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ViennaRNA-bindings 0.1.2.2 → 0.233.1.1

raw patch · 215 files changed

+120631/−52953 lines, 215 filesdep +QuickCheckdep +ViennaRNA-bindingsdep +tastydep ~base

Dependencies added: QuickCheck, ViennaRNA-bindings, tasty, tasty-hunit, tasty-silver, tasty-th

Dependency ranges changed: base

Files

BioInf/ViennaRNA/Bindings.hs view
@@ -1,14 +1,20 @@  -- | Bindings to important functions in the ViennaRNA library.+--+-- TODO Anything here that is not thread-safe should internally use+-- a mutex!  module BioInf.ViennaRNA.Bindings   ( module BioInf.ViennaRNA.Bindings   , CofoldF (..)+  , Duplex (..)   ) where  import qualified Data.Array.IArray as A +import BioInf.ViennaRNA.Bindings.FFI.Centroid as FFI import BioInf.ViennaRNA.Bindings.FFI.CoFold   as FFI+import BioInf.ViennaRNA.Bindings.FFI.Duplex   as FFI import BioInf.ViennaRNA.Bindings.FFI.Fold     as FFI import BioInf.ViennaRNA.Bindings.FFI.PartFunc as FFI @@ -18,12 +24,26 @@ mfe :: String -> IO (Double,String) mfe = ffiFold +mfeTemp :: Double -> String -> IO (Double,String)+mfeTemp = ffiFoldTemp++circmfe :: String -> IO (Double,String)+circmfe = ffiCircFold+ -- | Given a sequence and a structure, returns the energy of the -- sequence/structure pair.  eos :: String -> String -> IO Double eos i s = ffiEnergyOfStructure i s 0 +eosTemp :: Double -> String -> String -> IO Double+eosTemp t i s = ffiEnergyOfStructureTemp t i s 0++-- | Energy of a circular structure++eosCirc :: String -> String -> IO Double+eosCirc i s = ffiEnergyOfCircStructure i s 0+ -- | Given a string, calculates the partition function for said string. Returns -- the ensemble energy, a string with where each nucleotide position is -- annotated with the strength of the potential pairing, and the whole base@@ -35,8 +55,17 @@ partConstrained :: String -> String -> IO (Double, String, A.Array (Int,Int) Double) partConstrained = ffi_pf_fold_constrained +circPart :: String -> IO (Double,String,A.Array (Int,Int) Double)+circPart = ffi_pf_circ_fold +circPartConstrained :: String -> String -> IO (Double, String, A.Array (Int,Int) Double)+circPartConstrained = ffi_pf_circ_fold_constrained +-- | Centroid structure++centroidTemp :: Double -> String -> IO (Double,String)+centroidTemp t i = ffiCentroidTemp t i+ -- * RNAcofold  -- | Energy of struct for cofolded structures.@@ -58,4 +87,8 @@ copartConstrained :: String -> String -> Int -> IO (CofoldF,String,A.Array (Int,Int) Double) copartConstrained sq str c = ffiCoPartitionConstrained c sq str +-- | Fold a duplex structure++duplexFold :: String -> String -> IO Duplex+duplexFold = ffiDuplexFold
+ BioInf/ViennaRNA/Bindings/FFI/Centroid.chs view
@@ -0,0 +1,30 @@++module BioInf.ViennaRNA.Bindings.FFI.Centroid where++import Foreign.C.String+import Foreign.C.Types+import Foreign.Marshal.Alloc+import Foreign.Ptr+import GHC.Float+import Unsafe.Coerce++import BioInf.ViennaRNA.Bindings.FFI.Utils++++#include "ViennaRNA/fold.h"++++ffiCentroidTemp :: Double -> String -> IO (Double,String)+ffiCentroidTemp t inp =+  withCAString inp $ \cinp ->+  withCAString inp $ \struc -> do+  e <- fold_centroid_p (realToFrac t) cinp struc+  s <- peekCAString struc+  return (cd2d e, s)++++foreign import ccall "ffiwrap_centroid_temp" fold_centroid_p :: CDouble -> CString -> CString -> IO CDouble+
BioInf/ViennaRNA/Bindings/FFI/CoFold.chs view
@@ -1,5 +1,3 @@-{-# LANGUAGE ScopedTypeVariables #-}-{-# LANGUAGE ForeignFunctionInterface #-}  module BioInf.ViennaRNA.Bindings.FFI.CoFold   ( ffiCoFold@@ -25,10 +23,10 @@   -#include "cofold.h"-#include "data_structures.h"-#include "fold.h"-#include "part_func_co.h"+#include "ViennaRNA/cofold.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/part_func_co.h"  {#pointer *cofoldF as CofoldFPtr -> CofoldF #}
+ BioInf/ViennaRNA/Bindings/FFI/Duplex.chs view
@@ -0,0 +1,78 @@++module BioInf.ViennaRNA.Bindings.FFI.Duplex+  ( Duplex (..)+  , ffiDuplexFold+  ) where++import           Control.Applicative+import           Control.Monad+import           Foreign.C.String+import           Foreign.C.Types+import           Foreign.Marshal.Alloc+import           Foreign.Marshal.Array+import           Foreign.Ptr+import           Foreign.Storable+import           GHC.Float+import qualified Data.Array.IArray as A+import           Unsafe.Coerce++import           BioInf.ViennaRNA.Bindings.FFI.Utils++++#include "ViennaRNA/duplex.h"+#include "ViennaRNA/data_structures.h"++{#pointer *duplexT as DuplexPtr -> Duplex #}++data Duplex = Duplex+  { i                 :: {-# UNPACK #-} !Int+  , j                 :: {-# UNPACK #-} !Int+  , end               :: {-# UNPACK #-} !Int+  , structure         ::                !String+  , energy            :: {-# UNPACK #-} !Double+  , energyBacktrack   :: {-# UNPACK #-} !Double+  , openingBacktrackX :: {-# UNPACK #-} !Double+  , openingBacktrackY :: {-# UNPACK #-} !Double+  , offset            :: {-# UNPACK #-} !Int+  , dG1               :: {-# UNPACK #-} !Double+  , dG2               :: {-# UNPACK #-} !Double+  , ddG               :: {-# UNPACK #-} !Double+  , tb                :: {-# UNPACK #-} !Int+  , te                :: {-# UNPACK #-} !Int+  , qb                :: {-# UNPACK #-} !Int+  , qe                :: {-# UNPACK #-} !Int+  }+  deriving (Show)++instance Storable Duplex where+  sizeOf _ = {# sizeof duplexT #}+  alignment _ = sizeOf (undefined :: CDouble)+  peek p = Duplex+    <$> liftM fromIntegral ({# get duplexT->i #} p)+    <*> liftM fromIntegral ({# get duplexT->j #} p)+    <*> liftM fromIntegral ({# get duplexT->end #} p)+    <*> (peekCAString =<<  ({# get duplexT->structure #} p))+    <*> liftM realToFrac   ({# get duplexT->energy #} p)+    <*> liftM realToFrac   ({# get duplexT->energy_backtrack #} p)+    <*> liftM realToFrac   ({# get duplexT->opening_backtrack_x #} p)+    <*> liftM realToFrac   ({# get duplexT->opening_backtrack_y #} p)+    <*> liftM fromIntegral ({# get duplexT->offset #} p)+    <*> liftM realToFrac   ({# get duplexT->dG1 #} p)+    <*> liftM realToFrac   ({# get duplexT->dG2 #} p)+    <*> liftM realToFrac   ({# get duplexT->ddG #} p)+    <*> liftM fromIntegral ({# get duplexT->tb #} p)+    <*> liftM fromIntegral ({# get duplexT->te #} p)+    <*> liftM fromIntegral ({# get duplexT->qb #} p)+    <*> liftM fromIntegral ({# get duplexT->qe #} p)++ffiDuplexFold :: String -> String -> IO Duplex+ffiDuplexFold l r =+  withCAString l $ \cl  ->+  withCAString r $ \cr  ->+  alloca         $ \ptr -> do+  d <- duplexfold_p ptr cl cr >> peek ptr+  return d++foreign import ccall "ffiwrap_duplexfold" duplexfold_p :: DuplexPtr -> CString -> CString -> IO ()+
BioInf/ViennaRNA/Bindings/FFI/Fold.chs view
@@ -1,10 +1,5 @@-{-# LANGUAGE ForeignFunctionInterface #-}-{-# LANGUAGE CPP #-} -module BioInf.ViennaRNA.Bindings.FFI.Fold-  ( ffiFold-  , ffiEnergyOfStructure-  ) where+module BioInf.ViennaRNA.Bindings.FFI.Fold where  import Foreign.C.String import Foreign.C.Types@@ -17,7 +12,7 @@   -#include "fold.h"+#include "ViennaRNA/fold.h"  ffiFold :: String -> IO (Double,String) ffiFold inp = withCAString inp $ \cinp ->@@ -33,4 +28,42 @@     setCutPoint (-1)     >>  {#call energy_of_structure #} i s (fromIntegral verb :: CInt)     >>= (return . cf2d)++ffiEnergyOfCircStructure :: String -> String -> Int -> IO Double+ffiEnergyOfCircStructure inp struc verb =+  withCAString inp   $ \i ->+  withCAString struc $ \s ->+    setCutPoint (-1)+    >>  {#call energy_of_circ_structure #} i s (fromIntegral verb :: CInt)+    >>= (return . cf2d)++ffiCircFold :: String -> IO (Double,String)+ffiCircFold inp = withCAString inp $ \cinp ->+                  withCAString inp $ \struc -> do+  e <- {#call circfold #} cinp struc+  s <- peekCAString struc+  return (cf2d e, s)++++ffiFoldTemp :: Double -> String -> IO (Double,String)+ffiFoldTemp t inp =+  withCAString inp $ \cinp ->+  withCAString inp $ \struc -> do+  e <- fold_temp_p (realToFrac t) cinp struc+  s <- peekCAString struc+  return (cf2d e, s)++ffiEnergyOfStructureTemp :: Double -> String -> String -> Int -> IO Double+ffiEnergyOfStructureTemp t inp struc verb =+  withCAString inp   $ \i ->+  withCAString struc $ \s ->+    setCutPoint (-1)+    >>  eos_temp_p (realToFrac t) i s (fromIntegral verb :: CInt)+    >>= (return . cf2d)+++foreign import ccall "ffiwrap_fold_temp" fold_temp_p :: CFloat -> CString -> CString -> IO CFloat++foreign import ccall "ffiwrap_eos_temp" eos_temp_p :: CFloat -> CString -> CString -> CInt -> IO CFloat
BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs view
@@ -1,8 +1,9 @@-{-# LANGUAGE ForeignFunctionInterface #-}  module BioInf.ViennaRNA.Bindings.FFI.PartFunc   ( ffi_pf_fold+  , ffi_pf_circ_fold   , ffi_pf_fold_constrained+  , ffi_pf_circ_fold_constrained   ) where  import           Foreign.C.String@@ -18,7 +19,7 @@   -#include "part_func.h"+#include "ViennaRNA/part_func.h"  ffi_pf_fold :: String -> IO (Double,String,A.Array (Int,Int) Double) ffi_pf_fold i =@@ -33,6 +34,19 @@   let ar = A.accumArray (const id) 0 ((1,1),(n,n)) $ zip [ (ii,jj) | ii <- [n,n-1..1], jj <- [n,n-1..ii]] (drop 1 $ map unsafeCoerce xs)   return (cf2d e, s, ar) +ffi_pf_circ_fold :: String -> IO (Double,String,A.Array (Int,Int) Double)+ffi_pf_circ_fold i =+  withCAString i $ \ci -> do+  withCAString i $ \cs -> do+  let n = length i+  let z = n * (n+1) `div` 2 +1+  e  <- {#call pf_circ_fold #} ci cs+  s  <- peekCAString cs+  bp <- {#call export_bppm #}+  xs <- peekArray z (bp :: Ptr CDouble)+  let ar = A.accumArray (const id) 0 ((1,1),(n,n)) $ zip [ (ii,jj) | ii <- [n,n-1..1], jj <- [n,n-1..ii]] (drop 1 $ map unsafeCoerce xs)+  return (cf2d e, s, ar)+ ffi_pf_fold_constrained :: String -> String -> IO (Double,String,A.Array (Int,Int) Double) ffi_pf_fold_constrained i s =   withCAString i $ \ci ->@@ -46,7 +60,21 @@   let ar = A.accumArray (const id) 0 ((1,1),(n,n)) $ zip [ (ii,jj) | ii <- [n,n-1..1], jj <- [n,n-1..ii]] (drop 1 $ map unsafeCoerce xs)   return (cf2d e, s, ar) +ffi_pf_circ_fold_constrained :: String -> String -> IO (Double,String,A.Array (Int,Int) Double)+ffi_pf_circ_fold_constrained i s =+  withCAString i $ \ci -> do+  withCAString i $ \cs -> do+  let n = length i+  let z = n * (n+1) `div` 2 +1+  e  <- {#call ffiwrap_pf_circ_fold_constrained #} ci cs 1+  s  <- peekCAString cs+  bp <- {#call export_bppm #}+  xs <- peekArray z (bp :: Ptr CDouble)+  let ar = A.accumArray (const id) 0 ((1,1),(n,n)) $ zip [ (ii,jj) | ii <- [n,n-1..1], jj <- [n,n-1..ii]] (drop 1 $ map unsafeCoerce xs)+  return (cf2d e, s, ar)+ #c float ffiwrap_pf_fold_constrained (const char *sequence, char *structure, int constrained);+float ffiwrap_pf_circ_fold_constrained (const char *sequence, char *structure, int constrained); #endc
BioInf/ViennaRNA/Bindings/FFI/Utils.hs view
@@ -1,4 +1,3 @@-{-# LANGUAGE ForeignFunctionInterface #-}  module BioInf.ViennaRNA.Bindings.FFI.Utils where @@ -12,6 +11,9 @@  cf2d :: CFloat -> Double cf2d = float2Double . unsafeCoerce++cd2d :: CDouble -> Double+cd2d = unsafeCoerce  foreign import ccall "fold.h &cut_point" cut_point :: Ptr CInt
+ C/ViennaRNA/2Dfold.c view
@@ -0,0 +1,3750 @@+/*+      minimum free energy+      RNA secondary structure with+      basepair distance d_1 to reference structure 1 and distance d_2 to reference structure 2++*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/params.h"+#ifdef _OPENMP+#include <omp.h>+#endif+#include "ViennaRNA/2Dfold.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+int compute_2Dfold_F3 = 0;++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  mfe_linear(vrna_fold_compound_t *vc);+PRIVATE void  mfe_circ(vrna_fold_compound_t *vc);++PUBLIC  void  update_TwoDfold_params(TwoDfold_vars *vars);++PRIVATE void  backtrack_f5(unsigned int j, int k, int l, char *structure, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_c(unsigned int i, unsigned int j, int k, int l, char *structure, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_m(unsigned int i, unsigned int j, int k, int l, char *structure, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_m1(unsigned int i, unsigned int j, int k, int l, char *structure, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_fc(int k, int l, char *structure, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_m2(unsigned int i, int k, int l, char *structure, vrna_fold_compound_t *vc);++PRIVATE void  adjustArrayBoundaries(int ***array, int *k_min, int *k_max, int **l_min, int **l_max, int k_min_real, int k_max_real, int *l_min_real, int *l_max_real);+INLINE  PRIVATE void  preparePosteriorBoundaries(int size, int shift, int *min_k, int *max_k, int **min_l, int **max_l);+INLINE  PRIVATE void  updatePosteriorBoundaries(int d1, int d2, int *min_k, int *max_k, int **min_l, int **max_l);+INLINE  PRIVATE void  prepareBoundaries(int min_k_pre, int max_k_pre, int min_l_pre, int max_l_pre, int bpdist, int *min_k, int *max_k, int **min_l, int **max_l);+INLINE  PRIVATE void  prepareArray(int ***array, int min_k, int max_k, int *min_l, int *max_l);+INLINE  PRIVATE void  prepareArray2(unsigned long ***array, int min_k, int max_k, int *min_l, int *max_l);++++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++#if 0++PRIVATE void initialize_TwoDfold_vars(TwoDfold_vars *vars){+  update_TwoDfold_params(vars);+  /* this call updates the params in the ViennaRNA fold.o which is a global, so be careful+  *  whith calling it parallel... need a workarround or fix of ViennaRNA fold stuff+  */+  update_fold_params();+}++PUBLIC TwoDfold_solution **TwoDfold(TwoDfold_vars *vars, int distance1, int distance2){+  unsigned int i, d1, d2;+  unsigned int maxD1;+  unsigned int maxD2;+  unsigned int length;+  TwoDfold_solution **output;++  initialize_TwoDfold_vars(vars);+  if(fabs(vars->P->temperature - temperature)>1e-6) update_TwoDfold_params(vars);+  vars->S   = encode_sequence(vars->sequence, 0);+  vars->S1  = encode_sequence(vars->sequence, 1);++  make_ptypes(vars);++  maxD1 = vars->maxD1;+  maxD2 = vars->maxD2;++  if(distance1 >= 0){+    if((unsigned int)distance1 > maxD1)+      fprintf(stderr,+              "limiting maximum basepair distance 1 to %u\n",+              maxD1);+    else+      maxD1 = (unsigned int)distance1;+  }++  if(distance2 >= 0){+    if((unsigned int)distance2 > maxD2)+      fprintf(stderr,+              "limiting maximum basepair distance 2 to %u\n",+              maxD2);+    else+      maxD2 = (unsigned int)distance2;+  }++  vars->maxD1 = maxD1;+  vars->maxD2 = maxD2;+  output = (TwoDfold_solution **)vrna_alloc((vars->maxD1+1) * sizeof(TwoDfold_solution *));++  mfe_linear(vars);+  if(vars->circ) mfe_circ(vars);++  length = vars->seq_length;++  for(d1=0; d1<=maxD1;d1++){+    output[d1] = (TwoDfold_solution *)vrna_alloc((vars->maxD2+1)*sizeof(TwoDfold_solution));+#ifdef _OPENMP+  #pragma omp parallel for private(d2)+#endif+    for(d2=0; d2<=maxD2;d2++){+      output[d1][d2].en = (float)INF/(float)100.;+      output[d1][d2].s  = NULL;+    }+    if(     (d1 >= ((vars->circ) ? vars->k_min_values_fc : vars->k_min_values_f[length]))+        &&  (d1 <= ((vars->circ) ? vars->k_max_values_fc : vars->k_max_values_f[length]))){+#ifdef _OPENMP+  #pragma omp parallel for private(d2, i)+#endif+      for(  d2  = ((vars->circ) ? vars->l_min_values_fc[d1] : vars->l_min_values_f[length][d1]);+            d2 <= ((vars->circ) ? vars->l_max_values_fc[d1] : vars->l_max_values_f[length][d1]);+            d2 += 2){+        output[d1][d2].en = (float)((vars->circ) ? vars->E_Fc[d1][d2/2] : vars->E_F5[length][d1][d2/2])/(float)100.;+        if(vars->do_backtrack && (output[d1][d2].en != (float)INF/(float)100.)){+          char *mfe_structure = (char *)vrna_alloc(length+1);+          for(i=0;i<length;i++) mfe_structure[i] = '.';+          mfe_structure[i] = '\0';+          (vars->circ) ? backtrack_fc(d1, d2, mfe_structure, vars) : backtrack_f5(length, d1, d2, mfe_structure, vars);+          output[d1][d2].s = mfe_structure;+        }+      }+    }++  }+  return output;+}++#endif++PUBLIC vrna_sol_TwoD_t *+vrna_mfe_TwoD(vrna_fold_compound_t *vars,+              int distance1,+              int distance2){++  unsigned int  i, d1, d2;+  unsigned int  maxD1;+  unsigned int  maxD2;+  unsigned int  length;+  unsigned int  counter = 0;+  int           en = 0;+  vrna_sol_TwoD_t *output;+  vrna_md_t     *md;+  vrna_mx_mfe_t *matrices;++  maxD1 = vars->maxD1;+  maxD2 = vars->maxD2;+  matrices  = vars->matrices;+  md        = &(vars->params->model_details);++  if(distance1 >= 0){+    if((unsigned int)distance1 > maxD1)+      vrna_message_warning("vrna_mfe_TwoD@2Dfold.c: limiting maximum basepair distance 1 to %u\n",+                                  maxD1);+    else+      maxD1 = (unsigned int)distance1;+  }++  if(distance2 >= 0){+    if((unsigned int)distance2 > maxD2)+      vrna_message_warning("vrna_mfe_TwoD@2Dfold.c: limiting maximum basepair distance 2 to %u\n",+                                  maxD2);+    else+      maxD2 = (unsigned int)distance2;+  }++  vars->maxD1 = maxD1;+  vars->maxD2 = maxD2;+  output = (vrna_sol_TwoD_t *)vrna_alloc((((vars->maxD1+1)*(vars->maxD2+2))/2 + 2) * sizeof(vrna_sol_TwoD_t));++  mfe_linear(vars);+  if(md->circ) mfe_circ(vars);++  length = vars->length;++  for(d1=0; d1<=maxD1;d1++){+    if((d1 >= ((md->circ) ? matrices->k_min_Fc : matrices->k_min_F5[length]))+        &&  (d1 <= ((md->circ) ? matrices->k_max_Fc : matrices->k_max_F5[length]))){+      for(d2  = ((md->circ) ? matrices->l_min_Fc[d1] : matrices->l_min_F5[length][d1]);+          d2 <= ((md->circ) ? matrices->l_max_Fc[d1] : matrices->l_max_F5[length][d1]);+          d2 += 2){+        en = ((md->circ) ? matrices->E_Fc[d1][d2/2] : matrices->E_F5[length][d1][d2/2]);+        if(en == INF) continue;+        output[counter].k   = d1;+        output[counter].l   = d2;+        output[counter].en  = (float)en/(float)100.;+        if(md->backtrack){+          char *mfe_structure = (char *)vrna_alloc(length+1);+          for(i=0;i<length;i++) mfe_structure[i] = '.';+          mfe_structure[i] = '\0';+          (md->circ) ? backtrack_fc((int)d1, (int)d2, mfe_structure, vars) : backtrack_f5(length, (int)d1, (int)d2, mfe_structure, vars);+          output[counter].s = mfe_structure;+        }+        else output[counter].s = NULL;+        counter++;+      }+    }+  }++  /* store entry for remaining partition if it exists */+  en = ((md->circ) ? matrices->E_Fc_rem : matrices->E_F5_rem[length]);+  if(en != INF){+    output[counter].k   = -1;+    output[counter].l   = -1;+    output[counter].en  =  (float)en/(float)100.;+    if(md->backtrack){+      char *mfe_structure = (char *)vrna_alloc(length+1);+      for(i=0;i<length;i++) mfe_structure[i] = '.';+      mfe_structure[i] = '\0';+      (md->circ) ? backtrack_fc(-1, -1, mfe_structure, vars) : backtrack_f5(length, -1, -1, mfe_structure, vars);+      output[counter].s = mfe_structure;+    }+    else output[counter].s = NULL;+    counter++;+  }++  /* insert end-marker entry */+  output[counter].k = output[counter].l = INF;+  counter++;++  /* resize to actual dataset amount */+  output = (vrna_sol_TwoD_t *)vrna_realloc(output, sizeof(vrna_sol_TwoD_t) * counter);+  return output;+}+++PUBLIC char *+vrna_backtrack5_TwoD( vrna_fold_compound_t *vc,+                      int k,+                      int l,+                      unsigned int j){++  unsigned int i;+  char *mfe_structure = (char *)vrna_alloc(j+1);+  if(j < TURN + 2) return NULL;++  for(i=0; i < j; i++) mfe_structure[i] = '.';+  mfe_structure[i] = '\0';++  backtrack_f5(j, k, l, mfe_structure, vc);+  return mfe_structure;+}++PRIVATE void+mfe_linear(vrna_fold_compound_t *vc){++  unsigned int  d, i, j, ij, maxD1, maxD2, seq_length, dia, dib, dja, djb, *referenceBPs1, *referenceBPs2, *mm1, *mm2, *bpdist;+  int           cnt1, cnt2, cnt3, cnt4, d1, d2, energy, dangles, temp2, type, additional_en, *my_iindx, *jindx, circ, *rtype;+  short         *S1, *reference_pt1, *reference_pt2;+  char          *sequence, *ptype;+  vrna_param_t  *P;+  vrna_mx_mfe_t *matrices;+  vrna_md_t     *md;++  /* dereferenciate things we often need */+  P               = vc->params;+  md              = &(P->model_details);+  matrices        = vc->matrices;+  sequence        = vc->sequence;+  seq_length      = vc->length;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  rtype           = &(md->rtype[0]);+  reference_pt1   = vc->reference_pt1;+  reference_pt2   = vc->reference_pt2;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  mm1             = vc->mm1;+  mm2             = vc->mm2;+  bpdist          = vc->bpdist;+  dangles         = md->dangles;+  circ            = md->circ;++  for (d = TURN+2; d <= seq_length; d++) { /* i,j in [1..length] */+#ifdef _OPENMP+  #pragma omp parallel for private(additional_en, j, energy, temp2, i, ij, dia,dib,dja,djb,cnt1,cnt2,cnt3,cnt4, d1, d2)+#endif+    for (j = d; j <= seq_length; j++) {+      unsigned int p, q, pq, u, maxp, dij;+      int type_2, type, tt, no_close, base_d1, base_d2;++      i = j-d+1;+      dij = j - i - 1;+      ij = my_iindx[i]-j;+      type = ptype[jindx[j] + i];++      no_close = (((type==3)||(type==4))&&no_closingGU);++      if (type) {   /* we have a pair */+        /* increase or decrease distance-to-reference value depending whether (i,j) is included in+        *  reference or has to be introduced+        */+        base_d1 = ((unsigned int)reference_pt1[i] != j) ? 1 : -1;+        base_d2 = ((unsigned int)reference_pt2[i] != j) ? 1 : -1;++        /* HAIRPIN STRUCTURES */++        /* get distance to reference if closing the hairpin+        *  d = dbp(T_{i,j}, {i,j})+        */+        d1 = base_d1 + referenceBPs1[ij];+        d2 = base_d2 + referenceBPs2[ij];++        int min_k, max_k, min_l, max_l;+        int real_min_k, real_max_k, *min_l_real, *max_l_real;++        min_l = min_k = 0;+        max_k = mm1[ij] + referenceBPs1[ij];+        max_l = mm2[ij] + referenceBPs2[ij];++        prepareBoundaries(min_k,+                          max_k,+                          min_l,+                          max_l,+                          bpdist[ij],+                          &matrices->k_min_C[ij],+                          &matrices->k_max_C[ij],+                          &matrices->l_min_C[ij],+                          &matrices->l_max_C[ij]+                          );++        preparePosteriorBoundaries( matrices->k_max_C[ij] - matrices->k_min_C[ij] + 1,+                                    matrices->k_min_C[ij],+                                    &real_min_k,+                                    &real_max_k,+                                    &min_l_real,+                                    &max_l_real+                                  );++        prepareArray( &matrices->E_C[ij],+                      matrices->k_min_C[ij],+                      matrices->k_max_C[ij],+                      matrices->l_min_C[ij],+                      matrices->l_max_C[ij]+                    );++#ifdef COUNT_STATES+        prepareArray2( &matrices->N_C[ij],+                      matrices->k_min_C[ij],+                      matrices->k_max_C[ij],+                      matrices->l_min_C[ij],+                      matrices->l_max_C[ij]+                    );+#endif++        /* d1 and d2 are the distancies to both references introduced by closing a hairpin structure at (i,j) */+        if((d1 >= 0) && (d2 >= 0)){+          if(((unsigned int)d1<=maxD1) && ((unsigned int)d2 <= maxD2)){+            matrices->E_C[ij][d1][d2/2] = (no_close) ? FORBIDDEN : E_Hairpin(dij, type, S1[i+1], S1[j-1], sequence+i-1, P);+            updatePosteriorBoundaries(d1,+                                      d2,+                                      &real_min_k,+                                      &real_max_k,+                                      &min_l_real,+                                      &max_l_real+                                      );+#ifdef COUNT_STATES+            matrices->N_C[ij][d1][d2/2] = 1;+#endif+          }+          else{+            matrices->E_C_rem[ij] = (no_close) ? FORBIDDEN : E_Hairpin(dij, type, S1[i+1], S1[j-1], sequence+i-1, P);+          }+        }+        /* INTERIOR LOOP STRUCTURES */+        maxp = MIN2(j-2-TURN,i+MAXLOOP+1);+        for(p = i+1; p <= maxp; p++){+          unsigned int minq = p + TURN + 1;+          unsigned int ln_pre = dij + p;+          if(ln_pre > minq + MAXLOOP) minq = ln_pre - MAXLOOP - 1;+          for(q = minq; q < j; q++){+            pq = my_iindx[p]-q;+            /* set distance to reference structure... */+            type_2 = ptype[jindx[q] + p];++            if (type_2==0) continue;+            type_2 = rtype[type_2];++            /* get distance to reference if closing the interior loop+            *  d2 = dbp(S_{i,j}, S_{p.q} + {i,j})+            */+            d1 = base_d1 + referenceBPs1[ij] - referenceBPs1[pq];+            d2 = base_d2 + referenceBPs2[ij] - referenceBPs2[pq];++            if(no_closingGU)+              if(no_close||(type_2==3)||(type_2==4))+                if((p>i+1)||(q<j-1)) continue;  /* continue unless stack */++            energy = E_IntLoop(p-i-1, j-q-1, type, type_2, S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);++            if(matrices->E_C[pq] != NULL){+              for(cnt1 = matrices->k_min_C[pq]; cnt1 <= matrices->k_max_C[pq]; cnt1++){+                for(cnt2 = matrices->l_min_C[pq][cnt1]; cnt2 <= matrices->l_max_C[pq][cnt1]; cnt2+=2){+                  if(matrices->E_C[pq][cnt1][cnt2/2] != INF){+                    if(((cnt1 + d1) <= maxD1) && ((cnt2+d2) <= maxD2)){+                        matrices->E_C[ij][cnt1 + d1][(cnt2 + d2)/2] = MIN2( matrices->E_C[ij][cnt1 + d1][(cnt2 + d2)/2],+                                                                        matrices->E_C[pq][cnt1][cnt2/2] + energy+                                                                      );+                        updatePosteriorBoundaries(cnt1 + d1,+                                                  cnt2 + d2,+                                                  &real_min_k,+                                                  &real_max_k,+                                                  &min_l_real,+                                                  &max_l_real+                                                  );+#ifdef COUNT_STATES+                       matrices->N_C[ij][cnt1 + d1][(cnt2 + d2)/2] += matrices->N_C[pq][cnt1][cnt2/2];+#endif+                    }+                    /* collect all cases where d1+cnt1 or d2+cnt2 exceeds maxD1, maxD2, respectively */+                    else{+                      matrices->E_C_rem[ij] = MIN2(matrices->E_C_rem[ij], matrices->E_C[pq][cnt1][cnt2/2] + energy);+                    }+                  }+                }+              }+            }+            /* collect all contributions where C[pq] already lies outside k_max, l_max boundary */+            if(matrices->E_C_rem[pq] != INF){+              matrices->E_C_rem[ij] = MIN2(matrices->E_C_rem[ij], matrices->E_C_rem[pq] + energy);+            }+          } /* end q-loop */+        } /* end p-loop */++++        /* MULTI LOOP STRUCTURES */+        if(!no_close){++          /* dangle energies for multiloop closing stem */+          tt = rtype[type];+          temp2 = P->MLclosing;+          if(dangles == 2)+            temp2 += E_MLstem(tt, S1[j-1], S1[i+1], P);+          else+            temp2 += E_MLstem(tt, -1, -1, P);++          for(u=i+TURN+2; u<j-TURN-2;u++){+            int i1u   = my_iindx[i+1]-u;+            int u1j1  = my_iindx[u+1]-j+1;+            /* check all cases where either M or M1 are already out of scope of maxD1 and/or maxD2 */+            if(matrices->E_M_rem[i1u] != INF){+              for(cnt3 = matrices->k_min_M1[u1j1];+                  cnt3 <= matrices->k_max_M1[u1j1];+                  cnt3++)+                for(cnt4 = matrices->l_min_M1[u1j1][cnt3];+                    cnt4 <= matrices->l_max_M1[u1j1][cnt3];+                    cnt4+=2){+                  if(matrices->E_M1[u1j1][cnt3][cnt4/2]!= INF){+                    matrices->E_C_rem[ij] = MIN2(matrices->E_C_rem[ij],+                                              matrices->E_M_rem[i1u]+                                            + matrices->E_M1[u1j1][cnt3][cnt4/2]+                                            + temp2+                                              );+                  }+                }+              if(matrices->E_M1_rem[u1j1] != INF){+                matrices->E_C_rem[ij] = MIN2(matrices->E_C_rem[ij],+                                          matrices->E_M_rem[i1u]+                                        + matrices->E_M1_rem[u1j1]+                                        + temp2+                                          );+              }+            }+            if(matrices->E_M1_rem[u1j1] != INF){+              for(cnt1 = matrices->k_min_M[i1u];+                  cnt1 <= matrices->k_max_M[i1u];+                  cnt1++)+                for(cnt2 = matrices->l_min_M[i1u][cnt1];+                    cnt2 <= matrices->l_max_M[i1u][cnt1];+                    cnt2+=2)+                  if(matrices->E_M[i1u][cnt1][cnt2/2] != INF){+                    matrices->E_C_rem[ij] = MIN2(matrices->E_C_rem[ij],+                                              matrices->E_M[i1u][cnt1][cnt2/2]+                                            + matrices->E_M1_rem[u1j1]+                                            + temp2+                                              );+                  }+            }+            /* get distance to reference if closing the multiloop+            *  d = dbp(S_{i,j}, {i,j} + S_{i+1,u} + S_{u+1,j-1})+            */+            if(!matrices->E_M[i1u]) continue;+            if(!matrices->E_M1[u1j1]) continue;++            d1 = base_d1 + referenceBPs1[ij] - referenceBPs1[i1u] - referenceBPs1[u1j1];+            d2 = base_d2 + referenceBPs2[ij] - referenceBPs2[i1u] - referenceBPs2[u1j1];++            for(cnt1 = matrices->k_min_M[i1u];+                cnt1 <= matrices->k_max_M[i1u];+                cnt1++)+              for(cnt2 = matrices->l_min_M[i1u][cnt1];+                  cnt2 <= matrices->l_max_M[i1u][cnt1];+                  cnt2+=2)+                for(cnt3 = matrices->k_min_M1[u1j1];+                    cnt3 <= matrices->k_max_M1[u1j1];+                    cnt3++)+                  for(cnt4 = matrices->l_min_M1[u1j1][cnt3];+                      cnt4 <= matrices->l_max_M1[u1j1][cnt3];+                      cnt4+=2){+                    if((matrices->E_M[i1u][cnt1][cnt2/2] != INF) && (matrices->E_M1[u1j1][cnt3][cnt4/2]!= INF)){+                      if(((cnt1+cnt3+d1) <= maxD1) && ((cnt2+cnt4+d2) <= maxD2)){+                        matrices->E_C[ij][cnt1+cnt3+d1][(cnt2+cnt4+d2)/2] = MIN2( matrices->E_C[ij][cnt1+cnt3+d1][(cnt2+cnt4+d2)/2],+                                                                              matrices->E_M[i1u][cnt1][cnt2/2]+                                                                            + matrices->E_M1[u1j1][cnt3][cnt4/2]+                                                                            + temp2+                                                                            );+                        updatePosteriorBoundaries(cnt1 + cnt3 + d1,+                                                  cnt2 + cnt4 + d2,+                                                  &real_min_k,+                                                  &real_max_k,+                                                  &min_l_real,+                                                  &max_l_real+                                                );+#ifdef COUNT_STATES+                        matrices->N_C[ij][cnt1+cnt3+d1][(cnt2+cnt4+d2)/2] += matrices->N_M[i1u][cnt1][cnt2/2] * matrices->N_M1[u1j1][cnt3][cnt4/2];+#endif+                      }+                      /* collect all cases where d1+cnt1+cnt3 or d2+cnt2+cnt4 exceeds maxD1, maxD2, respectively */+                      else{+                        matrices->E_C_rem[ij] = MIN2(  matrices->E_C_rem[ij],+                                                    matrices->E_M[i1u][cnt1][cnt2/2]+                                                  + matrices->E_M1[u1j1][cnt3][cnt4/2]+                                                  + temp2+                                                  );+                      }+                    }+                  }+          }+        }++        /* resize and move memory portions of energy matrix E_C */+        adjustArrayBoundaries(&matrices->E_C[ij],+                              &matrices->k_min_C[ij],+                              &matrices->k_max_C[ij],+                              &matrices->l_min_C[ij],+                              &matrices->l_max_C[ij],+                              real_min_k,+                              real_max_k,+                              min_l_real,+                              max_l_real+                              );+#ifdef COUNT_STATES+        /* actually we should adjust the array boundaries here but we might never use the count states option more than once so what....*/+#endif+      } /* end >> if (pair) << */++++      /* done with c[i,j], now compute fML[i,j] */+      /* free ends ? -----------------------------------------*/+++      dia = referenceBPs1[ij] - referenceBPs1[my_iindx[i+1]-j];+      dib = referenceBPs2[ij] - referenceBPs2[my_iindx[i+1]-j];+      dja = referenceBPs1[ij] - referenceBPs1[ij+1];+      djb = referenceBPs2[ij] - referenceBPs2[ij+1];++      if(dangles==2)+        temp2 = E_MLstem(type, ((i > 1) || circ) ? S1[i-1] : -1, ((j < seq_length) || circ) ? S1[j+1] : -1, P);+      else+        temp2 = E_MLstem(type, -1, -1, P);++      int min_k_guess, max_k_guess, min_l_guess, max_l_guess;+      int min_k_real_m, max_k_real_m, *min_l_real_m, *max_l_real_m;+      int min_k_real_m1, max_k_real_m1, *min_l_real_m1, *max_l_real_m1;++      min_k_guess = min_l_guess = 0;+      max_k_guess = mm1[ij] + referenceBPs1[ij];+      max_l_guess = mm2[ij] + referenceBPs2[ij];++      prepareBoundaries(min_k_guess,+                        max_k_guess,+                        min_l_guess,+                        max_l_guess,+                        bpdist[ij],+                        &matrices->k_min_M[ij],+                        &matrices->k_max_M[ij],+                        &matrices->l_min_M[ij],+                        &matrices->l_max_M[ij]+                        );++      prepareBoundaries(min_k_guess,+                        max_k_guess,+                        min_l_guess,+                        max_l_guess,+                        bpdist[ij],+                        &matrices->k_min_M1[ij],+                        &matrices->k_max_M1[ij],+                        &matrices->l_min_M1[ij],+                        &matrices->l_max_M1[ij]+                        );++      preparePosteriorBoundaries( matrices->k_max_M[ij] - matrices->k_min_M[ij] + 1,+                                  matrices->k_min_M[ij],+                                  &min_k_real_m,+                                  &max_k_real_m,+                                  &min_l_real_m,+                                  &max_l_real_m+                                );+      preparePosteriorBoundaries( matrices->k_max_M1[ij] - matrices->k_min_M1[ij] + 1,+                                  matrices->k_min_M1[ij],+                                  &min_k_real_m1,+                                  &max_k_real_m1,+                                  &min_l_real_m1,+                                  &max_l_real_m1+                                );++      prepareArray( &matrices->E_M[ij],+                    matrices->k_min_M[ij],+                    matrices->k_max_M[ij],+                    matrices->l_min_M[ij],+                    matrices->l_max_M[ij]+                  );++      prepareArray( &matrices->E_M1[ij],+                    matrices->k_min_M1[ij],+                    matrices->k_max_M1[ij],+                    matrices->l_min_M1[ij],+                    matrices->l_max_M1[ij]+                  );+#ifdef COUNT_STATES+      prepareArray2( &matrices->N_M[ij],+                    matrices->k_min_M[ij],+                    matrices->k_max_M[ij],+                    matrices->l_min_M[ij],+                    matrices->l_max_M[ij]+                  );+      prepareArray2( &matrices->N_M1[ij],+                    matrices->k_min_M1[ij],+                    matrices->k_max_M1[ij],+                    matrices->l_min_M1[ij],+                    matrices->l_max_M1[ij]+                  );+#endif++      /* now to the actual computations... */+      /* 1st E_M[ij] = E_M1[ij] = E_C[ij] + b */+      if(matrices->E_C_rem[ij] != INF){+        matrices->E_M_rem[ij] = matrices->E_M1_rem[ij] = temp2 + matrices->E_C_rem[ij];+      }+      if(matrices->E_C[ij])+        for(cnt1 = matrices->k_min_C[ij]; cnt1 <= matrices->k_max_C[ij]; cnt1++){+          for(cnt2 = matrices->l_min_C[ij][cnt1]; cnt2 <= matrices->l_max_C[ij][cnt1]; cnt2+=2){+            if(matrices->E_C[ij][cnt1][cnt2/2] != INF){+              matrices->E_M[ij][cnt1][cnt2/2] = matrices->E_M1[ij][cnt1][cnt2/2] = temp2 + matrices->E_C[ij][cnt1][cnt2/2];+              updatePosteriorBoundaries(cnt1,+                                        cnt2,+                                        &min_k_real_m,+                                        &max_k_real_m,+                                        &min_l_real_m,+                                        &max_l_real_m+                                        );+              updatePosteriorBoundaries(cnt1,+                                        cnt2,+                                        &min_k_real_m1,+                                        &max_k_real_m1,+                                        &min_l_real_m1,+                                        &max_l_real_m1+                                        );+#ifdef COUNT_STATES+             matrices->N_M[ij][cnt1][cnt2/2] = matrices->N_M1[ij][cnt1][cnt2/2] = matrices->N_C[ij][cnt1][cnt2/2];+#endif+            }+          }+        }++      /* 2nd E_M[ij] = MIN(E_M[ij], E_M[i+1,j] + c) */+      if(matrices->E_M_rem[my_iindx[i+1]-j] != INF){+        matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                  matrices->E_M_rem[my_iindx[i+1]-j] + P->MLbase+                                  );+      }+      if(matrices->E_M[my_iindx[i+1]-j])+        for(cnt1 = matrices->k_min_M[my_iindx[i+1]-j];+            cnt1 <= matrices->k_max_M[my_iindx[i+1]-j];+            cnt1++){+          for(cnt2 = matrices->l_min_M[my_iindx[i+1]-j][cnt1];+              cnt2 <= matrices->l_max_M[my_iindx[i+1]-j][cnt1];+              cnt2+=2){+            if(matrices->E_M[my_iindx[i+1]-j][cnt1][cnt2/2] != INF){+              if(((cnt1 + dia) <= maxD1) && ((cnt2 + dib) <= maxD2)){+                matrices->E_M[ij][cnt1+dia][(cnt2+dib)/2] = MIN2( matrices->E_M[ij][cnt1+dia][(cnt2+dib)/2],+                                                              matrices->E_M[my_iindx[i+1]-j][cnt1][cnt2/2] + P->MLbase+                                                            );+                updatePosteriorBoundaries(cnt1 + dia,+                                          cnt2 + dib,+                                          &min_k_real_m,+                                          &max_k_real_m,+                                          &min_l_real_m,+                                          &max_l_real_m+                                          );+#ifdef COUNT_STATES+                matrices->N_M[ij][cnt1+dia][(cnt2+dib)/2] += matrices->N_M[my_iindx[i+1]-j][cnt1][cnt2/2];+#endif+              }+              /* collect all cases where dia+cnt1 or dib+cnt2 exceeds maxD1, maxD2, respectively */+              else{+                matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                          matrices->E_M[my_iindx[i+1]-j][cnt1][cnt2/2] + P->MLbase+                                          );+              }+            }+          }+        }++      /* 3rd E_M[ij] = MIN(E_M[ij], E_M[i,j-1] + c) */+      if(matrices->E_M_rem[ij+1] != INF){+        matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                  matrices->E_M_rem[ij+1] + P->MLbase+                                  );+      }+      if(matrices->E_M[ij+1])+        for(cnt1 = matrices->k_min_M[ij+1];+            cnt1 <= matrices->k_max_M[ij+1];+            cnt1++){+          for(cnt2 = matrices->l_min_M[ij+1][cnt1];+              cnt2 <= matrices->l_max_M[ij+1][cnt1];+              cnt2+=2){+            if(matrices->E_M[ij+1][cnt1][cnt2/2] != INF){+              if(((cnt1 + dja) <= maxD1) && ((cnt2 + djb) <= maxD2)){+                matrices->E_M[ij][cnt1+dja][(cnt2+djb)/2] = MIN2( matrices->E_M[ij][cnt1+dja][(cnt2+djb)/2],+                                                              matrices->E_M[ij+1][cnt1][cnt2/2] + P->MLbase+                                                            );+                updatePosteriorBoundaries(cnt1 + dja,+                                          cnt2 + djb,+                                          &min_k_real_m,+                                          &max_k_real_m,+                                          &min_l_real_m,+                                          &max_l_real_m+                                          );+#ifdef COUNT_STATES+                matrices->N_M[ij][cnt1+dja][(cnt2+djb)/2] += matrices->N_M[ij+1][cnt1][cnt2/2];+#endif+              }+              /* collect all cases where dja+cnt1 or djb+cnt2 exceeds maxD1, maxD2, respectively */+              else{+                matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                          matrices->E_M[ij+1][cnt1][cnt2/2] + P->MLbase+                                          );+              }+            }+          }+        }++      /* 4th E_M1[ij] = MIN(E_M1[ij], E_M1[i,j-1] + c) */+      if(matrices->E_M1_rem[ij+1] != INF){+        matrices->E_M1_rem[ij] = MIN2( matrices->E_M1_rem[ij],+                                    matrices->E_M1_rem[ij+1] + P->MLbase+                                  );+      }+      if(matrices->E_M1[ij+1])+        for(cnt1 = matrices->k_min_M1[ij+1];+            cnt1 <= matrices->k_max_M1[ij+1];+            cnt1++){+          for(cnt2 = matrices->l_min_M1[ij+1][cnt1];+              cnt2 <= matrices->l_max_M1[ij+1][cnt1];+              cnt2+=2){+            if(matrices->E_M1[ij+1][cnt1][cnt2/2] != INF){+              if(((cnt1 + dja) <= maxD1) && ((cnt2 + djb) <= maxD2)){+                matrices->E_M1[ij][cnt1+dja][(cnt2+djb)/2]  = MIN2( matrices->E_M1[ij][cnt1+dja][(cnt2+djb)/2],+                                                                matrices->E_M1[ij+1][cnt1][cnt2/2] + P->MLbase+                                                              );+                updatePosteriorBoundaries(cnt1 + dja,+                                          cnt2 + djb,+                                          &min_k_real_m1,+                                          &max_k_real_m1,+                                          &min_l_real_m1,+                                          &max_l_real_m1+                                          );+#ifdef COUNT_STATES+                matrices->N_M1[ij][cnt1+dja][(cnt2+djb)/2]  += matrices->N_M1[ij+1][cnt1][cnt2/2];+#endif+              }+              /* collect all cases where dja+cnt1 or djb+cnt2 exceeds maxD1, maxD2, respectively */+              else{+                matrices->E_M1_rem[ij] = MIN2( matrices->E_M1_rem[ij],+                                            matrices->E_M1[ij+1][cnt1][cnt2/2] + P->MLbase+                                          );+              }+            }+          }+        }+++      /* 5th E_M[ij] = MIN(E_M[ij], min(E_M[i,k] + E_M[k+1,j])) */+      if(j > TURN + 2)+      for (u = i+1+TURN; u <= j-2-TURN; u++){+        /* check all cases where M(i,u) and/or M(u+1,j) are already out of scope of maxD1 and/or maxD2 */+        if(matrices->E_M_rem[my_iindx[i]-u] != INF){+          for(cnt3 = matrices->k_min_M[my_iindx[u+1]-j];+              cnt3 <= matrices->k_max_M[my_iindx[u+1]-j];+              cnt3++){+            for(cnt4 = matrices->l_min_M[my_iindx[u+1]-j][cnt3];+                cnt4 <= matrices->l_max_M[my_iindx[u+1]-j][cnt3];+                cnt4+=2){+              if(matrices->E_M[my_iindx[u+1]-j][cnt3][cnt4/2] != INF){+                  matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                            matrices->E_M_rem[my_iindx[i]-u] + matrices->E_M[my_iindx[u+1]-j][cnt3][cnt4/2]+                                            );+              }+            }+          }+          if(matrices->E_M_rem[my_iindx[u+1]-j] != INF){+            matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                      matrices->E_M_rem[my_iindx[i]-u] + matrices->E_M_rem[my_iindx[u+1]-j]+                                      );+          }+        }+        if(matrices->E_M_rem[my_iindx[u+1]-j] != INF){+          for(cnt1 = matrices->k_min_M[my_iindx[i]-u];+              cnt1 <= matrices->k_max_M[my_iindx[i]-u];+              cnt1++){+            for(cnt2 = matrices->l_min_M[my_iindx[i]-u][cnt1];+                cnt2 <= matrices->l_max_M[my_iindx[i]-u][cnt1];+                cnt2+=2){+              if(matrices->E_M[my_iindx[i]-u][cnt1][cnt2/2] != INF){+                matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                          matrices->E_M[my_iindx[i]-u][cnt1][cnt2/2] + matrices->E_M_rem[my_iindx[u+1]-j]+                                          );+              }+            }+          }+        }+        if(!matrices->E_M[my_iindx[i]-u]) continue;+        if(!matrices->E_M[my_iindx[u+1]-j]) continue;++        dia = referenceBPs1[ij] - referenceBPs1[my_iindx[i]-u] - referenceBPs1[my_iindx[u+1]-j];+        dib = referenceBPs2[ij] - referenceBPs2[my_iindx[i]-u] - referenceBPs2[my_iindx[u+1]-j];++        for(cnt1 = matrices->k_min_M[my_iindx[i]-u];+            cnt1 <= matrices->k_max_M[my_iindx[i]-u];+            cnt1++){+          for(cnt2 = matrices->l_min_M[my_iindx[i]-u][cnt1];+              cnt2 <= matrices->l_max_M[my_iindx[i]-u][cnt1];+              cnt2+=2){+            for(cnt3 = matrices->k_min_M[my_iindx[u+1]-j];+                cnt3 <= matrices->k_max_M[my_iindx[u+1]-j];+                cnt3++){+              for(cnt4 = matrices->l_min_M[my_iindx[u+1]-j][cnt3];+                  cnt4 <= matrices->l_max_M[my_iindx[u+1]-j][cnt3];+                  cnt4+=2){+                if((matrices->E_M[my_iindx[i]-u][cnt1][cnt2/2] != INF) && (matrices->E_M[my_iindx[u+1]-j][cnt3][cnt4/2] != INF)){+                  if(((cnt1 + cnt3 + dia) <= maxD1) && ((cnt2 + cnt4 + dib) <= maxD2)){+                    matrices->E_M[ij][cnt1+cnt3+dia][(cnt2+cnt4+dib)/2] = MIN2( matrices->E_M[ij][cnt1+cnt3+dia][(cnt2+cnt4+dib)/2],+                                                                            matrices->E_M[my_iindx[i]-u][cnt1][cnt2/2]+                                                                          + matrices->E_M[my_iindx[u+1]-j][cnt3][cnt4/2]+                                                                          );+                    updatePosteriorBoundaries(cnt1 + cnt3 + dia,+                                              cnt2 + cnt4 + dib,+                                              &min_k_real_m,+                                              &max_k_real_m,+                                              &min_l_real_m,+                                              &max_l_real_m+                                              );+#ifdef COUNT_STATES+                    matrices->N_M[ij][cnt1+cnt3+dia][(cnt2+cnt4+dib)/2] += matrices->N_M[my_iindx[i]-u][cnt1][cnt2/2] * matrices->N_M1[my_iindx[u+1]-j][cnt3][cnt4/2];+#endif+                  }+                  /* collect all cases where dia+cnt1+cnt3 or dib+cnt2+cnt4 exceeds maxD1, maxD2, respectively */+                  else{+                    matrices->E_M_rem[ij] = MIN2(matrices->E_M_rem[ij],+                                              matrices->E_M[my_iindx[i]-u][cnt1][cnt2/2] + matrices->E_M[my_iindx[u+1]-j][cnt3][cnt4/2]+                                              );+                  }+                }+              }+            }+          }+        }+      }++      /* thats all folks for the multiloop decomposition... */++      adjustArrayBoundaries(&matrices->E_M[ij],+                            &matrices->k_min_M[ij],+                            &matrices->k_max_M[ij],+                            &matrices->l_min_M[ij],+                            &matrices->l_max_M[ij],+                            min_k_real_m,+                            max_k_real_m,+                            min_l_real_m,+                            max_l_real_m+                            );++      adjustArrayBoundaries(&matrices->E_M1[ij],+                            &matrices->k_min_M1[ij],+                            &matrices->k_max_M1[ij],+                            &matrices->l_min_M1[ij],+                            &matrices->l_max_M1[ij],+                            min_k_real_m1,+                            max_k_real_m1,+                            min_l_real_m1,+                            max_l_real_m1+                            );++#ifdef COUNT_STATES+        /* actually we should adjust the array boundaries here but we might never use the count states option more than once so what....*/+#endif+    } /* end of j-loop */+  }++  /* calculate energies of 5' and 3' fragments */++  /* prepare first entries in E_F5 */+  for(cnt1 = 1; cnt1 <= TURN+1; cnt1++){+    matrices->E_F5[cnt1] = (int **)vrna_alloc(sizeof(int *));+    matrices->E_F5[cnt1][0] = (int *)vrna_alloc(sizeof(int));+    matrices->E_F5[cnt1][0][0] = 0;+    matrices->E_F5_rem[cnt1] = INF;+    matrices->k_min_F5[cnt1] = matrices->k_max_F5[cnt1] = 0;+    matrices->l_min_F5[cnt1] = (int *)vrna_alloc(sizeof(int));+    matrices->l_max_F5[cnt1] = (int *)vrna_alloc(sizeof(int));+    matrices->l_min_F5[cnt1][0] = matrices->l_max_F5[cnt1][0] = 0;+#ifdef COUNT_STATES+    matrices->N_F5[cnt1] = (unsigned long **)vrna_alloc(sizeof(unsigned long *));+    matrices->N_F5[cnt1][0] = (unsigned long *)vrna_alloc(sizeof(unsigned long));+    matrices->N_F5[cnt1][0][0] = 1;+#endif++  }++++  for (j=TURN+2; j <= seq_length; j++) {++    unsigned int da = referenceBPs1[my_iindx[1]-j] - referenceBPs1[my_iindx[1]-j+1];+    unsigned int db = referenceBPs2[my_iindx[1]-j] - referenceBPs2[my_iindx[1]-j+1];++    type=ptype[jindx[j] + 1];+    additional_en = 0;+    if(type){+      if(dangles == 2)+        additional_en += E_ExtLoop(type, -1, j < seq_length ? S1[j+1] : -1, P);+      else+        additional_en += E_ExtLoop(type, -1, -1, P);+    }++    /* make min and max k guess for memory allocation */+    int min_k_guess, max_k_guess, min_l_guess, max_l_guess;+    int *min_l_real, *max_l_real, min_k_real, max_k_real;++    min_k_guess = min_l_guess = 0;+    max_k_guess = referenceBPs1[my_iindx[1]-j] + mm1[my_iindx[1]-j];+    max_l_guess = referenceBPs2[my_iindx[1]-j] + mm2[my_iindx[1]-j];++    prepareBoundaries(min_k_guess,+                      max_k_guess,+                      min_l_guess,+                      max_l_guess,+                      bpdist[my_iindx[1]-j],+                      &matrices->k_min_F5[j],+                      &matrices->k_max_F5[j],+                      &matrices->l_min_F5[j],+                      &matrices->l_max_F5[j]+                      );++    preparePosteriorBoundaries( matrices->k_max_F5[j] - matrices->k_min_F5[j] + 1,+                                matrices->k_min_F5[j],+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                              );++    prepareArray( &matrices->E_F5[j],+                  matrices->k_min_F5[j],+                  matrices->k_max_F5[j],+                  matrices->l_min_F5[j],+                  matrices->l_max_F5[j]+                );+#ifdef COUNT_STATES+    prepareArray2( &matrices->N_F5[j],+                  matrices->k_min_F5[j],+                  matrices->k_max_F5[j],+                  matrices->l_min_F5[j],+                  matrices->l_max_F5[j]+                );+#endif++    /* begin the actual computation of 5' end energies */++    /* j-1 is unpaired ... */+    matrices->E_F5_rem[j] = matrices->E_F5_rem[j-1];+    for(cnt1 = matrices->k_min_F5[j-1]; cnt1 <= matrices->k_max_F5[j-1]; cnt1++){+      for(cnt2 = matrices->l_min_F5[j-1][cnt1]; cnt2 <= matrices->l_max_F5[j-1][cnt1]; cnt2+=2){+        if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+          matrices->E_F5[j][cnt1+da][(cnt2+db)/2] = MIN2( matrices->E_F5[j][cnt1+da][(cnt2+db)/2],+                                                      matrices->E_F5[j-1][cnt1][cnt2/2]+                                                    );+          updatePosteriorBoundaries(cnt1 + da,+                                    cnt2 + db,+                                    &min_k_real,+                                    &max_k_real,+                                    &min_l_real,+                                    &max_l_real+                                    );+#ifdef COUNT_STATES+          matrices->N_F5[j][cnt1+da][(cnt2+db)/2] += matrices->N_F5[j-1][cnt1][cnt2/2];+#endif+        }+        /* collect all cases where da+cnt1 or db+cnt2 exceeds maxD1, maxD2, respectively */+        else{+          matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j], matrices->E_F5[j-1][cnt1][cnt2/2]);+        }+      }+    }+    /* j pairs with 1 */+    if(matrices->E_C_rem[my_iindx[1]-j] != INF){+      matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j], matrices->E_C_rem[my_iindx[1]-j] + additional_en);+    }+    if(matrices->E_C[my_iindx[1]-j])+      for(cnt1 = matrices->k_min_C[my_iindx[1]-j]; cnt1 <= matrices->k_max_C[my_iindx[1]-j]; cnt1++)+        for(cnt2 = matrices->l_min_C[my_iindx[1]-j][cnt1]; cnt2 <= matrices->l_max_C[my_iindx[1]-j][cnt1]; cnt2+=2){+          if(matrices->E_C[my_iindx[1]-j][cnt1][cnt2/2] != INF){+            matrices->E_F5[j][cnt1][cnt2/2] = MIN2( matrices->E_F5[j][cnt1][cnt2/2],+                                                matrices->E_C[my_iindx[1]-j][cnt1][cnt2/2]+ additional_en+                                              );+            updatePosteriorBoundaries(cnt1,+                                      cnt2,+                                      &min_k_real,+                                      &max_k_real,+                                      &min_l_real,+                                      &max_l_real+                                      );+#ifdef COUNT_STATES+            matrices->N_F5[j][cnt1][cnt2/2] += matrices->N_C[my_iindx[1]-j][cnt1][cnt2/2];+#endif+          }+        }++    /* j pairs with some other nucleotide -> see below */+    for (i=j-TURN-1; i>1; i--) {+      ij = my_iindx[i]-j;+      type = ptype[jindx[j] + i];+      if (type) {+        if(dangles == 2)+          additional_en = E_ExtLoop(type, S1[i-1], j < seq_length ? S1[j+1] : -1, P);+        else+          additional_en = E_ExtLoop(type, -1, -1, P);++        if(matrices->E_C_rem[ij] != INF){+          for(cnt3 = matrices->k_min_F5[i-1]; cnt3 <= matrices->k_max_F5[i-1]; cnt3++)+            for(cnt4 = matrices->l_min_F5[i-1][cnt3]; cnt4 <= matrices->l_max_F5[i-1][cnt3]; cnt4+=2){+              if(matrices->E_F5[i-1][cnt3][cnt4/2] != INF){+                matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j],+                                          matrices->E_F5[i-1][cnt3][cnt4/2] + matrices->E_C_rem[ij] + additional_en+                                          );+              }+            }+          if(matrices->E_F5_rem[i-1] != INF){+            matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j],+                                      matrices->E_F5_rem[i-1] + matrices->E_C_rem[ij] + additional_en+                                      );+          }+        }+        if((matrices->E_F5_rem[i-1] != INF) && (matrices->E_C[ij])){+          for(cnt1 = matrices->k_min_C[ij]; cnt1 <= matrices->k_max_C[ij]; cnt1++)+            for(cnt2 = matrices->l_min_C[ij][cnt1]; cnt2 <= matrices->l_max_C[ij][cnt1]; cnt2+=2)+              if(matrices->E_C[ij][cnt1][cnt2/2]!= INF){+                matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j],+                                          matrices->E_F5_rem[i-1] + matrices->E_C[ij][cnt1][cnt2/2] + additional_en+                                          );+              }+        }+        if(!matrices->E_C[ij]) continue;++        unsigned int d1a = referenceBPs1[my_iindx[1]-j] - referenceBPs1[ij] - referenceBPs1[my_iindx[1]-i+1];+        unsigned int d1b = referenceBPs2[my_iindx[1]-j] - referenceBPs2[ij] - referenceBPs2[my_iindx[1]-i+1];++        for(cnt1 = matrices->k_min_C[ij]; cnt1 <= matrices->k_max_C[ij]; cnt1++)+          for(cnt2 = matrices->l_min_C[ij][cnt1]; cnt2 <= matrices->l_max_C[ij][cnt1]; cnt2+=2)+            for(cnt3 = matrices->k_min_F5[i-1]; cnt3 <= matrices->k_max_F5[i-1]; cnt3++)+              for(cnt4 = matrices->l_min_F5[i-1][cnt3]; cnt4 <= matrices->l_max_F5[i-1][cnt3]; cnt4+=2){+                if(matrices->E_F5[i-1][cnt3][cnt4/2] != INF && matrices->E_C[ij][cnt1][cnt2/2]!= INF){+                  if(((cnt1 + cnt3 + d1a) <= maxD1) && ((cnt2 + cnt4 + d1b) <= maxD2)){+                    matrices->E_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2] = MIN2( matrices->E_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2],+                                                                            matrices->E_F5[i-1][cnt3][cnt4/2] + matrices->E_C[ij][cnt1][cnt2/2] + additional_en+                                                                          );+                    updatePosteriorBoundaries(cnt1 + cnt3 + d1a,+                                              cnt2 + cnt4 + d1b,+                                              &min_k_real,+                                              &max_k_real,+                                              &min_l_real,+                                              &max_l_real+                                              );+#ifdef COUNT_STATES+                    matrices->N_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2] += matrices->N_F5[i-1][cnt3][cnt4/2] * matrices->N_C[ij][cnt1][cnt2/2];+#endif+                  }+                  /* collect all cases where d1a+cnt1+cnt3 or d1b+cnt2+cnt4 exceeds maxD1, maxD2, respectively */+                  else{+                    matrices->E_F5_rem[j] = MIN2(matrices->E_F5_rem[j],+                                              matrices->E_F5[i-1][cnt3][cnt4/2] + matrices->E_C[ij][cnt1][cnt2/2] + additional_en+                                              );+                  }+                }+              }+      }+    }++    /* resize and move memory portions of energy matrix E_F5 */+    adjustArrayBoundaries(&matrices->E_F5[j],+                          &matrices->k_min_F5[j],+                          &matrices->k_max_F5[j],+                          &matrices->l_min_F5[j],+                          &matrices->l_max_F5[j],+                          min_k_real,+                          max_k_real,+                          min_l_real,+                          max_l_real+                          );++  } /* end of j-loop */+++  if(compute_2Dfold_F3){++    /* prepare first entries in E_F3 */+    for(cnt1 = seq_length; cnt1 >= seq_length-TURN-1; cnt1--){+      matrices->E_F3[cnt1]        = (int **)vrna_alloc(sizeof(int *));+      matrices->E_F3[cnt1][0]     = (int *) vrna_alloc(sizeof(int));+      matrices->E_F3[cnt1][0][0]  = 0;+      matrices->k_min_F3[cnt1]     = matrices->k_max_F3[cnt1] = 0;+      matrices->l_min_F3[cnt1]     = (int *)vrna_alloc(sizeof(int));+      matrices->l_max_F3[cnt1]     = (int *)vrna_alloc(sizeof(int));+      matrices->l_min_F3[cnt1][0]  = matrices->l_max_F3[cnt1][0] = 0;+    }+    /* begin calculations */+    for (j=seq_length-TURN-2; j >= 1; j--){++      unsigned int da = referenceBPs1[my_iindx[j]-seq_length] - referenceBPs1[my_iindx[j+1]-seq_length];+      unsigned int db = referenceBPs2[my_iindx[j]-seq_length] - referenceBPs2[my_iindx[j+1]-seq_length];++      type=ptype[jindx[seq_length] + j];+      additional_en = 0;+      if(type){+        if(dangles == 2)+          additional_en += E_ExtLoop(type, j > 1 ? S1[j-1] : -1, -1, P);+        else+          additional_en += E_ExtLoop(type, -1, -1, P);+      }++      /* make min and max k guess for memory allocation */+      int min_k_guess, max_k_guess, min_l_guess, max_l_guess;+      int *min_l_real, *max_l_real, min_k_real, max_k_real;++      min_k_guess = min_l_guess = 0;+      max_k_guess = referenceBPs1[my_iindx[j]-seq_length] + mm1[my_iindx[j]-seq_length];+      max_l_guess = referenceBPs2[my_iindx[j]-seq_length] + mm2[my_iindx[j]-seq_length];++      prepareBoundaries(min_k_guess,+                        max_k_guess,+                        min_l_guess,+                        max_l_guess,+                        bpdist[my_iindx[j]-seq_length],+                        &matrices->k_min_F3[j],+                        &matrices->k_max_F3[j],+                        &matrices->l_min_F3[j],+                        &matrices->l_max_F3[j]+                        );++      preparePosteriorBoundaries( matrices->k_max_F3[j] - matrices->k_min_F3[j] + 1,+                                  matrices->k_min_F3[j],+                                  &min_k_real,+                                  &max_k_real,+                                  &min_l_real,+                                  &max_l_real+                                );++      prepareArray( &matrices->E_F3[j],+                    matrices->k_min_F3[j],+                    matrices->k_max_F3[j],+                    matrices->l_min_F3[j],+                    matrices->l_max_F3[j]+                  );+      /* begin the actual computation of 5' end energies */++      /* j is unpaired ... */+      for(cnt1 = matrices->k_min_F3[j+1]; cnt1 <= matrices->k_max_F3[j+1]; cnt1++){+        for(cnt2 = matrices->l_min_F3[j+1][cnt1]; cnt2 <= matrices->l_max_F3[j+1][cnt1]; cnt2+=2){+          matrices->E_F3[j][cnt1+da][(cnt2+db)/2] = MIN2( matrices->E_F3[j][cnt1+da][(cnt2+db)/2],+                                                      matrices->E_F3[j+1][cnt1][cnt2/2]+                                                    );+          updatePosteriorBoundaries(cnt1 + da,+                                    cnt2 + db,+                                    &min_k_real,+                                    &max_k_real,+                                    &min_l_real,+                                    &max_l_real+                                    );+        }+      }+      /* j pairs with n */+      if(matrices->E_C[my_iindx[j]-seq_length])+        for(cnt1 = matrices->k_min_C[my_iindx[j]-seq_length]; cnt1 <= matrices->k_max_C[my_iindx[j]-seq_length]; cnt1++)+          for(cnt2 = matrices->l_min_C[my_iindx[j]-seq_length][cnt1]; cnt2 <= matrices->l_max_C[my_iindx[j]-seq_length][cnt1]; cnt2+=2){+            if(matrices->E_C[my_iindx[j]-seq_length][cnt1][cnt2/2] != INF){+              matrices->E_F3[j][cnt1][cnt2/2] = MIN2( matrices->E_F3[j][cnt1][cnt2/2],+                                                  matrices->E_C[my_iindx[j]-seq_length][cnt1][cnt2/2]+ additional_en+                                                );+              updatePosteriorBoundaries(cnt1,+                                        cnt2,+                                        &min_k_real,+                                        &max_k_real,+                                        &min_l_real,+                                        &max_l_real+                                        );+            }+          }++      /* j pairs with some other nucleotide -> see below */+      for (i=j-TURN-1; i>1; i--) {+        ij = my_iindx[i]-j;+        if(!matrices->E_C[ij]) continue;+        type = ptype[jindx[j] + i];+        if (type) {+          unsigned int d1a = referenceBPs1[my_iindx[1]-j] - referenceBPs1[ij] - referenceBPs1[my_iindx[1]-i+1];+          unsigned int d1b = referenceBPs2[my_iindx[1]-j] - referenceBPs2[ij] - referenceBPs2[my_iindx[1]-i+1];++          if(dangles == 2)+            additional_en = E_ExtLoop(type, S1[i-1], j < seq_length ? S1[j+1] : -1, P);+          else+            additional_en = E_ExtLoop(type, -1, -1, P);++          for(cnt1 = matrices->k_min_C[ij]; cnt1 <= matrices->k_max_C[ij]; cnt1++)+            for(cnt2 = matrices->l_min_C[ij][cnt1]; cnt2 <= matrices->l_max_C[ij][cnt1]; cnt2+=2)+              for(cnt3 = matrices->k_min_F5[i-1]; cnt3 <= matrices->k_max_F5[i-1]; cnt3++)+                for(cnt4 = matrices->l_min_F5[i-1][cnt3]; cnt4 <= matrices->l_max_F5[i-1][cnt3]; cnt4+=2){+                  if(matrices->E_F5[i-1][cnt3][cnt4/2] != INF && matrices->E_C[ij][cnt1][cnt2/2]!= INF){+                    matrices->E_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2] = MIN2( matrices->E_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2],+                                                                            matrices->E_F5[i-1][cnt3][cnt4/2] + matrices->E_C[ij][cnt1][cnt2/2] + additional_en+                                                                          );+                    updatePosteriorBoundaries(cnt1 + cnt3 + d1a,+                                              cnt2 + cnt4 + d1b,+                                              &min_k_real,+                                              &max_k_real,+                                              &min_l_real,+                                              &max_l_real+                                              );+#ifdef COUNT_STATES+                    matrices->N_F5[j][cnt1+cnt3+d1a][(cnt2+cnt4+d1b)/2] += matrices->N_F5[i-1][cnt3][cnt4/2] * matrices->N_C[ij][cnt1][cnt2/2];+#endif+                  }+                }+        }+      }++      /* resize and move memory portions of energy matrix E_F5 */+      adjustArrayBoundaries(&matrices->E_F5[j],+                            &matrices->k_min_F5[j],+                            &matrices->k_max_F5[j],+                            &matrices->l_min_F5[j],+                            &matrices->l_max_F5[j],+                            min_k_real,+                            max_k_real,+                            min_l_real,+                            max_l_real+                            );++    } /* end of j-loop */+++++  }+}+++/*---------------------------------------------------------------------------*/++/*---------------------------------------------------------------------------*/++PRIVATE void+backtrack_f5( unsigned int j,+              int k,+              int l,+              char *structure,+              vrna_fold_compound_t *vc){++  int           *my_iindx, *jindx, energy, type, dangles, cnt1, cnt2, cnt3, cnt4;+  int           **l_min_C, **l_max_C,**l_min_F5, **l_max_F5;+  int           *k_min_C, *k_max_C,*k_min_F5, *k_max_F5;+  int           ***E_C, ***E_F5;+  int           *E_C_rem, *E_F5_rem;+  unsigned int   i, ij, seq_length, maxD1, maxD2;+  short *S1;+  unsigned int   *referenceBPs1, *referenceBPs2;+  char  *ptype;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_mx_mfe_t   *matrices;+  unsigned int   da, db;++  P               = vc->params;+  md              = &(P->model_details);+  matrices        = vc->matrices;+  seq_length      = vc->length;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  dangles         = md->dangles;+  E_F5            = matrices->E_F5;+  l_min_F5  = matrices->l_min_F5;+  l_max_F5  = matrices->l_max_F5;+  k_min_F5  = matrices->k_min_F5;+  k_max_F5  = matrices->k_max_F5;++  E_C             = matrices->E_C;+  l_min_C    = matrices->l_min_C;+  l_max_C    = matrices->l_max_C;+  k_min_C    = matrices->k_min_C;+  k_max_C    = matrices->k_max_C;++  E_F5_rem       = matrices->E_F5_rem;+  E_C_rem        = matrices->E_C_rem;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;++  da = referenceBPs1[my_iindx[1]-j] - referenceBPs1[my_iindx[1]-j+1];+  db = referenceBPs2[my_iindx[1]-j] - referenceBPs2[my_iindx[1]-j+1];++  if(j<TURN+2) return;++  /* F5[j] == F5[j-1] ? */+  if(k == -1){+    if(E_F5_rem[j]==INF)+      return;+    else if(E_F5_rem[j] == E_F5_rem[j-1]){+      backtrack_f5(j-1,k,l,structure, vc);+      return;+    }+    else if(E_F5[j-1]){+      for(cnt1 =  k_min_F5[j-1];+        cnt1 <= k_max_F5[j-1];+        cnt1++){+        for(cnt2 = l_min_F5[j-1][cnt1];+            cnt2 <= l_max_F5[j-1][cnt1];+            cnt2+=2){+          if(((cnt1 + da) > maxD1) || ((cnt2 + db) > maxD2)){+            if(E_F5_rem[j] == E_F5[j-1][cnt1][cnt2/2]){+              backtrack_f5(j-1, cnt1, cnt2, structure, vc);+              return;+            }+          }+        }+      }+    }+  }+  else if((k >= da) && (l >= db)){+    if(E_F5[j-1]){+      if((k - da >= k_min_F5[j-1]) && (k - da <= k_max_F5[j-1])){+        if((l - db >= l_min_F5[j-1][k-da]) && (l - db <= l_max_F5[j-1][k-da]))+          if(E_F5[j-1][k-da][(l-db)/2] == E_F5[j][k][l/2]){+            backtrack_f5(j-1, k-da, l-db, structure, vc);+            return;+          }+      }+    }+  }++  type = ptype[jindx[j] + 1];+  if(type){+    if(dangles == 2)+      energy = E_ExtLoop(type, -1, j < seq_length ? S1[j+1] : -1, P);+    else+      energy = E_ExtLoop(type, -1, -1, P);++    if(k == -1){+      if(E_C_rem[my_iindx[1]-j] + energy == E_F5_rem[j]){+          backtrack_c(1, j, -1, -1, structure, vc);+          return;+      }+    }+    else if(k >= k_min_C[my_iindx[1]-j] && (k <= k_max_C[my_iindx[1]-j])){++      if((l >= l_min_C[my_iindx[1]-j][k]) && (l <= l_max_C[my_iindx[1]-j][k]))+        if(E_C[my_iindx[1]-j][k][l/2] + energy == E_F5[j][k][l/2]){+          backtrack_c(1, j, k, l, structure, vc);+          return;+        }+    }+  }++  for (i=j-TURN-1; i>1; i--) {+    ij = my_iindx[i]-j;+    type = ptype[jindx[j] + i];+    if (type) {+      unsigned int d1a = referenceBPs1[my_iindx[1]-j] - referenceBPs1[ij] - referenceBPs1[my_iindx[1]-i+1];+      unsigned int d1b = referenceBPs2[my_iindx[1]-j] - referenceBPs2[ij] - referenceBPs2[my_iindx[1]-i+1];++      if(dangles == 2)+        energy = E_ExtLoop(type, S1[i-1], j < seq_length ? S1[j+1] : -1, P);+      else+        energy = E_ExtLoop(type, -1, -1, P);++      if(k == -1){+        if(E_C_rem[ij] != INF){+          for(cnt1 = k_min_F5[i-1];+              cnt1 <= k_max_F5[i-1];+              cnt1++){+            for(cnt2 = l_min_F5[i-1][cnt1];+                cnt2 <= l_max_F5[i-1][cnt1];+                cnt2+=2){+              if(E_F5_rem[j] == (E_F5[i-1][cnt1][cnt2/2] + E_C_rem[ij] + energy)){+                backtrack_f5(i-1, cnt1, cnt2, structure, vc);+                backtrack_c(i,j,-1,-1,structure, vc);+                return;+              }+            }+          }+          if(E_F5_rem[j] == (E_F5_rem[i-1] + E_C_rem[ij] + energy)){+            backtrack_f5(i-1, -1, -1, structure, vc);+            backtrack_c(i,j,-1,-1,structure,vc);+            return;+          }+        }+        if(E_F5_rem[i-1] != INF){+          for(cnt1 = k_min_C[ij];+              cnt1 <= k_max_C[ij];+              cnt1++){+            for(cnt2 = l_min_C[ij][cnt1];+                cnt2 <= l_max_C[ij][cnt1];+                cnt2 += 2){+               if(E_F5_rem[j] == (E_F5_rem[i-1] + E_C[ij][cnt1][cnt2/2] + energy)){+                backtrack_f5(i-1,-1,-1,structure,vc);+                backtrack_c(i,j,cnt1,cnt2,structure,vc);+                return;+              }+            }+          }+        }+        for(cnt1 = k_min_F5[i-1];+            cnt1 <= k_max_F5[i-1];+            cnt1++)+          for(cnt2 = l_min_F5[i-1][cnt1];+              cnt2 <= l_max_F5[i-1][cnt1];+              cnt2 += 2)+            for(cnt3 = k_min_C[ij];+                cnt3 <= k_max_C[ij];+                cnt3++)+              for(cnt4 = l_min_C[ij][cnt3];+                  cnt4 <= l_max_C[ij][cnt3];+                  cnt4 += 2){+                if(((cnt1 + cnt3 + d1a)>maxD1) || ((cnt2+cnt4+d1b)>maxD2)){+                  if(E_F5_rem[j] == (E_F5[i-1][cnt1][cnt2/2] + E_C[ij][cnt3][cnt4/2] + energy)){+                    backtrack_f5(i-1,cnt1,cnt2,structure,vc);+                    backtrack_c(i,j,cnt3,cnt4,structure,vc);+                    return;+                  }+                }+              }+      }+      else if((k >= d1a) && (l >= d1b)){+        int k_f_max = MIN2(k-d1a, k_max_F5[i-1]);++        for(cnt1 = k_min_F5[i-1]; cnt1 <= k_f_max; cnt1++){+          int l_f_max = MIN2(l - d1b, l_max_F5[i-1][cnt1]);+          for(cnt2 = l_min_F5[i-1][cnt1]; cnt2 <= l_f_max; cnt2+=2){+            int k_c = k - d1a - cnt1;+            if((k_c >= k_min_C[ij]) && (k_c <= k_max_C[ij])){+              int l_c = l - d1b - cnt2;+              if((l_c >= l_min_C[ij][k_c]) && (l_c <= l_max_C[ij][k_c])){+                if(E_F5[j][k][l/2] == (E_F5[i-1][cnt1][cnt2/2] + E_C[ij][k_c][l_c/2] + energy)){+                  backtrack_f5(i-1, cnt1, cnt2, structure, vc);+                  backtrack_c(i, j, k_c, l_c, structure, vc);+                  return;+                }+              }+            }+          }++        }+      }+    }+  }+  vrna_message_error("backtracking failed in f5");+}++PRIVATE void+backtrack_c(unsigned int i,+            unsigned int j,+            int k,+            int l,+            char *structure,+            vrna_fold_compound_t *vc){++  unsigned int p, q, pq, ij, maxp, maxD1, maxD2;+  int *my_iindx, *jindx, type, type_2, energy, no_close, dangles, base_d1, base_d2, d1, d2, cnt1, cnt2, cnt3, cnt4, *rtype;+  int           **l_min_C, **l_max_C,**l_min_M, **l_max_M,**l_min_M1, **l_max_M1;+  int           *k_min_C, *k_max_C,*k_min_M, *k_max_M,*k_min_M1, *k_max_M1;+  int           ***E_C, ***E_M, ***E_M1, *E_C_rem, *E_M_rem, *E_M1_rem;+  short *S1;+  unsigned int   *referenceBPs1, *referenceBPs2;+  char  *ptype,  *sequence;+  vrna_param_t   *P;+  vrna_md_t       *md;+  vrna_mx_mfe_t   *matrices;++  P               = vc->params;+  md              = &(P->model_details);+  matrices        = vc->matrices;+  sequence        = vc->sequence;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  rtype           = &(md->rtype[0]);+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  dangles         = md->dangles;++  E_C             = matrices->E_C;+  l_min_C    = matrices->l_min_C;+  l_max_C    = matrices->l_max_C;+  k_min_C    = matrices->k_min_C;+  k_max_C    = matrices->k_max_C;++  E_M             = matrices->E_M;+  l_min_M  = matrices->l_min_M;+  l_max_M  = matrices->l_max_M;+  k_min_M  = matrices->k_min_M;+  k_max_M  = matrices->k_max_M;++  E_M1            = matrices->E_M1;+  l_min_M1 = matrices->l_min_M1;+  l_max_M1 = matrices->l_max_M1;+  k_min_M1 = matrices->k_min_M1;+  k_max_M1 = matrices->k_max_M1;++  E_C_rem        = matrices->E_C_rem;+  E_M_rem        = matrices->E_M_rem;+  E_M1_rem       = matrices->E_M1_rem;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+++  ij = my_iindx[i]-j;++  int e = (k==-1) ? E_C_rem[ij] : E_C[ij][k][l/2];++  type = ptype[jindx[j] + i];++  no_close = (((type==3)||(type==4))&&no_closingGU);+  structure[i-1] = '(';+  structure[j-1] = ')';++  base_d1 = ((unsigned int)vc->reference_pt1[i] != j) ? 1 : -1;+  base_d2 = ((unsigned int)vc->reference_pt2[i] != j) ? 1 : -1;++  base_d1 += referenceBPs1[ij];+  base_d2 += referenceBPs2[ij];++  if(k == -1){+    if(((unsigned int)base_d1 > maxD1) || ((unsigned int)base_d2 > maxD2)){+      if(e == E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], sequence+i-1, P)) return;+    }+  }+  else{+    if((unsigned int)base_d1 == k)+      if((unsigned int)base_d2 == l)+        if(E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], sequence+i-1, P) == e) return;+  }+  maxp = MIN2(j-2-TURN,i+MAXLOOP+1);+  for(p = i+1; p <= maxp; p++){+    unsigned int minq, ln_pre;+    minq = p + TURN + 1;+    ln_pre = j - i - 1;+    if(ln_pre > minq + MAXLOOP) minq = ln_pre - MAXLOOP - 1;+    for (q = minq; q < j; q++) {+      pq = my_iindx[p]-q;+      type_2 = ptype[jindx[q] + p];+      if (type_2==0) continue;+      type_2 = rtype[type_2];++      /* d2 = dbp(S_{i,j}, S_{p.q} + {i,j}) */+      d1 = base_d1 - referenceBPs1[pq];+      d2 = base_d2 - referenceBPs2[pq];++      energy = E_IntLoop(p-i-1, j-q-1, type, type_2, S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);+++      if(k == -1){+        if(E_C_rem[pq] != INF)+          if(e == (E_C_rem[pq] + energy)){+            backtrack_c(p,q,-1,-1,structure,vc);+            return;+          }+        if(E_C[pq])+        for(cnt1 = k_min_C[pq];+            cnt1 <= k_max_C[pq];+            cnt1++)+          for(cnt2 = l_min_C[pq][cnt1];+              cnt2 <= l_max_C[pq][cnt1];+              cnt2 += 2){+            if(((cnt1 + d1) > maxD1) || ((cnt2 + d2) > maxD2)){+              if(e == (E_C[pq][cnt1][cnt2/2] + energy)){+                backtrack_c(p,q,cnt1,cnt2,structure,vc);+                return;+              }+            }+          }+      }+      else{+        if(!E_C[pq]) continue;+        if(d1 <= k && d2 <= l){+          if((k-d1 >= k_min_C[pq]) && (k-d1) <= k_max_C[pq])+            if((l - d2 >= l_min_C[pq][k-d1]) && (l-d2 <= l_max_C[pq][k-d1]))+              if(E_C[pq][k-d1][(l-d2)/2] + energy == e){+                backtrack_c(p, q, k-d1, l-d2, structure, vc);+                return;+              }+        }+      }+    } /* end q-loop */+  } /* end p-loop */++  /* multi-loop decomposition ------------------------*/+  if(!no_close){+    unsigned int u;+    int tt;+    if(k==-1){+      for(u=i+TURN+2; u<j-TURN-2;u++){+        int i1u, u1j1;+        i1u   = my_iindx[i+1]-u;+        u1j1  = my_iindx[u+1]-j+1;+        tt = rtype[type];+        energy = P->MLclosing;+        if(dangles == 2)+          energy += E_MLstem(tt, S1[j-1], S1[i+1], P);+        else+          energy += E_MLstem(tt, -1, -1, P);+++        if(E_M_rem[i1u] != INF){+          if(E_M1[u1j1])+          for(cnt1 = k_min_M1[u1j1];+              cnt1 <= k_max_M1[u1j1];+              cnt1++)+            for(cnt2 = l_min_M1[u1j1][cnt1];+                cnt2 <= l_max_M1[u1j1][cnt1];+                cnt2 += 2){+              if(e == (E_M_rem[i1u] + E_M1[u1j1][cnt1][cnt2/2] + energy)){+                backtrack_m(i+1,u,-1,-1,structure,vc);+                backtrack_m1(u+1,j-1,cnt1,cnt2,structure,vc);+                return;+              }+            }+          if(E_M1_rem[u1j1] != INF){+            if(e == (E_M_rem[i1u] + E_M1_rem[u1j1] + energy)){+              backtrack_m(i+1, u, -1, -1, structure, vc);+              backtrack_m1(u+1, j-1, -1, -1, structure, vc);+              return;+            }+          }+        }+        if(E_M1_rem[u1j1] != INF){+          if(E_M[i1u])+          for(cnt1 = k_min_M[i1u];+              cnt1 <= k_max_M[i1u];+              cnt1++)+            for(cnt2 = l_min_M[i1u][cnt1];+                cnt2 <= l_max_M[i1u][cnt1];+                cnt2 += 2)+              if(e == (E_M[i1u][cnt1][cnt2/2] + E_M1_rem[u1j1] + energy)){+                backtrack_m(i+1,u,cnt1,cnt2,structure,vc);+                backtrack_m1(u+1,j-1,-1,-1,structure,vc);+                return;+              }+        }++        /* now all cases where we exceed the maxD1/D2 scope by combination of E_M and E_M1 */+        if(!E_M[i1u]) continue;+        if(!E_M1[u1j1]) continue;+        /* get distance to reference if closing this multiloop+        *  dist3 = dbp(S_{i,j}, {i,j} + S_{i+1.u} + S_{u+1,j-1})+        */+        d1 = base_d1 - referenceBPs1[i1u] - referenceBPs1[u1j1];+        d2 = base_d2 - referenceBPs2[i1u] - referenceBPs2[u1j1];+        +        for(cnt1 = matrices->k_min_M[i1u];+            cnt1 <= matrices->k_max_M[i1u];+            cnt1++)+          for(cnt2 = matrices->l_min_M[i1u][cnt1];+              cnt2 <= matrices->l_max_M[i1u][cnt1];+              cnt2+=2)+            for(cnt3 = matrices->k_min_M1[u1j1];+                cnt3 <= matrices->k_max_M1[u1j1];+                cnt3++)+              for(cnt4 = matrices->l_min_M1[u1j1][cnt3];+                  cnt4 <= matrices->l_max_M1[u1j1][cnt3];+                  cnt4+=2){+                if(((cnt1 + cnt3 + d1) > maxD1) || ((cnt2 + cnt4 + d2) > maxD2)){+                  if(e == (E_M[i1u][cnt1][cnt2/2] + E_M1[u1j1][cnt3][cnt4/2] + energy)){+                    backtrack_m(i+1,u,cnt1,cnt2,structure,vc);+                    backtrack_m1(u+1,j-1,cnt3,cnt4,structure,vc);+                    return;+                  }+                }+              }+      }+    }+    else{+      for(u=i+TURN+2; u<j-TURN-2;u++){+        int i1u, u1j1;+        i1u   = my_iindx[i+1]-u;+        u1j1  = my_iindx[u+1]-j+1;+        if(!E_M[i1u]) continue;+        if(!E_M1[u1j1]) continue;++        /* get distance to reference if closing this multiloop+        *  dist3 = dbp(S_{i,j}, {i,j} + S_{i+1.u} + S_{u+1,j-1})+        */+        d1 = base_d1 - referenceBPs1[i1u] - referenceBPs1[u1j1];+        d2 = base_d2 - referenceBPs2[i1u] - referenceBPs2[u1j1];++        tt = rtype[type];+        energy = P->MLclosing;+        if(dangles == 2)+          energy += E_MLstem(tt, S1[j-1], S1[i+1], P);+        else+          energy += E_MLstem(tt, -1, -1, P);++        if((d1 <= k) && (d2 <= l))+          for(cnt1 = k_min_M[i1u];+              cnt1 <= MIN2(k-d1, k_max_M[i1u]);+              cnt1++)+            for(cnt2 = l_min_M[i1u][cnt1];+                cnt2 <= MIN2(l-d2, l_max_M[i1u][cnt1]);+                cnt2+=2)+              if(     ((k-d1-cnt1) >= k_min_M1[u1j1])+                  &&  ((k-d1-cnt1) <= k_max_M1[u1j1]))+                if(     ((l-d2-cnt2) >= l_min_M1[u1j1][k-d1-cnt1])+                    &&  ((l-d2-cnt2) <= l_max_M1[u1j1][k-d1-cnt1]))+                  if(e == (energy + E_M[i1u][cnt1][cnt2/2] + E_M1[u1j1][k-d1-cnt1][(l-d2-cnt2)/2])){+                    backtrack_m(i+1, u, cnt1, cnt2, structure, vc);+                    backtrack_m1(u+1, j-1, k-d1-cnt1, l-d2-cnt2, structure, vc);+                    return;+                  }+      }+    }+  }+  vrna_message_error("backtracking failed in c");+}++PRIVATE void+backtrack_m(unsigned int i,+            unsigned int j,+            int k,+            int l,+            char *structure,+            vrna_fold_compound_t *vc){++  unsigned int u, ij, seq_length, base_d1, base_d2, d1, d2, maxD1, maxD2;+  int *my_iindx, *jindx, type, energy, dangles,circ, cnt1, cnt2, cnt3, cnt4;+  int           **l_min_C, **l_max_C,**l_min_M, **l_max_M;+  int           *k_min_C, *k_max_C,*k_min_M, *k_max_M;+  int           ***E_C, ***E_M, *E_C_rem, *E_M_rem;+  short *S1;+  unsigned int   *referenceBPs1, *referenceBPs2;+  char  *ptype;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_mx_mfe_t   *matrices;++  P           = vc->params;+  md          = &(P->model_details);+  matrices    = vc->matrices;+  seq_length  = vc->length;+  S1          = vc->sequence_encoding;+  circ        = md->circ;+  ptype       = vc->ptype;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  referenceBPs1  = vc->referenceBPs1;+  referenceBPs2  = vc->referenceBPs2;+  dangles     = md->dangles;++  E_C             = matrices->E_C;+  l_min_C    = matrices->l_min_C;+  l_max_C    = matrices->l_max_C;+  k_min_C    = matrices->k_min_C;+  k_max_C    = matrices->k_max_C;++  E_M             = matrices->E_M;+  l_min_M  = matrices->l_min_M;+  l_max_M  = matrices->l_max_M;+  k_min_M  = matrices->k_min_M;+  k_max_M  = matrices->k_max_M;++  E_C_rem        = matrices->E_C_rem;+  E_M_rem        = matrices->E_M_rem;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;++  ij = my_iindx[i]-j;+  int e = (k == -1) ? E_M_rem[ij] : E_M[ij][k][l/2];++  base_d1 = referenceBPs1[ij];+  base_d2 = referenceBPs2[ij];++  if(k == -1){+    /* new_fML = ML(i+1,j)+c */+    d1 = base_d1 - referenceBPs1[my_iindx[i+1]-j];+    d2 = base_d2 - referenceBPs2[my_iindx[i+1]-j];+    if(E_M_rem[my_iindx[i+1]-j] != INF){+      if(e == (E_M_rem[my_iindx[i+1]-j] + P->MLbase)){+        backtrack_m(i+1,j,-1,-1,structure,vc);+        return;+      }+    }+    if(E_M[my_iindx[i+1]-j])+    for(cnt1 = k_min_M[my_iindx[i+1]-j];+        cnt1 <= k_max_M[my_iindx[i+1]-j];+        cnt1++)+      for(cnt2 = l_min_M[my_iindx[i+1]-j][cnt1];+          cnt2 <= l_max_M[my_iindx[i+1]-j][cnt1];+          cnt2 += 2)+        if(((cnt1 + d1) > maxD1) || ((cnt2 + d2) > maxD2)){+          if(e == (E_M[my_iindx[i+1]-j][cnt1][cnt2/2] + P->MLbase)){+            backtrack_m(i+1,j,cnt1,cnt2,structure,vc);+            return;+          }+        }++    /* new_fML = min(ML(i,j-1) + c, new_fML) */+    d1 = base_d1 - referenceBPs1[ij+1];+    d2 = base_d2 - referenceBPs2[ij+1];+    if(E_M_rem[ij+1] != INF){+      if(e == (E_M_rem[ij+1] + P->MLbase)){+        backtrack_m(i,j-1,-1,-1,structure,vc);+        return;+      }+    }+    if(E_M[ij+1])+    for(cnt1 = k_min_M[ij+1];+        cnt1 <= k_max_M[ij+1];+        cnt1++)+      for(cnt2 = l_min_M[ij+1][cnt1];+          cnt2 <= l_max_M[ij+1][cnt1];+          cnt2 += 2)+        if(((cnt1 + d1) > maxD1) || ((cnt2 + d2) > maxD2)){+          if(e == (E_M[ij+1][cnt1][cnt2/2] + P->MLbase)){+            backtrack_m(i,j-1,cnt1,cnt2,structure,vc);+            return;+          }+        }++    /* new_fML = min(new_fML, C(i,j)+b) */+    if(E_C_rem[ij] != INF){+      type = ptype[jindx[j] + i];+      if(dangles == 2)+        energy = E_MLstem(type, ((i > 1) || circ) ? S1[i-1] : -1, ((j < seq_length) || circ) ? S1[j+1] : -1, P);+      else+        energy = E_MLstem(type, -1, -1, P);+      if(e == (E_C_rem[ij] + energy)){+        backtrack_c(i,j,-1,-1,structure,vc);+        return;+      }+    }++    /* modular decomposition -------------------------------*/+    for(u = i+1+TURN; u <= j-2-TURN; u++){+      int iu, uj;+      iu = my_iindx[i]-u;+      uj = my_iindx[u+1]-j;+      type = ptype[jindx[j] + u + 1];++      d1 = base_d1 - referenceBPs1[iu] - referenceBPs1[uj];+      d2 = base_d2 - referenceBPs2[iu] - referenceBPs2[uj];++      if(dangles == 2)+        energy = E_MLstem(type, S1[u], (j < seq_length) || circ ? S1[j+1] : -1, P);+      else+        energy = E_MLstem(type, -1, -1, P);++      if(E_M_rem[iu] != INF){+        if(E_C[uj])+        for(cnt1 = k_min_C[uj];+            cnt1 <= k_max_C[uj];+            cnt1++)+          for(cnt2 = l_min_C[uj][cnt1];+              cnt2 <= l_max_C[uj][cnt1];+              cnt2 += 2)+            if(e == (E_M_rem[iu] + E_C[uj][cnt1][cnt2/2] + energy)){+              backtrack_m(i,u,-1,-1,structure,vc);+              backtrack_c(u+1,j,cnt1,cnt2,structure, vc);+              return;+            }+        if(E_C_rem[uj] != INF){+          if(e == (E_M_rem[iu] + E_C_rem[uj] + energy)){+            backtrack_m(i,u,-1,-1,structure,vc);+            backtrack_c(u+1,j,-1,-1,structure,vc);+            return;+          }+        }+      }+      if(E_C_rem[uj] != INF){+        if(E_M[iu])+        for(cnt1 = k_min_M[iu];+            cnt1 <= k_max_M[iu];+            cnt1++)+          for(cnt2 = l_min_M[iu][cnt1];+              cnt2 <= l_max_M[iu][cnt1];+              cnt2 += 2)+            if(e == (E_M[iu][cnt1][cnt2/2] + E_C_rem[uj] + energy)){+              backtrack_m(i,u,cnt1,cnt2,structure,vc);+              backtrack_c(u+1,j,-1,-1,structure,vc);+              return;+            }+      }++      if(!E_M[iu]) continue;+      if(!E_C[uj]) continue;++      for(cnt1 = k_min_M[iu];+          cnt1 <= k_max_M[iu];+          cnt1++)+        for(cnt2 = l_min_M[iu][cnt1];+            cnt2 <= l_max_M[iu][cnt1];+            cnt2 += 2)+          for(cnt3 = k_min_C[uj];+              cnt3 <= k_max_C[uj];+              cnt3++){+            for(cnt4 = l_min_C[uj][cnt3];+                cnt4 <= l_max_C[uj][cnt3];+                cnt4 += 2)+              if(((cnt1 + cnt3 + d1) > maxD1) || ((cnt2 + cnt4 + d2) > maxD2))+                if(e == (E_M[iu][cnt1][cnt2/2] + E_C[uj][cnt3][cnt4/2] + energy)){+                  backtrack_m(i, u, cnt1, cnt2, structure, vc);+                  backtrack_c(u+1, j, cnt3, cnt4, structure, vc);+                  return;+                }+          }+    }++  } /* end if (k == -1) */+  else{+    d1 = base_d1 - referenceBPs1[my_iindx[i+1]-j];+    d2 = base_d2 - referenceBPs2[my_iindx[i+1]-j];+    /* new_fML = ML(i+1,j)+c */+    if(d1 <= k && d2 <= l)+      if((k-d1 >= k_min_M[my_iindx[i+1]-j]) && (k-d1 <= k_max_M[my_iindx[i+1]-j]))+        if((l-d2 >= l_min_M[my_iindx[i+1]-j][k-d1]) && (l-d2 <= l_max_M[my_iindx[i+1]-j][k-d1])){+          if(E_M[my_iindx[i+1]-j][k-d1][(l-d2)/2] + P->MLbase == e){+            backtrack_m(i+1, j, k-d1, l-d2, structure, vc);+            return;+          }+        }++    d1 = base_d1 - referenceBPs1[ij+1];+    d2 = base_d2 - referenceBPs2[ij+1];++    /* new_fML = min(ML(i,j-1) + c, new_fML) */+    if(E_M[ij+1])+      if(d1 <= k && d2 <= l)+        if((k-d1 >= k_min_M[ij+1]) && (k-d1 <= k_max_M[ij+1]))+          if((l-d2 >= l_min_M[ij+1][k-d1]) && (l-d2 <= l_max_M[ij+1][k-d1]))+            if(E_M[ij+1][k-d1][(l-d2)/2] + P->MLbase == e){+              backtrack_m(i, j-1, k-d1, l-d2, structure, vc);+              return;+            }++    /* new_fML = min(new_fML, C(i,j)+b) */+    if(E_C[ij]){+      type = ptype[jindx[j] + i];++      if(dangles == 2)+        energy = E_MLstem(type, ((i > 1) || circ) ? S1[i-1] : -1, ((j < seq_length) || circ) ? S1[j+1] : -1, P);+      else+        energy = E_MLstem(type, -1, -1, P);++      if((k >= k_min_C[ij]) && (k <= k_max_C[ij]))+        if((l >= l_min_C[ij][k]) && (l <= l_max_C[ij][k])){+          if(E_C[ij][k][l/2] + energy == e){+            backtrack_c(i, j, k, l, structure, vc);+            return;+          }+        }+    }++      /* modular decomposition -------------------------------*/++    for(u = i+1+TURN; u <= j-2-TURN; u++){+      if(!E_M[my_iindx[i]-u]) continue;+      if(!E_C[my_iindx[u+1]-j]) continue;+      type = ptype[jindx[j] + u + 1];++      d1 = base_d1 - referenceBPs1[my_iindx[i]-u] - referenceBPs1[my_iindx[u+1]-j];+      d2 = base_d2 - referenceBPs2[my_iindx[i]-u] - referenceBPs2[my_iindx[u+1]-j];++      if(dangles == 2)+        energy = E_MLstem(type, S1[u], ((j < seq_length) || circ) ? S1[j+1] : -1, P);+      else+        energy = E_MLstem(type, -1, -1, P);++      if(d1 <= k && d2 <= l)+        for(cnt1 = k_min_M[my_iindx[i]-u]; cnt1 <= MIN2(k-d1, k_max_M[my_iindx[i]-u]); cnt1++)+          for(cnt2 = l_min_M[my_iindx[i]-u][cnt1]; cnt2 <= MIN2(l-d2, l_max_M[my_iindx[i]-u][cnt1]); cnt2+=2)+            if((k-d1-cnt1 >= k_min_C[my_iindx[u+1]-j]) && (k-d1-cnt1 <= k_max_C[my_iindx[u+1]-j]))+              if((l-d2-cnt2 >= l_min_C[my_iindx[u+1]-j][k-d1-cnt1]) && (l-d2-cnt2 <= l_max_C[my_iindx[u+1]-j][k-d1-cnt1]))+                if(E_M[my_iindx[i]-u][cnt1][cnt2/2] + E_C[my_iindx[u+1]-j][k-d1-cnt1][(l-d2-cnt2)/2] + energy == e){+                  backtrack_m(i, u, cnt1, cnt2, structure, vc);+                  backtrack_c(u+1, j, k-d1-cnt1, l-d2-cnt2, structure, vc);+                  return;+                }+    }+  }+  vrna_message_error("backtracking failed in fML\n");+}++PRIVATE void+backtrack_m1( unsigned int i,+              unsigned int j,+              int k,+              int l,+              char *structure,+              vrna_fold_compound_t *vc){++  unsigned int  ij, seq_length, d1, d2, *referenceBPs1, *referenceBPs2, maxD1, maxD2;+  int           *my_iindx, *jindx, **l_min_C, **l_max_C,**l_min_M1, **l_max_M1;+  int           *k_min_C, *k_max_C,*k_min_M1, *k_max_M1, cnt1, cnt2;+  int           ***E_C, ***E_M1, *E_C_rem, *E_M1_rem, type, dangles, circ, energy, e_m1;++  short         *S1;+  char          *ptype;+  vrna_param_t  *P;+  vrna_md_t     *md;+  vrna_mx_mfe_t *matrices;++  P               = vc->params;+  md              = &(P->model_details);+  matrices        = vc->matrices;+  seq_length      = vc->length;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  circ            = md->circ;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  dangles         = md->dangles;++  E_C             = matrices->E_C;+  l_min_C    = matrices->l_min_C;+  l_max_C    = matrices->l_max_C;+  k_min_C    = matrices->k_min_C;+  k_max_C    = matrices->k_max_C;++  E_M1            = matrices->E_M1;+  l_min_M1 = matrices->l_min_M1;+  l_max_M1 = matrices->l_max_M1;+  k_min_M1 = matrices->k_min_M1;+  k_max_M1 = matrices->k_max_M1;++  E_C_rem        = matrices->E_C_rem;+  E_M1_rem       = matrices->E_M1_rem;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;++  ij    = my_iindx[i]-j;+  e_m1  = (k == -1) ? E_M1_rem[ij] : E_M1[ij][k][l/2];++  type = ptype[jindx[j] + i];+  d1 = referenceBPs1[ij] - referenceBPs1[ij+1];+  d2 = referenceBPs2[ij] - referenceBPs2[ij+1];++  if(dangles == 2)+    energy = E_MLstem(type, (i > 1) || circ ? S1[i-1] : -1, (j < seq_length) || circ ? S1[j+1] : -1, P);+  else+    energy = E_MLstem(type, -1, -1, P);++  if(k == -1){+    if(E_C_rem[ij] != INF){+      if(e_m1 == (E_C_rem[ij] + energy)){+        backtrack_c(i,j,-1,-1,structure,vc);+        return;+      }+    }+    if(E_M1_rem[ij+1] != INF){+      if(e_m1 == (E_M1_rem[ij+1] + P->MLbase)){+        backtrack_m1(i,j-1,-1,-1,structure,vc);+        return;+      }+    }+    for(cnt1 = k_min_M1[ij+1];+        cnt1 <= k_max_M1[ij+1];+        cnt1++)+      for(cnt2 = l_min_M1[ij+1][cnt1];+          cnt2 <= l_max_M1[ij+1][cnt1];+          cnt2 += 2)+        if(((cnt1 + d1) > maxD1) || ((cnt2 + d2) > maxD2)){+          if(e_m1  == (E_M1[ij+1][cnt1][cnt2/2] + P->MLbase)){+            backtrack_m1(i,j-1,cnt1,cnt2,structure,vc);+            return;+          }+        }+  }+  else{+    if(E_C[ij])+      if((k >= k_min_C[ij]) && (k <= k_max_C[ij]))+        if((l >= l_min_C[ij][k]) && (l <= l_max_C[ij][k]))+          if(E_C[ij][k][l/2] + energy == e_m1){+            backtrack_c(i, j, k, l, structure, vc);+            return;+          }++    if(d1 <= k && d2 <= l)+      if((k-d1 >= k_min_M1[ij+1]) && (k-d1 <= k_max_M1[ij+1]))+        if((l-d2 >= l_min_M1[ij+1][k-d1]) && (l-d2 <= l_max_M1[ij+1][k-d1]))+          if(E_M1[ij+1][k-d1][(l-d2)/2] + P->MLbase == e_m1){+            backtrack_m1(i, j-1, k-d1, l-d2, structure, vc);+            return;+          }+  }+  vrna_message_error("backtack failed in m1\n");+}++PRIVATE void+backtrack_fc( int k,+              int l,+              char *structure,+              vrna_fold_compound_t *vc){++  unsigned int   d, i, j, seq_length, base_d1, base_d2, d1, d2, maxD1, maxD2;+  int   *my_iindx, *jindx, energy, cnt1, cnt2, cnt3, cnt4, *rtype;+  short *S1;+  unsigned int   *referenceBPs1, *referenceBPs2;+  char  *sequence, *ptype;+  int **E_Fc, **E_FcH, **E_FcI, **E_FcM, ***E_C, ***E_M, ***E_M2;+  int *E_C_rem, *E_M_rem, *E_M2_rem, E_Fc_rem, E_FcH_rem, E_FcI_rem, E_FcM_rem;+  int **l_min_C, **l_max_C, *k_min_C, *k_max_C;+  int **l_min_M, **l_max_M, *k_min_M, *k_max_M;+  int **l_min_M2, **l_max_M2, *k_min_M2, *k_max_M2;+  int *l_min_FcH, *l_max_FcH, k_min_FcH, k_max_FcH;+  int *l_min_FcI, *l_max_FcI, k_min_FcI, k_max_FcI;+  int *l_min_FcM, *l_max_FcM, k_min_FcM, k_max_FcM;+  vrna_param_t   *P;+  vrna_md_t     *md;+  vrna_mx_mfe_t *matrices;++  P                 = vc->params;+  md                = &(P->model_details);+  matrices          = vc->matrices;+  sequence          = vc->sequence;+  seq_length        = vc->length;+  S1                = vc->sequence_encoding;+  ptype             = vc->ptype;+  rtype             = &(md->rtype[0]);+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  referenceBPs1     = vc->referenceBPs1;+  referenceBPs2     = vc->referenceBPs2;++  base_d1           = referenceBPs1[my_iindx[1]-seq_length];+  base_d2           = referenceBPs2[my_iindx[1]-seq_length];++  E_C               = matrices->E_C;+  l_min_C      = matrices->l_min_C;+  l_max_C      = matrices->l_max_C;+  k_min_C      = matrices->k_min_C;+  k_max_C      = matrices->k_max_C;++  E_M               = matrices->E_M;+  l_min_M    = matrices->l_min_M;+  l_max_M    = matrices->l_max_M;+  k_min_M    = matrices->k_min_M;+  k_max_M    = matrices->k_max_M;++  E_M2              = matrices->E_M2;+  l_min_M2   = matrices->l_min_M2;+  l_max_M2   = matrices->l_max_M2;+  k_min_M2   = matrices->k_min_M2;+  k_max_M2   = matrices->k_max_M2;++  E_Fc              = matrices->E_Fc;++  E_FcI             = matrices->E_FcI;+  l_min_FcI  = matrices->l_min_FcI;+  l_max_FcI  = matrices->l_max_FcI;+  k_min_FcI  = matrices->k_min_FcI;+  k_max_FcI  = matrices->k_max_FcI;++  E_FcH             = matrices->E_FcH;+  l_min_FcH  = matrices->l_min_FcH;+  l_max_FcH  = matrices->l_max_FcH;+  k_min_FcH  = matrices->k_min_FcH;+  k_max_FcH  = matrices->k_max_FcH;++  E_FcM             = matrices->E_FcM;+  l_min_FcM  = matrices->l_min_FcM;+  l_max_FcM  = matrices->l_max_FcM;+  k_min_FcM  = matrices->k_min_FcM;+  k_max_FcM  = matrices->k_max_FcM;++  E_C_rem          = matrices->E_C_rem;+  E_M_rem          = matrices->E_M_rem;+  E_M2_rem         = matrices->E_M2_rem;+  E_Fc_rem         = matrices->E_Fc_rem;+  E_FcH_rem        = matrices->E_FcH_rem;+  E_FcI_rem        = matrices->E_FcI_rem;+  E_FcM_rem        = matrices->E_FcM_rem;+  maxD1             = vc->maxD1;+  maxD2             = vc->maxD2;+++  if(k==-1){+    /* check if mfe might be open chain */+    if(E_Fc_rem == 0)+      if((referenceBPs1[my_iindx[1]-seq_length] > maxD1) || (referenceBPs2[my_iindx[1]-seq_length] > maxD2))+        return;++    /* check for hairpin configurations */+    if(E_Fc_rem == E_FcH_rem){+      for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+        for (j = d; j <= seq_length; j++) {+          unsigned int u, ij;+          int type, no_close;+          char loopseq[10];+          i = j-d+1;+          ij = my_iindx[i]-j;+          u = seq_length-j + i-1;+          if (u<TURN) continue;+          type = ptype[jindx[j] + i];+          no_close = (((type==3)||(type==4))&&no_closingGU);+          type=rtype[type];+          if (!type) continue;+          if(no_close) continue;++          d1 = base_d1 - referenceBPs1[ij];+          d2 = base_d2 - referenceBPs2[ij];+          if (u<7) {+            strcpy(loopseq , sequence+j-1);+            strncat(loopseq, sequence, i);+          }+          energy = E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, P);++          if(E_C_rem[ij] != INF){+            if(E_Fc_rem == (E_C_rem[ij] + energy)){+              backtrack_c(i,j,-1,-1,structure,vc);+              return;+            }+          }+          if(E_C[ij])+            for(cnt1 = k_min_C[ij];+                cnt1 <= k_max_C[ij];+                cnt1++)+              for(cnt2 = l_min_C[ij][cnt1];+                  cnt2 <= l_max_C[ij][cnt1];+                  cnt2 += 2)+                if(((cnt1 + d1) > maxD1) || ((cnt2 + d2) > maxD2))+                  if(E_Fc_rem == (E_C[ij][cnt1][cnt2/2] + energy)){+                    backtrack_c(i,j,cnt1,cnt2,structure,vc);+                    return;+                  }+        }+    }++    /* check for interior loop configurations */+    if(E_Fc_rem == E_FcI_rem){+      for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+        for (j = d; j <= seq_length; j++) {+          unsigned int u, ij, p, q, pq;+          int type, type_2;+          i = j-d+1;+          ij = my_iindx[i]-j;+          u = seq_length-j + i-1;+          if (u<TURN) continue;+          type = rtype[(unsigned int)ptype[jindx[j] + i]];+          if (!type) continue;++          for(p = j+1; p < seq_length ; p++){+            unsigned int u1, qmin, ln_pre;+            u1 = p-j-1;+            if (u1+i-1>MAXLOOP) break;+            qmin = p + TURN + 1;+            ln_pre = u1 + i + seq_length;+            if(ln_pre > qmin + MAXLOOP) qmin = ln_pre - MAXLOOP - 1;+            for(q = qmin; q <= seq_length; q++){+              unsigned int u2;+              pq = my_iindx[p]-q;+              type_2 = rtype[(unsigned int)ptype[jindx[q] + p]];+              if (type_2==0) continue;+              u2 = i-1 + seq_length-q;+              if (u1+u2>MAXLOOP) continue;+              energy = E_IntLoop(u1, u2, type, type_2, S1[j+1], S1[i-1], S1[p-1], S1[q+1], P);+              if(E_C_rem[ij] != INF){+                if(E_C[pq])+                  for(cnt1 = k_min_C[pq];+                      cnt1 <= k_max_C[pq];+                      cnt1++)+                    for(cnt2 = l_min_C[pq][cnt1];+                        cnt2 <= l_max_C[pq][cnt1];+                        cnt2 += 2)+                      if(E_Fc_rem == (E_C_rem[ij] + E_C[pq][cnt1][cnt2/2] + energy)){+                        backtrack_c(i,j,-1,-1,structure,vc);+                        backtrack_c(p,q,cnt1,cnt2,structure,vc);+                        return;+                      }+                if(E_C_rem[pq] != INF){+                  if(E_Fc_rem == (E_C_rem[ij] + E_C_rem[pq] + energy)){+                    backtrack_c(i,j,-1,-1,structure,vc);+                    backtrack_c(p,q,-1,-1,structure,vc);+                    return;+                  }+                }+              }+              if(E_C_rem[pq] != INF){+                if(E_C[ij])+                  for(cnt1 = k_min_C[ij];+                      cnt1 <= k_max_C[ij];+                      cnt1++)+                    for(cnt2 = l_min_C[ij][cnt1];+                        cnt2 <= l_max_C[ij][cnt1];+                        cnt2 += 2)+                      if(E_Fc_rem == (E_C[ij][cnt1][cnt2/2] + E_C_rem[pq] + energy)){+                        backtrack_c(i,j,cnt1,cnt2,structure,vc);+                        backtrack_c(p,q,-1,-1,structure,vc);+                        return;+                      }+              }++              if(!(E_C[ij])) continue;+              if(!(E_C[pq])) continue;++              /* get distance to reference if closing the interior loop+              *  d2a = dbp(T1_[1,n}, T1_{p,q} + T1_{i,j})+              *  d2b = dbp(T2_[1,n}, T2_{p,q} + T2_{i,j})+              */+              d1 = base_d1 - referenceBPs1[ij] - referenceBPs1[pq];+              d2 = base_d2 - referenceBPs2[ij] - referenceBPs2[pq];+              for(cnt1 = k_min_C[ij];+                  cnt1 <= k_max_C[ij];+                  cnt1++)+                for(cnt2 = l_min_C[ij][cnt1];+                    cnt2 <= l_max_C[ij][cnt1];+                    cnt2 += 2)+                  for(cnt3 = k_min_C[pq];+                      cnt3 <= k_max_C[pq];+                      cnt3++)+                    for(cnt4 = l_min_C[pq][cnt3];+                        cnt4 <= l_max_C[pq][cnt3];+                        cnt4 += 2)+                      if(((cnt1 + cnt3 + d1) > maxD1) || ((cnt2 + cnt4 + d2) > maxD2))+                        if(E_Fc_rem == (E_C[ij][cnt1][cnt2/2] + E_C[pq][cnt3][cnt4/2] + energy)){+                          backtrack_c(i, j, cnt1, cnt2, structure, vc);+                          backtrack_c(p, q, cnt3, cnt4, structure, vc);+                          return;+                        }+            } /* end for p */+          } /* end for q */+        }++    }++    /* check for multi loop configurations */+    if(E_Fc_rem == E_FcM_rem){+      if(seq_length > 2*TURN)+        for (i=TURN+1; i<seq_length-2*TURN; i++) {+          /* get distancies to references+          * d3a = dbp(T1_[1,n}, T1_{1,k} + T1_{k+1, n})+          * d3b = dbp(T2_[1,n}, T2_{1,k} + T2_{k+1, n})+          */+          if(E_M_rem[my_iindx[1]-i] != INF){+            if(E_M2[i+1])+              for(cnt1 = k_min_M2[i+1];+                  cnt1 <= k_max_M2[i+1];+                  cnt1++)+                for(cnt2 = l_min_M2[i+1][cnt1];+                    cnt2 <= l_max_M2[i+1][cnt1];+                    cnt2 += 2)+                  if(E_Fc_rem == (E_M_rem[my_iindx[1]-i] + E_M2[i+1][cnt1][cnt2/2] + P->MLclosing)){+                    backtrack_m(1,i,-1,-1,structure,vc);+                    backtrack_m2(i+1,cnt1,cnt2,structure,vc);+                    return;+                  }+            if(E_M2_rem[i+1] != INF){+              if(E_Fc_rem == (E_M_rem[my_iindx[1]-i] + E_M2_rem[i+1] + P->MLclosing)){+                backtrack_m(1,i,-1,-1,structure,vc);+                backtrack_m2(i+1,-1,-1,structure,vc);+                return;+              }+            }+          }+          if(E_M2_rem[i+1] != INF){+            if(E_M[my_iindx[1]-i])+              for(cnt1 = k_min_M[my_iindx[1]-i];+                  cnt1 <= k_max_M[my_iindx[1]-i];+                  cnt1++)+                for(cnt2 = l_min_M[my_iindx[1]-i][cnt1];+                    cnt2 <= l_max_M[my_iindx[1]-i][cnt1];+                    cnt2 += 2)+                  if(E_Fc_rem == (E_M[my_iindx[1]-i][cnt1][cnt2/2] + E_M2_rem[i+1] + P->MLclosing)){+                    backtrack_m(1,i,cnt1,cnt2,structure,vc);+                    backtrack_m2(i+1,-1,-1,structure,vc);+                    return;+                  }+          }++          if(!(E_M[my_iindx[1]-i])) continue;+          if(!(E_M2[i+1])) continue;++          d1 = base_d1 - referenceBPs1[my_iindx[1]-i] - referenceBPs1[my_iindx[i+1]-seq_length];+          d2 = base_d2 - referenceBPs2[my_iindx[1]-i] - referenceBPs2[my_iindx[i+1]-seq_length];+          for(cnt1 = k_min_M[my_iindx[1]-i];+              cnt1 <= k_max_M[my_iindx[1]-i];+              cnt1++)+            for(cnt2 = l_min_M[my_iindx[1]-i][cnt1];+                cnt2 <= l_max_M[my_iindx[1]-i][cnt1];+                cnt2 += 2)+              for(cnt3 = k_min_M2[i+1];+                  cnt3 <= k_max_M2[i+1];+                  cnt3++)+                for(cnt4 = l_min_M2[i+1][cnt3];+                    cnt4 <= l_max_M2[i+1][cnt3];+                    cnt4 += 2)+                  if(((cnt1 + cnt3 + d1) > maxD1) || ((cnt2 + cnt4 + d2) > maxD2)){+                    if(E_Fc_rem == (E_M[my_iindx[1]-i][cnt1][cnt2/2] + E_M2[i+1][cnt3][cnt4/2] + P->MLclosing)){+                      backtrack_m(1, i, cnt1, cnt2, structure, vc);+                      backtrack_m2(i+1, cnt3, cnt4, structure, vc);+                      return;+                    }+                  }+        }+    }+  }+  else{+    /* open chain ? */+    if(E_Fc[k][l/2] == 0)+      if((k == referenceBPs1[my_iindx[1]-seq_length]) && (l == referenceBPs2[my_iindx[1]-seq_length])){+        return;+      }+    if((k >= k_min_FcH) && (k <= k_max_FcH)){+      if((l >= l_min_FcH[k]) && (l <= l_max_FcH[k]))+        if(E_Fc[k][l/2] == E_FcH[k][l/2]){+          for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+            for (j = d; j <= seq_length; j++) {+              unsigned int u, ij;+              int type, no_close;+              char loopseq[10];+              i = j-d+1;+              ij = my_iindx[i]-j;+              if (!E_C[ij]) continue;+              u = seq_length-j + i-1;+              if (u<TURN) continue;++              type = ptype[jindx[j] + i];++              no_close = (((type==3)||(type==4))&&no_closingGU);++              type=rtype[type];++              if (!type) continue;+              if(no_close) continue;++              d1 = base_d1 - referenceBPs1[ij];+              d2 = base_d2 - referenceBPs2[ij];+              if (u<7) {+                strcpy(loopseq , sequence+j-1);+                strncat(loopseq, sequence, i);+              }+              energy = E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, P);+              if((k >= d1) && (l >= d2))+                if((k-d1 >= k_min_C[ij]) && (k-d1 <= k_max_C[ij]))+                  if((l-d2 >= l_min_C[ij][k-d1]) && (l-d2 <= l_max_C[ij][k-d1])){+                    if(E_Fc[k][l/2] == E_C[ij][k-d1][(l-d2)/2] + energy){+                      backtrack_c(i, j, k-d1, l-d2, structure, vc);+                      return;+                    }+                  }+            }+        }+    }++    if((k >= k_min_FcI) && (k <= k_max_FcI)){+      if((l >= l_min_FcI[k]) && (l <= l_max_FcI[k]))+        if(E_Fc[k][l/2] == E_FcI[k][l/2]){+          for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+            for (j = d; j <= seq_length; j++) {+              unsigned int u, ij, p, q, pq;+              int type, type_2;+              i = j-d+1;+              ij = my_iindx[i]-j;+              if(!E_C[ij]) continue;+              u = seq_length-j + i-1;+              if (u<TURN) continue;++              type = ptype[jindx[j] + i];++              type=rtype[type];++              if (!type) continue;++              for(p = j+1; p < seq_length ; p++){+                unsigned int u1, qmin, ln_pre;+                u1 = p-j-1;+                if (u1+i-1>MAXLOOP) break;+                qmin = p + TURN + 1;+                ln_pre = u1 + i + seq_length;+                if(ln_pre > qmin + MAXLOOP) qmin = ln_pre - MAXLOOP - 1;+                for(q = qmin; q <= seq_length; q++){+                  unsigned int u2;+                  pq = my_iindx[p]-q;+                  if(!E_C[pq]) continue;+                  type_2 = rtype[(unsigned int)ptype[jindx[q] + p]];+                  if (type_2==0) continue;+                  u2 = i-1 + seq_length-q;+                  if (u1+u2>MAXLOOP) continue;+                  /* get distance to reference if closing the interior loop+                  *  d2a = dbp(T1_[1,n}, T1_{p,q} + T1_{i,j})+                  *  d2b = dbp(T2_[1,n}, T2_{p,q} + T2_{i,j})+                  */+                  d1 = base_d1 - referenceBPs1[ij] - referenceBPs1[pq];+                  d2 = base_d2 - referenceBPs2[ij] - referenceBPs2[pq];+                  energy = E_IntLoop(u1, u2, type, type_2, S1[j+1], S1[i-1], S1[p-1], S1[q+1], P);+                  if((k >= d1) && (l >= d2))+                    for(cnt1 = k_min_C[ij]; cnt1 <= MIN2(k_max_C[ij], k - d1); cnt1++)+                      for(cnt2 = l_min_C[ij][cnt1]; cnt2 <= MIN2(l_max_C[ij][cnt1], l - d2); cnt2+=2)+                        if((k - d1 - cnt1 >= k_min_C[pq]) && (k - d1 - cnt1 <= k_max_C[pq]))+                          if((l - d2 - cnt2 >= l_min_C[pq][k-d1-cnt1]) && (l - d2 - cnt2 <= l_max_C[pq][k-d1-cnt1])){+                            if((E_C[ij][cnt1][cnt2/2] + E_C[pq][k-d1-cnt1][(l-d2-cnt2)/2] + energy) == E_Fc[k][l/2]){+                              backtrack_c(i, j, cnt1, cnt2, structure, vc);+                              backtrack_c(p, q, k - d1 - cnt1, l - d2 - cnt2, structure, vc);+                              return;+                            }+                          }+                }+              }+            }+        }+    }++    if((k >= k_min_FcM) && (k <= k_max_FcM)){+      if((l >= l_min_FcM[k]) && (l <= l_max_FcM[k]))+        if(E_Fc[k][l/2] == E_FcM[k][l/2]){+          if(seq_length > 2*TURN)+            for (i=TURN+1; i<seq_length-2*TURN; i++) {+              /* get distancies to references+              * d3a = dbp(T1_[1,n}, T1_{1,k} + T1_{k+1, n})+              * d3b = dbp(T2_[1,n}, T2_{1,k} + T2_{k+1, n})+              */+              if(!E_M[my_iindx[1]-i]) continue;+              if(!E_M2[i+1]) continue;+              d1 = base_d1 - referenceBPs1[my_iindx[1]-i] - referenceBPs1[my_iindx[i+1]-seq_length];+              d2 = base_d2 - referenceBPs2[my_iindx[1]-i] - referenceBPs2[my_iindx[i+1]-seq_length];+              if((k >= d1) && (l >= d2))+                for(cnt1 = k_min_M[my_iindx[1]-i]; cnt1 <= MIN2(k_max_M[my_iindx[1]-i], k-d1); cnt1++)+                  for(cnt2 = l_min_M[my_iindx[1]-i][cnt1]; cnt2 <= MIN2(l_max_M[my_iindx[1]-i][cnt1], l-d2); cnt2+=2)+                    if((k - d1 - cnt1 >= k_min_M2[i+1]) && (k - d1 - cnt1 <= k_max_M2[i+1]))+                      if((l - d2 - cnt2 >= l_min_M2[i+1][k-d1-cnt1]) && (l - d2 - cnt2 <= l_max_M2[i+1][k-d1-cnt1]))+                        if((E_M[my_iindx[1]-i][cnt1][cnt2/2] + E_M2[i+1][k-d1-cnt1][(l-d2-cnt2)/2] + P->MLclosing) == E_FcM[k][l/2]){+                          backtrack_m(1, i, cnt1, cnt2, structure, vc);+                          backtrack_m2(i+1, k - d1 - cnt1, l - d2 - cnt2, structure, vc);+                          return;+                        }+            }+        }+    }+  }+  vrna_message_error("backtack failed in fc\n");+}+++PRIVATE void+backtrack_m2( unsigned int i,+              int k,+              int l,+              char *structure,+              vrna_fold_compound_t *vc){++  unsigned int   j, ij, j3, n;+  unsigned int   *referenceBPs1, *referenceBPs2;+  unsigned int d1, d2, base_d1, base_d2, maxD1, maxD2;+  int *my_iindx, cnt1, cnt2, cnt3, cnt4;+  int ***E_M1, ***E_M2, *E_M2_rem, *E_M1_rem, e;+  int **l_min_M1, **l_max_M1, *k_min_M1, *k_max_M1;+  vrna_mx_mfe_t   *matrices;++  matrices        = vc->matrices;+  n               = vc->length;+  my_iindx        = vc->iindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;++  E_M1            = matrices->E_M1;+  l_min_M1 = matrices->l_min_M1;+  l_max_M1 = matrices->l_max_M1;+  k_min_M1 = matrices->k_min_M1;+  k_max_M1 = matrices->k_max_M1;++  E_M1_rem        = matrices->E_M1_rem;++  E_M2            = matrices->E_M2;++  E_M2_rem        = matrices->E_M2_rem;++  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;++  base_d1 = referenceBPs1[my_iindx[i]-n];+  base_d2 = referenceBPs2[my_iindx[i]-n];++  if(k == -1){+    e = E_M2_rem[i];+    for (j=i+TURN+1; j<n-TURN-1; j++){+      if(E_M1_rem[my_iindx[i]-j] != INF){+        if(E_M1[my_iindx[j+1]-n])+          for(cnt1 = k_min_M1[my_iindx[j+1]-n];+              cnt1 <= k_max_M1[my_iindx[j+1]-n];+              cnt1++)+            for(cnt2 = l_min_M1[my_iindx[j+1]-n][cnt1];+                cnt2 <= l_max_M1[my_iindx[j+1]-n][cnt1];+                cnt2++)+              if(e == E_M1_rem[my_iindx[i]-j] + E_M1[my_iindx[j+1]-n][cnt1][cnt2/2]){+                backtrack_m1(i, j, k, l, structure, vc);+                backtrack_m1(j+1, n, cnt1, cnt2, structure, vc);+                return;+              }+        if(E_M1_rem[my_iindx[j+1]-n] != INF){+          if(e == E_M1_rem[my_iindx[i]-j] + E_M1_rem[my_iindx[j+1]-n]){+            backtrack_m1(i, j, k, l, structure, vc);+            backtrack_m1(j+1, n, k, l, structure, vc);+            return;+          }+        }+      }+      if(E_M1_rem[my_iindx[j+1]-n] != INF){+        if(E_M1[my_iindx[i]-j])+          for(cnt1 = k_min_M1[my_iindx[i]-j];+              cnt1 <= k_max_M1[my_iindx[i]-j];+              cnt1++)+            for(cnt2 = l_min_M1[my_iindx[i]-j][cnt1];+                cnt2 <= l_max_M1[my_iindx[i]-j][cnt1];+                cnt2 += 2)+              if(e == E_M1[my_iindx[i]-j][cnt1][cnt2/2] + E_M1_rem[my_iindx[j+1]-n]){+                backtrack_m1(i, j, cnt1, cnt2, structure, vc);+                backtrack_m1(j+1, n, k, l, structure, vc);+                return;+              }+      }+++      if(!E_M1[my_iindx[i]-j]) continue;+      if(!E_M1[my_iindx[j+1]-n]) continue;++      d1 = referenceBPs1[my_iindx[i]-n] - referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[j+1]-n];+      d2 = referenceBPs2[my_iindx[i]-n] - referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[j+1]-n];++      for(cnt1 = k_min_M1[my_iindx[i]-j]; cnt1 <= k_max_M1[my_iindx[i]-j]; cnt1++)+        for(cnt2 = l_min_M1[my_iindx[i]-j][cnt1]; cnt2 <= l_max_M1[my_iindx[i]-j][cnt1]; cnt2+=2){+          for(cnt3 = k_min_M1[my_iindx[j+1]-n]; cnt3 <= k_max_M1[my_iindx[j+1]-n]; cnt3++)+            for(cnt4 = l_min_M1[my_iindx[j+1]-n][cnt3]; cnt4 <= l_max_M1[my_iindx[j+1]-n][cnt3]; cnt4+=2){+              if(((cnt1 + cnt3 + d1) > maxD1) || ((cnt2 + cnt4 + d2) > maxD2)){+                if(e == E_M1[my_iindx[i]-j][cnt1][cnt2/2] + E_M1[my_iindx[j+1]-n][cnt3][cnt4/2]){+                  backtrack_m1(i, j, cnt1, cnt2, structure, vc);+                  backtrack_m1(j+1, n, cnt3, cnt4, structure, vc);+                  return;+                }+              }+            }+        }+    }+  }+  else{+    for(j=i+TURN+1; j<n-TURN-1; j++){+      if(!E_M1[my_iindx[i]-j]) continue;+      if(!E_M1[my_iindx[j+1]-n]) continue;++      ij = my_iindx[i]-j;+      j3 = my_iindx[j+1]-n;+      d1 = base_d1 - referenceBPs1[ij] - referenceBPs1[j3];+      d2 = base_d2 - referenceBPs2[ij] - referenceBPs2[j3];++      for(cnt1 = k_min_M1[ij]; cnt1 <= MIN2(k_max_M1[ij], k - d1); cnt1++)+        for(cnt2 = l_min_M1[ij][cnt1]; cnt2 <= MIN2(l_max_M1[ij][cnt1], l-d2); cnt2+=2)+          if((k - d1 - cnt1 >= k_min_M1[j3]) && (k - d1 - cnt1 <= k_max_M1[j3]))+            if((l - d2 - cnt2 >= l_min_M1[j3][k - d1 - cnt1]) && (l - d2 - cnt2 <= l_max_M1[j3][k-d1-cnt1]))+              if(E_M1[ij][cnt1][cnt2/2] + E_M1[j3][k-d1-cnt1][(l-d2-cnt2)/2] == E_M2[i][k][l/2]){+                backtrack_m1(i, j, cnt1, cnt2, structure, vc);+                backtrack_m1(j+1, n, k-d1-cnt1, l-d2-cnt2, structure, vc);+                return;+              }+    }+  }+  vrna_message_error("backtack failed in m2\n");+}++PRIVATE void+mfe_circ(vrna_fold_compound_t *vc){++  unsigned int  d, i, j, maxD1, maxD2, seq_length, *referenceBPs1, *referenceBPs2, d1, d2, base_d1, base_d2, *mm1, *mm2, *bpdist;+  int           *my_iindx, *jindx, energy, cnt1, cnt2, cnt3, cnt4, *rtype;+  short         *S1;+  char          *sequence, *ptype;+  int           ***E_C, ***E_M, ***E_M1;+  int           *E_C_rem, *E_M_rem, *E_M1_rem;+  int           **l_min_C, **l_max_C, **l_min_M, **l_max_M, **l_min_M1, **l_max_M1;+  int           *k_min_C, *k_max_C,*k_min_M, *k_max_M,*k_min_M1, *k_max_M1;++  vrna_param_t  *P;+  vrna_md_t     *md;+  vrna_mx_mfe_t *matrices;++  P               = vc->params;+  md              = &(P->model_details);+  matrices        = vc->matrices;+  sequence        = vc->sequence;+  seq_length      = vc->length;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  rtype           = &(md->rtype[0]);+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  mm1             = vc->mm1;+  mm2             = vc->mm2;+  bpdist          = vc->bpdist;++  E_C             = matrices->E_C;+  l_min_C    = matrices->l_min_C;+  l_max_C    = matrices->l_max_C;+  k_min_C    = matrices->k_min_C;+  k_max_C    = matrices->k_max_C;++  E_M             = matrices->E_M;+  l_min_M  = matrices->l_min_M;+  l_max_M  = matrices->l_max_M;+  k_min_M  = matrices->k_min_M;+  k_max_M  = matrices->k_max_M;++  E_M1            = matrices->E_M1;+  l_min_M1 = matrices->l_min_M1;+  l_max_M1 = matrices->l_max_M1;+  k_min_M1 = matrices->k_min_M1;+  k_max_M1 = matrices->k_max_M1;++  E_C_rem        = matrices->E_C_rem;+  E_M_rem        = matrices->E_M_rem;+  E_M1_rem       = matrices->E_M1_rem;++#ifdef _OPENMP+  #pragma omp parallel for private(d1,d2,cnt1,cnt2,cnt3,cnt4,j, i)+#endif+  for(i=1; i<seq_length-TURN-1; i++){+    /* guess memory requirements for M2 */++    int min_k, max_k, max_l, min_l;+    int min_k_real, max_k_real, *min_l_real, *max_l_real;++    min_k = min_l = 0;+    max_k = mm1[my_iindx[i]-seq_length] + referenceBPs1[my_iindx[i] - seq_length];+    max_l = mm2[my_iindx[i]-seq_length] + referenceBPs2[my_iindx[i] - seq_length];++    prepareBoundaries(min_k,+                      max_k,+                      min_l,+                      max_l,+                      bpdist[my_iindx[i] - seq_length],+                      &matrices->k_min_M2[i],+                      &matrices->k_max_M2[i],+                      &matrices->l_min_M2[i],+                      &matrices->l_max_M2[i]+                      );++    prepareArray( &matrices->E_M2[i],+                  matrices->k_min_M2[i],+                  matrices->k_max_M2[i],+                  matrices->l_min_M2[i],+                  matrices->l_max_M2[i]+                 );++    preparePosteriorBoundaries( matrices->k_max_M2[i] - matrices->k_min_M2[i] + 1,+                                matrices->k_min_M2[i],+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                              );++    /* begin filling of M2 array */+    for (j=i+TURN+1; j<seq_length-TURN-1; j++){+      if(E_M1_rem[my_iindx[i]-j] != INF){+        if(E_M1[my_iindx[j+1]-seq_length])+          for(cnt1 = k_min_M1[my_iindx[j+1]-seq_length];+              cnt1 <= k_max_M1[my_iindx[j+1]-seq_length];+              cnt1++)+            for(cnt2 = l_min_M1[my_iindx[j+1]-seq_length][cnt1];+                cnt2 <= l_max_M1[my_iindx[j+1]-seq_length][cnt1];+                cnt2++)+              matrices->E_M2_rem[i] = MIN2(matrices->E_M2_rem[i],+                                  E_M1_rem[my_iindx[i]-j] + E_M1[my_iindx[j+1]-seq_length][cnt1][cnt2/2]+                                  );+        if(E_M1_rem[my_iindx[j+1]-seq_length] != INF)+          matrices->E_M2_rem[i] = MIN2(matrices->E_M2_rem[i], E_M1_rem[my_iindx[i]-j] + E_M1_rem[my_iindx[j+1]-seq_length]);+      }+      if(E_M1_rem[my_iindx[j+1]-seq_length] != INF){+        if(E_M1[my_iindx[i]-j])+          for(cnt1 = k_min_M1[my_iindx[i]-j];+              cnt1 <= k_max_M1[my_iindx[i]-j];+              cnt1++)+            for(cnt2 = l_min_M1[my_iindx[i]-j][cnt1];+                cnt2 <= l_max_M1[my_iindx[i]-j][cnt1];+                cnt2 += 2)+              matrices->E_M2_rem[i] = MIN2(matrices->E_M2_rem[i],+                                  E_M1[my_iindx[i]-j][cnt1][cnt2/2] + E_M1_rem[my_iindx[j+1]-seq_length]+                                  );+      }+++      if(!E_M1[my_iindx[i]-j]) continue;+      if(!E_M1[my_iindx[j+1]-seq_length]) continue;++      d1 = referenceBPs1[my_iindx[i]-seq_length] - referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[j+1]-seq_length];+      d2 = referenceBPs2[my_iindx[i]-seq_length] - referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[j+1]-seq_length];++      for(cnt1 = k_min_M1[my_iindx[i]-j]; cnt1 <= k_max_M1[my_iindx[i]-j]; cnt1++)+        for(cnt2 = l_min_M1[my_iindx[i]-j][cnt1]; cnt2 <= l_max_M1[my_iindx[i]-j][cnt1]; cnt2+=2){+          for(cnt3 = k_min_M1[my_iindx[j+1]-seq_length]; cnt3 <= k_max_M1[my_iindx[j+1]-seq_length]; cnt3++)+            for(cnt4 = l_min_M1[my_iindx[j+1]-seq_length][cnt3]; cnt4 <= l_max_M1[my_iindx[j+1]-seq_length][cnt3]; cnt4+=2){+              if(((cnt1 + cnt3 + d1) <= maxD1) && ((cnt2 + cnt4 + d2) <= maxD2)){+                matrices->E_M2[i][cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2] = MIN2( matrices->E_M2[i][cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2],+                                                                        E_M1[my_iindx[i]-j][cnt1][cnt2/2] + E_M1[my_iindx[j+1]-seq_length][cnt3][cnt4/2]+                                                                      );+                updatePosteriorBoundaries(cnt1+cnt3+d1,+                                          cnt2+cnt4+d2,+                                          &min_k_real,+                                          &max_k_real,+                                          &min_l_real,+                                          &max_l_real+                                          );+              }+              else{+                matrices->E_M2_rem[i] = MIN2(matrices->E_M2_rem[i],+                                    E_M1[my_iindx[i]-j][cnt1][cnt2/2] + E_M1[my_iindx[j+1]-seq_length][cnt3][cnt4/2]+                                    );+              }+            }+        }+    }++    /* resize and move memory portions of energy matrix E_M2 */+    adjustArrayBoundaries(&matrices->E_M2[i],+                          &matrices->k_min_M2[i],+                          &matrices->k_max_M2[i],+                          &matrices->l_min_M2[i],+                          &matrices->l_max_M2[i],+                          min_k_real,+                          max_k_real,+                          min_l_real,+                          max_l_real+                          );+  } /* end for i */++  base_d1 = referenceBPs1[my_iindx[1]-seq_length];+  base_d2 = referenceBPs2[my_iindx[1]-seq_length];++  /* guess memory requirements for E_FcH, E_FcI and E_FcM */++  int min_k, max_k, max_l, min_l;+  int min_k_real, max_k_real, min_k_real_fcH, max_k_real_fcH, min_k_real_fcI, max_k_real_fcI, min_k_real_fcM, max_k_real_fcM;+  int *min_l_real, *max_l_real, *min_l_real_fcH, *max_l_real_fcH, *min_l_real_fcI, *max_l_real_fcI,*min_l_real_fcM, *max_l_real_fcM;++  min_k = min_l = 0;++  max_k = mm1[my_iindx[1] - seq_length] + referenceBPs1[my_iindx[1] - seq_length];+  max_l = mm2[my_iindx[1] - seq_length] + referenceBPs2[my_iindx[1] - seq_length];++#ifdef _OPENMP+  #pragma omp sections+  {++  #pragma omp section+  {+#endif+  prepareBoundaries(min_k,+                    max_k,+                    min_l,+                    max_l,+                    bpdist[my_iindx[1] - seq_length],+                    &matrices->k_min_Fc,+                    &matrices->k_max_Fc,+                    &matrices->l_min_Fc,+                    &matrices->l_max_Fc+                    );+  prepareArray( &matrices->E_Fc,+                matrices->k_min_Fc,+                matrices->k_max_Fc,+                matrices->l_min_Fc,+                matrices->l_max_Fc+              );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  prepareBoundaries(min_k,+                    max_k,+                    min_l,+                    max_l,+                    bpdist[my_iindx[1] - seq_length],+                    &matrices->k_min_FcH,+                    &matrices->k_max_FcH,+                    &matrices->l_min_FcH,+                    &matrices->l_max_FcH+                    );+  prepareArray( &matrices->E_FcH,+                matrices->k_min_FcH,+                matrices->k_max_FcH,+                matrices->l_min_FcH,+                matrices->l_max_FcH+              );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  prepareBoundaries(min_k,+                    max_k,+                    min_l,+                    max_l,+                    bpdist[my_iindx[1] - seq_length],+                    &matrices->k_min_FcI,+                    &matrices->k_max_FcI,+                    &matrices->l_min_FcI,+                    &matrices->l_max_FcI+                    );+  prepareArray( &matrices->E_FcI,+                matrices->k_min_FcI,+                matrices->k_max_FcI,+                matrices->l_min_FcI,+                matrices->l_max_FcI+              );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  prepareBoundaries(min_k,+                    max_k,+                    min_l,+                    max_l,+                    bpdist[my_iindx[1] - seq_length],+                    &matrices->k_min_FcM,+                    &matrices->k_max_FcM,+                    &matrices->l_min_FcM,+                    &matrices->l_max_FcM+                    );+  prepareArray( &matrices->E_FcM,+                matrices->k_min_FcM,+                matrices->k_max_FcM,+                matrices->l_min_FcM,+                matrices->l_max_FcM+              );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  preparePosteriorBoundaries( max_k - min_k + 1,+                              min_k,+                              &min_k_real,+                              &max_k_real,+                              &min_l_real,+                              &max_l_real+                            );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  preparePosteriorBoundaries( max_k - min_k + 1,+                              min_k,+                              &min_k_real_fcH,+                              &max_k_real_fcH,+                              &min_l_real_fcH,+                              &max_l_real_fcH+                            );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  preparePosteriorBoundaries( max_k - min_k + 1,+                              min_k,+                              &min_k_real_fcI,+                              &max_k_real_fcI,+                              &min_l_real_fcI,+                              &max_l_real_fcI+                            );++#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  preparePosteriorBoundaries( max_k - min_k + 1,+                              min_k,+                              &min_k_real_fcM,+                              &max_k_real_fcM,+                              &min_l_real_fcM,+                              &max_l_real_fcM+                            );+#ifdef _OPENMP+  }+  }+#endif++  /* begin actual energy calculations */+#ifdef _OPENMP+  #pragma omp sections private(d, d1,d2,cnt1,cnt2,cnt3,cnt4,j, i, energy)+  {++  #pragma omp section+  {+#endif+  for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+    for (j = d; j <= seq_length; j++) {+      unsigned int  u, ij;+      int           type, no_close;+      char          loopseq[10];+      i = j-d+1;+      ij = my_iindx[i]-j;+      u = seq_length-j + i-1;+      if (u<TURN) continue;++      type = ptype[jindx[j] + i];++      no_close = (((type==3)||(type==4))&&no_closingGU);++      type=rtype[type];++      if (!type) continue;+      if(no_close) continue;++      d1 = base_d1 - referenceBPs1[ij];+      d2 = base_d2 - referenceBPs2[ij];+      if (u<7) {+        strcpy(loopseq , sequence+j-1);+        strncat(loopseq, sequence, i);+      }+      energy = E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, P);++      if(E_C_rem[ij] != INF)+        matrices->E_FcH_rem = MIN2(matrices->E_FcH_rem, E_C_rem[ij] + energy);++      if (!E_C[ij]) continue;+      for(cnt1 = k_min_C[ij]; cnt1 <= k_max_C[ij]; cnt1++)+        for(cnt2 = l_min_C[ij][cnt1]; cnt2 <= l_max_C[ij][cnt1]; cnt2 += 2){+          if(((cnt1 + d1) <= maxD1) && ((cnt2 + d2) <= maxD2)){+            matrices->E_FcH[cnt1 + d1][(cnt2+d2)/2] = MIN2( matrices->E_FcH[cnt1 + d1][(cnt2+d2)/2],+                                                  energy + E_C[ij][cnt1][cnt2/2]+                                                );+            updatePosteriorBoundaries(cnt1 + d1,+                                      cnt2 + d2,+                                      &min_k_real_fcH,+                                      &max_k_real_fcH,+                                      &min_l_real_fcH,+                                      &max_l_real_fcH+                                    );+          }+          else+            matrices->E_FcH_rem = MIN2(matrices->E_FcH_rem, energy + E_C[ij][cnt1][cnt2/2]);+        }+    }+  /* end of i-j loop */++  /* resize and move memory portions of energy matrix E_FcH */+  adjustArrayBoundaries(&matrices->E_FcH,+                        &matrices->k_min_FcH,+                        &matrices->k_max_FcH,+                        &matrices->l_min_FcH,+                        &matrices->l_max_FcH,+                        min_k_real_fcH,+                        max_k_real_fcH,+                        min_l_real_fcH,+                        max_l_real_fcH+                      );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+    for (j = d; j <= seq_length; j++) {+      unsigned int  u, ij, p, q, pq;+      int           type, type_2, no_close;+      i = j-d+1;+      ij = my_iindx[i]-j;+      u = seq_length-j + i-1;+      if (u<TURN) continue;++      type = ptype[jindx[j] + i];++      no_close = (((type==3)||(type==4))&&no_closingGU);++      type=rtype[type];++      if (!type) continue;+      if(no_close) continue;++      if(E_C_rem[ij] != INF){+        for(p = j+1; p < seq_length ; p++){+          unsigned int u1, qmin, ln_pre;+          u1 = p-j-1;+          if (u1+i-1>MAXLOOP) break;+          qmin = p + TURN + 1;+          ln_pre = u1 + i + seq_length;+          if(ln_pre > qmin + MAXLOOP) qmin = ln_pre - MAXLOOP - 1;+          for(q = qmin; q <= seq_length; q++){+            unsigned int u2;+            pq = my_iindx[p]-q;+            type_2 = rtype[(unsigned int)ptype[jindx[q] + p]];+            if (type_2==0) continue;+            u2 = i-1 + seq_length-q;+            if (u1+u2>MAXLOOP) continue;+            /* get distance to reference if closing the interior loop+            *  d2a = dbp(T1_[1,n}, T1_{p,q} + T1_{i,j})+            *  d2b = dbp(T2_[1,n}, T2_{p,q} + T2_{i,j})+            */+            d1 = base_d1 - referenceBPs1[ij] - referenceBPs1[pq];+            d2 = base_d2 - referenceBPs2[ij] - referenceBPs2[pq];+            energy = E_IntLoop(u1, u2, type, type_2, S1[j+1], S1[i-1], S1[p-1], S1[q+1], P);++            if(E_C_rem[pq] != INF)+              matrices->E_FcI_rem = MIN2(matrices->E_FcI_rem, E_C_rem[ij] + E_C_rem[pq] + energy);++            if(E_C[pq])+              for(cnt1 = k_min_C[pq];+                  cnt1 <= k_max_C[pq];+                  cnt1++)+                for(cnt2 = l_min_C[pq][cnt1];+                    cnt2 <= l_max_C[pq][cnt1];+                    cnt2 += 2)+                  matrices->E_FcI_rem = MIN2(matrices->E_FcI_rem, E_C_rem[ij] + E_C[pq][cnt1][cnt2/2] + energy);+          }+        }+      }++      if(E_C[ij]){+        for(p = j+1; p < seq_length ; p++){+          unsigned int u1, qmin, ln_pre;+          u1 = p-j-1;+          if (u1+i-1>MAXLOOP) break;+          qmin = p + TURN + 1;+          ln_pre = u1 + i + seq_length;+          if(ln_pre > qmin + MAXLOOP) qmin = ln_pre - MAXLOOP - 1;+          for(q = qmin; q <= seq_length; q++){+            unsigned int u2;+            pq = my_iindx[p]-q;+            type_2 = rtype[(unsigned int)ptype[jindx[q] + p]];+            if (type_2==0) continue;+            u2 = i-1 + seq_length-q;+            if (u1+u2>MAXLOOP) continue;+            /* get distance to reference if closing the interior loop+            *  d2a = dbp(T1_[1,n}, T1_{p,q} + T1_{i,j})+            *  d2b = dbp(T2_[1,n}, T2_{p,q} + T2_{i,j})+            */+            d1 = base_d1 - referenceBPs1[ij] - referenceBPs1[pq];+            d2 = base_d2 - referenceBPs2[ij] - referenceBPs2[pq];+            energy = E_IntLoop(u1, u2, type, type_2, S1[j+1], S1[i-1], S1[p-1], S1[q+1], P);+            if(E_C_rem[pq] != INF){+              for(cnt1 = k_min_C[ij];+                  cnt1 <= k_max_C[ij];+                  cnt1++)+                for(cnt2 = l_min_C[ij][cnt1];+                    cnt2 <= l_max_C[ij][cnt1];+                    cnt2 += 2)+                  matrices->E_FcI_rem = MIN2(matrices->E_FcI_rem, E_C[ij][cnt1][cnt2/2] + E_C_rem[pq] + energy);+            }++            if(E_C[pq])+              for(cnt1 = k_min_C[ij];+                  cnt1 <= k_max_C[ij];+                  cnt1++)+                for(cnt2 = l_min_C[ij][cnt1];+                    cnt2 <= l_max_C[ij][cnt1];+                    cnt2 += 2)+                  for(cnt3 = k_min_C[pq];+                      cnt3 <= k_max_C[pq];+                      cnt3++)+                    for(cnt4 = l_min_C[pq][cnt3];+                        cnt4 <= l_max_C[pq][cnt3];+                        cnt4 += 2){+                      if(((cnt1 + cnt3 + d1) <= maxD1) && ((cnt2 + cnt4 + d2) <= maxD2)){+                        matrices->E_FcI[cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2] = MIN2(+                                                                          matrices->E_FcI[cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2],+                                                                          E_C[ij][cnt1][cnt2/2]+                                                                        + E_C[pq][cnt3][cnt4/2]+                                                                        + energy+                                                                            );+                        updatePosteriorBoundaries(cnt1 + cnt3 + d1,+                                                  cnt2 + cnt4 + d2,+                                                  &min_k_real_fcI,+                                                  &max_k_real_fcI,+                                                  &min_l_real_fcI,+                                                  &max_l_real_fcI+                                                );+                      }+                      else{+                        matrices->E_FcI_rem = MIN2(+                                      matrices->E_FcI_rem,+                                      E_C[ij][cnt1][cnt2/2]+                                    + E_C[pq][cnt3][cnt4/2]+                                    + energy+                                          );+                      }+                    }+          }+        }+      }+    }+  /* end of i-j loop */++  /* resize and move memory portions of energy matrix E_FcI */+  adjustArrayBoundaries(&matrices->E_FcI,+                        &matrices->k_min_FcI,+                        &matrices->k_max_FcI,+                        &matrices->l_min_FcI,+                        &matrices->l_max_FcI,+                        min_k_real_fcI,+                        max_k_real_fcI,+                        min_l_real_fcI,+                        max_l_real_fcI+                      );+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  if(seq_length > 2*TURN){+    for (i=TURN+1; i<seq_length-2*TURN; i++) {+      /* get distancies to references+      * d3a = dbp(T1_[1,n}, T1_{1,k} + T1_{k+1, n})+      * d3b = dbp(T2_[1,n}, T2_{1,k} + T2_{k+1, n})+      */+      d1 = base_d1 - referenceBPs1[my_iindx[1]-i] - referenceBPs1[my_iindx[i+1]-seq_length];+      d2 = base_d2 - referenceBPs2[my_iindx[1]-i] - referenceBPs2[my_iindx[i+1]-seq_length];++      if(E_M_rem[my_iindx[1]-i] != INF){+        if(matrices->E_M2[i+1])+          for(cnt1 = matrices->k_min_M2[i+1];+              cnt1 <= matrices->k_max_M2[i+1];+              cnt1++)+            for(cnt2 = matrices->l_min_M2[i+1][cnt1];+                cnt2 <= matrices->l_max_M2[i+1][cnt1];+                cnt2 += 2)+              matrices->E_FcM_rem = MIN2(matrices->E_FcM_rem, E_M_rem[my_iindx[1]-i] + matrices->E_M2[i+1][cnt1][cnt2/2] + P->MLclosing);+        if(matrices->E_M2_rem[i+1] != INF)+          matrices->E_FcM_rem = MIN2(matrices->E_FcM_rem, E_M_rem[my_iindx[1]-i] + matrices->E_M2_rem[i+1] + P->MLclosing);+      }+      if(matrices->E_M2_rem[i+1] != INF){+        if(E_M[my_iindx[1]-i])+          for(cnt1 = k_min_M[my_iindx[1]-i];+              cnt1 <= k_max_M[my_iindx[1]-i];+              cnt1++)+            for(cnt2 = l_min_M[my_iindx[1]-i][cnt1];+                cnt2 <= l_max_M[my_iindx[1]-i][cnt1];+                cnt2 += 2)+              matrices->E_FcM_rem = MIN2(matrices->E_FcM_rem, E_M[my_iindx[1]-i][cnt1][cnt2/2] + matrices->E_M2_rem[i+1] + P->MLclosing);+      }++      if(!E_M[my_iindx[1]-i]) continue;+      if(!matrices->E_M2[i+1]) continue;+      for(cnt1 = k_min_M[my_iindx[1]-i]; cnt1 <= k_max_M[my_iindx[1]-i]; cnt1++)+        for(cnt2 = l_min_M[my_iindx[1]-i][cnt1]; cnt2 <= l_max_M[my_iindx[1]-i][cnt1]; cnt2 += 2)+          for(cnt3 = matrices->k_min_M2[i+1]; cnt3 <= matrices->k_max_M2[i+1]; cnt3++)+            for(cnt4 = matrices->l_min_M2[i+1][cnt3]; cnt4 <= matrices->l_max_M2[i+1][cnt3]; cnt4 += 2){+              if(((cnt1 + cnt3 + d1) <= maxD1) && ((cnt2 + cnt4 + d2) <= maxD2)){+                matrices->E_FcM[cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2] = MIN2(+                                                                  matrices->E_FcM[cnt1 + cnt3 + d1][(cnt2 + cnt4 + d2)/2],+                                                                  E_M[my_iindx[1]-i][cnt1][cnt2/2]+                                                                + matrices->E_M2[i+1][cnt3][cnt4/2]+                                                                + P->MLclosing+                                                                    );+                updatePosteriorBoundaries(cnt1 + cnt3 + d1,+                                          cnt2 + cnt4 + d2,+                                          &min_k_real_fcM,+                                          &max_k_real_fcM,+                                          &min_l_real_fcM,+                                          &max_l_real_fcM+                                        );+              }+              else{+                matrices->E_FcM_rem = MIN2(+                              matrices->E_FcM_rem,+                              E_M[my_iindx[1]-i][cnt1][cnt2/2]+                            + matrices->E_M2[i+1][cnt3][cnt4/2]+                            + P->MLclosing+                                  );+              }+            }+    }+  }+  /* resize and move memory portions of energy matrix E_FcM */+  adjustArrayBoundaries(&matrices->E_FcM,+                        &matrices->k_min_FcM,+                        &matrices->k_max_FcM,+                        &matrices->l_min_FcM,+                        &matrices->l_max_FcM,+                        min_k_real_fcM,+                        max_k_real_fcM,+                        min_l_real_fcM,+                        max_l_real_fcM+                      );+#ifdef _OPENMP+  }+  }+#endif++++  /* compute E_Fc_rem */+  matrices->E_Fc_rem = MIN2(matrices->E_FcH_rem, matrices->E_FcI_rem);+  matrices->E_Fc_rem = MIN2(matrices->E_Fc_rem, matrices->E_FcM_rem);+  /* add the case were structure is unfolded chain */+  if((referenceBPs1[my_iindx[1]-seq_length] > maxD1) || (referenceBPs2[my_iindx[1]-seq_length] > maxD2))+    matrices->E_Fc_rem = MIN2(matrices->E_Fc_rem, 0);+++  /* compute all E_Fc */+  for(cnt1 = matrices->k_min_FcH; cnt1 <= matrices->k_max_FcH; cnt1++)+    for(cnt2 = matrices->l_min_FcH[cnt1]; cnt2 <= matrices->l_max_FcH[cnt1]; cnt2 += 2){+      matrices->E_Fc[cnt1][cnt2/2] = MIN2(matrices->E_Fc[cnt1][cnt2/2],+                                      matrices->E_FcH[cnt1][cnt2/2]+                                      );+      updatePosteriorBoundaries(cnt1,+                                cnt2,+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                                );+    }+  for(cnt1 = matrices->k_min_FcI; cnt1 <= matrices->k_max_FcI; cnt1++)+    for(cnt2 = matrices->l_min_FcI[cnt1]; cnt2 <= matrices->l_max_FcI[cnt1]; cnt2 += 2){+      matrices->E_Fc[cnt1][cnt2/2] = MIN2(matrices->E_Fc[cnt1][cnt2/2],+                                      matrices->E_FcI[cnt1][cnt2/2]+                                      );+      updatePosteriorBoundaries(cnt1,+                                cnt2,+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                                );+    }+  for(cnt1 = matrices->k_min_FcM; cnt1 <= matrices->k_max_FcM; cnt1++)+    for(cnt2 = matrices->l_min_FcM[cnt1]; cnt2 <= matrices->l_max_FcM[cnt1]; cnt2 += 2){+      matrices->E_Fc[cnt1][cnt2/2] = MIN2(matrices->E_Fc[cnt1][cnt2/2],+                                      matrices->E_FcM[cnt1][cnt2/2]+                                      );+      updatePosteriorBoundaries(cnt1,+                                cnt2,+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                                );+    }+  /* add the case were structure is unfolded chain */+  matrices->E_Fc[referenceBPs1[my_iindx[1]-seq_length]][referenceBPs2[my_iindx[1]-seq_length]/2] = MIN2(matrices->E_Fc[referenceBPs1[my_iindx[1]-seq_length]][referenceBPs2[my_iindx[1]-seq_length]/2],+                                                                                                    0);+  updatePosteriorBoundaries(referenceBPs1[my_iindx[1]-seq_length],+                            referenceBPs2[my_iindx[1]-seq_length],+                            &min_k_real,+                            &max_k_real,+                            &min_l_real,+                            &max_l_real+                            );+++  adjustArrayBoundaries(&matrices->E_Fc,+                        &matrices->k_min_Fc,+                        &matrices->k_max_Fc,+                        &matrices->l_min_Fc,+                        &matrices->l_max_Fc,+                        min_k_real,+                        max_k_real,+                        min_l_real,+                        max_l_real+                      );++}+++++PRIVATE void adjustArrayBoundaries(int ***array, int *k_min, int *k_max, int **l_min, int **l_max, int k_min_post, int k_max_post, int *l_min_post, int *l_max_post){+  int cnt1;+  int k_diff_pre  = k_min_post - *k_min;+  int mem_size    = k_max_post - k_min_post + 1;++  if(k_min_post < INF){+    /* free all the unused memory behind actual data */+    for(cnt1 = k_max_post + 1; cnt1 <= *k_max; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }++    /* free unused memory before actual data */+    for(cnt1 = *k_min; cnt1 < k_min_post; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }+    /* move data to front and thereby eliminating unused memory in front of actual data */+    if(k_diff_pre > 0){+      memmove((int **)(*array),((int **)(*array)) + k_diff_pre, sizeof(int *) * mem_size);+      memmove((int *) (*l_min),((int *) (*l_min)) + k_diff_pre, sizeof(int)   * mem_size);+      memmove((int *) (*l_max),((int *) (*l_max)) + k_diff_pre, sizeof(int)   * mem_size);+    }++    /* reallocating memory to actual size used */+    *array  += *k_min;+    *array = (int **)realloc(*array, sizeof(int *) * mem_size);+    *array -= k_min_post;++    *l_min  += *k_min;+    *l_min = (int *)realloc(*l_min, sizeof(int) * mem_size);+    *l_min -= k_min_post;++    *l_max  += *k_min;+    *l_max = (int *)realloc(*l_max, sizeof(int) * mem_size);+    *l_max -= k_min_post;++    /* adjust l dimension of array */+    for(cnt1 = k_min_post; cnt1 <= k_max_post; cnt1++){+      if(l_min_post[cnt1] < INF){+        /* new memsize */+        mem_size        = (l_max_post[cnt1] - l_min_post[cnt1] + 1)/2 + 1;+        /* reshift the pointer */+        (*array)[cnt1]  += (*l_min)[cnt1]/2;++        int shift       = (l_min_post[cnt1]%2 == (*l_min)[cnt1]%2) ? 0 : 1;+        /* eliminate unused memory in front of actual data */+        unsigned int    start = (l_min_post[cnt1] - (*l_min)[cnt1])/2 + shift;+        if(start > 0)+          memmove((int *)((*array)[cnt1]), (int *)((*array)[cnt1])+start, sizeof(int) * mem_size);+        (*array)[cnt1]  = (int *) realloc((*array)[cnt1], sizeof(int) * mem_size);++        (*array)[cnt1]  -= l_min_post[cnt1]/2;+      }+      else{+        /* free according memory */+        (*array)[cnt1] += (*l_min)[cnt1]/2;+        free((*array)[cnt1]);+      }++      (*l_min)[cnt1] = l_min_post[cnt1];+      (*l_max)[cnt1] = l_max_post[cnt1];+    }+  }+  else{+    /* we have to free all unused memory */+    for(cnt1 = *k_min; cnt1 <= *k_max; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }+    (*l_min) += *k_min;+    (*l_max) += *k_min;+    free(*l_min);+    free(*l_max);+    (*array) += *k_min;+    free(*array);+    *array = NULL;+  }++  l_min_post  += *k_min;+  l_max_post  += *k_min;+  free(l_min_post);+  free(l_max_post);+  *k_min      = k_min_post;+  *k_max      = k_max_post;+}++PRIVATE INLINE void preparePosteriorBoundaries(int size, int shift, int *min_k, int *max_k, int **min_l, int **max_l){+  int i;+  *min_k  = INF;+  *max_k  = 0;++  *min_l  = (int *)vrna_alloc(sizeof(int) * size);+  *max_l  = (int *)vrna_alloc(sizeof(int) * size);++  for(i = 0; i < size; i++){+    (*min_l)[i] = INF;+    (*max_l)[i] = 0;+  }++  *min_l  -= shift;+  *max_l  -= shift;+}++PRIVATE INLINE void updatePosteriorBoundaries(int d1, int d2, int *min_k, int *max_k, int **min_l, int **max_l){+  (*min_l)[d1]  = MIN2((*min_l)[d1], d2);+  (*max_l)[d1]  = MAX2((*max_l)[d1], d2);+  *min_k        = MIN2(*min_k, d1);+  *max_k        = MAX2(*max_k, d1);+}++INLINE  PRIVATE void  prepareBoundaries(int min_k_pre, int max_k_pre, int min_l_pre, int max_l_pre, int bpdist, int *min_k, int *max_k, int **min_l, int **max_l){+  int cnt;+  int mem = max_k_pre - min_k_pre + 1;++  *min_k  = min_k_pre;+  *max_k  = max_k_pre;+  *min_l  = (int *) vrna_alloc(sizeof(int) * mem);+  *max_l  = (int *) vrna_alloc(sizeof(int) * mem);++  *min_l  -= min_k_pre;+  *max_l  -= min_k_pre;++  /* for each k guess the according minimum l*/+  for(cnt = min_k_pre; cnt <= max_k_pre; cnt++){+    (*min_l)[cnt] = min_l_pre;+    (*max_l)[cnt] = max_l_pre;+    while((*min_l)[cnt] + cnt < bpdist) (*min_l)[cnt]++;+    if((bpdist % 2) != (((*min_l)[cnt] + cnt) % 2)) (*min_l)[cnt]++;+  }+}++INLINE  PRIVATE void  prepareArray(int ***array, int min_k, int max_k, int *min_l, int *max_l){+  int i, j, mem;+  *array  = (int **)vrna_alloc(sizeof(int *) * (max_k - min_k + 1));+  *array  -= min_k;++  for(i = min_k; i <= max_k; i++){+    mem = (max_l[i] - min_l[i] + 1)/2 + 1;+    (*array)[i] = (int *)vrna_alloc(sizeof(int) * mem);+    for(j = 0; j < mem; j++)+      (*array)[i][j] = INF;+    (*array)[i]  -= min_l[i]/2;+  }+}++INLINE  PRIVATE void  prepareArray2(unsigned long ***array, int min_k, int max_k, int *min_l, int *max_l){+  int i, mem;+  *array  = (unsigned long **)vrna_alloc(sizeof(unsigned long *) * (max_k - min_k + 1));+  *array  -= min_k;++  for(i = min_k; i <= max_k; i++){+    mem = (max_l[i] - min_l[i] + 1)/2 + 1;+    (*array)[i] = (unsigned long *)vrna_alloc(sizeof(unsigned long) * mem);+    (*array)[i] -= min_l[i]/2;+  }+}++/*+#################################+# OLD API support               #+#################################+*/++/* crosslink data from vars->compatibility to TwoDfold_vars structure */+PRIVATE INLINE void+crosslink(TwoDfold_vars *vars){++  vrna_fold_compound_t  *c;+  vrna_mx_mfe_t       *m;++  c                     = vars->compatibility;+  m                     = c->matrices;+  vars->sequence        = c->sequence;+  vars->seq_length      = c->length;+  vars->reference_pt1   = c->reference_pt1;+  vars->reference_pt2   = c->reference_pt2;+  vars->referenceBPs1   = c->referenceBPs1;+  vars->referenceBPs2   = c->referenceBPs2;+  vars->bpdist          = c->bpdist;+  vars->do_backtrack    = 1;+  vars->dangles         = c->params->model_details.dangles;+  vars->circ            = c->params->model_details.circ;+  vars->temperature     = c->params->model_details.temperature;+  vars->ptype           = c->ptype_pf_compat;+  vars->P               = c->params;+  vars->S               = c->sequence_encoding2;+  vars->S1              = c->sequence_encoding;+  vars->my_iindx        = c->iindx;+  vars->mm1             = c->mm1;+  vars->mm2             = c->mm2;+  vars->maxD1           = c->maxD1;+  vars->maxD2           = c->maxD2;++  vars->E_C              = m->E_C;+  vars->l_min_values     = m->l_min_C;+  vars->l_max_values     = m->l_max_C;+  vars->k_min_values     = m->k_min_C;+  vars->k_max_values     = m->k_max_C;++  vars->E_F5             = m->E_F5;+  vars->l_min_values_f   = m->l_min_F5;+  vars->l_max_values_f   = m->l_max_F5;+  vars->k_min_values_f   = m->k_min_F5;+  vars->k_max_values_f   = m->k_max_F5;++  vars->E_F3             = m->E_F3;+  vars->l_min_values_f3  = m->l_min_F3;+  vars->l_max_values_f3  = m->l_max_F3;+  vars->k_min_values_f3  = m->k_min_F3;+  vars->k_max_values_f3  = m->k_max_F3;++  vars->E_M              = m->E_M;+  vars->l_min_values_m   = m->l_min_M;+  vars->l_max_values_m   = m->l_max_M;+  vars->k_min_values_m   = m->k_min_M;+  vars->k_max_values_m   = m->k_max_M;++  vars->E_M1             = m->E_M1;+  vars->l_min_values_m1  = m->l_min_M1;+  vars->l_max_values_m1  = m->l_max_M1;+  vars->k_min_values_m1  = m->k_min_M1;+  vars->k_max_values_m1  = m->k_max_M1;++#ifdef COUNT_STATES+  vars->N_C              = m->N_C;+  vars->N_F5             = m->N_F5;+  vars->N_M              = m->N_M;+  vars->N_M1             = m->N_M1;+#endif++  vars->E_M2_rem        = m->E_M2_rem;+  vars->E_M2            = m->E_M2;+  vars->l_min_values_m2 = m->l_min_M2;+  vars->l_max_values_m2 = m->l_max_M2;+  vars->k_min_values_m2 = m->k_min_M2;+  vars->k_max_values_m2 = m->k_max_M2;++  vars->E_Fc              = m->E_Fc;+  vars->E_FcH             = m->E_FcH;+  vars->E_FcI             = m->E_FcI;+  vars->E_FcM             = m->E_FcM;++  vars->E_Fc_rem         = m->E_Fc_rem;+  vars->E_FcH_rem        = m->E_FcH_rem;+  vars->E_FcI_rem        = m->E_FcI_rem;+  vars->E_FcM_rem        = m->E_FcM_rem;++  vars->E_C_rem          = m->E_C_rem;+  vars->E_M_rem          = m->E_M_rem;+  vars->E_M1_rem         = m->E_M1_rem;+  vars->E_F5_rem         = m->E_F5_rem;+}+++PUBLIC TwoDfold_vars *+get_TwoDfold_variables( const char *seq,+                        const char *structure1,+                        const char *structure2,+                        int circ){++  vrna_md_t           md;+  TwoDfold_vars       *vars;+  vrna_fold_compound_t  *c;+  vrna_mx_mfe_t       *m;++  set_model_details(&md);+  md.circ = circ;++  vars = (TwoDfold_vars *)vrna_alloc(sizeof(TwoDfold_vars));+  vars->compatibility = vrna_fold_compound_TwoD(seq, structure1, structure2, &md, VRNA_OPTION_MFE);++  crosslink(vars);++  return vars;+}++PUBLIC char *+TwoDfold_backtrack_f5(unsigned int j,+                      int k,+                      int l,+                      TwoDfold_vars *vars){++  return vrna_backtrack5_TwoD(vars->compatibility, k, l, j);+}++PUBLIC void+destroy_TwoDfold_variables(TwoDfold_vars *vars){++  if(vars == NULL) return;++  vrna_fold_compound_free(vars->compatibility);++  free(vars);+}++PUBLIC vrna_sol_TwoD_t *+TwoDfoldList( TwoDfold_vars *vars,+              int distance1,+              int distance2){++  vrna_sol_TwoD_t *sol;++  sol = vrna_mfe_TwoD(vars->compatibility, distance1, distance2);++  crosslink(vars);++  return sol;+}++PUBLIC void+update_TwoDfold_params(TwoDfold_vars *vars){++  vrna_md_t md;++  set_model_details(&md);++  free(vars->compatibility->params);+  vars->compatibility->params = vrna_params(&md);++  crosslink(vars);+}+
+ C/ViennaRNA/2Dfold.h view
@@ -0,0 +1,347 @@+#ifndef VIENNA_RNA_PACKAGE_TWO_D_FOLD_H+#define VIENNA_RNA_PACKAGE_TWO_D_FOLD_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file 2Dfold.h+ *  @ingroup kl_neighborhood+ *  @brief MFE structures for base pair distance classes+ *+ */++/**+ *  @addtogroup kl_neighborhood_mfe+ *  @brief Compute the minimum free energy (MFE) and secondary structures for a partitioning of+ *  the secondary structure space according to the base pair distance to two fixed reference structures+ *  basepair distance to two fixed reference structures+ *  @see For further details, we refer to Lorenz et al. 2009 @cite lorenz:2009+ *+ *  @{+ *  @ingroup  kl_neighborhood_mfe+ *+ */++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++/**+ *  @brief Solution element returned from vrna_mfe_TwoD()+ *+ *  This element contains free energy and structure for the appropriate+ *  kappa (k), lambda (l) neighborhood+ *  The datastructure contains two integer attributes 'k' and 'l'+ *  as well as an attribute 'en' of type float representing the free energy+ *  in kcal/mol and an attribute 's' of type char* containg the secondary+ *  structure representative,+ *+ *  A value of #INF in k denotes the end of a list+ *+ *  @see  vrna_mfe_TwoD()+ */+typedef struct vrna_sol_TwoD_t{+  int k;          /**<  @brief  Distance to first reference */+  int l;          /**<  @brief  Distance to second reference */+  float en;       /**<  @brief  Free energy in kcal/mol */+  char *s;        /**<  @brief  MFE representative structure in dot-bracket notation */+} vrna_sol_TwoD_t;++++/**+ * @brief Compute MFE's and representative for distance partitioning+ *+ * This function computes the minimum free energies and a representative+ * secondary structure for each distance class according to the two references+ * specified in the datastructure 'vars'.+ * The maximum basepair distance to each of both references may be set+ * by the arguments 'distance1' and 'distance2', respectively.+ * If both distance arguments are set to '-1', no restriction is assumed and+ * the calculation is performed for each distance class possible.+ *+ * The returned list contains an entry for each distance class. If a maximum+ * basepair distance to either of the references was passed, an entry with+ * k=l=-1 will be appended in the list, denoting the class where all structures+ * exceeding the maximum will be thrown into.+ * The end of the list is denoted by an attribute value of #INF in+ * the k-attribute of the list entry.+ *+ *  @see  vrna_fold_compound_TwoD(), vrna_fold_compound_free(), vrna_pf_TwoD()+ *        vrna_backtrack5_TwoD(), #vrna_sol_TwoD_t, #vrna_fold_compound_t+ *+ *  @param vc         The datastructure containing all precomputed folding attributes+ *  @param distance1  maximum distance to reference1 (-1 means no restriction)+ *  @param distance2  maximum distance to reference2 (-1 means no restriction)+ *  @return           A list of minimum free energies (and corresponding structures)+ *                    for each distance class+ */+vrna_sol_TwoD_t *+vrna_mfe_TwoD(vrna_fold_compound_t *vc,+              int distance1,+              int distance2);++/**+ * @brief Backtrack a minimum free energy structure from a 5' section of specified length+ *+ * This function allows one to backtrack a secondary structure beginning at the 5' end, a specified+ * length and residing in a specific distance class.+ * If the argument 'k' gets a value of -1, the structure that is backtracked is assumed to+ * reside in the distance class where all structures exceeding the maximum basepair distance+ * specified in vrna_mfe_TwoD() belong to.+ * @note The argument 'vars' must contain precalculated energy values in the energy matrices,+ * i.e. a call to vrna_mfe_TwoD() preceding this function is mandatory!+ *+ * @see vrna_mfe_TwoD()+ *+ * @param vc    The datastructure containing all precomputed folding attributes+ * @param j     The length in nucleotides beginning from the 5' end+ * @param k     distance to reference1 (may be -1)+ * @param l     distance to reference2+ */+char *+vrna_backtrack5_TwoD( vrna_fold_compound_t *vc,+                      int k,+                      int l,+                      unsigned int j);++#ifdef  VRNA_BACKWARD_COMPAT++#define TwoDfold_solution       vrna_sol_TwoD_t         /* restore compatibility of struct rename */++/**+ *  @brief Variables compound for 2Dfold MFE folding+ *+ *  @deprecated This data structure will be removed from the library soon!+ *              Use #vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(),+ *              vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!+ */+typedef struct TwoDfold_vars{+  vrna_param_t    *P;             /**<  @brief  Precomputed energy parameters and model details */+  int             do_backtrack;   /**<  @brief  Flag whether to do backtracing of the structure(s) or not */+  char            *ptype;         /**<  @brief  Precomputed array of pair types */+  char            *sequence;      /**<  @brief  The input sequence  */+  short           *S, *S1;        /**<  @brief  The input sequences in numeric form */+  unsigned int    maxD1;          /**<  @brief  Maximum allowed base pair distance to first reference */+  unsigned int    maxD2;          /**<  @brief  Maximum allowed base pair distance to second reference */+++  unsigned int    *mm1;           /**<  @brief  Maximum matching matrix, reference struct 1 disallowed */+  unsigned int    *mm2;           /**<  @brief  Maximum matching matrix, reference struct 2 disallowed */++  int             *my_iindx;      /**<  @brief  Index for moving in quadratic distancy dimensions */++  double          temperature;++  unsigned int    *referenceBPs1; /**<  @brief  Matrix containing number of basepairs of reference structure1 in interval [i,j] */+  unsigned int    *referenceBPs2; /**<  @brief  Matrix containing number of basepairs of reference structure2 in interval [i,j] */+  unsigned int    *bpdist;        /**<  @brief  Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */++  short           *reference_pt1;+  short           *reference_pt2;+  int             circ;+  int             dangles;+  unsigned int    seq_length;++  int             ***E_F5;+  int             ***E_F3;+  int             ***E_C;+  int             ***E_M;+  int             ***E_M1;+  int             ***E_M2;++  int             **E_Fc;+  int             **E_FcH;+  int             **E_FcI;+  int             **E_FcM;++  int             **l_min_values;+  int             **l_max_values;+  int             *k_min_values;+  int             *k_max_values;++  int             **l_min_values_m;+  int             **l_max_values_m;+  int             *k_min_values_m;+  int             *k_max_values_m;++  int             **l_min_values_m1;+  int             **l_max_values_m1;+  int             *k_min_values_m1;+  int             *k_max_values_m1;++  int             **l_min_values_f;+  int             **l_max_values_f;+  int             *k_min_values_f;+  int             *k_max_values_f;++  int             **l_min_values_f3;+  int             **l_max_values_f3;+  int             *k_min_values_f3;+  int             *k_max_values_f3;++  int             **l_min_values_m2;+  int             **l_max_values_m2;+  int             *k_min_values_m2;+  int             *k_max_values_m2;++  int             *l_min_values_fc;+  int             *l_max_values_fc;+  int             k_min_values_fc;+  int             k_max_values_fc;++  int             *l_min_values_fcH;+  int             *l_max_values_fcH;+  int             k_min_values_fcH;+  int             k_max_values_fcH;++  int             *l_min_values_fcI;+  int             *l_max_values_fcI;+  int             k_min_values_fcI;+  int             k_max_values_fcI;++  int             *l_min_values_fcM;+  int             *l_max_values_fcM;+  int             k_min_values_fcM;+  int             k_max_values_fcM;++  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */+  int             *E_F5_rem;+  int             *E_F3_rem;+  int             *E_C_rem;+  int             *E_M_rem;+  int             *E_M1_rem;+  int             *E_M2_rem;++  int             E_Fc_rem;+  int             E_FcH_rem;+  int             E_FcI_rem;+  int             E_FcM_rem;++#ifdef COUNT_STATES+  unsigned long             ***N_F5;+  unsigned long             ***N_C;+  unsigned long             ***N_M;+  unsigned long             ***N_M1;+#endif++  vrna_fold_compound_t *compatibility;+} TwoDfold_vars;++/**+ *  @brief Get a structure of type TwoDfold_vars prefilled with current global settings+ * + *  This function returns a datastructure of type TwoDfold_vars.+ *  The data fields inside the TwoDfold_vars are prefilled by global settings and all memory+ *  allocations necessary to start a computation are already done for the convenience of the user+ * + *  @note Make sure that the reference structures are compatible with the sequence according to Watson-Crick- and Wobble-base pairing+ * + *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!+ *+ *  @param seq          The RNA sequence+ *  @param structure1   The first reference structure in dot-bracket notation+ *  @param structure2   The second reference structure in dot-bracket notation+ *  @param circ         A switch to indicate the assumption to fold a circular instead of linear RNA (0=OFF, 1=ON)+ *  @returns            A datastructure prefilled with folding options and allocated memory+ */+DEPRECATED(TwoDfold_vars *+get_TwoDfold_variables( const char *seq,+                        const char *structure1,+                        const char *structure2,+                        int circ));++/**+ *  @brief Destroy a TwoDfold_vars datastructure without memory loss+ * + *  This function free's all allocated memory that depends on the datastructure given.+ * + *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!+ *+ *  @param our_variables  A pointer to the datastructure to be destroyed+ */+DEPRECATED(void +destroy_TwoDfold_variables(TwoDfold_vars *our_variables));++/**+ * @brief Compute MFE's and representative for distance partitioning+ *+ * This function computes the minimum free energies and a representative+ * secondary structure for each distance class according to the two references+ * specified in the datastructure 'vars'.+ * The maximum basepair distance to each of both references may be set+ * by the arguments 'distance1' and 'distance2', respectively.+ * If both distance arguments are set to '-1', no restriction is assumed and+ * the calculation is performed for each distance class possible.+ *+ * The returned list contains an entry for each distance class. If a maximum+ * basepair distance to either of the references was passed, an entry with+ * k=l=-1 will be appended in the list, denoting the class where all structures+ * exceeding the maximum will be thrown into.+ * The end of the list is denoted by an attribute value of #INF in+ * the k-attribute of the list entry.+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), and vrna_fold_compound_free() instead!+ *+ * @param vars      the datastructure containing all predefined folding attributes+ * @param distance1 maximum distance to reference1 (-1 means no restriction)+ * @param distance2 maximum distance to reference2 (-1 means no restriction)+ */+DEPRECATED(TwoDfold_solution *+TwoDfoldList( TwoDfold_vars *vars,+              int distance1,+              int distance2));++/**+ * @brief Backtrack a minimum free energy structure from a 5' section of specified length+ *+ * This function allows one to backtrack a secondary structure beginning at the 5' end, a specified+ * length and residing in a specific distance class.+ * If the argument 'k' gets a value of -1, the structure that is backtracked is assumed to+ * reside in the distance class where all structures exceeding the maximum basepair distance+ * specified in TwoDfold() belong to.+ * @note The argument 'vars' must contain precalculated energy values in the energy matrices,+ * i.e. a call to TwoDfold() preceding this function is mandatory!+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_mfe_TwoD(), vrna_backtrack5_TwoD(), and+ *              vrna_fold_compound_free() instead!+ *+ * @param j     The length in nucleotides beginning from the 5' end+ * @param k     distance to reference1 (may be -1)+ * @param l     distance to reference2+ * @param vars  the datastructure containing all predefined folding attributes+ */+DEPRECATED(char *TwoDfold_backtrack_f5(unsigned int j,+                            int k,+                            int l,+                            TwoDfold_vars *vars));++/**+ * + */+DEPRECATED(TwoDfold_solution **TwoDfold(TwoDfold_vars *our_variables,+                                        int distance1,+                                        int distance2));+++#endif++/**+ *  @}+ */++#endif
+ C/ViennaRNA/2Dpfold.c view
@@ -0,0 +1,4029 @@+/*+      minimum free energy+      RNA secondary structure with+      basepair distance d_1 to reference structure 1 and distance d_2 to reference structure 2++*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/2Dpfold.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  crosslink(TwoDpfold_vars *vars);++PRIVATE         void  pf2D_linear(vrna_fold_compound_t *vc);+PRIVATE         void  pf2D_circ(vrna_fold_compound_t *vc);+PRIVATE         char  *pbacktrack_circ( vrna_fold_compound_t *vc,+                                        int d1,+                                        int d2);++PRIVATE         void  backtrack(vrna_fold_compound_t *vc,+                                char *pstruc,+                                int d1,+                                int d2,+                                unsigned int i,+                                unsigned int j);+PRIVATE         void  backtrack_qm( vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2,+                                    unsigned int i,+                                    unsigned int j);+PRIVATE         void  backtrack_qm1(vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2,+                                    unsigned int i,+                                    unsigned int j);+PRIVATE         void  backtrack_qm2(vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2,+                                    unsigned int k);+PRIVATE         void  backtrack_qcH(vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2);+PRIVATE         void  backtrack_qcI(vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2);+PRIVATE         void  backtrack_qcM(vrna_fold_compound_t *vc,+                                    char *pstruc,+                                    int d1,+                                    int d2);++PRIVATE         void  adjustArrayBoundaries(+                        FLT_OR_DBL ***array,+                        int *k_min, int *k_max,+                        int **l_min, int **l_max,+                        int k_min_real, int k_max_real,+                        int *l_min_real, int *l_max_real);++INLINE  PRIVATE void  preparePosteriorBoundaries(+                        int size, int shift,+                        int *min_k, int *max_k,+                        int **min_l, int **max_l);+INLINE  PRIVATE void  updatePosteriorBoundaries(+                        int d1, int d2,+                        int *min_k, int *max_k,+                        int **min_l, int **max_l);+INLINE  PRIVATE void  prepareBoundaries(+                        int min_k_pre, int max_k_pre,+                        int min_l_pre, int max_l_pre,+                        int bpdist,+                        int *min_k, int *max_k,+                        int **min_l, int **max_l);+INLINE  PRIVATE void  prepareArray(+                        FLT_OR_DBL ***array,+                        int min_k, int max_k,+                        int *min_l, int *max_l);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC vrna_sol_TwoD_pf_t *+vrna_pf_TwoD( vrna_fold_compound_t *vc,+                int distance1,+                int distance2){++  unsigned int  maxD1 = 0, maxD2 = 0, counter = 0;+  int           cnt1, cnt2, k_min, k_max, l_min, l_max, ndx;+  FLT_OR_DBL    q = 0.;++  vrna_sol_TwoD_pf_t  *output;+  vrna_md_t           *md;+  vrna_mx_pf_t        *matrices;++  maxD1     = vc->maxD1;+  maxD2     = vc->maxD2;+  matrices  = vc->exp_matrices;+  md        = &(vc->exp_params->model_details);++  if(distance1 >= 0){+    if((unsigned int)distance1 > maxD1)+      vrna_message_warning("vrna_pf_TwoD@2Dpfold.c: limiting maximum basepair distance 1 to %u\n",+                                  maxD1);+    else+      maxD1 = (unsigned int)distance1;+  }++  if(distance2 >= 0){+    if((unsigned int)distance2 > maxD2)+      vrna_message_warning("vrna_pf_TwoD@2Dpfold.c: limiting maximum basepair distance 2 to %u\n",+                                  maxD2);+    else+      maxD2 = (unsigned int)distance2;+  }++  vc->maxD1 = maxD1;+  vc->maxD2 = maxD2;++  output = (vrna_sol_TwoD_pf_t *)vrna_alloc((((maxD1+1)*(maxD2+2))/2 + 2) * sizeof(vrna_sol_TwoD_pf_t));++  pf2D_linear(vc);+  if(md->circ) pf2D_circ(vc);++  ndx   = vc->iindx[1] - vc->length;+  k_min = (md->circ) ? matrices->k_min_Q_c: matrices->k_min_Q[ndx];+  k_max = (md->circ) ? matrices->k_max_Q_c: matrices->k_max_Q[ndx];++  for(cnt1 =  k_min;+      cnt1 <= k_max;+      cnt1++){+    l_min = (md->circ) ? matrices->l_min_Q_c[cnt1] : matrices->l_min_Q[ndx][cnt1];+    l_max = (md->circ) ? matrices->l_max_Q_c[cnt1] : matrices->l_max_Q[ndx][cnt1];+    for(cnt2 =  l_min;+        cnt2 <= l_max;+        cnt2 += 2){+      q = (md->circ) ? matrices->Q_c[cnt1][cnt2/2] : matrices->Q[ndx][cnt1][cnt2/2];+      if(q == 0.) continue;+      output[counter].k = cnt1;+      output[counter].l = cnt2;+      output[counter].q = q;+      counter++;+    }+  }++  /* store entry for remaining partition if it exists */+  q = (md->circ) ? matrices->Q_c_rem : matrices->Q_rem[ndx];+  if(q != 0.){+    output[counter].k = -1;+    output[counter].l = -1;+    output[counter].q = q;+    counter++;+  }++  /* insert end-marker entry */+  output[counter].k = output[counter].l = INF;+  counter++;++  /* resize to actual dataset amount */+  output = (vrna_sol_TwoD_pf_t *)vrna_realloc(output, sizeof(vrna_sol_TwoD_pf_t) * counter);+  return output;+}++#if 0+PUBLIC FLT_OR_DBL **TwoDpfold(TwoDpfold_vars *vars, int distance1, int distance2){+  unsigned int  i;+  unsigned int  maxD1 = 0;+  unsigned int  maxD2 = 0;+  unsigned int  mm;+  int           cnt1, cnt2;++  FLT_OR_DBL **output;++  initialize_TwoDpfold_vars(vars);++  vars->S   = encode_sequence(vars->sequence, 0);+  vars->S1  = encode_sequence(vars->sequence, 1);+  make_ptypes2(vars);++  for(i=1; i<=(unsigned int)vars->reference_pt1[0]; i++)+    if(i < (unsigned int)vars->reference_pt1[i]) maxD1++;+  for(i=1; i<=(unsigned int)vars->reference_pt2[0]; i++)+    if(i < (unsigned int)vars->reference_pt2[i]) maxD2++;+  mm    = maximumMatching(vars->sequence);+  maxD1 += mm;+  maxD2 += mm;++  if(distance1 >= 0){+    if((unsigned int)distance1 > maxD1)+      fprintf(stderr, "limiting maximum basepair distance 1 to %u\n", maxD1);+    maxD1 = (unsigned int)distance1;+  }++  if(distance2 >= 0){+    if((unsigned int)distance2 > maxD2)+      fprintf(stderr, "limiting maximum basepair distance 2 to %u\n", maxD2);+    maxD2 = (unsigned int)distance2;+  }+  vars->maxD1 = maxD1;+  vars->maxD2 = maxD2;+++  output = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL*) * (maxD1+1));+  pf2D_linear(vars);+  int ndx = vars->my_iindx[1] - vars->seq_length;+  for(cnt1 = vars->k_min_values[ndx]; cnt1 <= MIN2(vars->k_max_values[ndx], vars->maxD1); cnt1++){+    output[cnt1] = (FLT_OR_DBL *)vrna_alloc((vars->maxD2+1)*sizeof(FLT_OR_DBL));+    for(cnt2 = vars->l_min_values[ndx][cnt1]; cnt2 <= MIN2(vars->l_max_values[ndx][cnt1], vars->maxD2); cnt2+=2){+      output[cnt1][cnt2] = vars->Q[ndx][cnt1][cnt2/2];+    }+  }+  return output;+}++PUBLIC FLT_OR_DBL **TwoDpfold_circ(TwoDpfold_vars *vars, int distance1, int distance2){+  unsigned int i;+  unsigned int maxD1 = 0;+  unsigned int maxD2 = 0;+  unsigned int mm;+  int           cnt1, cnt2;+  FLT_OR_DBL **output;++  initialize_TwoDpfold_vars(vars);++  vars->S   = encode_sequence(vars->sequence, 0);+  vars->S1  = encode_sequence(vars->sequence, 1);+  make_ptypes2(vars);++  for(i=1; i<=(unsigned int)vars->reference_pt1[0]; i++)+    if(i < (unsigned int)vars->reference_pt1[i]) maxD1++;+  for(i=1; i<=(unsigned int)vars->reference_pt2[0]; i++)+    if(i < (unsigned int)vars->reference_pt2[i]) maxD2++;+  mm = maximumMatching(vars->sequence);+  maxD1 += mm;+  maxD2 += mm;++  if(distance1 >= 0){+    if((unsigned int)distance1 > maxD1)+      fprintf(stderr, "limiting maximum basepair distance 1 to %u\n", maxD1);+    maxD1 = (unsigned int)distance1;+  }++  if(distance2 >= 0){+    if((unsigned int)distance2 > maxD2)+      fprintf(stderr, "limiting maximum basepair distance 2 to %u\n", maxD2);+    maxD2 = (unsigned int)distance2;+  }+  vars->maxD1 = maxD1;+  vars->maxD2 = maxD2;++  output = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL*) * (maxD1+1));+  pf2D_linear(vars);+  pf2D_circ(vars);++  for(cnt1 = vars->k_min_values_qc; cnt1 <= MIN2(vars->k_max_values_qc, vars->maxD1); cnt1++){+    output[cnt1] = (FLT_OR_DBL *)vrna_alloc((vars->maxD2+1)*sizeof(FLT_OR_DBL));+    for(cnt2 = vars->l_min_values_qc[cnt1]; cnt2 <= MIN2(vars->l_max_values_qc[cnt1], vars->maxD2); cnt2+=2){+      output[cnt1][cnt2] = vars->Q_c[cnt1][cnt2/2];+    }+  }+  return output;+}++#endif++PRIVATE void+pf2D_linear(vrna_fold_compound_t *vc){++  char          *sequence, *ptype;+  short         *S1, *reference_pt1, *reference_pt2;+  unsigned int  *referenceBPs1, *referenceBPs2,+                d, i, j, ij, seq_length, maxD1,+                maxD2, *mm1, *mm2, *bpdist;+  int           *my_iindx, *jindx, circ, cnt1, cnt2, cnt3, cnt4, *rtype;+  double        max_real;+  FLT_OR_DBL    *scale, Qmax;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  vrna_md_t         *md;++  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  pf_params     = vc->exp_params;+  md            = &(pf_params->model_details);+  matrices      = vc->exp_matrices;+  sequence      = vc->sequence;+  seq_length    = vc->length;+  maxD1         = vc->maxD1;+  maxD2         = vc->maxD2;+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype;+  rtype         = &(md->rtype[0]);+  scale         = matrices->scale;+  reference_pt1 = vc->reference_pt1;+  reference_pt2 = vc->reference_pt2;+  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  referenceBPs1 = vc->referenceBPs1;+  referenceBPs2 = vc->referenceBPs2;+  dangles       = md->dangles;+  circ          = md->circ;+  mm1           = vc->mm1;+  mm2           = vc->mm2;+  bpdist        = vc->bpdist;+  Qmax          = 0.;++  /*array initialization ; qb,qm,q+    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */++  for (j = 1; j<=seq_length; j++)+    for (i=(j>TURN?(j-TURN):1); i<=j; i++){+      ij                        = my_iindx[i]-j;+      matrices->k_min_Q[ij]    = 0;+      matrices->k_max_Q[ij]    = 0;+      matrices->l_min_Q[ij]    = (int *)vrna_alloc(sizeof(int));+      matrices->l_max_Q[ij]    = (int *)vrna_alloc(sizeof(int));+      matrices->l_min_Q[ij][0] = 0;+      matrices->l_max_Q[ij][0] = 0;+      matrices->Q[ij]               = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *));+      matrices->Q[ij][0]            = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL));+      matrices->Q[ij][0][0]         = 1.0 * scale[j-i+1];+    }+++  for (d = TURN+2; d <= seq_length; d++) { /* i,j in [1..seq_length] */+#ifdef _OPENMP+  #pragma omp parallel for private(i, j, ij, cnt1, cnt2, cnt3, cnt4)+#endif+    for (j = d; j <= seq_length; j++) {+      unsigned int k,l, kl, u, ii, dij;+      int no_close, type, type_2, tt, da, db, base_da, base_db;+      FLT_OR_DBL  temp2, aux_en;++      i     = j-d+1;+      ij    = my_iindx[i]-j;+      dij   = j - i - 1;+      type  = ptype[jindx[j] + i];+++      no_close = (((type==3)||(type==4))&&no_closingGU);++      if (type) {   /* we have a pair */++        int k_min_Q_B, k_max_Q_B, l_min_Q_B, l_max_Q_B;+        int k_min_post_b, k_max_post_b, *l_min_post_b, *l_max_post_b;+        int update_b = 0;++        if(!matrices->Q_B[ij]){+          update_b = 1;+          k_min_Q_B = l_min_Q_B = 0;+          k_max_Q_B = mm1[ij] + referenceBPs1[ij];+          l_max_Q_B = mm2[ij] + referenceBPs2[ij];++          prepareBoundaries(k_min_Q_B,+                            k_max_Q_B,+                            l_min_Q_B,+                            l_max_Q_B,+                            bpdist[ij],+                            &matrices->k_min_Q_B[ij],+                            &matrices->k_max_Q_B[ij],+                            &matrices->l_min_Q_B[ij],+                            &matrices->l_max_Q_B[ij]+                            );+          preparePosteriorBoundaries( matrices->k_max_Q_B[ij] - matrices->k_min_Q_B[ij] + 1,+                                      matrices->k_min_Q_B[ij],+                                      &k_min_post_b,+                                      &k_max_post_b,+                                      &l_min_post_b,+                                      &l_max_post_b+                                  );++          prepareArray( &matrices->Q_B[ij],+                        matrices->k_min_Q_B[ij],+                        matrices->k_max_Q_B[ij],+                        matrices->l_min_Q_B[ij],+                        matrices->l_max_Q_B[ij]+                    );+        }+++        /* hairpin ----------------------------------------------*/++        /* get distance to reference if closing the hairpin+        *  d1a = dbp(T1_{i,j}, {i,j})+        */+        base_da = ((unsigned int)reference_pt1[i] != j) ? 1 : -1;+        base_db = ((unsigned int)reference_pt2[i] != j) ? 1 : -1;++        da = base_da + referenceBPs1[ij];+        db = base_db + referenceBPs2[ij];++        if(!no_close)+          if((da >= 0) && (db >= 0)){+            if(((unsigned int)da<=maxD1) && ((unsigned int)db <= maxD2)){+              matrices->Q_B[ij][da][db/2] = exp_E_Hairpin(dij, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[dij+2];+              if(update_b){+                updatePosteriorBoundaries( da,+                                           db,+                                           &k_min_post_b,+                                           &k_max_post_b,+                                           &l_min_post_b,+                                           &l_max_post_b+                                         );+              }+            }+            else{+              matrices->Q_B_rem[ij] = exp_E_Hairpin(dij, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[dij+2];+            }+          }+        /*--------------------------------------------------------+          check for elementary structures involving more than one+          closing pair.+        --------------------------------------------------------*/+        for (k = i+1; k <= MIN2(j-2-TURN,i+MAXLOOP+1) ; k++) {+          unsigned int minl, ln_pre;+          minl = k + TURN + 1;+          ln_pre = dij + k;+          if(ln_pre > minl + MAXLOOP) minl = ln_pre - MAXLOOP - 1;+          for (l = minl; l < j; l++) {+            kl = my_iindx[k] - l;+            type_2 = ptype[jindx[l] + k];++            if (type_2==0) continue;+            type_2 = rtype[type_2];+            aux_en = exp_E_IntLoop(k-i-1, j-l-1, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params) * scale[k-i+j-l];++            /* get distance to reference if closing the interior loop+            *  d2 = dbp(S_{i,j}, S_{k,l} + {i,j})+            */+            da = base_da + referenceBPs1[ij] - referenceBPs1[kl];+            db = base_db + referenceBPs2[ij] - referenceBPs2[kl];++            if(matrices->Q_B_rem[kl]){+              matrices->Q_B_rem[ij] += matrices->Q_B_rem[kl] * aux_en;+            }+            if(!matrices->Q_B[kl]) continue;+            for(cnt1 = matrices->k_min_Q_B[kl];+                cnt1 <= matrices->k_max_Q_B[kl];+                cnt1++)+              for(cnt2 = matrices->l_min_Q_B[kl][cnt1];+                  cnt2 <= matrices->l_max_Q_B[kl][cnt1];+                  cnt2 += 2){+                if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+                  matrices->Q_B[ij][cnt1 + da][(cnt2 + db)/2] += matrices->Q_B[kl][cnt1][cnt2/2] * aux_en;+                  if(update_b){+                    updatePosteriorBoundaries( da + cnt1,+                                               db + cnt2,+                                               &k_min_post_b,+                                               &k_max_post_b,+                                               &l_min_post_b,+                                               &l_max_post_b+                                             );+                  }+                }+                else{+                  matrices->Q_B_rem[ij] += matrices->Q_B[kl][cnt1][cnt2/2] * aux_en;+                }+              }++          } /* end l-loop */+        } /* end k-loop */++        /* multi-loop contribution ------------------------*/+        if(!no_close){+          for(u=i+TURN+2; u<j-TURN-2;u++){+            tt = rtype[type];+            temp2 = pf_params->expMLclosing * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params) * scale[2];++            if(matrices->Q_M_rem[my_iindx[i+1]-u]){+              if(matrices->Q_M1[jindx[j-1]+u+1])+                for(cnt1 = matrices->k_min_Q_M1[jindx[j-1]+u+1];+                    cnt1 <= matrices->k_max_Q_M1[jindx[j-1]+u+1];+                    cnt1++)+                  for(cnt2 = matrices->l_min_Q_M1[jindx[j-1]+u+1][cnt1];+                      cnt2 <= matrices->l_max_Q_M1[jindx[j-1]+u+1][cnt1];+                      cnt2 += 2)+                    matrices->Q_B_rem[ij] += matrices->Q_M_rem[my_iindx[i+1]-u] * matrices->Q_M1[jindx[j-1]+u+1][cnt1][cnt2/2] * temp2;++              if(matrices->Q_M1_rem[jindx[j-1]+u+1])+                matrices->Q_B_rem[ij] += matrices->Q_M_rem[my_iindx[i+1]-u] * matrices->Q_M1_rem[jindx[j-1]+u+1] * temp2;+            }+            if(matrices->Q_M1_rem[jindx[j-1]+u+1]){+              if(matrices->Q_M[my_iindx[i+1]-u])+                for(cnt1 = matrices->k_min_Q_M[my_iindx[i+1]-u];+                    cnt1 <= matrices->k_max_Q_M[my_iindx[i+1]-u];+                    cnt1++)+                  for(cnt2 = matrices->l_min_Q_M[my_iindx[i+1]-u][cnt1];+                      cnt2 <= matrices->l_max_Q_M[my_iindx[i+1]-u][cnt1];+                      cnt2 += 2)+                    matrices->Q_B_rem[ij] += matrices->Q_M[my_iindx[i+1]-u][cnt1][cnt2/2] * matrices->Q_M1_rem[jindx[j-1]+u+1] * temp2;+            }++            /* get distance to reference if closing the multiloop+            *  dist3 = dbp(S_{i,j}, {i,j} + S_{i+1,u} + S_{u+1,j-1})+            */+            da = base_da + referenceBPs1[ij] - referenceBPs1[my_iindx[i+1]-u] - referenceBPs1[my_iindx[u+1]-j+1];+            db = base_db + referenceBPs2[ij] - referenceBPs2[my_iindx[i+1]-u] - referenceBPs2[my_iindx[u+1]-j+1];++            if(!matrices->Q_M[my_iindx[i+1]-u]) continue;+            if(!matrices->Q_M1[jindx[j-1]+u+1]) continue;+            for(cnt1 = matrices->k_min_Q_M[my_iindx[i+1]-u];+                cnt1 <= matrices->k_max_Q_M[my_iindx[i+1]-u];+                cnt1++)+              for(cnt2 = matrices->l_min_Q_M[my_iindx[i+1]-u][cnt1];+                  cnt2 <= matrices->l_max_Q_M[my_iindx[i+1]-u][cnt1];+                  cnt2 += 2){+                for(cnt3 = matrices->k_min_Q_M1[jindx[j-1]+u+1];+                    cnt3 <= matrices->k_max_Q_M1[jindx[j-1]+u+1];+                    cnt3++)+                  for(cnt4 = matrices->l_min_Q_M1[jindx[j-1]+u+1][cnt3];+                      cnt4 <= matrices->l_max_Q_M1[jindx[j-1]+u+1][cnt3];+                      cnt4 += 2){+                    if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                      matrices->Q_B[ij][cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] +=  matrices->Q_M[my_iindx[i+1]-u][cnt1][cnt2/2]+                                                                              * matrices->Q_M1[jindx[j-1]+u+1][cnt3][cnt4/2]+                                                                              * temp2;+                      if(update_b){+                        updatePosteriorBoundaries( cnt1 + cnt3 + da,+                                                   cnt2 + cnt4 + db,+                                                   &k_min_post_b,+                                                   &k_max_post_b,+                                                   &l_min_post_b,+                                                   &l_max_post_b+                                                 );+                      }+                    }+                    else{+                      matrices->Q_B_rem[ij] +=  matrices->Q_M[my_iindx[i+1]-u][cnt1][cnt2/2]+                                    * matrices->Q_M1[jindx[j-1]+u+1][cnt3][cnt4/2]+                                    * temp2;+                    }+                  }++              }++          }+        }++        if(update_b){+          adjustArrayBoundaries(&matrices->Q_B[ij],+                                &matrices->k_min_Q_B[ij],+                                &matrices->k_max_Q_B[ij],+                                &matrices->l_min_Q_B[ij],+                                &matrices->l_max_Q_B[ij],+                                k_min_post_b,+                                k_max_post_b,+                                l_min_post_b,+                                l_max_post_b+                                );+        }+      } /* end >> if (pair) << */++      /* free ends ? -----------------------------------------*/++      int k_min_Q_M, k_max_Q_M, l_min_Q_M, l_max_Q_M;+      int k_min_post_m, k_max_post_m, *l_min_post_m, *l_max_post_m;+      int update_m = 0;+      int k_min_Q_M1, k_max_Q_M1, l_min_Q_M1, l_max_Q_M1;+      int k_min_post_m1, k_max_post_m1, *l_min_post_m1, *l_max_post_m1;+      int update_m1 = 0;++      if(!matrices->Q_M[ij]){+        update_m = 1;+        k_min_Q_M = l_min_Q_M = 0;+        k_max_Q_M = mm1[ij] + referenceBPs1[ij];+        l_max_Q_M = mm2[ij] + referenceBPs2[ij];++        prepareBoundaries(k_min_Q_M,+                          k_max_Q_M,+                          l_min_Q_M,+                          l_max_Q_M,+                          bpdist[ij],+                          &matrices->k_min_Q_M[ij],+                          &matrices->k_max_Q_M[ij],+                          &matrices->l_min_Q_M[ij],+                          &matrices->l_max_Q_M[ij]+                          );+        preparePosteriorBoundaries( matrices->k_max_Q_M[ij] - matrices->k_min_Q_M[ij] + 1,+                                    matrices->k_min_Q_M[ij],+                                    &k_min_post_m,+                                    &k_max_post_m,+                                    &l_min_post_m,+                                    &l_max_post_m+                                );++        prepareArray( &matrices->Q_M[ij],+                      matrices->k_min_Q_M[ij],+                      matrices->k_max_Q_M[ij],+                      matrices->l_min_Q_M[ij],+                      matrices->l_max_Q_M[ij]+                  );+      }+      if(!matrices->Q_M1[jindx[j]+i]){+        update_m1 = 1;+        k_min_Q_M1 = l_min_Q_M1 = 0;+        k_max_Q_M1 = mm1[ij] + referenceBPs1[ij];+        l_max_Q_M1 = mm2[ij] + referenceBPs2[ij];++        prepareBoundaries(k_min_Q_M1,+                          k_max_Q_M1,+                          l_min_Q_M1,+                          l_max_Q_M1,+                          bpdist[ij],+                          &matrices->k_min_Q_M1[jindx[j]+i],+                          &matrices->k_max_Q_M1[jindx[j]+i],+                          &matrices->l_min_Q_M1[jindx[j]+i],+                          &matrices->l_max_Q_M1[jindx[j]+i]+                          );+        preparePosteriorBoundaries( matrices->k_max_Q_M1[jindx[j]+i] - matrices->k_min_Q_M1[jindx[j]+i] + 1,+                                    matrices->k_min_Q_M1[jindx[j]+i],+                                    &k_min_post_m1,+                                    &k_max_post_m1,+                                    &l_min_post_m1,+                                    &l_max_post_m1+                                );++        prepareArray( &matrices->Q_M1[jindx[j]+i],+                      matrices->k_min_Q_M1[jindx[j]+i],+                      matrices->k_max_Q_M1[jindx[j]+i],+                      matrices->l_min_Q_M1[jindx[j]+i],+                      matrices->l_max_Q_M1[jindx[j]+i]+                  );+      }+++      /* j is unpaired */+      da = referenceBPs1[ij] - referenceBPs1[ij+1];+      db = referenceBPs2[ij] - referenceBPs2[ij+1];++      if(matrices->Q_M_rem[ij+1])+        matrices->Q_M_rem[ij] += matrices->Q_M_rem[ij+1] * pf_params->expMLbase * scale[1];++      if(matrices->Q_M[ij+1])+        for(cnt1 = matrices->k_min_Q_M[ij+1];+            cnt1 <= matrices->k_max_Q_M[ij+1];+            cnt1++){+          for(cnt2 = matrices->l_min_Q_M[ij+1][cnt1];+              cnt2 <= matrices->l_max_Q_M[ij+1][cnt1];+              cnt2 += 2){+            if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+              matrices->Q_M[ij][cnt1 + da][(cnt2 + db)/2] += matrices->Q_M[ij+1][cnt1][cnt2/2] * pf_params->expMLbase * scale[1];+              if(update_m){+                updatePosteriorBoundaries(cnt1 + da,+                                          cnt2 + db,+                                          &k_min_post_m,+                                          &k_max_post_m,+                                          &l_min_post_m,+                                          &l_max_post_m+                                          );+              }+            }+            else{+              matrices->Q_M_rem[ij] += matrices->Q_M[ij+1][cnt1][cnt2/2] * pf_params->expMLbase * scale[1];+            }+          }+        }++      if(matrices->Q_M1_rem[jindx[j-1]+i])+        matrices->Q_M1_rem[jindx[j]+i] += matrices->Q_M1_rem[jindx[j-1]+i] * pf_params->expMLbase * scale[1];++      if(matrices->Q_M1[jindx[j-1]+i])+        for(cnt1 = matrices->k_min_Q_M1[jindx[j-1]+i];+            cnt1 <= matrices->k_max_Q_M1[jindx[j-1]+i];+            cnt1++)+          for(cnt2 = matrices->l_min_Q_M1[jindx[j-1]+i][cnt1];+              cnt2 <= matrices->l_max_Q_M1[jindx[j-1]+i][cnt1];+              cnt2 += 2){+            if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+              matrices->Q_M1[jindx[j]+i][cnt1 + da][(cnt2 + db)/2] += matrices->Q_M1[jindx[j-1]+i][cnt1][cnt2/2] * pf_params->expMLbase * scale[1];+              if(update_m1){+                updatePosteriorBoundaries(cnt1 + da,+                                          cnt2 + db,+                                          &k_min_post_m1,+                                          &k_max_post_m1,+                                          &l_min_post_m1,+                                          &l_max_post_m1+                                          );+              }+            }+            else{+              matrices->Q_M1_rem[jindx[j]+i] += matrices->Q_M1[jindx[j-1]+i][cnt1][cnt2/2] * pf_params->expMLbase * scale[1];+            }+          }+++      /* j pairs with i */+      if((!no_close) && type){+        FLT_OR_DBL aux_en = exp_E_MLstem(type, (i>1) || circ ? S1[i-1] : -1, (j<seq_length) || circ ? S1[j+1] : -1, pf_params);++        if(matrices->Q_B_rem[ij]){+          matrices->Q_M_rem[ij]           += matrices->Q_B_rem[ij] * aux_en;+          matrices->Q_M1_rem[jindx[j]+i]  += matrices->Q_B_rem[ij] * aux_en;+        }++        if(matrices->Q_B[ij]){+          for(cnt1 = matrices->k_min_Q_B[ij];+              cnt1 <= matrices->k_max_Q_B[ij];+              cnt1++)+            for(cnt2 = matrices->l_min_Q_B[ij][cnt1];+                cnt2 <= matrices->l_max_Q_B[ij][cnt1];+                cnt2 += 2){+              matrices->Q_M[ij][cnt1][cnt2/2] += matrices->Q_B[ij][cnt1][cnt2/2] * aux_en;+              if(update_m){+                updatePosteriorBoundaries(cnt1,+                                          cnt2,+                                          &k_min_post_m,+                                          &k_max_post_m,+                                          &l_min_post_m,+                                          &l_max_post_m+                                          );+              }+              matrices->Q_M1[jindx[j]+i][cnt1][cnt2/2] += matrices->Q_B[ij][cnt1][cnt2/2] * aux_en;+              if(update_m1){+                updatePosteriorBoundaries(cnt1,+                                          cnt2,+                                          &k_min_post_m1,+                                          &k_max_post_m1,+                                          &l_min_post_m1,+                                          &l_max_post_m1+                                          );+              }+            }+        }+      }++      /* j pairs with k: i<k<j */+      ii = my_iindx[i];+      for (k=i+1; k<=j; k++){+        tt = ptype[jindx[j] + k];+        temp2 = exp_E_MLstem(tt, S1[k-1], (j<seq_length) || circ ? S1[j+1] : -1, pf_params);++        if(matrices->Q_B_rem[my_iindx[k]-j]){+          matrices->Q_M_rem[ij] += matrices->Q_B_rem[my_iindx[k]-j] * pow(pf_params->expMLbase, (double)(k-i)) * scale[k-i] * temp2;+          if(matrices->Q_M[ii-k+1])+            for(cnt1 = matrices->k_min_Q_M[ii-k+1];+                cnt1 <= matrices->k_max_Q_M[ii-k+1];+                cnt1++)+              for(cnt2 = matrices->l_min_Q_M[ii-k+1][cnt1];+                  cnt2 <= matrices->l_max_Q_M[ii-k+1][cnt1];+                  cnt2 += 2)+                matrices->Q_M_rem[ij] += matrices->Q_M[ii-k+1][cnt1][cnt2/2] * matrices->Q_B_rem[my_iindx[k]-j] * temp2;++          if(matrices->Q_M_rem[ii-k+1])+            matrices->Q_M_rem[ij] += matrices->Q_M_rem[ii-k+1] * matrices->Q_B_rem[my_iindx[k]-j] * temp2;+        }+        if(matrices->Q_M_rem[ii-k+1]){+          if(matrices->Q_B[my_iindx[k]-j])+            for(cnt1 = matrices->k_min_Q_B[my_iindx[k]-j];+                cnt1 <= matrices->k_max_Q_B[my_iindx[k]-j];+                cnt1++)+              for(cnt2 = matrices->l_min_Q_B[my_iindx[k]-j][cnt1];+                  cnt2 <= matrices->l_max_Q_B[my_iindx[k]-j][cnt1];+                  cnt2 += 2)+                matrices->Q_M_rem[ij] += matrices->Q_M_rem[my_iindx[k]-j] * matrices->Q_B[my_iindx[k]-j][cnt1][cnt2/2] * temp2;+        }++        /* add contributions of QM(i,k-1)*QB(k,j)*e^b and+        *  e^((k-i) * c) * QB(k,j) * e^b+        *  therefor we need d1a = dbp(T1_{i,j}, T1_{i,k-1} + T1_{k,j}),+        *  d1b = dbp(T2_{i,j}, T2_{i,k-1} + T2_{k,j})+        *  d1c = dbp(T1_{i,j}, T1_{k,j})circ = 0;+        *  d1d = dbp(T2_{i,j}, T2_{k,j})+        */+        da = referenceBPs1[ij] - referenceBPs1[my_iindx[k]-j];+        db = referenceBPs2[ij] - referenceBPs2[my_iindx[k]-j];++        if(!matrices->Q_B[my_iindx[k]-j]) continue;+        for(cnt1 = matrices->k_min_Q_B[my_iindx[k]-j];+            cnt1 <= matrices->k_max_Q_B[my_iindx[k]-j];+            cnt1++)+          for(cnt2 = matrices->l_min_Q_B[my_iindx[k]-j][cnt1];+              cnt2 <= matrices->l_max_Q_B[my_iindx[k]-j][cnt1];+              cnt2 += 2){+            if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+                matrices->Q_M[ij][cnt1 + da][(cnt2 + db)/2] += matrices->Q_B[my_iindx[k]-j][cnt1][cnt2/2] * pow(pf_params->expMLbase, (double)(k-i)) * scale[k-i] * temp2;+              if(update_m){+                updatePosteriorBoundaries(cnt1 + da,+                                          cnt2 + db,+                                          &k_min_post_m,+                                          &k_max_post_m,+                                          &l_min_post_m,+                                          &l_max_post_m+                                          );+              }+            }+            else{+              matrices->Q_M_rem[ij] += matrices->Q_B[my_iindx[k]-j][cnt1][cnt2/2] * pow(pf_params->expMLbase, (double)(k-i)) * scale[k-i] * temp2;+            }+          }++        if(!matrices->Q_M[ii-k+1]) continue;+        da -= referenceBPs1[ii-k+1];+        db -= referenceBPs2[ii-k+1];++        for(cnt1 = matrices->k_min_Q_M[ii-k+1];+            cnt1 <= matrices->k_max_Q_M[ii-k+1];+            cnt1++)+          for(cnt2 = matrices->l_min_Q_M[ii-k+1][cnt1];+              cnt2 <= matrices->l_max_Q_M[ii-k+1][cnt1];+              cnt2 += 2)+            for(cnt3 = matrices->k_min_Q_B[my_iindx[k]-j];+                cnt3 <= matrices->k_max_Q_B[my_iindx[k]-j];+                cnt3++)+              for(cnt4 = matrices->l_min_Q_B[my_iindx[k]-j][cnt3];+                  cnt4 <= matrices->l_max_Q_B[my_iindx[k]-j][cnt3];+                  cnt4 += 2){+                if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                  matrices->Q_M[ij][cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] += matrices->Q_M[ii-k+1][cnt1][cnt2/2] * matrices->Q_B[my_iindx[k]-j][cnt3][cnt4/2] * temp2;+                  if(update_m){+                    updatePosteriorBoundaries(cnt1 + cnt3 + da,+                                              cnt2 + cnt4 + db,+                                              &k_min_post_m,+                                              &k_max_post_m,+                                              &l_min_post_m,+                                              &l_max_post_m+                                              );+                  }+                }+                else{+                  matrices->Q_M_rem[ij] += matrices->Q_M[ii-k+1][cnt1][cnt2/2] * matrices->Q_B[my_iindx[k]-j][cnt3][cnt4/2] * temp2;+                }+              }+      }++      if(update_m){+        adjustArrayBoundaries(&matrices->Q_M[ij],+                              &matrices->k_min_Q_M[ij],+                              &matrices->k_max_Q_M[ij],+                              &matrices->l_min_Q_M[ij],+                              &matrices->l_max_Q_M[ij],+                              k_min_post_m,+                              k_max_post_m,+                              l_min_post_m,+                              l_max_post_m+                              );+      }+      if(update_m1){+        adjustArrayBoundaries(&matrices->Q_M1[jindx[j]+i],+                              &matrices->k_min_Q_M1[jindx[j]+i],+                              &matrices->k_max_Q_M1[jindx[j]+i],+                              &matrices->l_min_Q_M1[jindx[j]+i],+                              &matrices->l_max_Q_M1[jindx[j]+i],+                              k_min_post_m1,+                              k_max_post_m1,+                              l_min_post_m1,+                              l_max_post_m1+                              );+      }++      /* compute contributions for Q(i,j) */+      int k_min, k_max, l_min, l_max;+      int k_min_post, k_max_post, *l_min_post, *l_max_post;+      int update_q = 0;+      if(!matrices->Q[ij]){+        update_q = 1;+        k_min = l_min = 0;+        k_max = mm1[ij] + referenceBPs1[ij];+        l_max = mm2[ij] + referenceBPs2[ij];++        prepareBoundaries(k_min,+                          k_max,+                          l_min,+                          l_max,+                          bpdist[ij],+                          &matrices->k_min_Q[ij],+                          &matrices->k_max_Q[ij],+                          &matrices->l_min_Q[ij],+                          &matrices->l_max_Q[ij]+                          );+        preparePosteriorBoundaries( matrices->k_max_Q[ij] - matrices->k_min_Q[ij] + 1,+                                    matrices->k_min_Q[ij],+                                    &k_min_post,+                                    &k_max_post,+                                    &l_min_post,+                                    &l_max_post+                                );++        prepareArray( &matrices->Q[ij],+                      matrices->k_min_Q[ij],+                      matrices->k_max_Q[ij],+                      matrices->l_min_Q[ij],+                      matrices->l_max_Q[ij]+                  );+      }++      if (type){+        aux_en = exp_E_ExtLoop(type, (i>1) || circ ? S1[i-1] : -1, (j < seq_length) || circ ? S1[j+1] : -1, pf_params);++        if(matrices->Q_B_rem[ij])+          matrices->Q_rem[ij] += matrices->Q_B_rem[ij] * aux_en;++        if(matrices->Q_B[ij])+          for(cnt1 = matrices->k_min_Q_B[ij];+              cnt1 <= matrices->k_max_Q_B[ij];+              cnt1++)+            for(cnt2 = matrices->l_min_Q_B[ij][cnt1];+                cnt2 <= matrices->l_max_Q_B[ij][cnt1];+                cnt2 += 2){+              matrices->Q[ij][cnt1][cnt2/2] += matrices->Q_B[ij][cnt1][cnt2/2] * aux_en;+              if(update_q){+                updatePosteriorBoundaries(cnt1,+                                          cnt2,+                                          &k_min_post,+                                          &k_max_post,+                                          &l_min_post,+                                          &l_max_post+                                          );+              }+            }+      }++      /* j is unpaired */+      if(matrices->Q_rem[ij+1])+        matrices->Q_rem[ij] += matrices->Q_rem[ij+1] * scale[1];++      /* da = dbp(T1_{i,j}, T1_{i,j-1})+      *  db = dbp(T2_{i,j}, T2_{i,j-1})+      */+      da = referenceBPs1[ij] - referenceBPs1[ij+1];+      db = referenceBPs2[ij] - referenceBPs2[ij+1];+      if(matrices->Q[ij+1])+        for(cnt1 = matrices->k_min_Q[ij+1];+            cnt1 <= matrices->k_max_Q[ij+1];+            cnt1++)+          for(cnt2 = matrices->l_min_Q[ij+1][cnt1];+              cnt2 <= matrices->l_max_Q[ij+1][cnt1];+              cnt2 += 2){+            if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+              matrices->Q[ij][cnt1 + da][(cnt2 + db)/2] += matrices->Q[ij+1][cnt1][cnt2/2] * scale[1];+              if(update_q){+                updatePosteriorBoundaries(cnt1 + da,+                                          cnt2 + db,+                                          &k_min_post,+                                          &k_max_post,+                                          &l_min_post,+                                          &l_max_post+                                          );+              }+            }+            else{+              matrices->Q_rem[ij] += matrices->Q[ij+1][cnt1][cnt2/2] * scale[1];+            }+          }++      for(k=j-TURN-1; k>i; k--){+        tt = ptype[jindx[j] + k];+        temp2 = exp_E_ExtLoop(tt, S1[k-1], (j<seq_length) || circ ? S1[j+1] : -1, pf_params);++        if(matrices->Q_rem[my_iindx[i]-k+1]){+          if(matrices->Q_B[my_iindx[k]-j])+            for(cnt1 = matrices->k_min_Q_B[my_iindx[k]-j];+                cnt1 <=  matrices->k_max_Q_B[my_iindx[k]-j];+                cnt1++)+              for(cnt2 = matrices->l_min_Q_B[my_iindx[k]-j][cnt1];+                  cnt2 <= matrices->l_max_Q_B[my_iindx[k]-j][cnt1];+                  cnt2 += 2)+                matrices->Q_rem[ij] += matrices->Q_rem[my_iindx[i]-k+1] * matrices->Q_B[my_iindx[k]-j][cnt1][cnt2/2] * temp2;+          if(matrices->Q_B_rem[my_iindx[k]-j])+            matrices->Q_rem[ij] += matrices->Q_rem[my_iindx[i]-k+1] * matrices->Q_B_rem[my_iindx[k]-j] * temp2;+        }+        if(matrices->Q_B_rem[my_iindx[k]-j]){+          if(matrices->Q[my_iindx[i]-k+1])+            for(cnt1 = matrices->k_min_Q[my_iindx[i]-k+1];+                cnt1 <= matrices->k_max_Q[my_iindx[i]-k+1];+                cnt1++)+              for(cnt2 = matrices->l_min_Q[my_iindx[i]-k+1][cnt1];+                  cnt2 <= matrices->l_max_Q[my_iindx[i]-k+1][cnt1];+                  cnt2 += 2)+                matrices->Q_rem[ij] += matrices->Q[my_iindx[i]-k+1][cnt1][cnt2/2] * matrices->Q_B_rem[my_iindx[k]-j] * temp2;+        }++        /* da = dbp{T1_{i,j}, T1_{k,j}+        *  db = dbp{T2_{i,j}, T2_{k,j}}+        */+        da = referenceBPs1[ij] - referenceBPs1[my_iindx[k] - j] - referenceBPs1[my_iindx[i]-k+1];+        db = referenceBPs2[ij] - referenceBPs2[my_iindx[k] - j] - referenceBPs2[my_iindx[i]-k+1];+++        if(!matrices->Q[my_iindx[i]-k+1]) continue;+        if(!matrices->Q_B[my_iindx[k]-j]) continue;+        for(cnt1 = matrices->k_min_Q[my_iindx[i]-k+1];+            cnt1 <= matrices->k_max_Q[my_iindx[i]-k+1];+            cnt1++)+          for(cnt2 = matrices->l_min_Q[my_iindx[i]-k+1][cnt1];+              cnt2 <= matrices->l_max_Q[my_iindx[i]-k+1][cnt1];+              cnt2 += 2)+            for(cnt3 = matrices->k_min_Q_B[my_iindx[k]-j];+                cnt3 <= matrices->k_max_Q_B[my_iindx[k]-j];+                cnt3++)+              for(cnt4 = matrices->l_min_Q_B[my_iindx[k]-j][cnt3];+                  cnt4 <= matrices->l_max_Q_B[my_iindx[k]-j][cnt3];+                  cnt4 += 2){+                if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                    matrices->Q[ij][cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] += matrices->Q[my_iindx[i]-k+1][cnt1][cnt2/2] * matrices->Q_B[my_iindx[k]-j][cnt3][cnt4/2] * temp2;+                  if(update_q){+                    updatePosteriorBoundaries(cnt1 + cnt3 + da,+                                              cnt2 + cnt4 + db,+                                              &k_min_post,+                                              &k_max_post,+                                              &l_min_post,+                                              &l_max_post+                                              );+                  }+                }+                else{+                  matrices->Q_rem[ij] += matrices->Q[my_iindx[i]-k+1][cnt1][cnt2/2] * matrices->Q_B[my_iindx[k]-j][cnt3][cnt4/2] * temp2;+                }+              }+      }++      if(update_q){+        adjustArrayBoundaries(&matrices->Q[ij],+                              &matrices->k_min_Q[ij],+                              &matrices->k_max_Q[ij],+                              &matrices->l_min_Q[ij],+                              &matrices->l_max_Q[ij],+                              k_min_post,+                              k_max_post,+                              l_min_post,+                              l_max_post+                              );+      }+#if 1+      for(cnt1 = matrices->k_min_Q[ij];+          cnt1 <= matrices->k_max_Q[ij];+          cnt1++){+        for(cnt2 = matrices->l_min_Q[ij][cnt1];+            cnt2 <= matrices->l_max_Q[ij][cnt1];+            cnt2 += 2){+          if(matrices->Q[ij][cnt1][cnt2/2] > Qmax) {+            Qmax = matrices->Q[ij][cnt1][cnt2/2];+            if (Qmax > max_real/10.)+              vrna_message_warning("Q close to overflow: %u %u %g\n", i,j,matrices->Q[ij][cnt1][cnt2/2]);+          }+          if(matrices->Q[ij][cnt1][cnt2/2] >= max_real) {+            vrna_message_error("overflow in pf_fold while calculating q[%u,%u]\n"+                                      "use larger pf_scale", i,j);+          }+        }++      }+#endif++    } /* end of j-loop */+  }+}++/* calculate partition function for circular case */+/* NOTE: this is the postprocessing step ONLY     */+/* You have to call pf2D_linear first to calculate  */+/* complete circular case!!!                      */+PRIVATE void+pf2D_circ(vrna_fold_compound_t *vc){++  unsigned int  d, p, q, pq, k, l, kl, u, da, db, seq_length, maxD1, maxD2, base_d1, base_d2, *mm1, *mm2, *bpdist;+  int         *my_iindx, *jindx, type, cnt1, cnt2, cnt3, cnt4, *rtype;+  short       *S1;+  unsigned int  *referenceBPs1, *referenceBPs2;+  char        *sequence, *ptype;+  FLT_OR_DBL  *scale;+  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */+  vrna_md_t         *md;+  vrna_mx_pf_t     *matrices;++  pf_params       = vc->exp_params;+  md              = &(pf_params->model_details);+  matrices        = vc->exp_matrices;+  sequence        = vc->sequence;+  seq_length      = vc->length;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+  S1              = vc->sequence_encoding;+  ptype           = vc->ptype;+  rtype           = &(md->rtype[0]);+  scale           = matrices->scale;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  dangles         = md->dangles;+  mm1             = vc->mm1;+  mm2             = vc->mm2;+  bpdist          = vc->bpdist;++  FLT_OR_DBL      ***Q_B, ***Q_M, ***Q_M1;+  FLT_OR_DBL      *Q_B_rem, *Q_M_rem, *Q_M1_rem;+  int             **l_min_Q_B, **l_max_Q_B, **l_min_Q_M, **l_max_Q_M, **l_min_Q_M1, **l_max_Q_M1;+  int             *k_min_Q_B, *k_max_Q_B,*k_min_Q_M, *k_max_Q_M,*k_min_Q_M1, *k_max_Q_M1;++  Q_B             = matrices->Q_B;+  l_min_Q_B  = matrices->l_min_Q_B;+  l_max_Q_B  = matrices->l_max_Q_B;+  k_min_Q_B  = matrices->k_min_Q_B;+  k_max_Q_B  = matrices->k_max_Q_B;++  Q_M             = matrices->Q_M;+  l_min_Q_M  = matrices->l_min_Q_M;+  l_max_Q_M  = matrices->l_max_Q_M;+  k_min_Q_M  = matrices->k_min_Q_M;+  k_max_Q_M  = matrices->k_max_Q_M;++  Q_M1            = matrices->Q_M1;+  l_min_Q_M1 = matrices->l_min_Q_M1;+  l_max_Q_M1 = matrices->l_max_Q_M1;+  k_min_Q_M1 = matrices->k_min_Q_M1;+  k_max_Q_M1 = matrices->k_max_Q_M1;+++  Q_B_rem        = matrices->Q_B_rem;+  Q_M_rem        = matrices->Q_M_rem;+  Q_M1_rem       = matrices->Q_M1_rem;++  matrices->Q_c_rem   = 0.;+  matrices->Q_cH_rem  = 0.;+  matrices->Q_cI_rem  = 0.;+  matrices->Q_cM_rem  = 0.;+++  /* construct qm2 matrix from qm1 entries  */+#ifdef _OPENMP+  #pragma omp parallel for private(d, k, l, da, db, cnt1, cnt2, cnt3, cnt4)+#endif+  for(k=1; k<seq_length-TURN-1; k++){+    int k_min_Q_M2, k_max_Q_M2, l_min_Q_M2, l_max_Q_M2;+    int k_min_post_m2, k_max_post_m2, *l_min_post_m2, *l_max_post_m2;+    int update_m2 = 0;+    if(!matrices->Q_M2[k]){+      update_m2 = 1;+      k_min_Q_M2 = l_min_Q_M2 = 0;+      k_max_Q_M2 = mm1[my_iindx[k]-seq_length] + referenceBPs1[my_iindx[k] - seq_length];+      l_max_Q_M2 = mm2[my_iindx[k]-seq_length] + referenceBPs2[my_iindx[k] - seq_length];++      prepareBoundaries(k_min_Q_M2,+                        k_max_Q_M2,+                        l_min_Q_M2,+                        l_max_Q_M2,+                        bpdist[my_iindx[k]-seq_length],+                        &matrices->k_min_Q_M2[k],+                        &matrices->k_max_Q_M2[k],+                        &matrices->l_min_Q_M2[k],+                        &matrices->l_max_Q_M2[k]+                        );+      preparePosteriorBoundaries( matrices->k_max_Q_M2[k] - matrices->k_min_Q_M2[k] + 1,+                                  matrices->k_min_Q_M2[k],+                                  &k_min_post_m2,+                                  &k_max_post_m2,+                                  &l_min_post_m2,+                                  &l_max_post_m2+                              );++      prepareArray( &matrices->Q_M2[k],+                    matrices->k_min_Q_M2[k],+                    matrices->k_max_Q_M2[k],+                    matrices->l_min_Q_M2[k],+                    matrices->l_max_Q_M2[k]+                );+    }++    /* construct Q_M2 */+    for (l=k+TURN+1; l<seq_length-TURN-1; l++){+      if(Q_M1_rem[jindx[l]+k]){+        if(Q_M1[jindx[seq_length]+l+1]){+          for(cnt1 = k_min_Q_M1[jindx[seq_length]+l+1];+              cnt1 <= k_max_Q_M1[jindx[seq_length]+l+1];+              cnt1++)+            for(cnt2 = l_min_Q_M1[jindx[seq_length]+l+1][cnt1];+                cnt2 <= l_max_Q_M1[jindx[seq_length]+l+1][cnt1];+                cnt2 += 2)+              matrices->Q_M2_rem[k] += Q_M1_rem[jindx[l]+k] * Q_M1[jindx[seq_length]+l+1][cnt1][cnt2/2];+        }+        if(Q_M1_rem[jindx[seq_length]+l+1])+          matrices->Q_M2_rem[k] += Q_M1_rem[jindx[l]+k] * Q_M1_rem[jindx[seq_length]+l+1];      +      }+      if(Q_M1_rem[jindx[seq_length]+l+1]){+        if(Q_M1[jindx[l]+k])+          for(cnt1 = k_min_Q_M1[jindx[l]+k];+              cnt1 <= k_max_Q_M1[jindx[l]+k];+              cnt1++)+            for(cnt2 = l_min_Q_M1[jindx[l]+k][cnt1];+                cnt2 <= l_max_Q_M1[jindx[l]+k][cnt1];+                cnt2 += 2)+              matrices->Q_M2_rem[k] += Q_M1[jindx[l]+k][cnt1][cnt2/2]*Q_M1_rem[jindx[seq_length]+l+1];+      +      }++      if(matrices->Q_M1[jindx[l]+k] && matrices->Q_M1[jindx[seq_length] + l + 1]){+        da = referenceBPs1[my_iindx[k]-seq_length] - referenceBPs1[my_iindx[k]-l] - referenceBPs1[my_iindx[l+1]-seq_length];+        db = referenceBPs2[my_iindx[k]-seq_length] - referenceBPs2[my_iindx[k]-l] - referenceBPs2[my_iindx[l+1]-seq_length];+        for(cnt1 = k_min_Q_M1[jindx[l]+k]; cnt1 <= k_max_Q_M1[jindx[l]+k]; cnt1++)+          for(cnt2 = l_min_Q_M1[jindx[l]+k][cnt1]; cnt2 <= l_max_Q_M1[jindx[l]+k][cnt1]; cnt2+=2){+            for(cnt3 = k_min_Q_M1[jindx[seq_length] + l + 1]; cnt3 <= k_max_Q_M1[jindx[seq_length] + l + 1]; cnt3++)+              for(cnt4 = l_min_Q_M1[jindx[seq_length] + l + 1][cnt3]; cnt4 <= l_max_Q_M1[jindx[seq_length] + l + 1][cnt3]; cnt4+=2){+                if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                  matrices->Q_M2[k][cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] += Q_M1[jindx[l]+k][cnt1][cnt2/2] * Q_M1[jindx[seq_length] + l + 1][cnt3][cnt4/2];+                  if(update_m2){+                      updatePosteriorBoundaries(cnt1 + cnt3 + da,+                                                cnt2 + cnt4 + db,+                                                &k_min_post_m2,+                                                &k_max_post_m2,+                                                &l_min_post_m2,+                                                &l_max_post_m2+                                                );+                  }+                }+                else{+                  matrices->Q_M2_rem[k] += Q_M1[jindx[l]+k][cnt1][cnt2/2] * Q_M1[jindx[seq_length] + l + 1][cnt3][cnt4/2];+                }+              }+          }+      }+    }+    if(update_m2){+      adjustArrayBoundaries(&matrices->Q_M2[k],+                            &matrices->k_min_Q_M2[k],+                            &matrices->k_max_Q_M2[k],+                            &matrices->l_min_Q_M2[k],+                            &matrices->l_max_Q_M2[k],+                            k_min_post_m2,+                            k_max_post_m2,+                            l_min_post_m2,+                            l_max_post_m2+                            );+    }+  }++  base_d1 = referenceBPs1[my_iindx[1]-seq_length];+  base_d2 = referenceBPs2[my_iindx[1]-seq_length];++  int min_k, max_k, max_l, min_l;+  int min_k_real, max_k_real, min_k_real_qcH, max_k_real_qcH, min_k_real_qcI, max_k_real_qcI, min_k_real_qcM, max_k_real_qcM;+  int *min_l_real, *max_l_real, *min_l_real_qcH, *max_l_real_qcH, *min_l_real_qcI, *max_l_real_qcI,*min_l_real_qcM, *max_l_real_qcM;+  int update_c, update_cH, update_cI, update_cM;++  update_c = update_cH = update_cI = update_cM = 0;++  min_k = min_l = 0;++  max_k = mm1[my_iindx[1] - seq_length] + referenceBPs1[my_iindx[1] - seq_length];+  max_l = mm2[my_iindx[1] - seq_length] + referenceBPs2[my_iindx[1] - seq_length];++#ifdef _OPENMP+  #pragma omp sections+  {++  #pragma omp section+  {+#endif+  if(!matrices->Q_c){+    update_c = 1;+    prepareBoundaries(min_k,+                      max_k,+                      min_l,+                      max_l,+                      bpdist[my_iindx[1] - seq_length],+                      &matrices->k_min_Q_c,+                      &matrices->k_max_Q_c,+                      &matrices->l_min_Q_c,+                      &matrices->l_max_Q_c+                      );+    prepareArray( &matrices->Q_c,+                  matrices->k_min_Q_c,+                  matrices->k_max_Q_c,+                  matrices->l_min_Q_c,+                  matrices->l_max_Q_c+                );+    preparePosteriorBoundaries( max_k - min_k + 1,+                                min_k,+                                &min_k_real,+                                &max_k_real,+                                &min_l_real,+                                &max_l_real+                              );+  }+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  if(!matrices->Q_cH){+    update_cH = 1;+    prepareBoundaries(min_k,+                      max_k,+                      min_l,+                      max_l,+                      bpdist[my_iindx[1] - seq_length],+                      &matrices->k_min_Q_cH,+                      &matrices->k_max_Q_cH,+                      &matrices->l_min_Q_cH,+                      &matrices->l_max_Q_cH+                      );+    prepareArray( &matrices->Q_cH,+                  matrices->k_min_Q_cH,+                  matrices->k_max_Q_cH,+                  matrices->l_min_Q_cH,+                  matrices->l_max_Q_cH+                );+    preparePosteriorBoundaries( max_k - min_k + 1,+                                min_k,+                                &min_k_real_qcH,+                                &max_k_real_qcH,+                                &min_l_real_qcH,+                                &max_l_real_qcH+                              );+  }+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  if(!matrices->Q_cI){+    update_cI = 1;+    prepareBoundaries(min_k,+                      max_k,+                      min_l,+                      max_l,+                      bpdist[my_iindx[1] - seq_length],+                      &matrices->k_min_Q_cI,+                      &matrices->k_max_Q_cI,+                      &matrices->l_min_Q_cI,+                      &matrices->l_max_Q_cI+                      );+    prepareArray( &matrices->Q_cI,+                  matrices->k_min_Q_cI,+                  matrices->k_max_Q_cI,+                  matrices->l_min_Q_cI,+                  matrices->l_max_Q_cI+                );+    preparePosteriorBoundaries( max_k - min_k + 1,+                                min_k,+                                &min_k_real_qcI,+                                &max_k_real_qcI,+                                &min_l_real_qcI,+                                &max_l_real_qcI+                              );+  }+#ifdef _OPENMP+  }+  #pragma omp section+  {+#endif+  if(!matrices->Q_cM){+    update_cM = 1;+    prepareBoundaries(min_k,+                      max_k,+                      min_l,+                      max_l,+                      bpdist[my_iindx[1] - seq_length],+                      &matrices->k_min_Q_cM,+                      &matrices->k_max_Q_cM,+                      &matrices->l_min_Q_cM,+                      &matrices->l_max_Q_cM+                      );+    prepareArray( &matrices->Q_cM,+                  matrices->k_min_Q_cM,+                  matrices->k_max_Q_cM,+                  matrices->l_min_Q_cM,+                  matrices->l_max_Q_cM+                );+    preparePosteriorBoundaries( max_k - min_k + 1,+                                min_k,+                                &min_k_real_qcM,+                                &max_k_real_qcM,+                                &min_l_real_qcM,+                                &max_l_real_qcM+                              );+  }+#ifdef _OPENMP+  }+  }+#endif+++++  for (d = TURN+2; d <= seq_length; d++) /* i,j in [1..length] */+#ifdef _OPENMP+    #pragma omp parallel for private(p, q, pq, k, l, kl, u, da, db, type, cnt1, cnt2, cnt3, cnt4)+#endif+    for (q = d; q <= seq_length; q++) {+      FLT_OR_DBL qot;+      char loopseq[10];+      p = q - d + 1;+      pq = my_iindx[p]-q;++      /* 1. get exterior hairpin contribution  */+      u = seq_length-q + p-1;+      if (u<TURN) continue;+      type = ptype[jindx[q] + p];+      if (!type) continue;+      if(((type==3)||(type==4))&&no_closingGU) continue;++       /* cause we want to calc the exterior loops, we need the reversed pair type from now on  */+      type=rtype[type];++      if (u<7){+        strcpy(loopseq , sequence+q-1);+        strncat(loopseq, sequence, p);+      }+      /* get distance to reference if closing the hairpin+      *  da = dbp(T1_[1,n}, T1_{p,q})+      *  db = dbp(T2_{1,n}, T2_{p,q})+      */+      da = base_d1 - referenceBPs1[pq];+      db = base_d2 - referenceBPs2[pq];+      qot = exp_E_Hairpin(u, type, S1[q+1], S1[p-1],  loopseq, pf_params) * scale[u];+      +      if(Q_B_rem[pq])+        matrices->Q_cH_rem += Q_B_rem[pq] * qot;+      +      if(Q_B[pq]){+        for(cnt1 = k_min_Q_B[pq];+            cnt1 <= k_max_Q_B[pq];+            cnt1++)+          for(cnt2 = l_min_Q_B[pq][cnt1];+              cnt2 <= l_max_Q_B[pq][cnt1];+              cnt2 += 2){+            if(((cnt1 + da) <= maxD1) && ((cnt2 + db) <= maxD2)){+              matrices->Q_cH[cnt1 + da][(cnt2 + db)/2] += Q_B[pq][cnt1][cnt2/2] * qot;+              if(update_cH){+                updatePosteriorBoundaries(cnt1 + da,+                                      cnt2 + db,+                                      &min_k_real_qcH,+                                      &max_k_real_qcH,+                                      &min_l_real_qcH,+                                      &max_l_real_qcH+                                      );+              }+            }+            else{+              matrices->Q_cH_rem += Q_B[pq][cnt1][cnt2/2] * qot;+            }+          }+      }++      /* 2. exterior interior loops, i "define" the (k,l) pair as "outer pair"  */+      /* so "outer type" is rtype[type[k,l]] and inner type is type[p,q]        */+      if(Q_B_rem[pq])+        for(k=q+1; k < seq_length; k++){+          unsigned int ln1, lstart, ln_pre;+          ln1 = k - q - 1;+          if(ln1+p-1>MAXLOOP) break;+          lstart = k + TURN + 1;+          ln_pre = ln1 + p + seq_length;+          if(ln_pre > lstart + MAXLOOP) lstart = ln_pre - MAXLOOP - 1;+          for(l=lstart;l <= seq_length; l++){+            unsigned int ln2;+            int type2;+            kl = my_iindx[k]-l;+            ln2 = (p - 1) + (seq_length - l);++            if((ln1+ln2) > MAXLOOP) continue;++            type2 = ptype[jindx[l] + k];+            if(!type2) continue;++            qot = exp_E_IntLoop(ln2, ln1, rtype[type2], type, S1[l+1], S1[k-1], S1[p-1], S1[q+1], pf_params) * scale[ln1+ln2];++            if(Q_B_rem[kl])+              matrices->Q_cI_rem += Q_B_rem[pq] * Q_B_rem[kl] * qot;++            if(Q_B[kl])+              for(cnt1 = k_min_Q_B[kl];+                  cnt1 <= k_max_Q_B[kl];+                  cnt1++)+                for(cnt2 = l_min_Q_B[kl][cnt1];+                    cnt2 <= l_max_Q_B[kl][cnt1];+                    cnt2 += 2)+                  matrices->Q_cI_rem += Q_B_rem[pq] * Q_B[kl][cnt1][cnt2/2] * qot;+          }+        }++      if(Q_B[pq])+        for(k=q+1; k < seq_length; k++){+          unsigned int ln1, lstart, ln_pre;+          ln1 = k - q - 1;+          if(ln1+p-1>MAXLOOP) break;+          lstart = k + TURN + 1;+          ln_pre = ln1 + p + seq_length;+          if(ln_pre > lstart + MAXLOOP) lstart = ln_pre - MAXLOOP - 1;+          for(l=lstart;l <= seq_length; l++){+            unsigned int ln2;+            int type2;+            kl = my_iindx[k]-l;+            ln2 = (p - 1) + (seq_length - l);++            if((ln1+ln2) > MAXLOOP) continue;++            type2 = ptype[jindx[l] + k];+            if(!type2) continue;++            qot = exp_E_IntLoop(ln2, ln1, rtype[type2], type, S1[l+1], S1[k-1], S1[p-1], S1[q+1], pf_params) * scale[ln1+ln2];++            if(Q_B_rem[kl]){+              for(cnt1 = k_min_Q_B[pq];+                  cnt1 <= k_max_Q_B[pq];+                  cnt1++)+                for(cnt2 = l_min_Q_B[pq][cnt1];+                    cnt2 <= l_max_Q_B[pq][cnt1];+                    cnt2 += 2)+                  matrices->Q_cI_rem += Q_B[pq][cnt1][cnt2/2] * Q_B_rem[kl] * qot;+            }++            if(!Q_B[kl]) continue;++            /* get distance to reference if closing the interior loop+            *  d2a = dbp(T1_[1,n}, T1_{p,q} + T1_{k,l})+            *  d2b = dbp(T2_[1,n}, T2_{p,q} + T2_{k,l})+            */+            da = base_d1 - referenceBPs1[pq] - referenceBPs1[kl];+            db = base_d2 - referenceBPs2[pq] - referenceBPs2[kl];++            for(cnt1 = k_min_Q_B[pq]; cnt1 <= k_max_Q_B[pq]; cnt1++)+              for(cnt2 = l_min_Q_B[pq][cnt1]; cnt2 <= l_max_Q_B[pq][cnt1]; cnt2+=2)+                for(cnt3 = k_min_Q_B[kl]; cnt3 <= k_max_Q_B[kl]; cnt3++)+                  for(cnt4 = l_min_Q_B[kl][cnt3]; cnt4 <= l_max_Q_B[kl][cnt3]; cnt4+=2){+                    if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                      matrices->Q_cI[cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] += Q_B[pq][cnt1][cnt2/2] * Q_B[kl][cnt3][cnt4/2] * qot;+                      if(update_cI){+                        updatePosteriorBoundaries(cnt1 + cnt3 + da,+                                                cnt2 + cnt4 + db,+                                                &min_k_real_qcI,+                                                &max_k_real_qcI,+                                                &min_l_real_qcI,+                                                &max_l_real_qcI+                                                );+                      }+                    }+                    else{+                      matrices->Q_cI_rem += Q_B[pq][cnt1][cnt2/2] * Q_B[kl][cnt3][cnt4/2] * qot;+                    }+                  }+          }+        }+    }++  if(update_cH){+    adjustArrayBoundaries(&matrices->Q_cH,+                          &matrices->k_min_Q_cH,+                          &matrices->k_max_Q_cH,+                          &matrices->l_min_Q_cH,+                          &matrices->l_max_Q_cH,+                          min_k_real_qcH,+                          max_k_real_qcH,+                          min_l_real_qcH,+                          max_l_real_qcH+                        );+  }+  if(update_cI){+    adjustArrayBoundaries(&matrices->Q_cI,+                          &matrices->k_min_Q_cI,+                          &matrices->k_max_Q_cI,+                          &matrices->l_min_Q_cI,+                          &matrices->l_max_Q_cI,+                          min_k_real_qcI,+                          max_k_real_qcI,+                          min_l_real_qcI,+                          max_l_real_qcI+                        );+  }++  /* 3. Multiloops  */+  if(seq_length > 2*TURN-3)+#ifdef _OPENMP+  #pragma omp parallel for private(k, da, db, cnt1, cnt2, cnt3, cnt4)+#endif+    for(k=TURN+2; k<seq_length-2*TURN-3; k++){+      if(Q_M_rem[my_iindx[1]-k]){+        if(matrices->Q_M2[k+1])+          for(cnt1 = matrices->k_min_Q_M2[k+1];+              cnt1 <= matrices->k_max_Q_M2[k+1];+              cnt1++)+            for(cnt2 = matrices->l_min_Q_M2[k+1][cnt1];+                cnt2 <= matrices->l_max_Q_M2[k+1][cnt1];+                cnt2 += 2)+              matrices->Q_cM_rem += Q_M_rem[my_iindx[1]-k] * matrices->Q_M2[k+1][cnt1][cnt2/2] * pf_params->expMLclosing;+        if(matrices->Q_M2_rem[k+1])+          matrices->Q_cM_rem += Q_M_rem[my_iindx[1]-k] * matrices->Q_M2_rem[k+1] * pf_params->expMLclosing;+      }+      if(matrices->Q_M2_rem[k+1]){+        if(Q_M[my_iindx[1]-k])+          for(cnt1 = k_min_Q_M[my_iindx[1]-k];+              cnt1 <= k_max_Q_M[my_iindx[1]-k];+              cnt1++)+            for(cnt2 = l_min_Q_M[my_iindx[1]-k][cnt1];+                cnt2 <= l_max_Q_M[my_iindx[1]-k][cnt1];+                cnt2 += 2)+              matrices->Q_cM_rem += Q_M[my_iindx[1]-k][cnt1][cnt2/2] * matrices->Q_M2_rem[k+1] * pf_params->expMLclosing;+      }++      /* get distancies to references+      * d3a = dbp(T1_[1,n}, T1_{1,k} + T1_{k+1, n})+      * d3b = dbp(T2_[1,n}, T2_{1,k} + T2_{k+1, n})+      */+      da = base_d1 - referenceBPs1[my_iindx[1]-k] - referenceBPs1[my_iindx[k+1]-seq_length];+      db = base_d2 - referenceBPs2[my_iindx[1]-k] - referenceBPs2[my_iindx[k+1]-seq_length];+      if(Q_M[my_iindx[1]-k] && matrices->Q_M2[k+1])+        for(cnt1 = k_min_Q_M[my_iindx[1]-k]; cnt1 <= k_max_Q_M[my_iindx[1]-k]; cnt1++)+          for(cnt2 = l_min_Q_M[my_iindx[1]-k][cnt1]; cnt2 <= l_max_Q_M[my_iindx[1]-k][cnt1]; cnt2+=2)+            for(cnt3 = matrices->k_min_Q_M2[k+1]; cnt3 <= matrices->k_max_Q_M2[k+1]; cnt3++)+              for(cnt4 = matrices->l_min_Q_M2[k+1][cnt3]; cnt4 <= matrices->l_max_Q_M2[k+1][cnt3]; cnt4+=2){+                if(((cnt1 + cnt3 + da) <= maxD1) && ((cnt2 + cnt4 + db) <= maxD2)){+                  matrices->Q_cM[cnt1 + cnt3 + da][(cnt2 + cnt4 + db)/2] += Q_M[my_iindx[1]-k][cnt1][cnt2/2] * matrices->Q_M2[k+1][cnt3][cnt4/2] * pf_params->expMLclosing;+                  if(update_cM){+                    updatePosteriorBoundaries(cnt1 + cnt3 + da,+                                            cnt2 + cnt4 + db,+                                            &min_k_real_qcM,+                                            &max_k_real_qcM,+                                            &min_l_real_qcM,+                                            &max_l_real_qcM+                                            );+                  }+                }+                else{+                  matrices->Q_cM_rem += Q_M[my_iindx[1]-k][cnt1][cnt2/2] * matrices->Q_M2[k+1][cnt3][cnt4/2] * pf_params->expMLclosing;+                }+              }+    }+  if(update_cM){+    adjustArrayBoundaries(&matrices->Q_cM,+                          &matrices->k_min_Q_cM,+                          &matrices->k_max_Q_cM,+                          &matrices->l_min_Q_cM,+                          &matrices->l_max_Q_cM,+                          min_k_real_qcM,+                          max_k_real_qcM,+                          min_l_real_qcM,+                          max_l_real_qcM+                        );+  }++  for(cnt1 = matrices->k_min_Q_cH;+      cnt1 <= matrices->k_max_Q_cH;+      cnt1++)+    for(cnt2 = matrices->l_min_Q_cH[cnt1];+        cnt2 <= matrices->l_max_Q_cH[cnt1];+        cnt2 += 2){+      matrices->Q_c[cnt1][cnt2/2] += matrices->Q_cH[cnt1][cnt2/2];+      if(update_c){+        updatePosteriorBoundaries(cnt1,+                                  cnt2,+                                  &min_k_real,+                                  &max_k_real,+                                  &min_l_real,+                                  &max_l_real+                                  );+      }+    }+  for(cnt1 = matrices->k_min_Q_cI;+      cnt1 <= matrices->k_max_Q_cI;+      cnt1++)+    for(cnt2 = matrices->l_min_Q_cI[cnt1];+        cnt2 <= matrices->l_max_Q_cI[cnt1];+        cnt2 += 2){+      matrices->Q_c[cnt1][cnt2/2] += matrices->Q_cI[cnt1][cnt2/2];+      if(update_c){+        updatePosteriorBoundaries(cnt1,+                                  cnt2,+                                  &min_k_real,+                                  &max_k_real,+                                  &min_l_real,+                                  &max_l_real+                                  );+      }+    }+  for(cnt1 = matrices->k_min_Q_cM;+      cnt1 <= matrices->k_max_Q_cM;+      cnt1++)+    for(cnt2 = matrices->l_min_Q_cM[cnt1];+        cnt2 <= matrices->l_max_Q_cM[cnt1];+        cnt2 += 2){+      matrices->Q_c[cnt1][cnt2/2] += matrices->Q_cM[cnt1][cnt2/2];+      if(update_c){+        updatePosteriorBoundaries(cnt1,+                                  cnt2,+                                  &min_k_real,+                                  &max_k_real,+                                  &min_l_real,+                                  &max_l_real+                                  );+      }+    }++  matrices->Q_c_rem   = matrices->Q_cH_rem + matrices->Q_cI_rem + matrices->Q_cM_rem;++  /* add the case were structure is unfolded chain */+  if((referenceBPs1[my_iindx[1]-seq_length] <= maxD1) && (referenceBPs2[my_iindx[1]-seq_length] <= maxD2)){+    matrices->Q_c[referenceBPs1[my_iindx[1]-seq_length]][referenceBPs2[my_iindx[1]-seq_length]/2] += 1.0 * scale[seq_length];+    if(update_c){+      updatePosteriorBoundaries(referenceBPs1[my_iindx[1]-seq_length],+                              referenceBPs2[my_iindx[1]-seq_length],+                              &min_k_real,+                              &max_k_real,+                              &min_l_real,+                              &max_l_real+                              );+    }+  }+  else{+    matrices->Q_c_rem += 1.0 * scale[seq_length];+  }++  adjustArrayBoundaries(&matrices->Q_c,+                        &matrices->k_min_Q_c,+                        &matrices->k_max_Q_c,+                        &matrices->l_min_Q_c,+                        &matrices->l_max_Q_c,+                        min_k_real,+                        max_k_real,+                        min_l_real,+                        max_l_real+                      );+}++/*+* ###################################################+* stochastic backtracking+* ###################################################+*/++PUBLIC char *+vrna_pbacktrack_TwoD( vrna_fold_compound_t *vc,+                      int d1,+                      int d2){++  return vrna_pbacktrack5_TwoD(vc, d1, d2, vc->length);+}++PUBLIC char *+vrna_pbacktrack5_TwoD(vrna_fold_compound_t *vc,+                      int d1,+                      int d2,+                      unsigned int length){++  char            *pstruc, *ptype;+  short           *S1;+  unsigned int    i, j, n, start, maxD1, maxD2, da, db,+                  *referenceBPs1, *referenceBPs2;+  int             *my_iindx, *jindx, ij, cnt1, cnt2, cnt3, cnt4, type,+                  **l_min_Q, **l_max_Q,+                  **l_min_Q_B, **l_max_Q_B,+                  *k_min_Q, *k_max_Q,+                  *k_min_Q_B, *k_max_Q_B;+  FLT_OR_DBL      r, qt, *scale, ***Q, ***Q_B, *Q_rem, *Q_B_rem;+  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  n               = vc->length;+  pf_params       = vc->exp_params;+  md              = &(pf_params->model_details);+  matrices        = vc->exp_matrices;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  scale           = matrices->scale;+  ptype           = vc->ptype;+  S1              = vc->sequence_encoding;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;++  Q               = matrices->Q;+  l_min_Q    = matrices->l_min_Q;+  l_max_Q    = matrices->l_max_Q;+  k_min_Q    = matrices->k_min_Q;+  k_max_Q    = matrices->k_max_Q;++  Q_B             = matrices->Q_B;+  l_min_Q_B  = matrices->l_min_Q_B;+  l_max_Q_B  = matrices->l_max_Q_B;+  k_min_Q_B  = matrices->k_min_Q_B;+  k_max_Q_B  = matrices->k_max_Q_B;++  Q_rem           = matrices->Q_rem;+  Q_B_rem         = matrices->Q_B_rem;++  if(md->circ){+    if(n != length)+      vrna_message_error("vrna_pbacktrack_TwoD@2Dfold.c: cotranscriptional backtracking for circular RNAs not supported!");+    return pbacktrack_circ(vc, d1, d2);+  }++  if(length > n)+    vrna_message_error("vrna_pbacktrack_TwoD@2Dpfold.c: requested transcript length exceeds sequence length!");++#if 0+  if(d1 > maxD1)+    vrna_message_error("pbacktrack@2Dpfold.c: distance to 1st reference structure to high!");+  if(d2 > maxD2)+    vrna_message_error("pbacktrack@2Dpfold.c: distance to 2nd reference structure to high!");+#endif++  /* check whether the chosen neighborhood exists at all */+  int dumb = 1;+  ij = my_iindx[1]-length;+  if((d1 == -1) && (Q_rem[ij] != 0.)) dumb = 0;+  else{+    if((k_min_Q[ij] <= d1) && (k_max_Q[ij] >= d1)){+      int l_min = l_min_Q[ij][d1];+      if((d2 % 2) == (l_min%2))+        if((l_min <= d2) && (l_max_Q[ij][d1] >= d2))+          dumb = 0;+    }+  }+  if(dumb){+    vrna_message_error("neighborhood %d:%d is not in scope of calculated partition function!\n"+                              "pbacktrack@2Dpfold.c: exiting...",+                              d1, d2);+  }++  pstruc = vrna_alloc((length+1)*sizeof(char));++  for (i=0; i<length; i++) pstruc[i] = '.';+  pstruc[i] = '\0';++  start = 1;+  while (start<length) {+    int sn = my_iindx[start] - length;+    /* find i position of first pair */+    FLT_OR_DBL qln_i = 0, qln_i1 = 0;++    if(d1 == -1){+      qln_i = Q_rem[sn];++      /* open chain ? */+      if(   (maxD1 > referenceBPs1[sn])+        &&  (maxD2 > referenceBPs2[sn])){+        r = vrna_urn() * qln_i;+        if(scale[length-start+1] > r)+          return pstruc;+      }++      /* lets see if we find a base pair with i involved */+      for (i=start; i<length; i++) {+        r = vrna_urn() * qln_i;++        qln_i1 = Q_rem[my_iindx[i+1] - length];++        da = referenceBPs1[sn] - referenceBPs1[my_iindx[i+1] - length];+        db = referenceBPs2[sn] - referenceBPs2[my_iindx[i+1] - length];++        for(cnt1 = k_min_Q[my_iindx[i+1] - length];+            cnt1 <= k_max_Q[my_iindx[i+1] - length];+            cnt1++)+          for(cnt2 = l_min_Q[my_iindx[i+1] - length][cnt1];+              cnt2 <= l_max_Q[my_iindx[i+1] - length][cnt1];+              cnt2 += 2)+            if(((cnt1 + da) > maxD1) || ((cnt2 + db) > maxD2)){+              qln_i1 += Q[my_iindx[i+1] - length][cnt1][cnt2/2];+            }++        if(r > qln_i1*scale[1]) break;++        qln_i = qln_i1;+      }+      if (i>=length) break; /* no more pairs */++      /* i is paired, find pairing partner j */+      r = vrna_urn() * (qln_i - qln_i1*scale[1]);+      for (qt=0, j=i+TURN+1; j<length; j++) {+        ij = my_iindx[i]-j;+        type = ptype[jindx[j] + i];+        if (type) {+          cnt1 = cnt2 = cnt3 = cnt4 = -1;+          double qkl = exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, S1[j+1], pf_params);++          if(Q_B_rem[ij] != 0.){+            if(Q_rem[my_iindx[j+1]-length] != 0.){+              qt += qkl * Q_B_rem[ij] * Q_rem[my_iindx[j+1]-length];+              if(qt >= r)+                goto pbacktrack_ext_loop_early_escape_rem;+            }+            if(Q[my_iindx[j+1]-length])+              for(cnt3 = k_min_Q[my_iindx[j+1]-length];+                  cnt3 <= k_max_Q[my_iindx[j+1]-length];+                  cnt3++)+                for(cnt4 = l_min_Q[my_iindx[j+1]-length][cnt3];+                    cnt4 <= l_max_Q[my_iindx[j+1]-length][cnt3];+                    cnt4 += 2){+                  qt += qkl * Q_B_rem[ij] * Q[my_iindx[j+1]-length][cnt3][cnt4/2];+                  if(qt >= r)+                    goto pbacktrack_ext_loop_early_escape_rem;+                }+          }+          if(Q_rem[my_iindx[j+1]-length] != 0.){+            cnt3 = cnt4 = -1;+            if(Q_B[ij]){+              for(cnt1 = k_min_Q_B[ij];+                  cnt1 <= k_max_Q_B[ij];+                  cnt1++)+                for(cnt2 = l_min_Q_B[ij][cnt1];+                    cnt2 <= l_max_Q_B[ij][cnt1];+                    cnt2 += 2){+                  qt += qkl * Q_B[ij][cnt1][cnt2/2] * Q_rem[my_iindx[j+1]-length];+                  if(qt >= r)+                    goto pbacktrack_ext_loop_early_escape_rem;+                }+            }+          }+          /* if we still search for pairing partner j, we go on here... */+          if(Q_B[ij] && Q[my_iindx[j+1]-length]){+            da = referenceBPs1[sn] - referenceBPs1[ij] - referenceBPs1[my_iindx[j+1]-length];+            db = referenceBPs2[sn] - referenceBPs2[ij] - referenceBPs2[my_iindx[j+1]-length];+            for(cnt1 = k_min_Q_B[ij];+                cnt1 <= k_max_Q_B[ij];+                cnt1++)+              for(cnt2 = l_min_Q_B[ij][cnt1];+                  cnt2 <= l_max_Q_B[ij][cnt1];+                  cnt2 += 2)+                for(cnt3 = k_min_Q[my_iindx[j+1]-length];+                    cnt3 <= k_max_Q[my_iindx[j+1]-length];+                    cnt3++)+                  for(cnt4 = l_min_Q[my_iindx[j+1]-length][cnt3];+                      cnt4 <= l_max_Q[my_iindx[j+1]-length][cnt3];+                      cnt4 += 2)+                    if(((cnt1 + cnt3 + da) > maxD1) || ((cnt2 + cnt4 + db) > maxD2)){+                      qt += qkl * Q_B[ij][cnt1][cnt2/2] * Q[my_iindx[j+1]-length][cnt3][cnt4/2];+                      if(qt >= r)+                        goto pbacktrack_ext_loop_early_escape_rem;+                    }+          }+        } /* end if(type) */+      } /* end for(j) */+      cnt1 = cnt2 = cnt3 = cnt4 = -1;+      /* dont forget the case where i pairs with n */+      j = length;+      ij = my_iindx[i]-j;+      type = ptype[jindx[j] + i];+      if (type) {+        double qkl = exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);+        if(Q_B_rem[ij] != 0.){+          qt += qkl * Q_B_rem[ij];+          if(qt >= r)+            goto pbacktrack_ext_loop_early_escape_rem;+        }+        /* if we still search for pairing partner j, we go on here... */+        if(Q_B[ij]){+          da = referenceBPs1[sn] - referenceBPs1[ij];+          db = referenceBPs2[sn] - referenceBPs2[ij];+          for(cnt1 = k_min_Q_B[ij];+              cnt1 <= k_max_Q_B[ij];+              cnt1++)+            for(cnt2 = l_min_Q_B[ij][cnt1];+                cnt2 <= l_max_Q_B[ij][cnt1];+                cnt2 += 2)+              if(((cnt1 + da) > maxD1) || ((cnt2 + db) > maxD2)){+                qt += qkl * Q_B[ij][cnt1][cnt2/2];+                if(qt >= r)+                  goto pbacktrack_ext_loop_early_escape_rem;+              }+        }+      } /* end if(type) */+      j++;++pbacktrack_ext_loop_early_escape_rem:++      if (j==length+1){+        vrna_message_error("pbacktrack@2Dpfold.c: backtracking failed in ext loop (rem)");+      }++      /* finally start backtracking the first exterior stem */+      backtrack(vc, pstruc, cnt1, cnt2, i,j);+      if(j==length) break;+      start = j+1;+      d1 = cnt3;+      d2 = cnt4;++    } /* end if d1 ==-1 */+    else{+      qln_i = Q[sn][d1][d2/2];++      /* open chain ? */+      if(   (d1 == referenceBPs1[sn])+        &&  (d2 == referenceBPs2[sn])){+        r = vrna_urn() * qln_i;+        if(scale[length-start+1] > r)+          return pstruc;+      }++      for (i=start; i<length; i++) {+        r = vrna_urn() * qln_i;+        da = referenceBPs1[sn] - referenceBPs1[my_iindx[i+1] - length];+        db = referenceBPs2[sn] - referenceBPs2[my_iindx[i+1] - length];+        qln_i1 = 0;+        if(d1 >= da && d2 >= db)+          if(+              (d1-da >= k_min_Q[my_iindx[i+1] - length])+           && (d1 - da <= k_max_Q[my_iindx[i+1] - length]))+            if(+                  (d2 - db >= l_min_Q[my_iindx[i+1] - length][d1 - da])+              &&  (d2 - db <= l_max_Q[my_iindx[i+1] - length][d1 - da]))+              qln_i1 += Q[my_iindx[i+1] - length][d1-da][(d2-db)/2];+        if (r > qln_i1*scale[1])  break; /* i is paired */+        qln_i = qln_i1;+      }++      if (i>=length) break; /* no more pairs */++      /* now find the pairing partner j */+      r = vrna_urn() * (qln_i - qln_i1*scale[1]);++      for (qt=0, j=i+1; j<length; j++) {+        int type;+        ij = my_iindx[i]-j;+        type = ptype[jindx[j] + i];+        if (type) {+          double qkl = 1.0;+          qkl *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, S1[j+1], pf_params);++          da = referenceBPs1[sn] - referenceBPs1[ij] - referenceBPs1[my_iindx[j+1]-length];+          db = referenceBPs2[sn] - referenceBPs2[ij] - referenceBPs2[my_iindx[j+1]-length];++          if(   (d1 >= da)+            &&  (d2 >= db)+            &&  Q_B[ij]+            &&  Q[my_iindx[j+1]-length])+            for(cnt1 = k_min_Q_B[ij];+                cnt1 <= MIN2(k_max_Q_B[ij], d1-da);+                cnt1++)+              for(cnt2 = l_min_Q_B[ij][cnt1];+                  cnt2 <= MIN2(l_max_Q_B[ij][cnt1], d2-db);+                  cnt2+=2)+                if(   (d1-da-cnt1 >= k_min_Q[my_iindx[j+1]-length])+                  &&  (d1-da-cnt1 <= k_max_Q[my_iindx[j+1]-length]))+                  if(   (d2 - db - cnt2 >= l_min_Q[my_iindx[j+1]-length][d1-da-cnt1]) +                    &&  (d2 - db - cnt2 <= l_max_Q[my_iindx[j+1]-length][d1-da-cnt1])){+                    qt += qkl * Q_B[ij][cnt1][cnt2/2] * Q[my_iindx[j+1]-length][d1-da-cnt1][(d2-db-cnt2)/2];+                    if(qt >= r)+                      goto pbacktrack_ext_loop_early_escape;+                  }+        }+      }+      /* now dont forget the case j==n */+      j = length;+      ij = my_iindx[i]-j;+      int type = ptype[jindx[j] + i];+      if (type) {+        double qkl = 1.0;++        qkl *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);++        da = referenceBPs1[sn] - referenceBPs1[ij];+        db = referenceBPs2[sn] - referenceBPs2[ij];+        if(d1 >= da && d2 >= db){+          cnt1 = d1 - da;+          cnt2 = d2 - db;+          if((cnt1 >= k_min_Q_B[ij]) && (cnt1 <= k_max_Q_B[ij]))+            if((cnt2 >= l_min_Q_B[ij][cnt1]) && (cnt2 <= l_max_Q_B[ij][cnt1])){+              qt += qkl * Q_B[ij][cnt1][cnt2/2];+              if(qt >= r)+                goto pbacktrack_ext_loop_early_escape; /* j is paired */+            }+        }+      }+      j++;++pbacktrack_ext_loop_early_escape:++      if (j==length+1){+        vrna_message_error("pbacktrack@2Dpfold.c: backtracking failed in ext loop");+      }++      backtrack(vc, pstruc, cnt1, cnt2, i,j);++      if(j==length) break;+      start = j+1;+      d1 -= cnt1 + da;+      d2 -= cnt2 + db;+    } /* end if d1!=-1 */+  }+  return pstruc;+}+++PRIVATE char *+pbacktrack_circ(vrna_fold_compound_t *vc,+                int d1,+                int d2){++  char            *pstruc;+  unsigned int    i, n, maxD1, maxD2,+                  *referenceBPs1, *referenceBPs2;+  int             *my_iindx,+                  k_min_Q_c, k_max_Q_c,+                  k_min_Q_cH, k_max_Q_cH,+                  k_min_Q_cI, k_max_Q_cI,+                  k_min_Q_cM, k_max_Q_cM,+                  *l_min_Q_c, *l_max_Q_c,+                  *l_min_Q_cH, *l_max_Q_cH,+                  *l_min_Q_cI, *l_max_Q_cI,+                  *l_min_Q_cM, *l_max_Q_cM;+  FLT_OR_DBL      r, *scale, qot,+                  **Q_c, **Q_cH, **Q_cI, **Q_cM,+                  Q_c_rem, Q_cH_rem, Q_cI_rem, Q_cM_rem;+  vrna_mx_pf_t      *matrices;+  vrna_md_t         *md;+  vrna_exp_param_t  *pf_params;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  n                 = vc->length;+  maxD1             = vc->maxD1;+  maxD2             = vc->maxD2;+  my_iindx          = vc->iindx;+  scale             = matrices->scale;+  referenceBPs1     = vc->referenceBPs1;+  referenceBPs2     = vc->referenceBPs2;++  Q_c               = matrices->Q_c;+  l_min_Q_c   = matrices->l_min_Q_c;+  l_max_Q_c   = matrices->l_max_Q_c;+  k_min_Q_c   = matrices->k_min_Q_c;+  k_max_Q_c   = matrices->k_max_Q_c;++  Q_cH              = matrices->Q_cH;+  l_min_Q_cH  = matrices->l_min_Q_cH;+  l_max_Q_cH  = matrices->l_max_Q_cH;+  k_min_Q_cH  = matrices->k_min_Q_cH;+  k_max_Q_cH  = matrices->k_max_Q_cH;++  Q_cI              = matrices->Q_cI;+  l_min_Q_cI  = matrices->l_min_Q_cI;+  l_max_Q_cI  = matrices->l_max_Q_cI;+  k_min_Q_cI  = matrices->k_min_Q_cI;+  k_max_Q_cI  = matrices->k_max_Q_cI;++  Q_cM              = matrices->Q_cM;+  l_min_Q_cM  = matrices->l_min_Q_cM;+  l_max_Q_cM  = matrices->l_max_Q_cM;+  k_min_Q_cM  = matrices->k_min_Q_cM;+  k_max_Q_cM  = matrices->k_max_Q_cM;++  Q_c_rem           = matrices->Q_c_rem;+  Q_cH_rem          = matrices->Q_cH_rem;+  Q_cI_rem          = matrices->Q_cI_rem;+  Q_cM_rem          = matrices->Q_cM_rem;++  /* check whether the chosen neighborhood exists at all */+  int dumb = 1;+  if((d1 == -1) && (Q_c_rem != 0.)) dumb = 0;+  else{+    if((k_min_Q_c <= d1) && (k_max_Q_c >= d1)){+      int l_min = l_min_Q_c[d1];+      if((d2 % 2) == (l_min%2))+        if((l_min <= d2) && (l_max_Q_c[d1] >= d2))+          dumb = 0;+    }+  }+  if(dumb){+    vrna_message_error("neighborhood %d:%d is not in scope of calculated partition function!\n"+                              "pbacktrack_circ@2Dpfold.c: exiting cheerless...",+                              d1, d2);+  }++  pstruc = vrna_alloc((n+1)*sizeof(char));++  for (i=0; i<n; i++) pstruc[i] = '.';+  pstruc[i] = '\0';++  /* now we come to the actual backtracking process */++  qot = 0.;+  /* backtrack in rest-partition */+  if(d1 == -1){+    r = vrna_urn() * Q_c_rem;+    /* open chain ? */+    if((referenceBPs1[my_iindx[1]-n] > maxD1) || (referenceBPs2[my_iindx[1]-n] > maxD2)){+      qot = 1.0 * scale[n];+      if(qot >= r)+        goto pbacktrack_circ_escape;+    }+    qot += Q_cH_rem;+    if(qot >= r){+      backtrack_qcH(vc, pstruc, d1, d2);+      goto pbacktrack_circ_escape;+    }+    qot += Q_cI_rem;+    if(qot >= r){+      backtrack_qcI(vc, pstruc, d1, d2);+      goto pbacktrack_circ_escape;+    }+    qot += Q_cM_rem;+    if(qot >= r){+      backtrack_qcM(vc, pstruc, d1, d2);+      goto pbacktrack_circ_escape;+    }+    vrna_message_error("pbacktrack_circ@2Dpfold.c: backtracking failed in exterior loop! Exiting cheerless...");+  }+  /* normal backtracking */+  else{+    r = vrna_urn() * Q_c[d1][d2/2];++    /* open chain ? */+    if((referenceBPs1[my_iindx[1]-n] == d1) && (referenceBPs2[my_iindx[1]-n] == d2)){+      qot += 1.0 * scale[n];+      if(qot >= r)+        goto pbacktrack_circ_escape;+    }++    /* exterior hairpin loop ? */+    if((k_min_Q_cH <= d1) && (k_max_Q_cH >= d1)){+      int l_min = l_min_Q_cH[d1];+      if((d2 % 2) == (l_min%2))+        if((l_min <= d2) && (l_max_Q_cH[d1] >= d2)){+          qot += Q_cH[d1][d2/2];+          if(qot >= r){+            backtrack_qcH(vc, pstruc, d1, d2);+            goto pbacktrack_circ_escape;+          }+        }+    }++    /* exterior interior loop ? */+    if((k_min_Q_cI <= d1) && (k_max_Q_cI >= d1)){+      int l_min = l_min_Q_cI[d1];+      if((d2 % 2) == (l_min%2))+        if((l_min <= d2) && (l_max_Q_cI[d1] >= d2)){+          qot += Q_cI[d1][d2/2];+          if(qot >= r){+            backtrack_qcI(vc, pstruc, d1, d2);+            goto pbacktrack_circ_escape;+          }+        }+    }++    /* exterior multibranch loop ? */+    if((k_min_Q_cM <= d1) && (k_max_Q_cM >= d1)){+      int l_min = l_min_Q_cM[d1];+      if((d2 % 2) == (l_min%2))+        if((l_min <= d2) && (l_max_Q_cM[d1] >= d2)){+          qot += Q_cM[d1][d2/2];+          if(qot >= r){+            backtrack_qcM(vc, pstruc, d1, d2);+            goto pbacktrack_circ_escape;+          }+        }+    }+  }++pbacktrack_circ_escape:+  return pstruc;+}++++PRIVATE void+backtrack_qcH(vrna_fold_compound_t *vc,+              char *pstruc,+              int d1,+              int d2){++  char            *ptype, *sequence;+  short           *S1;+  unsigned int    i, j, n, maxD1, maxD2,+                  base_d1, base_d2, da, db,+                  *referenceBPs1, *referenceBPs2;+  int             u, *my_iindx, *jindx, ij, cnt1, cnt2,type,+                  **l_min_Q_B, **l_max_Q_B,+                  *k_min_Q_B, *k_max_Q_B, *rtype;+  FLT_OR_DBL      r, qt, *scale, qot,+                  ***Q_B, **Q_cH, *Q_B_rem,+                  Q_cH_rem;++  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  sequence          = vc->sequence;+  n                 = vc->length;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  scale             = matrices->scale;+  ptype             = vc->ptype;+  rtype           = &(md->rtype[0]);+  S1                = vc->sequence_encoding;+  referenceBPs1     = vc->referenceBPs1;+  referenceBPs2     = vc->referenceBPs2;+  maxD1             = vc->maxD1;+  maxD2             = vc->maxD2;++  Q_B_rem           = matrices->Q_B_rem;+  Q_B               = matrices->Q_B;+  l_min_Q_B    = matrices->l_min_Q_B;+  l_max_Q_B    = matrices->l_max_Q_B;+  k_min_Q_B    = matrices->k_min_Q_B;+  k_max_Q_B    = matrices->k_max_Q_B;++  Q_cH_rem          = matrices->Q_cH_rem;+  Q_cH              = matrices->Q_cH;++  qot = qt = 0.;++  base_d1 = referenceBPs1[my_iindx[1]-n];+  base_d2 = referenceBPs2[my_iindx[1]-n];++  if(d1 == -1){+    r = vrna_urn() * Q_cH_rem;+    for(i=1;i<n;i++)+      for(j=i+TURN+1;j<=n;j++){+        char loopseq[10];+        ij = my_iindx[i]-j;+        u = n-j + i-1;+        if (u<TURN) continue;+        type = ptype[jindx[j] + i];+        if (!type) continue;+        if(((type==3)||(type==4))&&no_closingGU) continue;+        type=rtype[type];+        if (u<7){+          strcpy(loopseq , sequence+j-1);+          strncat(loopseq, sequence, i);+        }+        qt  = exp_E_Hairpin(u, type,+                            S1[j+1], S1[i-1],+                            loopseq, pf_params)+              * scale[u];++        if(Q_B_rem[ij]){+          qot += Q_B_rem[ij] * qt;+          if(qot >= r){+            backtrack(vc, pstruc, d1, d2, i, j);+            return;+          }+        }++        da = base_d1 - referenceBPs1[ij];+        db = base_d2 - referenceBPs2[ij];++        if(Q_B[ij]){+          for(cnt1 = k_min_Q_B[ij];+              cnt1 <= k_max_Q_B[ij];+              cnt1++)+            for(cnt2 = l_min_Q_B[ij][cnt1];+                cnt2 <= l_max_Q_B[ij][cnt1];+                cnt2 += 2){+              if(     ((cnt1 + da) > maxD1)+                  ||  ((cnt2 + db) > maxD2)){+                qot += Q_B[ij][cnt1][cnt2/2] * qt;+                if(qot >= r){+                  backtrack(vc, pstruc, cnt1, cnt2, i, j);+                  return;+                }+              }+            }+        }+    }+  }+  else{+    r = vrna_urn() * Q_cH[d1][d2/2];+    for(i=1;i<n;i++)+      for(j=i+TURN+1;j<=n;j++){+        char loopseq[10];+        ij = my_iindx[i]-j;+        if(!Q_B[ij]) continue;+        u = n-j + i-1;+        if (u<TURN) continue;+        type = ptype[jindx[j] + i];+        if (!type) continue;+        if(((type==3)||(type==4))&&no_closingGU) continue;+        type=rtype[type];+        if (u<7){+          strcpy(loopseq , sequence+j-1);+          strncat(loopseq, sequence, i);+        }+        qt  = exp_E_Hairpin(u, type,+                            S1[j+1], S1[i-1],+                            loopseq, pf_params)+              * scale[u];+        da  = base_d1 - referenceBPs1[ij];+        db  = base_d2 - referenceBPs2[ij];++        for(cnt1 = k_min_Q_B[ij];+            cnt1 <= k_max_Q_B[ij];+            cnt1++)+          for(cnt2 = l_min_Q_B[ij][cnt1];+              cnt2 <= l_max_Q_B[ij][cnt1];+              cnt2 += 2){+            if( ((cnt1 + da) == d1)+                && ((cnt2 + db) == d2)){+              qot += Q_B[ij][cnt1][cnt2/2] * qt;+              if(qot >= r){+                backtrack(vc, pstruc, cnt1, cnt2, i, j);+                return;+              }+            }+          }+      }+  }+  vrna_message_error("backtrack_qcH@2Dpfold.c: failed to find closing pair!");+}++PRIVATE void  backtrack_qcI(vrna_fold_compound_t *vc,+                            char *pstruc,+                            int d1, int d2){++  char            *ptype;+  short           *S1;+  unsigned int    i, j, ij, p, q, pq, n, maxD1, maxD2,+                  base_d1, base_d2, da, db,+                  *referenceBPs1, *referenceBPs2;+  int             *my_iindx, *jindx, cnt1, cnt2, cnt3, cnt4, type,+                  **l_min_Q_B, **l_max_Q_B,+                  *k_min_Q_B, *k_max_Q_B, *rtype;+  FLT_OR_DBL      r, qt, *scale, qot,+                  ***Q_B, *Q_B_rem,+                  **Q_cI, Q_cI_rem;+  vrna_exp_param_t       *pf_params;+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  n                 = vc->length;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  scale             = matrices->scale;+  ptype             = vc->ptype;+  rtype           = &(md->rtype[0]);+  S1                = vc->sequence_encoding;+  referenceBPs1     = vc->referenceBPs1;+  referenceBPs2     = vc->referenceBPs2;+  maxD1             = vc->maxD1;+  maxD2             = vc->maxD2;++  Q_B               = matrices->Q_B;+  l_min_Q_B    = matrices->l_min_Q_B;+  l_max_Q_B    = matrices->l_max_Q_B;+  k_min_Q_B    = matrices->k_min_Q_B;+  k_max_Q_B    = matrices->k_max_Q_B;++  Q_cI              = matrices->Q_cI;+  Q_B_rem           = matrices->Q_B_rem;+  Q_cI_rem          = matrices->Q_cI_rem;++  qot = qt = 0.;++  base_d1 = referenceBPs1[my_iindx[1]-n];+  base_d2 = referenceBPs2[my_iindx[1]-n];++  if(d1 == -1){+    r = vrna_urn() * Q_cI_rem;+    for(i=1;i<n;i++)+      for(j=i+TURN+1;j<=n;j++){+        ij = my_iindx[i]-j;+        type = rtype[(unsigned int)ptype[jindx[j] + i]];+        if(!type) continue;++        if(Q_B_rem[ij])+          for(p=j+1; p < n; p++){+            unsigned int ln1, qstart, ln_pre;+            ln1 = p - j - 1;+            if(ln1+i-1>MAXLOOP) break;+            qstart = p + TURN + 1;+            ln_pre = ln1 + i + n;+            if(ln_pre > qstart + MAXLOOP)+              qstart = ln_pre - MAXLOOP - 1;+            for(q=qstart;q <= n; q++){+              unsigned int ln2;+              int type2;+              pq = my_iindx[p]-q;+              ln2 = (i - 1) + (n - q);+              if((ln1+ln2) > MAXLOOP) continue;+              type2 = ptype[jindx[q] + p];+              if(!type2) continue;+              qt  = exp_E_IntLoop(ln2, ln1,+                                  rtype[type2], type,+                                  S1[q+1], S1[p-1],+                                  S1[i-1], S1[j+1],+                                  pf_params)+                    * scale[ln1 + ln2];+              if(Q_B_rem[pq]){+                qot +=  Q_B_rem[ij] * Q_B_rem[pq] * qt;+                if(qot > r){+                  backtrack(vc, pstruc, d1, d2, i, j);+                  backtrack(vc, pstruc, d1, d2, p, q);+                  return;+                }+              }+              if(Q_B[pq])+                for(cnt1 = k_min_Q_B[pq];+                    cnt1 <= k_max_Q_B[pq];+                    cnt1++)+                  for(cnt2 = l_min_Q_B[pq][cnt1];+                      cnt2 <= l_max_Q_B[pq][cnt1];+                      cnt2 += 2){+                    qot +=  Q_B_rem[ij] * Q_B[pq][cnt1][cnt2/2] * qt;+                    if(qot > r){+                      backtrack(vc, pstruc, d1, d2, i, j);+                      backtrack(vc, pstruc, cnt1, cnt2, p, q);+                      return;+                    }+                  }+            }+          }++        if(Q_B[ij]){+          for(p=j+1; p < n; p++){+            unsigned int ln1, qstart, ln_pre;+            ln1 = p - j - 1;+            if(ln1+i-1>MAXLOOP) break;+            qstart = p + TURN + 1;+            ln_pre = ln1 + i + n;+            if(ln_pre > qstart + MAXLOOP)+              qstart = ln_pre - MAXLOOP - 1;+            for(q=qstart;q <= n; q++){+              unsigned int ln2;+              int type2;+              pq = my_iindx[p]-q;+              ln2 = (i - 1) + (n - q);+              if((ln1+ln2) > MAXLOOP) continue;+              type2 = ptype[jindx[q] + p];+              if(!type2) continue;+              qt  = exp_E_IntLoop(ln2, ln1,+                                  rtype[type2], type,+                                  S1[q+1], S1[p-1],+                                  S1[i-1], S1[j+1],+                                  pf_params)+                    * scale[ln1 + ln2];+              if(Q_B_rem[pq])+                for(cnt1 = k_min_Q_B[ij];+                    cnt1 <= k_max_Q_B[ij];+                    cnt1++)+                  for(cnt2 = l_min_Q_B[ij][cnt1];+                      cnt2 <= l_max_Q_B[ij][cnt1];+                      cnt2 += 2){+                    qot +=  Q_B[ij][cnt1][cnt2/2] * Q_B_rem[pq] * qt;+                    if(qot > r){+                      backtrack(vc, pstruc, cnt1, cnt2, i, j);+                      backtrack(vc, pstruc, d1, d2, p, q);+                      return;+                    }+                  }+              if(Q_B[pq]){+                da  = base_d1+                      - referenceBPs1[ij]+                      - referenceBPs1[pq];+                db  = base_d2+                      - referenceBPs2[ij]+                      - referenceBPs2[pq];+                for(cnt1 = k_min_Q_B[ij];+                    cnt1 <= k_max_Q_B[ij];+                    cnt1++)+                  for(cnt2 = l_min_Q_B[ij][cnt1];+                      cnt2 <= l_max_Q_B[ij][cnt1];+                      cnt2 += 2)+                    for(cnt3 = k_min_Q_B[pq];+                        cnt3 <= k_max_Q_B[pq];+                        cnt3++)+                      for(cnt4 = l_min_Q_B[pq][cnt3];+                          cnt4 <= l_max_Q_B[pq][cnt3];+                          cnt4 += 2){+                        if(     ((cnt1 + cnt3 + da) > maxD1)+                            ||  ((cnt2 + cnt4 + db) > maxD2)){+                          qot +=  Q_B[ij][cnt1][cnt2/2]+                                  * Q_B[pq][cnt3][cnt4/2]+                                  * qt;+                          if(qot > r){+                            backtrack(vc, pstruc, cnt1, cnt2, i, j);+                            backtrack(vc, pstruc, cnt3, cnt4, p, q);+                            return;+                          }+                        }+                      }+              }+            }+          }+        }++      }+  }+  else{+    r = vrna_urn() * Q_cI[d1][d2/2];+    for(i=1;i<n;i++)+      for(j=i+TURN+1;j<=n;j++){+        ij = my_iindx[i]-j;+        type = rtype[(unsigned int)ptype[jindx[j] + i]];+        if(!type) continue;+        if(!Q_B[ij]) continue;+        for(p=j+1; p < n; p++){+          unsigned int ln1, qstart, ln_pre;+          ln1 = p - j - 1;+          if(ln1+i-1>MAXLOOP) break;+          qstart = p + TURN + 1;+          ln_pre = ln1 + i + n;+          if(ln_pre > qstart + MAXLOOP)+            qstart = ln_pre - MAXLOOP - 1;+          for(q=qstart;q <= n; q++){+            unsigned int ln2;+            int type2;+            pq    = my_iindx[p]-q;+            if(!Q_B[pq]) continue;+            ln2   = (i - 1) + (n - q);+            if((ln1+ln2) > MAXLOOP) continue;+            type2 = ptype[jindx[q] + p];+            if(!type2) continue;+            qt  = exp_E_IntLoop( ln2, ln1,+                                rtype[type2], type,+                                S1[q+1], S1[p-1],+                                S1[i-1], S1[j+1],+                                pf_params)+                  * scale[ln1 + ln2];+            da  = base_d1+                  - referenceBPs1[ij]+                  - referenceBPs1[pq];+            db  = base_d2+                  - referenceBPs2[ij]+                  - referenceBPs2[pq];+            for(cnt1 = k_min_Q_B[ij];+                cnt1 <= k_max_Q_B[ij];+                cnt1++)+              for(cnt2 = l_min_Q_B[ij][cnt1];+                  cnt2 <= l_max_Q_B[ij][cnt1];+                  cnt2 += 2)+                for(cnt3 = k_min_Q_B[pq];+                    cnt3 <= k_max_Q_B[pq];+                    cnt3++)+                  for(cnt4 = l_min_Q_B[pq][cnt3];+                      cnt4 <= l_max_Q_B[pq][cnt3];+                      cnt4 += 2){+                    if(     ((cnt1 + cnt3 + da) == d1)+                        &&  ((cnt2 + cnt4 + db) == d2)){+                      qot +=  Q_B[ij][cnt1][cnt2/2]+                              * Q_B[pq][cnt3][cnt4/2]+                              * qt;+                      if(qot > r){+                        backtrack(vc, pstruc, cnt1, cnt2, i, j);+                        backtrack(vc, pstruc, cnt3, cnt4, p, q);+                        return;+                      }+                    }+                  }+          }+        }+      }+  }+}++PRIVATE void  backtrack_qcM(vrna_fold_compound_t *vc,+                            char *pstruc,+                            int d1, int d2){++  unsigned int  k, n, maxD1, maxD2, base_d1, base_d2,+                da, db, *referenceBPs1, *referenceBPs2;+  int           *my_iindx, cnt1, cnt2, cnt3, cnt4,+                **l_min_Q_M, **l_max_Q_M,+                **l_min_Q_M2, **l_max_Q_M2,+                *k_min_Q_M, *k_max_Q_M,+                *k_min_Q_M2, *k_max_Q_M2;+  FLT_OR_DBL    r, qt, qot,+                ***Q_M, ***Q_M2, **Q_cM,+                *Q_M_rem, *Q_M2_rem, Q_cM_rem;+  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  n                 = vc->length;+  my_iindx          = vc->iindx;+  referenceBPs1     = vc->referenceBPs1;+  referenceBPs2     = vc->referenceBPs2;+  maxD1             = vc->maxD1;+  maxD2             = vc->maxD2;++  Q_cM              = matrices->Q_cM;++  Q_M               = matrices->Q_M;+  l_min_Q_M    = matrices->l_min_Q_M;+  l_max_Q_M    = matrices->l_max_Q_M;+  k_min_Q_M    = matrices->k_min_Q_M;+  k_max_Q_M    = matrices->k_max_Q_M;++  Q_M2              = matrices->Q_M2;+  l_min_Q_M2   = matrices->l_min_Q_M2;+  l_max_Q_M2   = matrices->l_max_Q_M2;+  k_min_Q_M2   = matrices->k_min_Q_M2;+  k_max_Q_M2   = matrices->k_max_Q_M2;++  Q_cM_rem          = matrices->Q_cM_rem;+  Q_M_rem           = matrices->Q_M_rem;+  Q_M2_rem          = matrices->Q_M2_rem;++  base_d1 = referenceBPs1[my_iindx[1]-n];+  base_d2 = referenceBPs2[my_iindx[1]-n];+  qot     = qt = 0.;++  if(d1 == -1){+    r = vrna_urn() * Q_cM_rem;+    for(k = TURN + 2;+        k < n - 2 * TURN - 3;+        k++){++      if(Q_M_rem[my_iindx[1]-k]){++        if(Q_M2[k+1])+          for(cnt1 = k_min_Q_M2[k+1];+              cnt1 <= k_max_Q_M2[k+1];+              cnt1++)+            for(cnt2 = l_min_Q_M2[k+1][cnt1];+                cnt2 <= l_max_Q_M2[k+1][cnt1];+                cnt2 += 2){+              qot +=  Q_M_rem[my_iindx[1]-k]+                      * Q_M2[k+1][cnt1][cnt2/2]+                      * pf_params->expMLclosing;+              if(qot > r){+                backtrack_qm(vc, pstruc, d1, d2, 1, k);+                backtrack_qm2(vc, pstruc, cnt1, cnt2, k+1);+                return;+              }+            }++        if(Q_M2_rem[k+1]){+          qot +=  Q_M_rem[my_iindx[1]-k]+                  * Q_M2_rem[k+1]+                  * pf_params->expMLclosing;+          if(qot > r){+            backtrack_qm(vc, pstruc, d1, d2, 1, k);+            backtrack_qm2(vc, pstruc, d1, d2, k+1);+            return;+          }+        }++      }++      if(Q_M2_rem[k+1]){++        if(Q_M[my_iindx[1]-k])+          for(cnt1 = k_min_Q_M[my_iindx[1]-k];+              cnt1 <= k_max_Q_M[my_iindx[1]-k];+              cnt1++)+            for(cnt2 = l_min_Q_M[my_iindx[1]-k][cnt1];+                cnt2 <= l_max_Q_M[my_iindx[1]-k][cnt1];+                cnt2 += 2){+              qot +=  Q_M[my_iindx[1]-k][cnt1][cnt2/2]+                      * Q_M2_rem[k+1]+                      * pf_params->expMLclosing;+              if(qot > r){+                backtrack_qm(vc, pstruc, cnt1, cnt2, 1, k);+                backtrack_qm2(vc, pstruc, d1, d2, k+1);+                return;+              }+            }++      }++      da  = base_d1+            - referenceBPs1[my_iindx[1]-k]+            - referenceBPs1[my_iindx[k+1]-n];+      db  = base_d2+            - referenceBPs2[my_iindx[1]-k]+            - referenceBPs2[my_iindx[k+1]-n];++      if(     Q_M[my_iindx[1]-k]+          &&  Q_M2[k+1])+        for(cnt1 = k_min_Q_M[my_iindx[1]-k];+            cnt1 <= k_max_Q_M[my_iindx[1]-k];+            cnt1++)+          for(cnt2 = l_min_Q_M[my_iindx[1]-k][cnt1];+              cnt2 <= l_max_Q_M[my_iindx[1]-k][cnt1];+              cnt2 += 2)+            for(cnt3 = k_min_Q_M2[k+1];+                cnt3 <= k_max_Q_M2[k+1];+                cnt3++)+              for(cnt4 = l_min_Q_M2[k+1][cnt3];+                  cnt4 <= l_max_Q_M2[k+1][cnt3];+                  cnt4 += 2){+                if(     ((cnt1 + cnt3 + da) > maxD1)+                    ||  ((cnt2 + cnt4 + db) > maxD2)){+                  qot   +=  Q_M[my_iindx[1]-k][cnt1][cnt2/2]+                            * Q_M2[k+1][cnt3][cnt4/2]+                            * pf_params->expMLclosing;+                  if(qot > r){+                    backtrack_qm(vc, pstruc, cnt1, cnt2, 1, k);+                    backtrack_qm2(vc, pstruc, cnt3, cnt4, k+1);+                    return;+                  }+                }+              }++    }+  }+  else{+    r = vrna_urn() * Q_cM[d1][d2/2];+    for(k = TURN + 2;+        k < n - 2 * TURN - 3;+        k++){+      da  = base_d1+            - referenceBPs1[my_iindx[1]-k]+            - referenceBPs1[my_iindx[k+1]-n];+      db  = base_d2+            - referenceBPs2[my_iindx[1]-k]+            - referenceBPs2[my_iindx[k+1]-n];+        if(     Q_M[my_iindx[1]-k]+            &&  Q_M2[k+1])+          for(cnt1 = k_min_Q_M[my_iindx[1]-k];+              cnt1 <= k_max_Q_M[my_iindx[1]-k];+              cnt1++)+            for(cnt2 = l_min_Q_M[my_iindx[1]-k][cnt1];+                cnt2 <= l_max_Q_M[my_iindx[1]-k][cnt1];+                cnt2 += 2)+              for(cnt3 = k_min_Q_M2[k+1];+                  cnt3 <= k_max_Q_M2[k+1];+                  cnt3++)+                for(cnt4 = l_min_Q_M2[k+1][cnt3];+                    cnt4 <= l_max_Q_M2[k+1][cnt3];+                    cnt4 += 2)+                  if(     ((cnt1 + cnt3 + da) == d1)+                      &&  ((cnt2 + cnt4 + db) == d2)){+                    qot +=  Q_M[my_iindx[1]-k][cnt1][cnt2/2]+                            * Q_M2[k+1][cnt3][cnt4/2]+                            * pf_params->expMLclosing;+                    if(qot > r){+                      backtrack_qm(vc, pstruc, cnt1, cnt2, 1, k);+                      backtrack_qm2(vc, pstruc, cnt3, cnt4, k+1);+                      return;+                    }+                  }+    }+  }+  vrna_message_error("backtrack_qcM@2Dpfold.c: backtracking failed");+}++PRIVATE void+backtrack_qm2(vrna_fold_compound_t *vc,+              char *pstruc,+              int d1,+              int d2,+              unsigned int k){++  unsigned int  l, n, maxD1, maxD2, da, db,+                *referenceBPs1, *referenceBPs2;+  int           *my_iindx, *jindx, cnt1, cnt2, cnt3, cnt4,+                *k_min_Q_M1, *k_max_Q_M1,+                **l_min_Q_M1, **l_max_Q_M1;+  FLT_OR_DBL    r, qt, qot,+                ***Q_M2, ***Q_M1,+                *Q_M2_rem, *Q_M1_rem;++  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;++  n               = vc->length;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;++  Q_M1_rem        = matrices->Q_M1_rem;+  Q_M1            = matrices->Q_M1;+  l_min_Q_M1 = matrices->l_min_Q_M1;+  l_max_Q_M1 = matrices->l_max_Q_M1;+  k_min_Q_M1 = matrices->k_min_Q_M1;+  k_max_Q_M1 = matrices->k_max_Q_M1;++  Q_M2_rem        = matrices->Q_M2_rem;+  Q_M2            = matrices->Q_M2;++  qot = qt = 0.;++  if(d1 == -1){+    r = vrna_urn() * Q_M2_rem[k];+    for (l=k+TURN+1; l<n-TURN-1; l++){+      if(Q_M1_rem[jindx[l]+k]){+        if(Q_M1[jindx[n]+l+1]){+          for(cnt1 = k_min_Q_M1[jindx[n]+l+1];+              cnt1 <= k_max_Q_M1[jindx[n]+l+1];+              cnt1++)+            for(cnt2 = l_min_Q_M1[jindx[n]+l+1][cnt1];+                cnt2 <= l_max_Q_M1[jindx[n]+l+1][cnt1];+                cnt2 += 2){+              qot += Q_M1_rem[jindx[l]+k] * Q_M1[jindx[n]+l+1][cnt1][cnt2/2];+              if(qot > r){+                backtrack_qm1(vc, pstruc, d1, d2, k, l);+                backtrack_qm1(vc, pstruc, cnt1, cnt2, l+1, n);+                return;+              }+            }+        }+        if(Q_M1_rem[jindx[n]+l+1]){+          qot +=  Q_M1_rem[jindx[l]+k]+                  * Q_M1_rem[jindx[n]+l+1];+          if(qot > r){+            backtrack_qm1(vc, pstruc, d1, d2, k, l);+            backtrack_qm1(vc, pstruc, d1, d2, l+1, n);+            return;+          }+        }+      }+      if(Q_M1_rem[jindx[n]+l+1]){+        if(Q_M1[jindx[l]+k])+          for(cnt1 = k_min_Q_M1[jindx[l]+k];+              cnt1 <= k_max_Q_M1[jindx[l]+k];+              cnt1++)+            for(cnt2 = l_min_Q_M1[jindx[l]+k][cnt1];+                cnt2 <= l_max_Q_M1[jindx[l]+k][cnt1];+                cnt2 += 2){+              qot +=  Q_M1[jindx[l]+k][cnt1][cnt2/2]+                      * Q_M1_rem[jindx[n]+l+1];+              if(qot > r){+                backtrack_qm1(vc, pstruc, cnt1, cnt2, k, l);+                backtrack_qm1(vc, pstruc, d1, d2, l+1, n);+                return;+              }+            }+      }++      if(!Q_M1[jindx[l]+k]) continue;+      if(!Q_M1[jindx[n] + l + 1]) continue;++      da  = referenceBPs1[my_iindx[k]-n]+            - referenceBPs1[my_iindx[k]-l]+            - referenceBPs1[my_iindx[l+1]-n];+      db  = referenceBPs2[my_iindx[k]-n]+            - referenceBPs2[my_iindx[k]-l]+            - referenceBPs2[my_iindx[l+1]-n];+      for(cnt1 = k_min_Q_M1[jindx[l]+k];+          cnt1 <= k_max_Q_M1[jindx[l]+k];+          cnt1++)+        for(cnt2 = l_min_Q_M1[jindx[l]+k][cnt1];+            cnt2 <= l_max_Q_M1[jindx[l]+k][cnt1];+            cnt2 += 2){+          for(cnt3 = k_min_Q_M1[jindx[n] + l + 1];+              cnt3 <= k_max_Q_M1[jindx[n] + l + 1];+              cnt3++)+            for(cnt4 = l_min_Q_M1[jindx[n] + l + 1][cnt3];+                cnt4 <= l_max_Q_M1[jindx[n] + l + 1][cnt3];+                cnt4 += 2){+              if(    ((cnt1 + cnt3 + da) > maxD1)+                  || ((cnt2 + cnt4 + db) > maxD2)){+                qot +=  Q_M1[jindx[l]+k][cnt1][cnt2/2]+                        * Q_M1[jindx[n] + l + 1][cnt3][cnt4/2];+                if(qot > r){+                  backtrack_qm1(vc, pstruc, cnt1, cnt2, k, l);+                  backtrack_qm1(vc, pstruc, cnt3, cnt4, l+1, n);+                  return;+                }+              }+            }+        }+    }++  }+  else{+    r = vrna_urn() * Q_M2[k][d1][d2/2];+    for (l=k+TURN+1; l<n-TURN-1; l++){+      if(!Q_M1[jindx[l]+k]) continue;+      if(!Q_M1[jindx[n] + l + 1]) continue;++      da  = referenceBPs1[my_iindx[k]-n]+            - referenceBPs1[my_iindx[k]-l]+            - referenceBPs1[my_iindx[l+1]-n];+      db  = referenceBPs2[my_iindx[k]-n]+            - referenceBPs2[my_iindx[k]-l]+            - referenceBPs2[my_iindx[l+1]-n];+      for(cnt1 = k_min_Q_M1[jindx[l]+k];+          cnt1 <= k_max_Q_M1[jindx[l]+k];+          cnt1++)+        for(cnt2 = l_min_Q_M1[jindx[l]+k][cnt1];+            cnt2 <= l_max_Q_M1[jindx[l]+k][cnt1];+            cnt2 += 2){+          for(cnt3 = k_min_Q_M1[jindx[n] + l + 1];+              cnt3 <= k_max_Q_M1[jindx[n] + l + 1];+              cnt3++)+            for(cnt4 = l_min_Q_M1[jindx[n] + l + 1][cnt3];+                cnt4 <= l_max_Q_M1[jindx[n] + l + 1][cnt3];+                cnt4 += 2){+              if(     ((cnt1 + cnt3 + da) == d1)+                  &&  ((cnt2 + cnt4 + db) == d2)){+                qot +=  Q_M1[jindx[l]+k][cnt1][cnt2/2]+                        * Q_M1[jindx[n] + l + 1][cnt3][cnt4/2];+                if(qot > r){+                  backtrack_qm1(vc, pstruc, cnt1, cnt2, k, l);+                  backtrack_qm1(vc, pstruc, cnt3, cnt4, l+1, n);+                  return;+                }+              }+            }+        }+    }+  }+  vrna_message_error("backtrack_qm2@2Dpfold.c: backtracking failed");+}+++PRIVATE void+backtrack(vrna_fold_compound_t *vc,+          char *pstruc,+          int d1,+          int d2,+          unsigned int i,+          unsigned int j) {++  FLT_OR_DBL      *scale;+  unsigned int    maxD1, maxD2, base_d1, base_d2, da, db;+  unsigned int    *referenceBPs1, *referenceBPs2;+  char            *ptype, *sequence;+  short           *S1, *reference_pt1, *reference_pt2;+  int             *my_iindx, *jindx, ij, cnt1, cnt2, cnt3, cnt4, *rtype;+  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  sequence    = vc->sequence;+  maxD1       = vc->maxD1;+  maxD2       = vc->maxD2;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  scale       = matrices->scale;+  ptype       = vc->ptype;+  rtype           = &(md->rtype[0]);+  S1              = vc->sequence_encoding;+  reference_pt1   = vc->reference_pt1;+  reference_pt2   = vc->reference_pt2;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;++  FLT_OR_DBL  ***Q_B, ***Q_M, ***Q_M1, *Q_B_rem, *Q_M_rem, *Q_M1_rem;+  int         *k_min_Q_M, *k_max_Q_M,*k_min_Q_M1, *k_max_Q_M1,*k_min_Q_B, *k_max_Q_B;+  int         **l_min_Q_M, **l_max_Q_M,**l_min_Q_M1, **l_max_Q_M1,**l_min_Q_B, **l_max_Q_B;++  Q_B = matrices->Q_B;+  k_min_Q_B = matrices->k_min_Q_B;+  k_max_Q_B = matrices->k_max_Q_B;+  l_min_Q_B = matrices->l_min_Q_B;+  l_max_Q_B = matrices->l_max_Q_B;++  Q_M = matrices->Q_M;+  k_min_Q_M = matrices->k_min_Q_M;+  k_max_Q_M = matrices->k_max_Q_M;+  l_min_Q_M = matrices->l_min_Q_M;+  l_max_Q_M = matrices->l_max_Q_M;++  Q_M1 = matrices->Q_M1;+  k_min_Q_M1 = matrices->k_min_Q_M1;+  k_max_Q_M1 = matrices->k_max_Q_M1;+  l_min_Q_M1 = matrices->l_min_Q_M1;+  l_max_Q_M1 = matrices->l_max_Q_M1;++  Q_B_rem   = matrices->Q_B_rem;+  Q_M_rem   = matrices->Q_M_rem;+  Q_M1_rem  = matrices->Q_M1_rem;++  do {+    double r, qbt1 = 0.;+    unsigned int k, l, u, u1;+    int type;++    pstruc[i-1] = '('; pstruc[j-1] = ')';++    r = 0.;+    ij = my_iindx[i]-j;++    if(d1 == -1){+      r= vrna_urn() * Q_B_rem[ij];+      if(r == 0.) vrna_message_error("backtrack@2Dpfold.c: backtracking failed\n");+      +      type = ptype[jindx[j] + i];+      u = j-i-1;+      base_d1 = ((unsigned int)reference_pt1[i] != j) ? 1 : -1;+      base_d2 = ((unsigned int)reference_pt2[i] != j) ? 1 : -1;++      da = base_d1 + referenceBPs1[ij];+      db = base_d2 + referenceBPs2[ij];++      /* hairpin ? */+      if((da > maxD1) || (db > maxD2))+        if(!(((type==3)||(type==4))&&no_closingGU))+          qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[u+2];++      if (qbt1>=r) return; /* found the hairpin we're done */++      /* lets see if we form an interior loop */+      for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {+        unsigned int u_pre, lmin;+        u1 = k-i-1;+        lmin = k + TURN + 1;+        u_pre = u1 + j;+        /* lmin = MAX2(k + TURN + 1, u1 + j - 1 - MAXLOOP) */+        if(u_pre > lmin + MAXLOOP) lmin = u_pre - 1 - MAXLOOP;+        for (l=lmin; l<j; l++) {+          int type_2;+          type_2 = ptype[jindx[l]+k];+          if (type_2) {+            cnt1 = cnt2 = -1;+            da = base_d1 + referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[k]-l];+            db = base_d2 + referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[k]-l];+            type_2 = rtype[type_2];+            FLT_OR_DBL tmp_en = exp_E_IntLoop(u1, j-l-1, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params) * scale[u1+j-l+1];++            if(Q_B_rem[my_iindx[k]-l] != 0.){+              qbt1 += Q_B_rem[my_iindx[k]-l] * tmp_en;+              if(qbt1 > r) goto backtrack_int_early_escape_rem;+            }++            if(Q_B[my_iindx[k]-l])+              for(cnt1 = k_min_Q_B[my_iindx[k]-l];+                  cnt1 <= k_max_Q_B[my_iindx[k]-l];+                  cnt1++)+                for(cnt2 = l_min_Q_B[my_iindx[k]-l][cnt1];+                    cnt2 <= l_max_Q_B[my_iindx[k]-l][cnt1];+                    cnt2 += 2)+                  if(((cnt1 + da) > maxD1) || ((cnt2 + db) > maxD2)){+                    qbt1 += Q_B[my_iindx[k]-l][cnt1][cnt2/2] * tmp_en;+                    if(qbt1 > r) goto backtrack_int_early_escape_rem;+                  }+          }+        }+      }+backtrack_int_early_escape_rem:+      if (l<j) {+        i=k; j=l;+        d1 = cnt1;+        d2 = cnt2;+      }+      else break;+    }+    else{++      if((d1 >= k_min_Q_B[ij]) && (d1 <= k_max_Q_B[ij]))+        if((d2 >= l_min_Q_B[ij][d1]) && (d2 <= l_max_Q_B[ij][d1]))+          r = vrna_urn() * Q_B[ij][d1][d2/2];++      if(r == 0.) vrna_message_error("backtrack@2Dpfold.c: backtracking failed\n");++      type = ptype[jindx[j] + i];+      u = j-i-1;+      base_d1 = ((unsigned int)reference_pt1[i] != j) ? 1 : -1;+      base_d2 = ((unsigned int)reference_pt2[i] != j) ? 1 : -1;++      da = base_d1 + referenceBPs1[ij];+      db = base_d2 + referenceBPs2[ij];++      /*hairpin contribution*/+      if((da == d1) && (db == d2))+        if(!(((type==3)||(type==4))&&no_closingGU))+          qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[u+2];++      if (qbt1>=r) return; /* found the hairpin we're done */++      for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {+        unsigned int u_pre, lmin;+        u1 = k-i-1;+        lmin = k + TURN + 1;+        u_pre = u1 + j;+        /* lmin = MAX2(k + TURN + 1, u1 + j - 1 - MAXLOOP) */+        if(u_pre > lmin + MAXLOOP) lmin = u_pre - 1 - MAXLOOP;+        for (l=lmin; l<j; l++) {+          int type_2;+          type_2 = ptype[jindx[l]+k];+          if (type_2) {+            da = base_d1 + referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[k]-l];+            db = base_d2 + referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[k]-l];+            type_2 = rtype[type_2];+            FLT_OR_DBL tmp_en = exp_E_IntLoop(u1, j-l-1, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params) * scale[u1+j-l+1];+            if(d1 >= da && d2 >= db)+              if((d1 - da >= k_min_Q_B[my_iindx[k]-l]) && (d1 - da <= k_max_Q_B[my_iindx[k]-l]))+                if((d2 - db >= l_min_Q_B[my_iindx[k]-l][d1 - da]) && (d2 - db <= l_max_Q_B[my_iindx[k]-l][d1 - da])){+                  cnt1 = d1 - da;+                  cnt2 = d2 - db;+                  qbt1 += Q_B[my_iindx[k]-l][cnt1][cnt2/2] * tmp_en;+                  if(qbt1 > r) goto backtrack_int_early_escape;+                }+          }+        }+      }++backtrack_int_early_escape:+      if (l<j) {+        i=k; j=l;+        d1 = cnt1;+        d2 = cnt2;+      }+      else break;+    }+  } while (1);++  /* backtrack in multi-loop */+  {+    double r, qt;+    unsigned int k, ii, jj;++    base_d1 = ((unsigned int)reference_pt1[i] != j) ? 1 : -1;+    base_d2 = ((unsigned int)reference_pt2[i] != j) ? 1 : -1;++    base_d1 += referenceBPs1[my_iindx[i]-j];+    base_d2 += referenceBPs2[my_iindx[i]-j];++    i++; j--;+    /* find the first split index */+    ii = my_iindx[i]; /* ii-j=[i,j] */+    jj = jindx[j]; /* jj+i=[j,i] */+    if(d1 == -1){+      /* get total contribution for current part */+      for (qt=0., k=i+1; k<j; k++){+        if(Q_M_rem[ii-k+1] != 0.){+          if(Q_M1[jj+k])+            for(cnt1 = k_min_Q_M1[jj+k];+                cnt1 <= k_max_Q_M1[jj+k];+                cnt1++)+              for(cnt2 = l_min_Q_M1[jj+k][cnt1];+                  cnt2 <= l_max_Q_M1[jj+k][cnt1];+                  cnt2 += 2)+                qt += Q_M_rem[ii-k+1] * Q_M1[jj+k][cnt1][cnt2/2];+          if(Q_M1_rem[jj+k] != 0.)+            qt += Q_M_rem[ii-k+1] * Q_M1_rem[jj+k];+        }+        if(Q_M1_rem[jj+k] != 0.){+          if(Q_M[ii-k+1])+            for(cnt1 = k_min_Q_M[ii-k+1];+                cnt1 <= k_max_Q_M[ii-k+1];+                cnt1++)+              for(cnt2 = l_min_Q_M[ii-k+1][cnt1];+                  cnt2 <= l_max_Q_M[ii-k+1][cnt1];+                  cnt2 += 2)+                qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1_rem[jj+k];+        }+        /* calculate introduced distance to reference structures */+        if(!Q_M[ii-k+1]) continue;+        if(!Q_M1[jj+k]) continue;+        da = base_d1 - referenceBPs1[my_iindx[i]-k+1] - referenceBPs1[my_iindx[k]-j];+        db = base_d2 - referenceBPs2[my_iindx[i]-k+1] - referenceBPs2[my_iindx[k]-j];+        /* collect all contributing energies */+        for(cnt1 = k_min_Q_M[ii-k+1];+            cnt1 <= k_max_Q_M[ii-k+1];+            cnt1++)+          for(cnt2 = l_min_Q_M[ii-k+1][cnt1];+              cnt2 <= l_max_Q_M[ii-k+1][cnt1];+              cnt2 += 2)+            for(cnt3 = k_min_Q_M1[jj+k];+                cnt3 <= k_max_Q_M1[jj+k];+                cnt3++)+              for(cnt4 = l_min_Q_M1[jj+k][cnt3];+                  cnt4 <= l_max_Q_M1[jj+k][cnt3];+                  cnt4 += 2)+                if(((cnt1 + cnt3 + da) > maxD1) || ((cnt2 + cnt4 + db) > maxD2))+                  qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1[jj+k][cnt3][cnt4/2];+      }+      /* throw the dice */+      r = vrna_urn() * qt;+      for (qt=0., k=i+1; k<j; k++) {+        cnt1 = cnt2 = cnt3 = cnt4 = -1;+        if(Q_M_rem[ii-k+1] != 0.){+          if(Q_M1_rem[jj+k] != 0){+            qt += Q_M_rem[ii-k+1] * Q_M1_rem[jj+k];+            if(qt >= r) goto backtrack_ml_early_escape;+          }+          if(Q_M1[jj+k])+            for(cnt3 = k_min_Q_M1[jj+k];+                cnt3 <= k_max_Q_M1[jj+k];+                cnt3++)+              for(cnt4 = l_min_Q_M1[jj+k][cnt3];+                  cnt4 <= l_max_Q_M1[jj+k][cnt3];+                  cnt4 += 2){+                qt += Q_M_rem[ii-k+1] * Q_M1[jj+k][cnt3][cnt4/2];+                if(qt >= r) goto backtrack_ml_early_escape;+              }+        }+        if(Q_M1_rem[jj+k] != 0.){+          cnt3 = cnt4 = -1;+          if(Q_M[ii-k+1])+            for(cnt1 = k_min_Q_M[ii-k+1];+                cnt1 <= k_max_Q_M[ii-k+1];+                cnt1++)+              for(cnt2 = l_min_Q_M[ii-k+1][cnt1];+                  cnt2 <= l_max_Q_M[ii-k+1][cnt1];+                  cnt2 += 2){+                qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1_rem[jj+k];+                if(qt >= r) goto backtrack_ml_early_escape;+              }+        }+        /* calculate introduced distance to reference structures */+        da = base_d1 - referenceBPs1[my_iindx[i]-k+1] - referenceBPs1[my_iindx[k]-j];+        db = base_d2 - referenceBPs2[my_iindx[i]-k+1] - referenceBPs2[my_iindx[k]-j];+        /* collect all contributing energies */+        if(!Q_M[ii-k+1]) continue;+        if(!Q_M1[jj+k]) continue;+        for(cnt1 = k_min_Q_M[ii-k+1];+            cnt1 <= k_max_Q_M[ii-k+1];+            cnt1++)+          for(cnt2 = l_min_Q_M[ii-k+1][cnt1];+              cnt2 <= l_max_Q_M[ii-k+1][cnt1];+              cnt2 += 2)+            for(cnt3 = k_min_Q_M1[jj+k];+                cnt3 <= k_max_Q_M1[jj+k];+                cnt3++)+              for(cnt4 = l_min_Q_M1[jj+k][cnt3];+                  cnt4 <= l_max_Q_M1[jj+k][cnt3];+                  cnt4 += 2)+                if(((cnt1 + cnt3 + da) > maxD1) || ((cnt2 + cnt4 + db) > maxD2)){+                  qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1[jj+k][cnt3][cnt4/2];+                  if (qt>=r) goto backtrack_ml_early_escape;+                }+      }+    }+    else{+      /* get total contribution */+      for (qt=0., k=i+1; k<j; k++){+        /* calculate introduced distance to reference structures */+        da = base_d1 - referenceBPs1[my_iindx[i]-k+1] - referenceBPs1[my_iindx[k]-j];+        db = base_d2 - referenceBPs2[my_iindx[i]-k+1] - referenceBPs2[my_iindx[k]-j];+        /* collect all contributing energies */+        if(d1 >= da && d2 >= db && Q_M[ii-k+1] && Q_M1[jj+k])+          for(cnt1 = k_min_Q_M[ii-k+1]; cnt1 <= MIN2(k_max_Q_M[ii-k+1], d1-da); cnt1++)+            for(cnt2 = l_min_Q_M[ii-k+1][cnt1]; cnt2 <= MIN2(l_max_Q_M[ii-k+1][cnt1], d2 - db); cnt2+=2)+              if((d1-cnt1-da >= k_min_Q_M1[jj+k]) && (d1-cnt1-da <= k_max_Q_M1[jj+k]))+                if((d2 - cnt2 - db >= l_min_Q_M1[jj+k][d1-da-cnt1]) && (d2 - cnt2 - db <= l_max_Q_M1[jj+k][d1-cnt1-da]))+                  qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1[jj+k][d1-da-cnt1][(d2-db-cnt2)/2];+      }+      r = vrna_urn() * qt;+      for (qt=0., k=i+1; k<j; k++) {+        /* calculate introduced distance to reference structures */+        da = base_d1 - referenceBPs1[my_iindx[i]-k+1] - referenceBPs1[my_iindx[k]-j];+        db = base_d2 - referenceBPs2[my_iindx[i]-k+1] - referenceBPs2[my_iindx[k]-j];+        /* collect all contributing energies */+        if(d1 >= da && d2 >= db && Q_M[ii-k+1] && Q_M1[jj+k])+          for(cnt1 = k_min_Q_M[ii-k+1]; cnt1 <= MIN2(k_max_Q_M[ii-k+1], d1-da); cnt1++)+            for(cnt2 = l_min_Q_M[ii-k+1][cnt1]; cnt2 <= MIN2(l_max_Q_M[ii-k+1][cnt1], d2 - db); cnt2+=2)+              if((d1-cnt1-da >= k_min_Q_M1[jj+k]) && (d1-cnt1-da <= k_max_Q_M1[jj+k]))+                if((d2 - cnt2 - db >= l_min_Q_M1[jj+k][d1-da-cnt1]) && (d2 - cnt2 - db <= l_max_Q_M1[jj+k][d1-cnt1-da])){+                  cnt3 = d1-da-cnt1;+                  cnt4 = d2-db-cnt2;+                  qt += Q_M[ii-k+1][cnt1][cnt2/2] * Q_M1[jj+k][cnt3][cnt4/2];+                  if (qt>=r) goto backtrack_ml_early_escape;+                }+      }+    }+    if (k>=j) vrna_message_error("backtrack failed, can't find split index ");++backtrack_ml_early_escape:++    backtrack_qm1(vc, pstruc, cnt3, cnt4, k, j);++    j = k-1;+    backtrack_qm(vc, pstruc, cnt1, cnt2, i, j);+  }+}++PRIVATE void+backtrack_qm1(vrna_fold_compound_t *vc,+              char *pstruc,+              int d1,+              int d2,+              unsigned int i,+              unsigned int j){++  /* i is paired to l, i<l<j; backtrack in qm1 to find l */+  FLT_OR_DBL      r, qt, *scale;+  unsigned int    maxD1, maxD2, da, db;+  unsigned int    *referenceBPs1, *referenceBPs2;+  char            *ptype;+  short           *S1;+  int             *my_iindx, *jindx, cnt1, cnt2;++  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  maxD1           = vc->maxD1;+  maxD2           = vc->maxD2;+  my_iindx        = vc->iindx;+  jindx           = vc->jindx;+  scale           = matrices->scale;+  ptype           = vc->ptype;+  S1              = vc->sequence_encoding;+  referenceBPs1   = vc->referenceBPs1;+  referenceBPs2   = vc->referenceBPs2;++  FLT_OR_DBL  ***Q_B, ***Q_M1, *Q_B_rem, *Q_M1_rem;+  int         *k_min_Q_M1, *k_max_Q_M1,*k_min_Q_B, *k_max_Q_B;+  int         **l_min_Q_M1, **l_max_Q_M1,**l_min_Q_B, **l_max_Q_B;++  Q_B = matrices->Q_B;+  k_min_Q_B = matrices->k_min_Q_B;+  k_max_Q_B = matrices->k_max_Q_B;+  l_min_Q_B = matrices->l_min_Q_B;+  l_max_Q_B = matrices->l_max_Q_B;++  Q_M1 = matrices->Q_M1;+  k_min_Q_M1 = matrices->k_min_Q_M1;+  k_max_Q_M1 = matrices->k_max_Q_M1;+  l_min_Q_M1 = matrices->l_min_Q_M1;+  l_max_Q_M1 = matrices->l_max_Q_M1;++  Q_B_rem   = matrices->Q_B_rem;+  Q_M1_rem  = matrices->Q_M1_rem;++  unsigned int ii, l;+  int type;++  r = 0.;++  /* find qm1 contribution */+  if(d1 == -1)+    r = vrna_urn() * Q_M1_rem[jindx[j]+i];+  else{+    if((d1 >= k_min_Q_M1[jindx[j]+i]) && (d1 <= k_max_Q_M1[jindx[j]+i]))+      if((d2 >= l_min_Q_M1[jindx[j]+i][d1]) && (d2 <= l_max_Q_M1[jindx[j]+i][d1]))+        r = vrna_urn() * Q_M1[jindx[j]+i][d1][d2/2];+  }+  if(r == 0.) vrna_message_error("backtrack_qm1@2Dpfold.c: backtracking failed\n");++  ii = my_iindx[i];+  for (qt=0., l=i+TURN+1; l<=j; l++) {+    type = ptype[jindx[l] + i];+    if (type){+      FLT_OR_DBL tmp = exp_E_MLstem(type, S1[i-1], S1[l+1], pf_params) * pow(pf_params->expMLbase, j-l) * scale[j-l];+      /* compute the introduced distance to reference structures */+      da = referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[i]-l];+      db = referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[i]-l];+      cnt1 = cnt2 = -1;+      if(d1 == -1){+        if(Q_B_rem[ii-l] != 0.){+          qt += Q_B_rem[ii-l] * tmp;+          if(qt >= r) goto backtrack_qm1_early_escape;+        }+        if(Q_B[ii-l])+          for(cnt1 = k_min_Q_B[ii-l];+              cnt1 <= k_max_Q_B[ii-l];+              cnt1++)+            for(cnt2 = l_min_Q_B[ii-l][cnt1];+                cnt2 <= l_max_Q_B[ii-l][cnt1];+                cnt2 += 2)+              if(((cnt1 + da) > maxD1) || ((cnt2 + db) > maxD2)){+                qt += Q_B[ii-l][cnt1][cnt2/2] * tmp;+                if(qt >= r) goto backtrack_qm1_early_escape;+              }+      }+      else{+        /* get energy contributions */+        if(d1 >= da && d2 >= db)+          if((d1 - da >= k_min_Q_B[ii-l]) && (d1 - da <= k_max_Q_B[ii-l]))+            if((d2 - db >= l_min_Q_B[ii-l][d1-da]) && (d2 - db <= l_max_Q_B[ii-l][d1-da])){+              cnt1 = d1 - da;+              cnt2 = d2 - db;+              qt += Q_B[ii-l][cnt1][cnt2/2] * tmp;+              if (qt>=r) goto backtrack_qm1_early_escape;+            }+      }+    }+  }+  if (l>j) vrna_message_error("backtrack failed in qm1");+backtrack_qm1_early_escape:++  backtrack(vc, pstruc, cnt1, cnt2, i,l);+}++PRIVATE void+backtrack_qm( vrna_fold_compound_t *vc,+              char *pstruc,+              int d1,+              int d2,+              unsigned int i,+              unsigned int j){++  /* divide multiloop into qm and qm1  */+  FLT_OR_DBL      r, *scale;+  unsigned int    maxD1, maxD2, da, db, da2, db2;+  unsigned int    *referenceBPs1, *referenceBPs2;+  int             *my_iindx, *jindx, cnt1, cnt2, cnt3, cnt4;++  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */+  vrna_md_t         *md;+  vrna_mx_pf_t      *matrices;++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  matrices          = vc->exp_matrices;+  maxD1       = vc->maxD1;+  maxD2       = vc->maxD2;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  scale       = matrices->scale;+  referenceBPs1  = vc->referenceBPs1;+  referenceBPs2  = vc->referenceBPs2;++  FLT_OR_DBL  ***Q_M, ***Q_M1, *Q_M_rem, *Q_M1_rem;+  int         *k_min_Q_M, *k_max_Q_M,*k_min_Q_M1, *k_max_Q_M1;+  int         **l_min_Q_M, **l_max_Q_M,**l_min_Q_M1, **l_max_Q_M1;++  Q_M = matrices->Q_M;+  k_min_Q_M = matrices->k_min_Q_M;+  k_max_Q_M = matrices->k_max_Q_M;+  l_min_Q_M = matrices->l_min_Q_M;+  l_max_Q_M = matrices->l_max_Q_M;++  Q_M1 = matrices->Q_M1;+  k_min_Q_M1 = matrices->k_min_Q_M1;+  k_max_Q_M1 = matrices->k_max_Q_M1;+  l_min_Q_M1 = matrices->l_min_Q_M1;+  l_max_Q_M1 = matrices->l_max_Q_M1;+  Q_M_rem   = matrices->Q_M_rem;+  Q_M1_rem  = matrices->Q_M1_rem;++  double qmt = 0;+  unsigned int k;+  while(j>i){+    /* now backtrack  [i ... j] in qm[] */++    /* find qm contribution */+    if(d1 == -1)+      r = vrna_urn() * Q_M_rem[my_iindx[i]-j];+    else{+      if(Q_M[my_iindx[i]-j])+        if((d1 >= k_min_Q_M[my_iindx[i]-j]) && (d1 <= k_max_Q_M[my_iindx[i]-j]))+          if((d2 >= l_min_Q_M[my_iindx[i]-j][d1]) && (d2 <= l_max_Q_M[my_iindx[i]-j][d1]))+            r = vrna_urn() * Q_M[my_iindx[i]-j][d1][d2/2];+    }+    if(r == 0.) vrna_message_error("backtrack_qm@2Dpfold.c: backtracking failed in finding qm contribution\n");++    qmt = 0.;+    if(d1 == -1){+      if(Q_M1_rem[jindx[j]+i] != 0.){+        qmt += Q_M1_rem[jindx[j]+i];+        if(qmt >= r){+          backtrack_qm1(vc, pstruc, d1, d2, i, j);+          return;+        }+      }++      for(k=i+1; k<=j; k++){+        FLT_OR_DBL tmp = pow(pf_params->expMLbase, k-i) * scale[k-i];+        if(Q_M1_rem[jindx[j]+k] != 0.){+          qmt += Q_M1_rem[jindx[j]+k] * tmp;+          if(qmt >= r){+            backtrack_qm1(vc, pstruc, d1, d2, k, j);+            return;+          }+        }+        da2 = referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[k]-j];+        db2 = referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[k]-j];+        if(Q_M1[jindx[j]+k])+          for(cnt1 = k_min_Q_M1[jindx[j]+k];+              cnt1 <= k_max_Q_M1[jindx[j]+k];+              cnt1++)+            for(cnt2 = l_min_Q_M1[jindx[j]+k][cnt1];+                cnt2 <= l_max_Q_M1[jindx[j]+k][cnt1];+                cnt2 += 2)+              if(((cnt1 + da2) > maxD1) || ((cnt2 + db2) > maxD2)){+                qmt += Q_M1[jindx[j]+k][cnt1][cnt2/2] * tmp;+                if(qmt >= r){+                  backtrack_qm1(vc, pstruc, cnt1, cnt2, k, j);+                  return;+                }+              }++        da = da2 - referenceBPs1[my_iindx[i]-k+1];+        db = db2 - referenceBPs2[my_iindx[i]-k+1];++        cnt1 = cnt2 = cnt3 = cnt4 = -1;+        if(Q_M_rem[my_iindx[i]-k+1] != 0.){+          if(Q_M1_rem[jindx[j]+k] != 0.){+            qmt += Q_M_rem[my_iindx[i]-k+1] * Q_M1_rem[jindx[j]+k];+            if(qmt >= r) goto backtrack_qm_early_escape;+          }+          if(Q_M1[jindx[j]+k])+            for(cnt3 = k_min_Q_M1[jindx[j]+k];+                cnt3 <= k_max_Q_M1[jindx[j]+k];+                cnt3++)+              for(cnt4 = l_min_Q_M1[jindx[j]+k][cnt3];+                  cnt4 <= l_max_Q_M1[jindx[j]+k][cnt3];+                  cnt4 += 2){+                qmt += Q_M_rem[my_iindx[i]-k+1] * Q_M1[jindx[j]+k][cnt3][cnt4/2];+                if(qmt >= r) goto backtrack_qm_early_escape;+              }+        }+        if(Q_M1_rem[jindx[j]+k] != 0.){+          cnt3 = cnt4 = -1;+          if(Q_M[my_iindx[i]-k+1])+            for(cnt1 = k_min_Q_M[my_iindx[i]-k+1];+                cnt1 <= k_max_Q_M[my_iindx[i]-k+1];+                cnt1++)+              for(cnt2 = l_min_Q_M[my_iindx[i]-k+1][cnt1];+                  cnt2 <= l_max_Q_M[my_iindx[i]-k+1][cnt1];+                  cnt2 += 2){+                qmt += Q_M[my_iindx[i]-k+1][cnt1][cnt2/2] * Q_M1_rem[jindx[j]+k];+                if(qmt >= r) goto backtrack_qm_early_escape;+              }+        }++        if(!Q_M[my_iindx[i]-k+1]) continue;+        if(!Q_M1[jindx[j]+k]) continue;+        for(cnt1 = k_min_Q_M[my_iindx[i]-k+1];+            cnt1 <= k_max_Q_M[my_iindx[i]-k+1];+            cnt1++)+          for(cnt2 = l_min_Q_M[my_iindx[i]-k+1][cnt1];+              cnt2 <= l_max_Q_M[my_iindx[i]-k+1][cnt1];+              cnt2 += 2)+            for(cnt3 = k_min_Q_M1[jindx[j]+k];+                cnt3 <= k_max_Q_M1[jindx[j]+k];+                cnt3++)+              for(cnt4 = l_min_Q_M1[jindx[j]+k][cnt3];+                  cnt4 <= l_max_Q_M1[jindx[j]+k][cnt3];+                  cnt4 += 2)+                if(((cnt1 + cnt3 + da) > maxD1) || ((cnt2 + cnt4 + db) > maxD2)){+                  qmt += Q_M[my_iindx[i]-k+1][cnt1][cnt2/2] * Q_M1[jindx[j]+k][cnt3][cnt4/2];+                  if(qmt >= r) goto backtrack_qm_early_escape;+                }+      }++    }+    else{+      /* find corresponding qm1 contribution */+      if(Q_M1[jindx[j]+i])+        if((d1 >= k_min_Q_M1[jindx[j]+i]) && (d1 <= k_max_Q_M1[jindx[j]+i]))+          if((d2 >= l_min_Q_M1[jindx[j]+i][d1]) && (d2 <= l_max_Q_M1[jindx[j]+i][d1])){+            qmt = Q_M1[jindx[j]+i][d1][d2/2];+          }++      k=i;+      if(qmt<r){+        for(k=i+1; k<=j; k++){+          /* calculate introduced distancies to reference structures */+          da2 = referenceBPs1[my_iindx[i]-j] - referenceBPs1[my_iindx[k]-j];+          db2 = referenceBPs2[my_iindx[i]-j] - referenceBPs2[my_iindx[k]-j];+          da = da2 - referenceBPs1[my_iindx[i]-k+1];+          db = db2 - referenceBPs2[my_iindx[i]-k+1];+++          FLT_OR_DBL tmp = pow(pf_params->expMLbase, k-i) * scale[k-i];++          /* collect unpaired + qm1 contributions */+          if(d1 >= da2 && d2 >= db2)+            if((d1 - da2 >= k_min_Q_M1[jindx[j]+k]) && (d1 - da2 <= k_max_Q_M1[jindx[j]+k]))+              if((d2 - db2 >= l_min_Q_M1[jindx[j]+k][d1-da2]) && (d2 - db2 <= l_max_Q_M1[jindx[j]+k][d1-da2])){+                cnt3 = d1-da2;+                cnt4 = d2-db2;+                qmt += Q_M1[jindx[j]+k][cnt3][cnt4/2] * tmp;+                if(qmt >= r){+                  backtrack_qm1(vc, pstruc, cnt3, cnt4, k, j);+                  return;+                }+              }++          /* collect qm + qm1 contributions */+          if(d1 >= da && d2 >= db && Q_M[my_iindx[i]-k+1] && Q_M1[jindx[j]+k])+            for(cnt1 = k_min_Q_M[my_iindx[i]-k+1]; cnt1 <= MIN2(k_max_Q_M[my_iindx[i]-k+1], d1 - da); cnt1++)+              for(cnt2 = l_min_Q_M[my_iindx[i]-k+1][cnt1]; cnt2 <= MIN2(l_max_Q_M[my_iindx[i]-k+1][cnt1], d2 - db); cnt2+=2)+                if((d1 - da - cnt1 >= k_min_Q_M1[jindx[j]+k]) && (d1 - da - cnt1 <= k_max_Q_M1[jindx[j]+k]))+                  if((d2 - db - cnt2 >= l_min_Q_M1[jindx[j]+k][d1-da-cnt1]) && (d2 - db - cnt2 <= l_max_Q_M1[jindx[j]+k][d1-da-cnt1])){+                    cnt3 = d1 - da - cnt1;+                    cnt4 = d2 - db - cnt2;+                    qmt += Q_M[my_iindx[i]-k+1][cnt1][cnt2/2] * Q_M1[jindx[j]+k][cnt3][cnt4/2];+                    if(qmt >= r) goto backtrack_qm_early_escape;+                  }+        }+      }+      else{+        backtrack_qm1(vc, pstruc, d1, d2, k, j);+        return;+      }+    }++    if(k>j) vrna_message_error("backtrack_qm@2Dpfold.c: backtrack failed in qm");++backtrack_qm_early_escape:++    backtrack_qm1(vc, pstruc, cnt3, cnt4, k, j);++    if(k<i+TURN) break; /* no more pairs */++    d1 = cnt1;+    d2 = cnt2;+++    if(d1 == referenceBPs1[my_iindx[i]-k+1] && d2 == referenceBPs2[my_iindx[i]-k+1]){+      /* is interval [i,k] totally unpaired? */+      FLT_OR_DBL tmp = pow(pf_params->expMLbase, k-i) * scale[k-i];+      r = vrna_urn() * (Q_M[my_iindx[i]-k+1][d1][d2/2] + tmp);+      if(tmp >= r) return; /* no more pairs */+    }+    j = k-1;+  }+}+++++PRIVATE void  adjustArrayBoundaries(FLT_OR_DBL ***array,+                                    int *k_min, int *k_max,+                                    int **l_min, int **l_max,+                                    int k_min_post, int k_max_post,+                                    int *l_min_post, int *l_max_post){++  int cnt1;+  int k_diff_pre  = k_min_post - *k_min;+  int mem_size    = k_max_post - k_min_post + 1;++  if(k_min_post < INF){+    /* free all the unused memory behind actual data */+    for(cnt1 = k_max_post + 1; cnt1 <= *k_max; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }++    /* free unused memory before actual data */+    for(cnt1 = *k_min; cnt1 < k_min_post; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }+    /* move data to front and thereby eliminating unused memory in front of actual data */+    if(k_diff_pre > 0){+      memmove((FLT_OR_DBL **)(*array),((FLT_OR_DBL **)(*array)) + k_diff_pre, sizeof(FLT_OR_DBL *) * mem_size);+      memmove((int *) (*l_min),((int *) (*l_min)) + k_diff_pre, sizeof(int)   * mem_size);+      memmove((int *) (*l_max),((int *) (*l_max)) + k_diff_pre, sizeof(int)   * mem_size);+    }++    /* reallocating memory to actual size used */+    *array  +=  *k_min;+    *array  =   (FLT_OR_DBL **)realloc(*array, sizeof(FLT_OR_DBL *) * mem_size);+    *array  -=  k_min_post;++    *l_min  +=  *k_min;+    *l_min  =   (int *)realloc(*l_min, sizeof(int) * mem_size);+    *l_min  -=   k_min_post;++    *l_max  +=  *k_min;+    *l_max  =   (int *)realloc(*l_max, sizeof(int) * mem_size);+    *l_max  -=  k_min_post;+++    for(cnt1 = k_min_post; cnt1 <= k_max_post; cnt1++){+      if(l_min_post[cnt1] < INF){+        /* new memsize */+        mem_size        = (l_max_post[cnt1] - l_min_post[cnt1] + 1)/2 + 1;+        /* reshift the pointer */+        (*array)[cnt1]  += (*l_min)[cnt1]/2;++        int shift       = (l_min_post[cnt1]%2 == (*l_min)[cnt1]%2) ? 0 : 1;+        /* eliminate unused memory in front of actual data */+        unsigned int    start = (l_min_post[cnt1] - (*l_min)[cnt1])/2 + shift;+        if(start > 0)+          memmove((FLT_OR_DBL *)((*array)[cnt1]), (FLT_OR_DBL *)((*array)[cnt1])+start, sizeof(FLT_OR_DBL) * mem_size);+        (*array)[cnt1]  = (FLT_OR_DBL *) realloc((*array)[cnt1], sizeof(FLT_OR_DBL) * mem_size);++        (*array)[cnt1]  -= l_min_post[cnt1]/2;+      }+      else{+        /* free according memory */+        (*array)[cnt1] += (*l_min)[cnt1]/2;+        free((*array)[cnt1]);+      }++      (*l_min)[cnt1] = l_min_post[cnt1];+      (*l_max)[cnt1] = l_max_post[cnt1];+    }+  }+  else{+    /* we have to free all unused memory */+    for(cnt1 = *k_min; cnt1 <= *k_max; cnt1++){+      (*array)[cnt1] += (*l_min)[cnt1]/2;+      free((*array)[cnt1]);+    }+    (*l_min) += *k_min;+    (*l_max) += *k_min;+    free(*l_min);+    free(*l_max);+    (*array) += *k_min;+    free(*array);+    *array = NULL;+  }++  l_min_post  += *k_min;+  l_max_post  += *k_min;+  *k_min      = k_min_post;+  *k_max      = k_max_post;++  free(l_min_post);+  free(l_max_post);+}+++PRIVATE INLINE void preparePosteriorBoundaries(int size, int shift, int *min_k, int *max_k, int **min_l, int **max_l){+  int i;+  *min_k  = INF;+  *max_k  = 0;++  *min_l  = (int *)vrna_alloc(sizeof(int) * size);+  *max_l  = (int *)vrna_alloc(sizeof(int) * size);++  for(i = 0; i < size; i++){+    (*min_l)[i] = INF;+    (*max_l)[i] = 0;+  }++  *min_l  -= shift;+  *max_l  -= shift;+}++PRIVATE INLINE void updatePosteriorBoundaries(int d1, int d2, int *min_k, int *max_k, int **min_l, int **max_l){+  (*min_l)[d1]  = MIN2((*min_l)[d1], d2);+  (*max_l)[d1]  = MAX2((*max_l)[d1], d2);+  *min_k        = MIN2(*min_k, d1);+  *max_k        = MAX2(*max_k, d1);+}++PRIVATE INLINE  void  prepareBoundaries(int min_k_pre, int max_k_pre, int min_l_pre, int max_l_pre, int bpdist, int *min_k, int *max_k, int **min_l, int **max_l){+  int cnt;+  int mem = max_k_pre - min_k_pre + 1;++  *min_k  = min_k_pre;+  *max_k  = max_k_pre;+  *min_l  = (int *) vrna_alloc(sizeof(int) * mem);+  *max_l  = (int *) vrna_alloc(sizeof(int) * mem);++  *min_l  -= min_k_pre;+  *max_l  -= min_k_pre;++  /* for each k guess the according minimum l*/+  for(cnt = min_k_pre; cnt <= max_k_pre; cnt++){+    (*min_l)[cnt] = min_l_pre;+    (*max_l)[cnt] = max_l_pre;+    while((*min_l)[cnt] + cnt < bpdist) (*min_l)[cnt]++;+    if((bpdist % 2) != (((*min_l)[cnt] + cnt) % 2)) (*min_l)[cnt]++;+  }+}++PRIVATE INLINE  void  prepareArray(FLT_OR_DBL ***array, int min_k, int max_k, int *min_l, int *max_l){+  int i, mem;+  *array  = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (max_k - min_k + 1));+  *array  -= min_k;++  for(i = min_k; i <= max_k; i++){+    mem         = (max_l[i] - min_l[i] + 1)/2 + 1;+    (*array)[i] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * mem);+    (*array)[i] -= min_l[i]/2;+  }+}++/*+#################################+# DEPRECATED FUNCTIONS BELOW    #+#################################+*/+PRIVATE void+crosslink(TwoDpfold_vars *vars){++  vrna_fold_compound_t  *c;+  vrna_mx_pf_t        *m;++  c                     = vars->compatibility;+  m                     = c->exp_matrices;++  vars->sequence      = c->sequence;+  vars->seq_length    = c->length;+  vars->reference_pt1 = c->reference_pt1;+  vars->reference_pt2 = c->reference_pt2;+  vars->referenceBPs1 = c->referenceBPs1;+  vars->referenceBPs2 = c->referenceBPs2;+  vars->mm1           = c->mm1;+  vars->mm2           = c->mm2;+  vars->bpdist        = c->bpdist;+  vars->dangles       = c->exp_params->model_details.dangles;+  vars->circ          = c->exp_params->model_details.circ;+  vars->temperature   = c->exp_params->model_details.temperature;+  vars->init_temp     = c->exp_params->model_details.temperature;+  vars->pf_scale      = c->exp_params->pf_scale;+  vars->pf_params     = c->exp_params;++  vars->scale         = m->scale;+  vars->ptype         = c->ptype_pf_compat;+  vars->S             = c->sequence_encoding2;+  vars->S1            = c->sequence_encoding;++  vars->jindx         = c->jindx;+  vars->my_iindx      = c->iindx;+  vars->maxD1         = c->maxD1;+  vars->maxD2         = c->maxD2;++  vars->Q                = m->Q;+  vars->l_min_values     = m->l_min_Q;+  vars->l_max_values     = m->l_max_Q;+  vars->k_min_values     = m->k_min_Q;+  vars->k_max_values     = m->k_max_Q;++  vars->Q_B              = m->Q_B;+  vars->l_min_values_b   = m->l_min_Q_B;+  vars->l_max_values_b   = m->l_max_Q_B;+  vars->k_min_values_b   = m->k_min_Q_B;+  vars->k_max_values_b   = m->k_max_Q_B;++  vars->Q_M              = m->Q_M;+  vars->l_min_values_m   = m->l_min_Q_M;+  vars->l_max_values_m   = m->l_max_Q_M;+  vars->k_min_values_m   = m->k_min_Q_M;+  vars->k_max_values_m   = m->k_max_Q_M;++  vars->Q_M1             = m->Q_M1;+  vars->l_min_values_m1  = m->l_min_Q_M1;+  vars->l_max_values_m1  = m->l_max_Q_M1;+  vars->k_min_values_m1  = m->k_min_Q_M1;+  vars->k_max_values_m1  = m->k_max_Q_M1;++  vars->Q_M2_rem         = m->Q_M2_rem;+  vars->Q_M2             = m->Q_M2;+  vars->l_min_values_m2  = m->l_min_Q_M2;+  vars->l_max_values_m2  = m->l_max_Q_M2;+  vars->k_min_values_m2  = m->k_min_Q_M2;+  vars->k_max_values_m2  = m->k_max_Q_M2;++  vars->Q_c               = m->Q_c;+  vars->Q_cH              = m->Q_cH;+  vars->Q_cI              = m->Q_cI;+  vars->Q_cM              = m->Q_cM;+  vars->Q_c_rem           = m->Q_c_rem;+  vars->Q_cH_rem          = m->Q_cH_rem;+  vars->Q_cI_rem          = m->Q_cI_rem;+  vars->Q_cM_rem          = m->Q_cM_rem;++  vars->Q_rem             = m->Q_rem;+  vars->Q_B_rem           = m->Q_B_rem;+  vars->Q_M_rem           = m->Q_M_rem;+  vars->Q_M1_rem          = m->Q_M1_rem;+}++PUBLIC char *+TwoDpfold_pbacktrack( TwoDpfold_vars *vars,+                      int d1,+                      int d2){++  return vrna_pbacktrack_TwoD(vars->compatibility, d1, d2);+}++PUBLIC char *+TwoDpfold_pbacktrack5(TwoDpfold_vars *vars,+                      int d1,+                      int d2,+                      unsigned int length){++  return vrna_pbacktrack5_TwoD(vars->compatibility, d1, d2, length);+}++PUBLIC TwoDpfold_vars *+get_TwoDpfold_variables(const char *seq,+                        const char *structure1,+                        char *structure2,+                        int circ){++  vrna_md_t           md;+  TwoDpfold_vars      *vars;+  vrna_fold_compound_t  *c;+  vrna_mx_mfe_t       *m;++  set_model_details(&md);+  md.circ = circ;++  vars = (TwoDpfold_vars *)malloc(sizeof(TwoDpfold_vars));+  vars->compatibility = vrna_fold_compound_TwoD(seq, structure1, structure2, &md, VRNA_OPTION_PF);++  crosslink(vars);++  return vars;+}++PUBLIC void+destroy_TwoDpfold_variables(TwoDpfold_vars *vars){++  if(vars == NULL) return;++  vrna_fold_compound_free(vars->compatibility);++  free(vars);+}++vrna_sol_TwoD_pf_t *+TwoDpfoldList(TwoDpfold_vars *vars,+              int distance1,+              int distance2){++  vrna_sol_TwoD_pf_t *sol;++  sol = vrna_pf_TwoD(vars->compatibility, distance1, distance2);++  crosslink(vars);++  return sol;+}
+ C/ViennaRNA/2Dpfold.h view
@@ -0,0 +1,399 @@+#ifndef VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H+#define VIENNA_RNA_PACKAGE_TWO_D_PF_FOLD_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file 2Dpfold.h+ *  @ingroup kl_neighborhood+ *  @brief Partition function implementations for base pair distance classes+ *+ */++/**+ *  @addtogroup kl_neighborhood_pf+ *  @brief Compute the partition function and stochastically sample secondary structures for a partitioning of+ *  the secondary structure space according to the base pair distance to two fixed reference structures+ *+ *  @{+ *  @ingroup  kl_neighborhood_pf+ */++#include <ViennaRNA/data_structures.h>++/**+ *  @brief Solution element returned from vrna_pf_TwoD()+ *+ *  This element contains the partition function for the appropriate+ *  kappa (k), lambda (l) neighborhood+ *  The datastructure contains two integer attributes 'k' and 'l'+ *  as well as an attribute 'q' of type #FLT_OR_DBL+ *+ *  A value of #INF in k denotes the end of a list+ *+ *  @see  vrna_pf_TwoD()+ */+typedef struct vrna_sol_TwoD_pf_t{+  int k;          /**<  @brief  Distance to first reference */+  int l;          /**<  @brief  Distance to second reference */+  FLT_OR_DBL  q;  /**<  @brief  partition function */+} vrna_sol_TwoD_pf_t;++/**+ * @brief Compute the partition function for all distance classes+ *+ * This function computes the partition functions for all distance classes+ * according the two reference structures specified in the datastructure 'vars'.+ * Similar to vrna_mfe_TwoD() the arguments maxDistance1 and maxDistance2 specify+ * the maximum distance to both reference structures. A value of '-1' in either of+ * them makes the appropriate distance restrictionless, i.e. all basepair distancies+ * to the reference are taken into account during computation.+ * In case there is a restriction, the returned solution contains an entry where+ * the attribute k=l=-1 contains the partition function for all structures exceeding+ * the restriction.+ * A value of #INF in the attribute 'k' of the returned list denotes the end of the list+ *+ * @see vrna_fold_compound_TwoD(), vrna_fold_compound_free(), #vrna_fold_compound+ *      #vrna_sol_TwoD_pf_t+ *+ * @param vc            The datastructure containing all necessary folding attributes and matrices+ * @param maxDistance1  The maximum basepair distance to reference1 (may be -1)+ * @param maxDistance2  The maximum basepair distance to reference2 (may be -1)+ * @returns             A list of partition funtions for the corresponding distance classes+ */+vrna_sol_TwoD_pf_t  *+vrna_pf_TwoD(vrna_fold_compound_t *vc,+                  int maxDistance1,+                  int maxDistance2);++/** @} */ /* End of group kl_neighborhood_pf */++/**+ *  @addtogroup kl_neighborhood_stochbt+ *  @brief Contains functions related to stochastic backtracking from a specified distance class+ *  @{+ */++/**+ *  @brief Sample secondary structure representatives from a set of distance classes according to their + *  Boltzmann probability+ *+ *  If the argument 'd1' is set to '-1', the structure will be backtracked in the distance class+ *  where all structures exceeding the maximum basepair distance to either of the references reside.+ *+ *  @pre      The argument 'vars' must contain precalculated partition function matrices,+ *            i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!+ *+ *  @see      vrna_pf_TwoD()+ *+ *  @param[inout]  vc The #vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices+ *  @param[in]  d1    The distance to reference1 (may be -1)+ *  @param[in]  d2    The distance to reference2+ *  @returns    A sampled secondary structure in dot-bracket notation+ */+char *+vrna_pbacktrack_TwoD( vrna_fold_compound_t *vc,+                      int d1,+                      int d2);++/**+ * @brief Sample secondary structure representatives with a specified length from a set of distance classes according to their + *  Boltzmann probability+ *+ * This function does essentially the same as vrna_pbacktrack_TwoD() with the only difference that partial structures,+ * i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked+ *+ * @note      This function does not work (since it makes no sense) for circular RNA sequences!+ * @pre       The argument 'vars' must contain precalculated partition function matrices,+ *            i.e. a call to vrna_pf_TwoD() preceding this function is mandatory!+ *+ * @see       vrna_pbacktrack_TwoD(), vrna_pf_TwoD()+ *+ *  @param[inout] vc    The #vrna_fold_compound_t datastructure containing all necessary folding attributes and matrices+ *  @param[in]  d1      The distance to reference1 (may be -1)+ *  @param[in]  d2      The distance to reference2+ *  @param[in]  length  The length of the structure beginning from the 5' end+ *  @returns            A sampled secondary structure in dot-bracket notation+ */+char *+vrna_pbacktrack5_TwoD(vrna_fold_compound_t *vc,+                      int d1,+                      int d2,+                      unsigned int length);++/**+ *  @}+ */ /* End of group kl_neighborhood_stochbt */+++#ifdef  VRNA_BACKWARD_COMPAT++#define TwoDpfold_solution       vrna_sol_TwoD_pf_t         /* restore compatibility of struct rename */++/**+ *  @brief  Variables compound for 2Dfold partition function folding+ *+ *  @deprecated This data structure will be removed from the library soon!+ *              Use #vrna_fold_compound_t and the corresponding functions vrna_fold_compound_TwoD(),+ *              vrna_pf_TwoD(), and vrna_fold_compound_free() instead!+ */+typedef struct{++  unsigned int    alloc;+  char            *ptype;         /**<  @brief  Precomputed array of pair types */+  char            *sequence;      /**<  @brief  The input sequence  */+  short           *S, *S1;        /**<  @brief  The input sequences in numeric form */+  unsigned int    maxD1;          /**<  @brief  Maximum allowed base pair distance to first reference */+  unsigned int    maxD2;          /**<  @brief  Maximum allowed base pair distance to second reference */++  double          temperature;    /* temperature in last call to scale_pf_params */+  double          init_temp;      /* temperature in last call to scale_pf_params */+  FLT_OR_DBL      *scale;+  FLT_OR_DBL      pf_scale;+  vrna_exp_param_t  *pf_params;     /* holds all [unscaled] pf parameters */++  int             *my_iindx;      /**<  @brief  Index for moving in quadratic distancy dimensions */+  int             *jindx;         /**<  @brief  Index for moving in the triangular matrix qm1 */++  short           *reference_pt1;+  short           *reference_pt2;++  unsigned int    *referenceBPs1; /**<  @brief  Matrix containing number of basepairs of reference structure1 in interval [i,j] */+  unsigned int    *referenceBPs2; /**<  @brief  Matrix containing number of basepairs of reference structure2 in interval [i,j] */+  unsigned int    *bpdist;        /**<  @brief  Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */++  unsigned int    *mm1;           /**<  @brief  Maximum matching matrix, reference struct 1 disallowed */+  unsigned int    *mm2;           /**<  @brief  Maximum matching matrix, reference struct 2 disallowed */++  int             circ;+  int             dangles;+  unsigned int    seq_length;++  FLT_OR_DBL      ***Q;+  FLT_OR_DBL      ***Q_B;+  FLT_OR_DBL      ***Q_M;+  FLT_OR_DBL      ***Q_M1;+  FLT_OR_DBL      ***Q_M2;++  FLT_OR_DBL      **Q_c;+  FLT_OR_DBL      **Q_cH;+  FLT_OR_DBL      **Q_cI;+  FLT_OR_DBL      **Q_cM;++  int             **l_min_values;+  int             **l_max_values;+  int             *k_min_values;+  int             *k_max_values;++  int             **l_min_values_b;+  int             **l_max_values_b;+  int             *k_min_values_b;+  int             *k_max_values_b;++  int             **l_min_values_m;+  int             **l_max_values_m;+  int             *k_min_values_m;+  int             *k_max_values_m;++  int             **l_min_values_m1;+  int             **l_max_values_m1;+  int             *k_min_values_m1;+  int             *k_max_values_m1;++  int             **l_min_values_m2;+  int             **l_max_values_m2;+  int             *k_min_values_m2;+  int             *k_max_values_m2;++  int             *l_min_values_qc;+  int             *l_max_values_qc;+  int             k_min_values_qc;+  int             k_max_values_qc;++  int             *l_min_values_qcH;+  int             *l_max_values_qcH;+  int             k_min_values_qcH;+  int             k_max_values_qcH;++  int             *l_min_values_qcI;+  int             *l_max_values_qcI;+  int             k_min_values_qcI;+  int             k_max_values_qcI;++  int             *l_min_values_qcM;+  int             *l_max_values_qcM;+  int             k_min_values_qcM;+  int             k_max_values_qcM;++  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */+  FLT_OR_DBL      *Q_rem;+  FLT_OR_DBL      *Q_B_rem;+  FLT_OR_DBL      *Q_M_rem;+  FLT_OR_DBL      *Q_M1_rem;+  FLT_OR_DBL      *Q_M2_rem;++  FLT_OR_DBL      Q_c_rem;+  FLT_OR_DBL      Q_cH_rem;+  FLT_OR_DBL      Q_cI_rem;+  FLT_OR_DBL      Q_cM_rem;++  vrna_fold_compound_t *compatibility;+} TwoDpfold_vars;++/**+ * @brief Get a datastructure containing all necessary attributes and global folding switches+ *+ * This function prepares all necessary attributes and matrices etc which are needed for a call+ * of TwoDpfold() .+ * A snapshot of all current global model switches (dangles, temperature and so on) is done and+ * stored in the returned datastructure. Additionally, all matrices that will hold the partition+ * function values are prepared.+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!+ *+ * @param seq         the RNA sequence in uppercase format with letters from the alphabet {AUCG}+ * @param structure1  the first reference structure in dot-bracket notation+ * @param structure2  the second reference structure in dot-bracket notation+ * @param circ        a switch indicating if the sequence is linear (0) or circular (1)+ * @returns           the datastructure containing all necessary partition function attributes+ */+DEPRECATED(TwoDpfold_vars  *+get_TwoDpfold_variables(const char *seq,+                        const char *structure1,+                        char *structure2,+                        int circ));++/**+ * @brief Free all memory occupied by a TwoDpfold_vars datastructure+ *+ * This function free's all memory occupied by a datastructure obtained from from+ * get_TwoDpfold_variabless() or get_TwoDpfold_variables_from_MFE()+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!+ *+ * @see get_TwoDpfold_variables(), get_TwoDpfold_variables_from_MFE()+ *+ * @param vars   the datastructure to be free'd+ */+DEPRECATED(void +destroy_TwoDpfold_variables(TwoDpfold_vars *vars));++/**+ * @brief Compute the partition function for all distance classes+ *+ * This function computes the partition functions for all distance classes+ * according the two reference structures specified in the datastructure 'vars'.+ * Similar to TwoDfold() the arguments maxDistance1 and maxDistance2 specify+ * the maximum distance to both reference structures. A value of '-1' in either of+ * them makes the appropriate distance restrictionless, i.e. all basepair distancies+ * to the reference are taken into account during computation.+ * In case there is a restriction, the returned solution contains an entry where+ * the attribute k=l=-1 contains the partition function for all structures exceeding+ * the restriction.+ * A values of #INF in the attribute 'k' of the returned list denotes the end of the list+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_pf_TwoD(), and vrna_fold_compound_free() instead!+ *+ * @see get_TwoDpfold_variables(), destroy_TwoDpfold_variables(), #vrna_sol_TwoD_pf_t+ *+ * @param vars          the datastructure containing all necessary folding attributes and matrices+ * @param maxDistance1  the maximum basepair distance to reference1 (may be -1)+ * @param maxDistance2  the maximum basepair distance to reference2 (may be -1)+ * @returns             a list of partition funtions for the appropriate distance classes+ */+DEPRECATED(TwoDpfold_solution  *+TwoDpfoldList(TwoDpfold_vars *vars,+              int maxDistance1,+              int maxDistance2));++/**+ *  @brief Sample secondary structure representatives from a set of distance classes according to their + *  Boltzmann probability+ *+ *  If the argument 'd1' is set to '-1', the structure will be backtracked in the distance class+ *  where all structures exceeding the maximum basepair distance to either of the references reside.+ *+ *  @pre      The argument 'vars' must contain precalculated partition function matrices,+ *            i.e. a call to TwoDpfold() preceding this function is mandatory!+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack_TwoD(), and+ *              vrna_fold_compound_free() instead!+ *+ *  @see      TwoDpfold()+ *+ *  @param[in]  vars  the datastructure containing all necessary folding attributes and matrices+ *  @param[in]  d1    the distance to reference1 (may be -1)+ *  @param[in]  d2    the distance to reference2+ *  @returns    A sampled secondary structure in dot-bracket notation+ */+DEPRECATED(char *+TwoDpfold_pbacktrack( TwoDpfold_vars *vars,+                      int d1,+                      int d2));++/**+ * @brief Sample secondary structure representatives with a specified length from a set of distance classes according to their + *  Boltzmann probability+ *+ * This function does essentially the same as TwoDpfold_pbacktrack() with the only difference that partial structures,+ * i.e. structures beginning from the 5' end with a specified length of the sequence, are backtracked+ *+ * @note      This function does not work (since it makes no sense) for circular RNA sequences!+ * @pre       The argument 'vars' must contain precalculated partition function matrices,+ *            i.e. a call to TwoDpfold() preceding this function is mandatory!+ *+ *  @deprecated Use the new API that relies on #vrna_fold_compound_t and the corresponding functions+ *              vrna_fold_compound_TwoD(), vrna_pf_TwoD(), vrna_pbacktrack5_TwoD(), and+ *              vrna_fold_compound_free() instead!+ *+ * @see       TwoDpfold_pbacktrack(), TwoDpfold()+ *+ *  @param[in]  vars    the datastructure containing all necessary folding attributes and matrices+ *  @param[in]  d1      the distance to reference1 (may be -1)+ *  @param[in]  d2      the distance to reference2+ *  @param[in]  length  the length of the structure beginning from the 5' end+ *  @returns    A sampled secondary structure in dot-bracket notation+ */+DEPRECATED(char *+TwoDpfold_pbacktrack5(TwoDpfold_vars *vars,+                      int d1,+                      int d2,+                      unsigned int length));++/**+ * @brief+ *+ *+ */+DEPRECATED(FLT_OR_DBL          **TwoDpfold(TwoDpfold_vars *our_variables,+                                int maxDistance1,+                                int maxDistance2));++/**+ * @brief+ *+ *+ */+DEPRECATED(FLT_OR_DBL          **TwoDpfold_circ(+                                TwoDpfold_vars *our_variables,+                                int maxDistance1,+                                int maxDistance2));++#endif++#endif
+ C/ViennaRNA/LPfold.c view
@@ -0,0 +1,1373 @@+/*+  local pair probabilities for RNA secondary structures++  Stephan Bernhart, Ivo L Hofacker+  Vienna RNA package+*/+/*+  todo: compute energy z-score for each window++*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/PS_dot.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/LPfold.h"+#include "ViennaRNA/Lfold.h"++#ifdef _OPENMP+#include <omp.h>+#endif+++#define ISOLATED  256.0++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++PRIVATE float       cutoff;+PRIVATE int         num_p=0; /* for counting basepairs in pairlist pl, can actually be moved into pfl_fold */+PRIVATE FLT_OR_DBL  *expMLbase=NULL;+PRIVATE FLT_OR_DBL  **q=NULL, **qb=NULL, **qm=NULL, *qqm=NULL, *qqm1=NULL, *qq=NULL, *qq1=NULL, **pR=NULL, **qm2=NULL, **QI5=NULL,  **q2l=NULL, **qmb=NULL;/*,**QI3,*/+PRIVATE FLT_OR_DBL  *prml=NULL, *prm_l=NULL, *prm_l1=NULL, *q1k=NULL, *qln=NULL;+PRIVATE FLT_OR_DBL  *scale=NULL;+PRIVATE char        **ptype=NULL; /* precomputed array of pair types */+PRIVATE int         *jindx=NULL;+PRIVATE int         *my_iindx=NULL;+PRIVATE vrna_exp_param_t   *pf_params=NULL;+PRIVATE short       *S=NULL, *S1=NULL;+PRIVATE int         ulength;+PRIVATE int         pUoutput;+PRIVATE double      alpha = 1.0;++#ifdef _OPENMP++/* NOTE: all variables are assumed to be uninitialized if they are declared as threadprivate+*/+#pragma omp threadprivate(cutoff, num_p, scale, ptype, jindx, my_iindx, pf_params,\+                          expMLbase, q, qb, qm, qqm, qqm1, qq, qq1, pR, qm2, QI5, q2l, qmb,\+                          prml, prm_l, prm_l1, q1k, qln,\+                          S, S1, ulength, pUoutput, alpha)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE void  init_partfunc_L(int length, vrna_exp_param_t *parameters);+PRIVATE void  get_arrays_L(unsigned int length);+PRIVATE void  free_pf_arrays_L(void);+PRIVATE void  scale_pf_params(unsigned int length, vrna_exp_param_t *parameters);+PRIVATE void  GetPtype(int j, int pairsize, const short *S, int n);+PRIVATE void  FreeOldArrays(int i);+PRIVATE void  GetNewArrays(int j, int winSize);+PRIVATE void  printpbar(FLT_OR_DBL **prb,int winSize, int i, int n);+PRIVATE plist *get_deppp(plist *pl, int start, int pairsize, int length);+PRIVATE plist *get_plistW(plist *pl, int length, int start, FLT_OR_DBL **Tpr, int winSize);+PRIVATE void  print_plist(int length, int start, FLT_OR_DBL **Tpr, int winSize, FILE *fp);+PRIVATE void  compute_pU(int k, int ulength, double **pU, int winSize, int n, char *sequence);+PRIVATE void  putoutpU(double **pU,int k, int ulength, FILE *fp);+/*PRIVATE void make_ptypes(const short *S, const char *structure);*/++PRIVATE void putoutpU_splitup(double **pUx, int k, int ulength, FILE *fp, char ident);+PRIVATE void compute_pU_splitup(int k, int ulength, double **pU,  double **pUO, double **pUH, double **pUI, double **pUM, int winSize,int n, char *sequence);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PRIVATE void init_partfunc_L(int length, vrna_exp_param_t *parameters){+  if (length<1) vrna_message_error("init_partfunc_L: length must be greater 0");+#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+  free_pf_arrays_L(); /* free previous allocation */+#else+  free_pf_arrays_L(); /* free previous allocation */+#endif++#ifdef SUN4+  nonstandard_arithmetic();+#else+#ifdef HP9+  fpsetfastmode(1);+#endif+#endif+  make_pair_matrix();+  get_arrays_L((unsigned) length);+  scale_pf_params((unsigned) length, parameters);++}++PRIVATE void get_arrays_L(unsigned int length){+  /*arrays in 2 dimensions*/++  q         = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *)*(length+1));+  qb        = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *)*(length+1));+  qm        = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *)*(length+1));+  pR        = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *)*(length+1));+  q1k       = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+1));+  qln       = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  qq        = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  qq1       = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  qqm       = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  qqm1      = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  prm_l     = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  prm_l1    = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  prml      = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+2));+  expMLbase = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+1));+  scale     = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)  *(length+1));+  ptype     = (char **)       vrna_alloc(sizeof(char *)      *(length+2));++  if (ulength>0) {+    /* QI3 = (FLT_OR_DBL **) vrna_alloc((length+1)*sizeof(FLT_OR_DBL *));*/+    QI5 = (FLT_OR_DBL **) vrna_alloc((length+1)*sizeof(FLT_OR_DBL *));+    qmb = (FLT_OR_DBL **) vrna_alloc((length+1)*sizeof(FLT_OR_DBL *));+    qm2 = (FLT_OR_DBL **) vrna_alloc((length+1)*sizeof(FLT_OR_DBL *));+    q2l = (FLT_OR_DBL **) vrna_alloc((length+1)*sizeof(FLT_OR_DBL *));+  }+  my_iindx  = vrna_idx_row_wise(length);+  iindx     = vrna_idx_row_wise(length); /* for backward compatibility and Perl wrapper */+  jindx     = vrna_idx_col_wise(length);+}++PRIVATE void free_pf_arrays_L(void){+  if(q)         free(q);+  if(qb)        free(qb);+  if(qm)        free(qm);+  if(pR)        free(pR);+  if(qm2)       free(qm2);+  if(qq)        free(qq);+  if(qq1)       free(qq1);+  if(qqm)       free(qqm);+  if(qqm1)      free(qqm1);+  if(q1k)       free(q1k);+  if(qln)       free(qln);+  if(prm_l)     free(prm_l);+  if(prm_l1)    free(prm_l1);+  if(prml)      free(prml);+  if(expMLbase) free(expMLbase);+  if(scale)     free(scale);+  if(my_iindx)  free(my_iindx);+  if(iindx)     free(iindx); /* for backward compatibility and Perl wrapper */+  if(jindx)     free(jindx);+  if(ptype)     free(ptype);+  if(QI5)       free(QI5);+  if(qmb)       free(qmb);+  if(q2l)       free(q2l);+  if(pf_params) free(pf_params);++  q = qb = qm = pR = QI5 = qmb = qm2 = q2l = NULL;+  qq = qq1 = qqm = qqm1 = q1k = qln = prml = prm_l = prm_l1 = expMLbase = NULL;+  my_iindx = jindx = iindx = NULL;+  pf_params = NULL;+  ptype     = NULL;+  scale = NULL;++#ifdef SUN4+  standard_arithmetic();+#else+#ifdef HP9+  fpsetfastmode(0);+#endif+#endif++}++PUBLIC void update_pf_paramsLP(int length){+  update_pf_paramsLP_par(length, NULL);+}++PUBLIC void update_pf_paramsLP_par(int length, vrna_exp_param_t *parameters){+  init_partfunc_L(length, parameters);+}++PUBLIC plist *pfl_fold( char *sequence,+                        int winSize,+                        int pairSize,+                        float cutoffb,+                        double **pU,+                        plist **dpp2,+                        FILE *pUfp,+                        FILE *spup){+  return pfl_fold_par(sequence, winSize, pairSize, cutoffb, pU, dpp2, pUfp, spup, NULL);+}++PUBLIC plist *pfl_fold_par( char *sequence,+                            int winSize,+                            int pairSize,+                            float cutoffb,+                            double **pU,+                            plist **dpp2,+                            FILE *pUfp,+                            FILE *spup,+                            vrna_exp_param_t *parameters){++  int         n, m, i, j, k, l, u, u1, type, type_2, tt, ov, do_dpp, simply_putout, noGUclosure;+  double      max_real;+  FLT_OR_DBL  temp, Qmax, prm_MLb, prmt, prmt1, qbt1, *tmp, expMLclosing;+  plist       *dpp, *pl;+  int split=0;++  ov            = 0;+  Qmax          = 0;+  do_dpp        = 0;+  simply_putout = 0;+  dpp           = NULL;+  pl            = NULL;+  pUoutput      = 0;+  ulength       = 0;+  cutoff        = cutoffb;++  if(pU != NULL)  ulength       = (int)pU[0][0]+0.49;+  if(spup !=NULL) simply_putout = 1; /*can't have one without the other*/+  if(pUfp!=NULL)  pUoutput      = 1;+  else if((pUoutput)&&(ulength!=0)){+    vrna_message_warning("There was a problem with non existing File Pointer for unpaireds, terminating process\n");+    return pl;+  }+  dpp = *dpp2;+  if(dpp !=NULL)  do_dpp=1;++  /*here, I allocate memory for pU, if has to be saved, I allocate all in one go,+    if pU is put out and freed, I only allocate what I really need*/++  n = (int) strlen(sequence);++  /* allocate memory and initialize unpaired probabilities */+  if (ulength > 0) {+    if (pUoutput) {+      for (i = 1; i <= ulength; i++)+        pU[i] = (double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+    }+    else {+      for (i = 1; i <= n; i++)+        pU[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+    }+  }++  if (n < TURN + 2) {+    if (ulength > 0) {+      if (pUoutput) {+        for (i = 1; i <= ulength; i++) {+          for (j = 0; j < MAX2(MAXLOOP,ulength) + 1; j++)+            pU[i][j] = 1.;+        }+      }+      else {+        for (i = 1; i <= n; i++) {+          for (j = 0; j < MAX2(MAXLOOP,ulength) + 1; j++)+            pU[i][j] = 1.;+        }+      }+    }+    return pl;+  }++  /* always init everything since all global static variables are uninitialized when entering a thread */+  init_partfunc_L(n, parameters);++  expMLclosing  = pf_params->expMLclosing;+  noGUclosure   = pf_params->model_details.noGUclosure;+++  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  S   = encode_sequence(sequence, 0);+  S1  = encode_sequence(sequence, 1);++  /*  make_ptypes(S, structure); das machmadochlieber lokal, ey!*/++  /*array initialization ; qb,qm,q+    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */+  num_p = 0;+  pl    = (plist *)vrna_alloc(1000*sizeof(plist));+++  /*ALWAYS q[i][j] => i>j!!*/+  for (j=1; j<MIN2(TURN+2,n); j++) { /*allocate start*/+    GetNewArrays(j, winSize);+    GetPtype(j,pairSize,S,n);+    for (i=1; i<=j; i++) q[i][j]=scale[(j-i+1)];+  }+  for (j=TURN+2;j<=n+winSize; j++) {+    if (j<=n) {+      GetNewArrays(j, winSize);+      GetPtype(j,pairSize,S,n);+      for (i=MAX2(1,j-winSize); i<=j/*-TURN*/; i++)+        q[i][j]=scale[(j-i+1)];+      for (i=j-TURN-1;i>=MAX2(1,(j-winSize+1)); i--) {+        /* construction of partition function of segment i,j*/+        /*firstly that given i bound to j : qb(i,j) */+        u = j-i-1;+        type = ptype[i][j];+        if (type!=0) {+          /*hairpin contribution*/+          if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;+          else+            qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[u+2];++          /* interior loops with interior pair k,l */+          for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {+            u1 = k-i-1;+            for (l=MAX2(k+TURN+1,j-1-MAXLOOP+u1); l<j; l++) {+              type_2 = ptype[k][l];+              if (type_2) {+                type_2 = rtype[type_2];+                qbt1 += qb[k][l] *+                  exp_E_IntLoop(u1, j-l-1, type, type_2,+                                S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params) * scale[k-i+j-l];+              }+            }+          }+          /*multiple stem loop contribution*/+          temp = 0.0;+          for (k=i+2; k<=j-1; k++) temp += qm[i+1][k-1]*qqm1[k];+          tt = rtype[type];+          qbt1 += temp * expMLclosing * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params) * scale[2];++          qb[i][j] = qbt1;+        } /* end if (type!=0) */+        else qb[i][j] = 0.0;++        /* construction of qqm matrix containing final stem+           contributions to multiple loop partition function+           from segment i,j */+        qqm[i] = qqm1[i]*expMLbase[1];+        if (type) {+          qbt1 = qb[i][j] * exp_E_MLstem(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);+          qqm[i] += qbt1;+        }++        /*construction of qm matrix containing multiple loop+          partition function contributions from segment i,j */+        temp = 0.0;+        /*ii = my_iindx[i];   ii-k=[i,k-1] */+        /*new qm2 computation done here*/+        for (k=i+1; k<=j; k++) temp += (qm[i][k-1])*qqm[k];+        if (ulength>0) qm2[i][j]=temp;/*new qm2 computation done here*/+        for (k=i+1; k<=j; k++) temp += expMLbase[k-i] * qqm[k];+        qm[i][j] = (temp + qqm[i]);++        /*auxiliary matrix qq for cubic order q calculation below */+        qbt1 = qb[i][j];+        if (type) {+          qbt1 *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j < n) ? S1[j+1] : -1, pf_params);+        }+        qq[i] = qq1[i]*scale[1] + qbt1;++        /*construction of partition function for segment i,j */+        temp = 1.0*scale[1+j-i] + qq[i];+        for (k=i; k<=j-1; k++) temp += q[i][k]*qq[k+1];+        q[i][j] = temp;++        if (temp>Qmax) {+          Qmax = temp;+          if (Qmax>max_real/10.)+            vrna_message_warning("Q close to overflow: %d %d %g\n", i,j,temp);+        }+        if (temp>=max_real) {+          vrna_message_error("overflow in pf_fold while calculating q[%d,%d]\n"+                                    "use larger pf_scale", i,j);+        }+      } /*end for i*/+      tmp = qq1;  qq1 =qq;  qq =tmp;+      tmp = qqm1; qqm1=qqm; qqm=tmp;+    }++    /* just as a general service, I save here the free energy of the windows+       no output is generated, however,...+    */+    if ((j>=winSize) && (j<=n) && (ulength) && !(pUoutput)) {+      double Fwindow=0.;+      Fwindow=(-log(q[j-winSize+1][j])-winSize*log(pf_params->pf_scale))*pf_params->kT/1000.0;++      pU[j][0]=Fwindow;+      /*+      if (ulength>=winSize)+        pU[j][winSize]=scale[winSize]/q[j-winSize+1][j];+      */+    }+    if (j>winSize) {+      Qmax=0;+      /* i=j-winSize; */+      /* initialize multiloopfs */+      for (k=j-winSize; k<=MIN2(n,j); k++) {+        prml[k]=0;+        prm_l[k]=0;+        /*        prm_l1[k]=0;  others stay*/+      }+      prm_l1[j-winSize]=0;+      k=j-winSize;+      for (l=k+TURN+1; l<=MIN2(n,k+winSize-1); l++) {+        int a;+        pR[k][l] = 0; /* set zero at start */+        type=ptype[k][l];+        if (qb[k][l]==0) continue;++        for (a=MAX2(1,l-winSize+2); a<MIN2(k,n-winSize+2);a++)+          pR[k][l]+=q[a][k-1]*q[l+1][a+winSize-1]/q[a][a+winSize-1];++        if (l-k+1==winSize)+          pR[k][l]+=1./q[k][l];+        else {+          if (k+winSize-1<=n)          /* k outermost */+            pR[k][l]+=q[l+1][k+winSize-1]/q[k][k+winSize-1];+          if (l-winSize+1>=1)  /*l outermost*/+            pR[k][l]+=q[l-winSize+1][k-1]/q[l-winSize+1][l];+        }+        pR[k][l] *= exp_E_ExtLoop(type, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params);++        type_2 = ptype[k][l];+        type_2 = rtype[type_2];++        for (i=MAX2(MAX2(l-winSize+1,k-MAXLOOP-1),1); i<=k-1; i++) {+          for (m=l+1; m<=MIN2(MIN2(l+ MAXLOOP -k+i+2,i+winSize-1),n); m++) {+            type = ptype[i][m];+            if ((pR[i][m]>0))+              pR[k][l] += pR[i][m]*exp_E_IntLoop(k-i-1, m-l-1, type, type_2,+                                                 S1[i+1], S1[m-1], S1[k-1], S1[l+1], pf_params) * scale[k-i+m-l];+          }+        }+        if (ulength) { /* NOT IF WITHIN INNER LOOP */+          for (i=MAX2(MAX2(l-winSize+1,k-MAXLOOP-1),1); i<=k-1; i++) {+            for (m=l+1; m<=MIN2(MIN2(l+ MAXLOOP -k+i+2,i+winSize-1),n); m++) {+              type = ptype[i][m];+              if ((pR[i][m]>0)){+                temp=pR[i][m]*qb[k][l]*exp_E_IntLoop(k-i-1, m-l-1, type, type_2,+                                                     S1[i+1], S1[m-1], S1[k-1], S1[l+1], pf_params) * scale[k-i+m-l];+                QI5[l][m-l-1]+=temp;+                QI5[i][k-i-1]+=temp;+              }+            }+           }+        }+      }+      /* 3. bonding k,l as substem of multi-loop enclosed by i,m */+      prm_MLb = 0.;+      if(k>1) /*sonst nix!*/+        for (l=MIN2(n-1,k+winSize-2); l>=k+TURN+1; l--) { /* opposite direction */+          m=l+1;+          prmt = prmt1 = 0.0;+          tt = ptype[k-1][m]; tt=rtype[tt];+          prmt1 = pR[k-1][m] * expMLclosing * exp_E_MLstem(tt, S1[l], S1[k], pf_params);+          for (i=MAX2(1,l-winSize+2); i<k-1/*TURN*/; i++) {+            tt = ptype[i][m]; tt = rtype[tt];+            prmt += pR[i][m] * exp_E_MLstem(tt, S1[m-1], S1[i+1], pf_params) * qm[i+1][k-1];+          }+          tt = ptype[k][l];+          prmt *= expMLclosing;+          prml[ m] = prmt;+          prm_l[m] = prm_l1[m]*expMLbase[1]+prmt1;++          prm_MLb = prm_MLb*expMLbase[1] + prml[m];+          /* same as:    prm_MLb = 0;+             for (i=n; i>k; i--)  prm_MLb += prml[i]*expMLbase[k-i-1];+          */+          prml[m] = prml[ m] + prm_l[m];++          if (qb[k][l] == 0.) continue;++          temp = prm_MLb;++          if (ulength) {+            double dang;+            /* coefficient for computations of unpairedarrays */+            dang  =   qb[k][l] * exp_E_MLstem(tt, S1[k-1], S1[l+1], pf_params) * scale[2];+            for (m=MIN2(k+winSize-2,n);m>=l+2; m--){+              qmb[l][m-l-1] +=  prml[m]*dang;+              q2l[l][m-l-1] +=  (prml[m]-prm_l[m])*dang;+            }+          }++          for (m=MIN2(k+winSize-2,n);m>=l+2; m--)+            temp += prml[m]*qm[l+1][m-1];++          temp      *= exp_E_MLstem(tt, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params) * scale[2];+          pR[k][l]  += temp;++          if (pR[k][l]>Qmax) {+            Qmax = pR[k][l];+            if (Qmax>max_real/10.)+              vrna_message_warning("P close to overflow: %d %d %g %g\n",+                                          i, m, pR[k][l], qb[k][l]);+          }+          if (pR[k][l]>=max_real) {+            ov++;+            pR[k][l]=FLT_MAX;+          }++        } /* end for (l=..) */+      tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;++      /* end for (l=..)   */+      if ((ulength)&&(k-MAXLOOP-1>0)){+        /* if (pUoutput) pU[k-MAXLOOP-1]=(double *)vrna_alloc((ulength+2)*sizeof(double)); */+        if(split){ /*generate the new arrays, if you want them somewhere else, you have to generate them and overgive them ;)*/+          double **pUO;+          double **pUI;+          double **pUM;+          double **pUH;+          pUO= (double **)  vrna_alloc((n+1)*sizeof(double *));+          pUI= (double **)  vrna_alloc((n+1)*sizeof(double *));+          pUM= (double **)  vrna_alloc((n+1)*sizeof(double *));+          pUH= (double **)  vrna_alloc((n+1)*sizeof(double *));+          if (pUoutput) {+            for (i=1; i<=ulength; i++) {+              pUH[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+              pUI[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+              pUO[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+              pUM[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+            }+          }+          //dont want to have that yet?+          /*  else {+            for (i=1; i<=n; i++) pU[i]=(double *)vrna_alloc((MAX2(MAXLOOP,ulength)+2)*sizeof(double));+            }*/+          compute_pU_splitup(k-MAXLOOP-1,ulength,pU,pUO,pUH, pUI, pUM, winSize, n, sequence);+          if (pUoutput) {+            putoutpU_splitup(pUO,k-MAXLOOP-1, ulength, pUfp,'E');+            putoutpU_splitup(pUH,k-MAXLOOP-1, ulength, pUfp,'H');+            putoutpU_splitup(pUI,k-MAXLOOP-1, ulength, pUfp,'I');+            putoutpU_splitup(pUM,k-MAXLOOP-1, ulength, pUfp,'M');+          }+        }+        else {+        compute_pU(k-MAXLOOP-1,ulength,pU, winSize, n, sequence);++        /* here, we put out and free pUs not in use any more (hopefully) */+        if (pUoutput)+          putoutpU(pU,k-MAXLOOP-1, ulength, pUfp);+      }+      }++      if (j-(2*winSize+MAXLOOP+1)>0) {+        printpbar(pR,winSize,j-(2*winSize+MAXLOOP+1),n);+        if (simply_putout) {+          print_plist(n, j-(2*winSize+MAXLOOP+1), pR, winSize, spup);+        }+        else{+          pl=get_plistW(pl, n, j-(2*winSize+MAXLOOP+1), pR, winSize);+        }+        if (do_dpp)dpp=get_deppp(dpp,j-(2*winSize-MAXLOOP),pairSize, n);+        FreeOldArrays(j-(2*winSize+MAXLOOP+1));+      }+    }   /* end if (do_backtrack)*/++  }/* end for j */++  /* finish output and free */+  for (j=MAX2(1,n-MAXLOOP); j<=n;j++) {+    /* if (pUoutput) pU[j]=(double *)vrna_alloc((ulength+2)*sizeof(double)); */+    if (ulength) compute_pU(j,ulength,pU, winSize, n, sequence);+    /*here, we put out and free pUs not in use any more (hopefully)*/+    if (pUoutput) putoutpU(pU,j, ulength, pUfp);+  }+  for (j=MAX2(n-winSize-MAXLOOP,1); j<=n; j++) {+    printpbar(pR,winSize,j,n);+    if (simply_putout) {+      print_plist(n, j, pR, winSize, spup);+    }+    else {+      pl=get_plistW(pl, n, j, pR, winSize);+    }+    if ((do_dpp)&&j<n) dpp=get_deppp(dpp,j,pairSize, n);+    FreeOldArrays(j);+  }+  /* free_pf_arrays_L(); */+  free(S);+  free(S1);+  S = S1 = NULL;+  if(ov > 0)+    vrna_message_warning("%d overflows occurred while backtracking;\n"+                                "you might try a smaller pf_scale than %g\n",+                                ov, pf_params->pf_scale);+  *dpp2=dpp;++  return pl;+}++PRIVATE void scale_pf_params(unsigned int length, vrna_exp_param_t *parameters){+  unsigned int i;+  double  kT, scaling_factor;++  if(pf_params) free(pf_params);++  if(parameters){+    pf_params = vrna_exp_params_copy(parameters);+  } else {+    vrna_md_t  md;+    set_model_details(&md);+    pf_params = vrna_exp_params(&md);+  }++  scaling_factor = pf_params->pf_scale;+  kT = pf_params->kT;   /* kT in cal/mol  */++   /* scaling factors (to avoid overflows) */+  if (scaling_factor == -1) { /* mean energy for random sequences: 184.3*length cal */+    scaling_factor = exp(-(-185+(pf_params->temperature-37.)*7.27)/kT);+    if (scaling_factor<1) scaling_factor=1;+    pf_params->pf_scale = scaling_factor;+  }+  scale[0] = 1.;+  scale[1] = 1./scaling_factor;+  expMLbase[0] = 1;+  expMLbase[1] = pf_params->expMLbase/scaling_factor;+  for (i=2; i<=length; i++) {+    scale[i] = scale[i/2]*scale[i-(i/2)];+    expMLbase[i] = pow(pf_params->expMLbase, (double)i) * scale[i];+  }+}++PRIVATE void printpbar(FLT_OR_DBL **prb,int winSize, int i, int n) {+  int j;+  int howoften=0; /* how many samples do we have for this pair */+  int pairdist;++  for (j=i+TURN; j<MIN2(i+winSize,n+1); j++) {+    pairdist=(j-i+1);+    /*4cases*/+    howoften=MIN2(winSize-pairdist+1,i); /*pairdist,start*/+    howoften=MIN2(howoften,n-j+1);       /*end*/+    howoften=MIN2(howoften,n-winSize+1); /*windowsize*/+    prb[i][j] *= qb[i][j]/howoften;+  }+  return;+}++PRIVATE void FreeOldArrays(int i) {+  /*free arrays no longer needed*/+  free(pR[i]+i);+  free(q[i]+i);+  free(qb[i]+i);+  free(qm[i]+i);+  if (ulength!=0) {+    free(qm2[i]+i);+    free(QI5[i]);+    free(qmb[i]);+    free(q2l[i]);+  }+  free(ptype[i]+i);+  return;+}++PRIVATE void GetNewArrays(int j, int winSize) {+  /*allocate new part of arrays*/+  pR[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+  pR[j]-=j;+  q[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+  q[j]-=j;+  qb[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+  qb[j]-=j;+  qm[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+  qm[j]-=j;+  if (ulength!=0) {+    qm2[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+    qm2[j]-=j;+    QI5[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+    qmb[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+    q2l[j]=(FLT_OR_DBL *)vrna_alloc((winSize+1)*sizeof(FLT_OR_DBL));+  }+  ptype[j]=(char *)vrna_alloc((winSize+1)*sizeof(char));+  ptype[j]-=j;+  return;+}+++PRIVATE void GetPtype(int i, int winSize,const short *S,int n) {+  /*make new entries in ptype array*/+  int j;+  int type;+  for (j=i; j<=MIN2(i+winSize,n); j++) {+    type = pair[S[i]][S[j]];+    ptype[i][j] = (char) type;+  }+  return;+}+++PRIVATE plist *get_plistW(plist *pl, int length,+                                 int start, FLT_OR_DBL **Tpr, int winSize) {+  /* get pair probibilities out of pr array */+  int  j,  max_p;+  max_p=1000;+  while (max_p<num_p)+    max_p*=2;++  for (j=start+1; j<=MIN2(start+winSize, length); j++) {+    if (Tpr[start][j]<cutoff) continue;+    if (num_p==max_p-1) {+      max_p*=2;+      pl=(plist *)vrna_realloc(pl,max_p*sizeof(plist));+    }+    pl[num_p].i=start;+    pl[num_p].j=j;+    pl[num_p++].p=Tpr[start][j];+  }++  /* mark end of data with zeroes */+  pl[num_p].i=0;+  pl[num_p].j=0;+  pl[num_p].p=0.;+  /* pl=(plist *)vrna_realloc(pl,(count)*sizeof(plist)); */+  return pl;+}+++PRIVATE plist *get_deppp(plist *pl, int start, int pairsize, int length) {+  /* compute dependent pair probabilities */+  int i, j, count=0;+  double tmp;+  plist *temp;+  temp=(plist *)vrna_alloc(pairsize*sizeof(plist)); /* holds temporary deppp */+  for (j=start+TURN; j<MIN2(start+pairsize,length); j++) {++    if ((qb[start][j]*qb[start-1][(j+1)])>10e-200) {+      int type=ptype[start-1][j+1];+      int type_2=rtype[(unsigned char)ptype[start][j]];+      tmp=qb[start][j]/qb[start-1][(j+1)]*exp_E_IntLoop(0, 0, type, type_2,+                                                        S1[start], S1[j], S1[start-1], S1[j+1], pf_params) * scale[2];+       temp[count].i=start;+      temp[count].j=j;+      temp[count++].p=tmp;+    }+  }+  /* write it to list of deppps */+  for (i=0; pl[i].i!=0; i++);+  pl=(plist *)vrna_realloc(pl,(i+count+1)*sizeof(plist));+  for (j=0; j<count; j++) {+    pl[i+j].i=temp[j].i;+    pl[i+j].j=temp[j].j;+    pl[i+j].p=temp[j].p;+  }+  pl[i+count].i=0;+  pl[i+count].j=0;+  pl[i+count].p=0;+  free(temp);+  return pl;+}+++PRIVATE void print_plist(int length,int start, FLT_OR_DBL **Tpr, int winSize, FILE *fp) {+  /* print out of pr array, do not save */+  int  j;+++  for (j=start+1; j<=MIN2(start+winSize, length); j++) {+    if (Tpr[start][j]<cutoff) continue;+    fprintf(fp,"%d  %d  %g\n",start,j,Tpr[start][j]);+  }++  /* mark end of data with zeroes */++  return ;+}++PRIVATE void compute_pU(int k, int ulength, double **pU, int winSize,int n, char *sequence) {+/*  here, we try to add a function computing all unpaired probabilities starting at some i,+    going down to $unpaired, to be unpaired, i.e. a list with entries from 1 to unpaired for+    every i, with the probability of a stretch of length x, starting at i-x+1, to be unpaired+*/+  int startu;+  int i5;+  int j3, len, obp;+  double temp;+  double *QBE;+  FLT_OR_DBL  expMLclosing      = pf_params->expMLclosing;++  QBE=(double *) vrna_alloc((MAX2(ulength,MAXLOOP)+2)*sizeof(double));++  /* first, we will */+  /* for k<=ulength, pU[k][k]=0, because no bp can enclose it */+  if (pUoutput&&k+ulength<=n)  pU[k+ulength]=(double *)vrna_alloc((ulength+2)*sizeof(double));+  /*compute pu[k+ulength][ulength] */+   for (i5=MAX2(k+ulength-winSize+1,1);i5<=k;i5++) {+    for (j3=k+ulength+1; j3<=MIN2(n,i5+winSize-1); j3++) {+      /*  if (k>400) {+        printf("i%d j%d  ",i5,j3);+        fflush(stdout);+        } */+      if (ptype[i5][j3]!=0) {/**/+        /* (.. >-----|..........)+          i5  j     j+ulength  j3              */+        /*Multiloops*/+        temp = (i5<k) ? qm2[i5+1][k] * expMLbase[j3-k-1] : 0.; /* (..{}{}-----|......) */++        if(j3-1>k+ulength)+          temp  +=  qm2[k+ulength+1][j3-1] * expMLbase[k+ulength-i5]; /* (..|-----|{}{}) */++        if((i5<k)&&(j3-1>k+ulength))+          temp  +=  qm[i5+1][k] * qm[k+ulength+1][j3-1] * expMLbase[ulength]; /* ({}|-----|{}) */++        /* add dangles, multloopclosing etc. */+        temp  *=  exp_E_MLstem(rtype[(unsigned char)ptype[i5][j3]], S1[j3-1], S1[i5+1], pf_params) * scale[2] * expMLclosing;+        /*add hairpins*/+        temp  +=  exp_E_Hairpin(j3-i5-1, ptype[i5][j3], S1[i5+1], S1[j3-1], sequence+i5-1, pf_params) * scale[j3-i5+1];+        /*add outer probability*/+        temp *= pR[i5][j3];+        pU[k+ulength][ulength] += temp;++      }+    }+   }+   /* code doubling to avoid if within loop */+#if 0+  /*initialization for interior loops,+    it is not recomended to have verysmall ulengths!!*/+  if (ulength<MAXLOOP) {+    int k5;+    int l3;+    int outype;+    /* kl bp is 5' */+    /* MAXLOOP>((l5-k5-1)+(j3-l3-1)+      k-winSize+ulength<i5<k-TURN-1;+      k+ulength<j3<=k+MAXLOOP+1+      if i then use l3, it is easier by far:+      j3-MAXLOOP<=l3<=k+      i5<k5<k-TURN k5<=i5+l3+2+MAXLOOP-j3+      k5+TURN<l3<=k+    */+    for (i5=MAX2(k+ulength-winSize,1);i5<k-TURN-1;i5++) {++      for (j3=k+ulength+1; j3<=MIN2(n,MIN2(i5+winSize-1,k+MAXLOOP+1)); j3++) {+        double temp=0;+        if (outype=ptype[i5][j3]>0) /* oder so halt */+          for (l3=MAX2(i5+TURN+1,j3-MAXLOOP-1); l3<=k; l3++){+            for (k5=i5+1; k5<=MIN2(l3-TURN-1,MAXLOOP+i5+l3+2-j3); k5++){+              if (ptype[k5][l3]) {+                temp+= qb[k5][l3]*expLoopEnergy(k5-i5-1, j3-l3-1, outype, rtype[ptype[k5][l3]], S1[i5+1], S1[j3-1], S1[k5-1], S1[l3+1]);+              }+            }+          }+        temp*=pR[i5][j3];+        pU[k+ulength][ulength]+= temp;+      }+    }+    /* kl bp is 3' */+    /*+      k+ulength-MAXLOOP<=i5<=k+      k+ulength+1+TURN<j3<i5+winSize+      k+ulength+1<=k5<i5+MAXLOOP+2 || k5<j3-TURN+      k5<l3<j3 || j3-k5-i5-2-ML<=l3<j3+    */+    for (i5=MAX2(1,MAX2(k+ulength-winSize,k+ulength-MAXLOOP));i5<=k; i5++){+      for (j3=k+ulength+TURN+2; j3<MIN2(n+1,i5+winSize); j3++) {+        double temp = 0;+        if (outype=ptype[i5][j3]>0) /* oder so halt */+          for (k5=k+ulength+1; k5<MIN2(j3-TURN-1,i5+MAXLOOP+2); k5++) {+            for (l3=MAX2(k5+TURN+1,j3+k5-i5-2-MAXLOOP); l3<j3; l3++) {+              if (ptype[k5][l3])+                temp += qb[k5][l3]*expLoopEnergy(k5-i5-1, j3-l3-1, outype, rtype[ptype[k5][l3]], S1[i5+1], S1[j3-1], S1[k5-1], S1[l3+1]);+            }+          }+        temp*=pR[i5][j3];+        pU[k+ulength][ulength]+= temp;+      }+    }+  }+  /* Add up Is QI5[l][m-l-1] QI3 */+  /* Add up Interior loop terms */+  temp=0.;++  for (len=winSize; len>=ulength; len--) temp+=QI3[k][len];+  for (;len>0; len--) {+    temp += QI3[k][len];+    QBE[len] += temp;+  }+#endif+  temp=0.;+  for (len=winSize; len>=MAX2(ulength,MAXLOOP); len--) temp+=QI5[k][len];+  for (;len>0; len--) {+    temp += QI5[k][len];+    QBE[len] += temp;  /* replace QBE with QI */+  }+  /* Add Hairpinenergy to QBE */+  temp=0.;+  for(obp = MIN2(n, k + winSize - 1); obp > k + ulength; obp--)+    if(ptype[k][obp])+      temp += pR[k][obp] * exp_E_Hairpin(obp-k-1, ptype[k][obp], S1[k+1], S1[obp-1], sequence+k-1, pf_params) * scale[obp-k+1];+  for(obp = MIN2(n, MIN2(k + winSize - 1, k + ulength)); obp > k + 1; obp--){+    if (ptype[k][obp])+      temp += pR[k][obp] * exp_E_Hairpin(obp-k-1, ptype[k][obp], S1[k+1], S1[obp-1], sequence+k-1, pf_params) * scale[obp-k+1];+    QBE[obp-k-1] += temp;  /* add hairpins to QBE (all in one array) */+  }+  /* doubling the code to get the if out of the loop */++  /* Add up Multiloopterms  qmb[l][m]+=prml[m]*dang;+    q2l[l][m]+=(prml[m]-prm_l[m])*dang; */++  temp=0.;+  for(len = winSize; len >= ulength; len--)+    temp += q2l[k][len] * expMLbase[len];+  for( ; len > 0; len--){+    temp += q2l[k][len] * expMLbase[len];+    QBE[len] += temp; /* add (()()____) type cont. to I3 */+  }+  for(len = 1; len < ulength; len++){+    for(obp = k + len + TURN; obp <= MIN2(n, k + winSize - 1); obp++){+      /* add (()___()) */+      QBE[len] += qmb[k][obp-k-1] * qm[k+len+1/*2*/][obp-1] * expMLbase[len];+    }+  }+  for (len=1; len<ulength; len++) {+    for (obp=k+len+TURN+TURN; obp<=MIN2(n,k+winSize-1); obp++) {+      if (ptype[k][obp]) {+        temp      =   exp_E_MLstem(rtype[(unsigned char)ptype[k][obp]], S1[obp-1], S1[k+1], pf_params) * scale[2] * expMLbase[len] * expMLclosing; /* k:obp */+        QBE[len]  +=  pR[k][obp] * temp * qm2[k+len+1][obp-1]; /* add (___()()) */+      }+    }+  }+  /* After computing all these contributions in QBE[len], that k is paired+    and the unpaired stretch is AT LEAST len long, we start to add that to+    the old unpaired thingies; */+  for(len = 1; len < MIN2(MAX2(ulength, MAXLOOP), n - k); len++){+    pU[k+len][len] += pU[k+len][len+1] + QBE[len];+  }++  /*open chain*/+  if ((ulength>=winSize)&&(k>=ulength)) {+    pU[k][winSize]=scale[winSize]/q[k-winSize+1][k];+  }+  /* now the not enclosed by any base pair terms for whatever it is we do not need anymore...+    ... which should be e.g; k, again */+  for(startu = MIN2(ulength, k); startu > 0; startu--){+    temp=0.;+    for(i5 = MAX2(1, k - winSize + 2); i5 <= MIN2(k - startu, n - winSize + 1); i5++){+      temp += q[i5][k - startu] * q[k + 1][i5 + winSize - 1] * scale[startu]/q[i5][i5 + winSize - 1];+    }+    /* the 2 Cases where the borders are on the edge of the interval */+    if((k >= winSize) && (startu + 1 <= winSize))+      temp += q[k - winSize + 1][k - startu]*scale[startu]/q[k - winSize + 1][k];+    if((k <= n - winSize+ startu) && (k - startu >= 0) && (k < n) && (startu + 1 <= winSize))+      temp += q[k + 1][k - startu + winSize] * scale[startu] / q[k - startu + 1][k - startu + winSize];++    /* Divide by number of possible windows */+    pU[k][startu] += temp;+    {+      int leftmost, rightmost;++      leftmost      = MAX2(1, k - winSize + 1);+      rightmost     = MIN2(n - winSize + 1, k - startu + 1);+      pU[k][startu] /= (rightmost - leftmost + 1);+    }+  }+  free(QBE);+  return;+}+++PRIVATE void putoutpU(double **pUx, int k, int ulength, FILE *fp) {+  /*put out unpaireds for k, and free pU[k], make sure we don't need pU[k] any more!!*/+  /*could use that for hairpins, also!*/+  int i;+  fprintf(fp,"%d\t",k);+  for (i=1; i<=MIN2(ulength,k); i++) {+    fprintf(fp,"%.5g\t",pUx[k][i]);+  }+  fprintf(fp,"\n");+  free(pUx[k]);+}+PRIVATE void putoutpU_splitup(double **pUx, int k, int ulength, FILE *fp, char ident) {+  /*put out unpaireds for k, and free pU[k], make sure we don't need pU[k] any more!!*/+  /*could use that for hairpins, also!*/+  int i;+  fprintf(fp,"%d\t",k);+  for (i=1; i<=MIN2(ulength,k); i++) {+    fprintf(fp,"%.5g\t",pUx[k][i]);+  }+  fprintf(fp,"\t%c\n",ident);+  free(pUx[k]);+}++PUBLIC void putoutpU_prob(double **pU,int length, int ulength, FILE *fp, int energies) {+  putoutpU_prob_par(pU, length, ulength, fp, energies, pf_params);+}+++PUBLIC void putoutpU_prob_par(double **pU,int length, int ulength, FILE *fp, int energies, vrna_exp_param_t *parameters){+  /*put out unpaireds */+  int i,k;+  double kT = parameters->kT/1000.0;+  double temp;+  if (energies) fprintf(fp,"#opening energies\n #i$\tl=");+  else  fprintf(fp,"#unpaired probabilities\n #i$\tl=");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pU[k][i])*kT;+      else temp=pU[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\n");+    free(pU[k]);+  }+  fflush(fp);+}++PUBLIC void putoutpU_prob_bin(double **pU,int length, int ulength, FILE *fp, int energies) {+  putoutpU_prob_bin_par(pU, length, ulength, fp, energies, pf_params);+}++PUBLIC void putoutpU_prob_bin_par(double **pU,int length, int ulength, FILE *fp, int energies, vrna_exp_param_t *parameters) {++  /*put out unpaireds */+  int i,k;+  double kT= parameters->kT/1000.0;+  int *p;+  p = (int*) vrna_alloc(sizeof(int)*1);+  /* write first line */+  p[0]=ulength; /* u length */+  fwrite(p,sizeof(int),1,fp);+  p[0]=length; /* seq length */+  fwrite(p,sizeof(int),1,fp);+  for (k=3; k<=(length+20); k++){ /* all the other lines are set to 1000000 because we are at ulength=0 */+    p[0]=1000000;+    fwrite(p,sizeof(int),1,fp);+  }+  /* data */+  for (i=1; i<=ulength; i++) {+    for (k=1; k<=11; k++){/* write first ten entries to 1000000 */+      p[0]=1000000;+      fwrite(p,sizeof(int),1,fp);+    }+    for (k=1; k<=length; k++){/* write data now */+      if (i>k) {+        p[0]=1000000;         /* check if u > pos */+        fwrite(p,sizeof(int),1,fp);+        continue;+      }+      else{+        p[0]= (int) rint(100 *(-log(pU[k][i])*kT));+        fwrite(p,sizeof(int),1,fp);+      }+    }+    for (k=1; k<=9; k++){/* finish by writing the last 10 entries */+      p[0]=1000000;+      fwrite(p,sizeof(int),1,fp);+    }+  }+  /* free pU array; */+  for (k=1; k<=length; k++){+    free(pU[k]);+  }+  free(p);+  fflush(fp);+}+++/*+ Here: Space for questions...+*/+PRIVATE void compute_pU_splitup(int k, int ulength, double **pU,  double **pUO, double **pUH, double **pUI, double **pUM, int winSize,int n, char *sequence) {+/*  here, we try to add a function computing all unpaired probabilities starting at some i,+    going down to $unpaired, to be unpaired, i.e. a list with entries from 1 to unpaired for+    every i, with the probability of a stretch of length x, starting at i-x+1, to be unpaired+*/+  int startu;+  int i5;+  int j3, len, obp;+  double temp;+  double *QBE;+  double *QBI;+  double *QBM;+  double *QBH;+  +  FLT_OR_DBL  expMLclosing      = pf_params->expMLclosing;++  QBE=(double *) vrna_alloc((MAX2(ulength,MAXLOOP)+2)*sizeof(double));+  QBM=(double *) vrna_alloc((MAX2(ulength,MAXLOOP)+2)*sizeof(double));+  QBI=(double *) vrna_alloc((MAX2(ulength,MAXLOOP)+2)*sizeof(double));+  QBH=(double *) vrna_alloc((MAX2(ulength,MAXLOOP)+2)*sizeof(double));++  /* first, we will */+  /* for k<=ulength, pU[k][k]=0, because no bp can enclose it */+  if (pUoutput&&k+ulength<=n)  pU[k+ulength]=(double *)vrna_alloc((ulength+2)*sizeof(double));+  /*compute pu[k+ulength][ulength] */+   for (i5=MAX2(k+ulength-winSize+1,1);i5<=k;i5++) {+    for (j3=k+ulength+1; j3<=MIN2(n,i5+winSize-1); j3++) {+      /*  if (k>400) {+        printf("i%d j%d  ",i5,j3);+        fflush(stdout);+        } */+      if (ptype[i5][j3]!=0) {/**/+        /* (.. >-----|..........)+          i5  j     j+ulength  j3              */+        /*Multiloops*/+        temp = (i5<k) ? qm2[i5+1][k] * expMLbase[j3-k-1] : 0.; /* (..{}{}-----|......) */++        if(j3-1>k+ulength)+          temp  +=  qm2[k+ulength+1][j3-1] * expMLbase[k+ulength-i5]; /* (..|-----|{}{}) */++        if((i5<k)&&(j3-1>k+ulength))+          temp  +=  qm[i5+1][k] * qm[k+ulength+1][j3-1] * expMLbase[ulength]; /* ({}|-----|{}) */++        /* add dangles, multloopclosing etc. */+        temp  *=  exp_E_MLstem(rtype[(unsigned char)ptype[i5][j3]], S1[j3-1], S1[i5+1], pf_params) * scale[2] * expMLclosing;+        /*add hairpins*/+        temp  +=  exp_E_Hairpin(j3-i5-1, ptype[i5][j3], S1[i5+1], S1[j3-1], sequence+i5-1, pf_params) * scale[j3-i5+1];+        /*add outer probability*/+        temp *= pR[i5][j3];+        pU[k+ulength][ulength] += temp;++      }+    }+   }+   /* code doubling to avoid if within loop */+  temp=0.;+  for (len=winSize; len>=MAX2(ulength,MAXLOOP); len--) temp+=QI5[k][len];+  for (;len>0; len--) {+    temp += QI5[k][len];+    QBI[len] += temp; +    QBE[len] += temp;  /* replace QBE with QI */+  }+  /* Add Hairpinenergy to QBE */+  temp=0.;+  for(obp = MIN2(n, k + winSize - 1); obp > k + ulength; obp--)+    if(ptype[k][obp])+      temp += pR[k][obp] * exp_E_Hairpin(obp-k-1, ptype[k][obp], S1[k+1], S1[obp-1], sequence+k-1, pf_params) * scale[obp-k+1];+  for(obp = MIN2(n, MIN2(k + winSize - 1, k + ulength)); obp > k + 1; obp--){+    if (ptype[k][obp])+      temp += pR[k][obp] * exp_E_Hairpin(obp-k-1, ptype[k][obp], S1[k+1], S1[obp-1], sequence+k-1, pf_params) * scale[obp-k+1];+    QBH[obp-k-1] += temp;+    QBE[obp-k-1] += temp;  /* add hairpins to QBE (all in one array) */+  }+  /* doubling the code to get the if out of the loop */++  /* Add up Multiloopterms  qmb[l][m]+=prml[m]*dang;+    q2l[l][m]+=(prml[m]-prm_l[m])*dang; */++  temp=0.;+  for(len = winSize; len >= ulength; len--)+    temp += q2l[k][len] * expMLbase[len];+  for( ; len > 0; len--){+    temp += q2l[k][len] * expMLbase[len];+    QBM[len] += temp; +    QBE[len] += temp; /* add (()()____) type cont. to I3 */+  }+  for(len = 1; len < ulength; len++){+    for(obp = k + len + TURN; obp <= MIN2(n, k + winSize - 1); obp++){+      /* add (()___()) */+      QBM[len] += qmb[k][obp-k-1] * qm[k+len+1/*2*/][obp-1] * expMLbase[len];+      QBE[len] += qmb[k][obp-k-1] * qm[k+len+1/*2*/][obp-1] * expMLbase[len];+    }+  }+  for (len=1; len<ulength; len++) {+    for (obp=k+len+TURN+TURN; obp<=MIN2(n,k+winSize-1); obp++) {+      if (ptype[k][obp]) {+        temp      =   exp_E_MLstem(rtype[(unsigned char)ptype[k][obp]], S1[obp-1], S1[k+1], pf_params) * scale[2] * expMLbase[len] * expMLclosing; /* k:obp */+        QBE[len]  +=  pR[k][obp] * temp * qm2[k+len+1][obp-1]; /* add (___()()) */+        QBM[len]  +=  pR[k][obp] * temp * qm2[k+len+1][obp-1]; /* add (___()()) */+      }+    }+  }+  /* After computing all these contributions in QBE[len], that k is paired+    and the unpaired stretch is AT LEAST len long, we start to add that to+    the old unpaired thingies; */+  for(len = 1; len < MIN2(MAX2(ulength, MAXLOOP), n - k); len++){+    pU[k+len][len] += pU[k+len][len+1] + QBE[len];+    pUH[k+len][len] += pUH[k+len][len+1] + QBH[len];+    pUM[k+len][len] += pUM[k+len][len+1] + QBM[len];+    pUI[k+len][len] += pUI[k+len][len+1] + QBI[len];+    +  }++  /* open chain */+  if ((ulength>=winSize)&&(k>=ulength)) {+    pUO[k][winSize]=scale[winSize]/q[k-winSize+1][k];+  }+  /*open chain*/+  if ((ulength>=winSize)&&(k>=ulength)) {+    pU[k][winSize]=scale[winSize]/q[k-winSize+1][k];+  }+  /* now the not enclosed by any base pair terms for whatever it is we do not need anymore...+    ... which should be e.g; k, again */+  for(startu = MIN2(ulength, k); startu > 0; startu--){+    temp=0.;+    for(i5 = MAX2(1, k - winSize + 2); i5 <= MIN2(k - startu, n - winSize + 1); i5++){+      temp += q[i5][k - startu] * q[k + 1][i5 + winSize - 1] * scale[startu]/q[i5][i5 + winSize - 1];+    }+    /* the 2 Cases where the borders are on the edge of the interval */+    if((k >= winSize) && (startu + 1 <= winSize))+      temp += q[k - winSize + 1][k - startu]*scale[startu]/q[k - winSize + 1][k];+    if((k <= n - winSize+ startu) && (k - startu >= 0) && (k < n) && (startu + 1 <= winSize))+      temp += q[k + 1][k - startu + winSize] * scale[startu] / q[k - startu + 1][k - startu + winSize];++    /* Divide by number of possible windows */+    pU[k][startu] += temp;+    pUO[k][startu] += temp;+    +    {+      int leftmost, rightmost;++      leftmost      = MAX2(1, k - winSize + 1);+      rightmost     = MIN2(n - winSize + 1, k - startu + 1);+      pU[k][startu] /= (rightmost - leftmost + 1);+      /*Do we want to make a distinction between those?*/+      pUH[k][startu] /= (rightmost - leftmost + 1);+      pUO[k][startu] /= (rightmost - leftmost + 1);+      pUI[k][startu] /= (rightmost - leftmost + 1);+      pUM[k][startu] /= (rightmost - leftmost + 1);+    }+  }+  free(QBE);+  free(QBI);+  free(QBH);+  free(QBM);+  return;+}+PUBLIC void putoutpU_prob_splitup(double **pU, double **pUO, double **pUH, double **pUI, double **pUM, int length, int ulength, FILE *fp, int energies) {+  /*put out unpaireds */+  int i,k;+  double kT= (temperature+K0)*GASCONST/1000.0;+  double temp;+  if (energies) fprintf(fp,"#opening energies\n #i$\tl=");+  else  fprintf(fp,"#unpaired probabilities\n #i$\tl=");+  +  fprintf(fp,"Total\n");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pU[k][i])*kT;+      else temp=pU[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\tT\n");+    free(pU[k]);+  }+  fprintf(fp,"\n###################################################################\nHairpin\n");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pUH[k][i])*kT;+      else temp=pUH[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\tH\n");+    free(pUH[k]);+  }+  fprintf(fp,"\n###################################################################\nInterior\n");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pUI[k][i])*kT;+      else temp=pUI[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\tI\n");+    free(pUI[k]);+  }+  fprintf(fp,"\n###################################################################\nMultiloop\n");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pUM[k][i])*kT;+      else temp=pUM[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\tM\n");+    free(pUM[k]);+  }+  fprintf(fp,"\n###################################################################\nExterior\n");+  for (i=1; i<=ulength; i++) {+    fprintf(fp,"%d\t", i);+  }+  fprintf(fp,"\t E\n");++  for (k=1; k<=length; k++){+    fprintf(fp,"%d\t",k);+    for (i=1; i<=ulength; i++) {+      if (i>k) {+        fprintf(fp,"NA\t");+        continue;+      }+      if (energies) temp=-log(pUO[k][i])*kT;+      else temp=pUO[k][i];+      fprintf(fp,"%.7g\t",temp);+    }+    fprintf(fp,"\n");+    free(pU[k]);+  }+  fflush(fp);+}+++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC void init_pf_foldLP(int length){ /* DO NOTHING */}+
+ C/ViennaRNA/LPfold.h view
@@ -0,0 +1,167 @@+#ifndef VIENNA_RNA_PACKAGE_LPFOLD_H+#define VIENNA_RNA_PACKAGE_LPFOLD_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     LPfold.h+ *  @ingroup  local_fold+ *  @brief    Partition function implementation for the Lfold algorithm+ *+ */+++/**+ *  \brief+ *+ *  \ingroup local_pf_fold+ * + *  \param  length+ */+void update_pf_paramsLP(int length);++/**+ *  \brief+ *+ *  \ingroup local_pf_fold+ * + */+void update_pf_paramsLP_par(int length, vrna_exp_param_t *parameters);++/**+ *  \brief Compute partition functions for locally stable secondary structures+ * + *  pfl_fold computes partition functions for every window of size+ *  'winSize' possible in a RNA molecule, allowing only pairs with a span+ *  smaller than 'pairSize'. It returns the mean pair probabilities averaged+ *  over all windows containing the pair in 'pl'. 'winSize' should+ *  always be >= 'pairSize'. Note that in contrast to Lfold(),+ *  bases outside of the window do not influence the structure at all. Only+ *  probabilities higher than 'cutoffb' are kept.+ * + *  If 'pU' is supplied (i.e is not the NULL pointer), pfl_fold()+ *  will also compute the mean probability that regions of length 'u' and smaller are + *  unpaired. The parameter 'u' is supplied in 'pup[0][0]'. On return+ *  the 'pup' array will contain these probabilities, with the entry on+ *  'pup[x][y]' containing the mean probability that x and the y-1+ *  preceding bases are unpaired. The 'pU' array needs to be large+ *  enough to hold n+1 float* entries, where n is the sequence length.+ * + *  If an array dpp2 is supplied, the probability of base pair (i,j)+ *  given that there already exists a base pair (i+1,j-1) is also+ *  computed and saved in this array. If pUfp is given (i.e. not NULL), pU+ *  is not saved but put out imediately. If spup is given (i.e. is not NULL),+ *  the pair probabilities in pl are not saved but put out imediately.+ *+ *  \ingroup local_pf_fold+ * + *  \param  sequence  RNA sequence+ *  \param  winSize   size of the window+ *  \param  pairSize  maximum size of base pair+ *  \param  cutoffb   cutoffb for base pairs+ *  \param  pU        array holding all unpaired probabilities   + *  \param  dpp2  array of dependent pair probabilities    + *  \param  pUfp     file pointer for pU + *  \param  spup     file pointer for pair probabilities   + *  \return list of pair probabilities       + */+plist *pfl_fold(char *sequence,+                int winSize,+                int pairSize,+                float cutoffb,+                double **pU,+                plist **dpp2,+                FILE *pUfp,+                FILE *spup);++/**+ *  \brief Compute partition functions for locally stable secondary structures+ * + *  \ingroup local_pf_fold+ * + */+plist *pfl_fold_par(char *sequence,+                    int winSize,+                    int pairSize,+                    float cutoffb,+                    double **pU,+                    plist **dpp2,+                    FILE *pUfp,+                    FILE *spup,+                    vrna_exp_param_t *parameters);+++void putoutpU_prob_par( double **pU,+                        int length,+                        int ulength,+                        FILE *fp,+                        int energies,+                        vrna_exp_param_t *parameters);+++/**+ *  \brief Writes the unpaired probabilities (pU) or opening energies into a file+ * + *  Can write either the unpaired probabilities (accessibilities) pU or+ *  the opening energies -log(pU)kT into a file+ * + *  \ingroup local_pf_fold+ * + *  \param  pU       pair probabilities+ *  \param  length   length of RNA sequence + *  \param  ulength  maximum length of unpaired stretch + *  \param  fp file pointer of destination file       + *  \param  energies  switch to put out as  opening energies + */+void    putoutpU_prob(double **pU,+                      int length,+                      int ulength,+                      FILE *fp,+                      int energies);++void putoutpU_prob_bin_par( double **pU,+                            int length,+                            int ulength,+                            FILE *fp,+                            int energies,+                            vrna_exp_param_t *parameters);++/**+ *  \brief Writes the unpaired probabilities (pU) or opening energies into a binary file + * + *  Can write either the unpaired probabilities (accessibilities) pU or+ *  the opening energies -log(pU)kT into a file+ * + *  \ingroup local_pf_fold+ * + *  \param  pU       pair probabilities+ *  \param  length   length of RNA sequence + *  \param  ulength  maximum length of unpaired stretch + *  \param  fp file pointer of destination file       + *  \param  energies  switch to put out as  opening energies + */+void    putoutpU_prob_bin(double **pU,+                          int length,+                          int ulength,+                          FILE *fp,+                          int energies);++/**+ *  Dunno if this function was ever used by external programs linking to RNAlib, but it+ *  was declared PUBLIC before.+ *  Anyway, never use this function as it will be removed soon and does nothing at all+ */+DEPRECATED(void init_pf_foldLP(int length));++#endif
+ C/ViennaRNA/Lfold.c view
@@ -0,0 +1,1413 @@+/*+                  minimum free energy+                  RNA secondary structure prediction+                  with maximum distance base pairs++                  c Ivo Hofacker, Peter Stadler++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/Lfold.h"++#ifdef USE_SVM+#include "svm.h"+#include "svm_utils.h"+#endif++#define MAXSECTORS                  500   /* dimension for a backtrack array */+#define INT_CLOSE_TO_UNDERFLOW(i)   ((i) <= (INT_MIN/16))+#define UNDERFLOW_CORRECTION        (INT_MIN/32)++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE float wrap_Lfold( vrna_fold_compound_t *vc,+                          int with_zsc,+                          double min_z,+                          FILE *file);+PRIVATE void  make_ptypes(vrna_fold_compound_t *vc,+                          int i);+PRIVATE char  *backtrack( vrna_fold_compound_t *vc,+                          int start,+                          int maxdist);+PRIVATE int   fill_arrays(vrna_fold_compound_t *vc,+                          int with_zsc,+                          double min_z,+#ifdef USE_SVM+                          struct svm_model *avg_model,+                          struct svm_model *sd_model,+#endif+                          int *underflow,+                          FILE *output);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_Lfold( const char *string,+            int window_size,+            FILE  *file){++  float               energy;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  vrna_md_set_default(&md);++  md.window_size = window_size;+  md.max_bp_span = window_size;++  vc  = vrna_fold_compound(string, &md, VRNA_OPTION_WINDOW);++  energy = wrap_Lfold(vc, 0, 0.0, file);++  vrna_fold_compound_free(vc);++  return energy;+}++PUBLIC float+vrna_mfe_window( vrna_fold_compound_t *vc,+            FILE *file){++  return wrap_Lfold(vc, 0, 0.0, file);+}++#ifdef USE_SVM++PUBLIC float+vrna_Lfoldz(const char *string,+            int window_size,+            double min_z,+            FILE *file){++  float               energy;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  vrna_md_set_default(&md);++  md.window_size = window_size;+  md.max_bp_span = window_size;++  vc  = vrna_fold_compound(string, &md, VRNA_OPTION_WINDOW);++  energy = wrap_Lfold(vc, 1, min_z, file);++  vrna_fold_compound_free(vc);++  return energy;+}++PUBLIC float+vrna_mfe_window_zscore( vrna_fold_compound_t *vc,+             double min_z,+             FILE *file){++  return wrap_Lfold(vc, 1, min_z, file);+}++#endif++/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/++PRIVATE float+wrap_Lfold( vrna_fold_compound_t *vc,+            int with_zsc,+            double min_z,+            FILE *file){++  int     i, energy, underflow, n, maxdist;+  float   mfe_local;+  FILE    *out;++#ifdef USE_SVM+  struct svm_model  *avg_model = NULL;+  struct svm_model  *sd_model = NULL;+#endif++  if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_MFE | VRNA_OPTION_WINDOW)){+    vrna_message_warning("vrna_mfe_window@Lfold.c: Failed to prepare vrna_fold_compound");+    return (float)(INF/100.);+  }+++  n       = vc->length;+  maxdist = vc->window_size;+  out     = (file) ? file : stdout;++  for(i = n; (i >= (int)n - (int)maxdist - 4) && (i > 0); i--)+    make_ptypes(vc, i);++#ifdef USE_SVM  /*svm*/+  if(with_zsc){+    avg_model = svm_load_model_string(avg_model_string);+    sd_model  = svm_load_model_string(sd_model_string);+  }+#endif++  /* keep track of how many times we were close to an integer underflow */+  underflow = 0;++#ifdef USE_SVM+  energy = fill_arrays(vc, with_zsc, min_z, avg_model, sd_model, &underflow, out);+  if(with_zsc){+    svm_free_model_content(avg_model);+    svm_free_model_content(sd_model);+  }+#else+  energy = fill_arrays(vc, with_zsc, min_z, &underflow, out);+#endif++  mfe_local = (underflow > 0) ? ((float)underflow * (float)(UNDERFLOW_CORRECTION)) / 100. : 0.;+  mfe_local += (float)energy/100.;++  return mfe_local;+}++PRIVATE int+fill_arrays(vrna_fold_compound_t *vc,+            int zsc,+            double min_z,+#ifdef USE_SVM+            struct svm_model *avg_model,+            struct svm_model *sd_model,+#endif+            int *underflow,+            FILE *output){++  /* fill "c", "fML" and "f3" arrays and return  optimal energy */++  int   i, j, k, length, energy, maxdist;+  int   **c, **fML, *f3, **ggg;+  int   decomp, new_fML;+  int   no_close, type, type_2, tt, with_gquad, dangle_model, noLP, noGUclosure, turn;+  int   *rtype;+  int   fij;+  int   lind;++  int   *cc = NULL;        /* linear array for calculating canonical structures */+  int   *cc1 = NULL;       /*   "     "        */+  int   *Fmi = NULL;       /* holds row i of fML (avoids jumps in memory) */+  int   *DMLi = NULL;      /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */+  int   *DMLi1 = NULL;     /*             MIN(fML[i+1,k]+fML[k+1,j])  */+  int   *DMLi2 = NULL;     /*             MIN(fML[i+2,k]+fML[k+1,j])  */++  short         *S, *S1;+  char          *string, **ptype, *prev;+  vrna_param_t  *P;+  vrna_md_t     *md;+++  string        = vc->sequence;+  length        = vc->length;+  S             = vc->sequence_encoding2;+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype_local;+  maxdist       = vc->window_size;+  P             = vc->params;+  md            = &(P->model_details);+  dangle_model  = md->dangles;+  with_gquad    = md->gquad;+  noLP          = md->noLP;+  noGUclosure   = md->noGUclosure;+  turn          = md->min_loop_size;+  rtype         = &(md->rtype[0]);++  prev          = NULL;++  c           = vc->matrices->c_local;+  fML         = vc->matrices->fML_local;+  f3          = vc->matrices->f3_local;+  ggg         = vc->matrices->ggg_local;++  cc    = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+  cc1   = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+  Fmi   = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+  DMLi  = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+  DMLi1 = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+  DMLi2 = (int *)   vrna_alloc(sizeof(int)   *(maxdist+5));+++  for (j=0; j<maxdist+5; j++)+    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;+  for (j=length; j>length-maxdist-4; j--) {+    for (i=(length-maxdist-4>0)?length-maxdist-4:1 ; i<j; i++)+      c[i][j-i] = fML[i][j-i] = INF;+  }++  if(with_gquad){+    vrna_gquad_mx_local_update(vc, length - maxdist - 4);+    ggg = vc->matrices->ggg_local;+  }++  for (i = length-turn-1; i >= 1; i--) { /* i,j in [1..length] */+    for (j = i+turn+1; j <= length && j <= i+maxdist; j++) {+      int p, q;+      type = ptype[i][j-i];++      no_close = (((type==3)||(type==4))&&noGUclosure);++      if (type) {   /* we have a pair */+        int new_c=0, stackEnergy=INF;+        /* hairpin ----------------------------------------------*/++        new_c = (no_close) ? FORBIDDEN : E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], string+i-1, P);++        /*--------------------------------------------------------+          check for elementary structures involving more than one+          closing pair.+          --------------------------------------------------------*/++        for (p = i+1; p <= MIN2(j-2-turn,i+MAXLOOP+1) ; p++){+          int minq = j-i+p-MAXLOOP-2;+          if (minq<p+1+turn) minq = p+1+turn;+          for (q = minq; q < j; q++) {+            type_2 = ptype[p][q-p];++            if (type_2==0) continue;+            type_2 = rtype[type_2];++            if (noGUclosure)+              if (no_close||(type_2==3)||(type_2==4))+                if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */++            energy = E_IntLoop(p-i-1, j-q-1, type, type_2, S1[i+1], S1[j-1], S1[p-1], S1[q+1],P);+            new_c = MIN2(new_c, energy + c[p][q-p]);+            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */+          } /* end q-loop */+        } /* end p-loop */++        /* multi-loop decomposition ------------------------*/+        if (!no_close) {+          decomp  = DMLi1[j-1-(i+1)];+          tt      = rtype[type];+          switch(dangle_model){+            /* no dangle_model */+            case 0:   decomp += E_MLstem(tt, -1, -1, P);+                      break;+            /* double dangle_model */+            case 2:   decomp += E_MLstem(tt, S1[j-1], S1[i+1], P);+                      break;+            /* normal dangle_model, aka dangle_model = 1 */+            default:  decomp += E_MLstem(tt, -1, -1, P);+                      decomp = MIN2(decomp, DMLi2[j-1-(i+2)] + E_MLstem(tt, -1, S1[i+1], P) + P->MLbase);+                      decomp = MIN2(decomp, DMLi2[j-2-(i+2)] + E_MLstem(tt, S1[j-1], S1[i+1], P) + 2*P->MLbase);+                      decomp = MIN2(decomp, DMLi1[j-2-(i+1)] + E_MLstem(tt, S1[j-1], -1, P) + P->MLbase);+                      break;+          }+          new_c = MIN2(new_c, decomp + P->MLclosing);+        }++        /* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */++        if (dangle_model==3) {+          decomp = INF;+          for (k = i+2+turn; k < j-2-turn; k++) {+            type_2 = ptype[i+1][k-i-1]; type_2 = rtype[type_2];+            if (type_2)+              decomp = MIN2(decomp, c[i+1][k-i-1]+P->stack[type][type_2]++                            fML[k+1][j-1-k-1]);+            type_2 = ptype[k+1][j-1-k-1]; type_2 = rtype[type_2];+            if (type_2)+              decomp = MIN2(decomp, c[k+1][j-1-k-1]+P->stack[type][type_2]++                            fML[i+1][k-i-1]);+          }+          /* no TermAU penalty if coax stack */+          decomp += 2*P->MLintern[1] + P->MLclosing;+          new_c = MIN2(new_c, decomp);+        }++        if(with_gquad){+          /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */+          if (!no_close) {+            tt = rtype[type];+            energy = E_GQuad_IntLoop_L(i, j, type, S1, ggg, maxdist, P);+            new_c = MIN2(new_c, energy);+          }+        }++        new_c = MIN2(new_c, cc1[j-1-(i+1)]+stackEnergy);+        cc[j-i] = new_c;+        if (noLP)+          c[i][j-i] = cc1[j-1-(i+1)]+stackEnergy;+        else+          c[i][j-i] = cc[j-i];++      } /* end >> if (pair) << */++      else c[i][j-i] = INF;++      /* done with c[i,j], now compute fML[i,j] */+      /* free ends ? -----------------------------------------*/+      new_fML = INF;+      switch(dangle_model){+        /* no dangle_model */+        case 0:   new_fML = fML[i+1][j-i-1] + P->MLbase;+                  new_fML = MIN2(new_fML, fML[i][j-1-i] + P->MLbase);+                  new_fML = MIN2(new_fML, c[i][j-i] + E_MLstem(type, -1, -1, P));+                  break;+        /* double dangle_model */+        case 2:   new_fML = fML[i+1][j-i-1] + P->MLbase;+                  new_fML = MIN2(fML[i][j-1-i] + P->MLbase, new_fML);+                  new_fML = MIN2(new_fML,  c[i][j-i] + E_MLstem(type, (i>1) ? S1[i-1] : -1, (j<length) ? S1[j+1] : -1, P));+                  break;+        /* normal dangle_model, aka dangle_model = 1 */+        default:  /* i unpaired */+                  new_fML = fML[i+1][j-i-1] + P->MLbase;+                  /* j unpaired */+                  new_fML = MIN2(new_fML, fML[i][j-1-i] + P->MLbase);+                  /* i,j */+                  if(type) new_fML = MIN2(new_fML, c[i][j-i] + E_MLstem(type, -1, -1, P));+                  /* i+1,j */+                  tt = ptype[i+1][j-i-1];+                  if(tt) new_fML = MIN2(new_fML, c[i+1][j-i-1] + E_MLstem(tt, S1[i], -1, P) + P->MLbase);+                  /* i, j-1 */+                  tt = ptype[i][j-1-i];+                  if(tt) new_fML = MIN2(new_fML, c[i][j-1-i] + E_MLstem(tt, -1, S1[j], P) + P->MLbase);+                  /* i+1,j-1 */+                  tt = ptype[i+1][j-1-i-1];+                  if(tt) new_fML = MIN2(new_fML, c[i+1][j-1-i-1] + E_MLstem(tt, S1[i], S1[j], P) + 2*P->MLbase);+                  break;+      }++      if(with_gquad){+        new_fML = MIN2(new_fML, ggg[i][j - i] + E_MLstem(0, -1, -1, P));+      }++      /* modular decomposition -------------------------------*/+      for (decomp = INF, k = i+1+turn; k <= j-2-turn; k++)+        decomp = MIN2(decomp, Fmi[k-i]+fML[k+1][j-k-1]);++      DMLi[j-i] = decomp;               /* store for use in ML decompositon */+      new_fML   = MIN2(new_fML, decomp);++      /* coaxial stacking */+      if (dangle_model==3) {+        /* additional ML decomposition as two coaxially stacked helices */+        for (decomp = INF, k = i+1+turn; k <= j-2-turn; k++) {+          type = ptype[i][k-i]; type = rtype[type];+          type_2 = ptype[k+1][j-k-1]; type_2 = rtype[type_2];+          if (type && type_2)+            decomp = MIN2(decomp,+                          c[i][k-i]+c[k+1][j-k-1]+P->stack[type][type_2]);+        }++        decomp += 2*P->MLintern[1];          /* no TermAU penalty if coax stack */+#if 0+        /* This is needed for Y shaped ML loops with coax stacking of+           interior pairts, but backtracking will fail if activated */+        DMLi[j-i] = MIN2(DMLi[j-i], decomp);+        DMLi[j-i] = MIN2(DMLi[j-i], DMLi[j-1-i]+P->MLbase);+        DMLi[j-i] = MIN2(DMLi[j-i], DMLi1[j-(i+1)]+P->MLbase);+        new_fML = MIN2(new_fML, DMLi[j-i]);+#endif+        new_fML = MIN2(new_fML, decomp);+      }+      fML[i][j-i] = Fmi[j-i] = new_fML;     /* substring energy */+    } /* for (j...) */++    /* calculate energies of 5' and 3' fragments */+    {+      static int do_backtrack = 0, prev_i=0;+      char *ss=NULL;+      double prevz = 0.;++      /* first case: i stays unpaired */+      f3[i] = f3[i+1];++      /* next all cases where i is paired */+      switch(dangle_model){+        /* dont use dangling end and mismatch contributions at all */+        case 0:   for(j=i+turn+1; j<length && j<=i+maxdist; j++){+                    type = ptype[i][j-i];++                    if(with_gquad){+                      f3[i] = MIN2(f3[i], f3[j+1] + ggg[i][j-i]);+                    }++                    if(type)+                      f3[i] = MIN2(f3[i], f3[j+1] + c[i][j-i] + E_ExtLoop(type, -1, -1, P));+                  }+                  if(length<=i+maxdist){+                    j=length;++                    if(with_gquad){+                      f3[i] = MIN2(f3[i], ggg[i][j-i]);+                    }++                    type = ptype[i][j-i];+                    if(type)+                      f3[i] = MIN2(f3[i], c[i][j-i] + E_ExtLoop(type, -1, -1, P));+                  }+                  break;+        /* always use dangle_model on both sides */+        case 2:   for(j=i+turn+1; j<length && j<=i+maxdist; j++){+                    type = ptype[i][j-i];++                    if(with_gquad){+                      if(ggg[i][j-i] != INF)+                        f3[i] = MIN2(f3[i], f3[j+1] + ggg[i][j-i]);+                    }++                    if(type)+                      f3[i] = MIN2(f3[i], f3[j+1] + c[i][j-i] + E_ExtLoop(type, (i>1) ? S1[i-1] : -1, S1[j+1], P));+                  }+                  if(length<=i+maxdist){+                    j=length;++                    if(with_gquad){+                      f3[i] = MIN2(f3[i], ggg[i][j-i]);+                    }++                    type = ptype[i][j-i];+                    if(type)+                      f3[i] = MIN2(f3[i], c[i][j-i] + E_ExtLoop(type, (i>1) ? S1[i-1] : -1, -1, P));+                  }+                  break;+        /* normal dangle_model, aka dangle_model = 1 */+        default:  for(j=i+turn+1; j<length && j<=i+maxdist; j++){+                    type = ptype[i][j-i];++                    if(with_gquad){+                      f3[i] = MIN2(f3[i], f3[j+1] + ggg[i][j-i]);+                    }++                    if(type){+                      f3[i] = MIN2(f3[i], f3[j+1] + c[i][j-i] + E_ExtLoop(type, -1, -1, P));+                      f3[i] = MIN2(f3[i], ((j+2<=length) ? f3[j+2] : 0) + c[i][j-i] + E_ExtLoop(type, -1, S1[j+1], P));+                    }+                    type = ptype[i+1][j-i-1];+                    if(type){+                      f3[i] = MIN2(f3[i], f3[j+1] + c[i+1][j-i-1] + E_ExtLoop(type, S1[i], -1, P));+                      f3[i] = MIN2(f3[i], ((j + 1 < length) ? f3[j+2] : 0) + c[i+1][j-i-1] + E_ExtLoop(type, S1[i], S1[j+1], P));+                    }+                  }+                  if(length<=i+maxdist){+                    j     = length;++                    if(with_gquad){+                      f3[i] = MIN2(f3[i], ggg[i][j-i]);+                    }++                    type  = ptype[i][j-i];+                    if(type)+                      f3[i] = MIN2(f3[i], c[i][j-i] + E_ExtLoop(type, -1, -1, P));+                    type  = ptype[i+1][j-i-1];+                    if(type)+                      f3[i] = MIN2(f3[i], c[i+1][j-i-1] + E_ExtLoop(type, S1[i], -1, P));+                  }+                  break;+      } /* switch(dangle_model)... */++      /* backtrack partial structure */+      if (f3[i] < f3[i+1]){+        do_backtrack=1;+      }+      else if (do_backtrack) {+        int pairpartner; /*i+1?? is paired with pairpartner*/+        int cc;+        int traced2=0;+        fij = f3[i+1];+        lind=i+1;+        /*start "short" backtrack*/++        /*get paired base*/+        while(fij==f3[lind+1])+          lind++;++        /*get pairpartner*/+        for (pairpartner = lind + turn; pairpartner <= lind + maxdist; pairpartner++){+          type = ptype[lind][pairpartner-lind];+          switch(dangle_model){+            case 0:   if(type){+                        cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, -1, P);+                        if(fij == cc + f3[pairpartner + 1])+                          traced2 = 1;+                      }+                      else if(with_gquad) {+                        cc = ggg[lind][pairpartner-lind];+                        if(fij == cc + f3[pairpartner + 1])+                          traced2 = 1;+                      }++                      break;+            case 2:   if(type){+                        cc = c[lind][pairpartner-lind] + E_ExtLoop(type, (lind > 1) ? S1[lind-1] : -1, (pairpartner < length) ? S1[pairpartner+1] : -1, P);+                        if(fij == cc + f3[pairpartner + 1])+                          traced2 = 1;+                      }+                      else if(with_gquad){+                        cc = ggg[lind][pairpartner-lind];+                        if(fij == cc + f3[pairpartner + 1])+                          traced2 = 1;+                      }++                      break;+            default:  if(type){+                        cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, -1, P);+                        if(fij == cc + f3[pairpartner + 1]){+                          traced2 = 1;+                          break;+                        }+                        else if(pairpartner < length){+                          cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, S1[pairpartner+1], P);+                          if(fij == cc + f3[pairpartner + 2]){+                            traced2 = 1;+                            break;+                          }+                        }+                      }+                      else if(with_gquad){+                        cc = ggg[lind][pairpartner-lind];+                        if(fij == cc + f3[pairpartner + 1])+                          traced2 = 1;+                      }++                      type = ptype[lind+1][pairpartner-lind-1];+                      if(type){+                        cc = c[lind+1][pairpartner-(lind+1)] + E_ExtLoop(type, S1[lind], -1, P);+                        if(fij == cc + f3[pairpartner+1]){+                          traced2 = 1;+                          break;+                        }+                        else if(pairpartner < length){+                          cc = c[lind+1][pairpartner-(lind+1)] + E_ExtLoop(type, S1[lind], S1[pairpartner+1], P);+                          if(fij == cc + f3[pairpartner+2])+                            traced2 = 1;+                        }+                      }+                      break;+          }+          if(traced2) break;+        }+        if (!traced2) vrna_message_error("backtrack failed in short backtrack 1");+        if (zsc){+#ifdef USE_SVM+          int info_avg;+          double average_free_energy;+          double sd_free_energy;+          double my_z;+          int *AUGC = get_seq_composition(S, lind-1, MIN2((pairpartner+1),length), length);+          /*\svm*/+          average_free_energy = avg_regression(AUGC[0], AUGC[1], AUGC[2], AUGC[3], AUGC[4], avg_model, &info_avg);+          if (info_avg == 0)  {+            double difference;+            double min_sd = minimal_sd(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4]);+            difference=(fij-f3[pairpartner+1])/100.-average_free_energy;+            if ( difference - ( min_z * min_sd ) <= 0.0001 ) {+              sd_free_energy = sd_regression(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4],sd_model);+              my_z=difference/sd_free_energy;+              if (my_z<=min_z){+                ss =  backtrack(vc, lind, pairpartner+1);+                if (prev) {+                  if ((i+strlen(ss)<prev_i+strlen(prev)) ||+                      strncmp(ss+prev_i-i,prev,strlen(prev))) { /* ss does not contain prev */+                    if (dangle_model==2)+                      fprintf(output, ".%s (%6.2f) %4d z= %.3f\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)-1])/100., prev_i-1, prevz);+                    else+                      fprintf(output, "%s (%6.2f) %4d z=%.3f\n ", prev, (f3[prev_i]-f3[prev_i+strlen(prev)])/100., prev_i, prevz);+                  }+                  free(prev);+                }+                prev=ss; prev_i = lind; prevz=my_z;+              }+            }++          }+          free(AUGC);+          do_backtrack=0;+#endif+        }+        else {+          /* original code for Lfold*/+          ss =  backtrack(vc, lind , pairpartner+1);+          if (prev) {+            if ((i+strlen(ss)<prev_i+strlen(prev)) || strncmp(ss+prev_i-i,prev,strlen(prev))){+              /* ss does not contain prev */+              if (dangle_model==2){+                fprintf(output, ".%s (%6.2f) %4d\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)-1])/100., prev_i-1);+              } else+                fprintf(output, "%s (%6.2f) %4d\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)])/100., prev_i);+            }+            free(prev);+          }+          prev=ss;+          prev_i = lind;+          do_backtrack=0;+        }+      }+      if (i==1) {+        if (prev) {+          if(zsc) {+            if (dangle_model==2)+              fprintf(output, ".%s (%6.2f) %4d z= %.2f\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)-1])/100., prev_i-1, prevz);+           else+              fprintf(output, "%s (%6.2f) %4dz= %.2f \n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)])/100., prev_i, prevz);+          }+          else {+            if (dangle_model==2)+              fprintf(output, ".%s (%6.2f) %4d\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)-1])/100., prev_i-1);+            else+              fprintf(output, "%s (%6.2f) %4d\n", prev, (f3[prev_i]-f3[prev_i+strlen(prev)])/100., prev_i);+          }+          free(prev); prev=NULL;+        } else if ((f3[i]<0) && (!zsc)) do_backtrack=1;++        if (do_backtrack) {+          int pairpartner; /*i+1?? is paired with pairpartner*/+          int cc;+          double average_free_energy;+          double sd_free_energy;+          int info_avg;+          double my_z;+          int traced2 = 0;+          fij = f3[i];+          lind=i;+          while(fij==f3[lind+1]) lind++;+          /*get pairpartner*/+          for(pairpartner = lind + turn; pairpartner <= lind + maxdist; pairpartner++){+            type = ptype[lind][pairpartner-lind];+            switch(dangle_model){+              case 0:   if(type){+                          cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, -1, P);+                          if(fij == cc + f3[pairpartner + 1])+                            traced2 = 1;+                        }+                        else if(with_gquad){+                          cc = ggg[lind][pairpartner-lind];+                          if(fij == cc + f3[pairpartner + 1])+                            traced2 = 1;+                        }++                        break;+              case 2:   if(type){+                          cc = c[lind][pairpartner-lind] + E_ExtLoop(type, (lind > 1) ? S1[lind-1] : -1, (pairpartner < length) ? S1[pairpartner+1] : -1, P);+                          if(fij == cc + f3[pairpartner + 1])+                            traced2 = 1;+                        }+                        else if(with_gquad){+                          cc = ggg[lind][pairpartner-lind];+                          if(fij == cc + f3[pairpartner + 1])+                            traced2 = 1;+                        }++                        break;+              default:  if(type){+                          cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, -1, P);+                          if(fij == cc + f3[pairpartner + 1]){+                            traced2 = 1;+                            break;+                          }+                          else if(pairpartner < length){+                            cc = c[lind][pairpartner-lind] + E_ExtLoop(type, -1, S1[pairpartner + 1], P);+                            if(fij == cc + f3[pairpartner + 1]){+                              traced2 = 1;+                              break;+                            }+                          }+                        }+                        else if(with_gquad){+                          cc = ggg[lind][pairpartner-lind];+                          if(fij == cc + f3[pairpartner + 1])+                            traced2 = 1;+                        }++                        type = ptype[lind+1][pairpartner-lind-1];+                        if(type){+                          cc = c[lind+1][pairpartner-(lind+1)] + E_ExtLoop(type, S1[lind], -1, P);+                          if(fij == cc + f3[pairpartner+1]){+                            traced2 = 1;+                            break;+                          }+                          else if (pairpartner < length){+                            cc = c[lind+1][pairpartner-(lind+1)] + E_ExtLoop(type, S1[lind], S1[pairpartner+1], P);+                            if(fij == cc + f3[pairpartner + 2]){+                              traced2 =1;+                              break;+                            }+                          }+                        }+            }+            if(traced2) break;+          }+          if (!traced2) vrna_message_error("backtrack failed in short backtrack 2");++          if(zsc){+#ifdef USE_SVM+            int *AUGC = get_seq_composition(S, lind-1, MIN2((pairpartner+1),length), length);+            average_free_energy = avg_regression(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4],avg_model,&info_avg);+            if (info_avg == 0)  {+              double difference;+              double min_sd = minimal_sd(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4]);+              difference=(fij-f3[pairpartner+1])/100.-average_free_energy;+              if ( difference - ( min_z * min_sd ) <= 0.0001 ) {+                sd_free_energy = sd_regression(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4],sd_model);+                my_z=difference/sd_free_energy;+                if (my_z<=min_z){+                  ss =  backtrack(vc, lind , pairpartner+1);+                  fprintf(output, "%s (%6.2f) %4d z= %.2f\n", ss, (f3[lind]-f3[lind+strlen(ss)-1])/100., lind, my_z);+                }+              }+            }+            free(AUGC);+#endif+          }+          else {+            ss =  backtrack(vc, lind , pairpartner+1);+            if (dangle_model==2)+              fprintf(output, "%s (%6.2f) %4d\n", ss, (f3[lind]-f3[lind+strlen(ss)-1])/100., 1);+            else+              fprintf(output, "%s (%6.2f) %4d\n", ss, (f3[lind]-f3[lind+strlen(ss)])/100., 1);+            free(ss);+          }+        }+        do_backtrack=0;+      }+    }+    {+      int ii, *FF; /* rotate the auxilliary arrays */++      /* check for values close to integer underflow */+      if(INT_CLOSE_TO_UNDERFLOW(f3[i])){+        /* correct f3 free energies and increase underflow counter */+        int cnt, cnt2;+        for(cnt=i; cnt <= length && cnt <= lind + maxdist + 2; cnt++) {+          f3[cnt] -= UNDERFLOW_CORRECTION;+        }+        (*underflow)++;+      }++      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for(j = 0; j < maxdist + 5; j++){+        cc[j] = Fmi[j] = DMLi[j] = INF;+      }++      /*+        rotate the DP matrices+        NOTE: here we rotate them only locally, i.e. their+        actual configuration within vc remains intact+      */+      if( i + maxdist + 4 <= length ){+        c[i - 1]                = c[i + maxdist + 4];+        c[i + maxdist + 4]      = NULL;+        fML[i - 1]              = fML[i + maxdist + 4];+        fML[i + maxdist + 4]    = NULL;+        ptype[i - 1]            = ptype[i + maxdist + 4];+        ptype[i + maxdist + 4]  = NULL;+        if( i > 1 ){+          make_ptypes(vc, i - 1);+          if(with_gquad){+            vrna_gquad_mx_local_update(vc, i - 1);+            ggg = vc->matrices->ggg_local;+          }+        }+        for(ii = 0; ii < maxdist + 5; ii++){+          c[i - 1][ii]    = INF;+          fML[i - 1][ii]  = INF;+        }+      }++    }+  }++  free(cc);+  free(cc1);+  free(Fmi);+  free(DMLi);+  free(DMLi1);+  free(DMLi2);++  return f3[1];+}++PRIVATE char *+backtrack(vrna_fold_compound_t *vc,+          int start,+          int maxdist){++  /*------------------------------------------------------------------+    trace back through the "c", "f3" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This is fast, since only few structure elements are recalculated.+    ------------------------------------------------------------------*/+  sect          sector[MAXSECTORS];   /* backtracking sectors */+  int           i, j, k, length, energy, new, no_close, type, type_2, tt, s=0;+  int           with_gquad, bt_type, turn, dangle_model, noLP, noGUclosure, *rtype;+  int           **c, **fML, *f3, **ggg;+  char          *string, *structure, **ptype;+  short         *S, *S1;+  vrna_param_t  *P;+  vrna_md_t     *md;++  string        = vc->sequence;+  length        = vc->length;+  S             = vc->sequence_encoding2;+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype_local;+  P             = vc->params;+  md            = &(P->model_details);+  dangle_model  = md->dangles;+  noLP          = md->noLP;+  noGUclosure   = md->noGUclosure;+  with_gquad    = md->gquad;+  bt_type       = md->backtrack_type;+  turn          = md->min_loop_size;+  rtype         = &(md->rtype[0]);++  c       = vc->matrices->c_local;+  fML     = vc->matrices->fML_local;+  f3      = vc->matrices->f3_local;+  ggg     = vc->matrices->ggg_local;++  /* length = strlen(string); */+  sector[++s].i = start;+  sector[s].j   = MIN2(length, maxdist+1);+  sector[s].ml  = (bt_type=='M') ? 1 : ((bt_type=='C')?2:0);++  structure = (char *) vrna_alloc((MIN2(length-start, maxdist)+3)*sizeof(char));+  for (i=0; i<=MIN2(length-start, maxdist); i++) structure[i] = '-';++  while (s>0) {+    int ml, fij, cij, traced, i1, j1, mm, mm5, mm3, mm53, p, q, jj=0, gq=0;+    int canonical = 1;     /* (i,j) closes a canonical structure */+    i  = sector[s].i;+    j  = sector[s].j;+    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to+                              occur in the fML- (1) or in the f-array (0) */+    if (ml==2) {+      structure[i-start] = '(';+      structure[j-start] = ')';+      goto repeat1;+    }++    if (j < i + turn + 1) continue; /* no more pairs in this interval */++    fij = (ml)? fML[i][j-i] : f3[i];++    if (ml == 0) { /* backtrack in f3 */++      if (fij == f3[i+1]) {+        sector[++s].i = i+1;+        sector[s].j   = j;+        sector[s].ml  = ml;+        continue;+      }+      /* i or i+1 is paired. Find pairing partner */+      switch(dangle_model){+        case 0:   for(traced = 0, k=j; k>i+turn; k--){++                    if(with_gquad){+                      if(fij == ggg[i][k-i] + f3[k+1]){+                        /* found the decomposition */+                        traced = i; jj = k + 1; gq = 1;+                        break;+                      }+                    }++                    jj    = k+1;+                    type  = ptype[i][k-i];+                    if(type)+                      if(fij == c[i][k-i] + E_ExtLoop(type, -1, -1, P) + f3[k+1]){+                        traced = i;+                        break;+                      }+                  }+                  break;+        case 2:   for(traced = 0, k=j; k>i+turn; k--){++                    if(with_gquad){+                      if(fij == ggg[i][k-i] + f3[k+1]){+                        /* found the decomposition */+                        traced = i; jj = k + 1; gq = 1;+                        break;+                      }+                    }++                    jj    = k+1;+                    type  = ptype[i][k-i];+                    if(type)+                      if(fij == c[i][k-i] + E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (k<length) ? S1[k+1] : -1, P) + f3[k+1]){+                        traced = i;+                        break;+                      }+                  }+                  break;+        default:  for(traced = 0,k=j; k>i+turn; k--){++                    if(with_gquad){+                      if(fij == ggg[i][k-i] + f3[k+1]){+                        /* found the decomposition */+                        traced = i; jj = k + 1; gq = 1;+                        break;+                      }+                    }++                    jj = k+1;+                    type = ptype[i+1][k-(i+1)];+                    if(type){+                      if(fij == c[i+1][k-(i+1)] + E_ExtLoop(type, S1[i], -1, P) + f3[k+1]){+                        traced=i+1;+                      }+                      if(k < length){+                        if(fij == c[i+1][k-(i+1)] + E_ExtLoop(type, S1[i], S1[k+1], P) + f3[k+2]){+                          traced  = i+1;+                          jj      = k+2;+                        }+                      }+                    }+                    type = ptype[i][k-i];+                    if(type){+                      if(fij == c[i][k-i] + E_ExtLoop(type, -1, -1, P) + f3[k+1]){+                        traced = i;+                      }+                      if(k<length){+                        if(fij == c[i][k-i] + E_ExtLoop(type, -1, S1[k+1], P) + f3[k+2]){+                          traced  = i;+                          jj      = k+2;+                        }+                      }+                    }+                    if(traced) break;+                  }+                  break;+      } /* switch(dangle_model)...*/++      if (!traced) vrna_message_error("backtrack failed in f3");+      if (j==length) { /* backtrack only one component, unless j==length */+        sector[++s].i = jj;+        sector[s].j   = j;+        sector[s].ml  = ml;+      }+      i=traced; j=k;++      if(with_gquad && gq){+        /* goto backtrace of gquadruplex */+        goto repeat_gquad;+      }++      structure[i-start] = '('; structure[j-start] = ')';+      if (((jj==j+2) || (dangle_model==2)) && (j < length)) structure[j+1-start] = '.';+      goto repeat1;+    }+    else { /* trace back in fML array */+      if (fML[i][j-1-i]+P->MLbase == fij) {  /* 3' end is unpaired */+        sector[++s].i = i;+        sector[s].j   = j-1;+        sector[s].ml  = ml;+        continue;+      }+      if (fML[i+1][j-(i+1)]+P->MLbase == fij) { /* 5' end is unpaired */+        sector[++s].i = i+1;+        sector[s].j   = j;+        sector[s].ml  = ml;+        continue;+      }++      if(with_gquad){+        if(fij == ggg[i][j-i] + E_MLstem(0, -1, -1, P)){+          /* go to backtracing of quadruplex */+          goto repeat_gquad;+        }+      }++      switch(dangle_model){+        case 0:   tt = ptype[i][j-i];+                  if(fij == c[i][j-i] + E_MLstem(tt, -1, -1, P)){+                    structure[i-start] = '(';+                    structure[j-start] = ')';+                    goto repeat1;+                  }+                  break;+        case 2:   tt = ptype[i][j-i];+                  if(fij == c[i][j-i] + E_MLstem(tt, (i>1) ? S1[i-1] : -1, (j < length) ? S1[j+1] : -1, P)){+                    structure[i-start] = '(';+                    structure[j-start] = ')';+                    goto repeat1;+                  }+                  break;+        default:  tt = ptype[i][j-i];+                  if(fij == c[i][j-i] + E_MLstem(tt, -1, -1, P)){+                    structure[i-start] = '(';+                    structure[j-start] = ')';+                    goto repeat1;+                  }+                  tt = ptype[i+1][j-(i+1)];+                  if(fij == c[i+1][j-(i+1)] + E_MLstem(tt, S1[i], -1, P) + P->MLbase){+                    structure[++i-start] = '(';+                    structure[j-start] = ')';+                    goto repeat1;+                  }+                  tt = ptype[i][j-1-i];+                  if(fij == c[i][j-1-i] + E_MLstem(tt, -1, S1[j], P) + P->MLbase){+                    structure[i-start] = '(';+                    structure[--j-start] = ')';+                    goto repeat1;+                  }+                  tt = ptype[i+1][j-1-(i+1)];+                  if(fij == c[i+1][j-1-(i+1)] + E_MLstem(tt, S1[i], S1[j], P) + 2*P->MLbase){+                    structure[++i-start] = '(';+                    structure[--j-start] = ')';+                    goto repeat1;+                  }+                  break;+      } /* switch(dangle_model)... */++      /* modular decomposition */+      for (k = i+1+turn; k <= j-2-turn; k++)+        if (fij == (fML[i][k-i]+fML[k+1][j-(k+1)]))+          break;++      if ((dangle_model==3)&&(k>j-2-turn)) { /* must be coax stack */+        ml = 2;+        for (k = i+1+turn; k <= j-2-turn; k++) {+          type = ptype[i][k-i];  type= rtype[type];+          type_2 = ptype[k+1][j-(k+1)]; type_2= rtype[type_2];+          if (type && type_2)+            if (fij == c[i][k-i]+c[k+1][j-(k+1)]+P->stack[type][type_2]++                       2*P->MLintern[1])+              break;+        }+      }++      sector[++s].i = i;+      sector[s].j   = k;+      sector[s].ml  = ml;+      sector[++s].i = k+1;+      sector[s].j   = j;+      sector[s].ml  = ml;++      if (k>j-2-turn) vrna_message_error("backtrack failed in fML");+      continue;+    }++  repeat1:++    /*----- begin of "repeat:" -----*/+    if (canonical)  cij = c[i][j-i];++    type = ptype[i][j-i];+++    if (noLP)+      if (cij == c[i][j-i]) {+        /* (i.j) closes canonical structures, thus+           (i+1.j-1) must be a pair                */+        type_2 = ptype[i+1][j-1-(i+1)]; type_2 = rtype[type_2];+        cij -= P->stack[type][type_2];+        structure[i+1-start] = '('; structure[j-1-start] = ')';+        i++; j--;+        canonical=0;+        goto repeat1;+      }+    canonical = 1;+++    no_close = (((type==3)||(type==4))&&noGUclosure);+    if (no_close) {+      if (cij == FORBIDDEN) continue;+    } else+      if (cij == E_Hairpin(j-i-1, type, S1[i+1], S1[j-1],string+i-1, P))+        continue;++    for (p = i+1; p <= MIN2(j-2-turn,i+MAXLOOP+1); p++) {+      int minq;+      minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+turn) minq = p+1+turn;+      for (q = j-1; q >= minq; q--) {++        type_2 = ptype[p][q-p];+        if (type_2==0) continue;+        type_2 = rtype[type_2];+        if (noGUclosure)+          if (no_close||(type_2==3)||(type_2==4))+            if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */++        /* energy = oldLoopEnergy(i, j, p, q, type, type_2); */+        energy = E_IntLoop(p-i-1, j-q-1, type, type_2, S1[i+1], S1[j-1], S1[p-1], S1[q+1],P);++        new = energy+c[p][q-p];+        traced = (cij == new);+        if (traced) {+          structure[p-start] = '(';+          structure[q-start] = ')';+          i = p, j = q;+          goto repeat1;+        }+      }+    }++    /* end of repeat: --------------------------------------------------*/++    /* (i.j) must close a multi-loop */+    tt = rtype[type];+    i1 = i+1; j1 = j-1;++    if(with_gquad){+      /*+        The case that is handled here actually resembles something like+        an interior loop where the enclosing base pair is of regular+        kind and the enclosed pair is not a canonical one but a g-quadruplex+        that should then be decomposed further...+      */+      if(backtrack_GQuad_IntLoop_L(cij, i, j, type, S, ggg, maxdist, &p, &q, P)){+        i = p; j = q;+        goto repeat_gquad;+      }+    }++    sector[s+1].ml  = sector[s+2].ml = 1;++    switch(dangle_model){+      case 0:   mm = P->MLclosing + E_MLstem(tt, -1, -1, P);+                for(k = i+2+turn; k < j-2-turn; k++){+                  if(cij == fML[i+1][k-(i+1)] + fML[k+1][j-1-(k+1)] + mm)+                    break;+                }+                break;+      case 2:   mm = P->MLclosing + E_MLstem(tt, S1[j-1], S1[i+1], P);+                for(k = i+2+turn; k < j-2-turn; k++){+                  if(cij == fML[i+1][k-(i+1)] + fML[k+1][j-1-(k+1)] + mm)+                    break;+                }+                break;+      default:  mm    = P->MLclosing + E_MLstem(tt, -1, -1, P);+                mm5   = P->MLclosing + E_MLstem(tt, S1[j-1], -1, P) + P->MLbase;+                mm3   = P->MLclosing + E_MLstem(tt, -1, S1[i+1], P) + P->MLbase;+                mm53  = P->MLclosing + E_MLstem(tt, S1[j-1], S1[i+1], P) + 2*P->MLbase;+                for(k = i+2+turn; k < j-2-turn; k++){+                  if(cij == fML[i+1][k-(i+1)] + fML[k+1][j-1-(k+1)] + mm)+                    break;+                  else if(cij == fML[i+2][k-(i+2)] + fML[k+1][j-1-(k+1)] + mm3){+                    i1 = i+2;+                    break;+                  }+                  else if(cij == fML[i+1][k-(i+1)] + fML[k+1][j-2-(k+1)] + mm5){+                    j1 = j-2;+                    break;+                  }+                  else if(cij == fML[i+2][k-(i+2)] + fML[k+1][j-2-(k+1)] + mm53){+                    i1 = i+2;+                    j1 = j-2;+                    break;+                  }+                  /* coaxial stacking of (i.j) with (i+1.k) or (k.j-1) */+                  /* use MLintern[1] since coax stacked pairs don't get TerminalAU */+                  if (dangle_model==3) {+                    int en;+                    type_2 = ptype[i+1][k-(i+1)]; type_2 = rtype[type_2];+                    if (type_2) {+                      en = c[i+1][k-(i+1)]+P->stack[type][type_2]+fML[k+1][j-1-(k+1)];+                      if (cij == en+2*P->MLintern[1]+P->MLclosing) {+                        ml = 2;+                        sector[s+1].ml  = 2;+                        break;+                      }+                    }+                    type_2 = ptype[k+1][j-1-(k+1)]; type_2 = rtype[type_2];+                    if (type_2) {+                      en = c[k+1][j-1-(k+1)]+P->stack[type][type_2]+fML[i+1][k-(i+1)];+                      if (cij == en+2*P->MLintern[1]+P->MLclosing) {+                        sector[s+2].ml = 2;+                        break;+                      }+                    }+                  }+                }+                break;+    } /* switch(dangle_model)... */++    if (k<=j-3-turn) { /* found the decomposition */+      sector[++s].i = i1;+      sector[s].j   = k;+      sector[++s].i = k+1;+      sector[s].j   = j1;+    } else {+#if 0+      /* Y shaped ML loops fon't work yet */+      if (dangle_model==3) {+        /* (i,j) must close a Y shaped ML loop with coax stacking */+        if (cij ==  fML[i+1][j-2-(i+2)] + mm + d3 + d5 + P->MLbase + P->MLbase) {+          i1 = i+2;+          j1 = j-2;+        } else if (cij ==  fML[i+1][j-2-(i+1)] + mm + d5 + P->MLbase)+          j1 = j-2;+        else if (cij ==  fML[i+2][j-1-(i+2)] + mm + d3 + P->MLbase)+          i1 = i+2;+        else /* last chance */+          if (cij != fML[i+1][j-1-(i+1)] + mm + P->MLbase)+            fprintf(stderr,  "backtracking failed in repeat");+        /* if we arrive here we can express cij via fML[i1,j1]+dangle_model */+        sector[++s].i = i1;+        sector[s].j   = j1;+      }+      else+#endif+        vrna_message_error("backtracking failed in repeat");+    }++    continue; /* this is a workarround to not accidentally proceed in the following block */++  repeat_gquad:+    /*+      now we do some fancy stuff to backtrace the stacksize and linker lengths+      of the g-quadruplex that should reside within position i,j+    */+    {+      int l[3], L, a;+      L = -1;++      get_gquad_pattern_mfe(S, i, j, P, &L, l);+      if(L != -1){+        /* fill the G's of the quadruplex into the structure string */+        for(a=0;a<L;a++){+          structure[i+a-start] = '+';+          structure[i+L+l[0]+a-start] = '+';+          structure[i+L+l[0]+L+l[1]+a-start] = '+';+          structure[i+L+l[0]+L+l[1]+L+l[2]+a-start] = '+';+        }+        goto repeat_gquad_exit;+      }+      vrna_message_error("backtracking failed in repeat_gquad");+    }+  repeat_gquad_exit:+    __asm("nop");++  }++  for (i=strlen(structure)-1; i>0 && structure[i] == '-'; i--)+    structure[i] = '\0';+  for (;i>=0; i--)+   if (structure[i]=='-') structure[i]='.';++  return structure;+}++PRIVATE void+make_ptypes(vrna_fold_compound_t *vc, int i){++  int       j, k, type, n, maxdist, turn, noLP;+  short     *S;+  char      **ptype;+  vrna_md_t *md;++  n       = (int)vc->length;+  S       = vc->sequence_encoding2;+  ptype   = vc->ptype_local;+  maxdist = vc->window_size;+  md      = &(vc->params->model_details);+  turn    = md->min_loop_size;+  noLP    = md->noLP;++  for(k = turn + 1; k < maxdist; k++){+    j = i + k;+    if (j > n)+      break;+    type = md->pair[S[i]][S[j]];++    if(noLP && type){+      if(!ptype[i + 1][j - 1 - i - 1])+        if(j == n || i == 1 || (!md->pair[S[i - 1]][S[j + 1]]))+          type = 0;+    }+    ptype[i][j - i] = type;+  }+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++#ifdef  VRNA_BACKWARD_COMPAT++PUBLIC float Lfold( const char *string,+                    char *structure,+                    int window_size){++  float               energy;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  set_model_details(&md);++  md.window_size = window_size;+  md.max_bp_span = window_size;++  vc  = vrna_fold_compound(string, &md, VRNA_OPTION_WINDOW);++  energy = wrap_Lfold(vc, 0, 0.0, NULL);++  vrna_fold_compound_free(vc);++  return energy;+}++PUBLIC float+Lfoldz( const char *string,+        char *structure,+        int window_size,+        int zsc,+        double min_z){++  float               energy;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  set_model_details(&md);++  md.window_size = window_size;+  md.max_bp_span = window_size;++  vc  = vrna_fold_compound(string, &md, VRNA_OPTION_WINDOW);++#ifndef USE_SVM+  zsc = 0;  /* deactivate z-scoring if no compiled-in svm support is available */+#endif++  energy = wrap_Lfold(vc, zsc, min_z, NULL);++  vrna_fold_compound_free(vc);++  return energy;+}++#endif
+ C/ViennaRNA/Lfold.h view
@@ -0,0 +1,136 @@+#ifndef VIENNA_RNA_PACKAGE_LFOLD_H+#define VIENNA_RNA_PACKAGE_LFOLD_H++/**+ *  @file Lfold.h+ *  @ingroup  local_fold+ *  @brief    Functions for locally optimal MFE structure prediction+ */++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++#include <ViennaRNA/mfe.h>++/**+ *  @brief Local MFE prediction using a sliding window approach (simplified interface)+ * + *  This simplified interface to vrna_mfe_window() computes the MFE and locally+ *  optimal secondary structure using default options. Structures are predicted+ *  using a sliding window approach, where base pairs may not span outside the+ *  window. Memory required for dynamic programming (DP) matrices will+ *  be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled+ *  matrices are not available any more for any post-processing.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe_window(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @ingroup local_mfe_fold+ *+ *  @see  vrna_mfe_window(), vrna_Lfoldz(), vrna_mfe_window_zscore(), vrna_fold_compound(),+ *        #vrna_fold_compound_t+ *+ *  @param  string      The nucleic acid sequence+ *  @param  window_size The window size for locally optimal structures+ *  @param  file        The output file handle where predictions are written to (if NULL, output is written to stdout)+ */+float+vrna_Lfold( const char *string,+            int window_size,+            FILE  *file);++#ifdef USE_SVM+/**+ *  @brief Local MFE prediction using a sliding window approach with z-score cut-off (simplified interface)+ * + *  This simplified interface to vrna_mfe_window_zscore() computes the MFE and locally+ *  optimal secondary structure using default options. Structures are predicted+ *  using a sliding window approach, where base pairs may not span outside the+ *  window. Memory required for dynamic programming (DP) matrices will+ *  be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled+ *  matrices are not available any more for any post-processing.+ *  This function is the z-score version of vrna_Lfold(), i.e.+ *  only predictions above a certain z-score cut-off value are+ *  printed.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe_window(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @ingroup local_mfe_fold+ *+ *  @see  vrna_mfe_window_zscore(), vrna_Lfold(), vrna_mfe_window(), vrna_fold_compound(),+ *        #vrna_fold_compound_t+ *+ *  @param  string      The nucleic acid sequence+ *  @param  window_size The window size for locally optimal structures+ *  @param  min_z       The minimal z-score for a predicted structure to appear in the output+ *  @param  file        The output file handle where predictions are written to (if NULL, output is written to stdout)+ */+float+vrna_Lfoldz(const char *string,+            int window_size,+            double min_z,+            FILE *file);++#endif+++/**+ *  @addtogroup local_consensus_fold+ *  @{+ *+ *  @}+ */++/**+ *  @brief+ *+ *  @ingroup local_consensus_fold+ * + *  @param strings+ *  @param structure+ *  @param maxdist+ *  @return+ */+float aliLfold( const char **strings,+                char *structure,+                int maxdist);++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief The local analog to fold().+ * + *  Computes the minimum free energy structure including only base pairs+ *  with a span smaller than 'maxdist'+ *+ *  @ingroup local_mfe_fold+ *+ *  @deprecated Use vrna_mfe_window() instead!+ */+DEPRECATED(float Lfold(const char *string, char *structure, int maxdist));++/**+ *  @brief+ * + *  @ingroup local_mfe_fold+ * + *  @deprecated Use vrna_mfe_window_zscore() instead!+ */+DEPRECATED(float Lfoldz(const char *string, char *structure, int maxdist, int zsc, double min_z));++#endif++#endif
+ C/ViennaRNA/MEA.c view
@@ -0,0 +1,288 @@+/*+                               MEA.c+                 c  Ivo L Hofacker, Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <float.h>    /* #defines DBL_EPSILON */+#include <math.h>+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/MEA.h"++/* compute an MEA structure, i.e. the structure maximising+   EA = \sum_{(i,j) \in S} 2\gamma p_{i,j} + \sum_{i is unpaired} p^u_i++   This can be computed by a variant of the Nussinov recursion:+   M(i,j) = min(M(i,j-1)+pu[j], min_k M(i,k-1)+C(k,j)+   C(i,j) = 2*gamma*p_ij + M(i+1,j-1)++   Just for fun, we implement it as a sparse DP algorithm.+   At any time we store only the current and previous row of M.+   The C matrix is implemented as a sparse matrix:+   For each j we store in C[j] a list of values (i, MEA([i..j])), containing+   the MEA over all structures closed by (i,j).+   The list is sparse since only C values where C(i,j)==M(i,j) can+   contribute to the optimal solution.+*/++typedef struct Litem {+  int i;+  double A;+} Litem;++typedef struct List {+  unsigned size;   /* allocated space */+  unsigned nelem;+  Litem *list;+} List;++PRIVATE int comp_plist(const void *a, const void *b);+PRIVATE plist *prune_sort(plist *p, double *pu, int n, double gamma, short *S, int gq);+PRIVATE void pushC(List *c, int i, double a);++struct MEAdat{+  plist *pl;+  double *pu;+  double gamma;+  List *C;+  double *Mi;+  char * structure;+};++PRIVATE void mea_backtrack(const struct MEAdat *bdat, int i, int j, int paired, short *S, vrna_exp_param_t *pf);++PUBLIC float MEA(plist *p, char *structure, double gamma) {+  return MEA_seq(p, NULL, structure, gamma, NULL);+}++PUBLIC float MEA_seq(plist *p, const char *sequence, char *structure, double gamma, vrna_exp_param_t *pf){++  int i,j,n;+  Litem *li;+  plist *pp, *pl;+  short *S = NULL;+  int with_gquad = 0;++  List *C;+  double MEA, *Mi, *Mi1, *tmp, *pu;+  struct MEAdat bdat;++  n = strlen(structure);+  for (i=0; i<n; i++) structure[i] = '.';++  if(sequence){+    if(pf){+      S = vrna_seq_encode(sequence, &(pf->model_details));+    } else {+      vrna_exp_param_t *pf_params;+      vrna_md_t         md;+      set_model_details(&md);+      pf_params = vrna_exp_params(&md);+      S = vrna_seq_encode(sequence, &(pf_params->model_details));+      with_gquad = pf_params->model_details.gquad;+      free(pf_params);+    }+  }+  if(pf)+    with_gquad = pf->model_details.gquad;++  pu = vrna_alloc(sizeof(double)*(n+1));+  pp = pl = prune_sort(p, pu, n, gamma, S, with_gquad);++  C = (List*) vrna_alloc((n+1)*(sizeof(List)));++  Mi = (double *) vrna_alloc((n+1)*sizeof(double));+  Mi1 = (double *) vrna_alloc((n+1)*sizeof(double));++  for (i=n; i>0; i--) {+    Mi[i] = pu[i];+    for (j=i+1; j<=n; j++) {+      double EA;+      Mi[j] = Mi[j-1] + pu[j];+      for (li=C[j].list; li<C[j].list+C[j].nelem; li++) {+        EA = li->A + Mi[(li->i) -1];+        Mi[j] = MAX2(Mi[j], EA);+      }+      if (pp->i == i && pp->j ==j) {+        EA = 2*gamma*pp->p +  Mi1[j-1];+        if (Mi[j]<EA) {+          Mi[j]=EA;+          pushC(&C[j], i, EA); /* only push into C[j] list if optimal */+        }+        pp++;+      }++    }+    tmp = Mi1; Mi1 = Mi; Mi = tmp;+  }++  MEA = Mi1[n];++  bdat.structure = structure; bdat.gamma = gamma;+  bdat.C = C;  bdat.Mi=Mi1; bdat.pl=pl; bdat.pu = pu;+  mea_backtrack(&bdat, 1, n, 0, S, pf);+  free(Mi); free(Mi1); free(pl); free(pu);+  for (i=1; i<=n; i++)+    if (C[i].list) free(C[i].list);+  free(C);+  if(S) free(S);+  return MEA;+}++PRIVATE int comp_plist(const void *a, const void *b) {+  plist *A, *B;+  int di;+  A = (plist *)a;+  B = (plist *)b;+  di = (B->i - A->i);+  if (di!=0) return di;+  return (A->j - B->j);+}+++PRIVATE plist *prune_sort(plist *p, double *pu, int n, double gamma, short *S, int gq){+  /*+     produce a list containing all base pairs with+     2*gamma*p_ij > p^u_i + p^u_j+     already sorted to be in the order we need them within the DP+  */+  unsigned size, i, nump = 0;+  plist *pp, *pc, *pc2;++  for (i=1; i<=n; i++) pu[i]=1.;++  for (pc=p; pc->i >0; pc++) {+    pu[pc->i] -= pc->p;+    pu[pc->j] -= pc->p;+  }++  if(gq){+    if(!S) vrna_message_error("no sequence information available in MEA gquad!");+    /* remove probabilities that i or j are enclosed by a gquad */+    for (i=1; i<=n; i++){+      for(pc2 = p; pc2->i > 0; pc2++){+        /* skip all non-gquads */+        if(S[pc2->i] != 3) continue;+        if(S[pc2->j] != 3) continue;+        /* remove only if i is enclosed */+        if((pc2->i < i) && (pc2->j > i))+          pu[i] -= pc2->p;+      }+    }+  }++  size = n+1;+  pp = vrna_alloc(sizeof(plist)*(n+1));+  for (pc=p; pc->i >0; pc++) {+    if (pc->i > n) vrna_message_error("mismatch between plist and structure in MEA()");+    if (pc->p*2*gamma > pu[pc->i] + pu[pc->j]) {+      if (nump+1 >= size) {+        size += size/2 + 1;+        pp = vrna_realloc(pp, size*sizeof(plist));+      }+      pp[nump++] = *pc;+    }+  }+  pp[nump].i = pp[nump].j = pp[nump].p = 0;+  qsort(pp, nump, sizeof(plist), comp_plist);+  return pp;+}++PRIVATE void pushC(List *c, int i, double a) {+  if (c->nelem+1>=c->size) {+    c->size = MAX2(8,c->size*sqrt(2));+    c->list = vrna_realloc(c->list, sizeof(Litem)*c->size);+  }+  c->list[c->nelem].i = i;+  c->list[c->nelem].A = a;+  c->nelem++;+}++PRIVATE void mea_backtrack(const struct MEAdat *bdat, int i, int j, int pair, short *S, vrna_exp_param_t *pf){+  /* backtrack structure for the interval [i..j] */+  /* recursively calls itself, recomputes the necessary parts of the M matrix */+  List *C; Litem *li;+  double *Mi, prec;+  double *pu;+  int fail=1;+  int gq = 0;+  if(pf)+    gq = pf->model_details.gquad;+++  C = bdat->C;+  Mi = bdat->Mi;+  pu = bdat->pu;++  if (pair) {+    int k;+    /* if pair == 1, insert pair and re-compute Mi values */+    /* else Mi is already filled */+    if(gq){+      if((S[i] == 3) && (S[j] == 3)){+        int L, l[3];+        get_gquad_pattern_pf(S, i, j, pf, &L, l);+        for(k=0;k<L;k++){+          bdat->structure[i+k-1]\+          = bdat->structure[i+k+L+l[0]-1]\+          = bdat->structure[i+k+2*L+l[0]+l[1]-1]\+          = bdat->structure[i+k+3*L+l[0]+l[1]+l[2]-1]\+          = '+';+        }+        return;+      } else {+        bdat->structure[i-1] = '(';+        bdat->structure[j-1] = ')';+        i++; j--;+        /* We've done this before in MEA() but didn't keep the results */+        Mi[i-1]=0; Mi[i]=pu[i];+        for (k=i+1; k<=j; k++) {+          Mi[k] = Mi[k-1] + pu[k];+          for (li=C[k].list; li<C[k].list+C[k].nelem && li->i >= i; li++) {+            double EA;+            EA = li->A + Mi[(li->i) -1];+            Mi[k] = MAX2(Mi[k], EA);+          }+        }+      }+    } else {+      bdat->structure[i-1] = '(';+      bdat->structure[j-1] = ')';+      i++; j--;+      /* We've done this before in MEA() but didn't keep the results */+      Mi[i-1]=0; Mi[i]=pu[i];+      for (k=i+1; k<=j; k++) {+        Mi[k] = Mi[k-1] + pu[k];+        for (li=C[k].list; li<C[k].list+C[k].nelem && li->i >= i; li++) {+          double EA;+          EA = li->A + Mi[(li->i) -1];+          Mi[k] = MAX2(Mi[k], EA);+        }+      }+    }+  }++  prec = DBL_EPSILON * Mi[j];+  /* Mi values are filled, do the backtrace */+  while (j>i && Mi[j] <= Mi[j-1] + pu[j] + prec) {+    bdat->structure[j-1]='.';+    j--;+  }+  for (li=C[j].list; li<C[j].list + C[j].nelem && li->i >= i; li++) {+    if (Mi[j] <= li->A + Mi[(li->i) -1] + prec) {+      if (li->i > i+3) mea_backtrack(bdat, i, (li->i)-1, 0, S, pf);+      mea_backtrack(bdat, li->i, j, 1, S, pf);+      fail = 0;+    }+  }+  if (fail && j>i) vrna_message_error("backtrack failed for MEA()");+}
+ C/ViennaRNA/MEA.h view
@@ -0,0 +1,36 @@+#ifndef VIENNA_RNA_PACKAGE_MEA_H+#define VIENNA_RNA_PACKAGE_MEA_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++/**+ *  @file MEA.h+ *  @ingroup subopt_and_representatives+ *  @brief Computes a MEA (maximum expected accuracy) structure.+ */++/**+ *  @brief Computes a MEA (maximum expected accuracy) structure.+ *+ *  @ingroup  mea_fold+ *+ *  The algorithm maximizes the expected accuracy+ *  @f[ A(S) = \sum_{(i,j) \in S} 2 \gamma p_{ij} + \sum_{i \notin S} p^u_i @f]+ *  Higher values of @f$\gamma@f$ result in more base pairs of lower+ *  probability and thus higher sensitivity. Low values of @f$\gamma@f$ result in structures+ *  containing only highly likely pairs (high specificity).+ *  The code of the MEA function also demonstrates the use of sparse dynamic+ *  programming scheme to reduce the time and memory complexity of folding.+ */+float MEA(plist *p,+          char *structure,+          double gamma);++float MEA_seq(plist *p,+              const char *sequence,+              char *structure,+              double gamma,+              vrna_exp_param_t *pf);++#endif
+ C/ViennaRNA/PKplex.h view
@@ -0,0 +1,25 @@+#ifndef PKPLEX_H+#define PKPLEX_H++#include <ViennaRNA/data_structures.h>++extern dupVar *PlexHits;+extern int    PlexHitsArrayLength;+extern int    NumberOfHits;+extern int    verbose;+++/**+ *  \brief + */+dupVar  **PKLduplexfold_XS( const char *s1,+                            int **access_s1,+                            const int threshold,+                            const int alignment_length,+                            const int delta);++int     arraySize(duplexT **array);++void    freeDuplexT(duplexT **array);++#endif
+ C/ViennaRNA/PS_dot.c view
@@ -0,0 +1,1293 @@+/*+        PostScript and GML output for RNA secondary structures+                    and pair probability matrices++                 c  Ivo Hofacker and Peter F Stadler+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <string.h>+#include <ctype.h>+#include "ViennaRNA/model.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/PS_dot.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/gquad.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++#define SIZE 452.+#define PMIN 0.00001++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++static const char *RNAdp_prolog =+"%This file contains the square roots of the base pair probabilities in the form\n"+"% i  j  sqrt(p(i,j)) ubox\n\n"+"%%BeginProlog\n"+"/DPdict 100 dict def\n"+"DPdict begin\n"+"/logscale false def\n"+"/lpmin 1e-05 log def\n\n"+"/DataVisible  [ true true true true] def\n"+"/DataTitles   [ false false false false ] def\n\n"+"/min { 2 copy gt { exch } if pop } bind def\n\n"+"/max { 2 copy lt { exch } if pop } bind def\n\n"+"/box { %size x y box - draws box centered on x,y\n"+"   2 index 0.5 mul sub            % x -= 0.5\n"+"   exch 2 index 0.5 mul sub exch  % y -= 0.5\n"+"   3 -1 roll dup rectfill\n"+"} bind def\n\n"+"/ubox {\n"+"   logscale {\n"+"      log dup add lpmin div 1 exch sub dup 0 lt { pop 0 } if\n"+"   } if\n"+"   3 1 roll\n"+"   exch len exch sub 1 add box\n"+"} bind def\n\n"+"/lbox {\n"+"   3 1 roll\n"+"   len exch sub 1 add box\n"+"} bind def\n\n"+"/drawseq {\n"+"% print sequence along all 4 sides\n"+"[ [0.7 -0.3 0 ]\n"+"  [0.7 0.7 len add 0]\n"+"  [-0.3 len sub -0.4 -90]\n"+"  [-0.3 len sub 0.7 len add -90]\n"+"] {\n"+"   gsave\n"+"    aload pop rotate translate\n"+"    0 1 len 1 sub {\n"+"     dup 0 moveto\n"+"     sequence exch 1 getinterval\n"+"     show\n"+"    } for\n"+"   grestore\n"+"  } forall\n"+"} bind def\n\n"+"/drawgrid{\n"+"  gsave\n"+"  0.5 dup translate"+"  0.01 setlinewidth\n"+"  len log 0.9 sub cvi 10 exch exp  % grid spacing\n"+"  dup 1 gt {\n"+"     dup dup 20 div dup 2 array astore exch 40 div setdash\n"+"  } { [0.3 0.7] 0.1 setdash } ifelse\n"+"  0 exch len {\n"+"     dup dup\n"+"     0 moveto\n"+"     len lineto\n"+"     dup\n"+"     len exch sub 0 exch moveto\n"+"     len exch len exch sub lineto\n"+"     stroke\n"+"  } for\n"+"  [] 0 setdash\n"+"  0.04 setlinewidth\n"+"  currentdict /cutpoint known {\n"+"    cutpoint 1 sub\n"+"    dup dup -1 moveto len 1 add lineto\n"+"    len exch sub dup\n"+"    -1 exch moveto len 1 add exch lineto\n"+"    stroke\n"+"  } if\n"+"  %% draw diagonal\n"+"  0 len moveto len 0 lineto stroke\n"+"  grestore\n"+"} bind def\n\n"+"/drawTitle {\n"+"  currentdict /DPtitle known {\n"+"    % center title text\n"+"    /Helvetica findfont 10 scalefont setfont\n"+"    360 705 moveto DPtitle dup stringwidth pop 2 div neg 0 rmoveto show\n"+"  } if\n"+"} bind def\n\n"+"/prepareCoords {\n"+"  0 1 3 {\n"+"    % check whether we want to display current data\n"+"    dup DataVisible exch get\n"+"    {\n"+"      % check whether we've actually got some data\n"+"      DataSource exch get dup currentdict exch known {\n"+"        % data source s_j is present, so find length of array\n"+"        currentdict exch get length \n"+"      } { pop 0 } ifelse\n"+"    } if\n"+"  } for\n"+"  exch dup 5 -1 roll add 4 -1 roll dup 5 1 roll 4 -1 roll add max\n"+"  len add 3 add 700 exch div dup scale\n"+"  exch 1 add exch 1 add translate\n"+"} bind def\n\n";++static const char *RNAdp_sd =+"/utri{ % i j prob utri\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95  0.33\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub\n"+"  moveto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n\n";++static const char *RNAdp_ud =+"/uUDmotif{ % i j uUDmotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95 0.6\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub\n"+"  moveto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n"+"/lUDmotif{ % i j lUDmotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95 0.6\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  dup len exch sub dup 4 -1 roll 1 sub dup 3 1 roll dup len exch sub\n"+"  moveto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n\n";++static const char *RNAdp_sc_motifs =+"/uHmotif{ % i j uHmotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95  0.99\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  exch 1 sub dup len exch sub dup 4 -1 roll dup 3 1 roll dup len exch sub\n"+"  moveto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n"+"/lHmotif{ % i j lHmotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95  0.99\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  dup len exch sub dup 4 -1 roll 1 sub dup 3 1 roll dup len exch sub\n"+"  moveto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n"+"/uImotif{ % i j k l uImotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95  0.99\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  1 sub dup 5 1 roll exch len exch sub dup 5 1 roll 3 -1 roll dup\n"+"  5 1 roll exch 4 1 roll 3 1 roll exch 1 sub len exch sub dup 3 1 roll\n"+"  moveto lineto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n"+"/lImotif{ % i j k l lImotif\n"+"  gsave\n"+"  0.5 dup translate\n"+"  1 min 2 div\n"+"  0.85 mul 0.15 add 0.95  0.99\n"+"  3 1 roll % prepare hsb color\n"+"  sethsbcolor\n"+"  % now produce the coordinates for lines\n"+"  4 -1 roll 1 sub dup 5 1 roll exch 1 sub len exch sub dup 3 -1 roll exch\n"+"  5 -1 roll len exch sub dup 6 -1 roll dup 3 1 roll 7 4 roll\n"+"  moveto lineto lineto lineto closepath fill\n"+"  grestore\n"+"} bind def\n";++static const char *RNAdp_prolog_turn =+"/drawseq_turn {"+"% print sequence at bottom\n"+"   gsave\n"+"   len 2 sqrt div dup neg 0.28 add exch 0.78 sub translate\n"+"    0 1 len 1 sub {\n"+"     dup dup 2 sqrt mul 0 moveto\n"+"     sequence exch 1 getinterval\n"+"     show\n"+"    } for\n"+"   grestore\n"+"} bind def\n"+"/drawgrid_turn{\n"+"  0.01 setlinewidth\n"+"  len log 0.9 sub cvi 10 exch exp  % grid spacing\n"+"  dup 1 gt {\n"+"     dup dup 20 div dup 2 array astore exch 40 div setdash\n"+"  } { [0.3 0.7] 0.1 setdash } ifelse\n"+"  0 exch len {    %for (0, gridspacing, len) \n"+"     dup dup      %duplicate what - gridspacing??\n"+"     dup len exch sub moveto     %moveto diagonal?\n"+"     dup winSize gt\n"+"     {dup dup len exch sub winSize add lineto}\n"+"     {dup len lineto}ifelse\n"+"     dup len exch sub moveto  %moveto diagonal?\n"+"     dup len winSize sub le\n"+"     {dup dup len exch sub dup winSize exch sub len add exch lineto}\n"+"     {dup dup len exch sub len exch lineto}ifelse"+"     stroke pop pop\n"+"  } for\n"+"  len log 0.9 sub cvi 10 exch exp  % grid spacing\n"+"      dup 1 gt {\n"+"          dup dup 20 div dup 2 array astore exch 40 div setdash\n"+"      } { [0.3 0.7] 0.1 setdash } ifelse\n"+"      0 exch len {    %for (0, gridspacing, len) \n"+"     dup dup      %duplicate what - gridspacing??\n"+"     dup len exch sub moveto     %moveto diagonal?\n"+"     len exch sub 0.7 sub exch 0.7 sub exch lineto\n"+"     stroke\n"+"   }for\n"+" winSize len moveto  len winSize  lineto stroke\n"+"  [] 0 setdash\n"+"  0.04 setlinewidth \n"+"  currentdict /cutpoint known {\n"+"    cutpoint 1 sub\n"+"    dup dup -1 moveto len 1 add lineto\n"+"    len exch sub dup\n"+"    -1 exch moveto len 1 add exch lineto\n"+"   stroke\n"+"  } if\n"+"  0.5 neg dup translate\n"+"} bind def \n\n";++static const char *RNAdp_linear_data =+"/drawDataSquareBottom { % x v n dataSquareBottom draw box\n"+"  len add 2 add exch lbox\n"+"} bind def\n\n"+"/drawDataSquareTop { % x v n dataSquareBottom draw box\n"+"  neg 1 sub exch lbox\n"+"} bind def\n\n"+"/drawDataSquareLeft { % y v n dataSquareBottom draw box\n"+"  neg 1 sub 3 1 roll lbox\n"+"} bind def\n\n"+"/drawDataSquareRight { % y v n dataSquareBottom draw box\n"+"  % use size x y box to draw box\n"+"  2 add len add 3 1 roll lbox\n"+"} bind def\n\n"+"/drawDataSquareBottomHSB { % x v h s b n dataSquareBottomHSB draw box\n"+"  % use size x y box to draw box\n"+"  len add 2 add 5 1 roll sethsbcolor lbox\n"+"} bind def\n\n"+"/drawDataSquareTopHSB { % x v h s b n dataSquareBottomHSB draw box\n"+"  % use size x y box to draw box\n"+"  neg 1 sub 5 1 roll sethsbcolor lbox\n"+"} bind def\n\n"+"/drawDataSquareLeftHSB { % x v h s b n dataSquareLeftHSB draw box\n"+"  % use size x y box to draw box\n"+"  neg 1 sub 6 1 roll sethsbcolor lbox\n"+"} bind def\n\n"+"/drawDataSquareRightHSB { % x v h s b n dataSquareLeftHSB draw box\n"+"  % use size x y box to draw box\n"+"  2 add len add 6 1 roll sethsbcolor lbox\n"+"} bind def\n\n"+"/drawDataTitleBottom {\n"+"  /Helvetica findfont 0.95 scalefont setfont\n"+"  0 -1.4 3 -1 roll sub moveto \n"+"  dup stringwidth pop neg 0 rmoveto   \n"+"  show\n"+"} bind def\n\n"+"/drawDataTitleTop {\n"+"  /Helvetica findfont 0.95 scalefont setfont\n"+"  0 len 1.6 add 3 -1 roll add moveto \n"+"  dup stringwidth pop neg 0 rmoveto   \n"+"  show\n"+"} bind def\n\n"+"/drawDataTitleLeft {\n"+"  /Helvetica findfont 0.95 scalefont setfont\n"+"  neg 1.4 sub len 1 add moveto \n"+"  dup stringwidth pop 0 exch rmoveto -90 rotate\n"+"  show 90 rotate\n"+"} bind def\n\n"+"/drawDataTitleRight {\n"+"  /Helvetica findfont 0.95 scalefont setfont\n"+"  1.6 add len add len 1 add moveto \n"+"  dup stringwidth pop 0 exch rmoveto -90 rotate\n"+"  show 90 rotate\n"+"} bind def\n\n"+"% do not modify the arrays below unless you know what you're doing!\n"+"/DataSource     [ /topData /leftData /bottomData /rightData ] def\n"+"/DataDrawBox    [ /drawDataSquareTop  /drawDataSquareLeft /drawDataSquareBottom /drawDataSquareRight] def\n"+"/DataDrawBoxHSB [ /drawDataSquareTopHSB /drawDataSquareLeftHSB /drawDataSquareBottomHSB /drawDataSquareRightHSB ] def\n"+"/DataDrawTitle  [ /drawDataTitleTop /drawDataTitleLeft /drawDataTitleBottom /drawDataTitleRight ] def\n\n"+"% this is the logic to parse the auxiliary linear data\n"+"% given in arrays topData, leftData, bottomData, and rightData\n"+"% See also the Boolean arrays DataVisible and DataTitles that\n"+"% are used to control which part of data will be visible\n"+"/drawData {\n"+"  0 1 3 {\n"+"    % check whether we want to display current data\n"+"    dup DataVisible exch get\n"+"    {\n"+"      % check whether we've actually got some data\n"+"      dup DataSource exch get dup currentdict exch known {\n"+"        % data source s_j is present, so we load the\n"+"        % corresponding data array a and loop over all data sets a[i]\n"+"        currentdict exch get dup length 1 sub 0 1 3 -1 roll {\n"+"          dup dup\n"+"          % now on stack: j a i i i\n\n"+"          % load data set, i.e. a[i]\n"+"          4 -1 roll         % j i i i a\n"+"          dup 3 -1 roll get dup % j i i a a[i] a[i]\n\n"+"          % 1. check whether we need to process data set title\n"+"          6 -1 roll dup 7 1 roll DataTitles exch get {\n"+"            % get current title drawing function key\n"+"            6 -1 roll dup 7 1 roll DataDrawTitle exch get\n"+"            % now on stack: ... j i i a a[i] a[i] title_draw_key\n\n"+"            % get current title and execute drawing function\n"+"            exch 0 get exch currentdict exch get 5 -1 roll exch exec\n"+"          } { % remove unused variables\n"+"              pop 3 -1 roll pop\n"+"          } ifelse\n"+"          % now on stack: ... j i a a[i]\n\n"+"          % 2. process actual data a[k] for 1 <= k < n\n"+"          dup length 1 sub 1 exch getinterval { \n"+"            % on stack: j i a a[i][k]\n"+"            gsave\n"+"            dup length 2 eq { % print black box if two-valued\n"+"              % get box drawing function\n"+"              4 -1 roll dup 5 1 roll DataDrawBox exch get currentdict exch get exch\n"+"              aload pop 5 -1 roll dup 6 1 roll 4 -1 roll exec\n"+"            } {\n"+"              dup length 5 eq { % print box with hsb color\n"+"                % get box drawing function\n"+"                4 -1 roll dup 5 1 roll DataDrawBoxHSB exch get currentdict exch get exch\n"+"                % on stack: j i a f a[i]\n"+"                % load data array and prepare for drawing\n"+"                aload pop 8 -1 roll dup 9 1 roll 7 -1 roll exec\n"+"              } { pop } ifelse\n"+"            } ifelse\n"+"            grestore\n"+"          } forall\n"+"          exch pop \n"+"          % left on stack: j a\n"+"        } for\n"+"        \n"+"      } if\n"+"    } if\n"+"  } for\n"+"} bind def\n\n";+++#define dp_add_lindata(data_var, data, title_var, title, size, avail)  \+  (title_var)[size] = title; \+  (data_var)[size]  = data; \+  if((++size) == (avail)){ \+    avail *= 1.2; \+    data_var  = (vrna_data_lin_t **)vrna_realloc(data_var, sizeof(vrna_data_lin_t *) * avail); \+    title_var = (char **)vrna_realloc(title_var, sizeof(char *) * avail); \+  }+++#define dp_finalize_lindata(data_var, title_var, size) \+  (data_var)[size]  = NULL; \+  (title_var)[size] = NULL; \+  (data_var)        = (vrna_data_lin_t **)vrna_realloc(data_var, sizeof(vrna_data_lin_t *) * (size + 1)); \+  (title_var)       = (char **)vrna_realloc(title_var, sizeof(char *) * (size + 1));+++#define DP_MACRO_NONE         0U+#define DP_MACRO_LINEAR_DATA  1U+#define DP_MACRO_SC_MOTIFS    2U+#define DP_MACRO_SD           4U+#define DP_MACRO_UD           8U++#define DP_MACRO_ALL          (DP_MACRO_LINEAR_DATA | DP_MACRO_SC_MOTIFS | DP_MACRO_SD | DP_MACRO_UD)++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE FILE  *PS_dot_common(const char *seq, int cp, const char *wastlfile, char *comment, int winsize, unsigned int options);+PRIVATE int   sort_plist_by_type_desc(const void *p1, const void *p2);+PRIVATE int   sort_plist_by_prob_asc(const void *p1, const void *p2);+PRIVATE void  EPS_footer(FILE *eps);+PRIVATE void  EPS_print_title(FILE *eps, const char *title);+PRIVATE void  EPS_print_seq(FILE *eps, const char *sequence);+PRIVATE void  EPS_print_header(FILE *eps, int bbox[4], const char *comment, unsigned int options);+PRIVATE void  EPS_print_ud_data(FILE *eps, plist *pl, plist *mf);+PRIVATE void  EPS_print_sd_motif_data(FILE *eps, plist *pl, plist *mf);+PRIVATE void  EPS_print_sc_motif_data(FILE *eps, plist *pl, plist *mf);+PRIVATE void  EPS_print_bpp_data(FILE *eps, plist *pl, plist *mf);+PRIVATE void  EPS_print_linear_data_top(FILE *eps, const char **data_title, vrna_data_lin_t **data);+PRIVATE void  EPS_print_linear_data_left(FILE *eps, const char **data_title, vrna_data_lin_t **data);+PRIVATE void  EPS_print_linear_data_bottom(FILE *eps, const char **data_title, vrna_data_lin_t **data);+PRIVATE void  EPS_print_linear_data_right(FILE *eps, const char **data_title, vrna_data_lin_t **data);+PRIVATE void  EPS_print_linear_data(FILE *eps, const char *varname, const char **data_title, vrna_data_lin_t **data);+PRIVATE vrna_data_lin_t *plist_to_accessibility(plist *pl, unsigned int length);+PRIVATE vrna_data_lin_t *plist_to_ud_motif_prob(plist *pl, unsigned int length);+PRIVATE void  EPS_print_sd_data(FILE *eps, vrna_plist_t *pl, vrna_plist_t *mf);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC int+PS_color_dot_plot(char *seq,+                  cpair *pi,+                  char *wastlfile){++  /* produce color PostScript dot plot from cpair */++  FILE *wastl;+  int i;++  wastl = PS_dot_common(seq, cut_point, wastlfile, NULL, 0, DP_MACRO_NONE);+  if (wastl==NULL)  return 0; /* return 0 for failure */++  fprintf(wastl, "/hsb {\n"+          "dup 0.3 mul 1 exch sub sethsbcolor\n"+          "} bind def\n\n");++  fprintf(wastl,  "\n%%draw the grid\ndrawgrid\n\n");+  fprintf(wastl,"%%start of base pair probability data\n");++  /* print boxes */+   i=0;+   while (pi[i].j>0) {+     fprintf(wastl,"%1.2f %1.2f hsb %d %d %1.6f ubox\n",+             pi[i].hue, pi[i].sat, pi[i].i, pi[i].j, sqrt(pi[i].p));++     if (pi[i].mfe)+       fprintf(wastl,"%1.2f %1.2f hsb %d %d %1.4f lbox\n",+               pi[i].hue, pi[i].sat, pi[i].i, pi[i].j, pi[i].p);+     i++;+   }++   EPS_footer(wastl);++   fclose(wastl);+   return 1; /* success */+}+++PUBLIC int+PS_dot_plot_list( char *seq,+                  char *wastlfile,+                  plist *pl,+                  plist *mf,+                  char *comment){++  return vrna_plot_dp_PS_list(seq, cut_point, wastlfile, pl, mf, comment);+}+++PUBLIC int+vrna_plot_dp_PS_list( char *seq,+                      int cp,+                      char *wastlfile,+                      plist *pl,+                      plist *mf,+                      char *comment){++  FILE *wastl;+  int pl_size, gq_num;+  double tmp;+  plist *pl1;++  wastl = PS_dot_common(seq, cp, wastlfile, comment, 0, DP_MACRO_ALL);++  if (wastl==NULL) return 0; /* return 0 for failure */++  fprintf(wastl,"%%data starts here\n");++  /* sort the plist to bring all gquad triangles to the front */+  for(gq_num = pl_size = 0, pl1 = pl; pl1->i > 0; pl1++, pl_size++)+    if(pl1->type == 1) gq_num++;+  qsort(pl, pl_size, sizeof(plist), sort_plist_by_type_desc);+  /* sort all gquad triangles by probability to bring lower probs to the front */+  qsort(pl, gq_num, sizeof(plist), sort_plist_by_prob_asc);++  EPS_print_sd_data(wastl, pl, mf);+  EPS_print_sc_motif_data(wastl, pl, mf);++  fprintf(wastl, "\n%%draw the grid\ndrawgrid\n\n");+  fprintf(wastl,"%%start of base pair probability data\n");++  EPS_print_bpp_data(wastl, pl, mf);++  EPS_footer(wastl);++  fclose(wastl);+  return 1; /* success */+}+++PUBLIC int+vrna_plot_dp_EPS( const char              *filename,+                  const char              *sequence,+                  vrna_plist_t            *upper,+                  vrna_plist_t            *lower,+                  vrna_dotplot_auxdata_t  *auxdata,+                  unsigned int            options){++  char            **lintoptitle,**linbottomtitle,**linlefttitle,**linrighttitle,+                  *c, *comment, *title;+  int             pl_size, gq_num, i, lintop_num, lintop_size, linbottom_num,+                  linbottom_size, linleft_num, linleft_size, linright_num,+                  linright_size, bbox[4];+  double          tmp;+  FILE            *fh;+  plist           *pl1;+  vrna_data_lin_t **lintop, **linbottom, **linleft, **linright, *ud_lin, *access;++  fh = fopen(filename, "w");+  if(!fh){+    vrna_message_warning("can't open %s for dot plot", filename);+    return 0; /* return 0 for failure */+  }++  comment = title = NULL;++  lintop_num      = 0;+  lintop_size     = 5;+  linbottom_num   = 0;+  linbottom_size  = 5;+  linleft_num     = 0;+  linleft_size    = 5;+  linright_num    = 0;+  linright_size   = 5;+  bbox[0]         = 0;+  bbox[1]         = 0;+  bbox[2]         = 700;+  bbox[3]         = 720;+  access          = NULL;+  ud_lin          = NULL;+  lintop          = (vrna_data_lin_t **)vrna_alloc(sizeof(vrna_data_lin_t *) * lintop_size);+  lintoptitle     = (char **)vrna_alloc(sizeof(char *) * lintop_size);+  linbottom       = (vrna_data_lin_t **)vrna_alloc(sizeof(vrna_data_lin_t *) * linbottom_size);+  linbottomtitle  = (char **)vrna_alloc(sizeof(char *) * linbottom_size);+  linleft         = (vrna_data_lin_t **)vrna_alloc(sizeof(vrna_data_lin_t *) * linleft_size);+  linlefttitle    = (char **)vrna_alloc(sizeof(char *) * linleft_size);+  linright        = (vrna_data_lin_t **)vrna_alloc(sizeof(vrna_data_lin_t *) * linright_size);+  linrighttitle   = (char **)vrna_alloc(sizeof(char *) * linright_size);++  /* prepare linear data and retrieve number of additional linear data lines to correct bounding box */+  if(options & VRNA_PLOT_PROBABILITIES_UD_LIN){+    ud_lin = plist_to_ud_motif_prob(upper, strlen(sequence));+    if(ud_lin){+      dp_add_lindata(lintop, ud_lin, lintoptitle, "Protein binding", lintop_num, lintop_size);+      dp_add_lindata(linleft, ud_lin, linlefttitle, "Protein binding", linleft_num, linleft_size);+      dp_add_lindata(linbottom, ud_lin, linbottomtitle, "Protein binding", linbottom_num, linbottom_size);+      dp_add_lindata(linright, ud_lin, linrighttitle, "Protein binding", linright_num, linright_size);+    }+  }++  if(options & VRNA_PLOT_PROBABILITIES_ACC){+    access = plist_to_accessibility(upper, strlen(sequence));+    dp_add_lindata(lintop, access, lintoptitle, "Accessibility", lintop_num, lintop_size);+  }++  if(auxdata){+    if(auxdata->top){+      for(i = 0; auxdata->top[i]; i++){+        dp_add_lindata(lintop, auxdata->top[i], lintoptitle, auxdata->top_title[i], lintop_num, lintop_size);+      }+    }+    if(auxdata->bottom){+      for(i = 0; auxdata->bottom[i]; i++){+        dp_add_lindata(linbottom, auxdata->bottom[i], linbottomtitle, auxdata->bottom_title[i], linbottom_num, linbottom_size);+      }+    }+    if(auxdata->left){+      for(i = 0; auxdata->left[i]; i++){+        dp_add_lindata(linleft, auxdata->left[i], linlefttitle, auxdata->left_title[i], linleft_num, linleft_size);+      }+    }+    if(auxdata->right){+      for(i = 0; auxdata->right[i]; i++){+        dp_add_lindata(linright, auxdata->right[i], linrighttitle, auxdata->right_title[i], linright_num, linright_size);+      }+    }+  }++  dp_finalize_lindata(lintop, lintoptitle, lintop_num);+  dp_finalize_lindata(linbottom, linbottomtitle, linbottom_num);+  dp_finalize_lindata(linleft, linlefttitle, linleft_num);+  dp_finalize_lindata(linright, linrighttitle, linright_num);++  if(auxdata){+    comment = auxdata->comment;+    title   = (auxdata->title) ? strdup(auxdata->title) : NULL;+  }++  if(!title){+    title = strdup(filename);+    if((c=strrchr(title, '_')))+      *c='\0';+  }++  /* start printing postscript file */+  EPS_print_header(fh, bbox, comment, DP_MACRO_ALL);+  EPS_print_title(fh, title);+  EPS_print_seq(fh, sequence);++  fprintf(fh,"%% BEGIN linear data array\n\n");+  EPS_print_linear_data_top(fh, (const char **)lintoptitle, lintop);+  EPS_print_linear_data_left(fh, (const char **)linlefttitle, linleft);+  EPS_print_linear_data_bottom(fh, (const char **)linbottomtitle, linbottom);+  EPS_print_linear_data_right(fh, (const char **)linrighttitle, linright);+  fprintf(fh,"%% END linear data arrays\n");++  fprintf(fh, "\n%%Finally, prepare canvas\n\n"+              "%%draw title\ndrawTitle\n\n"+              "%%prepare coordinate system, draw grid and sequence\n"+              "/Helvetica findfont 0.95 scalefont setfont\n\n"+              "%%prepare coordinate system\nprepareCoords\n\n"+              "%%draw sequence arround grid\ndrawseq\n\n"+              "%%draw grid\ndrawgrid\n\n"+              "%%draw auxiliary linear data (if available)\ndrawData\n\n");++  fprintf(fh,"%%data (commands) starts here\n");++  if(options & VRNA_PLOT_PROBABILITIES_SD){+    EPS_print_sd_data(fh, upper, lower);+  }++  if(options & VRNA_PLOT_PROBABILITIES_UD){+    EPS_print_ud_data(fh, upper, lower);+  }+++  EPS_print_sc_motif_data(fh, upper, lower);+  EPS_print_bpp_data(fh, upper, lower);++  EPS_footer(fh);++  fclose(fh);+  free(lintoptitle);+  free(lintop);+  free(linbottomtitle);+  free(linbottom);+  free(linlefttitle);+  free(linleft);+  free(linrighttitle);+  free(linright);+  free(access);+  free(ud_lin);+  free(title);++  return 1; /* success */+}+++PUBLIC int+PS_color_dot_plot_turn( char *seq,+                        cpair *pi,+                        char *wastlfile,+                        int winSize) {++  /* produce color PostScript dot plot from cpair */++  FILE *wastl;+  int i;++  wastl = PS_dot_common(seq, cut_point, wastlfile, NULL, winSize, DP_MACRO_NONE);+  if (wastl==NULL)+    return 0; /* return 0 for failure */++  fprintf(wastl, "/hsb {\n"+          "dup 0.3 mul 1 exch sub sethsbcolor\n"+          "} bind def\n\n"+          "%%BEGIN DATA\n");++  if(winSize > 0)+    fprintf(wastl, "\n%%draw the grid\ndrawgrid_turn\n\n");+  else+    fprintf(wastl,  "\n%%draw the grid\ndrawgrid\n\n");+  fprintf(wastl,"%%start of base pair probability data\n");++  /* print boxes */+   i=0;+   while (pi[i].j>0) {+     fprintf(wastl,"%1.2f %1.2f hsb %d %d %1.6f ubox\n",+             pi[i].hue, pi[i].sat, pi[i].i, pi[i].j, sqrt(pi[i].p));/*sqrt??*/++     if (pi[i].mfe)+       fprintf(wastl,"%1.2f %1.2f hsb %d %d %1.4f lbox\n",+               pi[i].hue, pi[i].sat, pi[i].i, pi[i].j, pi[i].p);+     i++;+   }++   EPS_footer(wastl);++   fclose(wastl);+   return 1; /* success */+}+++PUBLIC int+PS_dot_plot_turn( char *seq,+                  plist *pl,+                  char *wastlfile,+                  int winSize) {++  /* produce color PostScript dot plot from cpair */++  FILE *wastl;+  int i;++  wastl = PS_dot_common(seq, cut_point, wastlfile, NULL, winSize, DP_MACRO_NONE);+  if (wastl==NULL)+    return 0; /* return 0 for failure */++  if(winSize > 0)+    fprintf(wastl, "\n%%draw the grid\ndrawgrid_turn\n\n");+  else+    fprintf(wastl,  "\n%%draw the grid\ndrawgrid\n\n");+  fprintf(wastl,"%%start of base pair probability data\n");+  /* print boxes */+  i=0;+  if (pl) {+    while (pl[i].j>0) {+      fprintf(wastl,"%d %d %1.4f ubox\n",+              pl[i].i, pl[i].j, sqrt(pl[i].p));+      i++;+    }+  }++  EPS_footer(wastl);++  fclose(wastl);+  return 1; /* success */+}+++/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/++PRIVATE void+EPS_footer(FILE *eps){++   fprintf(eps,"showpage\n"+               "end\n"+               "%%%%EOF\n");+}+++PRIVATE void+EPS_print_title(FILE *eps, const char *title){++  unsigned int i;++  fprintf(eps,"/DPtitle {\n  (%s)\n} def\n\n", title);+}+++PRIVATE void+EPS_print_seq(FILE *eps, const char *sequence){++  unsigned int i;++  fprintf(eps,"/sequence { (\\\n");+  for(i = 0; i < strlen(sequence); i += 255)+    fprintf(eps, "%.255s\\\n", sequence + i);+  fprintf(eps,") } def\n\n"+              "/len { sequence length } bind def\n\n");+}+++PRIVATE void+EPS_print_header( FILE          *eps,+                  int           bbox[4],+                  const char    *comment,+                  unsigned int  options){++  fprintf(eps,+          "%%!PS-Adobe-3.0 EPSF-3.0\n"+          "%%%%Title: RNA Dot Plot\n"+          "%%%%Creator: ViennaRNA-%s\n"+          "%%%%CreationDate: %s", VERSION, vrna_time_stamp());++  fprintf(eps, "%%%%BoundingBox: %d %d %d %d\n", bbox[0], bbox[1], bbox[2], bbox[3]);++  fprintf(eps,+          "%%%%DocumentFonts: Helvetica\n"+          "%%%%Pages: 1\n"+          "%%%%EndComments\n\n"+          "%%Options: %s\n", option_string());++  if(comment)+    fprintf(eps,"%% %s\n",comment);++  fprintf(eps,"%s", RNAdp_prolog);++  /* add auxiliary macros */+  if(options & DP_MACRO_SD){  /* gquads et al. */+    fprintf(eps,"%s", RNAdp_sd);+  }++  if(options & DP_MACRO_UD){  /* unstructured domains */+    fprintf(eps,"%s", RNAdp_ud);+  }++  if(options & DP_MACRO_SC_MOTIFS){ /* soft constraint motifs */+    fprintf(eps,"%s", RNAdp_sc_motifs);+  }++  if(options & DP_MACRO_LINEAR_DATA){ /* linear data */+    fprintf(eps,"%s", RNAdp_linear_data);+  }++  fprintf(eps, "end\n%%EndProlog\n\nDPdict begin\n\n");+}+++PRIVATE void+EPS_print_sd_data(FILE          *eps,+                  vrna_plist_t  *pl,+                  vrna_plist_t  *mf){++  int     pl_size, gq_num;+  double  tmp;+  plist   *pl1;++  /* sort the plist to bring all gquad triangles to the front */+  for(gq_num = pl_size = 0, pl1 = pl; pl1->i > 0; pl1++, pl_size++)+    if(pl1->type == VRNA_PLIST_TYPE_GQUAD) gq_num++;++  qsort(pl, pl_size, sizeof(plist), sort_plist_by_type_desc);++  /* sort all gquad triangles by probability to bring lower probs to the front */+  qsort(pl, gq_num, sizeof(plist), sort_plist_by_prob_asc);++  /* print triangles for g-quadruplexes in upper half */+  fprintf(eps,"\n%%start of quadruplex data\n");++  for (pl1=pl; pl1->i > 0; pl1++) {+    if(pl1->type == VRNA_PLIST_TYPE_GQUAD){+      tmp = sqrt(pl1->p);+      fprintf(eps, "%d %d %1.9f utri\n", pl1->i, pl1->j, tmp);+    }+  }+}+++PRIVATE void+EPS_print_sc_motif_data(FILE          *eps,+                        vrna_plist_t  *pl,+                        vrna_plist_t  *mf){++  int     pl_size;+  double  tmp;+  plist   *pl1;++  /* print triangles for hairpin loop motifs in upper half */+  fprintf(eps,"\n%%start of Hmotif data\n");+  for (pl1=pl; pl1->i > 0; pl1++) {+    if(pl1->type == VRNA_PLIST_TYPE_H_MOTIF){+      tmp = sqrt(pl1->p);+      fprintf(eps, "%d %d %1.9f uHmotif\n", pl1->i, pl1->j, tmp);+    }+  }+  for (pl1=mf; pl1->i > 0; pl1++) {+    if(pl1->type == VRNA_PLIST_TYPE_H_MOTIF){+      tmp = sqrt(pl1->p);+      fprintf(eps, "%d %d %1.9f lHmotif\n", pl1->i, pl1->j, tmp);+    }+  }++  /* print triangles for interior loop motifs in upper half */+  fprintf(eps,"\n%%start of Imotif data\n");+  int   a,b;+  float ppp;+  a = b = 0;+  for (pl1=pl; pl1->i > 0; pl1++) {+    if(pl1->type == VRNA_PLIST_TYPE_I_MOTIF){+      if(a == 0){+        a = pl1->i;+        b = pl1->j;+        ppp = tmp = sqrt(pl1->p);+      } else {+        fprintf(eps, "%d %d %d %d %1.9f uImotif\n", a, b, pl1->i, pl1->j, ppp);+        a = b = 0;+      }+    }+  }+  for (a = b= 0, pl1=mf; pl1->i > 0; pl1++) {+    if(pl1->type == VRNA_PLIST_TYPE_I_MOTIF){+      if(a == 0){+        a = pl1->i;+        b = pl1->j;+        ppp = sqrt(pl1->p);+      } else {+        fprintf(eps, "%d %d %d %d %1.9f lImotif\n", a, b, pl1->i, pl1->j, ppp);+        a = b = 0;+      }+    }+  }+}+++PRIVATE void+EPS_print_bpp_data( FILE          *eps,+                    vrna_plist_t  *pl,+                    vrna_plist_t  *mf){++  int     pl_size;+  double  tmp;+  plist   *pl1;++  fprintf(eps,"%%start of base pair probability data\n");++  /* print boxes in upper right half*/+  for (pl1 = pl; pl1->i>0; pl1++) {+    tmp = sqrt(pl1->p);+    if(pl1->type == VRNA_PLIST_TYPE_BASEPAIR)+        fprintf(eps,"%d %d %1.9f ubox\n", pl1->i, pl1->j, tmp);+  }+++  /* print boxes in lower left half (mfe) */+  for (pl1=mf; pl1->i>0; pl1++) {+    tmp = sqrt(pl1->p);+    if(pl1->type == VRNA_PLIST_TYPE_BASEPAIR)+      fprintf(eps,"%d %d %1.7f lbox\n", pl1->i, pl1->j, tmp);+  }+}+++PRIVATE void+EPS_print_ud_data(FILE          *eps,+                  vrna_plist_t  *pl,+                  vrna_plist_t  *mf){++  int     pl_size;+  double  tmp;+  plist   *pl1;++  /* print triangles for unstructured domain motifs in upper half */+  fprintf(eps,"\n%%start of unstructured domain motif data\n");+  for(pl1 = pl; pl1->i > 0; pl1++){+    if(pl1->type == VRNA_PLIST_TYPE_UD_MOTIF){+      tmp = sqrt(pl1->p);+      fprintf(eps, "%d %d %1.9f uUDmotif\n", pl1->i, pl1->j, tmp);+    }+  }+  for(pl1 = mf; pl1->i > 0; pl1++){+    if(pl1->type == VRNA_PLIST_TYPE_UD_MOTIF){+      tmp = sqrt(pl1->p);+      fprintf(eps, "%d %d %1.9f lUDmotif\n", pl1->i, pl1->j, tmp);+    }+  }+}+++PRIVATE void+EPS_print_linear_data_top(FILE            *eps,+                          const char      **data_title,+                          vrna_data_lin_t **data){++  EPS_print_linear_data(eps, "topData", data_title, data);+}+++PRIVATE void+EPS_print_linear_data_left( FILE            *eps,+                            const char      **data_title,+                            vrna_data_lin_t **data){++  EPS_print_linear_data(eps, "leftData", data_title, data);+}+++PRIVATE void+EPS_print_linear_data_bottom( FILE            *eps,+                              const char      **data_title,+                              vrna_data_lin_t **data){++  EPS_print_linear_data(eps, "bottomData", data_title, data);+}+++PRIVATE void+EPS_print_linear_data_right(FILE            *eps,+                            const char      **data_title,+                            vrna_data_lin_t **data){++  EPS_print_linear_data(eps, "rightData", data_title, data);+}+++PRIVATE void+EPS_print_linear_data(FILE            *eps,+                      const char      *varname,+                      const char      **data_title,+                      vrna_data_lin_t **data){++  int             n, i;+  vrna_data_lin_t *ptr;++  /* count number of data sets */+  for(n = 0; data_title[n]; n++);++  fprintf(eps, "/%s [\n", varname);+  for(i = 0; i < n; i++){+    fprintf(eps, "[ (%s)\n", data_title[i]);+    for(ptr = data[i]; ptr->position > 0; ptr++){+      if((ptr->color.hue + ptr->color.sat + ptr->color.bri) == 0.){+        fprintf(eps, "  [ %d %1.9f ]\n", ptr->position, ptr->value);+      } else {+        fprintf(eps, "  [ %d %1.9f %1.4f %1.4f %1.4f]\n", ptr->position, ptr->value, ptr->color.hue, ptr->color.sat, ptr->color.bri);+      }+    }+    fprintf(eps, "]\n");+  }+  fprintf(eps, "] def\n\n");+}+++/*---------------------------------------------------------------------------*/+++static int sort_plist_by_type_desc(const void *p1, const void *p2){+  if(((plist*)p1)->type > ((plist*)p2)->type) return -1;+  if(((plist*)p1)->type < ((plist*)p2)->type) return 1;+  return 0;+}++static int sort_plist_by_prob_asc(const void *p1, const void *p2){+  if(((plist*)p1)->p > ((plist*)p2)->p) return 1;+  if(((plist*)p1)->p < ((plist*)p2)->p) return -1;+  return 0;+}+++PRIVATE vrna_data_lin_t *+plist_to_accessibility(plist *pl, unsigned int length){++  int   n, i;+  plist *ptr;++  vrna_data_lin_t *data = NULL;++  data = (vrna_data_lin_t *)vrna_alloc(sizeof(vrna_data_lin_t) * (length + 1));++  for(ptr = pl; ptr->i > 0; ptr++){+    if(ptr->type == VRNA_PLIST_TYPE_BASEPAIR){+      data[ptr->i - 1].value += ptr->p;+      data[ptr->j - 1].value += ptr->p;+    }+  }++  /* go through the entire list and square-root probabilities again */+  for(i = 0; i < length; i++){+    data[i].position = i + 1;+    data[i].value    = sqrt((double)(1. - data[i].value));+  }++  data[length].position = 0; /* end marker */++  return data;+}++PRIVATE vrna_data_lin_t *+plist_to_ud_motif_prob(plist *pl, unsigned int length){++  int   n, i;+  plist *ptr;++  vrna_data_lin_t *data = NULL;++  data = (vrna_data_lin_t *)vrna_alloc(sizeof(vrna_data_lin_t) * (length + 1));++  for(ptr = pl; ptr->i > 0; ptr++){+    if(ptr->type == VRNA_PLIST_TYPE_UD_MOTIF){+      for(i = ptr->i; i <= ptr->j; i++){+        data[i - 1].value += ptr->p;+      }+    }+  }++  /*  go through the entire list, remove entries with 0 probability,+      and square-root probabilities again+  */+  unsigned int actual_length  = length;+  unsigned int actual_pos     = 1;+  for(i = 0; i < actual_length; i++, actual_pos++){+    if(data[i].value == 0.){+      memmove(data + i, data + i + 1, sizeof(vrna_data_lin_t) * (actual_length - i));+      actual_length--;+      i--;+    } else {+      data[i].position  = actual_pos;+      data[i].value     = sqrt(data[i].value);+      data[i].color.hue = 0.6;+      data[i].color.sat = 0.8;+      data[i].color.bri = 0.95;+    }+  }++  if(actual_length > 0){+    data[actual_length].position = 0; /* end marker */+    data = (vrna_data_lin_t *)vrna_realloc(data, sizeof(vrna_data_lin_t) * (actual_length + 1));+    return data;+  } else {+    free(data);+    return NULL;+  }+}++++PRIVATE FILE *+PS_dot_common(const char *seq,+              int cp,+              const char *wastlfile,+              char *comment,+              int winsize,+              unsigned int options){++  /* write PS header etc for all dot plot variants */+  FILE *wastl;+  char *name, *c;+  int i;++  wastl = fopen(wastlfile,"w");+  if (wastl==NULL) {+    vrna_message_warning("can't open %s for dot plot", wastlfile);+    return NULL; /* return 0 for failure */+  }+  name = strdup(wastlfile);+  if((c=strrchr(name, '_')))+    *c='\0';++  int bbox[4];+  if(winsize > 0){+    bbox[0] = 66;+    bbox[1] = 530;+    bbox[2] = 520;+    bbox[3] = 650;+  } else {+    bbox[0] = 66;+    bbox[1] = 211;+    bbox[2] = 518;+    bbox[3] = 662;+  }++  EPS_print_header(wastl, bbox, comment, options);++  EPS_print_title(wastl, name);++  EPS_print_seq(wastl, seq);++  if (winsize>0)+    fprintf(wastl,"/winSize %d def\n",winsize);++  if (cp>0) fprintf(wastl,"/cutpoint %d def\n\n", cp);+++  if (winsize>0)+  fprintf(wastl,"292 416 translate\n"+          "72 6 mul len 1 add winSize add 2 sqrt mul div dup scale\n");+  else+    fprintf(wastl,"72 216 translate\n"+          "72 6 mul len 1 add div dup scale\n");+  fprintf(wastl, "/Helvetica findfont 0.95 scalefont setfont\n\n");++  if (winsize>0) {+    fprintf(wastl, "%s", RNAdp_prolog_turn);+    fprintf(wastl,"0.5 dup translate\n"+          "drawseq_turn\n"+          "45 rotate\n\n");+  }+  else+    fprintf(wastl,"drawseq\n");++  free(name);+  return(wastl);+}++#ifdef VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++int PS_dot_plot(char *string, char *wastlfile) {+  /* this is just a wrapper to call PS_dot_plot_list */+  int i, j, k, length, maxl, mf_num;+  plist *pl;+  plist *mf;++  length = strlen(string);+  maxl = 2*length;+  pl = (plist *)vrna_alloc(maxl*sizeof(plist));+  k=0;+  /*make plist out of pr array*/+  for (i=1; i<length; i++)+    for (j=i+1; j<=length; j++) {+      if (pr[iindx[i]-j]<PMIN) continue;+      if (k>=maxl-1) {+        maxl *= 2;+        pl = (plist *)vrna_realloc(pl,maxl*sizeof(plist));+      }+      pl[k].i = i;+      pl[k].j = j;+      pl[k++].p = pr[iindx[i]-j];+    }+  pl[k].i=0;+  pl[k].j=0;+  pl[k++].p=0.;+  /*make plist out of base_pair array*/+  mf_num = base_pair ? base_pair[0].i : 0;+  mf = (plist *)vrna_alloc((mf_num+1)*sizeof(plist));+  for (k=0; k<mf_num; k++) {+    mf[k].i = base_pair[k+1].i;+    mf[k].j = base_pair[k+1].j;+    mf[k].p = 0.95*0.95;+  }+  mf[k].i=0;+  mf[k].j=0;+  mf[k].p=0.;+  i = PS_dot_plot_list(string, wastlfile, pl, mf, "");+  free(mf);+  free(pl);+  return (i);+}++#endif+
+ C/ViennaRNA/PS_dot.h view
@@ -0,0 +1,148 @@+#ifndef VIENNA_RNA_PACKAGE_PS_DOT_H+#define VIENNA_RNA_PACKAGE_PS_DOT_H+++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/plot_structure.h>+#include <ViennaRNA/plot_aln.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file PS_dot.h+ *  @ingroup   plotting_utils+ *  @brief Various functions for plotting RNA secondary structures, dot-plots and other+ *  visualizations+ */++/**+ *  @{+ *  @ingroup   plotting_utils+ */++#define VRNA_PLOT_PROBABILITIES_BP        1U+#define VRNA_PLOT_PROBABILITIES_ACC       2U++#define VRNA_PLOT_PROBABILITIES_UD        4U+#define VRNA_PLOT_PROBABILITIES_UD_LIN    8U++#define VRNA_PLOT_PROBABILITIES_SD        16U++#define VRNA_PLOT_PROBABILITIES_SC_MOTIF  32U+#define VRNA_PLOT_PROBABILITIES_SC_UP     64U+#define VRNA_PLOT_PROBABILITIES_SC_BP     128U++#define VRNA_PLOT_PROBABILITIES_DEFAULT   (   VRNA_PLOT_PROBABILITIES_BP \+                                            | VRNA_PLOT_PROBABILITIES_SD \+                                            | VRNA_PLOT_PROBABILITIES_SC_MOTIF \+                                            | VRNA_PLOT_PROBABILITIES_UD_LIN )+typedef struct {+  char            *comment;+  char            *title;++  vrna_data_lin_t **top;+  char            **top_title;++  vrna_data_lin_t **bottom;+  char            **bottom_title;++  vrna_data_lin_t **left;+  char            **left_title;++  vrna_data_lin_t **right;+  char            **right_title;+} vrna_dotplot_auxdata_t;+++int+vrna_plot_dp_EPS( const char              *filename,+                  const char              *sequence,+                  vrna_plist_t            *upper,+                  vrna_plist_t            *lower,+                  vrna_dotplot_auxdata_t  *auxdata,+                  unsigned int            options);++int PS_color_dot_plot(char *string,+                      cpair *pi,+                      char *filename);++int PS_color_dot_plot_turn( char *seq,+                            cpair *pi,+                            char *filename,+                            int winSize);++/**+ *  @brief Produce a postscript dot-plot from two pair lists+ *+ *  This function reads two plist structures (e.g. base pair probabilities and a secondary structure)+ *  as produced by assign_plist_from_pr() and assign_plist_from_db() and produces a postscript+ *  "dot plot" that is written to 'filename'.\n+ *  Using base pair probabilities in the first and mfe structure in the second plist, the resulting+ *  "dot plot" represents each base pairing probability by a square of corresponding area in a upper+ *  triangle matrix. The lower part of the matrix contains the minimum free energy structure.+ *+ *  @see assign_plist_from_pr(), assign_plist_from_db()+ *+ *  @param seq      The RNA sequence+ *  @param filename A filename for the postscript output+ *  @param pl       The base pair probability pairlist+ *  @param mf       The mfe secondary structure pairlist+ *  @param comment  A comment+ *  @return         1 if postscript was successfully written, 0 otherwise+ */+int PS_dot_plot_list( char *seq,+                      char *filename,+                      plist *pl,+                      plist *mf,+                      char *comment);++int vrna_plot_dp_PS_list( char *seq,+                          int cp,+                          char *wastlfile,+                          plist *pl,+                          plist *mf,+                          char *comment);++int PS_dot_plot_turn( char *seq,+                      plist *pl,+                      char *filename,+                      int winSize);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  Wrapper to PS_dot_plot_list+ *+ *  @brief Produce postscript dot-plot+ *+ *  Reads base pair probabilities produced by pf_fold() from the+ *  global array #pr and the pair list #base_pair produced by+ *  fold() and produces a postscript "dot plot" that is written to+ *  'filename'. The "dot plot" represents each base pairing+ *  probability by a square of corresponding area in a upper triangle+ *  matrix. The lower part of the matrix contains the minimum free energy+ *  @note DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE+ *+ *  @deprecated This function is deprecated and will be removed soon! Use @ref PS_dot_plot_list() instead!+ */+DEPRECATED(int PS_dot_plot( char *string,+                            char *file));++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/ProfileAln.c view
@@ -0,0 +1,273 @@+/*+   Fast, but crude, pairwise structural Alignments of RNA sequences++   Possible structures of each RNA are encoded in a linear+   "probability profile", by computing for each base the probability+   of being unpaired, or paired upstream or downstream. These profiles+   can be aligned using standard string alignment.++   The is an extension of the old method in ProfileDist.c with the+   following changes:+   - use sequence as well as structure profile for scoring+   - use similarity alignment instead of distance (maybe add local alinment)+   - use affine gap costs++	  C Ivo L Hofacker, Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include <math.h>+#include <float.h>+#include "ViennaRNA/dist_vars.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/profiledist.h"+#include "ViennaRNA/ProfileAln.h"+++#define EQUAL(x,y)     (fabs((x)-(y)) <= fabs(x)*2*FLT_EPSILON)++PRIVATE int *alignment[2];++PRIVATE void    sprint_aligned_bppm(const float *T1, const char *seq1,+				    const float *T2, const char *seq2);+PRIVATE double  PrfEditScore(const float *p1, const float *p2,+			     char c1, char c2);+PRIVATE double  average(double x, double y);++PRIVATE double  open=-1.5, ext=-0.666;  /* defaults from clustalw */+PRIVATE double  seqw=0.5;+PRIVATE int     free_ends=1;            /* whether to use free end gaps */++/*---------------------------------------------------------------------------*/++PRIVATE float **newmat(int l1, int l2) {+  float **a;+  int i;+  a = (float **) vrna_alloc((l1+1)*sizeof(float *));+  for (i=0; i<=l1; i++) a[i] = (float *) vrna_alloc((l2+1)*sizeof(float));+  return a;+}++PUBLIC float profile_aln(const float *T1, const char *seq1,+			 const float *T2, const char *seq2)+{+  /* align the 2 probability profiles T1, T2 */+  /* This is like a Needleman-Wunsch alignment, with affine gap-costs+     ala Gotoh. The score looks at both seq and pair profile */++  float  **S, **E, **F, tot_score;+  int    i, j, length1, length2;++  length1 = strlen(seq1);+  length2 = strlen(seq2);+  S = newmat(length1, length2);+  E = newmat(length1, length2);+  F = newmat(length1, length2);++  E[0][0] = F[0][0] = open - ext;+  S[0][0] = 0;+  for (i=1; i<=length1; i++) F[i][0] = -9999; /* impossible */+  for (j=1; j<=length2; j++) E[0][j] = -9999; /* impossible */+  if (!free_ends) {+    for (i=1; i<=length1; i++) S[i][0] = E[i][0] = E[i-1][0] +ext;+    for (j=1; j<=length2; j++) S[0][j] = F[0][j] = F[0][j-1] +ext;+  }++  for (i=1; i<=length1; i++) {+    for (j=1; j<=length2; j++) {+      float M;+      E[i][j] = MAX2(E[i-1][j]+ext, S[i-1][j]+open);+      F[i][j] = MAX2(F[i][j-1]+ext, S[i][j-1]+open);+      M = S[i-1][j-1] + PrfEditScore(T1+3*i,T2+3*j, seq1[i-1], seq2[j-1]);+      S[i][j] = MAX3(M, E[i][j], F[i][j]);+    }+  }++  if (edit_backtrack) {+    double score=0;+    char state = 'S';+    int pos, i,j;+    alignment[0] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));+    alignment[1] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));++    pos = length1+length2;+    i   = length1;+    j   = length2;++    tot_score = S[length1][length2];++    if (free_ends) {+      /* find starting point for backtracking,+	 search for highest entry in last row or column */+      int imax=0;+      for (i=1; i<=length1; i++) {+	if (S[i][length2]>score) {+	  score=S[i][length2];+	  imax=i;+	}+      }+      for (j=1; j<=length2; j++) {+	if (S[length1][j]>score) {+	  score=S[length1][j];+	  imax=-j;+	}+      }+      if (imax<0) {+	for (j=length2; j> -imax; j--) {+	  alignment[0][pos] = 0;+	  alignment[1][pos--] = j;+	}+	i=length1;+      } else {+	for (i=length1; i>imax; i--) {+	  alignment[0][pos] = i;+	  alignment[1][pos--] = 0;+	}+	j=length2;+      }+      tot_score=score;+    }++    while (i>0 && j>0) {+      switch (state) {+      case 'E':+	score = E[i][j];+	alignment[0][pos] = i;+	alignment[1][pos--] = 0;+	if (EQUAL(score, S[i-1][j] + open)) state = 'S';+	i--;+	break;+      case 'F':+	score = F[i][j];+	alignment[0][pos] = 0;+	alignment[1][pos--] = j;+	if (EQUAL(score, S[i][j-1] + open)) state = 'S';+	j--;+	break;+      case 'S':+	score = S[i][j];+	if (EQUAL(score, E[i][j])) state = 'E';+	else if (EQUAL(score, F[i][j])) state = 'F';+	else if (EQUAL(score, S[i-1][j-1] ++		       PrfEditScore(T1+3*i,T2+3*j, seq1[i-1], seq2[j-1]))) {+	  alignment[0][pos] = i;+	  alignment[1][pos--] = j;+	  i--; j--;+	}+	else vrna_message_error("backtrack of alignment failed");+	break;+      }+    }++    for (; j>0; j--) {+      alignment[0][pos] = 0;+      alignment[1][pos--] = j;+    }+    for (; i>0; i--) {+      alignment[0][pos] = i;+      alignment[1][pos--] = 0;+    }++    for(i=pos+1; i<=length1+length2; i++){+      alignment[0][i-pos] = alignment[0][i];+      alignment[1][i-pos] = alignment[1][i];+    }+    alignment[0][0] = length1+length2-pos;   /* length of alignment */++    sprint_aligned_bppm(T1,seq1, T2,seq2);+    free(alignment[0]);+    free(alignment[1]);+  }+  for (i=0; i<=length1; i++) {+    free(S[i]); free(E[i]); free(F[i]);+  }+  free(S); free(E); free(F);++  return tot_score;+}+++/*---------------------------------------------------------------------------*/+PRIVATE inline double average(double x, double y) {+  /*+     As in Bonhoeffer et al (1993) 'RNA Multi Structure Landscapes',+     Eur. Biophys. J. 22: 13-24 we have chosen  the geometric mean.+  */+  return (float) sqrt(x*y);+}++PRIVATE double PrfEditScore(const float *p1, const float *p2, char c1, char c2)+{+  double  score;+  int    k;++  for(score=0.,k=0; k<3; k++)+    score += average(p1[k],p2[k]);++  score *= (1- seqw);+  if (c1==c2) score +=  seqw;+  else if (((c1=='A') && (c2=='G')) ||+	   ((c1=='G') && (c2=='A')) ||+	   ((c1=='C') && (c2=='U')) ||+	   ((c1=='U') && (c2=='C')))+    score += 0.5*seqw;+  else score -= 0.9*seqw;+  return score;+}++/*---------------------------------------------------------------------------*/++PRIVATE void sprint_aligned_bppm(const float *T1, const char *seq1,+				 const float *T2, const char *seq2) {+   int     i, length;+   length = alignment[0][0];+   for (i=0; i<4; i++) {+     if (aligned_line[i] != NULL) free(aligned_line[i]);+     aligned_line[i] = (char *) vrna_alloc((length+1)*sizeof(char));+   }+   for(i=1; i<=length; i++){+      if (alignment[0][i]==0)+	aligned_line[0][i-1] = aligned_line[2][i-1] = '_';+      else {+	aligned_line[0][i-1] = vrna_bpp_symbol(T1+alignment[0][i]*3);+	aligned_line[2][i-1] = seq1[alignment[0][i]-1];+      }+      if (alignment[1][i]==0)+	aligned_line[1][i-1] = aligned_line[3][i-1] = '_';+      else {+	aligned_line[1][i-1] = vrna_bpp_symbol(T2+alignment[1][i]*3);+	aligned_line[3][i-1] = seq2[alignment[1][i]-1];+      }+   }+}++PUBLIC int set_paln_params(double gap_open, double gap_ext,+			   double seq_weight, int freeends) {+  open = (gap_open>0) ? -gap_open : gap_open;+  ext = (gap_ext>0) ? -gap_ext : gap_ext;+  if (open > ext)+    vrna_message_warning( "Gap extension penalty is smaller than "+                          "gap open. Do you realy want this?");+  seqw = seq_weight;+  if (seqw<0) {+    seqw = 0;+    vrna_message_warning("Sequence weight set to 0 (must be in [0..1])");+  } else+  if (seqw>1) {+    seqw = 1;+    vrna_message_warning("Sequence weight set to 1 (must be in [0..1])");+  }+  free_ends = (freeends) ? 1 : 0;+  return 0;+}++/*---------------------------------------------------------------------------*/
+ C/ViennaRNA/ProfileAln.h view
@@ -0,0 +1,14 @@+#ifndef VIENNA_RNA_PACKAGE_PROFILEALN_H+#define VIENNA_RNA_PACKAGE_PROFILEALN_H++float profile_aln(const float *T1,+                  const char *seq1,+                  const float *T2,+                  const char *seq2);++int set_paln_params(double gap_open,+                    double gap_ext,+                    double seqweight,+                    int free_ends);++#endif
+ C/ViennaRNA/ProfileDist.c view
@@ -0,0 +1,247 @@+/*+	  Functions for handling the Base Pair Probability Matrix+		      Peter F Stadler, Ivo L Hofacker+			    Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include <math.h>+#include "ViennaRNA/dist_vars.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/profiledist.h"++PRIVATE int *alignment[2];++PRIVATE void    sprint_aligned_bppm(const float *T1, const float *T2);+PRIVATE double  PrfEditCost(int i, int j, const float *T1, const float *T2);+PRIVATE double  average(double x, double y);++/*---------------------------------------------------------------------------*/++PUBLIC float profile_edit_distance(const float *T1, const float *T2)+{+  /* align the 2 probability profiles T1, T2 */+  /* This is like a Needleman-Wunsch alignment,+     we should really use affine gap-costs ala Gotoh */++  float    **distance;+  short    **i_point, **j_point;++  int           i, j, i1, j1, pos, length1,length2;+  float         minus, plus, change, temp;++  length1 = (int) T1[0];+  length2 = (int) T2[0];+  distance = (float **)     vrna_alloc((length1 +1)*sizeof(float *));+  if(edit_backtrack){+    i_point  = (short **)  vrna_alloc((length1 +1)*sizeof(short *));+    j_point  = (short **)  vrna_alloc((length1 +1)*sizeof(short *));+  }+  for(i=0; i<= length1; i++){+    distance[i] = (float *) vrna_alloc( (length2+1)*sizeof(float));+    if(edit_backtrack){+      i_point[i]  = (short *) vrna_alloc( (length2+1)*sizeof(short));+      j_point[i]  = (short *) vrna_alloc( (length2+1)*sizeof(short));+    }+  }++  for(i = 1; i <= length1; i++) {+    distance[i][0] = distance[i-1][0]+PrfEditCost(i,0,T1,T2);+    if(edit_backtrack){ i_point[i][0] = (short) i-1; j_point[i][0] = 0;   }+  }+  for(j = 1; j <= length2; j++) {+    distance[0][j] = distance[0][j-1]+PrfEditCost(0,j,T1,T2);+    if(edit_backtrack){ i_point[0][j] = 0;   j_point[0][j] = (short) j-1; }+  }+  for (i = 1; i <= length1; i++) {+    for (j = 1; j <= length2 ; j++) {+      minus  = distance[i-1][j]  + PrfEditCost(i,0,T1,T2);+      plus   = distance[i][j-1]  + PrfEditCost(0,j,T1,T2);+      change = distance[i-1][j-1]+ PrfEditCost(i,j,T1,T2);++      distance[i][j] = MIN3(minus, plus, change);+      /* printf("%g ", distance[i][j]); */++      if(edit_backtrack){+	if(distance[i][j] == change) {+	  i_point[i][j]= (short)i-1; j_point[i][j]= (short) j-1;  }+	else if(distance[i][j] == plus) {+	  i_point[i][j]= (short)i  ; j_point[i][j]= (short)j-1;  }+	else {+	  i_point[i][j]= (short)i-1; j_point[i][j]= (short)j  ;  }+      }+    }+    /* printf("\n"); */+  }+  /* printf("\n"); */+  temp = distance[length1][length2];+  for(i=0;i<=length1;i++)+    free(distance[i]);+  free(distance);++  if(edit_backtrack){+    alignment[0] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));+    alignment[1] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));++    pos = length1+length2;+    i   = length1;+    j   = length2;+    while( (i>0)||(j>0) ) {+      i1 = i_point[i][j];+      j1 = j_point[i][j];+      if( ((i-i1)==1)&&((j-j1)==1) )  {  /* substitution    */+	alignment[0][pos] = i;+	alignment[1][pos] = j;+      }+      if( ((i-i1)==1)&&(j==j1) )      {  /* Deletion in [1] */+	alignment[0][pos] = i;+	alignment[1][pos] = 0;+      }+      if( (i==i1)&&((j-j1)==1)  )      {  /* Deletion in [0] */+	alignment[0][pos] = 0;+	alignment[1][pos] = j;+      }+      pos--;+      i = i1;+      j = j1;+    }+    for(i=pos+1; i<=length1+length2; i++){+      alignment[0][i-pos] = alignment[0][i];+      alignment[1][i-pos] = alignment[1][i];+    }+    alignment[0][0] = length1+length2-pos;   /* length of alignment */++    for(i=0; i<=length1; i++){+      free(i_point[i]); free(j_point[i]);+    }+    free(i_point); free(j_point);+    sprint_aligned_bppm(T1,T2);+    free(alignment[0]);+    free(alignment[1]);+  }++  return temp;+}+++/*---------------------------------------------------------------------------*/++PRIVATE double PrfEditCost(int i, int j, const float *T1, const float *T2)+{+  double  dist;+  int    k, kmax;++  kmax = (int) T1[1];+  if ((int) T2[1] != kmax) vrna_message_error("inconsistent Profiles in PrfEditCost");++  if(i==0) {+    for(dist = 0. ,k=0 ; k<kmax ; k++)+      dist += T2[j*kmax+k];+  }+  if(j==0) {+    for(dist = 0. ,k=0 ; k<kmax ; k++)+      dist += T1[i*kmax+k];+  }+  if((i>0)&&(j>0)) {+    for(dist = 2.,k=0; k<kmax; k++)+      dist -= 2.*average(T1[i*kmax+k],T2[j*kmax+k]);+  }+  return dist;+}++/*---------------------------------------------------------------------------*/++PRIVATE double average(double x, double y)++/* can be essentially anything that fulfils :+   1.)     a(x,y)  =  a(y,x)+   2.)     a(x,y) >=  0       for 0<= x,y <= 1+   3.)     a(x,y) <=  (x+y)/2+   4.)     a(x,x) >=  a(x,y)  for 0<= x,y <= 1+   As in Bonhoeffer et al (1993) 'RNA Multi Structure Landscapes',+   Eur. Biophys. J. 22: 13-24 we have chosen  the geometric mean.+*/++{+    float a;+    a = (float) sqrt(x*y);+    return a;+}++/*---------------------------------------------------------------------------*/++PUBLIC float *Make_bp_profile_bppm(FLT_OR_DBL *bppm, int length){+   int i,j;+   int L=3;+   float *P; /* P[i*3+0] unpaired, P[i*3+1] upstream, P[i*3+2] downstream p */+   int *index = vrna_idx_row_wise((unsigned) length);++   P =  (float *) vrna_alloc((length+1)*3*sizeof(float));+   /* indices start at 1 use first entries to store length and dimension */+   P[0] = (float) length;+   P[1] = (float) L;++   for( i=1; i<length; i++)+     for( j=i+1; j<=length; j++ ) {+       P[i*L+1] += bppm[index[i]-j];+       P[j*L+2] += bppm[index[i]-j];+     }+   for( i=1; i<=length; i++)+     P[i*3+0] = 1 - P[i*3+1] - P[i*3+2];++   free(index);++   return (float *) P;+}++/*---------------------------------------------------------------------------*/++PRIVATE void sprint_aligned_bppm(const float *T1, const float *T2)+{+   int     i, length;+   length = alignment[0][0];+   aligned_line[0] = (char *) vrna_alloc((length+1)*sizeof(char));+   aligned_line[1] = (char *) vrna_alloc((length+1)*sizeof(char));+   for(i=1; i<=length; i++){+      if(alignment[0][i] ==0) aligned_line[0][i-1] = '_';+      else { aligned_line[0][i-1] = vrna_bpp_symbol(T1+alignment[0][i]*3); }+      if(alignment[1][i] ==0) aligned_line[1][i-1] = '_';+      else { aligned_line[1][i-1] = vrna_bpp_symbol(T2+alignment[1][i]*3); }+   }+}++/*---------------------------------------------------------------------------*/++PUBLIC void print_bppm(const float *T)+{+   int i;+   for(i=1; i<=( (int)T[0]); i++)+      printf("%c",vrna_bpp_symbol(T+i*3));+   printf("\n");+}++/*---------------------------------------------------------------------------*/++PUBLIC void     free_profile(float *T)+{+   free(T);+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC float *Make_bp_profile(int length){+   return Make_bp_profile_bppm(pr, length);+}++
+ C/ViennaRNA/RNAstruct.c view
@@ -0,0 +1,579 @@+/*+		parse and convert secondary structures+	   Walter Fontana, Ivo L Hofacker, Peter F Stadler+			Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/RNAstruct.h"++#define PRIVATE  static+#define PUBLIC++#define MAXLEN    10000+++PRIVATE char *aux_struct(const char *structure);++/* on return from parse_structure(), b2C() or b2Shapiro() ... */+PUBLIC int    loop_size[STRUC];       /* contains loop sizes of a structure */+PUBLIC int    helix_size[STRUC];      /* contains helix sizes of a structure */+PUBLIC int    loop_degree[STRUC];     /* contains loop degrees of a structure */+PUBLIC int    loops;                  /* n of loops and stacks in a structure */+PUBLIC int    unpaired, pairs;        /* n of unpaired digits and pairs */++/*---------------------------------------------------------------------------*/++PRIVATE char *aux_struct(const char* structure )+{+   short        *match_paren;+   int          i, o, p;+   char        *string;++   string = (char *) vrna_alloc(sizeof(char)*(strlen(structure)+1));+   match_paren = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/2+1));+   strcpy(string, structure);++   i = o = 0;+   while (string[i]) {+      switch (string[i]) {+       case '.': break;+       case '(':+	 match_paren[++o]=i;+	 break;+       case ')':+	 p=i;+	 while ((string[p+1]==')')&&(match_paren[o-1]==match_paren[o]-1)) {+	    p++; o--;+	 }+	 string[p]=']';+	 i=p;+	 string[match_paren[o]]='[';+	 o--;+	 break;+       default:+	 vrna_message_error("Junk in structure at aux_structure\n");+      }+      i++;+   }+   free(match_paren);+   return(string);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *b2HIT(const char *structure)+{++   int            i, u, p, l;+   char          *string, *temp, *HIT, tt[10];++   temp = (char *) vrna_alloc(strlen(structure)*4+4);+   string = aux_struct( structure );++   strcpy(temp,"(");+   i=p=u=0; l=1;+   while (string[i]) {+      switch(string[i]) {+       case '.':+	 u++; break;+       case '[':+	 if (u>0) {+	    sprintf(tt, "(U%d)" , u);+	    strcat(temp+l, tt);+	    l+=strlen(tt);+	    u=0;+	 }+	 strcat(temp+l, "("); l++;+	 break;+       case ')':+	 if (u>0) {+	    sprintf(tt, "(U%d)" , u);+	    strcat(temp+l, tt);+	    l+=strlen(tt);+	    u=0;+	 }+	 p++;+	 break;+       case ']':+	 if (u>0) {+	    sprintf(tt, "(U%d)" , u);+	    strcat(temp+l, tt);+	    l+=strlen(tt);+	    u=0;+	 }+	 sprintf(tt,"P%d)", p+1);+	 strcat(temp+l, tt);+	 l+=strlen(tt);+	 p=0;+	 break;+      }+      i++;+   }+   if (u>0) {+      sprintf(tt, "(U%d)" , u);+      strcat(temp+l, tt);+      l+=strlen(tt);+   }+   strcat(temp+l, "R)");++   free( string );++   HIT = (char *) vrna_alloc(sizeof(char)*(strlen(temp)+2));+   strcpy(HIT, temp);+   free(temp);+   return(HIT);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *b2C(const char *structure )+{+   short *bulge, *loop;++   int    i, lp, p, l;+   char  *string, *Coarse, *temp;++   bulge = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));+   loop = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));+   temp = (char *) vrna_alloc(4*strlen(structure)+2);++   for (i = 0; i < STRUC; i++) {+      loop_size[i] = helix_size[i] = 0;+   }+   loop_degree[0]=0;         /* open structure has degree 0 */+   pairs = unpaired = loops = lp = 0;+   loop[0]=0;++   string = aux_struct( structure );++   i=p=l=0;+   temp[l++] = '(';+   while (string[i]) {+      switch(string[i]) {+       case '.':+	 loop_size[loop[lp]]++;+	 break;+       case '[':+	 temp[l++]='(';+	 if ((i>0)&&(string[i-1]=='(')) bulge[lp]=1;+	 lp++;+	 loop_degree[++loops]=1;+	 loop[lp]=loops;+	 bulge[lp]=0;+	 break;+       case ')':+	 if (string[i-1]==']') bulge[lp]=1;+	 p++;+	 break;+       case ']':+	 if (string[i-1]==']') bulge[lp]=1;+	 switch (loop_degree[loop[lp]]) {+	  case 1:  temp[l++]='H'; break;           /* hairpin */+	  case 2:+	    if (bulge[lp]==1)+	       temp[l++] = 'B';                    /* bulge */+	    else+	       temp[l++] = 'I';                    /* internal loop */+	    break;+	  default: temp[l++] = 'M';                /* multiloop */+	 }+	 temp[l++] = ')';+	 pairs+=p+1;+	 p=0;+	 loop_degree[loop[--lp]]++;+	 break;+      }+      i++;+   }+   temp[l++] = 'R';+   temp[l++] = ')';+   temp[l]='\0';+   free(string);+   Coarse = (char *) vrna_alloc(sizeof(char)*(strlen(temp)+2));+   strcpy(Coarse, temp);+   free(temp);+   free(bulge); free(loop);+   return(Coarse);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *b2Shapiro(const char *structure )+{++   short *bulge, *loop;++   int            i, lp, p, l, k;+   char          *string, *Shapiro, *temp, tt[10];++   bulge = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));+   loop = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));+   temp = (char *) vrna_alloc(4*strlen(structure)+3);++   for (i = 0; i < STRUC; i++) {+      loop_size[i] = helix_size[i] = 0;+   }+   loop_degree[0]=0;         /* open structure has degree 0 */+   pairs = unpaired = loops = lp = 0;+   loop[0]=0;++   string = aux_struct( structure );++   i=p=l=0;+   temp[l++] = '(';    /* root */+   while (string[i]) {+      switch(string[i]) {+       case '.':+	 unpaired++;+	 loop_size[loop[lp]]++;+	 break;+       case '[':+	 temp[l++]='(';+	 temp[l++]='(';+	 if ((i>0)&&(string[i-1]=='(' || string[i-1]=='['))+	   bulge[lp]=1;+	 lp++;+	 loop_degree[++loops]=1;+	 loop[lp]=loops;+	 bulge[lp]=0;+	 break;+       case ')':+	 if (string[i-1]==']') bulge[lp]=1;+	 p++;+	 break;+       case ']':+	 if (string[i-1]==']') bulge[lp]=1;+	 switch (loop_degree[loop[lp]]) {+	  case 1:  temp[l++]='H'; break;           /* hairpin */+	  case 2:+	    if (bulge[lp]==1)+	       temp[l++] = 'B';                    /* bulge */+	    else+	       temp[l++] = 'I';                    /* internal loop */+	    break;+	  default: temp[l++] = 'M';                /* multiloop */+	 }+	 helix_size[loop[lp]]=p+1;++         sprintf(tt, "%d)" , loop_size[loop[lp]]);+         for(k=0; k<strlen(tt); k++) temp[l++] = tt[k];+	 sprintf(tt, "S%d)" , helix_size[loop[lp]]);+         for(k=0; k<strlen(tt); k++) temp[l++] = tt[k];++	 pairs+=p+1;+	 p=0;+	 loop_degree[loop[--lp]]++;+	 break;+      }+      i++;+   }++   *tt = '\0';+   if (loop_size[0]) sprintf(tt, "E%d)" , loop_size[0]);+   strcat(tt,"R)");+   temp[l]='\0';+   strcat(temp, tt);+   Shapiro = (char *) vrna_alloc(sizeof(char)*(strlen(temp)+2));+   if (loop_size[0]) {+      Shapiro[0]='(';+      strcpy(Shapiro+1, temp);+   } else strcpy(Shapiro, temp);+   free(string);+   free(temp);+   free(loop); free(bulge);+   return Shapiro;+}+++++/*---------------------------------------------------------------------------*/++PUBLIC void parse_structure(const char *structure)++/*-----------------------------------------------------------------------------++    upon return from parse_structure():++    loops    ....................... number of loops or stacks in structure.+    loop_size[1 <= i <= loops] ..... size of i-th loop.+    loop_size[0] ................... number of external digits.+    loop_degree[1 <= i <= loops] ... degree (branches) of i-th loop.+    loop_degree[0] ................. number of components.+    helix_size[1 <= i <= loops] .... size of i-th stack.+    unpaired ....................... n of unpaired digits.+    pairs .......................... n of base pairs.++-----------------------------------------------------------------------------*/++{+   short  *bulge, *loop;++   int            i, lp, p;+   char          *string, *temp;++   temp = (char *)  vrna_alloc(strlen(structure)*4+2);+   bulge = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));+   loop = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/3+1));++   for (i = 0; i < STRUC; i++) {+      loop_size[i] = helix_size[i] = 0;+   }+   loop[0] = loop_degree[0]=0;         /* open structure has degree 0 */+   pairs = unpaired = loops = lp = 0;+   *temp='\0';++   string = aux_struct(structure);++   i=p=0;+   while (string[i]) {+      switch(string[i]) {+       case '.':+	 unpaired++;+	 loop_size[loop[lp]]++;+	 break;+       case '[':+	 if ((i>0)&&(string[i-1]=='(')) bulge[lp]=1;+	 lp++;+	 loop_degree[++loops]=1;+	 loop[lp]=loops;+	 bulge[lp]=0;+	 break;+       case ')':+	 if (string[i-1]==']') bulge[lp]=1;+	 p++;+	 break;+       case ']':+	 if (string[i-1]==']') bulge[lp]=1;+	 helix_size[loop[lp]]=p+1;+	 pairs+=p+1;+	 p=0;+	 loop_degree[loop[--lp]]++;+	 break;+      }+      i++;+   }+   free(string);+   free(bulge); free(loop);+   free(temp);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *add_root(const char *structure)+{+    char *xS;+    xS = (char *) vrna_alloc(sizeof(char)*(strlen(structure)+4));+    xS[0] = '(';+    strcat(xS,structure);+    strcat(xS,"R)");+    return xS;+}+++/*---------------------------------------------------------------------------*/++PUBLIC char *expand_Shapiro(const char *structure)+{+   char  *xS, *temp;+   int  i, l;++   temp = (char *) vrna_alloc(4*strlen(structure)+2);++   i = 1;+   l = 1;+   temp[0] = '(';+   while (i<strlen(structure)-1) {+      temp[l++] = structure[i];+      if      (structure[i] == '(') temp[l++] = '(';+      else if (structure[i] == ')') {+	 temp[l++] = 'S';+	 temp[l++] = ')';+      }+      i++;+   }+   temp[l++] = ')';+   temp[l] = '\0';++   xS = (char *) vrna_alloc(sizeof(char)*(strlen(temp)+1));+   strcpy(xS, temp);+   free(temp);+   return (xS);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *expand_Full(const char *structure)+{+    char *xF, *temp;+    int  i, l;++    temp = (char *) vrna_alloc(4*strlen(structure)+2);++    i = 0;+    l = 0;+    while (structure[i]) {+        if      (structure[i] == '(') temp[l++] = '(';+        else if (structure[i] == ')') {+            temp[l++] = 'P';+	    temp[l++] = ')';+        }+        else {+            temp[l++] = '(';+            temp[l++] = 'U';+            temp[l++] = ')';+        }+        i++;+     }+     temp[l] = '\0';++     xF = (char *) vrna_alloc(sizeof(char)*(l+5));+     strcpy(xF, "(");+     strcat(xF, temp);+     strcat(xF, "R)");+     free(temp);+     return (xF);+}++/*---------------------------------------------------------------------------*/++PUBLIC char *unexpand_Full(const char *structure)+{+   short        *match_paren;+   char id[10], *full, *temp;+   int    i, j, k, l, o, w;++   temp = (char *) vrna_alloc(4*strlen(structure)+2);+   match_paren = (short *) vrna_alloc(sizeof(short)*(strlen(structure)/2+1));++   i = strlen(structure)-1;+   l = o = 0; k=9;+   id[9]='\0';+   while (i>=0) {+     switch (structure[i]) {+     case '(':+       for (j=0; j<match_paren[o]; j++) temp[l++]='(';+       match_paren[o--] = 0;+       break;+     case 'U':+       w=1;+       sscanf(id+k, "%d", &w);+       for (j=0; j<w; j++) temp[l++]='.';+       k=9;+       break;+     case 'P':+           w=1;+       sscanf(id+k, "%d", &w);+       for (j=0; j<w; j++) temp[l++]=')';+       match_paren[o]=w;+       k=9;+       break;+     case 'R':+       break;+     case ')':+       o++;+       break;+     default:+       id[--k]=structure[i];+     }+     i--;+   }++   temp[l] = '\0';+   full = (char *) vrna_alloc(sizeof(char)*(l+1));+   for (i=0; i<l; i++) full[i]=temp[l-i-1];+   full[l]='\0';+   free(temp);+   free(match_paren);+   return full;+}+++/*---------------------------------------------------------------------------*/++PUBLIC char *unweight(const char *structure)+{+   int i,l;+   char *full, *temp;++   temp = (char *) vrna_alloc(4*strlen(structure)+1);++   i=l=0;+   while (structure[i]) {+      if (!isdigit((int)structure[i])) temp[l++]=structure[i];+      i++;+   }+   temp[l]='\0';+   full = (char *) vrna_alloc(sizeof(char)*(l+1));+   strcpy(full, temp);+   free(temp);+   return full;+}++/*---------------------------------------------------------------------------*/++PUBLIC void unexpand_aligned_F(char *align[2])+{+   char *t0, *t1;+   int i,l;++   t0 = (char *) vrna_alloc(strlen(align[0])+1);+   t1 = (char *) vrna_alloc(strlen(align[0])+1);++   for (i=0, l=0; i<strlen(align[0]); i++) {+      switch (align[0][i]) {+       case '(':+       case ')':+	 t0[l] = align[0][i];+	 t1[l++]=align[1][i];+	 break;+       case 'U':+	 switch (align[1][i]) {+	  case 'U':+	    t0[l-1]=t1[l-1]='.';+	    break;+	  case '_':+	    t0[l-1]='.';+	    t1[l-1]='_';+	    break;+	  case 'P':+	    t0[l-1]='_'; t0[l]='.';+	    t1[l-1]='('; t1[l]=')'; l++;+	 }+	 while (align[0][i]!=')') i++;+	 break;+       case '_':+	 switch (align[1][i]) {+	  case '(':+	  case ')':+	    t0[l] = align[0][i];+	    t1[l++]=align[1][i];+	    break;+	  case 'U':+	    while (align[1][i]!=')') i++;+	    t1[l-1]='.';+	    t0[l-1]='_';+	    break;+	 }+       case 'P':+	 if (align[1][i]=='U') {+	    t1[l-1]='_'; t1[l]='.'; t0[l++]=')';+	    while (align[0][i]!=')') i++;+	 }+	 break;+      }+   }+   t0[l-1]=t1[l-1]='\0';+   strcpy(align[0], t0+1);+   strcpy(align[1], t1+1);+   free(t0); free(t1);+}
+ C/ViennaRNA/RNAstruct.h view
@@ -0,0 +1,160 @@+#ifndef VIENNA_RNA_PACKAGE_RNASTRUCT_H+#define VIENNA_RNA_PACKAGE_RNASTRUCT_H++/**+ *  @addtogroup   struct_utils+ *+ *  @{+ *+ *  @file RNAstruct.h+ *  @brief Parsing and Coarse Graining of Structures+ * + *   Example:+ *  @verbatim+ *   .((..(((...)))..((..)))).   is the bracket or full tree+ *   becomes expanded:   - expand_Full() -+ *   ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)+ *   HIT:                - b2HIT() -+ *   ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)+ *   Coarse:             - b2C() -+ *   ((H)((H)M)R)+ *   becomes expanded:   - expand_Shapiro() -+ *   (((((H)S)((H)S)M)S)R)+ *   weighted Shapiro:   - b2Shapiro() -+ *   ((((((H3)S3)((H2)S2)M4)S2)E2)R)+ *  @endverbatim+ */++#define STRUC     2000++/**+ *  @brief Converts the full structure from bracket notation to the HIT+ *  notation including root.+ * + *  @param structure+ *  @return+ */+char *b2HIT(const char *structure);             /* Full   -> HIT    [incl. root] */++/**+ *  @brief Converts the full structure from bracket notation to the a+ *  coarse grained notation using the 'H' 'B' 'I' 'M' and 'R' identifiers.+ * + *  @param structure+ *  @return+ */+char *b2C(const char *structure);               /* Full   -> Coarse [incl. root] */++/**+ *  @brief Converts the full structure from bracket notation to the+ *  <i>weighted</i> coarse grained notation using the 'H' 'B' 'I' 'M' 'S' 'E' and+ *  'R' identifiers.+ * + *  @param structure+ *  @return+ */+char *b2Shapiro(const char *structure);         /* Full -> weighted Shapiro [i.r.] */++/**+ *  @brief Adds a root to an un-rooted tree in any except bracket notation.+ * + *  @param  structure+ *  @return+ */+char *add_root(const char *structure);                   /* {Tree} -> ({Tree}R)          */++/**+ *  @brief Inserts missing 'S' identifiers in unweighted coarse grained structures+ *  as obtained from b2C().+ * + *  @param coarse+ *  @return+ */+char  *expand_Shapiro(const char *coarse);++/* add S for stacks to coarse struct */+/**+ *  @brief Convert the full structure from bracket notation to the+ *  expanded notation including root.+ * + *  @param structure+ *  @return + */+char  *expand_Full(const char *structure);      /* Full   -> FFull         */++/**+ *  @brief Restores the bracket notation from an expanded full or HIT tree, that is+ *  any tree using only identifiers 'U' 'P' and 'R'.+ * + *  @param ffull+ *  @return + */+char  *unexpand_Full(const char *ffull);        /* FFull  -> Full          */++/**+ *  @brief Strip weights from any weighted tree.+ * + *  @param wcoarse+ *  @return+ */+char  *unweight(const char *wcoarse);           /* remove weights from coarse struct */++/**+ *  @brief Converts two aligned structures in expanded notation.+ * + *  Takes two aligned structures as produced by+ *  tree_edit_distance() function back to bracket notation with '_'+ *  as the gap character. The result overwrites the input.+ * + *  @param align+ */+void   unexpand_aligned_F(char *align[2]);++/**+ *  @brief Collects a statistic of structure elements of the full structure in+ *  bracket notation.+ * + *  The function writes to the following global variables:+ *  #loop_size, #loop_degree, #helix_size, #loops, #pairs, #unpaired+ * + *  @param structure+ *  @return+ */+void   parse_structure(const char *structure);  /* make structure statistics */++/**+ *  @brief contains a list of all loop sizes. loop_size[0] contains the+ *  number of external bases.+ */+extern int    loop_size[STRUC];       /* loop sizes of a structure */++/**+ *  @brief contains a list of all stack sizes.+ */+extern int    helix_size[STRUC];      /* helix sizes of a structure */++/**+ *  @brief contains the corresponding list of loop degrees.+ */+extern int    loop_degree[STRUC];     /* loop degrees of a structure */++/**+ *  @brief contains the number of loops ( and therefore of stacks ).+ */+extern int    loops;                  /* n of loops and stacks */++/**+ *  @brief contains the number of unpaired bases.+ */+extern int    unpaired;++/**+ *  @brief contains the number of base pairs in the last parsed structure.+ */+extern int    pairs;        /* n of unpaired digits and pairs */++/**+ * @}+ */++#endif
+ C/ViennaRNA/aliLfold.c view
@@ -0,0 +1,963 @@+/*+                  minimum free energy consensus+                  RNA secondary structure prediction+                  with maximum distance base pairs++                  c Ivo Hofacker, Stephan Bernhart++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/ribo.h"+#include "ViennaRNA/alifold.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/loop_energies.h"++#ifdef _OPENMP+#include <omp.h>+#endif+++#define PAREN++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */+#define MAXSECTORS      500     /* dimension for a backtrack array */+#define LOCALITY        0.      /* locality parameter for base-pairs */+#define UNIT 100+#define MINPSCORE -2 * UNIT+#define NONE -10000 /* score for forbidden pairs */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE vrna_param_t    *P = NULL;+PRIVATE int             **c = NULL;       /* energy array, given that i-j pair */+PRIVATE int             *cc = NULL;       /* linear array for calculating canonical structures */+PRIVATE int             *cc1 = NULL;      /*   "     "        */+PRIVATE int             *f3 = NULL;       /* energy of 5' end */+PRIVATE int             **fML = NULL;     /* multi-loop auxiliary energy array */+PRIVATE int             *Fmi = NULL;      /* holds row i of fML (avoids jumps in memory) */+PRIVATE int             *DMLi = NULL;     /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */+PRIVATE int             *DMLi1 = NULL;    /*             MIN(fML[i+1,k]+fML[k+1,j])  */+PRIVATE int             *DMLi2 = NULL;    /*             MIN(fML[i+2,k]+fML[k+1,j])  */+PRIVATE int             **pscore = NULL;  /* precomputed array of pair types */+PRIVATE unsigned int    length;+PRIVATE short           **S = NULL;+PRIVATE short           **S5 = NULL;      /*S5[s][i] holds next base 5' of i in sequence s*/+PRIVATE short           **S3 = NULL;      /*Sl[s][i] holds next base 3' of i in sequence s*/+PRIVATE char            **Ss = NULL;+PRIVATE unsigned short  **a2s = NULL;+PRIVATE float           **dm = NULL;+PRIVATE int             olddm[7][7]= {{0,0,0,0,0,0,0}, /* hamming distance between pairs PRIVATE needed??*/+                                      {0,0,2,2,1,2,2} /* CG */,+                                      {0,2,0,1,2,2,2} /* GC */,+                                      {0,2,1,0,2,1,2} /* GU */,+                                      {0,1,2,2,0,2,1} /* UG */,+                                      {0,2,2,1,2,0,2} /* AU */,+                                      {0,2,2,2,1,2,0} /* UA */};+PRIVATE int             energyout;+PRIVATE int             energyprev;++#ifdef _OPENMP++/* NOTE: all variables are assumed to be uninitialized if they are declared as threadprivate+*/+#pragma omp threadprivate(P, c, cc, cc1, f3, fML, Fmi, DMLi, DMLi1, DMLi2, pscore, length, S, dm, S5, S3, Ss, a2s, energyout, energyprev)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  initialize_aliLfold(int length, int maxdist);+PRIVATE void  free_aliL_arrays(int maxdist);+PRIVATE void  get_arrays(unsigned int size, int maxdist);+PRIVATE short *encode_seq(const char *sequence, short *s5, short *s3, char *ss, unsigned short *as);+PRIVATE void  make_pscores(const char ** AS, const char *structure,int maxdist, int start);+PRIVATE int   fill_arrays(const char **strings, int maxdist, char *structure);+PRIVATE char  *backtrack(const char **strings, int start, int maxdist);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PRIVATE void initialize_aliLfold(int length, int maxdist){+  if (length<1) vrna_message_error("initialize_fold: argument must be greater 0");+  get_arrays((unsigned) length, maxdist);+  make_pair_matrix();+  if(P) free(P);+  vrna_md_t   md;+  set_model_details(&md);+  P = vrna_params(&md);+}++/*--------------------------------------------------------------------------*/++PRIVATE void get_arrays(unsigned int size, int maxdist)+{+  int i;+  c       = (int **)vrna_alloc(sizeof(int *)*(size+1));+  fML     = (int **)vrna_alloc(sizeof(int *)*(size+1));+  pscore  = (int **)vrna_alloc(sizeof(int *)*(size+1));+  f3      = (int *) vrna_alloc(sizeof(int)*(size+2));  /* has to be one longer */+  cc      = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  cc1     = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  Fmi     = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  DMLi    = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  DMLi1   = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  DMLi2   = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+  for (i=size; i>(int)size-maxdist-5 && i>=0; i--) {+    c[i]      = (int *) vrna_alloc(sizeof(int) *(maxdist+5));+    fML[i]    = (int *) vrna_alloc(sizeof(int) *(maxdist+5));+    pscore[i] = (int *) vrna_alloc(sizeof(int )*(maxdist+5));+  }++}++/*--------------------------------------------------------------------------*/++PRIVATE void free_aliL_arrays(int maxdist) {+  int i;+  for(i=0; i<maxdist+5 && i<=length; i++){+    free(c[i]);+    free(fML[i]);+    free(pscore[i]);+  }+  free(c);+  free(fML);+  free(f3);+  free(cc);+  free(cc1);+  free(pscore);+  free(Fmi);+  free(DMLi);+  free(DMLi1);+  free(DMLi2);+}++/*--------------------------------------------------------------------------*/+PUBLIC float aliLfold(const char **strings, char *structure, int maxdist) {+  int length, energy, s, n_seq, i, j;+  length = (int) strlen(strings[0]);+  if (maxdist>length) maxdist = length;+  initialize_aliLfold(length, maxdist);++  for (s=0; strings[s]!=NULL; s++);+  n_seq = s;+  S   = (short **)          vrna_alloc(n_seq*sizeof(short *));+  S5  = (short **)          vrna_alloc(n_seq*sizeof(short *));+  S3  = (short **)          vrna_alloc(n_seq*sizeof(short *));+  a2s = (unsigned short **) vrna_alloc(n_seq*sizeof(unsigned short *));+  Ss  = (char **)           vrna_alloc(n_seq*sizeof(char *));++  for (s=0; s<n_seq; s++) {+    if (strlen(strings[s]) != length) vrna_message_error("uneqal seqence lengths");+    S5[s]   = (short *)           vrna_alloc((length+2)*sizeof(short));+    S3[s]   = (short *)           vrna_alloc((length+2)*sizeof(short));+    a2s[s]  = (unsigned short *)  vrna_alloc((length+2)*sizeof(unsigned short));+    Ss[s]   = (char *)            vrna_alloc((length+2)*sizeof(char));+    S[s]    = encode_seq(strings[s], S5[s],S3[s],Ss[s],a2s[s]);+  }++  if (ribo) {+    if (RibosumFile !=NULL) dm=readribosum(RibosumFile);+    else dm=get_ribosum(strings, n_seq, S[0][0]);+  }+  else { /*use usual matrix*/+    dm=(float **)vrna_alloc(7*sizeof(float*));+    for (i=0; i<7;i++) {+      dm[i]=(float *)vrna_alloc(7*sizeof(float));+      for (j=0; j<7; j++)+        dm[i][j] = (float) olddm[i][j];+    }+  }++  for (i=length; i>=(int)length-(int)maxdist-4 && i>0; i--)+    make_pscores((const char **) strings,structure,maxdist,i);++  energy = fill_arrays(strings, maxdist, structure);++  free_aliL_arrays(maxdist);+  return (float) energy/100.;+}++PRIVATE int fill_arrays(const char **strings, int maxdist, char *structure) {+  /* fill "c", "fML" and "f3" arrays and return  optimal energy */++  int   i, j, k, length, energy;+  int   decomp, new_fML,MLenergy ;+  int   *type, type_2, tt, s, n_seq, lastf, lastf2, thisj, lastj;++  lastf = lastf2 = INF;++  /* int   bonus=0;*/++  length = (int) strlen(strings[0]);+  for (s=0; strings[s]!=NULL; s++);+  n_seq = s;+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  for (j=0; j<maxdist+5; j++)+    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;+  for (j=length; j>length-maxdist-3; j--) {+    for (i=(length-maxdist-2>0)?length-maxdist-2:1 ; i<j; i++)+      c[i][j-i] = fML[i][j-i] = INF;+  }++  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */+    for (j = i+1; j<=length && j<=i+TURN; j++) {+      c[i][j-i]=fML[i][j-i]=INF;+    }+   for (j = i+TURN+1; j <= length && j <= i+maxdist; j++) {+      int p, q, psc;+      /* bonus = 0;*/+      for (s=0; s<n_seq; s++) {+        type[s] = pair[S[s][i]][S[s][j]];+        if (type[s]==0) type[s]=7;+      }++      psc = pscore[i][j-i];++      if (psc>=cv_fact*MINPSCORE) {   /* we have a pair 2 consider */+        int new_c=0, stackEnergy=INF;+        /* hairpin ----------------------------------------------*/+        for (new_c=s=0; s<n_seq; s++){+          if((a2s[s][j-1] - a2s[s][i]) < 3) new_c += 600;+          else new_c += E_Hairpin(a2s[s][j-1]-a2s[s][i],type[s],S3[s][i],S5[s][j],Ss[s]+(a2s[s][i-1]), P);+        }+        /*--------------------------------------------------------+          check for elementary structures involving more than one+          closing pair.+          --------------------------------------------------------*/+        for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {+          int minq = j-i+p-MAXLOOP-2;+          if (minq<p+1+TURN) minq = p+1+TURN;+          for (q = minq; q < j; q++) {+            if (pscore[p][q-p]<MINPSCORE) continue;+++            for (energy = s=0; s<n_seq; s++) {+              type_2 = pair[S[s][q]][S[s][p]]; /* q,p not p,q! */+              if (type_2 == 0) type_2 = 7;+              energy += E_IntLoop(a2s[s][p-1]-a2s[s][i],+                                  a2s[s][j-1]-a2s[s][q],+                                  type[s],+                                  type_2,+                                  S3[s][i],+                                  S5[s][j],+                                  S5[s][p],+                                  S3[s][q],+                                  P);+            }+            new_c = MIN2(energy+c[p][q-p], new_c);+            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */++          } /* end q-loop */+        } /* end p-loop */+++        /* multi-loop decomposition ------------------------*/+        decomp = DMLi1[j-1-(i+1)];+        if (dangles) {+          for (s=0; s<n_seq; s++) {+            tt = rtype[type[s]];+            decomp += E_MLstem(tt, S5[s][j], S3[s][i], P);+          }+        }+        else{+          for(s=0; s<n_seq; s++){+            tt = rtype[type[s]];+            decomp += E_MLstem(tt, -1, -1, P);+          }+        }+        MLenergy = decomp + n_seq*P->MLclosing;+        new_c = MIN2(new_c, MLenergy);++        new_c = MIN2(new_c, cc1[j-1-(i+1)]+stackEnergy);+        cc[j-i] = new_c - psc; /* add covariance bonnus/penalty */+        if (noLonelyPairs)+          c[i][j-i] = cc1[j-1-(i+1)]+stackEnergy-psc;+        else+          c[i][j-i] = cc[j-i];++      } /* end >> if (pair) << */+      else c[i][j-i] = INF;+++      /* done with c[i,j], now compute fML[i,j] */+      /* free ends ? -----------------------------------------*/++      new_fML = fML[i+1][j-i-1]+n_seq*P->MLbase;+      new_fML = MIN2(fML[i][j-1-i]+n_seq*P->MLbase, new_fML);+      energy = c[i][j-i]/*+P->MLintern[type]*/;+      if(dangles){+        for (s=0; s<n_seq; s++) {+          energy += E_MLstem(type[s], (i > 1) ? S5[s][i] : -1, (j < length) ? S3[s][j] : -1, P);+        }+      }+      else{+        for (s=0; s<n_seq; s++) {+          energy += E_MLstem(type[s], -1, -1, P);+        }+      }+      new_fML = MIN2(energy, new_fML);++      /* modular decomposition -------------------------------*/++      for (decomp = INF, k = i+1+TURN; k <= j-2-TURN; k++)+        decomp = MIN2(decomp, Fmi[k-i]+fML[k+1][j-k-1]);++      DMLi[j-i] = decomp;               /* store for use in ML decompositon */+      new_fML = MIN2(new_fML,decomp);++++      fML[i][j-i] = Fmi[j-i] = new_fML;     /* substring energy */++    } /* for (j...) */++    /* calculate energies of 5' and 3' fragments */+    {+      static int do_backtrack = 0, prev_i=0;+      static char * prev=NULL;+      char *ss;+      int thisf=0;+      f3[i] = f3[i+1];+      for (j=i+TURN+1; j<length && j<=i+maxdist; j++) {+        if(c[i][j-i]<INF) {+        /*        if (c[j+1]<INF) {*/+          energy = c[i][j-i];+          if(dangles){+            for(s = 0; s < n_seq; s++){+              tt = pair[S[s][i]][S[s][j]];+              if(tt==0) tt=7;+              energy += E_ExtLoop(tt, (i>1) ? S5[s][i] : -1, S3[s][j], P);+            }+          }+          else{+            for(s = 0; s < n_seq; s++){+              tt = pair[S[s][i]][S[s][j]];+              if(tt==0) tt=7;+              energy += E_ExtLoop(tt, -1, -1, P);+            }+          }+          if (energy/(j-i+1) < thisf){+            thisf = energy/(j-i+1);+            thisj = j;+          }+          energy += f3[j+1];+          if(f3[i] > energy){+            f3[i] = energy;+          }+        }+      }+      if(length <= i+maxdist){+        j = length;+        if(c[i][j-i]<INF) {+          energy = c[i][j-i];+          if(dangles){+            for (s=0; s<n_seq; s++) {+              tt = pair[S[s][i]][S[s][j]];+              if(tt==0) tt=7;+              energy += E_ExtLoop(tt, (i>1) ? S5[s][i] : -1, -1, P);+            }+          }+          else{+            for (s=0; s<n_seq; s++) {+              tt = pair[S[s][i]][S[s][j]];+              if(tt==0) tt=7;+              energy += E_ExtLoop(tt, -1, -1, P);+            }+          }+          /*  thisf=MIN2(energy/(j-i+1),thisf); ???*/+          if (energy/(j-i+1) < thisf){+            thisf = energy/(j-i+1);+            thisj = j;+          }+          f3[i] = MIN2(f3[i], energy);+        }+      }+      /* backtrack partial structure */+      /* if (i+maxdist<length) {*/+      if (i<length-1){+        if (f3[i] != f3[i+1]) {+          do_backtrack    = 1;+          backtrack_type  = 'F';+          if (prev_i==0) {+            prev          =  backtrack(strings, i , MIN2(maxdist,length-i));+            prev_i        = i;+            do_backtrack  = 0;+            lastf2        = lastf;+            energyprev    = f3[i];+          }+        }+        else if((thisf < lastf) && (thisf < lastf2) && ((thisf/(n_seq*100)) < -0.01)){ /*?????????*/+          do_backtrack    = 2;+          backtrack_type  = 'C';+        }+        else if (do_backtrack){+          if(do_backtrack == 1){+            ss =  backtrack(strings, i+1 , MIN2(maxdist,length-i)/*+1*/);+            energyout = f3[i] - f3[i+strlen(ss)-1];/*??*/+          }+          else {+            ss =  backtrack(strings, i+1 , lastj-i-2);+            energyout=c[i+1][lastj-(i+1)];+            if(dangles){+              for (s=0; s<n_seq; s++) {+                int type;+                type = pair[S[s][i+1]][S[s][lastj-i]]; if (type==0) type=7;+                energyout += E_ExtLoop(type, (i>1) ? S5[s][i+1] : -1, S3[s][lastj-i], P);+              }+            }+            else{+              for (s=0; s<n_seq; s++) {+                int type;+                type = pair[S[s][i+1]][S[s][lastj-i]]; if (type==0) type=7;+                energyout += E_ExtLoop(type, -1, -1, P);+              }+            }+          }++          if((prev_i + strlen(prev) > i+1+strlen(ss)) || (do_backtrack==2)){+            char *outstr = (char *)vrna_alloc(sizeof(char) * (strlen(prev)+1));+            strncpy(outstr, strings[0]+prev_i-1, strlen(prev));+            outstr[strlen(prev)] = '\0';+            if (csv==1)  printf("%s , %6.2f, %4d, %4d\n",prev, energyprev/(100.*n_seq), prev_i,prev_i + (int)strlen(prev)-1);+            /* if(do_backtrack==1)*/+            else {+              printf("%s (%6.2f) %4d - %4d\n",prev, energyprev/(100.*n_seq), prev_i,prev_i + (int)strlen(prev)-1);+            }+            free(outstr);+          }+          free(prev);+          prev = ss;+          energyprev = energyout;+          prev_i = i+1;+          do_backtrack = 0;+          backtrack_type='F';+        }+      }+      lastf2 = lastf;+      lastf  = thisf;+      lastj  = thisj;+++      if (i==1) {+        char *outstr = NULL;+        if (prev) {+          outstr = (char *)vrna_alloc(sizeof(char) *(strlen(prev) + 1));+          strncpy(outstr, strings[0]+prev_i-1, strlen(prev));+          outstr[strlen(prev)] = '\0';+          if(csv==1)+            printf("%s ,%6.2f, %4d, %4d\n", prev, (energyprev)/(100.*n_seq), prev_i,prev_i + (int)strlen(prev)-1);+          else{+            printf("%s (%6.2f) %4d - %4d\n", prev, (energyprev)/(100.*n_seq), prev_i,prev_i + (int)strlen(prev)-1);+          }+        }+        if ((f3[prev_i] != f3[1]) || !prev){+          ss      =  backtrack(strings, i , maxdist);+          if(outstr) free(outstr);+          outstr  = (char *)vrna_alloc(sizeof(char) * (strlen(ss) + 1));+          strncpy(outstr, strings[0], strlen(ss));+          outstr[strlen(ss)] = '\0';+          printf("%s \n", outstr);+          if(csv==1)+            printf("%s ,%6.2f ,%4d ,%4d\n", ss, (f3[1]-f3[1 + strlen(ss)-1])/(100.*n_seq), 1, (int)strlen(ss)-1);+          else{+            printf("%s (%6.2f) %4d - %4d\n", ss, (f3[1]-f3[1 + strlen(ss)-1])/(100.*n_seq), 1, (int)strlen(ss)-1);+          }+          free(ss);+        }+        if(prev)    free(prev);+        if(outstr)  free(outstr);+      }+    }+    {+      int ii, *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=0; j< maxdist+5; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+      if (i<=length-maxdist-4) {+        c[i-1] = c[i+maxdist+4]; c[i+maxdist+4] = NULL;+        fML[i-1] = fML[i+maxdist+4]; fML[i+maxdist+4]=NULL;+        pscore[i-1] = pscore[i+maxdist+4]; pscore[i+maxdist+4] = NULL;+        if(i > 1)+          make_pscores((const char**) strings, structure, maxdist, i-1);+        for(ii=0; ii<maxdist+5; ii++) {+          c[i-1][ii] = fML[i-1][ii] = INF;+        }+      }+    }+  }++  return f3[1];+}++PRIVATE char * backtrack(const char **strings, int start, int maxdist) {+  /*------------------------------------------------------------------+    trace back through the "c", "f3" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This is fast, since only few structure elements are recalculated.+    ------------------------------------------------------------------*/+  sect  sector[MAXSECTORS];   /* backtracking sectors */++  int   i, j, k, energy;+  int   *type, type_2, tt, n_seq;+  /*int   bonus;*/+  int   s=0, ss;+  char *structure;+  for (s=0; strings[s]!=NULL; s++);+  n_seq = s;+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  s=0;+  length = strlen(strings[0]);+  sector[++s].i = start;+  sector[s].j = MIN2(length, start+maxdist+1);+  sector[s].ml = (backtrack_type=='M') ? 1 : ((backtrack_type=='C')?2:0);++  structure = (char *) vrna_alloc((MIN2(length-start, maxdist)+3)*sizeof(char));+  for (i=0; i<=MIN2(length-start, maxdist); i++) structure[i] = '.';++  while (s>0) {+    int ml, fij, cij, traced, i1, j1, mm, p, q, jj=0;+    int canonical = 1;     /* (i,j) closes a canonical structure */+    i  = sector[s].i;+    j  = sector[s].j;+    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to+                              occur in the fML- (1) or in the f-array (0) */+    if (ml==2) {+      structure[i-start] = '(';+      structure[j-start] = ')';+      goto repeat1;+    }++    if (j < i+TURN+1) continue; /* no more pairs in this interval */++    fij = (ml)? fML[i][j-i] : f3[i];++    if (ml == 0) { /* backtrack in f3 */++      if (fij == f3[i+1]) {+        sector[++s].i = i+1;+        sector[s].j   = j;+        sector[s].ml  = ml;+        continue;+      }+      /* i is paired. Find pairing partner */+      for (k=i+TURN+1,traced=0; k<=j; k++) {+        int cc;+        jj = k+1;+        cc = c[i][k-(i)];+        if (cc<INF) {+          if(dangles){+            for (ss=0; ss<n_seq; ss++) {+              type[ss] = pair[S[ss][i]][S[ss][k]];+              if (type[ss]==0) type[ss]=7;+              cc += E_ExtLoop(type[ss], (i>1) ? S5[ss][i] : -1, (k<length) ? S3[ss][k] : -1, P);+            }+          }+          else{+            for (ss=0; ss<n_seq; ss++) {+              type[ss] = pair[S[ss][i]][S[ss][k]];+              if (type[ss]==0) type[ss]=7;+              cc += E_ExtLoop(type[ss], -1, -1, P);+            }+          }+          if (fij == cc + f3[k+1]) traced=i;+        }+        if (traced) break;+      }++      if (!traced) vrna_message_error("backtrack failed in f3");+      if (j==length) { /* backtrack only one component, unless j==length */+        sector[++s].i = jj;+        sector[s].j   = j;+        sector[s].ml  = ml;+      }+      i=traced; j=k;+      structure[i-start] = '('; structure[j-start] = ')';+      goto repeat1;+    }+    else { /* trace back in fML array */+      if (fML[i][j-1-i]+n_seq*P->MLbase == fij) {  /* 3' end is unpaired */+        sector[++s].i = i;+        sector[s].j   = j-1;+        sector[s].ml  = ml;+        continue;+      }+      if (fML[i+1][j-(i+1)]+n_seq*P->MLbase == fij) { /* 5' end is unpaired */+        sector[++s].i = i+1;+        sector[s].j   = j;+        sector[s].ml  = ml;+        continue;+      }++      cij = c[i][j-i] ;+      if(dangles){+        for (ss=0; ss<n_seq; ss++) {+          tt  = pair[S[ss][i]][S[ss][j]];+          if (tt==0) tt=7;+          cij += E_MLstem(tt, (i>1) ? S5[ss][i] : -1, (j<length) ? S3[ss][j] : -1, P);+        }+      }+      else{+        for (ss=0; ss<n_seq; ss++) {+          tt  = pair[S[ss][i]][S[ss][j]];+          if (tt==0) tt=7;+          cij += E_MLstem(tt, -1, -1, P);+        }+      }++      if(fij==cij){+        /* found a pair */+        structure[i-start] = '('; structure[j-start] = ')';+        goto repeat1;+      }++      for (k = i+1+TURN; k <= j-2-TURN; k++)+        if (fij == (fML[i][k-i]+fML[k+1][j-(k+1)]))+          break;++      sector[++s].i = i;+      sector[s].j   = k;+      sector[s].ml  = ml;+      sector[++s].i = k+1;+      sector[s].j   = j;+      sector[s].ml  = ml;++      if (k>j-2-TURN) vrna_message_error("backtrack failed in fML");+      continue;+    }++  repeat1:++    /*----- begin of "repeat:" -----*/+    if (canonical)  cij = c[i][j-i];++    for (ss=0; ss<n_seq; ss++) {+      type[ss] = pair[S[ss][i]][S[ss][j]];+      if (type[ss]==0) type[ss] = 7;+    }++    /*    bonus = 0;*/++    if (noLonelyPairs)+      if (cij == c[i][j-i]) {+        /* (i.j) closes canonical structures, thus+           (i+1.j-1) must be a pair                */+        for (ss=0; ss<n_seq; ss++) {+          type_2 = pair[S[ss][j-1]][S[ss][i+1]];  /* j,i not i,j */+          if (type_2==0) type_2 = 7;+          cij -= P->stack[type[ss]][type_2];+        }+        cij += pscore[i][j-i];+        structure[i+1-start] = '('; structure[j-1-start] = ')';+        i++; j--;+        canonical=0;+        goto repeat1;+      }+    canonical = 1;+    cij += pscore[i][j-i];++    {+      int cc=0;+      for (ss=0; ss<n_seq; ss++){+        if((a2s[ss][j-1] - a2s[ss][i]) < 3) cc += 600;+        else cc += E_Hairpin(a2s[ss][j-1] - a2s[ss][i], type[ss], S3[ss][i], S5[ss][j], Ss[ss] + a2s[ss][i-1], P);+      }+      if (cij == cc) /* found hairpin */+        continue;+    }++    for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1); p++) {+      int minq;+      minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+TURN) minq = p+1+TURN;+      for (q = j-1; q >= minq; q--) {+        if (c[p][q-p]>=INF) continue;+         for (ss=energy=0; ss<n_seq; ss++) {+          type_2 = pair[S[ss][q]][S[ss][p]];  /* q,p not p,q */+          if (type_2==0) type_2 = 7;+          energy += E_IntLoop(a2s[ss][p-1] - a2s[ss][i],+                              a2s[ss][j-1] - a2s[ss][q],+                              type[ss],+                              type_2,+                              S3[ss][i],+                              S5[ss][j],+                              S5[ss][p],+                              S3[ss][q],+                              P);+        }+        traced = (cij == energy+c[p][q-p]);+        if (traced) {+          structure[p-start] = '(';+          structure[q-start] = ')';+          i = p, j = q;+          goto repeat1;+        }+      }+    }++    /* end of repeat: --------------------------------------------------*/++    /* (i.j) must close a multi-loop */+    mm = n_seq*P->MLclosing;+    if(dangles){+      for (ss=0; ss<n_seq; ss++) {+        tt = rtype[type[ss]];+        mm += E_MLstem(tt, S5[ss][j],S3[ss][i], P);+      }+    }+    else{+      for (ss=0; ss<n_seq; ss++) {+        tt = rtype[type[ss]];+        mm += E_MLstem(tt, -1, -1, P);+      }+    }+    i1 = i+1; j1 = j-1;+    sector[s+1].ml  = sector[s+2].ml = 1;++    for (k = i+TURN+2; k < j-TURN-2; k++){+      if(cij == fML[i+1][k-(i+1)] + fML[k+1][j-1-(k+1)] + mm) break;+    }+    if (k<=j-3-TURN){ /* found the decomposition */+      sector[++s].i = i1;+      sector[s].j   = k;+      sector[++s].i = k+1;+      sector[s].j   = j1;+    } else {+        vrna_message_error("backtracking failed in repeat");+    }++  }+  if (start+maxdist<length) {+    for (i=strlen(structure); i>0 && structure[i-1] == '.'; i--)+      structure[i] = '\0';+  }+  return structure;+}++/*---------------------------------------------------------------------------*/+PRIVATE short *encode_seq(const char *sequence, short *s5, short *s3, char *ss, unsigned short *as){+  unsigned int    i,l;+  short           *S;+  unsigned short  p;++  l     = strlen(sequence);+  S     = (short *) vrna_alloc(sizeof(short)*(l+2));+  S[0]  = (short) l;++  s5[0]=s5[1]=0;+  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++) {+    short ctemp = (short)encode_char(toupper(sequence[i-1]));+    S[i]  = ctemp ;+  }++   if (oldAliEn) {+     /*use alignment sequences in all energy evaluations*/+     ss[0]=sequence[0];+     for (i=1; i<l; i++) {+       s5[i]=S[i-1];+       s3[i]=S[i+1];+       ss[i]= sequence[i];+       as[i]=i;+     }+     ss[l] = sequence[l];+     as[l]=l;+     s5[l]=S[l-1];+     s3[l]=0;+     S[l+1] = S[1];+     s5[1]=0;+     if (1) {+       s5[1]=S[l];+       s3[l]=S[1];+       ss[l+1]=S[1];+     }+     return S;+   }+   else {+     if (1) {+       for (i=l; i>0; i--) {+         char c5;+         c5=sequence[i-1];+         if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.')) continue;+         s5[1] = S[i];+         break;+       }+       for (i=1; i<=l; i++) {+         char c3;+         c3 = sequence[i-1];+         if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.')) continue;+         s3[l] = S[i];+         break;+       }+     } else  s5[1]=s3[l]=0;++     for (i=1,p=0; i<=l; i++) {+       char c5;+       c5=sequence[i-1];+       if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.'))+         s5[i+1]=s5[i];+       else { /* no gap */+         ss[p++]=sequence[i-1]; /*start at 0!!*/+         s5[i+1]=S[i];+       }+       as[i]=p;+     }+     for (i=l; i>=1; i--) {+       char c3;+       c3=sequence[i-1];+       if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.'))+         s3[i-1]=s3[i];+       else+         s3[i-1]=S[i];+     }+   }++   return S;+}++PRIVATE double cov_score(const char **AS, int i, int j) {+  int n_seq,k,l,s;+  double score;+  int pfreq[8]={0,0,0,0,0,0,0,0};+  for (n_seq=0; AS[n_seq]!=NULL; n_seq++);+  for (s=0; s<n_seq; s++) {+    int type;+    if (S[s][i]==0 && S[s][j]==0) type = 7; /* gap-gap  */+    else {+      if ((AS[s][i] == '~')||(AS[s][j] == '~')) type = 7;+      else type = pair[S[s][i]][S[s][j]];+    }++    pfreq[type]++;+  }+  if (pfreq[0]*2+pfreq[7]>n_seq)+    return NONE;+  else+    for (k=1,score=0.; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+      for (l=k; l<=6; l++)+        /* scores for replacements between pairtypes    */+        /* consistent or compensatory mutations score 1 or 2  */+        score += pfreq[k]*pfreq[l]*dm[k][l];++  /* counter examples score -1, gap-gap scores -0.25   */+  return cv_fact * ((UNIT*score)/n_seq - nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));+}++PRIVATE void make_pscores(const char ** AS,+                          const char *structure, int maxd, int i) {+  /* calculate co-variance bonus for each pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */+  int n,j,l;+  n=S[0][0];  /* length of seqs */++  /*first allocate space:*/+  pscore[i]=(int *)vrna_alloc((maxd+5)*sizeof(int));+  /*  pscore[start]-=start;*/+  /*fill pscore[start], too close*/+  for (j=i+1; (j<i+TURN+1) && (j<=n); j++) {+    pscore[i][j-i] = NONE;+  }+  for (j=i+TURN+1; ((j<=n) && (j<=i+maxd)); j++) {+    pscore[i][j-i] = cov_score(AS, i, j);+  }++  if (noLonelyPairs) { /* remove unwanted lonely pairs */+    int otype=0, ntype=0;+    for (j=i+TURN; ((j<n)&&(j<i+maxd)); j++) {+      if ((i>1) && (j<n)) otype = cov_score(AS, i-1, j+1);+      if (i<n) ntype=pscore[i+1][j-1-(i+1)];+      else ntype=NONE;++      if ((otype<-4*UNIT)&&(ntype<-4*UNIT))  /* worse than 2 counterex */+        pscore[i][j-i] = NONE; /* i.j can only form isolated pairs */+    }+  }++  if (fold_constrained&&(structure!=NULL)) {+    int psij, hx, *stack;+    stack = (int *) vrna_alloc(sizeof(int)*(n+1));+    hx=psij=0;+    /* for(hx=0, j=i+TURN; ((j<=i+maxd)&&(j<=n)); j++) {*/+    switch (structure[i-1]) {+    case 'x': /* can't pair */+      for (l=i+TURN+1; l<=i+maxd; l++) pscore[i][l-i] = NONE;+      break;+    case '(':+        hx=1;+        psij=1;+        for (l=i+1; l<=i+maxd; l++) {+          switch (structure[l-1]) {+          case '(':+            hx++;+            pscore[i][l-i] = NONE;+            break;+          case ')':+            hx--;+            if (hx!=0) pscore[i][l-i] = NONE;+            break;+          default:+            pscore[i][l-i] = NONE;+          }+          /* fallthrough */+                }+    case ')':+      for (l=i+TURN+1; l<=i+maxd; l++) pscore[i][l-i] = NONE;+      break;+    case '>':+      for (l=i+TURN+1; l<=i+maxd; l++) pscore[i][l-i] = NONE;+      break;++    }+    if (!psij) for (l=i+1; l<=i+maxd; l++) { /*no '(' constraint on i*/+      switch (structure[l-1]) {+      case '(':+        pscore[i][l-i] = NONE;+        break;+      case '<':+        pscore[i][l-i] = NONE;+        break;+      case 'x':+        pscore[i][l-i] = NONE;+        break;+      case ')':+         pscore[i][l-i] = NONE;+        break;+      }+    }+    if (hx!=0) {+      vrna_message_error("%s\nunbalanced brackets in constraint string", structure);+    }+    free(stack);+  }+}
+ C/ViennaRNA/ali_plex.c view
@@ -0,0 +1,1308 @@+/*+           compute the duplex structure of two RNA strands,+                allowing only inter-strand base pairs.+         see cofold() for computing hybrid structures without+                             restriction.+                             Ivo Hofacker+                          Vienna RNA package++*/+++/*+  library containing the function used in rnaplex+  the program rnaplex uses the following function+  Lduplexfold: finds high scoring segments+  it stores the end-position of these segments in an array+  and call then for each of these positions the duplexfold function+  which allows one to make backtracking for each of the high scoring position+  It allows one to find suboptimal partially overlapping (depends on a a parameter)+  duplexes between a long RNA and a shorter one.+  Contrarly to RNAduplex, the energy model is not in E~log(N),+  where N is the length of an interial loop but used an affine model,+  where the extension and begin parameter are fitted to the energy+  parameter used by RNAduplex. This allows one to check for duplex between a short RNA(20nt)+  and a long one at the speed of 1Mnt/s. At this speed the whole genome (3Gnt) can be analyzed for one siRNA+  in about 50 minutes.+  The algorithm is based on an idea by Durbin and Eddy:when the alginment reach a value larger than a+  given threshold this value is stored in an array. When the alignment score goes+  then under this threshold, the alignemnent begin from this value, in that way the backtracking allow us+  to find all non-overlapping high-scoring segments.+  For more information check "durbin, biological sequence analysis"+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/ali_plex.h"+++#define PUBLIC+#define PRIVATE static++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */+#define ARRAY 32          /*array size*/+#define UNIT 100+#define MINPSCORE -2 * UNIT+/**+*** Due to the great similarity between functions,+*** more annotation can be found in plex.c+**/++PRIVATE short *encode_seq(const char *seq);+PRIVATE void  update_dfold_params(void);+/**+*** aliduplexfold(_XS)/alibacktrack(_XS) computes duplex interaction with standard energy and considers extension_cost+*** alifind_max(_XS)/aliplot_max(_XS) find suboptimals and MFE+**/+PRIVATE duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);+PRIVATE char *    alibacktrack(int i, int j, const short *s1[], const short *s2[], const int extension_cost);+PRIVATE void      alifind_max(const int *position, const int *position_j,const int delta, const int threshold,+                           const int alignment_length, const char *s1[], const char *s2[], const int extension_cost, const int fast);+PRIVATE void      aliplot_max(const int max, const int max_pos, const int max_pos_j,+                           const int alignment_length, const char *s1[], const char *s2[], const int extension_cost, const int fast);+PRIVATE duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1,+                                 const int **access_s2, const int i_pos, const int j_pos, const int threshold,const int i_flag, const int j_flag);+PRIVATE char *    alibacktrack_XS(int i, int j, const short *s1[], const short *s2[], const int** access_s1, const int** access_s2,const int i_flag, const int j_flag);+PRIVATE void  alifind_max_XS(const int *position, const int *position_j,+                                 const int delta,  const int threshold, const int alignment_length,+                                 const char* s1[], const char* s2[],+                                 const int **access_s1, const int **access_s2, const int fast);+PRIVATE void aliplot_max_XS(const int max, const int max_pos, const int max_pos_j,+                            const int alignment_length, const char *s1[], const char* s2[],+                            const int **access_s1, const int **access_s2, const int fast);++/**+*** computes covariance score+**/++PRIVATE int covscore(const int *types, int n_seq);++extern double cv_fact; /* from alifold.c, default 1 */+extern double nc_fact;+++/*@unused@*/++#define MAXSECTORS      500     /* dimension for a backtrack array */+#define LOCALITY        0.      /* locality parameter for base-pairs */++PRIVATE vrna_param_t *P = NULL;+PRIVATE int   **c = NULL;+PRIVATE int  **lc = NULL, **lin = NULL, **lbx = NULL, **lby = NULL,**linx = NULL, **liny = NULL;+++++PRIVATE int   n1,n2;+PRIVATE int n3, n4;+PRIVATE int delay_free=0;+++/*-----------------------------------------------------------------------duplexfold_XS---------------------------------------------------------------------------*/++++/*----------------------------------------------ALIDUPLEXFOLD-----------------------------------------------------------------------------------------------------------*/+PRIVATE duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost) {+  int i, j, s, n_seq, Emin=INF, i_min=0, j_min=0;+  char *struc;+  duplexT mfe;+  vrna_md_t   md;+  short **S1, **S2;+  int *type;+  n3 = (int) strlen(s1[0]);+  n4 = (int) strlen(s2[0]);+  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; s2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in aliduplexfold()\n");++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=1; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));++  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n3) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n4) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_seq(s1[s]);+    S2[s] = encode_seq(s2[s]);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  for (i=1; i<=n3; i++) {+    for (j=n4; j>0; j--) {+      int k,l,E,psc;+      for (s=0; s<n_seq; s++) {+        type[s] = pair[S1[s][i]][S2[s][j]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      c[i][j] = (psc>=MINPSCORE) ? (n_seq*(P->DuplexInit + 2*extension_cost)) : INF;+      if (psc<MINPSCORE) continue;+      for (s=0; s<n_seq; s++) {+        c[i][j] += E_ExtLoop(type[s], (i>1) ? S1[s][i-1] : -1, (j<n4) ? S2[s][j+1] : -1, P) + 2*extension_cost;+      }+      for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+        for (l=j+1; l<=n4; l++) {+          int type2;+          if (i-k+l-j-2>MAXLOOP) break;+          if (c[k][l]>INF/2) continue;+          for (E=s=0; s<n_seq; s++) {+            type2 = pair[S1[s][k]][S2[s][l]];+            if (type2==0) type2=7;+            E += E_IntLoop(i-k-1, l-j-1, type2, rtype[type[s]],+                           S1[s][k+1], S2[s][l-1], S1[s][i-1], S2[s][j+1],P) + (i-k+l-j)*extension_cost;+          }+          c[i][j] = MIN2(c[i][j], c[k][l]+E);+        }+      }+      c[i][j] -= psc;+      E = c[i][j];+      for (s=0; s<n_seq; s++) {+        E += E_ExtLoop(rtype[type[s]], (j>1) ? S2[s][j-1] : -1, (i<n3) ? S1[s][i+1] : -1, P) +2*extension_cost;+      }+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      }+    }+  }+  struc = alibacktrack(i_min, j_min, (const short int**) S1, (const short int**) S2 , extension_cost);+  if (i_min<n3) i_min++;+  if (j_min>1 ) j_min--;+  int size;+  size=strlen(struc)-1;+  Emin-=size * n_seq * extension_cost;+  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (float) (Emin/(100.*n_seq));+  mfe.structure = struc;+  if (!delay_free) {+    for (i=1; i<=n3; i++) free(c[i]);+    free(c);+  }+  for (s=0; s<n_seq; s++) {+    free(S1[s]); free(S2[s]);+  }+  free(S1); free(S2); free(type);+  return mfe;+}+++PRIVATE char *alibacktrack(int i, int j, const short *S1[], const short *S2[], const int extension_cost) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, *type, type2, E, traced, i0, j0, s, n_seq;+  char *st1, *st2, *struc;++  n3 = (int) S1[0][0];+  n4 = (int) S2[0][0];++  for (s=0; S1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; S2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in alibacktrack()\n");++  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  i0=MIN2(i+1,n3); j0=MAX2(j-1,1);++  while (i>0 && j<=n4) {+    int psc;+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    for (s=0; s<n_seq; s++) {+      type[s] = pair[S1[s][i]][S2[s][j]];+    }+    psc = covscore(type, n_seq);+    for (s=0; s<n_seq; s++) if (type[s]==0) type[s] = 7;+    E += psc;+    for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+      for (l=j+1; l<=n4; l++) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        if (c[k][l]>INF/2) continue;+        for (s=LE=0; s<n_seq; s++) {+          type2 = pair[S1[s][k]][S2[s][l]];+          if (type2==0) type2=7;+          LE += E_IntLoop(i-k-1, l-j-1, type2, rtype[type[s]],+                          S1[s][k+1], S2[s][l-1], S1[s][i-1], S2[s][j+1],P)+(i-k+l-j)*extension_cost;+        }+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      for (s=0; s<n_seq; s++) {+        E -= E_ExtLoop(type[s], (i>1) ? S1[s][i-1] : -1, (j<n4) ? S2[s][j+1] : -1, P) + 2*extension_cost;+      }+      if (E != n_seq*P->DuplexInit + n_seq*2*extension_cost) {+        vrna_message_error("backtrack failed in aliduplex");+      } else break;+    }+  }+  if (i>1)  i--;+  if (j<n4) j++;++  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&");+  strcat(struc, st2+j0-1);++  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2); free(type);++  return struc;+}++duplexT** aliLduplexfold(const char *s1[], const char *s2[], const int threshold, const int extension_cost, const int alignment_length, const int delta, const int fast,const int il_a, const int il_b, const int b_a, const int b_b)+{+  short **S1, **S2;+  int *type, type2;+  int i, j,s,n_seq;+  s=0;+  int bopen=b_b;+  int bext=b_a+extension_cost;+  int iopen=il_b;+  int iext_s=2*(il_a+extension_cost);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a+extension_cost;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  int temp;+  int min_j_colonne;+  int max=INF;+  /* FOLLOWING NEXT 4 LINE DEFINES AN ARRAY CONTAINING POSITION OF THE SUBOPT IN S1 */+  int *position; /* contains the position of the hits with energy > E */+  int *position_j;+++  n1 = (int) strlen(s1[0]);+  n2 = (int) strlen(s2[0]);+  for (s=0; s1[s]; s++);+  n_seq = s;+  for (s=0; s2[s]; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in aliduplexfold()\n");++  position = (int *) vrna_alloc((delta+(n1)+4+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+(n1)+4+delta) * sizeof(int));++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)){+    update_dfold_params();+  }++  lc   = (int**) vrna_alloc(sizeof(int *) * 5);+  lin  = (int**) vrna_alloc(sizeof(int *) * 5);+  lbx  = (int**) vrna_alloc(sizeof(int *) * 5);+  lby  = (int**) vrna_alloc(sizeof(int *) * 5);+  linx = (int**) vrna_alloc(sizeof(int *) * 5);+  liny = (int**) vrna_alloc(sizeof(int *) * 5);++  for (i=0; i<=4; i++){+    lc[i]  = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lin[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lbx[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lby[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    linx[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+    liny[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+  }+++  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_seq(s1[s]);+    S2[s] = encode_seq(s2[s]);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  /**+  *** array initialization+  **/+  for(j=n2;j>=0;j--) {+    lbx[0][j]=lbx[1][j]=lbx[2][j]=lbx[3][j]    = lbx[4][j] =INF;+    lin[0][j]=lin[1][j]=lin[2][j]=lin[3][j]    = lin[4][j] =INF;+    lc[0][j] =lc[1][j] =lc[2][j] = lc[3][j]    =  lc[4][j] =INF;+    lby[0][j]=lby[1][j]=lby[2][j]=lby[3][j]    = lby[4][j] =INF;+    liny[0][j]=liny[1][j]=liny[2][j]=liny[3][j]=liny[4][j]=INF;+    linx[0][j]=linx[1][j]=linx[2][j]=linx[3][j]=linx[4][j]=INF;+  }+  i=10;+  i_length= n1 - 9 ;+  while(i < i_length) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    j=n2-9;+    while (9 < --j) {+      int psc;+      for (s=0; s<n_seq; s++) {+        type[s] = pair[S1[s][i]][S2[s][j]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      lc[idx][j] = (psc>=MINPSCORE) ? (n_seq*P->DuplexInit + 2*n_seq*extension_cost) : INF;+      /**+      *** Update matrix. It is the average over all sequence of a given structure element+      *** c_stack -> stacking of c+      *** c_10, c01 -> stack from bulge+      *** c_nm -> arrives in stack from nxm loop+      *** c_in -> arrives in stack from interior loop+      *** c_bx -> arrives in stack from large bulge on target+      *** c_by -> arrives in stack from large bulge on query+      ***+      **/+      int c_stack, c_10, c_01, c_11, c_22, c_21, c_12, c_23, c_32, c_in, c_in2x, c_in2y, c_bx, c_by, c_inx, c_iny;  /* matrix c */+      int in, in_x, in_y, in_xy; /*  in begin, in_x assymetric, in_y assymetric, in_xy symetric; */+      int inx, inx_x;+      int iny, iny_y;+      int bx, bx_x;+      int by, by_y;+      in=lc[idx_1][j+1]; in_x=lin[idx_1][j]; in_y=lin[idx][j+1]; in_xy=lin[idx_1][j+1];+      inx=lc[idx_1][j+1]; inx_x=linx[idx_1][j];+      iny=lc[idx_1][j+1]; iny_y=liny[idx][j+1];+      bx=lc[idx_1][j]; bx_x=lbx[idx_1][j];+      by=lc[idx][j+1]; by_y=lby[idx][j+1];+      c_stack=lc[idx_1][j+1]; c_01=lc[idx_1][j+2];c_10=lc[idx_2][j+1];+      c_12=lc[idx_2][j+3];c_21=lc[idx_3][j+2];c_11=lc[idx_2][j+2];+      c_22=lc[idx_3][j+3];c_32=lc[idx_4][j+3];c_23=lc[idx_3][j+4];+      c_in=lin[idx_3][j+3];c_in2x=lin[idx_4][j+2];c_in2y=lin[idx_2][j+4];+      c_inx=linx[idx_3][j+1]; c_iny=liny[idx_1][j+3];+      c_bx=lbx[idx_2][j+1];c_by=lby[idx_1][j+2];+      for (s=0; s<n_seq; s++) {+        type2 = pair[S2[s][j+1]][S1[s][i-1]];+        in   +=P->mismatchI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s;+        in_x +=iext_ass;+        in_y +=iext_ass;+        in_xy+=iext_s;+        inx  +=P->mismatch1nI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s;+        inx_x+=iext_ass;+        iny  +=P->mismatch1nI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s;+        iny_y+=iext_ass;+        type2=pair[S2[s][j]][S1[s][i-1]];+        bx   +=bopen+bext+(type2>2?P->TerminalAU:0);+        bx_x +=bext;+        type2=pair[S2[s][j+1]][S1[s][i]];+        by   +=bopen+bext+(type2>2?P->TerminalAU:0);+        by_y +=bext;+      }+      lin [idx][j]=MIN2(in, MIN2(in_x, MIN2(in_y, in_xy)));+      linx[idx][j]=MIN2(inx_x, inx);+      liny[idx][j]=MIN2(iny_y, iny);+      lby[idx][j] =MIN2(by, by_y);+      lbx[idx][j] =MIN2(bx, bx_x);++      if (psc<MINPSCORE) continue;+      for (s=0; s<n_seq; s++) {+        lc[idx][j]+=E_ExtLoop(type[s], S1[s][i-1],S2[s][j+1], P) + 2*extension_cost;+      }+      for (s=0; s<n_seq; s++) {+        type2=pair[S1[s][i-1]][S2[s][j+1]];if (type2==0) type2=7;+        c_stack+=E_IntLoop(0,0,type2, rtype[type[s]],S1[s][i], S2[s][j], S1[s][i-1], S2[s][j+1], P)+2*extension_cost;+        type2=pair[S1[s][i-1]][S2[s][j+2]];if (type2==0) type2=7;+        c_01   +=E_IntLoop(0,1,type2, rtype[type[s]],S1[s][i], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+3*extension_cost;+        type2=pair[S1[s][i-2]][S2[s][j+1]]; if (type2==0) type2=7;+        c_10   +=E_IntLoop(1,0,type2, rtype[type[s]],S1[s][i-1], S2[s][j], S1[s][i-1], S2[s][j+1], P)+3*extension_cost;+        type2=pair[S1[s][i-2]][S2[s][j+2]]; if (type2==0) type2=7;+        c_11   +=E_IntLoop(1,1,type2, rtype[type[s]],S1[s][i-1], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+4*extension_cost;+        type2 = pair[S1[s][i-3]][S2[s][j+3]];if (type2==0) type2=7;+        c_22   +=E_IntLoop(2,2,type2, rtype[type[s]],S1[s][i-2], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+6*extension_cost;+        type2 = pair[S1[s][i-3]][S2[s][j+2]];if (type2==0) type2=7;+        c_21   +=E_IntLoop(2,1,type2, rtype[type[s]],S1[s][i-2], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+5*extension_cost;+        type2 = pair[S1[s][i-2]][S2[s][j+3]];if (type2==0) type2=7;+        c_12   +=E_IntLoop(1,2,type2, rtype[type[s]],S1[s][i-1], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+5*extension_cost;+        type2 = pair[S1[s][i-4]][S2[s][j+3]];if (type2==0) type2=7;+        c_32   +=E_IntLoop(3,2,type2, rtype[type[s]],S1[s][i-3], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+7*extension_cost;+        type2 = pair[S1[s][i-3]][S2[s][j+4]];if (type2==0) type2=7;+        c_23   +=E_IntLoop(2,3,type2, rtype[type[s]],S1[s][i-2], S2[s][j+3], S1[s][i-1], S2[s][j+1], P)+7*extension_cost;+        c_in   +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+2*extension_cost+2*iext_s;+        c_in2x +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_s+2*iext_ass+2*extension_cost;+        c_in2y +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_s+2*iext_ass+2*extension_cost;+        c_inx  +=P->mismatch1nI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_ass+iext_ass+2*extension_cost;+        c_iny  +=P->mismatch1nI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_ass+iext_ass+2*extension_cost;+        int bAU;+        bAU=(type[s]>2?P->TerminalAU:0);+        c_bx   +=2*extension_cost+bext+bAU;+        c_by   +=2*extension_cost+bext+bAU;+      }+      lc[idx][j] =MIN2(lc[idx][j],+                       MIN2(c_stack,+                            MIN2(c_10,+                                 MIN2(c_01,+                                      MIN2(c_11,+                                           MIN2(c_21,+                                                MIN2(c_12,+                                                     MIN2(c_22,+                                                          MIN2(c_23,+                                                               MIN2(c_32,+                                                                    MIN2(c_bx,+                                                                         MIN2(c_by,+                                                                              MIN2(c_in,+                                                                                   MIN2(c_in2x,+                                                                                        MIN2(c_in2y,+                                                                                             MIN2(c_inx,c_iny)+                                                                                             )+                                                                                        )+                                                                                   )+                                                                              )+                                                                         )+                                                                    )+                                                               )+                                                          )+                                                     )+                                                )+                                           )+                                      )+                                 )+                            )+                       );+      lc[idx][j]-=psc;+      temp=lc[idx][j];+      for (s=0; s<n_seq; s++) {+        temp+=E_ExtLoop(rtype[type[s]], S2[s][j-1],S1[s][i+1],P)+2*extension_cost;+      }+      if(min_colonne > temp){+        min_colonne=temp;+        min_j_colonne=j;+      }+    }+    if(max>=min_colonne){+            max=min_colonne;+            max_pos=i;+        max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    i++;+  }+  /* printf("MAX:%d ",max); */+  for (s=0; s<n_seq; s++) {free(S1[s]);free(S2[s]);}+  free(S1); free(S2);+  if(max<threshold){+    alifind_max(position, position_j, delta, threshold, alignment_length, s1, s2, extension_cost, fast);+  }+  aliplot_max(max, max_pos, max_pos_j,alignment_length, s1, s2, extension_cost,fast);+  for (i=0; i<=4; i++) {free(lc[i]);free(lin[i]);free(lbx[i]);free(lby[i]);free(linx[i]);free(liny[i]);}+  /* free(lc[0]);free(lin[0]);free(lbx[0]);free(lby[0]);free(linx[0]);free(liny[0]); */+  free(lc);free(lin);free(lbx);free(lby);free(linx);free(liny);+  free(position);+  free(position_j);+  free(type);+  return NULL;+}+++PRIVATE void alifind_max(const int *position, const int *position_j,+                         const int delta, const int threshold, const int alignment_length,+                         const char *s1[], const char *s2[],+                         const int extension_cost, const int fast){+  int n_seq=0;+  for (n_seq=0; s1[n_seq]!=NULL; n_seq++);+  int pos=n1-9;+  if(fast==1){+    while(10<pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/(n_seq*100));+        pos=MAX2(10,pos+temp_min-delta);+      }+    }+  }+  else{+    pos=n1-9;+    while(pos-- > 10) {+      /* printf("delta %d position:%d value:%d\n", delta, pos, position[pos]); */+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* printf("%d %d %d\n", pos, max_pos_j,position[pos+delta]); */+        int begin_t=MAX2(11, pos-alignment_length+1);+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1);+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length-1);+        char **s3, **s4;+        s3 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+        s4 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+        int i;+        for(i=0; i<n_seq; i++){+          s3[i] = (char*) vrna_alloc(sizeof(char)*(end_t-begin_t+2));+          s4[i] = (char*) vrna_alloc(sizeof(char)*(end_q-begin_q+2));+          strncpy(s3[i], (s1[i]+begin_t-1), end_t - begin_t +1);+          strncpy(s4[i], (s2[i]+begin_q-1), end_q - begin_q +1);+          s3[i][end_t - begin_t +1]='\0';+          s4[i][end_q - begin_q +1]='\0';+        }+        duplexT test;+        test = aliduplexfold((const char**)s3, (const char**)s4, extension_cost);+        /* printf("test %d threshold %d",test.energy*100,(threshold/n_seq)); */+        if(test.energy * 100 < (int) (threshold/n_seq)){+          int l1=strchr(test.structure, '&')-test.structure;+                   printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure,+                 begin_t -10 +test.i-l1,+                 begin_t -10 +test.i-1,+                 begin_q -10 + test.j - 1,+                 begin_q-11 + test.j + (int)strlen(test.structure) -l1 -2 , test.energy);+          pos=MAX2(10,pos+temp_min-delta);++        }+        for(i=0;i<n_seq;i++){+          free(s3[i]);free(s4[i]);+        }+        free(s3);free(s4);+        free(test.structure);+      }+    }+  }+}+PRIVATE void aliplot_max(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1[], const char *s2[], const int extension_cost, const int fast)+{+  int n_seq;+  for (n_seq=0; !(s1[n_seq]==NULL); n_seq++);+  n1 = strlen(s1[0]); /* get length of alignment */+  n2 = strlen(s2[0]); /* get length of alignment */+  if(fast==1){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n",+           max_pos-10, max_pos_j-10, (double) ((double)max)/(100*n_seq));+  }+  else{+    int begin_t=MAX2(11, max_pos-alignment_length+1);+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1);+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length-1);+    char **s3, **s4;+    s3 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+    s4 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+    int i;+    for(i=0; i<n_seq; i++){+      s3[i] = (char*) vrna_alloc(sizeof(char)*(end_t-begin_t+2));+      s4[i] = (char*) vrna_alloc(sizeof(char)*(end_q-begin_q+2));+      strncpy(s3[i], (s1[i]+begin_t-1), end_t - begin_t +1);+      strncpy(s4[i], (s2[i]+begin_q-1), end_q - begin_q +1);+      s3[i][end_t - begin_t +1]='\0';+      s4[i][end_q - begin_q +1]='\0';+    }+    duplexT test;+    s3[n_seq]=s4[n_seq]=NULL;+    test = aliduplexfold((const char**) s3,(const char**) s4, extension_cost);+    int l1=strchr(test.structure, '&')-test.structure;+    printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n",+           test.structure,+           begin_t -10 +test.i-l1,+           begin_t -10 +test.i-1,+           begin_q-10 + test.j - 1,+           begin_q -11 + test.j + (int)strlen(test.structure) - l1 - 2,+           test.energy);+    for(i=0; i<n_seq ; i++){+      free(s3[i]);free(s4[i]);+    }+    free(s3);free(s4);+    free(test.structure);+  }+}++PRIVATE duplexT aliduplexfold_XS(const char *s1[], const char *s2[],+                                 const int **access_s1, const int **access_s2,+                                 const int i_pos, const int j_pos, const int threshold,+                                 const int i_flag, const int j_flag){+  int i,j,s,p,q, Emin=INF, l_min=0, k_min=0;+  char *struc;+  short **S1,**S2;+  int *type,*type2;+  struc=NULL;+  duplexT mfe;+  vrna_md_t   md;+  int n_seq;+  n3 = (int) strlen(s1[0]);+  n4 = (int) strlen(s2[0]);+  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; s2[s]!=NULL; s++);+  /* printf("%d \n",i_pos); */++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  for (i=0; i<=n3; i++){+    for(j=0;j<=n4;j++){+      c[i][j]=INF;+    }+  }+  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n3) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n4) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_seq(s1[s]);+    S2[s] = encode_seq(s2[s]);+  }+  type =  (int *) vrna_alloc(n_seq*sizeof(int));+  type2 = (int *) vrna_alloc(n_seq*sizeof(int));+  int type3, E, k,l;+  i=n3-i_flag; j=1+j_flag;+  for (s=0; s<n_seq; s++) {+    type[s] = pair[S1[s][i]][S2[s][j]];+  }+  c[i][j] = n_seq*P->DuplexInit - covscore(type,n_seq);+  for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+  for (s=0; s<n_seq; s++) {+    c[i][j]+=E_ExtLoop(rtype[type[s]], (j_flag ? S2[s][j-1] : -1) , (i_flag ? S1[s][i+1] : -1),  P);+  }+  k_min=i; l_min=j; Emin=c[i][j];+  for (k=i; k>1 ; k--) {+    if(k<i) c[k+1][0]=INF;+    for (l=j; l<=n4-1; l++) {+      if(!(k==i && l==j)){+        c[k][l]=INF;+      }+      int psc2;+      for(s=0;s<n_seq;s++){+        type2[s] = pair[S1[s][k]][S2[s][l]];+      }+      psc2=covscore(type2, n_seq);+      if (psc2<MINPSCORE) continue;+      for (s=0; s<n_seq; s++) if (type2[s]==0) type2[s]=7;+      for (p=k+1; p<= n3 -i_flag && p<k+MAXLOOP-1; p++) {+        for (q = l-1; q >= 1+j_flag; q--) {+          if (p-k+l-q-2>MAXLOOP) break;+          for(E=s=0;s<n_seq;s++){+            type3=pair[S1[s][p]][S2[s][q]];+            if(type3==0) type3=7;+            E += E_IntLoop(p-k-1, l-q-1, type2[s], rtype[type3],+                           S1[s][k+1], S2[s][l-1], S1[s][p-1], S2[s][q+1],P);+          }+          c[k][l] = MIN2(c[k][l], c[p][q]+E);+        }+      }+      c[k][l]-=psc2;+      E = c[k][l];+      E+=n_seq*(access_s1[i-k+1][i_pos]+access_s2[l-1][j_pos+(l-1)-1]);+      for (s=0; s<n_seq; s++) {+        E+=E_ExtLoop(type2[s], (k>1) ? S1[s][k-1] : -1, (l<n4) ? S2[s][l+1] : -1, P);+      }+      if (E<Emin) {+        Emin=E; k_min=k; l_min=l;+      }+    }+  }+  if(Emin > threshold-1){+    mfe.structure=NULL;+    mfe.energy=INF;+    for (i=0; i<=n3; i++) free(c[i]);+    free(c);+    for(i=0; i<=n_seq;i++){+      free(S1[i]);+      free(S2[i]);+    }+    free(S1); free(S2); /* free(SS1); free(SS2); */+    free(type);free(type2);+    return mfe;+    } else{+    struc = alibacktrack_XS(k_min, l_min,(const short int**)S1,(const short int**)S2,access_s1, access_s2,i_flag,j_flag);+    }+  int dx_5, dx_3, dy_5, dy_3,dGx,dGy;+  dx_5=0; dx_3=0; dy_5=0; dy_3=0;dGx=0;dGy=0;+  dGx =n_seq*(access_s1[i-k_min+1][i_pos]);dx_3=0; dx_5=0;+  dGy =n_seq*access_s2[l_min-j+1][j_pos + (l_min-1)-1];+  mfe.tb=i_pos -9 - i + k_min -1 -dx_5;+  mfe.te=i_pos -9 -1 + dx_3;+  mfe.qb=j_pos -9 -1 - dy_5;+  mfe.qe=j_pos + l_min -3 -9 + dy_3;+  mfe.ddG=(double) (Emin *0.01);+  mfe.dG1=(double) (dGx*(0.01));+  mfe.dG2=(double) (dGy*(0.01));+  mfe.energy= mfe.ddG - mfe.dG1 - mfe.dG2;+  mfe.structure = struc;+  for (i=0; i<=n3; i++) free(c[i]);+  free(c);+  for(i=0; i<=n_seq;i++){+    free(S1[i]);+    free(S2[i]);+  }+  free(S1); free(S2); free(type);free(type2);+  return mfe;+}++PRIVATE char *alibacktrack_XS(int i, int j, const short *S1[], const short *S2[],+                              const int** access_s1, const int ** access_s2, const int i_flag, const int j_flag) {+  int n3,n4,k, l, *type, type2, E, traced, i0, j0,s,n_seq,psc;+  char *st1=NULL, *st2=NULL, *struc=NULL;++  n3 = (int) S1[0][0];+  n4 = (int) S2[0][0];+  for (s=0; S1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; S2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in alibacktrack()\n");++  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  i0=i;/*MAX2(i-1,1);*/j0=j;/*MIN2(j+1,n4);*/+  while (i<=n3-i_flag && j>=1+j_flag) {+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    for (s=0; s<n_seq; s++) {+      type[s] = pair[S1[s][i]][S2[s][j]];+    }+    psc = covscore(type,n_seq);+    for (s=0; s<n_seq; s++) if (type[s]==0) type[s] = 7;+    E += psc;+    for (k=i+1; k<=n3 && k>i-MAXLOOP-2; k++) {+      for (l=j-1; l>=1; l--) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        for (s=LE=0; s<n_seq; s++) {+          type2 = pair[S1[s][k]][S2[s][l]];+          if (type2==0) type2=7;+          LE += E_IntLoop(k-i-1, j-l-1, type[s], rtype[type2],+                          S1[s][i+1], S2[s][j-1], S1[s][k-1], S2[s][l+1],P);+        }+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      for (s=0; s<n_seq; s++) {+        if (type[s]>2) E -= P->TerminalAU;+      }+      break;+      if (E != n_seq*P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex bal");+      } else break;+    }+  }+  struc = (char *) vrna_alloc(i-i0+1+j0-j+1+2);+  for (k=MAX2(i0,1); k<=i; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j; k<=j0; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i0-1,0)); strcat(struc, "&");+  strcat(struc, st2+j-1);+  free(st1);+  free(st2);+  free(type);+  return struc;+}++duplexT** aliLduplexfold_XS(const char*s1[], const char* s2[], const int **access_s1, const int **access_s2, const int threshold, const int alignment_length, const int delta,  const int fast,const int il_a, const int il_b, const int b_a, const int b_b)+{+  short **S1, **S2;+  int *type,type2;+  int i, j,s,n_seq;+  s=0;+  int bopen=b_b;+  int bext=b_a;+  int iopen=il_b;+  int iext_s=2*(il_a);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  int temp;+  int min_j_colonne;+  int max=INF;+  /* FOLLOWING NEXT 4 LINE DEFINES AN ARRAY CONTAINING POSITION OF THE SUBOPT IN S1 */+  int *position; /* contains the position of the hits with energy > E */+  int *position_j;+  int maxPenalty[4];++  n1 = (int) strlen(s1[0]);+  n2 = (int) strlen(s2[0]);+  for (s=0; s1[s]; s++);+  n_seq = s;+  for (s=0; s2[s]; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in aliduplexfold()\n");++  position = (int *) vrna_alloc((delta+(n1)+4+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+(n1)+4+delta) * sizeof(int));++  /**+  *** extension penalty, computed only once, further reduce the computation time+  **/+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)){+    update_dfold_params();+  }+  maxPenalty[0]=(int) -1*P->stack[2][2]/2;+  maxPenalty[1]=(int) -1*P->stack[2][2];+  maxPenalty[2]=(int) -3*P->stack[2][2]/2;+  maxPenalty[3]=(int) -2*P->stack[2][2];+++  lc   = (int**) vrna_alloc(sizeof(int *) * 5);+  lin  = (int**) vrna_alloc(sizeof(int *) * 5);+  lbx  = (int**) vrna_alloc(sizeof(int *) * 5);+  lby  = (int**) vrna_alloc(sizeof(int *) * 5);+  linx = (int**) vrna_alloc(sizeof(int *) * 5);+  liny = (int**) vrna_alloc(sizeof(int *) * 5);++  for (i=0; i<=4; i++){+    lc[i]  = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lin[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lbx[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lby[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    linx[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+    liny[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+  }+++  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_seq(s1[s]);+    S2[s] = encode_seq(s2[s]);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  /**+  *** array initialization+  **/++  for(j=n2+4;j>=0;j--) {+    lbx[0][j]=lbx[1][j]=lbx[2][j]=lbx[3][j]    = lbx[4][j] =INF;+    lin[0][j]=lin[1][j]=lin[2][j]=lin[3][j]    = lin[4][j] =INF;+    lc[0][j] =lc[1][j] =lc[2][j] = lc[3][j]    =  lc[4][j] =INF;+    lby[0][j]=lby[1][j]=lby[2][j]=lby[3][j]    = lby[4][j] =INF;+    liny[0][j]=liny[1][j]=liny[2][j]=liny[3][j]=liny[4][j]=INF;+    linx[0][j]=linx[1][j]=linx[2][j]=linx[3][j]=linx[4][j]=INF;+  }+  i=10;+  i_length= n1 - 9 ;+  int di1,di2,di3,di4; /* contains accessibility penalty */+  while(i < i_length) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;++    di1 = access_s1[5][i]   - access_s1[4][i-1];+    di2 = access_s1[5][i-1] - access_s1[4][i-2] + di1;+    di3 = access_s1[5][i-2] - access_s1[4][i-3] + di2;+    di4 = access_s1[5][i-3] - access_s1[4][i-4] + di3;+    di1=MIN2(di1,maxPenalty[0]);+    di2=MIN2(di2,maxPenalty[1]);+    di3=MIN2(di3,maxPenalty[2]);+    di4=MIN2(di3,maxPenalty[3]);+    j=n2-9;+    while (9 < --j) {+      int dj1,dj2,dj3,dj4;+      dj1 = access_s2[5][j+4] - access_s2[4][j+4];+      dj2 = access_s2[5][j+5] - access_s2[4][j+5] + dj1;+      dj3 = access_s2[5][j+6] - access_s2[4][j+6] + dj2;+      dj4 = access_s2[5][j+7] - access_s2[4][j+7] + dj3;+      dj1=MIN2(dj1,maxPenalty[0]);+      dj2=MIN2(dj2,maxPenalty[1]);+      dj3=MIN2(dj3,maxPenalty[2]);+      dj4=MIN2(dj4,maxPenalty[3]);+      int psc;+      for (s=0; s<n_seq; s++) { /* initialize type1 */+        type[s] = pair[S1[s][i]][S2[s][j]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      lc[idx][j] = ((psc >= MINPSCORE) ? n_seq*(P->DuplexInit) : INF);+      int c_stack, c_10, c_01, c_11, c_22, c_21, c_12, c_23, c_32, c_in, c_in2x, c_in2y, c_bx, c_by, c_inx, c_iny;  /* matrix c */+      int in,  in_x, in_y, in_xy; /*  in begin, in_x assymetric, in_y assymetric, in_xy symetric; */+      int inx, inx_x;+      int iny, iny_y;+      int bx,  bx_x;+      int by,  by_y;+      in=lc[idx_1][j+1]; in_x=lin[idx_1][j]; in_y=lin[idx][j+1]; in_xy=lin[idx_1][j+1];+      inx=lc[idx_1][j+1]; inx_x=linx[idx_1][j];+      iny=lc[idx_1][j+1]; iny_y=liny[idx][j+1];+      bx=lc[idx_1][j]; bx_x=lbx[idx_1][j];+      by=lc[idx][j+1]; by_y=lby[idx][j+1];+      c_stack=lc[idx_1][j+1]; c_01=lc[idx_1][j+2];c_10=lc[idx_2][j+1];+      c_12=lc[idx_2][j+3];c_21=lc[idx_3][j+2];c_11=lc[idx_2][j+2];+      c_22=lc[idx_3][j+3];c_32=lc[idx_4][j+3];c_23=lc[idx_3][j+4];+      c_in=lin[idx_3][j+3];c_in2x=lin[idx_4][j+2];c_in2y=lin[idx_2][j+4];+      c_inx=linx[idx_3][j+1]; c_iny=liny[idx_1][j+3];+      c_bx=lbx[idx_2][j+1];c_by=lby[idx_1][j+2];+      for (s=0; s<n_seq; s++) {+        type2 = pair[S2[s][j+1]][S1[s][i-1]];+        in   +=P->mismatchI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s+di1+dj1;+        in_x +=iext_ass+di1;+        in_y +=iext_ass+dj1;+        in_xy+=iext_s+di1+dj1;+        inx  +=P->mismatch1nI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s+di1+dj1;+        inx_x+=iext_ass+di1;+        iny  +=P->mismatch1nI[type2][S2[s][j]][S1[s][i]]+iopen+iext_s+di1+dj1;+        iny_y+=iext_ass+dj1;+        type2=pair[S2[s][j]][S1[s][i-1]];+        bx   +=bopen+bext+(type2>2?P->TerminalAU:0)+di1;+        bx_x +=bext+di1;+        type2=pair[S2[s][j+1]][S1[s][i]];+        by   +=bopen+bext+(type2>2?P->TerminalAU:0)+dj1;+        by_y +=bext+dj1;+      }+      lin[idx][j]=MIN2(in, MIN2(in_x, MIN2(in_y, in_xy)));+      linx[idx][j]=MIN2(inx_x, inx);+      liny[idx][j]=MIN2(iny_y, iny);+      lby[idx][j]=MIN2(by, by_y);+      lbx[idx][j]=MIN2(bx, bx_x);+      if (psc<MINPSCORE) continue;+      for (s=0; s<n_seq; s++) {+        lc[idx][j]+=E_ExtLoop(type[s], S1[s][i-1],S2[s][j+1],P);+      }+      for (s=0; s<n_seq; s++) {+        type2=pair[S1[s][i-1]][S2[s][j+1]];if (type2==0) type2=7;+        c_stack+=E_IntLoop(0,0,type2, rtype[type[s]],S1[s][i], S2[s][j], S1[s][i-1], S2[s][j+1], P)+di1+dj1;+        type2=pair[S1[s][i-1]][S2[s][j+2]];if (type2==0) type2=7;+        c_01   +=E_IntLoop(0,1,type2, rtype[type[s]],S1[s][i], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+di1+dj2;+        type2=pair[S1[s][i-2]][S2[s][j+1]];if (type2==0) type2=7;+        c_10   +=E_IntLoop(1,0,type2, rtype[type[s]],S1[s][i-1], S2[s][j], S1[s][i-1], S2[s][j+1], P)+di2+dj1;+        type2=pair[S1[s][i-2]][S2[s][j+2]];if (type2==0) type2=7;+        c_11   +=E_IntLoop(1,1,type2, rtype[type[s]],S1[s][i-1], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+di2+dj2;+        type2=pair[S1[s][i-3]][S2[s][j+3]];if (type2==0) type2=7;+        c_22   +=E_IntLoop(2,2,type2, rtype[type[s]],S1[s][i-2], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+di3+dj3;+        type2= pair[S1[s][i-3]][S2[s][j+2]];if (type2==0) type2=7;+        c_21   +=E_IntLoop(2,1,type2, rtype[type[s]],S1[s][i-2], S2[s][j+1], S1[s][i-1], S2[s][j+1], P)+di3+dj2;+        type2= pair[S1[s][i-2]][S2[s][j+3]];if (type2==0) type2=7;+        c_12   +=E_IntLoop(1,2,type2, rtype[type[s]],S1[s][i-1], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+di2+dj3;+        type2 = pair[S1[s][i-4]][S2[s][j+3]];if (type2==0) type2=7;+        c_32   +=E_IntLoop(3,2,type2, rtype[type[s]],S1[s][i-3], S2[s][j+2], S1[s][i-1], S2[s][j+1], P)+di4+dj3;+        type2 = pair[S1[s][i-3]][S2[s][j+4]];if (type2==0) type2=7;+        c_23   +=E_IntLoop(2,3,type2, rtype[type[s]],S1[s][i-2], S2[s][j+3], S1[s][i-1], S2[s][j+1], P)+dj4+di3;+        c_in   +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+di3+dj3+2*iext_s;+        c_in2x +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_s+2*iext_ass+di4+dj2;+        c_in2y +=P->mismatchI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_s+2*iext_ass+di2+dj4;+        c_inx  +=P->mismatch1nI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_ass+iext_ass+di3+dj1;+        c_iny  +=P->mismatch1nI[rtype[type[s]]][S1[s][i-1]][S2[s][j+1]]+iext_ass+iext_ass+di1+dj3;+        int bAU;+        bAU=(type[s]>2?P->TerminalAU:0);+        c_bx   +=di2+dj1+bext+bAU;+        c_by   +=di1+dj2+bext+bAU;+      }+      lc[idx][j] =MIN2(lc[idx][j],+                       MIN2(c_stack,+                            MIN2(c_10,+                                 MIN2(c_01,+                                      MIN2(c_11,+                                           MIN2(c_21,+                                                MIN2(c_12,+                                                     MIN2(c_22,+                                                          MIN2(c_23,+                                                               MIN2(c_32,+                                                                    MIN2(c_bx,+                                                                         MIN2(c_by,+                                                                              MIN2(c_in,+                                                                                   MIN2(c_in2x,+                                                                                        MIN2(c_in2y,+                                                                                             MIN2(c_inx,c_iny)+                                                                                             )+                                                                                        )+                                                                                   )+                                                                              )+                                                                         )+                                                                    )+                                                               )+                                                          )+                                                     )+                                                )+                                           )+                                      )+                                 )+                            )+                       );+      lc[idx][j]-=psc;+      temp=lc[idx][j];++      for (s=0; s<n_seq; s++) {+        temp+=E_ExtLoop(rtype[type[s]], S2[s][j-1],S1[s][i+1],P);+      }+      if(min_colonne > temp){+        min_colonne=temp;+        min_j_colonne=j;+      }+    }+    if(max>=min_colonne){+            max=min_colonne;+            max_pos=i;+        max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    i++;+  }+  /* printf("MAX: %d",max); */+  for (s=0; s<n_seq; s++) {free(S1[s]);free(S2[s]);}+  free(S1); free(S2);+  if(max<threshold){+    alifind_max_XS(position, position_j, delta, threshold, alignment_length, s1, s2,access_s1,access_s2, fast);+  }+  aliplot_max_XS(max, max_pos, max_pos_j,alignment_length, s1, s2, access_s1, access_s2, fast);+  for (i=0; i<=4; i++) {free(lc[i]);free(lin[i]);free(lbx[i]);free(lby[i]);free(linx[i]);free(liny[i]);}+  /* free(lc[0]);free(lin[0]);free(lbx[0]);free(lby[0]);free(linx[0]);free(liny[0]); */+  free(lc);free(lin);free(lbx);free(lby);free(linx);free(liny);+  free(position);+  free(position_j);+  free(type);+  return NULL;+}+++++PRIVATE void alifind_max_XS(const int *position, const int *position_j,+                                const int delta, const int threshold, const int alignment_length,+                                const char *s1[], const char *s2[],+                                const int **access_s1, const int **access_s2, const int fast){++  int n_seq=0;+  for (n_seq=0; s1[n_seq]!=NULL; n_seq++);+  int pos=n1-9;+  if(fast==1){+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        /*+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/100);+        */+        pos=MAX2(10,pos+temp_min-delta);+      }+    }+  }+  else{+    pos=n1-9;+    while( pos-- > 10 ) {+      /* printf("delta %d position:%d value:%d\n", delta, pos, position[pos]); */+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+           if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta]; /* position on j */+        int begin_t=MAX2(11, pos-alignment_length);+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1);+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length-1);+        int i_flag;+        int j_flag;+        i_flag = (end_t   ==  pos+1?1:0);+        j_flag = (begin_q == max_pos_j-1?1:0);+        char **s3, **s4;+        s3 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+        s4 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+        int i;+        for(i=0; i<n_seq; i++){+          s3[i] = (char*) vrna_alloc(sizeof(char)*(end_t-begin_t+2));+          s4[i] = (char*) vrna_alloc(sizeof(char)*(end_q-begin_q+2));+          strncpy(s3[i], (s1[i]+begin_t), end_t - begin_t +1);+          strncpy(s4[i], (s2[i]+begin_q), end_q - begin_q +1);+          s3[i][end_t - begin_t +1]='\0';+          s4[i][end_q - begin_q +1]='\0';+        }+        duplexT test;+        test = aliduplexfold_XS((const char**) s3, (const char**) s4, access_s1, access_s2,pos, max_pos_j,threshold,i_flag,j_flag);+        /*         printf("position %d approximation %d test %d threshold %d\n", pos, position[pos+delta], (int)test.energy,(int)(threshold/n_seq)); */+        if(test.energy*100  < (int) (threshold/n_seq)){+        printf("%s %3d,%-3d: %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f)\n", test.structure,+               test.tb,test.te,test.qb,test.qe, test.ddG/n_seq, test.energy/n_seq, test.dG1/n_seq, test.dG2/n_seq);+        free(test.structure);+	pos=MAX2(10,pos+temp_min-delta);+        }+        for(i=0;i<n_seq;i++){+          free(s3[i]);free(s4[i]);+        }+        free(s3);free(s4);+        /* free(test.structure); */+      }++    }+  }+}++PRIVATE void aliplot_max_XS(const int max, const int max_pos, const int max_pos_j,const int alignment_length,+                            const char *s1[], const char* s2[],const int **access_s1, const int **access_s2,+                            const int fast){++  int n_seq;+  for (n_seq=0; !(s1[n_seq]==NULL); n_seq++);+  n1 = strlen(s1[0]); /* get length of alignment */+  n2 = strlen(s2[0]); /* get length of alignme */++  if(fast){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n",+           max_pos-10, max_pos_j-10, (double) ((double)max)/(100*n_seq));+  }+  else{+    int begin_t=MAX2(11, max_pos-alignment_length); /* only get the position that binds.. */+    int end_t  =MIN2(n1-10, max_pos+1);              /* ..no dangles */+    int begin_q=MAX2(11, max_pos_j-1);+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length-1);+    int i_flag;+    int j_flag;+    i_flag = (end_t   == max_pos+1?1:0);+    j_flag = (begin_q == max_pos_j-1?1:0);+    char **s3, **s4;+    s3 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+    s4 = (char**) vrna_alloc(sizeof(char*)*(n_seq+1));+    int i;+    for(i=0; i<n_seq; i++){+      s3[i] = (char*) vrna_alloc(sizeof(char)*(end_t-begin_t+2));+      s4[i] = (char*) vrna_alloc(sizeof(char)*(end_q-begin_q+2));+      strncpy(s3[i], (s1[i]+begin_t), end_t - begin_t +1);+      strncpy(s4[i], (s2[i]+begin_q), end_q - begin_q +1);+      s3[i][end_t - begin_t +1]='\0';+      s4[i][end_q - begin_q +1]='\0';+    }+    duplexT test;+    test = aliduplexfold_XS((const char**) s3, (const char**) s4, access_s1, access_s2,max_pos, max_pos_j,INF,i_flag,j_flag);+    printf("%s %3d,%-3d: %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f)\n", test.structure,+           test.tb,test.te,test.qb,test.qe, test.ddG/n_seq, test.energy/n_seq, test.dG1/n_seq, test.dG2/n_seq);+    free(test.structure);+    for(i=0;i<n_seq;i++){+      free(s3[i]);free(s4[i]);+    }+    free(s3);free(s4);+  }+}++PRIVATE int covscore(const int *types, int n_seq) {+  /* calculate co-variance bonus for a pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */+#define NONE -10000 /* score for forbidden pairs */+  int k,l,s,score, pscore;+  int dm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                {0,0,2,2,1,2,2} /* CG */,+                {0,2,0,1,2,2,2} /* GC */,+                {0,2,1,0,2,1,2} /* GU */,+                {0,1,2,2,0,2,1} /* UG */,+                {0,2,2,1,2,0,2} /* AU */,+                {0,2,2,2,1,2,0} /* UA */};++  int pfreq[8]={0,0,0,0,0,0,0,0};+  for (s=0; s<n_seq; s++)+    pfreq[types[s]]++;++  if (pfreq[0]*2>n_seq) return NONE;+  for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+    for (l=k+1; l<=6; l++)+      /* scores for replacements between pairtypes    */+      /* consistent or compensatory mutations score 1 or 2  */+      score += pfreq[k]*pfreq[l]*dm[k][l];++  /* counter examples score -1, gap-gap scores -0.25   */+  pscore = cv_fact *+    ((UNIT*score)/n_seq - nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));+  return pscore;+}+++PRIVATE void update_dfold_params(void)+{+  vrna_md_t md;+  if(P) free(P);+  set_model_details(&md);+  P = vrna_params(&md);+  make_pair_matrix();+}++++PRIVATE short * encode_seq(const char *sequence) {+  unsigned int i,l;+  short *S;+  l = strlen(sequence);+  S = (short *) vrna_alloc(sizeof(short)*(l+2));+  S[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    S[i]= (short) encode_char(toupper(sequence[i-1]));++  /* for circular folding add first base at position n+1 */+  S[l+1] = S[1];++  return S;+}
+ C/ViennaRNA/ali_plex.h view
@@ -0,0 +1,40 @@+#ifndef VIENNA_RNA_PACKAGE_ALI_PLEX_H+#define VIENNA_RNA_PACKAGE_ALI_PLEX_H++#include <ViennaRNA/data_structures.h>+/**+*** aliLduplexfold computes the duplexes between two alignments+**/+duplexT** aliLduplexfold( const char *s1[],+                          const char *s2[],+                          const int threshold,+                          const int extension_cost,+                          const int alignment_length,+                          const int delta,+                          const int fast,+                          const int il_a,+                          const int il_b,+                          const int b_a,+                          const int b_b);+/**+*** aliLduplexfold computes the duplexes between two alignments. It also takes the average accessibility into account+**/+duplexT** aliLduplexfold_XS(const char* s1[],+                            const char* s2[],+                            const int **access_s1,+                            const int **access_s2, +                            const int threshold,+                            const int alignment_length,+                            const int delta,+                            const int fast,+                            const int il_a,+                            const int il_b,+                            const int b_a,+                            const int b_b);++/*+extern duplexT aliduplexfold(const char *s1[], const char *s2[], const int extension_cost);+extern duplexT aliduplexfold_XS(const char *s1[], const char *s2[],const int **access_s1, +const int **access_s2, const int i_pos, const int j_pos, const int threshold);+*/+#endif
+ C/ViennaRNA/alicircfold.inc view
@@ -0,0 +1,148 @@+/* -*-C-*- */+/* this file contains code for alifolding circular RNAs */+/* it's #include'd into alifold.c */++PRIVATE void+fill_arrays_comparative_circ( vrna_fold_compound_t *vc,+                              sect bt_stack[],+                              int *bt){++  /* variant of alifold() for circular RNAs */+  /* auxiliarry arrays:+     fM2 = multiloop region with exactly two stems, extending to 3' end+     for stupid dangles=1 case we also need:+     fM_d3 = multiloop region with >= 2 stems, starting at pos 2+             (a pair (k,n) will form 3' dangle with pos 1)+     fM_d5 = multiloop region with >= 2 stems, extending to pos n-1+             (a pair (1,k) will form a 5' dangle with pos n)+  */+  int               Fc, FcH, FcI, FcM, Hi, Hj, Ii, Ij, Ip, Iq, ip, iq, Mi, FcMd3, FcMd5;+  int               i, j, ij, u, length, new_c, fm, n_seq, s;+  int               *indx, *c, *fML, *fM2;+  char              *hard_constraints;+  unsigned short    **a2s;+  vrna_param_t      *P;+  vrna_hc_t         *hc;+  vrna_sc_t         **sc;++  a2s               = vc->a2s;+  P                 = vc->params;+  indx              = vc->jindx;     /* index for moving in the triangle matrices c[] and fMl[]*/+  c                 = vc->matrices->c;     /* energy array, given that i-j pair */+  fML               = vc->matrices->fML;     /* multi-loop auxiliary energy array */+  fM2               = vc->matrices->fM2;+  hc                = vc->hc;+  sc                = vc->scs;+  hard_constraints  = hc->matrix;+  n_seq             = vc->n_seq;+  length            = vc->length;++  /* extra arrays for circfold() */+  FcH = FcI= FcM = FcMd3= FcMd5= INF;++  if(hc->up_ext[1] >= length){+    Fc = 0;+    if(sc){+      for(s = 0; s < n_seq; s++){+        if(sc[s]->energy_up)+          Fc += sc[s]->energy_up[1][a2s[s][length] - 1];+      }+    }+  } else {+    Fc = INF;+  }++  for (i=1; i<length; i++)+    for (j=i+TURN+1; j <= length; j++) {+      u = length-j + i-1;+      if (u<TURN) continue;++      ij = indx[j]+i;++      if (!hard_constraints[ij])+        continue;++      /* exterior hairpin case */+      new_c =   vrna_E_hp_loop(vc, j, i)+              + c[ij];++      if (new_c<FcH) {+        FcH = new_c;+        Hi  = i;+        Hj  = j;+      }++      /* exterior interior loop case */+      ip = iq = 0;+      new_c =   vrna_E_ext_int_loop(vc, i, j, &ip, &iq)+              + c[ij];++      if(ip != 0){+        if(new_c < FcI){+          FcI = new_c;+          Ii  = i;+          Ij  = j;+          Ip  = ip;+          Iq  = iq;+        }+      }+    }+  Fc = MIN2(Fc, FcH);+  Fc = MIN2(Fc, FcI);++  /* compute the fM2 array (multi loops with exactly 2 helices) */+  /* to get a unique ML decomposition, just use fM1 instead of fML+     below. However, that will not work with dangles==1  */+  for (i=1; i<length-TURN; i++) {+    fM2[i] = INF;+    for (u=i+TURN; u<length-TURN; u++)+      fM2[i] = MIN2(fM2[i], fML[indx[u]+i] + fML[indx[length]+u+1]);+  }++  for (i=TURN+1; i<length-2*TURN; i++) {+    fm = fML[indx[i]+1]+fM2[i+1]+n_seq*P->MLclosing;+    if (fm<FcM) {+      FcM=fm; Mi=i;+    }+  }+  Fc = MIN2(Fc, FcM);++  if (FcH==Fc) {+    bt_stack[++(*bt)].i = Hi;+    bt_stack[(*bt)].j = Hj;+    bt_stack[(*bt)].ml = 2;+  }+  else if (FcI==Fc) {+    bt_stack[++(*bt)].i = Ii;+    bt_stack[(*bt)].j = Ij;+    bt_stack[(*bt)].ml = 2;+    bt_stack[++(*bt)].i = Ip;+    bt_stack[(*bt)].j = Iq;+    bt_stack[(*bt)].ml = 2;+  }+  else if (FcM==Fc) { /* grumpf we found a Multiloop */+    /* backtrack in fM2 */+    fm = fM2[Mi+1];+    for (u=Mi+TURN+1; u<length-TURN; u++)+      if (fm == fML[indx[u]+Mi+1] + fML[indx[length]+u+1]) {+        bt_stack[++(*bt)].i=Mi+1;+        bt_stack[(*bt)].j=u;+        bt_stack[(*bt)].ml = 1;+        bt_stack[++(*bt)].i=u+1;+        bt_stack[(*bt)].j=length;+        bt_stack[(*bt)].ml = 1;+        break;+      }+    bt_stack[++(*bt)].i = 1;+    bt_stack[(*bt)].j = Mi;+    bt_stack[(*bt)].ml = 1;+  } else { /* must be totally unstructured */+    bt_stack[++(*bt)].i = 1;+    bt_stack[(*bt)].j = 1;+    bt_stack[(*bt)].ml = 0;+  }+  vc->matrices->FcH = FcH;+  vc->matrices->FcI = FcI;+  vc->matrices->FcM = FcM;+  vc->matrices->Fc  = Fc;+}
+ C/ViennaRNA/alifold.c view
@@ -0,0 +1,307 @@+/*+                  minimum free energy folding+                  for a set of aligned sequences++                  c Ivo Hofacker++                  Vienna RNA package+*/++/**+*** \file alifold.c+**/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/mfe.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/eval.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/ribo.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/alifold.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/loop_energies.h"++#ifdef _OPENMP+#include <omp.h>+#endif++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++#define MAXSECTORS        500     /* dimension for a backtrack array */++/* some backward compatibility stuff */+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;+PRIVATE int                 backward_compat           = 0;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT+PRIVATE float   wrap_alifold( const char **strings,+                              char *structure,+                              vrna_param_t *parameters,+                              int is_constrained,+                              int is_circular);+#endif++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_alifold( const char **strings,+              char *structure){++  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);++  vc  = vrna_fold_compound_comparative(strings, &md, VRNA_OPTION_DEFAULT);+  mfe = vrna_mfe(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;+}++PUBLIC float+vrna_circalifold( const char **sequences,+                  char *structure){++  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.circ = 1;++  vc  = vrna_fold_compound_comparative(sequences, &md, VRNA_OPTION_DEFAULT);+  mfe = vrna_mfe(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;+}++++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++#ifdef  VRNA_BACKWARD_COMPAT++PRIVATE float+wrap_alifold( const char **strings,+              char *structure,+              vrna_param_t *parameters,+              int is_constrained,+              int is_circular){++  vrna_fold_compound_t  *vc;+  vrna_param_t          *P;+  float                 mfe;++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++  /* we need the parameter structure for hard constraints */+  if(parameters){+    P = vrna_params_copy(parameters);+  } else {+    vrna_md_t md;+    set_model_details(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }+  P->model_details.circ = is_circular;++  vc = vrna_fold_compound_comparative(strings, &(P->model_details), VRNA_OPTION_DEFAULT);++  if(parameters){ /* replace params if necessary */+    free(vc->params);+    vc->params = P;+  } else {+    free(P);+  }++  /* handle hard constraints in pseudo dot-bracket format if passed via simple interface */+  if(is_constrained && structure)+    vrna_constraints_add(vc, (const char *)structure, VRNA_CONSTRAINT_DB_DEFAULT);++  if(backward_compat_compound && backward_compat)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;++  /* call mfe() function without backtracking */+  mfe = vrna_mfe(vc, NULL);++  /* backtrack structure */+  if(structure && vc->params->model_details.backtrack){+    char            *ss;+    int             length;+    sect            bt_stack[MAXSECTORS];+    vrna_bp_stack_t *bp;++    length  = vc->length;+    bp      = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4*(1+length/2))); /* add a guess of how many G's may be involved in a G quadruplex */++    vrna_backtrack_from_intervals(vc, bp, bt_stack, 0);++    ss = vrna_db_from_bp_stack(bp, length);+    strncpy(structure, ss, length + 1);+    free(ss);++    if(base_pair)+      free(base_pair);+    base_pair = bp;+  }++  return mfe;+}+++PUBLIC void+free_alifold_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound  = NULL;+    backward_compat           = 0;+  }+}++PUBLIC float+alifold(const char **strings,+        char *structure){++  return wrap_alifold(strings, structure, NULL, fold_constrained, 0);+}++PUBLIC float circalifold( const char **strings,+                          char *structure) {++  return wrap_alifold(strings, structure, NULL, fold_constrained, 1);+}++PUBLIC void +update_alifold_params(void){++  vrna_fold_compound_t *v;++  if(backward_compat_compound && backward_compat){+    v = backward_compat_compound;++    if(v->params)+      free(v->params);++    vrna_md_t md;+    set_model_details(&md);+    v->params = vrna_params(&md);+  }+}++PUBLIC float+energy_of_ali_gquad_structure(const char **sequences,+                              const char *structure,+                              int n_seq,+                              float *energy){++  unsigned int  n;+  short         *pt;+  int           *loop_idx;++  if(sequences[0] != NULL){+    +    vrna_fold_compound_t  *vc;++    vrna_md_t md;+    set_model_details(&md);+    md.gquad = 1;++    vc = vrna_fold_compound_comparative(sequences, &md, VRNA_OPTION_EVAL_ONLY);++    energy[0] = vrna_eval_structure(vc, structure);+    energy[1] = vrna_eval_covar_structure(vc, structure);++    vrna_fold_compound_free(vc);+  }+  else vrna_message_error("energy_of_alistruct(): no sequences in alignment!");++  return energy[0];++}++PUBLIC  float+energy_of_alistruct(const char **sequences,+                    const char *structure,+                    int n_seq,+                    float *energy){++  short         *pt;++  if(sequences[0] != NULL){+    vrna_fold_compound_t  *vc;++    vrna_md_t md;+    set_model_details(&md);++    vc = vrna_fold_compound_comparative(sequences, &md, VRNA_OPTION_EVAL_ONLY);++    energy[0] = vrna_eval_structure(vc, structure);+    energy[1] = vrna_eval_covar_structure(vc, structure);++    vrna_fold_compound_free(vc);+  }+  else vrna_message_error("energy_of_alistruct(): no sequences in alignment!");++  return energy[0];+}++#endif
+ C/ViennaRNA/alifold.h view
@@ -0,0 +1,416 @@+#ifndef VIENNA_RNA_PACKAGE_ALIFOLD_H+#define VIENNA_RNA_PACKAGE_ALIFOLD_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/ribo.h>+#include <ViennaRNA/mfe.h>+#include <ViennaRNA/part_func.h>+#include <ViennaRNA/aln_util.h>+#include <ViennaRNA/boltzmann_sampling.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file alifold.h+ *  @ingroup consensus_fold+ *  @brief Functions for comparative structure prediction using RNA sequence alignments+ *+ */++/*+##############################################+# MFE VARIANTS OF THE ALIFOLD IMPLEMENTATION #+##############################################+*/++/**+ *  @brief  Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure+ *          for an RNA sequence alignment using a comparative method+ *+ *  @ingroup consensus_mfe_fold+ *+ *  This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary+ *  structure for an RNA sequence alignment using default options. Memory required for dynamic programming+ *  (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the+ *  recursively filled matrices are not available any more for any post-processing, e.g. suboptimal+ *  backtracking, etc.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_circalifold(), vrna_mfe(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequences  RNA sequence alignment+ *  @param structure  A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_alifold( const char **sequences,+              char *structure);++/**+ *  @brief  Compute Minimum Free Energy (MFE), and a corresponding consensus secondary structure+ *          for a sequence alignment of circular RNAs using a comparative method+ *+ *  @ingroup consensus_mfe_fold+ *+ *  This simplified interface to vrna_mfe() computes the MFE and, if required, a consensus secondary+ *  structure for an RNA sequence alignment using default options. Memory required for dynamic programming+ *  (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the+ *  recursively filled matrices are not available any more for any post-processing, e.g. suboptimal+ *  backtracking, etc.+ *+ *  Folding of circular RNA sequences is handled as a post-processing step of the forward+ *  recursions. See @cite hofacker:2006 for further details.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_alifold(), vrna_mfe(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequences  Sequence alignment of circular RNAs+ *  @param structure  A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_circalifold( const char **sequences,+                  char *structure);++/*+#############################################################+# PARTITION FUNCTION VARIANTS OF THE ALIFOLD IMPLEMENTATION #+#############################################################+*/++/**+ *  @brief  Compute Partition function @f$Q@f$ (and base pair probabilities) for an RNA+ *          sequence alignment using a comparative method+ *+ *  @ingroup consensus_pf_fold+ *+ *  This simplified interface to vrna_pf() computes the partition function and, if required,+ *  base pair probabilities for an RNA sequence alignment using default options. Memory required for+ *  dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of+ *  this function, the recursively filled matrices are not available any more for any post-processing.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_pf(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_pf_circalifold(), vrna_pf(), vrna_fold_compound_comparative(), #vrna_fold_compound_t+ *+ *  @param sequences  RNA sequence alignment+ *  @param structure  A pointer to the character array where position-wise pairing propensity+ *                    will be stored. (Maybe NULL)+ *  @param pl         A pointer to a list of #vrna_plist_t to store pairing probabilities (Maybe NULL)+ *  @return The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+float vrna_pf_alifold(const char **sequences, char *structure, vrna_plist_t **pl);++/**+ *  @brief  Compute Partition function @f$Q@f$ (and base pair probabilities) for an alignment+ *          of circular RNA sequences using a comparative method+ *+ *  @ingroup consensus_pf_fold+ *+ *  This simplified interface to vrna_pf() computes the partition function and, if required,+ *  base pair probabilities for an RNA sequence alignment using default options. Memory required for+ *  dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of+ *  this function, the recursively filled matrices are not available any more for any post-processing.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_pf(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  Folding of circular RNA sequences is handled as a post-processing step of the forward+ *  recursions. See @cite hofacker:2006 for further details.+ *+ *  @see vrna_pf_alifold(), vrna_pf(), vrna_fold_compound_comparative(), #vrna_fold_compound_t+ *+ *  @param sequences  Sequence alignment of circular RNAs+ *  @param structure  A pointer to the character array where position-wise pairing propensity+ *                    will be stored. (Maybe NULL)+ *  @param pl         A pointer to a list of #vrna_plist_t to store pairing probabilities (Maybe NULL)+ *  @return The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+float vrna_pf_circalifold(const char **sequences, char *structure, vrna_plist_t **pl);++#ifdef  VRNA_BACKWARD_COMPAT++/*+#################################################+# DEPRECATED FUNCTIONS                          #+#################################################+*/+++/**+ *  @brief Compute MFE and according consensus structure of an alignment of sequences+ * + *  This function predicts the consensus structure for the aligned 'sequences'+ *  and returns the minimum free energy; the mfe structure in bracket+ *  notation is returned in 'structure'.+ * + *  Sufficient space must be allocated for 'structure' before calling+ *  alifold().+ * + *  @ingroup consensus_mfe_fold+ * + *  @deprecated Usage of this function is discouraged! Use vrna_alifold(), or vrna_mfe() instead!+ *  @see vrna_alifold(), vrna_mfe()+ *+ *  @param strings    A pointer to a NULL terminated array of character arrays+ *  @param structure  A pointer to a character array that may contain a constraining consensus structure+ *                    (will be overwritten by a consensus structure that exhibits the MFE)+ *  @return           The free energy score in kcal/mol+ */+DEPRECATED(float alifold( const char **strings, char *structure));++/**+ *  @brief Compute MFE and according structure of an alignment of sequences assuming the sequences are circular instead of linear+ * + *  @ingroup consensus_mfe_fold+ * + *  @deprecated Usage of this function is discouraged! Use vrna_alicircfold(), and vrna_mfe() instead!+ *  @see vrna_alicircfold(), vrna_alifold(), vrna_mfe()+ * + *  @param strings    A pointer to a NULL terminated array of character arrays+ *  @param structure  A pointer to a character array that may contain a constraining consensus structure+ *                    (will be overwritten by a consensus structure that exhibits the MFE)+ *  @return           The free energy score in kcal/mol+ */+DEPRECATED(float circalifold( const char **strings, char *structure));++/**+ *  @brief Free the memory occupied by MFE alifold functions+ * + *  @deprecated Usage of this function is discouraged! It only+ *  affects memory being free'd that was allocated by an old API+ *  function before. Release of memory occupied by the newly introduced+ *  #vrna_fold_compound_t is handled by vrna_vrna_fold_compound_free()+ *+ *  @see vrna_vrna_fold_compound_free()+ *+ *  @ingroup consensus_mfe_fold+ * + */+DEPRECATED(void free_alifold_arrays(void));++/**+ *  @brief Calculate the free energy of a consensus structure given a set of aligned sequences+ * + *  @ingroup consensus_fold+ *+ *  @deprecated Usage of this function is discouraged! Use vrna_eval_structure(), and vrna_eval_covar_structure() instead!+ *+ *  @param  sequences   The NULL terminated array of sequences+ *  @param  structure   The consensus structure+ *  @param  n_seq       The number of sequences in the alignment+ *  @param  energy      A pointer to an array of at least two floats that will hold the free energies+ *                      (energy[0] will contain the free energy, energy[1] will be filled with the covariance energy term)+ *  @returns free energy in kcal/mol+ * + */+DEPRECATED(float energy_of_alistruct(const char **sequences, const char *structure, int n_seq, float *energy));++DEPRECATED(float energy_of_ali_gquad_structure(const char **sequences, const char *structure, int n_seq, float *energy));++/**+ *  @brief This variable controls the weight of the covariance term in the+ *  energy function of alignment folding algorithms+ * + *  @ingroup consensus_fold+ *+ *  @deprecated See #vrna_md_t.cv_fact, and vrna_mfe() to avoid using global variables+ *+ *  Default is 1.+ */+DEPRECATED(extern  double  cv_fact);+/**+ *  @brief This variable controls the magnitude of the penalty for non-compatible sequences in+ *  the covariance term of alignment folding algorithms.+ * + *  @ingroup consensus_fold+ * + *  @deprecated See #vrna_md_t.nc_fact, and vrna_mfe() to avoid using global variables+ *+ *  Default is 1.+ */+DEPRECATED(extern  double  nc_fact);++/**+ *  @brief+ * + *  @ingroup consensus_pf_fold+ * + *  @deprecated Use vrna_pf() instead+ *+ *  @param  sequences+ *  @param  structure+ *  @param  pl+ *  @param  parameters+ *  @param  calculate_bppm+ *  @param  is_constrained+ *  @param  is_circular+ *  @return+ */+DEPRECATED(float alipf_fold_par( const char **sequences,+                      char *structure,+                      vrna_plist_t **pl,+                      vrna_exp_param_t *parameters,+                      int calculate_bppm,+                      int is_constrained,+                      int is_circular));++/**+ *  @brief+ * + *  The partition function version of alifold() works in analogy to+ *  pf_fold(). Pair probabilities and information about sequence+ *  covariations are returned via the 'pi' variable as a list of+ *  #vrna_pinfo_t structs. The list is terminated by the first entry with+ *  pi.i = 0.+ * + *  @ingroup consensus_pf_fold+ * + *  @deprecated Use vrna_pf() instead+ *+ *  @param sequences+ *  @param structure+ *  @param pl+ *  @return+ */+DEPRECATED(float alipf_fold( const char **sequences, char *structure, vrna_plist_t **pl));++/**+ *  @brief+ * + *  @ingroup consensus_pf_fold+ *+ *  @deprecated Use vrna_pf() instead+ * + *  @param sequences+ *  @param structure+ *  @param pl+ *  @return+ */+DEPRECATED(float alipf_circ_fold(const char **sequences, char *structure, vrna_plist_t **pl));+++/**+ *  @brief Get a pointer to the base pair probability array+ * + *  Accessing the base pair probabilities for a pair (i,j) is achieved by+ *  @verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; @endverbatim+ * + *  @ingroup consensus_pf_fold+ *+ *  @deprecated Usage of this function is discouraged! The new #vrna_fold_compound_t+ *  allows direct access to the folding matrices, including the pair probabilities!+ *  The pair probability array returned here reflects the one of the latest call+ *  to vrna_pf(), or any of the old API calls for consensus structure+ *  partition function folding.+ * + *  @see #vrna_fold_compound_t, vrna_fold_compound_comparative(), and vrna_pf()+ *+ *  @return A pointer to the base pair probability array+ */+DEPRECATED(FLT_OR_DBL *export_ali_bppm(void));++/**+ *  @brief Free the memory occupied by folding matrices allocated by alipf_fold, alipf_circ_fold, etc.+ *+ *  @ingroup consensus_pf_fold+ * + *  @deprecated Usage of this function is discouraged! This function only free's memory+ *  allocated by old API function calls. Memory allocated by any of the new API calls (starting with vrna_)+ *  will be not affected!+ *+ *  @see #vrna_fold_compound_t, vrna_vrna_fold_compound_free()+ *+ */+DEPRECATED(void  free_alipf_arrays(void));++/**+ *  @brief Sample a consensus secondary structure from the Boltzmann ensemble according its probability+ * + *  @ingroup consensus_stochbt+ *+ *  @deprecated Use vrna_pbacktrack() instead!+ *+ *  @param  prob  to be described (berni)+ *  @return       A sampled consensus secondary structure in dot-bracket notation+ */+DEPRECATED(char  *alipbacktrack(double *prob));++/**+ *  @brief Get pointers to (almost) all relavant arrays used in alifold's partition function computation+ *+ *  @ingroup consensus_fold+ *+ *  @note To obtain meaningful pointers, call alipf_fold first!+ *+ *  @see pf_alifold(), alipf_circ_fold()+ *+ *  @deprecated It is discouraged to use this function! The new #vrna_fold_compound_t allows+ *  direct access to all necessary consensus structure prediction related variables!+ *+ *  @see #vrna_fold_compound_t, vrna_fold_compound_comparative(), vrna_pf()+ *+ *  @param S_p      A pointer to the 'S' array (integer representation of nucleotides)+ *  @param S5_p     A pointer to the 'S5' array+ *  @param S3_p     A pointer to the 'S3' array+ *  @param a2s_p    A pointer to the pair type matrix+ *  @param Ss_p     A pointer to the 'Ss' array+ *  @param qb_p     A pointer to the Q<sup>B</sup> matrix+ *  @param qm_p     A pointer to the Q<sup>M</sup> matrix+ *  @param q1k_p    A pointer to the 5' slice of the Q matrix (@f$q1k(k) = Q(1, k)@f$)+ *  @param qln_p    A pointer to the 3' slice of the Q matrix (@f$qln(l) = Q(l, n)@f$)+ *  @param pscore   A pointer to the start of a pscore list+ *  @return         Non Zero if everything went fine, 0 otherwise+ */+DEPRECATED(int get_alipf_arrays(short ***S_p,+                     short ***S5_p,+                     short ***S3_p,+                     unsigned short ***a2s_p,+                     char ***Ss_p,+                     FLT_OR_DBL **qb_p,+                     FLT_OR_DBL **qm_p,+                     FLT_OR_DBL **q1k_p,+                     FLT_OR_DBL **qln_p,+                     short **pscore));+++/**+ *  @brief Update the energy parameters for alifold function+ *+ *  Call this to recalculate the pair matrix and energy parameters after a+ *  change in folding parameters like #temperature+ *+ *  @ingroup  consensus_fold+ *  @deprecated Usage of this function is discouraged! The new API uses #vrna_fold_compound_t+ *  to lump all folding related necessities together, including the energy parameters. Use+ *  vrna_update_fold_params() to update the energy parameters within a #vrna_fold_compound_t.+ */+DEPRECATED(void update_alifold_params(void));++#endif+++#endif
+ C/ViennaRNA/alipfold.c view
@@ -0,0 +1,345 @@+/*+                  partiton function and base pair probabilities+                  for RNA secvondary structures+                  of a set of aligned sequences++                  Ivo L Hofacker+                  Vienna RNA package+*/++/**+*** \file alipfold.c+**/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MIN */+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/PS_dot.h"+#include "ViennaRNA/ribo.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/eval.h"+#include "ViennaRNA/mfe.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/structure_utils.h"+#include "ViennaRNA/alifold.h"++#ifdef _OPENMP+#include <omp.h>+#endif++/*+#################################+# PUBLIC GLOBAL VARIABLES       #+#################################+*/++/*+#################################+# PRIVATE GLOBAL VARIABLES      #+#################################+*/++/* some backward compatibility stuff */+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;+PRIVATE int                   backward_compat           = 0;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE float     wrap_alipf_fold(const char **sequences,+                                  char *structure,+                                  plist **pl,+                                  vrna_exp_param_t *parameters,+                                  int calculate_bppm,+                                  int is_constrained,+                                  int is_circular);++++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_pf_alifold(const char **strings,+                char *structure,+                vrna_plist_t **pl){++  float                 free_energy;+  double                mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);++  /* no need to backtrack MFE structure */+  md.backtrack = 0;++  if(!pl){ /* no need for pair probability computations if we do not store them somewhere */+    md.compute_bpp = 0;+  }++  vc  = vrna_fold_compound_comparative(strings, &md, VRNA_OPTION_DEFAULT);+  mfe = (double)vrna_pf(vc, structure);+  vrna_exp_params_rescale(vc, &mfe);+  free_energy = vrna_pf(vc, structure);++  /* fill plist */+  if(pl){+    *pl = vrna_plist_from_probs(vc, /*cut_off:*/ 1e-6);+  }++  vrna_fold_compound_free(vc);++  return free_energy;+}++PUBLIC float+vrna_pf_circalifold(const char **sequences,+                    char *structure,+                    vrna_plist_t **pl){++  float                 free_energy;+  double                mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.circ = 1;++  /* no need to backtrack MFE structure */+  md.backtrack = 0;++  if(!pl){ /* no need for pair probability computations if we do not store them somewhere */+    md.compute_bpp = 0;+  }++  vc  = vrna_fold_compound_comparative(sequences, &md, VRNA_OPTION_DEFAULT);+  mfe = (double)vrna_mfe(vc, structure);+  vrna_exp_params_rescale(vc, &mfe);+  free_energy = vrna_pf(vc, structure);++  /* fill plist */+  if(pl){+    *pl = vrna_plist_from_probs(vc, /*cut_off:*/ 1e-6);+  }++  vrna_fold_compound_free(vc);++  return free_energy;+}++++/*-----------------------------------------------------------------*/+PRIVATE float+wrap_alipf_fold(const char **sequences,+                char *structure,+                plist **pl,+                vrna_exp_param_t *parameters,+                int calculate_bppm,+                int is_constrained,+                int is_circular){++  int                 n_seq;+  float               free_energy;+  vrna_fold_compound_t  *vc;+  vrna_exp_param_t    *exp_params;++  if(sequences == NULL) return 0.;++  for(n_seq=0;sequences[n_seq];n_seq++); /* count the sequences */+  +  vc                  = NULL;++  /* we need vrna_exp_param_t datastructure to correctly init default hard constraints */+  if(parameters)+    exp_params = vrna_exp_params_copy(parameters);+  else{+    vrna_md_t md;+    set_model_details(&md); /* get global default parameters */+    exp_params = vrna_exp_params_comparative(n_seq, &md);+  }+  exp_params->model_details.circ        = is_circular;+  exp_params->model_details.compute_bpp = calculate_bppm;++  vc = vrna_fold_compound_comparative(sequences, &(exp_params->model_details), VRNA_OPTION_PF);++  if(parameters){ /* replace exp_params if necessary */+    free(vc->exp_params);+    vc->exp_params = exp_params;+  } else {+    free(exp_params);+  }+  vc->exp_params->pf_scale = pf_scale;++  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound && backward_compat_compound)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  iindx                     = backward_compat_compound->iindx;+  backward_compat           = 1;++  free_energy = vrna_pf(vc, structure);+  +  /* fill plist */+  if(pl && calculate_bppm){+    *pl = vrna_plist_from_probs(vc, /*cut_off:*/ 1e-6);+  }++  return free_energy;+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC float+alipf_fold( const char **sequences,+                  char *structure,+                  plist **pl){++  return wrap_alipf_fold(sequences, structure, pl, NULL, do_backtrack, fold_constrained, 0);+}++PUBLIC float+alipf_circ_fold(const char **sequences,+                      char *structure,+                      plist **pl){++  return wrap_alipf_fold(sequences, structure, pl, NULL, do_backtrack, fold_constrained, 1);+}++PUBLIC float+alipf_fold_par( const char **sequences,+                char *structure,+                plist **pl,+                vrna_exp_param_t *parameters,+                int calculate_bppm,+                int is_constrained,+                int is_circular){++  return wrap_alipf_fold(sequences, structure, pl, parameters, calculate_bppm, is_constrained, is_circular);+}++PUBLIC FLT_OR_DBL *+alipf_export_bppm(void){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->probs)+        return backward_compat_compound->exp_matrices->probs;++  return NULL;+}++PUBLIC FLT_OR_DBL *+export_ali_bppm(void){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->probs)+        return backward_compat_compound->exp_matrices->probs;++  return NULL;+}++/*brauch ma nurnoch pscores!*/+PUBLIC char *+alipbacktrack(double *prob){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices){+      vrna_exp_param_t *params = backward_compat_compound->exp_params;+      int n     = backward_compat_compound->length;+      int n_seq = backward_compat_compound->n_seq;+      int *idx  = backward_compat_compound->iindx;+      double Q  = (double)backward_compat_compound->exp_matrices->q[idx[1]-n];+      char *s   = vrna_pbacktrack(backward_compat_compound);+      double e  = (double)vrna_eval_structure(backward_compat_compound, s);+      e        -= (double)vrna_eval_covar_structure(backward_compat_compound, s);+      double fe = (-log(Q)-n*log(params->pf_scale))*params->kT/(1000.0 * n_seq);+      *prob     = exp((fe - e)/params->kT);+      return s;+    }+  return NULL;+}++/*-------------------------------------------------------------------------*/+/* make arrays used for alipf_fold available to other routines */+PUBLIC int+get_alipf_arrays( short ***S_p,+                  short ***S5_p,+                  short ***S3_p,+                  unsigned short ***a2s_p,+                  char ***Ss_p,+                  FLT_OR_DBL **qb_p,+                  FLT_OR_DBL **qm_p,+                  FLT_OR_DBL **q1k_p,+                  FLT_OR_DBL **qln_p,+                  short **pscore_p) {++  if(backward_compat_compound){+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->qb){+        *S_p      = backward_compat_compound->S;+        *S5_p     = backward_compat_compound->S5;+        *S3_p     = backward_compat_compound->S3;+        *a2s_p    = backward_compat_compound->a2s;+        *Ss_p     = backward_compat_compound->Ss;+        *qb_p     = backward_compat_compound->exp_matrices->qb;+        *qm_p     = backward_compat_compound->exp_matrices->qm;+        *q1k_p    = backward_compat_compound->exp_matrices->q1k;+        *qln_p    = backward_compat_compound->exp_matrices->qln;+        *pscore_p = backward_compat_compound->pscore_pf_compat;+        return 1;+      }+  }+  return 0;+}++PUBLIC void+free_alipf_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound  = NULL;+    backward_compat           = 0;+    iindx                     = NULL;+  }+}
+ C/ViennaRNA/aln_util.c view
@@ -0,0 +1,617 @@+/*+                               aln_util.c+               Helper functions frelated to alignments+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <errno.h>+#include <time.h>+#include <string.h>+#include <ctype.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/model.h"+#include "ViennaRNA/ribo.h"+#include "ViennaRNA/aln_util.h"++#define MAX_NUM_NAMES    500+int read_clustal(FILE *clust, char *AlignedSeqs[], char *names[]) {+   char *line, name[100]="", *seq;+   int  n, nn=0, num_seq = 0, i;++   if ((line=vrna_read_line(clust)) == NULL) {+     vrna_message_warning("Empty CLUSTAL file"); return 0;+   }++   if ((strncmp(line,"CLUSTAL", 7) !=0) && (!strstr(line,"STOCKHOLM"))) {+     vrna_message_warning("This doesn't look like a CLUSTAL/STOCKHOLM file, sorry");+     free(line); return 0;+   }+   free(line);+   line = vrna_read_line(clust);++   while (line!=NULL) {+    if(strncmp(line, "//", 2) == 0){+      free(line);+      break;+    }++    if (((n=strlen(line))<4) || isspace((int)line[0])) {+      /* skip non-sequence line */+      free(line); line = vrna_read_line(clust);+      nn=0; /* reset seqence number */+      continue;+    }+    /* skip comments */+    if(line[0] == '#'){+      free(line);+      line = vrna_read_line(clust);+      continue;+    }++     seq = (char *) vrna_alloc( (n+1)*sizeof(char) );+     sscanf(line,"%99s %s", name, seq);++    for(i=0;i<strlen(seq);i++){+      if(seq[i] == '.') seq[i] = '-'; /* replace '.' gaps by '-' */+      /* comment the next line and think about something more difficult to deal with+         lowercase sequence letters if you really want to */+      seq[i] = toupper(seq[i]);+    }++     if (nn == num_seq) { /* first time */+       names[nn] = strdup(name);+       AlignedSeqs[nn] = strdup(seq);+     }+     else {+       if (strcmp(name, names[nn])!=0) {+         /* name doesn't match */+         vrna_message_warning("Sorry, your file is messed up (inconsitent seq-names)");+         free(line); free(seq);+         return 0;+       }+       AlignedSeqs[nn] = (char *)+         vrna_realloc(AlignedSeqs[nn], strlen(seq)+strlen(AlignedSeqs[nn])+1);+       strcat(AlignedSeqs[nn], seq);+     }+     nn++;+     if (nn>num_seq) num_seq = nn;+     free(seq);+     free(line);+     if (num_seq>=MAX_NUM_NAMES) {+       vrna_message_warning("Too many sequences in CLUSTAL/STOCKHOLM file");+       return 0;+     }++     line = vrna_read_line(clust);+   }++   AlignedSeqs[num_seq] = NULL;+   names[num_seq] = NULL;+   if (num_seq == 0) {+     vrna_message_warning("No sequences found in CLUSTAL/STOCKHOLM file");+     return 0;+   }+   n = strlen(AlignedSeqs[0]);+   for (nn=1; nn<num_seq; nn++) {+     if (strlen(AlignedSeqs[nn])!=n) {+       vrna_message_warning("Sorry, your file is messed up.\n"+                            "Unequal lengths!");+       return 0;+     }+   }++   vrna_message_info(stderr, "%d sequences; length of alignment %d.", nn, n);+   return num_seq;+}++char *consensus(const char *AS[]) {+  /* simple consensus sequence (most frequent character) */+  char *string;+  int i,n;++  string = NULL;++  if(AS){+    n = strlen(AS[0]);+    string = (char *) vrna_alloc((n+1)*sizeof(char));+    for (i=0; i<n; i++) {+      int s,c,fm, freq[8] = {0,0,0,0,0,0,0,0};+      for (s=0; AS[s]!=NULL; s++)+        freq[encode_char(AS[s][i])]++;+      for (s=c=fm=0; s<8; s++) /* find the most frequent char */+        if (freq[s]>fm) {c=s, fm=freq[c];}+      if (s>4) s++; /* skip T */+      string[i]=Law_and_Order[c];+    }+  }+  return string;+}++/* IUP nucleotide classes indexed by a bit string of the present bases */+/* A C AC G AG CG ACG U AU CU ACU GU AGU CGU ACGU */+static char IUP[17] = "-ACMGRSVUWYHKDBN";+char *consens_mis(const char*AS[]) {+  /* MIS displays the 'most informative sequence' (Freyhult et al 2004),+     elements in columns with frequency greater than the background+     frequency are projected into iupac notation. Columns where gaps are+     over-represented are in lower case. */++  char *cons;+  int i, s, n, N, c;+  int bgfreq[8] = {0,0,0,0,0,0,0,0};++  cons = NULL;++  if(AS){+    n = strlen(AS[0]);+    for (N=0; AS[N]!=NULL; N++);+    cons = (char *) vrna_alloc((n+1)*sizeof(char));++    for (i=0; i<n; i++)+      for (s=0; s<N; s++) {+        c = encode_char(AS[s][i]);+        if (c>4) c=5;+        bgfreq[c]++;+      }++    for (i=0; i<n; i++) {+      int freq[8] = {0,0,0,0,0,0,0,0};+      int code = 0;+      for (s=0; s<N; s++) {+        c = encode_char(AS[s][i]);+        if (c>4) c=5;+        freq[c]++;+      }+      for (c=4; c>0; c--) {+        code <<=1;+        if (freq[c]*n>=bgfreq[c]) code++;+      }+      cons[i] = IUP[code];+      if (freq[0]*n>bgfreq[0])+        cons[i] = tolower(IUP[code]);+    }+  }+  return cons;+}++PUBLIC char *+get_ungapped_sequence(const char *seq){++  char  *tmp_sequence, *b;+  int   i;++  tmp_sequence = strdup(seq);++  b = tmp_sequence;+  i = 0;+  do{+    if((*b=='-')||(*b=='_')||(*b=='~')||(*b=='.')) continue;+    tmp_sequence[i] = *b;+    i++;+  }while(*(++b));++  tmp_sequence = (char *)vrna_realloc(tmp_sequence, (i+1)*sizeof(char));+  tmp_sequence[i] = '\0';++  return tmp_sequence;+}++PUBLIC int+vrna_aln_mpi(const char **alignment){++  int   i, j, k, s, n_seq, n, pairnum = 0, sumident = 0;+  float ident = 0;++  if(alignment){+    n = (int)strlen(alignment[0]);+    for(s = 0; alignment[s]; s++);+    n_seq = s;++    for(j = 0; j < n_seq - 1; j++)+      for(k = j + 1; k < n_seq; k++) {+        ident = 0;+        for (i = 1; i <= n; i++){+          if(alignment[k][i] == alignment[j][i])+            ident++;+          pairnum++;+        }+        sumident+=ident;+      }++    if(pairnum > 0)+      return (int) (sumident*100/pairnum);+  }+  return 0;+}++/*---------------------------------------------------------------------------*/+PRIVATE int+compare_pinfo(const void *pi1,+              const void *pi2){++  vrna_pinfo_t *p1, *p2;+  int  i, nc1, nc2;+  p1 = (vrna_pinfo_t *)pi1;  p2 = (vrna_pinfo_t *)pi2;+  for (nc1=nc2=0, i=1; i<=6; i++) {+    if (p1->bp[i]>0) nc1++;+    if (p2->bp[i]>0) nc2++;+  }+  /* sort mostly by probability, add+     epsilon * comp_mutations/(non-compatible+1) to break ties */+  return (p1->p + 0.01*nc1/(p1->bp[0]+1.)) <+         (p2->p + 0.01*nc2/(p2->bp[0]+1.)) ? 1 : -1;+}++PUBLIC vrna_pinfo_t *+vrna_aln_pinfo( vrna_fold_compound_t *vc,+                const char *structure,+                double threshold){++  int i,j, num_p=0, max_p = 64;+  vrna_pinfo_t *pi;+  double *duck, p;+  short *ptable = NULL;++  short **S = vc->S;+  char **AS = vc->sequences;+  int n_seq = vc->n_seq;+  int n     = vc->length;+  int         *my_iindx = vc->iindx;+  FLT_OR_DBL  *probs    = vc->exp_matrices->probs;+  vrna_md_t   *md = &(vc->exp_params->model_details);++  max_p = 64; pi = vrna_alloc(max_p*sizeof(vrna_pinfo_t));+  duck =  (double *) vrna_alloc((n+1)*sizeof(double));+  if(structure)+    ptable = vrna_ptable(structure);++  for (i=1; i<n; i++)+    for (j=i+TURN+1; j<=n; j++) {+      if ((p=probs[my_iindx[i]-j])>=threshold) {+        duck[i] -=  p * log(p);+        duck[j] -=  p * log(p);++        int type, s;+        pi[num_p].i   = i;+        pi[num_p].j   = j;+        pi[num_p].p   = p;+        pi[num_p].ent = duck[i]+duck[j]-p*log(p);++        for (type=0; type<8; type++) pi[num_p].bp[type]=0;+        for (s=0; s<n_seq; s++) {+          type = md->pair[S[s][i]][S[s][j]];+          if(S[s][i]==0 && S[s][j]==0) type = 7; /* gap-gap  */+          if ((AS[s][i-1] == '-')||(AS[s][j-1] == '-')) type = 7;+          if ((AS[s][i-1] == '~')||(AS[s][j-1] == '~')) type = 7;+          pi[num_p].bp[type]++;+        }+        if(ptable)+          pi[num_p].comp = (ptable[i] == j) ? 1:0;++        num_p++;+        if (num_p>=max_p) {+          max_p *= 2;+          pi = vrna_realloc(pi, max_p * sizeof(vrna_pinfo_t));+        }+      }+    }+  free(duck);+  pi = vrna_realloc(pi, (num_p+1)*sizeof(vrna_pinfo_t));+  pi[num_p].i=0;+  qsort(pi, num_p, sizeof(vrna_pinfo_t), compare_pinfo );++  free(ptable);+  return pi;+}+++PUBLIC int *+vrna_aln_pscore(const char  **alignment,+                vrna_md_t   *md){++  /* calculate co-variance bonus for each pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */++#define NONE -10000 /* score for forbidden pairs */++  int         i, j, k, l, s, n, n_seq, *indx, turn, max_span;+  float       **dm;+  vrna_md_t   md_default;+  int         *pscore;+  short       **S;++  int olddm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                  {0,0,2,2,1,2,2} /* CG */,+                  {0,2,0,1,2,2,2} /* GC */,+                  {0,2,1,0,2,1,2} /* GU */,+                  {0,1,2,2,0,2,1} /* UG */,+                  {0,2,2,1,2,0,2} /* AU */,+                  {0,2,2,2,1,2,0} /* UA */};++  pscore = NULL;++  if(!md){+    vrna_md_set_default(&md_default);+    md = &md_default;+  }++  if(alignment){+    /* length of alignment */+    n = (int)strlen(alignment[0]);++    /* count number of sequences */+    for(s = 0; alignment[s]; s++);+    n_seq = s;++    /* make numeric encoding of sequences */+    S = (short **)vrna_alloc(sizeof(short *) * (n_seq + 1));+    for(s = 0; s < n_seq; s++){+      S[s] = vrna_seq_encode_simple(alignment[s], md);+    }++    indx  = vrna_idx_col_wise(n);++    turn    = md->min_loop_size;++    pscore = (int *)vrna_alloc(sizeof(int) * ((n+1)*(n+2)/2 + 2));++    if (md->ribo) {+      if (RibosumFile !=NULL) dm=readribosum(RibosumFile);+      else dm=get_ribosum(alignment, n_seq, n);+    }+    else { /*use usual matrix*/+      dm = vrna_alloc(7*sizeof(float*));+      for (i=0; i<7;i++) {+        dm[i] = vrna_alloc(7*sizeof(float));+        for (j=0; j<7; j++)+          dm[i][j] = (float) olddm[i][j];+      }+    }++    max_span = md->max_bp_span;+    if((max_span < turn+2) || (max_span > n))+      max_span = n;+    for (i=1; i<n; i++) {+      for (j=i+1; (j<i+turn+1) && (j<=n); j++)+        pscore[indx[j]+i] = NONE;+      for (j=i+turn+1; j<=n; j++) {+        int pfreq[8]={0,0,0,0,0,0,0,0};+        double score;+        for (s=0; s<n_seq; s++) {+          int type;+          if (S[s][i]==0 && S[s][j]==0) type = 7; /* gap-gap  */+          else {+            if ((alignment[s][i] == '~')||(alignment[s][j] == '~')) type = 7;+            else type = md->pair[S[s][i]][S[s][j]];+          }+          pfreq[type]++;+        }+        if (pfreq[0]*2+pfreq[7]>n_seq) { pscore[indx[j]+i] = NONE; continue;}+        for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+          for (l=k; l<=6; l++)+            score += pfreq[k]*pfreq[l]*dm[k][l];+        /* counter examples score -1, gap-gap scores -0.25   */+        pscore[indx[j]+i] = md->cv_fact *+          ((UNIT*score)/n_seq - md->nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));++        if((j - i + 1) > max_span){+          pscore[indx[j]+i] = NONE;+        }+      }+    }++    if (md->noLP) /* remove unwanted pairs */+      for (k=1; k<n-turn-1; k++)+        for (l=1; l<=2; l++) {+          int type,ntype=0,otype=0;+          i=k; j = i+turn+l;+          type = pscore[indx[j]+i];+          while ((i>=1)&&(j<=n)) {+            if ((i>1)&&(j<n)) ntype = pscore[indx[j+1]+i-1];+            if ((otype<md->cv_fact*MINPSCORE)&&(ntype<md->cv_fact*MINPSCORE))  /* too many counterexamples */+              pscore[indx[j]+i] = NONE; /* i.j can only form isolated pairs */+            otype =  type;+            type  = ntype;+            i--; j++;+          }+        }++    /*free dm */+    for (i=0; i<7;i++) {+      free(dm[i]);+    }+    free(dm);++    for(s = 0; s < n_seq; s++){+      free(S[s]);+    }+    free(S);++    free(indx);+  }++  return pscore;+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC int+get_mpi(char *Alseq[],+        int n_seq,+        int length,+        int *mini){++  int   i, j, k, pairnum = 0, sumident = 0;+  float ident = 0, minimum = 1.;++  for(j=0; j<n_seq-1; j++)+    for(k=j+1; k<n_seq; k++) {+      ident=0;+      for (i=1; i<=length; i++){+        if (Alseq[k][i]==Alseq[j][i]) ident++;+        pairnum++;+      }+      if ((ident/length)<minimum) minimum=ident/(float)length;+      sumident+=ident;+    }+  mini[0]=(int)(minimum*100.);+  if (pairnum>0)   return (int) (sumident*100/pairnum);+  else return 0;+}++PUBLIC void+alloc_sequence_arrays(const char **sequences,+                      short ***S,+                      short ***S5,+                      short ***S3,+                      unsigned short ***a2s,+                      char ***Ss,+                      int circ){++  unsigned int s, n_seq, length;+  if(sequences[0] != NULL){+    length = strlen(sequences[0]);+    for (s=0; sequences[s] != NULL; s++);+    n_seq = s;+    *S    = (short **)          vrna_alloc((n_seq+1) * sizeof(short *));+    *S5   = (short **)          vrna_alloc((n_seq+1) * sizeof(short *));+    *S3   = (short **)          vrna_alloc((n_seq+1) * sizeof(short *));+    *a2s  = (unsigned short **) vrna_alloc((n_seq+1) * sizeof(unsigned short *));+    *Ss   = (char **)           vrna_alloc((n_seq+1) * sizeof(char *));+    for (s=0; s<n_seq; s++) {+      if(strlen(sequences[s]) != length) vrna_message_error("uneqal seqence lengths");+      (*S5)[s]  = (short *)         vrna_alloc((length + 2) * sizeof(short));+      (*S3)[s]  = (short *)         vrna_alloc((length + 2) * sizeof(short));+      (*a2s)[s] = (unsigned short *)vrna_alloc((length + 2) * sizeof(unsigned short));+      (*Ss)[s]  = (char *)          vrna_alloc((length + 2) * sizeof(char));+      (*S)[s]   = (short *)         vrna_alloc((length + 2) * sizeof(short));+      encode_ali_sequence(sequences[s], (*S)[s], (*S5)[s], (*S3)[s], (*Ss)[s], (*a2s)[s], circ);+    }+    (*S5)[n_seq]  = NULL;+    (*S3)[n_seq]  = NULL;+    (*a2s)[n_seq] = NULL;+    (*Ss)[n_seq]  = NULL;+    (*S)[n_seq]   = NULL;+  }+  else vrna_message_error("alloc_sequence_arrays: no sequences in the alignment!");+}++PUBLIC void+free_sequence_arrays( unsigned int n_seq,+                      short ***S,+                      short ***S5,+                      short ***S3,+                      unsigned short ***a2s,+                      char ***Ss){++  unsigned int s;+  for (s=0; s<n_seq; s++) {+    free((*S)[s]);+    free((*S5)[s]);+    free((*S3)[s]);+    free((*a2s)[s]);+    free((*Ss)[s]);+  }+  free(*S);   *S    = NULL;+  free(*S5);  *S5   = NULL;+  free(*S3);  *S3   = NULL;+  free(*a2s); *a2s  = NULL;+  free(*Ss);  *Ss   = NULL;+}++PUBLIC void+encode_ali_sequence(const char *sequence,+                    short *S,+                    short *s5,+                    short *s3,+                    char *ss,+                    unsigned short *as,+                    int circular){++  unsigned int i,l;+  unsigned short p;+  l     = strlen(sequence);+  S[0]  = (short) l;+  s5[0] = s5[1] = 0;++  /* make numerical encoding of sequence */+  for(i=1; i<=l; i++){+    short ctemp;+    ctemp=(short) encode_char(toupper(sequence[i-1]));+    S[i]= ctemp ;+  }++  if (oldAliEn){+    /* use alignment sequences in all energy evaluations */+    ss[0]=sequence[0];+    for(i=1; i<l; i++){+      s5[i] = S[i-1];+      s3[i] = S[i+1];+      ss[i] = sequence[i];+      as[i] = i;+    }+    ss[l]   = sequence[l];+    as[l]   = l;+    s5[l]   = S[l-1];+    s3[l]   = 0;+    S[l+1]  = S[1];+    s5[1]   = 0;+    if (circular) {+      s5[1]   = S[l];+      s3[l]   = S[1];+      ss[l+1] = S[1];+    }+  }+  else{+    if(circular){+      for(i=l; i>0; i--){+        char c5;+        c5 = sequence[i-1];+        if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.')) continue;+        s5[1] = S[i];+        break;+      }+      for (i=1; i<=l; i++) {+        char c3;+        c3 = sequence[i-1];+        if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.')) continue;+        s3[l] = S[i];+        break;+      }+    }+    else  s5[1]=s3[l]=0;++    for(i=1,p=0; i<=l; i++){+      char c5;+      c5 = sequence[i-1];+      if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.'))+        s5[i+1]=s5[i];+      else { /* no gap */+        ss[p++]=sequence[i-1]; /*start at 0!!*/+        s5[i+1]=S[i];+      }+      as[i]=p;+    }+    for (i=l; i>=1; i--) {+      char c3;+      c3 = sequence[i-1];+      if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.'))+        s3[i-1]=s3[i];+      else+        s3[i-1]=S[i];+    }+  }+}+
+ C/ViennaRNA/aln_util.h view
@@ -0,0 +1,206 @@+#ifndef VIENNA_RNA_PACKAGE_ALN_UTIL_H+#define VIENNA_RNA_PACKAGE_ALN_UTIL_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file aln_util.h+ *  @ingroup utils+ *  @brief Various utility- and helper-functions for sequence alignments and comparative structure prediction+ */++/**+ *  @{+ *  @ingroup   aln_utils+ *+ */++/** @brief Typename for the base pair info repesenting data structure #vrna_pinfo_s */+typedef struct vrna_pinfo_s     vrna_pinfo_t;++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT+++#ifdef VRNA_BACKWARD_COMPAT++/* the following typedefs are for backward compatibility only */++/**+ *  @brief Old typename of #vrna_pinfo_s+ *  @deprecated Use #vrna_pinfo_t instead!+*/+typedef struct vrna_pinfo_s     pair_info;++#endif++/**+ *  @brief A base pair info structure+ *+ *  For each base pair (i,j) with i,j in [0, n-1] the structure lists:+ *  - its probability 'p'+ *  - an entropy-like measure for its well-definedness 'ent'+ *  - the frequency of each type of pair in 'bp[]'+ *    + 'bp[0]' contains the number of non-compatible sequences+ *    + 'bp[1]' the number of CG pairs, etc.+ */+struct vrna_pinfo_s {+   unsigned i;    /**<  @brief  nucleotide position i */+   unsigned j;    /**<  @brief  nucleotide position j */+   float p;       /**< @brief  Probability */+   float ent;     /**< @brief  Pseudo entropy for @f$ p(i,j) = S_i + S_j - p_ij*ln(p_ij) @f$ */+   short bp[8];   /**< @brief  Frequencies of pair_types */+   char comp;     /**< @brief  1 iff pair is in mfe structure */+};++int read_clustal( FILE *clust,+                  char *AlignedSeqs[],+                  char *names[]);++char *consensus(const char *AS[]);++char *consens_mis(const char *AS[]);++char *+get_ungapped_sequence(const char *seq);++/**+ *  @brief Get the mean pairwise identity in steps from ?to?(ident)+ * + *  @ingroup consensus_fold+ * + *  @param alignment  Aligned sequences+ *  @return       The mean pairwise identity+ */+int vrna_aln_mpi( const char **alignment);++/**+ *  \brief Retrieve an array of #vrna_pinfo_t structures from precomputed pair probabilities+ *+ *  This array of structures contains information about positionwise pair probabilies,+ *  base pair entropy and more+ *+ *  \see #vrna_pinfo_t, and vrna_pf()+ *+ *  \param  vc          The #vrna_fold_compound_t of type #VRNA_FC_TYPE_COMPARATIVE with precomputed partition function matrices+ *  \param  structure   An optional structure in dot-bracket notation (Maybe NULL)+ *  \param  threshold   Do not include results with pair probabilities below threshold+ *  \return             The #vrna_pinfo_t array+ */+vrna_pinfo_t *vrna_aln_pinfo(vrna_fold_compound_t *vc,+                                  const char *structure,+                                  double threshold);++int *+vrna_aln_pscore(const char  **alignment,+                vrna_md_t   *md);+++/**+ *  @brief Get the mean pairwise identity in steps from ?to?(ident)+ * + *  @ingroup consensus_fold+ *+ *  @deprecated Use vrna_aln_mpi() as a replacement+ *+ *  @param Alseq+ *  @param n_seq  The number of sequences in the alignment+ *  @param length The length of the alignment+ *  @param mini+ *  @return       The mean pairwise identity+ */+DEPRECATED(int get_mpi(char *Alseq[], int n_seq, int length, int *mini));++/*+#############################################################+# some helper functions that might be useful in the library #+#############################################################+*/++/**+ *  @brief Get arrays with encoded sequence of the alignment+ *+ *  this function assumes that in S, S5, s3, ss and as enough+ *  space is already allocated (size must be at least sequence length+2)+ * + *  @ingroup consensus_fold+ * + *  @param sequence The gapped sequence from the alignment+ *  @param S        pointer to an array that holds encoded sequence+ *  @param s5      pointer to an array that holds the next base 5' of alignment position i+ *  @param s3      pointer to an array that holds the next base 3' of alignment position i+ *  @param ss+ *  @param as+ *  @param circ    assume the molecules to be circular instead of linear (circ=0)+ */+void encode_ali_sequence( const char *sequence,+                          short *S,+                          short *s5,+                          short *s3,+                          char *ss,+                          unsigned short *as,+                          int circ);++/**+ *  @brief Allocate memory for sequence array used to deal with aligned sequences+ * + *  Note that these arrays will also be initialized according to the sequence alignment given+ * + *  @ingroup consensus_fold+ * + *  @see free_sequence_arrays()+ * + *  @param sequences  The aligned sequences+ *  @param S          A pointer to the array of encoded sequences+ *  @param S5         A pointer to the array that contains the next 5' nucleotide of a sequence position+ *  @param S3         A pointer to the array that contains the next 3' nucleotide of a sequence position+ *  @param a2s        A pointer to the array that contains the alignment to sequence position mapping+ *  @param Ss         A pointer to the array that contains the ungapped sequence+ *  @param circ       assume the molecules to be circular instead of linear (circ=0)+ */+void  alloc_sequence_arrays(const char **sequences,+                            short ***S,+                            short ***S5,+                            short ***S3,+                            unsigned short ***a2s,+                            char ***Ss,+                            int circ);++/**+ *  @brief Free the memory of the sequence arrays used to deal with aligned sequences+ * + *  This function frees the memory previously allocated with alloc_sequence_arrays()+ * + *  @ingroup consensus_fold+ * + *  @see alloc_sequence_arrays()+ * + *  @param n_seq      The number of aligned sequences+ *  @param S          A pointer to the array of encoded sequences+ *  @param S5         A pointer to the array that contains the next 5' nucleotide of a sequence position+ *  @param S3         A pointer to the array that contains the next 3' nucleotide of a sequence position+ *  @param a2s        A pointer to the array that contains the alignment to sequence position mapping+ *  @param Ss         A pointer to the array that contains the ungapped sequence+ */+void  free_sequence_arrays( unsigned int n_seq,+                            short ***S,+                            short ***S5,+                            short ***S3,+                            unsigned short ***a2s,+                            char ***Ss);+++/**+ * @}+ */+++#endif
+ C/ViennaRNA/alphabet.c view
@@ -0,0 +1,399 @@+/*+    alphabet.c+    +    Code for handling nucleotide and base pair alphabet+    +    Part of the ViennaRNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/alphabet.h"++/*+  For now, we neglect all non-standard nucleotides in an input sequence, i.e. only+  ACGTUN is allowed.++  However, the standard nucleotide ambiguity code table would allow for many more:++  A = Adenylic acid+  C = Cytidylic acid+  G = Guanylic acid+  T = Thymidylic acid+  U = Uridylic acid+  I = Inosylic acid+  R = A or G = puRine+  Y = C or T = pYrimidine+  K = G or T = Keto+  M = A or C = aMino+  S = G or C = Strong base pair+  W = A or T = Weak base pair+  B = not A (G or C or T)+  D = not C (A or G or T)+  H = not G (A or C or T)+  V = not T/U (A or C or G)+  N = aNy base  (by convention, X is used for unknown amino acids, N for unknown nucleotides)++  For the future, we aim to accept all of the above codes.+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE const char Law_and_Order[] = "_ACGUTXKI";++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE char  *wrap_get_ptypes(const short *S, vrna_md_t *md);  /* provides backward compatibility for old ptypes array in pf computations */++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC unsigned int+vrna_sequence_length_max(unsigned int options){++  if(options & VRNA_OPTION_WINDOW)+    return (unsigned int)INT_MAX;++/*+  return (unsigned int)sqrt((double)INT_MAX);+*/+  /*+      many functions in RNAlib still rely on the sequence length+      at pos 0 in the integer encoded sequence array S. Since this+      encoding is stored in a short * array, the maximum length+      of any sequence is SHRT_MAX+  */+  return (unsigned int)SHRT_MAX;+}+++PUBLIC int+vrna_nucleotide_IUPAC_identity( char nt,+                                char mask){++  char n1,n2,*p;++  p   = NULL;+  n1  = toupper(nt);+  n2  = toupper(mask);++  switch(n1){+    case 'A': p = strchr("ARMWDHVN", n2);+              break;+    case 'C': p = strchr("CYMSBHVN", n2);+              break;+    case 'G': p = strchr("GRKSBDVN", n2);+              break;+    case 'T': p = strchr("TYKWBDHN", n2);+              break;+    case 'U': p = strchr("UYKWBDHN", n2);+              break;+    case 'I': p = strchr("IN", n2);+              break;+    case 'R': p = strchr("AGR", n2);+              break;+    case 'Y': p = strchr("CTUY", n2);+              break;+    case 'K': p = strchr("GTUK", n2);+              break;+    case 'M': p = strchr("ACM", n2);+              break;+    case 'S': p = strchr("GCS", n2);+              break;+    case 'W': p = strchr("ATUW", n2);+              break;+    case 'B': p = strchr("GCTBU", n2);+              break;+    case 'D': p = strchr("AGTUD", n2);+              break;+    case 'H': p = strchr("ACTUH", n2);+              break;+    case 'V': p = strchr("ACGV", n2);+              break;+    case 'N': p = strchr("ACGTUN", n2);+              break;+  }++  return (p) ? 1 : 0;+}+++PUBLIC char *+vrna_ptypes(const short *S,+                vrna_md_t *md){++  char *ptype;+  int n,i,j,k,l,*idx;+  int min_loop_size = md->min_loop_size;++  n     = S[0];++  if((unsigned int)n > vrna_sequence_length_max(VRNA_OPTION_DEFAULT)){+    vrna_message_warning("vrna_ptypes@alphabet.c: sequence length of %d exceeds addressable range", n);+    return NULL;+  }++  ptype = (char *)vrna_alloc(sizeof(char)*((n*(n+1))/2+2));+  idx   = vrna_idx_col_wise(n);++  for (k=1; k<n-min_loop_size; k++)+    for (l=1; l<=2; l++) {+      int type,ntype=0,otype=0;+      i=k; j = i+min_loop_size+l; if (j>n) continue;+      type = md->pair[S[i]][S[j]];+      while ((i>=1)&&(j<=n)) {+        if ((i>1)&&(j<n)) ntype = md->pair[S[i-1]][S[j+1]];+        if (md->noLP && (!otype) && (!ntype))+          type = 0; /* i.j can only form isolated pairs */+        ptype[idx[j]+i] = (char) type;+        otype =  type;+        type  = ntype;+        i--; j++;+      }+    }+  free(idx);+  return ptype;+}++PUBLIC short *+vrna_seq_encode(const char *sequence,+                vrna_md_t *md){++  unsigned int  i, l;+  short         *S = NULL;+  +  if(sequence && md){+    S = vrna_seq_encode_simple(sequence, md);++    l = (unsigned int)strlen(sequence);++    for(i=1; i<=l; i++)+      S[i] = md->alias[S[i]];++    S[l+1] = S[1];+    S[0] = S[l];+  }++  return S;+}++PUBLIC short *+vrna_seq_encode_simple( const char *sequence,+                        vrna_md_t *md){++  unsigned int  i, l;+  short         *S = NULL;++  if(sequence && md){+    l = (unsigned int)strlen(sequence);+    S = (short *) vrna_alloc(sizeof(short)*(l+2));++    for(i=1; i<=l; i++) /* make numerical encoding of sequence */+      S[i]= (short) vrna_nucleotide_encode(toupper(sequence[i-1]), md);++    S[l+1] = S[1];+    S[0] = (short) l;+  }++  return S;+}++PUBLIC  int+vrna_nucleotide_encode( char c,+                        vrna_md_t *md){++  /* return numerical representation of nucleotide used e.g. in vrna_md_t.pair[][] */+  int code = -1;++  if(md){+    if (md->energy_set>0) code = (int) (c-'A')+1;+    else {+      const char *pos;+      pos = strchr(Law_and_Order, c);+      if (pos==NULL) code=0;+      else code = (int) (pos-Law_and_Order);+      if (code>5) code = 0;+      if (code>4) code--; /* make T and U equivalent */+    }+  }++  return code;+}++PUBLIC  char+vrna_nucleotide_decode( int enc,+                        vrna_md_t *md){++  if(md){+    if(md->energy_set > 0)+      return (char)enc + 'A' - 1;+    else+      return (char)Law_and_Order[enc];+  } else {+    return (char)0;+  }+}++PUBLIC void+vrna_aln_encode(const char *sequence,+                    short **S_p,+                    short **s5_p,+                    short **s3_p,+                    char **ss_p,+                    unsigned short **as_p,+                    vrna_md_t *md){++  unsigned  int   i,l;+  unsigned  short p;++  l     = strlen(sequence);++  (*s5_p)   = (short *)         vrna_alloc((l + 2) * sizeof(short));+  (*s3_p)   = (short *)         vrna_alloc((l + 2) * sizeof(short));+  (*as_p)  = (unsigned short *)vrna_alloc((l + 2) * sizeof(unsigned short));+  (*ss_p)   = (char *)          vrna_alloc((l + 2) * sizeof(char));++  /* make numerical encoding of sequence */+  (*S_p)    = vrna_seq_encode_simple(sequence, md);++  (*s5_p)[0] = (*s5_p)[1] = 0;++  if(md->oldAliEn){+    /* use alignment sequences in all energy evaluations */+    (*ss_p)[0]=sequence[0];+    for(i=1; i<l; i++){+      (*s5_p)[i] = (*S_p)[i-1];+      (*s3_p)[i] = (*S_p)[i+1];+      (*ss_p)[i] = sequence[i];+      (*as_p)[i] = i;+    }+    (*ss_p)[l]   = sequence[l];+    (*as_p)[l]   = l;+    (*s5_p)[l]   = (*S_p)[l-1];+    (*s3_p)[l]   = 0;+    (*S_p)[l+1]  = (*S_p)[1];+    (*s5_p)[1]   = 0;+    if(md->circ){+      (*s5_p)[1]   = (*S_p)[l];+      (*s3_p)[l]   = (*S_p)[1];+      (*ss_p)[l+1] = (*S_p)[1];+    }+  }+  else{+    if(md->circ){+      for(i=l; i>0; i--){+        char c5;+        c5 = sequence[i-1];+        if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.')) continue;+        (*s5_p)[1] = (*S_p)[i];+        break;+      }+      for (i=1; i<=l; i++) {+        char c3;+        c3 = sequence[i-1];+        if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.')) continue;+        (*s3_p)[l] = (*S_p)[i];+        break;+      }+    }+    else  (*s5_p)[1]=(*s3_p)[l]=0;++    for(i=1,p=0; i<=l; i++){+      char c5;+      c5 = sequence[i-1];+      if ((c5=='-')||(c5=='_')||(c5=='~')||(c5=='.'))+        (*s5_p)[i+1]=(*s5_p)[i];+      else { /* no gap */+        (*ss_p)[p++]=sequence[i-1]; /*start at 0!!*/+        (*s5_p)[i+1]=(*S_p)[i];+      }+      (*as_p)[i]=p;+    }+    for (i=l; i>=1; i--) {+      char c3;+      c3 = sequence[i-1];+      if ((c3=='-')||(c3=='_')||(c3=='~')||(c3=='.'))+        (*s3_p)[i-1]=(*s3_p)[i];+      else+        (*s3_p)[i-1]=(*S_p)[i];+    }+  }+}++PRIVATE char *+wrap_get_ptypes(const short *S,+                vrna_md_t *md){++  char *ptype;+  int n,i,j,k,l,*idx;++  n     = S[0];+  ptype = (char *)vrna_alloc(sizeof(char)*((n*(n+1))/2+2));+  idx   = vrna_idx_row_wise(n);+  int min_loop_size = md->min_loop_size;++  for (k=1; k<n-min_loop_size; k++)+    for (l=1; l<=2; l++) {+      int type,ntype=0,otype=0;+      i=k; j = i+min_loop_size+l; if (j>n) continue;+      type = md->pair[S[i]][S[j]];+      while ((i>=1)&&(j<=n)) {+        if ((i>1)&&(j<n)) ntype = md->pair[S[i-1]][S[j+1]];+        if (md->noLP && (!otype) && (!ntype))+          type = 0; /* i.j can only form isolated pairs */+        ptype[idx[i]-j] = (char) type;+        otype =  type;+        type  = ntype;+        i--; j++;+      }+    }+  free(idx);+  return ptype;+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC char *+get_ptypes( const short *S,+            vrna_md_t *md,+            unsigned int idx_type){++  if(S){+    if((unsigned int)S[0] > vrna_sequence_length_max(VRNA_OPTION_DEFAULT)){+      vrna_message_warning("get_ptypes@alphabet.c: sequence length of %d exceeds addressable range", (int)S[0]);+      return NULL;+    }++    if(idx_type)+      return wrap_get_ptypes(S, md);+    else+      return vrna_ptypes(S, md);+  } else {+    return NULL;+  }+}++#endif+
+ C/ViennaRNA/alphabet.h view
@@ -0,0 +1,107 @@+#ifndef VIENNA_RNA_PACKAGE_ALPHABET_H+#define VIENNA_RNA_PACKAGE_ALPHABET_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     alphabet.h+ *  @ingroup  utils+ *  @brief    Functions to process, convert, and generally handle different nucleotide+ *            and/or base pair alphabets+ */++/**+ *  @{+ *  @ingroup utils+ */++#include <ViennaRNA/model.h>++unsigned int vrna_sequence_length_max(unsigned int options);++int vrna_nucleotide_IUPAC_identity(char a, char b);++/**+ *  @brief Get an array of the numerical encoding for each possible base pair (i,j)+ *+ *  @note This array is always indexed in column-wise order, in contrast to previously+ *  different indexing between mfe and pf variants!+ *+ *  @see  vrna_idx_col_wise(), #vrna_fold_compound_t+ *+ */+char  *vrna_ptypes( const short *S,+                    vrna_md_t *md);++/**+ *  @brief Get a numerical representation of the nucleotide sequence+ *+ */+short *vrna_seq_encode( const char *sequence,+                        vrna_md_t *md);++/**+ *  @brief Get a numerical representation of the nucleotide sequence (simple version)+ *+ */+short *vrna_seq_encode_simple(const char *sequence,+                              vrna_md_t *md);++/**+ *  @brief  Encode a nucleotide character to numerical value+ *+ *  This function encodes a nucleotide character to its numerical representation as required by many functions in RNAlib.+ *+ *  @see  vrna_nucleotide_decode(), vrna_seq_encode()+ *+ *  @param  c   The nucleotide character to encode+ *  @param  md  The model details that determine the kind of encoding+ *  @return     The encoded nucleotide+ */+int vrna_nucleotide_encode( char c,+                            vrna_md_t *md);++/**+ *  @brief  Decode a numerical representation of a nucleotide back into nucleotide alphabet+ *+ *  This function decodes a numerical representation of a nucleotide character back into nucleotide alphabet+ *+ *  @see  vrna_nucleotide_encode(), vrna_seq_encode()+ *+ *  @param  enc The encoded nucleotide+ *  @param  md  The model details that determine the kind of decoding+ *  @return     The decoded nucleotide character+ */+char vrna_nucleotide_decode(int enc,+                            vrna_md_t *md);++void vrna_aln_encode( const char *sequence,+                      short **S_p,+                      short **s5_p,+                      short **s3_p,+                      char **ss_p,+                      unsigned short **as_p,+                      vrna_md_t *md);++/**+ *  @}+ */++#ifdef  VRNA_BACKWARD_COMPAT++DEPRECATED(char  *get_ptypes(const short *S, vrna_md_t *md, unsigned int idx_type));++#endif++#endif
+ C/ViennaRNA/boltzmann_sampling.c view
@@ -0,0 +1,1109 @@+/*+                  partiton function for RNA secondary structures++                  Ivo L Hofacker + Ronny Lorenz+                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/boltzmann_sampling.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  backtrack(int i, int j, char *pstruc, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_qm(int i, int j, char *pstruc, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_qm1(int i,int j, char *pstruc, vrna_fold_compound_t *vc);+PRIVATE void  backtrack_qm2(int u, int n, char *pstruc, vrna_fold_compound_t *vc);+PRIVATE char  *wrap_pbacktrack_circ(vrna_fold_compound_t *vc);++PRIVATE void  backtrack_comparative(vrna_fold_compound_t *vc, char *pstruc, int i, int j, double *prob);+PRIVATE void  backtrack_qm1_comparative(vrna_fold_compound_t *vc, char *pstruc, int i,int j, double *prob);++/*+ *  @brief Sample a consensus secondary structure from the Boltzmann ensemble according its probability+ * + *  @ingroup consensus_stochbt+ *+ *  @see vrna_pf() for precomputing the partition function matrices, and+ *+ *  @param  vc    The #vrna_fold_compound_t of type #VRNA_FC_TYPE_COMPARATIVE with precomputed partition function matrices+ *  @param  prob  to be described (berni)+ *  @return       A sampled consensus secondary structure in dot-bracket notation+ */+PRIVATE char *pbacktrack_comparative(vrna_fold_compound_t *vc, double *prob);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++/*+  stochastic backtracking in pf_fold arrays+  returns random structure S with Boltzman probabilty+  p(S) = exp(-E(S)/kT)/Z+*/+PUBLIC char *+vrna_pbacktrack(vrna_fold_compound_t *vc){++  char    *structure  = NULL;+  double  prob        = 1.;++  if(vc && vc->exp_params){+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:     if(vc->exp_params->model_details.circ){+                                        return wrap_pbacktrack_circ(vc);+                                      } else {+                                        return vrna_pbacktrack5(vc, vc->length);+                                      }+                                      break;++        case VRNA_FC_TYPE_COMPARATIVE:  return pbacktrack_comparative(vc, &prob);+                                      break;++        default:                      vrna_message_warning("unrecognized fold compound type");+                                      return structure;+                                      break;+      }+  }++  return structure;+}++PUBLIC char *+vrna_pbacktrack5( vrna_fold_compound_t *vc,+                  int length){++  FLT_OR_DBL        r, qt, q_temp, qkl;+  int               i,j,ij, n, k, u, start, type;+  char              *pstruc;+  int               *my_iindx, *jindx, hc_decompose, *hc_up_ext;+  FLT_OR_DBL        *q, *qb, *q1k, *qln, *scale;+  char              *ptype, *hard_constraints;+  short             *S1;+  vrna_mx_pf_t      *matrices;+  vrna_hc_t         *hc;+  vrna_sc_t         *sc;+  vrna_exp_param_t  *pf_params;++  n         = vc->length;++  pf_params = vc->exp_params;+  my_iindx  = vc->iindx;+  jindx     = vc->jindx;+  matrices  = vc->exp_matrices;++  hc        = vc->hc;+  sc        = vc->sc;+  ptype     = vc->ptype;+  S1        = vc->sequence_encoding;++  q         = matrices->q;+  qb        = matrices->qb;+  q1k       = matrices->q1k;+  qln       = matrices->qln;+  scale     = matrices->scale;++  hard_constraints  = hc->matrix;+  hc_up_ext         = hc->up_ext;++  if(length > n)+    vrna_message_error("part_func.c@pbacktrack5: 3'-end exceeds sequence length");+  else if(length < 1)+    vrna_message_error("part_func.c@pbacktrack5: 3'-end too small");++/*+  if (init_length<1)+    vrna_message_error("can't backtrack without pf arrays.\n"+            "Call pf_fold() before pbacktrack()");+*/++  pstruc = vrna_alloc((length+1)*sizeof(char));++  for (i=0; i<length; i++)+    pstruc[i] = '.';++  if(!(q1k && qln)){+    matrices->q1k = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+1));+    matrices->qln = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+    q1k           = matrices->q1k;+    qln           = matrices->qln;+    for (k=1; k<=n; k++) {+      q1k[k] = q[my_iindx[1] - k];+      qln[k] = q[my_iindx[k] - n];+    }+    q1k[0] = 1.0;+    qln[n+1] = 1.0;+  }+++#ifdef WITH_BOUSTROPHEDON+  j = length;+  while (j > 1) {+  /* find i position of first pair */+    for (; j>1; j--){+      if(hc_up_ext[j]){+        r = vrna_urn() * q[my_iindx[1] - j];+        q_temp = q[my_iindx[1] - j + 1] * scale[1];++        if(sc){+          if (sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[j][1];++          if(sc->exp_f)+            q_temp *= sc->exp_f(1, j, 1, j-1, VRNA_DECOMP_EXT_EXT, sc->data);+        }++        if (r > q_temp)  break; /* i is paired */+      }+    }+    if (j<=1) break; /* no more pairs */++    /* now find the pairing partner i */+    r = vrna_urn() * (q[my_iindx[1] - j] - q_temp);+    u = j - 1;++    for (qt=0, k=1; k<j; k++) {+      /* apply alternating boustrophedon scheme to variable i */+      i             = (int)(1 + (u - 1)*((k - 1) % 2)) + (int)((1-(2*((k - 1) % 2)))*((k - 1)/2));+      ij            = my_iindx[i]-j;+      type          = ptype[jindx[j] + i];+      hc_decompose  = hard_constraints[jindx[j] + i];+      if (hc_decompose & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {++        if(type == 0)+          type = 7;++        qkl = qb[ij] * exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);++        if (i > 1){+          qkl *= q[my_iindx[1] - i + 1];+          if(sc){+            if(sc->exp_f)+              qkl *= sc->exp_f(1, j, i-1, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+          }+        } else {+          if(sc){+            if(sc->exp_f)+              qkl *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_STEM, sc->data);+          }+        }++        qt += qkl;+        if (qt > r) break; /* j is paired */+      }+    }+    if (k==j) vrna_message_error("backtracking failed in ext loop");+    backtrack(i,j, pstruc, vc);+    j = i - 1;+  }+#else+  start = 1;+  while (start<length) {+  /* find i position of first pair */+    for (i=start; i<length; i++) {+      if(hc_up_ext[i]){+        r = vrna_urn() * qln[i];+        q_temp = qln[i+1]*scale[1];++        if(sc){+          if (sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[i][1];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, length, i+1, length, VRNA_DECOMP_EXT_EXT, sc->data);+        }++        if (r > q_temp)  break; /* i is paired */+      }+    }+    if (i>=length) break; /* no more pairs */+    /* now find the pairing partner j */+    r = vrna_urn() * (qln[i] - q_temp);+    for (qt=0, j=i+1; j<=length; j++) {+      ij            = my_iindx[i]-j;+      type          = ptype[jindx[j] + i];+      hc_decompose  = hard_constraints[jindx[j] + i];+      if (hc_decompose & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {++        if(type == 0)+          type = 7;++        qkl = qb[ij] * exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);++        if (j<length){+          qkl *= qln[j+1];+          if(sc){+            if(sc->exp_f)+              qkl *= sc->exp_f(i, length, j, j+1, VRNA_DECOMP_EXT_STEM_EXT, sc->data);+          }+        } else {+          if(sc){+            if(sc->exp_f)+              qkl *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_STEM, sc->data);+          }+        }++        qt += qkl;+        if (qt > r) break; /* j is paired */+      }+    }+    if (j==length+1) vrna_message_error("backtracking failed in ext loop");+    start = j+1;+    backtrack(i,j, pstruc, vc);+  }+#endif+  return pstruc;+}++PRIVATE void+backtrack_qm( int i,+              int j,+              char *pstruc,+              vrna_fold_compound_t *vc){++  /* divide multiloop into qm and qm1  */+  FLT_OR_DBL        qmt, r, q_temp;+  int               k, n, u, cnt, span, turn;+  FLT_OR_DBL        *qm, *qm1, *expMLbase;+  int               *my_iindx, *jindx, *hc_up_ml;+  vrna_sc_t         *sc;+  vrna_hc_t         *hc;++  n = j;+  vrna_mx_pf_t  *matrices = vc->exp_matrices;++  my_iindx  = vc->iindx;+  jindx     = vc->jindx;++  hc        = vc->hc;+  sc        = vc->sc;+  hc_up_ml  = hc->up_ml;++  qm        = matrices->qm;+  qm1       = matrices->qm1;+  expMLbase = matrices->expMLbase;++  turn      = vc->exp_params->model_details.min_loop_size;++  while(j>i){+    /* now backtrack  [i ... j] in qm[] */+    r   = vrna_urn() * qm[my_iindx[i] - j];+    qmt = qm1[jindx[j]+i];+    k = cnt  = i;+    if(qmt<r)+      for(span = j - i,cnt=i+1; cnt<=j; cnt++){+#ifdef WITH_BOUSTROPHEDON+        k = (int)(i + 1 + span * ((cnt - i - 1) % 2)) + (int)((1 - (2 * ((cnt - i - 1) % 2))) * ((cnt - i) / 2));+#else+        k = cnt;+#endif+        q_temp = 0.;+        u = k - i;+        /* [i...k] is unpaired */+        if(hc_up_ml[i] >= u){+          q_temp += expMLbase[u] * qm1[jindx[j]+k];++          if(sc){+            if(sc->exp_energy_up)+              q_temp *= sc->exp_energy_up[i][u];++            if(sc->exp_f)+              q_temp *= sc->exp_f(i, j, k, j, VRNA_DECOMP_ML_ML, sc->data);+          }++          qmt += q_temp;+        }++        /* split between k-1, k */+        q_temp = qm[my_iindx[i]-(k-1)] * qm1[jindx[j]+k];++        if(sc){+          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, k-1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+        }++        qmt += q_temp;++        if(qmt >= r){ break;}+      }+    if(cnt>j) vrna_message_error("backtrack failed in qm");++    backtrack_qm1(k, j, pstruc, vc);++    if(k<i+turn) break; /* no more pairs */++    u = k - i;+    /* check whether we make the decision to leave [i..k-1] unpaired */+    if(hc_up_ml[i] >= u){+      q_temp = expMLbase[u];++      if(sc){+        if(sc->exp_energy_up)+          q_temp *= sc->exp_energy_up[i][u];++        if(sc->exp_f)+          q_temp *= sc->exp_f(i, k-1, i, k-1, VRNA_DECOMP_ML_UP, sc->data);+      }++      r = vrna_urn() * (qm[my_iindx[i]-(k-1)] + q_temp);+      if(q_temp >= r) break;+    }+    j = k-1;+  }+}++PRIVATE void+backtrack_qm1(int i,+              int j,+              char *pstruc,+              vrna_fold_compound_t *vc){++  /* i is paired to l, i<l<j; backtrack in qm1 to find l */+  int           ii, l, il, type, n, turn;+  FLT_OR_DBL    qt, r, q_temp;+  FLT_OR_DBL    *qm1, *qb, *expMLbase;+  vrna_mx_pf_t  *matrices;+  int           u, *my_iindx, *jindx, *hc_up_ml;+  char          *ptype, *hard_constraints;+  short         *S1;+  vrna_sc_t     *sc;+  vrna_hc_t     *hc;+  vrna_exp_param_t  *pf_params;+++  pf_params = vc->exp_params;+  my_iindx  = vc->iindx;+  jindx     = vc->jindx;++  ptype     = vc->ptype;++  sc        = vc->sc;+  hc        = vc->hc;+  hc_up_ml  = hc->up_ml;+  hard_constraints  = hc->matrix;++  matrices  = vc->exp_matrices;+  qb        = matrices->qb;+  qm1       = matrices->qm1;+  expMLbase = matrices->expMLbase;+  S1        = vc->sequence_encoding;++  turn      = pf_params->model_details.min_loop_size;++  n = j;+  r = vrna_urn() * qm1[jindx[j]+i];+  ii = my_iindx[i];+  for (qt=0., l=j; l > i + turn; l--) {+    il = jindx[l] + i;+    if(hard_constraints[il] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+      u = j - l;+      if(hc_up_ml[l+1] >= u){+        type = ptype[il];++        if(type == 0)+          type = 7;++        q_temp =  qb[ii-l]+                  * exp_E_MLstem(type, S1[i-1], S1[l+1], pf_params)+                  * expMLbase[j-l];++        if(sc){+          if(sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[l+1][j-l];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, i, l, VRNA_DECOMP_ML_STEM, sc->data);+        }++        qt += q_temp;+        if (qt>=r) break;+      } else {+        l = i + turn;+        break;+      }+    }+  }+  if (l < i + turn + 1) vrna_message_error("backtrack failed in qm1");+  backtrack(i, l, pstruc, vc);+}++PRIVATE void+backtrack_qm2(int k,+              int n,+              char *pstruc,+              vrna_fold_compound_t *vc){++  FLT_OR_DBL  qom2t, r;+  int         u, turn;+  FLT_OR_DBL  *qm1, *qm2;+  int         *jindx;++  jindx     = vc->jindx;+  qm1       = vc->exp_matrices->qm1;+  qm2       = vc->exp_matrices->qm2;+  turn      = vc->exp_params->model_details.min_loop_size;++  r= vrna_urn()*qm2[k];+  /* we have to search for our barrier u between qm1 and qm1  */+  for (qom2t = 0.,u=k+turn+1; u<n-turn-1; u++){+    qom2t += qm1[jindx[u]+k]*qm1[jindx[n]+(u+1)];+    if(qom2t > r) break;+  }+  if(u==n-turn) vrna_message_error("backtrack failed in qm2");+  backtrack_qm1(k, u, pstruc, vc);+  backtrack_qm1(u+1, n, pstruc, vc);+}++PRIVATE void+backtrack(int i,+          int j,+          char *pstruc,+          vrna_fold_compound_t *vc){++  char              *ptype, *sequence, *hard_constraints, hc_decompose;+  vrna_exp_param_t  *pf_params;+  FLT_OR_DBL        *qb, *qm, *qm1, *scale, tmp;+  FLT_OR_DBL        r, qbt1, qt, q_temp;+  vrna_mx_pf_t      *matrices;+  int               *my_iindx, *jindx, *hc_up_int, *hc_up_hp;+  vrna_sc_t         *sc;+  vrna_hc_t         *hc;+  short             *S1;++  sequence    = vc->sequence;+  pf_params   = vc->exp_params;+  ptype       = vc->ptype;+  S1          = vc->sequence_encoding;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;++  sc          = vc->sc;+  hc          = vc->hc;+  hc_up_hp    = hc->up_hp;+  hc_up_int   = hc->up_int;+  hard_constraints  = hc->matrix;++  matrices    = vc->exp_matrices;+  qb          = matrices->qb;+  qm          = matrices->qm;+  qm1         = matrices->qm1;+  scale       = matrices->scale;++  int noGUclosure = pf_params->model_details.noGUclosure;+  int turn        = pf_params->model_details.min_loop_size;+  int   *rtype    = &(pf_params->model_details.rtype[0]);+  int n;+  n = j;+  do {+    int k, l, kl, u, u1, u2, max_k, min_l;+    unsigned char type;+    k = i;+    l = j;++    pstruc[i-1] = '('; pstruc[j-1] = ')';++    r = vrna_urn() * qb[my_iindx[i]-j];+    tmp = qb[my_iindx[i]-j];+    type = (unsigned char)ptype[jindx[j] + i];+    hc_decompose = hard_constraints[jindx[j] + i];+    if(hc_decompose & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){ /* hairpin contribution */++      if(type == 0)+        type = 7;++      u = j-i-1;++      if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;+      else{+        q_temp = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[u+2];++        if(sc){+          if(sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[i+1][u];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+        }++        qbt1 = q_temp;++      }+      if (qbt1>=r) return; /* found the hairpin we're done */+    }++    if(hc_decompose & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){ /* interior loop contributions */++      if(type == 0)+        type = 7;++      max_k = i + MAXLOOP + 1;+      max_k = MIN2(max_k, j - turn - 2);+      max_k = MIN2(max_k, i + 1 + hc_up_int[i+1]);+      for (k = i + 1; k<=max_k; k++) {+        u1    = k-i-1;+        min_l = MAX2(k+turn+1,j-1-MAXLOOP+u1);+        kl    = my_iindx[k] - j + 1;+        for (u2 = 0, l=j-1; l>=min_l; l--, kl++, u2++){+          if(hc_up_int[l+1] < u2) break;+          if(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC){+            unsigned char type_2 = (unsigned char)ptype[jindx[l] + k];+            type_2 = rtype[type_2];++            if(type_2 == 0)+              type_2 = 7;++            /* add *scale[u1+u2+2] */+            q_temp = qb[kl]+                     * scale[u1+u2+2]+                     * exp_E_IntLoop(u1, u2, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params);++            if(sc){+              if(sc->exp_energy_up)+                q_temp *=   sc->exp_energy_up[i+1][u1]+                          * sc->exp_energy_up[l+1][u2];++              if(sc->exp_energy_stack)+                if((i + 1 == k) && (j - 1 == l))+                  q_temp *=   sc->exp_energy_stack[i]+                            * sc->exp_energy_stack[k]+                            * sc->exp_energy_stack[l]+                            * sc->exp_energy_stack[j];++              if(sc->exp_f)+                q_temp *= sc->exp_f(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);+            }++            qbt1 += q_temp;+            if (qbt1 >= r) break;+          }+        }+        if (qbt1 >= r) break;+      }+      if (k <= max_k) {+        i=k; j=l;+      } else { /* interior loop contributions did not exceed threshold, so we break */+        break;+      }+    } else { /* must not be interior loop, so we break out */+      break;+    }+  } while (1);++  /* backtrack in multi-loop */+  {+    int k, ii, jj, tt;+    FLT_OR_DBL closingPair;+    tt = rtype[(unsigned char)ptype[jindx[j] + i]];+    closingPair =   pf_params->expMLclosing+                  * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params)+                  * scale[2];+    if(sc){+      if(sc->exp_f)+        closingPair *= sc->exp_f(i, j, i, j, VRNA_DECOMP_PAIR_ML, sc->data);+    }++    i++; j--;+    /* find the first split index */+    ii = my_iindx[i]; /* ii-j=[i,j] */+    jj = jindx[j]; /* jj+i=[j,i] */+    for (qt=qbt1, k=i+1; k<j; k++) {++      q_temp = qm[ii-(k-1)] * qm1[jj+k] * closingPair;++      if(sc){+        if(sc->exp_f)+          q_temp *= sc->exp_f(i, j, k-1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+      }++      qt += q_temp;+      qbt1 += q_temp;+      if (qt>=r) break;+    }+    if (k>=j){+      vrna_message_error("backtrack failed, can't find split index ");+    }++    backtrack_qm1(k, j, pstruc, vc);++    j = k-1;+    backtrack_qm(i, j, pstruc, vc);+  }+}++PRIVATE char *+wrap_pbacktrack_circ(vrna_fold_compound_t *vc){++  FLT_OR_DBL  r, qt;+  int         i, j, k, l, n;+  vrna_exp_param_t   *pf_params;+  FLT_OR_DBL  qo, qmo;+  FLT_OR_DBL  *scale, *qb, *qm, *qm2;+  char        *sequence, *ptype, *pstruc;+  int         *my_iindx, *jindx;+  short       *S1;++  vrna_mx_pf_t *matrices;++  pf_params     = vc->exp_params;+  matrices      = vc->exp_matrices;+  ptype         = vc->ptype;+  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  S1            = vc->sequence_encoding;++  qo            = matrices->qo;+  qmo           = matrices->qmo;+  qb            = matrices->qb;+  qm            = matrices->qm;+  qm2           = matrices->qm2;+  scale         = matrices->scale;++  FLT_OR_DBL  expMLclosing  = pf_params->expMLclosing;+  int         *rtype        = &(pf_params->model_details.rtype[0]);+  int         turn          = pf_params->model_details.min_loop_size;++  sequence  = vc->sequence;+  n         = vc->length;++/*+  if (init_length<1)+    vrna_message_error("can't backtrack without pf arrays.\n"+      "Call pf_circ_fold() before pbacktrack_circ()");+*/++  pstruc = vrna_alloc((n+1)*sizeof(char));++  /* initialize pstruct with single bases  */+  for (i=0; i<n; i++) pstruc[i] = '.';++  qt = 1.0*scale[n];+  r = vrna_urn() * qo;++  /* open chain? */+  if(qt > r) return pstruc;++  for(i=1; (i < n); i++){+    for(j=i+turn+1;(j<=n); j++){++      int type, u;+      /* 1. first check, wether we can do a hairpin loop  */+      u = n-j + i-1;+      if (u<turn) continue;++      type = ptype[jindx[j] + i];+      if (!type) continue;++      type=rtype[type];++      char loopseq[10];+      if (u<7){+        strcpy(loopseq , sequence+j-1);+        strncat(loopseq, sequence, i);+      }++      qt += qb[my_iindx[i]-j] * exp_E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, pf_params) * scale[u];+      /* found a hairpin? so backtrack in the enclosed part and we're done  */+      if(qt>r){ backtrack(i,j, pstruc, vc); return pstruc;}++      /* 2. search for (k,l) with which we can close an interior loop  */+      for(k=j+1; (k < n); k++){+        int ln1, lstart;+        ln1 = k - j - 1;+        if(ln1+i-1>MAXLOOP) break;++        lstart = ln1+i-1+n-MAXLOOP;+        if(lstart<k+turn+1) lstart = k + turn + 1;+        for(l=lstart; (l <= n); l++){+            int ln2, type2;+            ln2 = (i - 1) + (n - l);+            if((ln1+ln2) > MAXLOOP) continue;++            type2 = ptype[jindx[l] + k];+            if(!type) continue;+            type2 = rtype[type2];+            qt += qb[my_iindx[i]-j] * qb[my_iindx[k]-l] * exp_E_IntLoop(ln2, ln1, type2, type, S1[l+1], S1[k-1], S1[i-1], S1[j+1], pf_params) * scale[ln1 + ln2];+            /* found an exterior interior loop? also this time, we can go straight  */+            /* forward and backtracking the both enclosed parts and we're done      */+            if(qt>r){ backtrack(i,j, pstruc, vc); backtrack(k,l, pstruc, vc); return pstruc;}+        }+      } /* end of kl double loop */+    }+  } /* end of ij double loop  */+  {+    /* as we reach this part, we have to search for our barrier between qm and qm2  */+    qt = 0.;+    r = vrna_urn()*qmo;+    for(k=turn+2; k<n-2*turn-3; k++){+      qt += qm[my_iindx[1]-k] * qm2[k+1] * expMLclosing;+      /* backtrack in qm and qm2 if we've found a valid barrier k  */+      if(qt>r){ backtrack_qm(1,k, pstruc, vc); backtrack_qm2(k+1,n, pstruc, vc); return pstruc;}+    }+  }+  /* if we reach the actual end of this function, an error has occured  */+  /* cause we HAVE TO find an exterior loop or an open chain!!!         */+  vrna_message_error("backtracking failed in exterior loop");+  return pstruc;+}+++PRIVATE char *+pbacktrack_comparative( vrna_fold_compound_t *vc,+                        double *prob){++  FLT_OR_DBL  r, gr, qt;+  int         k,i,j, start,s;+  FLT_OR_DBL      probs=1;+  char        *pstruc = NULL;++  int               n_seq       = vc->n_seq;+  int               n           = vc->length;+  short             **S         = vc->S;+  short             **S5        = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+  short             **S3        = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+  vrna_exp_param_t  *pf_params  = vc->exp_params;+  vrna_mx_pf_t      *matrices   = vc->exp_matrices;+  vrna_md_t         *md         = &(pf_params->model_details);+  int               *my_iindx   = vc->iindx;+  vrna_hc_t         *hc         = vc->hc;+  vrna_sc_t         **sc        = vc->scs;+  FLT_OR_DBL        *q          = matrices->q;+  FLT_OR_DBL        *qb         = matrices->qb;++  if((matrices->q1k == NULL) || (matrices->qln == NULL)){+    free(matrices->q1k);+    matrices->q1k = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+1));+    free(matrices->qln);+    matrices->qln = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  }++  FLT_OR_DBL *q1k   = matrices->q1k;+  FLT_OR_DBL *qln   = matrices->qln;+  FLT_OR_DBL *scale = matrices->scale;++  for (k=1; k<=n; k++) {+    q1k[k] = q[my_iindx[1] - k];+    qln[k] = q[my_iindx[k] - n];+  }+  q1k[0] = 1.0;+  qln[n+1] = 1.0;++  pstruc = vrna_alloc((n+1)*sizeof(char));++  for (i=0; i<n; i++)+    pstruc[i] = '.';+++  start = 1;+  while (start<n) {+  /* find i position of first pair */+    probs=1.;+    for (i=start; i<n; i++) {+      gr = vrna_urn() * qln[i];+      if (gr > qln[i+1]*scale[1]) {+        *prob=*prob*probs*(1-qln[i+1]*scale[1]/qln[i]);+        break; /* i is paired */+      }+      probs*=qln[i+1]*scale[1]/qln[i];+    }+    if (i>=n) {+      *prob=*prob*probs;+      break; /* no more pairs */+    }+    /* now find the pairing partner j */+    r = vrna_urn() * (qln[i] - qln[i+1]*scale[1]);+    for (qt=0, j=i+1; j<=n; j++) {+      int xtype;+      /*  type = ptype[my_iindx[i]-j];+          if (type) {*/+      FLT_OR_DBL qkl;+      if (qb[my_iindx[i]-j]>0) {+        qkl = qb[my_iindx[i]-j]*qln[j+1];  /*if psc too small qb=0!*/+        for (s=0; s< n_seq; s++) {+          xtype=md->pair[S[s][i]][S[s][j]];+          if (xtype==0) xtype=7;+          qkl *= exp_E_ExtLoop(xtype, (i>1) ? S5[s][i] : -1, (j<n) ? S3[s][j] : -1, pf_params);+        }+        qt += qkl; /*?*exp(pscore[jindx[j]+i]/kTn)*/+        if (qt > r) {+          *prob=*prob*(qkl/(qln[i] - qln[i+1]*scale[1]));/*probs*=qkl;*/+          break; /* j is paired */+        }+      }+    }+    if (j==n+1) vrna_message_error("backtracking failed in ext loop");+    start = j+1;+    backtrack_comparative(vc, pstruc, i, j, prob); /*?*/+  }++  return pstruc;+}+++PRIVATE void+backtrack_comparative(vrna_fold_compound_t *vc,+          char *pstruc,+          int i,+          int j,+          double *prob){++  int               n_seq       = vc->n_seq;+  short             **S         = vc->S;+  short             **S5        = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+  short             **S3        = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+  char              **Ss        = vc->Ss;+  unsigned short    **a2s       = vc->a2s;+  vrna_exp_param_t  *pf_params  = vc->exp_params;+  vrna_mx_pf_t      *matrices   = vc->exp_matrices;+  vrna_md_t         *md         = &(pf_params->model_details);+  int               *my_iindx   = vc->iindx;+  int               *jindx      = vc->jindx;+  vrna_hc_t         *hc         = vc->hc;+  vrna_sc_t         **sc        = vc->scs;+  FLT_OR_DBL        *qb         = matrices->qb;+  FLT_OR_DBL        *qm         = matrices->qm;+  FLT_OR_DBL        *qm1        = matrices->qm1;+  int               *pscore     = vc->pscore;     /* precomputed array of pair types */++  FLT_OR_DBL        *scale        = matrices->scale;+  FLT_OR_DBL        *expMLbase    = matrices->expMLbase;++  /*backtrack given i,j basepair!*/+  FLT_OR_DBL kTn = pf_params->kT/10.;+  int *type = (int *)vrna_alloc(sizeof(int) * n_seq);++  do {+    FLT_OR_DBL  r, qbt1, max_k, min_l;+    int         k, l, u, u1, u2, s;+    pstruc[i-1] = '('; pstruc[j-1] = ')';+    for (s=0; s<n_seq; s++) {+      type[s] = md->pair[S[s][i]][S[s][j]];+      if (type[s]==0) type[s]=7;+    }+    r = vrna_urn() * (qb[my_iindx[i]-j]/exp(pscore[jindx[j]+i]/kTn)); /*?*exp(pscore[jindx[j]+i]/kTn)*/++    qbt1=1.;+    for (s=0; s<n_seq; s++){+      u = a2s[s][j-1]-a2s[s][i];+      if (a2s[s][i]<1) continue;+      char loopseq[10];+      if(u < 9){+        strncpy(loopseq, Ss[s]+a2s[s][i]-1, 10);+      }+      qbt1 *= exp_E_Hairpin(u, type[s], S3[s][i], S5[s][j], loopseq, pf_params);+    }+    qbt1 *= scale[j-i+1];++    if (qbt1>r) {+      *prob=*prob*qbt1/(qb[my_iindx[i]-j]/exp(pscore[jindx[j]+i]/kTn));/*probs*=qbt1;*/+      free(type);+      return; /* found the hairpin we're done */+    }+++    max_k = MIN2(i+MAXLOOP+1,j-TURN-2);+    l = MAX2(i+TURN+2,j-MAXLOOP-1);+    for (k=i+1; k<=max_k; k++){+      min_l = MAX2(k+TURN+1,j-1-MAXLOOP+k-i-1);++      for (l=min_l; l<j; l++){+        FLT_OR_DBL qloop=1;+        int type_2;+        if (qb[my_iindx[k]-l]==0) {qloop=0; continue;}+        for (s=0; s<n_seq; s++) {+          u1      = a2s[s][k-1] - a2s[s][i]/*??*/;+          u2      = a2s[s][j-1] - a2s[s][l];+          type_2  = md->pair[S[s][l]][S[s][k]];+          if(type_2 == 0) type_2 = 7;++          qloop *= exp_E_IntLoop(u1, u2, type[s], type_2, S3[s][i], S5[s][j],S5[s][k], S3[s][l], pf_params);+        }++        if(sc)+          for (s=0; s<n_seq; s++) {+            if(sc[s]){+              int u1 = a2s[s][k-1] - a2s[s][i];+              int u2 = a2s[s][j-1] - a2s[s][l];+              if(u1 + u2 == 0)+                if(sc[s]->exp_energy_stack){+                  if(S[s][i] && S[s][j] && S[s][k] && S[s][l]){ /* don't allow gaps in stack */+                    qloop *=    sc[s]->exp_energy_stack[i]+                              * sc[s]->exp_energy_stack[k]+                              * sc[s]->exp_energy_stack[l]+                              * sc[s]->exp_energy_stack[j];+                  }+                }+            }+          }++        qbt1 += qb[my_iindx[k]-l] * qloop * scale[k-i+j-l];++        if (qbt1 > r) {+         *prob =  *prob+                  * qb[my_iindx[k]-l]+                  * qloop+                  * scale[k-i+j-l]+                  / (   qb[my_iindx[i]-j]+                      / exp(pscore[jindx[j]+i] / kTn));+         /*+          prob*=qb[my_iindx[k]-l] * qloop * scale[k-i+j-l];+         */+          break;+        }+      }+      if (qbt1 > r) break;+    }+    if (l<j) {+      i=k; j=l;+    }+    else {+      *prob=*prob*(1-qbt1/(qb[my_iindx[i]-j]/exp(pscore[jindx[j]+i]/kTn)));+      break;+    }+  } while (1);++  /* backtrack in multi-loop */+  {+    FLT_OR_DBL r, qt;+    int k, ii, jj;+    FLT_OR_DBL qttemp=0;;+    i++; j--;+    /* find the first split index */+    ii = my_iindx[i]; /* ii-j=[i,j] */+    jj = jindx[j]; /* jj+i=[j,i] */+    for (qt=0., k=i+1; k<j; k++) qttemp += qm[ii-(k-1)]*qm1[jj+k];+    r = vrna_urn() * qttemp;+    for (qt=0., k=i+1; k<j; k++) {+      qt += qm[ii-(k-1)]*qm1[jj+k];+      if (qt>=r){+        *prob = *prob+                * qm[ii-(k-1)]+                * qm1[jj+k]+                / qttemp;/*qttemp;*/+        /*        prob*=qm[ii-(k-1)]*qm1[jj+k];*/+        break;+      }+    }+    if (k>=j) vrna_message_error("backtrack failed, can't find split index ");++    backtrack_qm1_comparative(vc, pstruc, k, j, prob);++    j = k-1;+    while (j>i) {+      /* now backtrack  [i ... j] in qm[] */+      jj = jindx[j];/*habides??*/+      ii = my_iindx[i];+      r = vrna_urn() * qm[ii - j];+      qt = qm1[jj+i]; k=i;+      if (qt<r)+        for (k=i+1; k<=j; k++) {+          qt += (qm[ii-(k-1)]+expMLbase[k-i]/*n_seq??*/)*qm1[jj+k];+          if (qt >= r) {+            *prob = *prob+                    * (qm[ii-(k-1)] + expMLbase[k-i])+                    * qm1[jj+k]+                    / qm[ii - j];/*???*/+            /*            probs*=qt;*/+            break;+          }+        }+      else {+        *prob = *prob * qt / qm[ii - j];/*??*/+      }+      if (k>j) vrna_message_error("backtrack failed in qm");++      backtrack_qm1_comparative(vc, pstruc, k, j, prob);++      if (k<i+TURN) break; /* no more pairs */+      r = vrna_urn() * (qm[ii-(k-1)] + expMLbase[k-i]);+      if (expMLbase[k-i] >= r) {+        *prob = *prob * expMLbase[k-i] / (qm[ii-(k-1)] + expMLbase[k-i]);+        break; /* no more pairs */+      }+      j = k-1;+      /* whatishere?? */+    }+  }+  free(type);+}++PRIVATE void+backtrack_qm1_comparative(vrna_fold_compound_t *vc,+              char *pstruc,+              int i,+              int j,+              double *prob){++  int               n_seq       = vc->n_seq;+  short             **S         = vc->S;+  short             **S5        = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+  short             **S3        = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+  vrna_exp_param_t  *pf_params  = vc->exp_params;+  vrna_mx_pf_t      *matrices   = vc->exp_matrices;+  vrna_md_t         *md         = &(pf_params->model_details);+  int               *my_iindx   = vc->iindx;+  int               *jindx      = vc->jindx;+  vrna_hc_t         *hc         = vc->hc;+  vrna_sc_t         **sc        = vc->scs;+  FLT_OR_DBL        *qb         = matrices->qb;+  FLT_OR_DBL        *qm1        = matrices->qm1;+  FLT_OR_DBL        *expMLbase    = matrices->expMLbase;++  /* i is paired to l, i<l<j; backtrack in qm1 to find l */+  int ii, l, xtype,s;+  FLT_OR_DBL qt, r, tempz;+  r = vrna_urn() * qm1[jindx[j]+i];+  ii = my_iindx[i];+  for (qt=0., l=i+TURN+1; l<=j; l++) {+    if (qb[ii-l]==0) continue;+    tempz=1.;+    for (s=0; s<n_seq; s++) {+      xtype = md->pair[S[s][i]][S[s][l]];+      if (xtype==0) xtype=7;+      tempz *= exp_E_MLstem(xtype, S5[s][i], S3[s][l], pf_params);+    }+    qt +=  qb[ii-l]*tempz*expMLbase[j-l];+    if (qt>=r) {+      *prob = *prob+              * qb[ii-l]+              * tempz+              * expMLbase[j-l]+              / qm1[jindx[j]+i];+      /* probs*=qb[ii-l]*tempz*expMLbase[j-l];*/+      break;+    }+  }+  if (l>j) vrna_message_error("backtrack failed in qm1");++  backtrack_comparative(vc, pstruc, i, l, prob);+}+
+ C/ViennaRNA/boltzmann_sampling.h view
@@ -0,0 +1,46 @@+#ifndef VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H+#define VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H++#include <ViennaRNA/data_structures.h>++/**+ *  @file boltzmann_sampling.h+ *  @ingroup subopt_and_representatives+ *  @brief Boltzmann Sampling of secondary structures from the ensemble+ *+ *  A.k.a. Stochastic backtracking+ */++/**+ *  @brief Sample a secondary structure of a subsequence from the Boltzmann ensemble according its probability+ *+ *  @ingroup subopt_stochbt+ *  @pre    The fold compound has to be obtained using the #VRNA_OPTION_HYBRID option in vrna_fold_compound()+ *  @pre    vrna_pf() has to be called first to fill the partition function matrices+ *+ *  @param  vc      The fold compound data structure+ *  @param  length  The length of the subsequence to consider (starting with 5' end)+ *  @return         A sampled secondary structure in dot-bracket notation+ */+char    *vrna_pbacktrack5(vrna_fold_compound_t *vc, int length);++/**+ *  @brief Sample a secondary structure (consensus structure) from the Boltzmann ensemble according its probability+ *+ *  @ingroup subopt_stochbt+ *  @pre    The dynamic programming (DP) matrices have to allow for unique multibranch loop decomposition, i.e.+ *          the vrna_md_t.uniq_ML flag has to be non-zero before calling vrna_fold_compound()+ *  @pre    vrna_pf() has to be called first to fill the partition function matrices+ *+ *  @note This function is polymorphic. It accepts #vrna_fold_compound_t of type+ *        #VRNA_FC_TYPE_SINGLE, and #VRNA_FC_TYPE_COMPARATIVE.+ *+ *  @note The function will automagically detect cicular RNAs based on the model_details in exp_params as+ *        provided via the #vrna_fold_compound_t+ *+ *  @param  vc      The fold compound data structure+ *  @return         A sampled secondary structure in dot-bracket notation+ */+char    *vrna_pbacktrack(vrna_fold_compound_t *vc);++#endif
+ C/ViennaRNA/c_plex.c view
@@ -0,0 +1,1194 @@+/*+           compute the duplex structure of two RNA strands,+                allowing only inter-strand base pairs.+         see cofold() for computing hybrid structures without+                             restriction.+                             Ivo Hofacker+                          Vienna RNA package++*/+++/*+  library containing the function used in rnaplex+  the program rnaplex uses the following function+  Lduplexfold: finds high scoring segments+  it stores the end-position of these segments in an array+  and call then for each of these positions the duplexfold function+  which allows one to make backtracking for each of the high scoring position+  It allows one to find suboptimal partially overlapping (depends on a a parameter)+  duplexes between a long RNA and a shorter one.+  Contrarly to RNAduplex, the energy model is not in E~log(N),+  where N is the length of an interial loop but used an affine model,+  where the extension and begin parameter are fitted to the energy+  parameter used by RNAduplex. This allows one to check for duplex between a short RNA(20nt)+  and a long one at the speed of 1Mnt/s. At this speed the whole genome (3Gnt) can be analyzed for one siRNA+  in about 50 minutes.+  The algorithm is based on an idea by Durbin and Eddy:when the alginment reach a value larger than a+  given threshold this value is stored in an array. When the alignment score goes+  then under this threshold, the alignemnent begin from this value, in that way the backtracking allow us+  to find all non-overlapping high-scoring segments.+  For more information check "durbin, biological sequence analysis"+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/ali_plex.h"+#include "ViennaRNA/loop_energies.h"++/* int subopt_sorted=0; */++#define PUBLIC+#define PRIVATE static++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */+#define ARRAY 32          /*array size*/+#define UNIT 100+#define MINPSCORE -2 * UNIT+PRIVATE void  encode_seqs(const char *s1, const char *s2);+PRIVATE short *encode_seq(const char *seq);+/* PRIVATE void  my_encode_seq(const char *s1, const char *s2); */+PRIVATE void  update_dfold_params(void);+/* PRIVATE int   compare(const void *sub1, const void *sub2); */+/* PRIVATE int   compare_XS(const void *sub1, const void *sub2); */+/* PRIVATE duplexT* backtrack(int threshold, const int extension_cost); */+/* static void  print_struct(duplexT const *dup); */++/* PRIVATE int   print_struct(duplexT const *dup); */+/* PRIVATE int   get_rescaled_energy(duplexT const *dup); */++PRIVATE char * backtrack_C(int i, int j, const int extension_cost, const char * structure, int *E);+PRIVATE void   find_max_C(const int *position, const int *position_j, const int delta, const int threshold, const int constthreshold, const int length, const char *s1, const char *s2, const int extension_cost, const int fast, const char* structure);+PRIVATE void   plot_max_C(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast, const char* structure);+++PRIVATE char *   backtrack_CXS(int i, int j, const int** access_s1, const int** access_s2, const char* structure, int *E);+PRIVATE void find_max_CXS(const int *position, const int *position_j,const int delta, const int threshold, const int constthreshold, const int alignment_length, const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast,const char* structure);+PRIVATE void     plot_max_CXS(const int max, const int max_pos, const int max_pos_j, const int alignment_length,const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast, const char* structure);+PRIVATE duplexT duplexfold_C(const char *s1, const char *s2, const int extension_cost, const char* structure);+PRIVATE duplexT duplexfold_CXS(const char *s1, const char *s2,const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold ,const char* structure);+++/*@unused@*/++#define MAXSECTORS      500     /* dimension for a backtrack array */+#define LOCALITY        0.      /* locality parameter for base-pairs */++#define MIN2(A, B)      ((A) < (B) ? (A) : (B))+#define MAX2(A, B)      ((A) > (B) ? (A) : (B))++PRIVATE vrna_param_t *P = NULL;+PRIVATE int   **c = NULL;/*, **in, **bx, **by;*/      /* energy array used in duplexfold */+/* PRIVATE int ****c_XS; */+PRIVATE int  **lc = NULL, **lin = NULL, **lbx = NULL, **lby = NULL, **linx = NULL, **liny = NULL;   /* energy array used in Lduplexfold+                                             this arrays contains only 3 columns+                                             In this way I reduce my memory use and+                                             I can make most of my computation and+                                             accession in the computer cash+                                             which is the main performance boost*/++++/*PRIVATE int last_cell;                    this variable is the last_cell containing+                                            the information about the alignment+                                            useful only if there is an alignment+                                            which extends till the last nucleotide of+                                            the long sequence*/++PRIVATE short  *S1 = NULL, *SS1 = NULL, *S2 = NULL, *SS2 = NULL;/*contains the sequences*/+PRIVATE int   n1,n2;    /* sequence lengths */+PRIVATE int n3, n4; /*sequence length for the duplex*/;+PRIVATE int delay_free=0;+++/*-----------------------------------------------------------------------duplexfold_XS---------------------------------------------------------------------------*/++PRIVATE duplexT duplexfold_CXS(const char *s1, const char *s2, const int **access_s1, const int **access_s2,+                               const int i_pos, const int j_pos, const int threshold, const char* structure) {+  int i, j,p,q,Emin=INF, l_min=0, k_min=0;+  char *struc;+  struc=NULL;+  duplexT mfe;+  vrna_md_t md;+  int bonus=-10000;+  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);++  int *previous_const;+  previous_const=(int *) vrna_alloc(sizeof(int) * (n4+1));+  j=0;+  previous_const[j]=1;+  int prev_temp = 1;+  while(j++<n4){+    if(structure[j-1]=='|'){+      previous_const[j]=prev_temp;+      prev_temp=j;+    }+    else{+      previous_const[j]=prev_temp;+    }+  }++  set_model_details(&md);++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  for (i=0; i<=n3; i++){+    for(j=0;j<=n4;j++){+      c[i][j]=INF;+    }+  }+  encode_seqs(s1, s2);+  int type, type2, type3, E, k,l;+  i=n3-1; j=2;+  type = pair[S1[i]][S2[j]];+  if(!type){+    printf("Error during initialization of the duplex in duplexfold_XS\n");+    mfe.structure=NULL;+    mfe.energy = INF;+    return mfe;+  }+  c[i][j] = P->DuplexInit + (structure[j-1]=='|' ? bonus : 0 ); /* check if first pair is constrained  */+  if(!(structure[j-2] == '|')){+    c[i][j]+=P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]];+  }+  else{+    c[i][j]+=P->dangle3[rtype[type]][SS1[i+1]];+  }+  if (type>2) c[i][j] += P->TerminalAU;+  for (k=i-1; k>0 ; k--) {+    c[k+1][0]=INF;+    for (l=j+1; l<=n4; l++) {+      c[k][l]=INF;+      int bonus_2 = (structure[l-1]=='|'? bonus : 0 ); /* check if position is constrained and prepare bonus accordingly */+      type2 = pair[S1[k]][S2[l]];+      if (!type2) continue;+      for (p=k+1; p< n3 && p<k+MAXLOOP-1; p++){+        for (q = l-1; q >= previous_const[l] && q > 1; q--) {+          if (p-k+l-q-2>MAXLOOP) break;+          type3=pair[S1[p]][S2[q]];+          if(!type3) continue;+          E = E_IntLoop(p-k-1, l-q-1, type2, rtype[type3],SS1[k+1], SS2[l-1], SS1[p-1], SS2[q+1],P) + bonus_2;+          c[k][l] = MIN2(c[k][l], c[p][q]+E);+        }+      }+      E = c[k][l];+      if (type2>2) E += P->TerminalAU;+      E+=access_s1[i-k+1][i_pos]+access_s2[l-1][j_pos+(l-1)-1];+      if (k>1 && l<n4 && !(structure[l]=='|') ){+        E+=P->mismatchExt[type2][SS1[k-1]][SS2[l+1]];+      }+      else if(k>1){+        E += P->dangle5[type2][SS1[k-1]];+      }+      else if(l<n4 && !(structure[l]=='|')){+        E += P->dangle3[type2][SS2[l+1]];+      }+      if (E<Emin) {+        Emin=E; k_min=k; l_min=l;+      }+    }+  }+  free(previous_const);+  if(Emin  > threshold){+    mfe.energy=INF;+    mfe.ddG=INF;+    mfe.structure=NULL;+    for (i=0; i<=n3; i++) free(c[i]);+    free(c);+    free(S1); free(S2); free(SS1); free(SS2);+    return mfe;+  } else{+    struc = backtrack_CXS(k_min, l_min, access_s1, access_s2,structure,&Emin);+  }+++  /* lets take care of the dangles */+  /* find best combination  */+  int dx_5, dx_3, dy_5, dy_3,dGx,dGy,bonus_x;+  dx_5=0; dx_3=0; dy_5=0; dy_3=0;dGx=0;dGy=0;bonus_x=0;+  dGx = access_s1[i-k_min+1][i_pos];dx_3=0; dx_5=0;bonus_x=0;+  dGy = access_s2[l_min-j+1][j_pos + (l_min-1)-1];+  mfe.tb=i_pos -9 - i + k_min -1 -dx_5;+  mfe.te=i_pos -9 -1 + dx_3;+  mfe.qb=j_pos -9 -1 - dy_5;+  mfe.qe=j_pos + l_min -3 -9 + dy_3;+  mfe.ddG=(double) Emin * 0.01;+  mfe.dG1=(double) dGx*0.01 ;+  mfe.dG2=(double) dGy*0.01 ;+  /* mfe.energy += bonus_y + bonus_x; */+  mfe.energy= mfe.ddG - mfe.dG1 - mfe.dG2;++  mfe.structure = struc;+  for (i=0; i<=n3; i++) free(c[i]);+  free(c);+  free(S1); free(S2); free(SS1); free(SS2);+  return mfe;+}+++PRIVATE char *backtrack_CXS (int i, int j, const int **access_s1,const int **access_s2,const char* structure, int *Emin ) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;+  int *previous_const;+  int bonus=-10000;+  previous_const=(int *) vrna_alloc(sizeof(int) * (n4+1));+  int j_temp=0;+  previous_const[j_temp]=1;+  int prev_temp = 1;+  while(j_temp++<n4){+    if(structure[j_temp-1]=='|'){+      previous_const[j_temp]=prev_temp;+      prev_temp=j_temp;+    }+    else{+      previous_const[j_temp]=prev_temp;+    }+  }+  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  i0=i;/*MAX2(i-1,1);*/j0=j;/*MIN2(j+1,n4);*/+  while (i<=n3-1 && j>=2) {+    int bonus_2 = (structure[j-1]== '|'? bonus: 0);+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    type = pair[S1[i]][S2[j]];+    if (!type) vrna_message_error("backtrack failed in fold duplex bli");+    for (k=i+1; k<=n3 && k>i-MAXLOOP-2; k++) {+      for (l=j-1; l >= previous_const[j] && l>=1; l--) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        type2 = pair[S1[k]][S2[l]];+        if (!type2) continue;+        LE = E_IntLoop(k-i-1, j-l-1, type, rtype[type2], SS1[i+1], SS2[j-1], SS1[k-1], SS2[l+1],P) + bonus_2;+        if (E == c[k][l]+LE) {+          *Emin-=bonus_2;+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      if(i<n3 && j>1 && !(structure[j-2]=='|')){+        E -= P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]];+      }+      else if (i<n3){+        E -= P->dangle3[rtype[type]][SS1[i+1]];/* +access_s1[1][i+1]; */+      }+      else if (j>1){+        E -= (!(structure[j-2]=='|') ? P->dangle5[rtype[type]][SS2[j-1]] : 0);/* +access_s2[1][j+1]; */+      }+      if (type>2) E -= P->TerminalAU;++      /* break; */+      if (E != P->DuplexInit + bonus_2)  {+        vrna_message_error("backtrack failed in fold duplex bal");+      } else {+        *Emin-=bonus_2;+        break;+      }+    }+  }+  /* if (i<n3)  i++; */+  /* if (j>1)   j--; */+  struc = (char *) vrna_alloc(i-i0+1+j0-j+1+2);+  for (k=MAX2(i0,1); k<=i; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j; k<=j0; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i0-1,0)); strcat(struc, "&");+  strcat(struc, st2+j-1);+  free(st1); free(st2);free(previous_const);+  return struc;+}+++duplexT** Lduplexfold_CXS(const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int threshold, const int alignment_length, const int delta, const int fast, const char* structure,const int il_a, const int il_b, const int b_a, const int b_b)/* , const int target_dead, const int query_dead) */+{++  int i, j;+  int bopen=b_b;+  int bext=b_a;+  int iopen=il_b;+  int iext_s=2*il_a;/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  /* int temp; */+  int min_j_colonne;+  int max=INF;+  int bonus=-10000;+  int constthreshold=0; /* minimal threshold corresponding to a structure complying to all constraints */+  int maxPenalty[4];+  vrna_md_t   md;++  i=0;+  while(structure[i]!='\0'){+    if(structure[i]=='|') constthreshold+=bonus;+    i++;+  }+  int *position; /* contains the position of the hits with energy > E */+  int *position_j;+  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  position = (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));++  set_model_details(&md);++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)){+    update_dfold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  encode_seqs(s1,s2);++  maxPenalty[0]=(int) -1*P->stack[2][2]/2;+  maxPenalty[1]=(int) -1*P->stack[2][2];+  maxPenalty[2]=(int) -3*P->stack[2][2]/2;+  maxPenalty[3]=(int) -2*P->stack[2][2];++  lc   = (int**) vrna_alloc(sizeof(int *) * 5);+  lin  = (int**) vrna_alloc(sizeof(int *) * 5);+  lbx  = (int**) vrna_alloc(sizeof(int *) * 5);+  lby  = (int**) vrna_alloc(sizeof(int *) * 5);+  linx = (int**) vrna_alloc(sizeof(int *) * 5);+  liny = (int**) vrna_alloc(sizeof(int *) * 5);++  for (i=0; i<=4; i++){+    lc[i]  = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lin[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lbx[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lby[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    linx[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+    liny[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+  }+  for(j=n2;j>=0;j--) {+    lbx[0][j]=lbx[1][j]=lbx[2][j]=lbx[3][j]    = lbx[4][j] =INF;+    lin[0][j]=lin[1][j]=lin[2][j]=lin[3][j]    = lin[4][j] =INF;+    lc[0][j] =lc[1][j] =lc[2][j] = lc[3][j]    =  lc[4][j] =INF;+    lby[0][j]=lby[1][j]=lby[2][j]=lby[3][j]    = lby[4][j] =INF;+    liny[0][j]=liny[1][j]=liny[2][j]=liny[3][j]=liny[4][j]=INF;+    linx[0][j]=linx[1][j]=linx[2][j]=linx[3][j]=linx[4][j]=INF;+  }++  i=10 /*target_dead*/; /* start from 2 (        i=4) because no structure allowed to begin with a single base pair */+  i_length= n1 - 9  /*- target_dead*/ ;+  while(i < i_length) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    int di1,di2,di3,di4;+    di1 = access_s1[5][i]   - access_s1[4][i-1];+    di2 = access_s1[5][i-1] - access_s1[4][i-2] + di1;+    di3 = access_s1[5][i-2] - access_s1[4][i-3] + di2;+    di4 = access_s1[5][i-3] - access_s1[4][i-4] + di3;+    di1=MIN2(di1,maxPenalty[0]);+    di2=MIN2(di2,maxPenalty[1]);+    di3=MIN2(di3,maxPenalty[2]);+    di4=MIN2(di4,maxPenalty[3]);+    j=n2 - 9 /*- query_dead*/; /* start from n2-1 because no structure allow to begin with a single base pair  */+    while (--j > 9/*query_dead - 1*/) {+      /* ----------------------------------------------------------update lin lbx lby matrix */+      int bonus_2 = (structure[j-1]=='|' ? bonus :0 );+      int dj1,dj2,dj3,dj4;+      dj1 = access_s2[5][j+4] - access_s2[4][j+4];+      dj2 = access_s2[5][j+5] - access_s2[4][j+5] + dj1;+      dj3 = access_s2[5][j+6] - access_s2[4][j+6] + dj2;+      dj4 = access_s2[5][j+7] - access_s2[4][j+7] + dj3;+      dj1=MIN2(dj1,maxPenalty[0]);+      dj2=MIN2(dj2,maxPenalty[1]);+      dj3=MIN2(dj3,maxPenalty[2]);+      dj4=MIN2(dj4,maxPenalty[3]);+      int type2, type,temp;+      type  = pair[S1[i]][S2[j]];+      lc[idx][j]= type ? P->DuplexInit + bonus_2 : INF;+      if(!bonus_2){+        type2=pair[S2[j+1]][S1[i-1]];+        lin[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,lin[idx_1][j]+iext_ass + di1);+        lin[idx][j]=MIN2(lin[idx][j],lin[idx][j+1]+iext_ass + dj1);+        lin[idx][j]=MIN2(lin[idx][j],lin[idx_1][j+1]+iext_s + di1 + dj1);+        linx[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,linx[idx_1][j]+iext_ass + di1);+        liny[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,liny[idx][j+1]+iext_ass + dj1);+        type2=pair[S2[j+1]][S1[i]];+        lby[idx][j]=MIN2(lby[idx][j+1]+bext + dj1 ,+                         lc[idx][j+1]+bopen+bext+(type2>2?P->TerminalAU:0)+dj1);+      }+      else{+        lin[idx][j] = lby[idx][j] = linx[idx][j]= liny[idx][j]=INF; /* all loop containing "|" are rejected */+      }+      type2=pair[S2[j]][S1[i-1]];+      lbx[idx][j]=MIN2(lbx[idx_1][j]+bext + di1, lc[idx_1][j]+bopen+bext+(type2>2?P->TerminalAU:0) + di1);+      /* --------------------------------------------------------------- end update recursion */+      if(!type){continue;}+      if(!(structure[j]=='|')){+        lc[idx][j]+=P->mismatchExt[type][SS1[i-1]][SS2[j+1]];+      }+      else{+        lc[idx][j]+=P->dangle5[type][SS1[i-1]];+      }+      lc[idx][j]+=(type>2?P->TerminalAU:0);+      /* type > 2 -> no GC or CG pair */+      /* ------------------------------------------------------------------update c  matrix  */+      /*  Be careful, no lc may come from a region where a "|" is in a loop, avoided in lin = lby = INF ... jedoch fuer klein loops muss man aufpassen .. */+      if((type2=pair[S1[i-1]][S2[j+1]]))+        lc[idx][j]=MIN2(lc[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+di1+dj1, lc[idx][j]); /* 0x0+1x1 */+      if((type2=pair[S1[i-2]][S2[j+1]]))+        lc[idx][j]=MIN2(lc[idx_2][j+1]+E_IntLoop(1,0,type2, rtype[type],SS1[i-1], SS2[j], SS1[i-1], SS2[j+1], P)+di2+dj1,lc[idx][j]);/* 0x1 +1x1 */+      /* kleine loops checks wird in den folgenden if test gemacht. */+      if(!(structure[j]=='|')){+        if((type2=pair[S1[i-1]][S2[j+2]]))+          lc[idx][j]=MIN2(lc[idx_1][j+2]+E_IntLoop(0,1,type2, rtype[type],SS1[i], SS2[j+1], SS1[i-1], SS2[j+1], P)+di1+dj2,lc[idx][j]);/* 1x0 + 1x1 */+        if((type2=pair[S1[i-2]][S2[j+2]]))+          lc[idx][j]=MIN2(lc[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+di2+dj2, lc[idx][j]); /*  1x1 +1x1 */+        if((type2 = pair[S1[i-3]][S2[j+2]]))+          lc[idx][j]=MIN2(lc[idx_3][j+2]+E_IntLoop(2,1,type2, rtype[type],SS1[i-2], SS2[j+1], SS1[i-1], SS2[j+1], P)+di3+dj2, lc[idx][j]); /*  2x1 +1x1 */+        if(!(structure[j+1]=='|')){+          if((type2 = pair[S1[i-3]][S2[j+3]]))+            lc[idx][j]=MIN2(lc[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+di3+dj3,lc[idx][j]);/* 2x2 + 1x1 */+          if((type2 = pair[S1[i-2]][S2[j+3]]))+            lc[idx][j]=MIN2(lc[idx_2][j+3]+E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P)+di2+dj3, lc[idx][j]);/*  1x2 +1x1 */+          if((type2 = pair[S1[i-4]][S2[j+3]]))+            lc[idx][j]=MIN2(lc[idx_4][j+3]+E_IntLoop(3,2,type2, rtype[type],SS1[i-3], SS2[j+2], SS1[i-1], SS2[j+1], P)+di4+dj3, lc[idx][j]);+          if(!(structure[j+2]=='|')){+            if((type2 = pair[S1[i-3]][S2[j+4]]))+              lc[idx][j]=MIN2(lc[idx_3][j+4]+E_IntLoop(2,3,type2, rtype[type],SS1[i-2], SS2[j+3], SS1[i-1], SS2[j+1], P)+di3+dj4, lc[idx][j]);+          }+        }+      }+      /* internal->stack  */+      lc[idx][j]=MIN2(lin[idx_3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+di3+dj3+2*iext_s, lc[idx][j]);+      lc[idx][j]=MIN2(lin[idx_4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di4+dj2, lc[idx][j]);+      lc[idx][j]=MIN2(lin[idx_2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di2+dj4, lc[idx][j]);+      lc[idx][j]=MIN2(linx[idx_3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di3+dj1, lc[idx][j]);+      lc[idx][j]=MIN2(liny[idx_1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+dj3+di1, lc[idx][j]);+      /* bulge -> stack */+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      lc[idx][j]=MIN2(lbx[idx_2][j+1]+di2+dj1+bext+bAU, lc[idx][j]);+      /* min2=by[i][j+1]; */+      lc[idx][j]=MIN2(lby[idx_1][j+2]+di1+dj2+bext+bAU, lc[idx][j]);+      lc[idx][j]+=bonus_2;+      /* if(j<=const5end){ */+      temp=min_colonne;+      min_colonne=MIN2(lc[idx][j]+(type>2?P->TerminalAU:0)++                       (!(structure[j-2]=='|') ?+                        P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]] : P->dangle3[rtype[type]][SS1[i+1]]),+                       min_colonne);+      if(temp>min_colonne){+        min_j_colonne=j;+      }+      /* } */+      /* ---------------------------------------------------------------------end update */+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    i++;+  }+  /* printf("MAX :%d ", max); */+  free(S1); free(S2); free(SS1); free(SS2);+  if(max<threshold+constthreshold){+    find_max_CXS(position, position_j, delta, threshold+constthreshold, constthreshold, alignment_length, s1, s2, access_s1, access_s2, fast, structure);+  }+  if(max<constthreshold){+    plot_max_CXS(max, max_pos, max_pos_j,alignment_length, s1, s2, access_s1, access_s2,fast,structure);+  }+  for (i=0; i<=4; i++) {free(lc[i]);free(lin[i]);free(lbx[i]);free(lby[i]);free(linx[i]);free(liny[i]);}+  /* free(lc[0]);free(lin[0]);free(lbx[0]);free(lby[0]); */+  free(lc);free(lin);free(lbx);free(lby);free(linx);free(liny);+  free(position);+  free(position_j);+  return NULL;+}++PRIVATE void find_max_CXS(const int *position, const int *position_j,const int delta, const int threshold, const int constthreshold, const int alignment_length, const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast, const char* structure){+  int pos=n1-9;+  if(fast==1){+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/100);+        pos=MAX2(10,pos+temp_min-delta);+      }+    }+  }+  else{+    pos=n1-9;+    while( pos-- > 10 ){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min; /* position on i */+        int max_pos_j;+        max_pos_j=position_j[pos+delta]; /* position on j */+        /* int begin_t=MAX2(9, pos-alignment_length); */+        /* int end_t  =MIN2(n1-10, pos); */+        /* int begin_q=MAX2(9, max_pos_j-2); */+        /* int end_q  =MIN2(n2-10, max_pos_j+alignment_length-2); */+        int begin_t=MAX2(9,pos-alignment_length);+        int end_t  =pos;+        int begin_q=max_pos_j-2;+        int end_q  =MIN2(n2-9,max_pos_j+alignment_length-2);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+        char *local_structure = (char*) vrna_alloc(sizeof(char) * ( end_q - begin_q +2));+        strncpy(s3, (s1+begin_t),  end_t - begin_t+1);+        strncpy(s4, (s2+begin_q) , end_q - begin_q+1 );+        strncpy(local_structure, (structure+begin_q), end_q - begin_q +1);+        s3[end_t -begin_t +1 ]='\0';+        s4[end_q -begin_q +1 ]='\0';+        local_structure[end_q - begin_q +1]='\0';+        duplexT test;+        test = duplexfold_CXS(s3,s4,access_s1,access_s2,pos, max_pos_j,threshold,local_structure);+        if(test.energy * 100 < (threshold - constthreshold)){+          int l1=strchr(test.structure, '&')-test.structure;+          int dL = strrchr(structure,'|') - strchr(structure,'|');+          dL+=1;+          if(dL <=  strlen(test.structure)-l1-1){+            printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f)\n", test.structure,+                   test.tb,test.te,test.qb,test.qe, test.ddG, test.energy, test.dG1, test.dG2);+            pos=MAX2(10,pos+temp_min-delta);+          }+        }+        free(s3);free(s4);+        free(test.structure);+        free(local_structure);+      }+    }+  }+}+++PRIVATE void plot_max_CXS(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int ** access_s1, const int ** access_s2, const int fast, const char* structure)+{+  if(fast==1){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n", max_pos-3, max_pos_j, ((double)max)/100);+  }+  else{+    int begin_t=MAX2(9,max_pos-alignment_length);+    int end_t  =max_pos;+    int begin_q=max_pos_j-2;+    int end_q  =MIN2(n2-9,max_pos_j+alignment_length-2);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+    char *local_structure = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+    strncpy(s3, (s1+begin_t),  end_t - begin_t+1);+    strncpy(s4, (s2+begin_q) , end_q - begin_q+1 );+    strncpy(local_structure, (structure+begin_q) , end_q - begin_q +1 );+    s3[end_t -begin_t +1 ]='\0';+    s4[end_q -begin_q +1 ]='\0';+    local_structure[end_q - begin_q +1]='\0';+    duplexT test;+    test = duplexfold_CXS(s3,s4,access_s1,access_s2,max_pos, max_pos_j,INF,local_structure);+    int l1=  strchr(test.structure, '&')-test.structure;+    int dL = strrchr(structure,'|') - strchr(structure,'|');+    dL+=1;+    if(dL<=strlen(test.structure)-l1-1){+      printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f)\n", test.structure,+             test.tb,test.te,test.qb,test.qe, test.ddG, test.energy, test.dG1, test.dG2);+    }+    free(s3);free(s4);free(test.structure);free(local_structure);++  }+}+++/*---------------------------------------------------------duplexfold----------------------------------------------------------------------------------*/+++PRIVATE duplexT duplexfold_C(const char *s1, const char *s2, const int extension_cost, const char* structure ) {+  int i, j, l1, Emin=INF, i_min=0, j_min=0;+  char *struc;+  duplexT mfe;+  vrna_md_t   md;+  int bonus=-10000;+  int *previous_const; /* for each "|" constraint returns the position of the next "|" constraint */++  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  previous_const=(int *) vrna_alloc(sizeof(int) * (n4+1));+  j=n4+1;+  previous_const[j-1]=n4;+  int prev_temp = n4;+  while(--j){+    if(structure[j-1]=='|'){+      previous_const[j-1]=prev_temp;+      prev_temp=j;+    }+    else{+      previous_const[j-1]=prev_temp;+    }+  }+  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  encode_seqs(s1, s2);+  for (i=1; i<=n3; i++) {+    for (j=n4; j>0; j--) {+      int type, type2, E, k,l;+      int bonus_2 = (structure[j-1]=='|'? bonus: 0);+      type = pair[S1[i]][S2[j]];+      c[i][j] = type ? P->DuplexInit +2 * extension_cost + bonus_2: INF;+      if(!type){ continue;}+      if(j<n4 && i>1 && !(structure[j]=='|') ) {+        c[i][j]+=P->mismatchExt[type][SS1[i-1]][SS2[j+1]]+2*extension_cost;+      }+      else if(i>1){+        c[i][j] += P->dangle5[type][SS1[i-1]]+ extension_cost;+      }+      else if(j<n4 && !(structure[j]=='|')){+        c[i][j] += P->dangle3[type][SS2[j+1]]+ extension_cost;+      }+      if (type>2) c[i][j] += P->TerminalAU;+      for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+        for (l=j+1; l<=previous_const[j]; l++) {+          if (i-k+l-j-2>MAXLOOP) break;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          E = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                        SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P)+(i-k+l-j)*extension_cost + bonus_2;+          c[i][j] = MIN2(c[i][j], c[k][l]+E);+        }+      }+      E = c[i][j];+      if(i<n3 && j>1 && !(structure[j-2]=='|')){+        E+= P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]]+2*extension_cost;+      }+      else if (i<n3){+        E += P->dangle3[rtype[type]][SS1[i+1]]+extension_cost;+      }+      else if (j>1 && !(structure[j-2]=='|')){+        E += P->dangle5[rtype[type]][SS2[j-1]]+extension_cost;+      }+      if (type>2) E += P->TerminalAU;++      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      }+    }+  }+  struc = backtrack_C(i_min, j_min, extension_cost,structure,&Emin);+  if (i_min<n3) i_min++;+  if (j_min>1 ) j_min--;+  l1 = strchr(struc, '&')-struc;+  int size;+  size=strlen(struc)-1;+  Emin-= size * (extension_cost);+  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (double) Emin/100.;+  mfe.structure = struc;+  free(previous_const);+  if (!delay_free) {+    for (i=0; i<=n3; i++) free(c[i]);++    free(c);+    free(S1); free(S2); free(SS1); free(SS2);+  }+  return mfe;+}++PRIVATE char *backtrack_C(int i, int j, const int extension_cost, const char* structure, int *Emin) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0, *previous_const;+  char *st1, *st2, *struc;+  int bonus=-10000;+  previous_const=(int *) vrna_alloc(sizeof(int) * (n4+1)); /* encodes the position of the constraints */+  int j_temp=n4+1;+  previous_const[j_temp-1]=n4;+  int prev_temp = n4;+  while(--j_temp){+    if(structure[j_temp-1]=='|'){+      previous_const[j_temp-1]=prev_temp;+      prev_temp=j_temp;+    }+    else{+      previous_const[j_temp-1]=prev_temp;+    }+  }+  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  i0=MIN2(i+1,n3); j0=MAX2(j-1,1);+  while (i>0 && j<=n4) {+    int bonus_2 = (structure[j-1]== '|'? bonus: 0);+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    type = pair[S1[i]][S2[j]];+    if (!type) vrna_message_error("backtrack failed in fold duplex a");+    for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+      for (l=j+1; l<=previous_const[j]; l++) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        type2 = pair[S1[k]][S2[l]];+        if (!type2) continue;+        LE = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                       SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P)+(i-k+l-j)*extension_cost + bonus_2;+        if (E == c[k][l]+LE) {+          *Emin-=bonus_2;+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {++      if (i>1 && j<n4 && !(structure[j]=='|')){+        E -=P->mismatchExt[type][SS1[i-1]][SS2[j+1]]+2*extension_cost;+      }+      else if(i>1){+        E -= P->dangle5[type][SS1[i-1]]+extension_cost;+      }+      else if (j<n4 && !(structure[j]=='|')){+        E -= P->dangle3[type][SS2[j+1]]+ extension_cost;+      }+      /* if (j<n4) E -= P->dangle3[type][SS2[j+1]]+extension_cost; */+      if (type>2) E -= P->TerminalAU;+      if (E != P->DuplexInit+2*extension_cost + bonus_2) {+        vrna_message_error("backtrack failed in fold duplex b");+      } else {+        *Emin-=bonus_2;+        break;+      }+    }+  }+  if (i>1)  i--;+  if (j<n4) j++;++  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&");+  strcat(struc, st2+j0-1);++  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2);+  free(previous_const);+  return struc;+}+++++duplexT ** Lduplexfold_C(const char *s1, const char *s2, const int threshold, const int extension_cost, const int alignment_length, const int delta, const int fast, const char* structure, const int il_a, const int il_b, const int b_a, const int b_b)+{+  /* duplexT test = duplexfold_C(s1, s2, extension_cost,structure); */++  int i, j;+  int bopen=b_b;+  int bext=b_a+extension_cost;+  int iopen=il_b;+  int iext_s=2*(il_a+extension_cost);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a+extension_cost;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j=10;+  int temp;+  int min_j_colonne=11;+  int max=INF;+  int bonus = -10000;+  int constthreshold=0; /* minimal threshold corresponding to a structure complying to all constraints */+  i=0;+  while(structure[i]!='\0'){+    if(structure[i]=='|') constthreshold+=bonus;+    i++;+  }+  /* FOLLOWING NEXT 4 LINE DEFINES AN ARRAY CONTAINING POSITION OF THE SUBOPT IN S1 */+  /* int nsubopt=10;  */ /* total number of subopt */+  int *position; /* contains the position of the hits with energy > E */+  int *position_j;+  /*   int const5end; */ /* position of the 5'most constraint. Only interaction reaching this position are taken into account. */+  /* const5end = strchr(structure,'|') - structure; */+  /* const5end++; */+  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  /* delta_check is the minimal distance allowed for two hits to be accepted */+  /* if both hits are closer, reject the smaller ( in term of position)  hits  */+  position = (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  /* i want to implement a function that, given a position in a long sequence and a small sequence, */+  /* duplexfold them at this position and report the result at the command line */+  /* for this i first need to rewrite backtrack in order to remove the printf functio */+  /* END OF DEFINITION FOR NEEDED SUBOPT DATA  */++  if ((!P) || (fabs(P->temperature - temperature)>1e-6))+  update_dfold_params();++  lc   = (int**) vrna_alloc(sizeof(int *) * 5);+  lin  = (int**) vrna_alloc(sizeof(int *) * 5);+  lbx  = (int**) vrna_alloc(sizeof(int *) * 5);+  lby  = (int**) vrna_alloc(sizeof(int *) * 5);+  linx = (int**) vrna_alloc(sizeof(int *) * 5);+  liny = (int**) vrna_alloc(sizeof(int *) * 5);++  for (i=0; i<=4; i++){+    lc[i]  = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lin[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lbx[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    lby[i] = (int *) vrna_alloc(sizeof(int) * (n2+5));+    linx[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+    liny[i]= (int *) vrna_alloc(sizeof(int) * (n2+5));+  }+  for(j=n2;j>=0;j--) {+    lbx[0][j]=lbx[1][j]=lbx[2][j]=lbx[3][j]    = lbx[4][j] =INF;+    lin[0][j]=lin[1][j]=lin[2][j]=lin[3][j]    = lin[4][j] =INF;+    lc[0][j] =lc[1][j] =lc[2][j] = lc[3][j]    =  lc[4][j] =INF;+    lby[0][j]=lby[1][j]=lby[2][j]=lby[3][j]    = lby[4][j] =INF;+    liny[0][j]=liny[1][j]=liny[2][j]=liny[3][j]=liny[4][j]=INF;+    linx[0][j]=linx[1][j]=linx[2][j]=linx[3][j]=linx[4][j]=INF;+  }+  encode_seqs(s1,s2);+  i=10;+  i_length= n1 - 9 ;+  while(i < i_length) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    j=n2-9;+    while (9 < --j) {+      int bonus_2 = (structure[j-1]=='|' ? bonus : 0) ;+      int type, type2;+      type = pair[S1[i]][S2[j]];+      lc[idx][j]=type ? P->DuplexInit + 2*extension_cost + bonus_2 : INF; /* to avoid that previous value influence result should actually not be erforderlich */+      if(!bonus_2){+        type2=pair[S2[j+1]][S1[i-1]];+        lin[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s, lin[idx_1][j]+iext_ass);+        lin[idx][j]=MIN2(lin[idx][j],lin[idx][j+1]+iext_ass);+        lin[idx][j]=MIN2(lin[idx][j],lin[idx_1][j+1]+iext_s);+        linx[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,linx[idx_1][j]+iext_ass);+        liny[idx][j]=MIN2(lc[idx_1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,liny[idx][j+1]+iext_ass);+        type2=pair[S2[j+1]][S1[i]];+        lby[idx][j]=MIN2(lby[idx][j+1]+bext, lc[idx][j+1]+bopen+bext+(type2>2?P->TerminalAU:0));+      }+      else{+        lin[idx][j] = lby[idx][j] = linx[idx][j]= liny[idx][j]=INF;+      }+      type2=pair[S2[j]][S1[i-1]];+      lbx[idx][j]=MIN2(lbx[idx_1][j]+bext, lc[idx_1][j]+bopen+bext+(type2>2?P->TerminalAU:0));+      /* --------------------------------------------------------------- end update recursion */+      if(!type){continue;}+      if(!(structure[j]=='|')){+        lc[idx][j]+=P->mismatchExt[type][SS1[i-1]][SS2[j+1]]+2*extension_cost;+      }+      else{+        lc[idx][j]+=P->dangle5[type][SS1[i-1]]+extension_cost;+      }+      lc[idx][j]+=(type>2?P->TerminalAU:0);+      /* type > 2 -> no GC or CG pair */+      /* ------------------------------------------------------------------update c  matrix  */+      /*  Be careful, no lc may come from a region where a "|" is in a loop, avoided in lin = lby = INF ... jedoch fuer klein loops muss man aufpassen .. */+      type2=pair[S1[i-1]][S2[j+1]];+      lc[idx][j]=MIN2(lc[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+2*extension_cost, lc[idx][j]);+      type2=pair[S1[i-2]][S2[j+1]];+      lc[idx][j]=MIN2(lc[idx_2][j+1]+E_IntLoop(1,0,type2, rtype[type],SS1[i-1], SS2[j], SS1[i-1], SS2[j+1], P)+3*extension_cost,lc[idx][j]);+      /* kleine loops checks wird in den folgenden if test gemacht. */+      if(!(structure[j]=='|')){+        type2=pair[S1[i-1]][S2[j+2]];+        lc[idx][j]=MIN2(lc[idx_1][j+2]+E_IntLoop(0,1,type2, rtype[type],SS1[i], SS2[j+1], SS1[i-1], SS2[j+1], P)+3*extension_cost,lc[idx][j]);+        type2=pair[S1[i-2]][S2[j+2]];+        lc[idx][j]=MIN2(lc[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+4*extension_cost, lc[idx][j]);+        type2 = pair[S1[i-3]][S2[j+2]];+        lc[idx][j]=MIN2(lc[idx_3][j+2]+E_IntLoop(2,1,type2, rtype[type],SS1[i-2], SS2[j+1], SS1[i-1], SS2[j+1], P)+5*extension_cost, lc[idx][j]);+        if(!(structure[j+1]=='|')){+          type2 = pair[S1[i-3]][S2[j+3]];+          lc[idx][j]=MIN2(lc[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+6*extension_cost,lc[idx][j]);+          type2 = pair[S1[i-2]][S2[j+3]];+          lc[idx][j]=MIN2(lc[idx_2][j+3]+E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P)+5*extension_cost, lc[idx][j]);+          type2 = pair[S1[i-4]][S2[j+3]];+          lc[idx][j]=MIN2(lc[idx_4][j+3]+E_IntLoop(3,2,type2, rtype[type],SS1[i-3], SS2[j+2], SS1[i-1], SS2[j+1], P)+7*extension_cost, lc[idx][j]);+          if(!(structure[j+2]=='|')){+            type2 = pair[S1[i-3]][S2[j+4]];+            lc[idx][j]=MIN2(lc[idx_3][j+4]+E_IntLoop(2,3,type2, rtype[type],SS1[i-2], SS2[j+3], SS1[i-1], SS2[j+1], P)+7*extension_cost, lc[idx][j]);+          }+        }+      }+      /* internal->stack  */+      lc[idx][j]=MIN2(lin[idx_3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*extension_cost+2*iext_s, lc[idx][j]);+      lc[idx][j]=MIN2(lin[idx_4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, lc[idx][j]);+      lc[idx][j]=MIN2(lin[idx_2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, lc[idx][j]);+      lc[idx][j]=MIN2(linx[idx_3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, lc[idx][j]);+      lc[idx][j]=MIN2(liny[idx_1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, lc[idx][j]);+      /* bulge -> stack */+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      lc[idx][j]=MIN2(lbx[idx_2][j+1]+2*extension_cost+bext+bAU, lc[idx][j]);+      /* min2=by[i][j+1]; */+      lc[idx][j]=MIN2(lby[idx_1][j+2]+2*extension_cost+bext+bAU, lc[idx][j]);+      lc[idx][j]+=bonus_2;+      /*       if(j<=const5end){ */+      temp=min_colonne;+      min_colonne=MIN2(lc[idx][j]+(type>2?P->TerminalAU:0)++                       (!(structure[j-2]=='|') ?+                        P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]]+2*extension_cost :+                        P->dangle3[rtype[type]][SS1[i+1]]+extension_cost),+                       min_colonne);+      if(temp>min_colonne){+        min_j_colonne=j;+        /*         } */+      }+      /* ---------------------------------------------------------------------end update       */+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    i++;+  }+  free(S1); free(S2); free(SS1); free(SS2);+  /* printf("MAX: %d",max); */+  if(max<threshold+constthreshold){+    find_max_C(position, position_j, delta, threshold+constthreshold, constthreshold, alignment_length, s1, s2, extension_cost, fast, structure);+  }+  if(max<constthreshold){+    plot_max_C(max, max_pos, max_pos_j,alignment_length, s1, s2, extension_cost,fast,structure);+  }+  for (i=0; i<=4; i++) {free(lc[i]);free(lin[i]);free(lbx[i]);free(lby[i]);free(linx[i]);free(liny[i]);}+  /*  free(lc[0]);free(lin[0]);free(lbx[0]);free(lby[0]); */+  free(lc);free(lin);free(lbx);free(lby);free(linx);free(liny);+  free(position);+  free(position_j);+  return NULL;+}+++PRIVATE void find_max_C(const int *position, const int *position_j,const int delta, const int threshold, const int constthreshold, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast,const char* structure){+  int pos=n1-9;+  if(fast==1){+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/100);+        pos=MAX2(10,pos-delta);+      }+    }+  }+  else{+    pos=n1-9;+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* max_pos_j und pos entsprechen die realen position+           in der erweiterten sequenz.+           pos=1 -> position 1 in the sequence (and not 0 like in C)+           max_pos_j -> position 1 in the sequence ( not 0 like in C)+        */+        int begin_t=MAX2(11, pos-alignment_length+1);+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1);+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length-2);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+        char *local_structure = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+        strncpy(s3, (s1+begin_t-1),  end_t - begin_t +1);+        strncpy(s4, (s2+begin_q-1) , end_q - begin_q +1);+        strncpy(local_structure, (structure+begin_q-1) , end_q - begin_q +1 );+        s3[end_t -begin_t +1 ]='\0';+        s4[end_q -begin_q +1 ]='\0';+        local_structure[end_q - begin_q +1]='\0';+        duplexT test;+        test = duplexfold_C(s3, s4, extension_cost,local_structure);+        if(test.energy * 100 < (threshold-constthreshold)){+          int l1=strchr(test.structure, '&')-test.structure;+          int dL = strrchr(structure,'|') - strchr(structure,'|');+          dL+=1;+          if(dL <=  strlen(test.structure)-l1-1){+            printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure,+                   begin_t-10+test.i-l1,+                   begin_t-10+test.i-1,+                   begin_q-10 + test.j-1 ,+                   (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2,+                   test.energy);+            pos=MAX2(10,pos-delta);+          }+        }+        free(s3);free(s4);+        free(test.structure);+        free(local_structure);+      }+    }+  }+}+PRIVATE void plot_max_C(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast,const char* structure)+{+  if(fast==1){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n", max_pos-10, max_pos_j-10, ((double)max)/100);+  }+  else{+    duplexT test;+    int begin_t=MAX2(11, max_pos-alignment_length+1);+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1);+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length-2);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+    char *local_structure = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+    strncpy(s3, (s1+begin_t-1),  end_t - begin_t + 1);+    strncpy(s4, (s2+begin_q-1) , end_q - begin_q +1 );+    strncpy(local_structure, (structure+begin_q-1) , end_q - begin_q +1 );+    s3[end_t -begin_t +1 ]='\0';+    s4[end_q -begin_q +1 ]='\0';+    local_structure[end_q - begin_q +1]='\0';+    test = duplexfold_C(s3, s4, extension_cost,local_structure);+    int l1=strchr(test.structure, '&')-test.structure;+    int dL = strrchr(structure,'|') - strchr(structure,'|');+    dL+=1;+    if(dL <=  strlen(test.structure)-l1-1){+      printf("%s %3d,%-3d : %3d,%-3d (%5.2f)\n", test.structure,+             begin_t-10+test.i-l1, begin_t-10+test.i-1, begin_q-10 +test.j-1 ,+             (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2  , test.energy);+      free(s3);free(s4);free(test.structure);+    }+    free(local_structure);+  }+}+++PRIVATE void update_dfold_params(void)+{+  vrna_md_t md;+  if(P)+    free(P);+  set_model_details(&md);+  P = vrna_params(&md);+  make_pair_matrix();+}++/*---------------------------------------------------------------------------*/+++PRIVATE void encode_seqs(const char *s1, const char *s2) {+  unsigned int i,l;++  l = strlen(s1);+  S1 = encode_seq(s1);+  SS1= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS1 exists only for the special X K and I bases and energy_set!=0 */++  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS1[i] = alias[S1[i]];   /* for mismatches of nostandard bases */+  }++  l = strlen(s2);+  S2 = encode_seq(s2);+  SS2= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS2 exists only for the special X K and I bases and energy_set!=0 */++  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS2[i] = alias[S2[i]];   /* for mismatches of nostandard bases */+  }+}+++PRIVATE short * encode_seq(const char *sequence) {+  unsigned int i,l;+  short *S;+  l = strlen(sequence);+  S = (short *) vrna_alloc(sizeof(short)*(l+2));+  S[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    S[i]= (short) encode_char(toupper(sequence[i-1]));++  /* for circular folding add first base at position n+1 */+  S[l+1] = S[1];++  return S;+}++
+ C/ViennaRNA/centroid.c view
@@ -0,0 +1,204 @@+/*+                  centroid structure prediction++                  Ivo L Hofacker + Ronny Lorenz+                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/centroid.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC char *+vrna_centroid_from_plist( int length,+                          double *dist,+                          vrna_plist_t *pl){++  /* compute the centroid structure of the ensemble, i.e. the strutcure+     with the minimal average distance to all other structures+     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}+     Thus, the centroid is simply the structure containing all pairs with+     p_ij>0.5 */+  int i;+  char *centroid;++  if (pl==NULL)+    vrna_message_error("vrna_centroid_from_plist@centroid.c: pl==NULL!");++  *dist = 0.;+  centroid = (char *) vrna_alloc((length+1)*sizeof(char));+  for (i=0; i<length; i++) centroid[i]='.';+  for (i=0; pl[i].i>0; i++){+    if ((pl[i].p)>0.5) {+      centroid[pl[i].i-1] = '(';+      centroid[pl[i].j-1] = ')';+      *dist += (1-pl[i].p);+    } else+      *dist += pl[i].p;+  }+  centroid[length] = '\0';+  return centroid;+}++PUBLIC char *+vrna_centroid_from_probs( int length,+                          double *dist,+                          FLT_OR_DBL *probs){++  /* compute the centroid structure of the ensemble, i.e. the strutcure+     with the minimal average distance to all other structures+     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}+     Thus, the centroid is simply the structure containing all pairs with+     p_ij>0.5 */+  int i,j;+  FLT_OR_DBL p;+  char  *centroid;+  int   *index = vrna_idx_row_wise(length);++  if (probs == NULL)+    vrna_message_error("vrna_centroid_from_probs@centroid.c: probs==NULL!");++  *dist = 0.;+  centroid = (char *) vrna_alloc((length+1)*sizeof(char));+  for (i=0; i<length; i++) centroid[i]='.';+  for (i=1; i<=length; i++)+    for (j=i+TURN+1; j<=length; j++) {+      if ((p=probs[index[i]-j])>0.5) {+        centroid[i-1] = '(';+        centroid[j-1] = ')';+        *dist += (1-p);+      } else+        *dist += p;+    }+  free(index);+  centroid[length] = '\0';+  return centroid;+}++PUBLIC char *+vrna_centroid(vrna_fold_compound_t *vc,+             double *dist){++  /* compute the centroid structure of the ensemble, i.e. the strutcure+     with the minimal average distance to all other structures+     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}+     Thus, the centroid is simply the structure containing all pairs with+     p_ij>0.5 */+  int i,j, k, length;+  FLT_OR_DBL p;+  char  *centroid;+  short *S;+  vrna_mx_pf_t      *matrices;+  FLT_OR_DBL        *probs;+  int               *my_iindx;+  vrna_exp_param_t  *pf_params;+++  if(!vc){+    vrna_message_error("vrna_centroid@centroid.c: run vrna_pf_fold first!");+  } else if( !vc->exp_matrices->probs){+    vrna_message_error("vrna_centroid@centroid.c: probs==NULL!");+  }++  length      = vc->length;+  pf_params   = vc->exp_params;+  S           = vc->sequence_encoding2;+  my_iindx    = vc->iindx;++  matrices    = vc->exp_matrices;+  probs       = matrices->probs;++  *dist = 0.;+  centroid = (char *) vrna_alloc((length+1)*sizeof(char));+  for (i=0; i<length; i++) centroid[i]='.';+  for (i=1; i<=length; i++)+    for (j=i+TURN+1; j<=length; j++) {+      if ((p=probs[my_iindx[i]-j])>0.5) {+        if(pf_params->model_details.gquad){+          /* check for presence of gquadruplex */+          if((S[i] == 3) && (S[j] == 3)){+            int L, l[3];+            get_gquad_pattern_pf(S, i, j, pf_params, &L, l);+            for(k=0;k<L;k++){+              centroid[i+k-1]\+              = centroid[i+k+L+l[0]-1]\+              = centroid[i+k+2*L+l[0]+l[1]-1]\+              = centroid[i+k+3*L+l[0]+l[1]+l[2]-1]\+              = '+';+            }+            /* skip everything within the gquad */+            i = j; j = j+TURN+1;+            *dist += (1-p); /* right? */+            break;+          }+        }+        /* regular base pair */+        centroid[i-1] = '(';+        centroid[j-1] = ')';+        *dist += (1-p);+      } else+        *dist += p;+    }++  centroid[length] = '\0';+  return centroid;+}+++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/+++/* this function is a threadsafe replacement for centroid() */+PUBLIC char *+get_centroid_struct_pl( int length,+                        double *dist,+                        vrna_plist_t *pl){++  return vrna_centroid_from_plist(length, dist, pl);+}++/* this function is a threadsafe replacement for centroid() */+PUBLIC char *+get_centroid_struct_pr( int length,+                        double *dist,+                        FLT_OR_DBL *probs){++  return vrna_centroid_from_probs(length, dist, probs);+}+
+ C/ViennaRNA/centroid.h view
@@ -0,0 +1,103 @@+#ifndef VIENNA_RNA_PACKAGE_CENTROID_H+#define VIENNA_RNA_PACKAGE_CENTROID_H++#include <ViennaRNA/data_structures.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file   centroid.h+ *  @ingroup subopt_and_representatives+ *  @brief  Centroid structure computation+ */++/**+ *  @brief Get the centroid structure of the ensemble+ * + *  The centroid is the structure with the minimal average distance to all other structures+ *  \n @f$ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} @f$ \n+ *  Thus, the centroid is simply the structure containing all pairs with @f$p_ij>0.5@f$+ *  The distance of the centroid to the ensemble is written to the memory adressed by @a dist.+ * + *  @ingroup              centroid_fold+ *  @param[in]    vc      The fold compound data structure+ *  @param[out]   dist    A pointer to the distance variable where the centroid distance will be written to+ *  @return               The centroid structure of the ensemble in dot-bracket notation+ */+char *vrna_centroid(vrna_fold_compound_t *vc,+                    double *dist);++/**+ *  @brief Get the centroid structure of the ensemble+ * + *  This function is a threadsafe replacement for @ref centroid() with a #vrna_plist_t input+ * + *  The centroid is the structure with the minimal average distance to all other structures+ *  \n @f$ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} @f$ \n+ *  Thus, the centroid is simply the structure containing all pairs with @f$p_ij>0.5@f$+ *  The distance of the centroid to the ensemble is written to the memory adressed by @a dist.+ *+ *  @ingroup            centroid_fold+ *  @param[in]  length  The length of the sequence+ *  @param[out] dist    A pointer to the distance variable where the centroid distance will be written to+ *  @param[in]  pl      A pair list containing base pair probability information about the ensemble+ *  @return             The centroid structure of the ensemble in dot-bracket notation+ */+char  *vrna_centroid_from_plist(int length,+                                double *dist,+                                vrna_plist_t *pl);++/**+ *  @brief Get the centroid structure of the ensemble+ * + *  This function is a threadsafe replacement for @ref centroid() with a probability array input+ * + *  The centroid is the structure with the minimal average distance to all other structures+ *  \n @f$ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} @f$ \n+ *  Thus, the centroid is simply the structure containing all pairs with @f$p_ij>0.5@f$+ *  The distance of the centroid to the ensemble is written to the memory adressed by @a dist.+ * + *  @ingroup              centroid_fold+ *  @param[in]    length  The length of the sequence+ *  @param[out]   dist    A pointer to the distance variable where the centroid distance will be written to+ *  @param[in]    probs   An upper triangular matrix containing base pair probabilities (access via iindx @ref vrna_idx_row_wise() )+ *  @return               The centroid structure of the ensemble in dot-bracket notation+ */+char  *vrna_centroid_from_probs(int length,+                                double *dist,+                                FLT_OR_DBL *probs);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Get the centroid structure of the ensemble+ *+ *  @deprecated This function was renamed to vrna_centroid_from_plist()+ */+DEPRECATED(char  *get_centroid_struct_pl(int length,+                              double *dist,+                              vrna_plist_t *pl));++/**+ *  @brief Get the centroid structure of the ensemble+ *+ *  @deprecated This function was renamed to vrna_centroid_from_probs()+ */+DEPRECATED(char  *get_centroid_struct_pr(int length,+                              double *dist,+                              FLT_OR_DBL *pr));++#endif++#endif
+ C/ViennaRNA/circfold.inc view
@@ -0,0 +1,246 @@+/* -*-C-*- */+/* this file contains code for folding circular RNAs */+/* it's #include'd into fold.c */++PRIVATE void+fill_arrays_circ( vrna_fold_compound_t *vc,+                  sect bt_stack[],+                  int *bt){++  /* variant of fold() for circular RNAs */+  /* auxiliarry arrays:+     fM2 = multiloop region with exactly two stems, extending to 3' end+     for stupid dangles=1 case we also need:+     fM_d3 = multiloop region with >= 2 stems, starting at pos 2+             (a pair (k,n) will form 3' dangle with pos 1)+     fM_d5 = multiloop region with >= 2 stems, extending to pos n-1+             (a pair (1,k) will form a 5' dangle with pos n)+  */+  int               Hi, Hj, Ii, Ij, Ip, Iq, ip, iq, Mi;+  int               *fM_d3, *fM_d5, Md3i, Md5i, FcMd3, FcMd5;+  int               FcH, FcI, FcM, Fc, *fM2;+  int               i,j, ij, u, length, new_c, fm, type;+  int               *my_c, *my_fML, *indx, dangle_model, turn;+  vrna_param_t      *P;+  char              *ptype, *hard_constraints;+  short             *S1;+  vrna_hc_t         *hc;+  vrna_sc_t         *sc;++  P                 = vc->params;+  ptype             = vc->ptype;+  indx              = vc->jindx;+  S1                = vc->sequence_encoding;++  dangle_model      = P->model_details.dangles;+  turn              = P->model_details.min_loop_size;++  hc                = vc->hc;+  sc                = vc->sc;+  hard_constraints  = hc->matrix;++  my_c              = vc->matrices->c;+  my_fML            = vc->matrices->fML;+  fM2               = vc->matrices->fM2;++  length            = vc->length;++  FcH = FcI = FcM = FcMd3 = FcMd5 = INF;++  if(hc->up_ext[1] >= length){+    Fc = 0;+    if(sc){+      if(sc->energy_up)+        Fc += sc->energy_up[1][length];+    }+  } else {+    Fc = INF;+  }++  for(i = 1; i < length; i++)+    for(j = i + turn + 1; j <= length; j++){+      u = length-j + i-1;+      if (u<TURN) continue;++      ij = indx[j] + i;++      if (!hard_constraints[ij])+        continue;++      /* exterior hairpin case */+      new_c =   vrna_E_hp_loop(vc, j, i)+              + my_c[ij];++      if (new_c<FcH) {+        FcH = new_c;+        Hi  = i;+        Hj  = j;+      }++      /* exterior interior loop case */+      ip = iq = 0;+      new_c =   vrna_E_ext_int_loop(vc, i, j, &ip, &iq)+              + my_c[ij];++      if(ip != 0){+        if(new_c < FcI){+          FcI = new_c;+          Ii  = i;+          Ij  = j;+          Ip  = ip;+          Iq  = iq;+        }+      }+    } /* end of i,j loop */+  Fc = MIN2(Fc, FcH);+  Fc = MIN2(Fc, FcI);+  /* compute the fM2 array (multi loops with exactly 2 helices) */+  /* to get a unique ML decomposition, just use fM1 instead of fML+     below. However, that will not work with dangle_model==1  */+  for (i=1; i<length-TURN; i++) {+    fM2[i] = INF;+    for (u=i+TURN; u<length-TURN; u++)+      fM2[i] = MIN2(fM2[i], my_fML[indx[u]+i] + my_fML[indx[length]+u+1]);+  }++  for (i=TURN+1; i<length-2*TURN; i++) {+    fm = my_fML[indx[i]+1]+fM2[i+1]+P->MLclosing;+    if (fm<FcM) {+      FcM=fm; Mi=i;+    }+  }+  Fc = MIN2(Fc, FcM);++  if ((dangle_model == 1) || (dangle_model == 3)){+    fM_d3 =  (int *) vrna_alloc(sizeof(int)*(length+2));+    fM_d5 =  (int *) vrna_alloc(sizeof(int)*(length+2));++    for (i=TURN+1; i<length-TURN; i++) {+      fM_d3[i] = INF;+      for (u=2+TURN; u<i-TURN; u++)+        fM_d3[i] = MIN2(fM_d3[i], my_fML[indx[u]+2] + my_fML[indx[i]+u+1]);+    }++    for (i=2*TURN+1; i<length-TURN; i++) {+      type = ptype[indx[length]+i+1];+      if(hard_constraints[indx[length] + i + 1] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+        if(hc->up_ml[1]){+          fm = fM_d3[i]+my_c[indx[length]+i+1]+E_MLstem(type, -1, S1[1], P) + P->MLclosing;+          if (fm<FcMd3) {+            FcMd3=fm; Md3i=i;+          }++          if(hc->up_ml[i]){+            fm = fM_d3[i-1]+my_c[indx[length]+i+1]+E_MLstem(type, S1[i], S1[1], P) + P->MLclosing;+            if (fm<FcMd3) {+              FcMd3=fm; Md3i=-i;+            }+          }+        }+      }+    }++    for (i=TURN+1; i<length-TURN; i++) {+      fM_d5[i] = INF;+      for (u=i+TURN; u<length-TURN; u++)+        fM_d5[i] = MIN2(fM_d5[i], my_fML[indx[u]+i] + my_fML[indx[length-1]+u+1]);+    }++    for (i=TURN+1; i<length-2*TURN; i++) {+      if(hard_constraints[indx[i]+1] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+        type = ptype[indx[i]+1];+        if(hc->up_ml[length]){+          fm = E_MLstem(type, S1[length], -1, P) + my_c[indx[i]+1] + fM_d5[i+1] + P->MLclosing;+          if (fm<FcMd5) {+            FcMd5=fm; Md5i=i;+          }+          if(hc->up_ml[i+1]){+            fm = E_MLstem(type, S1[length], S1[i+1], P) + my_c[indx[i]+1] + fM_d5[i+2] + P->MLclosing;+            if (fm<FcMd5) {+              FcMd5=fm; Md5i=-i;+            }+          }+        }+      }+    }++    if (FcMd5<MIN2(Fc,FcMd3)) {+      /* looks like we have to do this ... */+      bt_stack[++(*bt)].i = 1;+      bt_stack[(*bt)].j = (Md5i>0)?Md5i:-Md5i;+      bt_stack[(*bt)].ml = 2;+      i = (Md5i>0)?Md5i+1 : -Md5i+2; /* let's backtrack fm_d5[Md5i+1] */+      for (u=i+TURN; u<length-TURN; u++)+        if (fM_d5[i] == my_fML[indx[u]+i] + my_fML[indx[length-1]+u+1]) {+          bt_stack[++(*bt)].i = i;+          bt_stack[(*bt)].j = u;+          bt_stack[(*bt)].ml = 1;+          bt_stack[++(*bt)].i =u+1;+          bt_stack[(*bt)].j = length-1;+          bt_stack[(*bt)].ml = 1;+          break;+        }+      Fc = FcMd5;+    } else if (FcMd3<Fc) {+      /* here we go again... */+      bt_stack[++(*bt)].i = (Md3i>0)?Md3i+1:-Md3i+1;+      bt_stack[(*bt)].j = length;+      bt_stack[(*bt)].ml = 2;+      i = (Md3i>0)? Md3i : -Md3i-1; /* let's backtrack fm_d3[Md3i] */+      for (u=2+TURN; u<i-TURN; u++)+        if (fM_d3[i] == my_fML[indx[u]+2] + my_fML[indx[i]+u+1]) {+          bt_stack[++(*bt)].i = 2;+          bt_stack[(*bt)].j = u;+          bt_stack[(*bt)].ml = 1;+          bt_stack[++(*bt)].i =u+1;+          bt_stack[(*bt)].j = i;+          bt_stack[(*bt)].ml = 1;+          break;+        }+      Fc = FcMd3;+    }+    free(fM_d3);+    free(fM_d5);+  }+  else if(Fc < 0){+    if (FcH==Fc) {+      bt_stack[++(*bt)].i = Hi;+      bt_stack[(*bt)].j = Hj;+      bt_stack[(*bt)].ml = 2;+    }+    else if (FcI==Fc) {+      bt_stack[++(*bt)].i = Ii;+      bt_stack[(*bt)].j = Ij;+      bt_stack[(*bt)].ml = 2;+      bt_stack[++(*bt)].i = Ip;+      bt_stack[(*bt)].j = Iq;+      bt_stack[(*bt)].ml = 2;+    }+    else if (FcM==Fc) { /* grumpf we found a Multiloop */+      /* backtrack in fM2 */+      fm = fM2[Mi+1];+      for (u=Mi+TURN+1; u<length-TURN; u++)+        if (fm == my_fML[indx[u]+Mi+1] + my_fML[indx[length]+u+1]) {+                bt_stack[++(*bt)].i=Mi+1;+                bt_stack[(*bt)].j=u;+                bt_stack[(*bt)].ml = 1;+                bt_stack[++(*bt)].i=u+1;+                bt_stack[(*bt)].j=length;+                bt_stack[(*bt)].ml = 1;+                break;+        }+      bt_stack[++(*bt)].i = 1;+      bt_stack[(*bt)].j = Mi;+      bt_stack[(*bt)].ml = 1;+    }+  } else { /* unstructured */+    bt_stack[++(*bt)].i = 1;+    bt_stack[(*bt)].j = 1;+    bt_stack[(*bt)].ml = 0;+  }+  vc->matrices->FcH = FcH;+  vc->matrices->FcI = FcI;+  vc->matrices->FcM = FcM;+  vc->matrices->Fc  = Fc;+}+
+ C/ViennaRNA/cofold.c view
@@ -0,0 +1,1222 @@+/*+                  minimum free energy+                  RNA secondary structure prediction++                  c Ivo Hofacker, Chrisoph Flamm+                  original implementation by+                  Walter Fontana++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/subopt.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/cofold.h"++#ifdef  VRNA_BACKWARD_COMPAT++#ifdef _OPENMP+#include <omp.h>+#endif++#endif++#define MAXSECTORS        500     /* dimension for a backtrack array */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++/* some backward compatibility stuff */+PRIVATE int                 backward_compat           = 0;+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;++PRIVATE float   mfe1, mfe2;       /* minimum free energies of the monomers */++#ifdef _OPENMP++#pragma omp threadprivate(mfe1, mfe2, backward_compat_compound, backward_compat)++#endif++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE void  backtrack(sect bt_stack[], vrna_bp_stack_t *bp_list, vrna_fold_compound_t *vc);+PRIVATE int   fill_arrays(vrna_fold_compound_t *vc, int zuker);+PRIVATE void  free_end(int *array, int i, int start, vrna_fold_compound_t *vc);+PRIVATE void  doubleseq(vrna_fold_compound_t *vc);  /* do magic */+PRIVATE void  halfseq(vrna_fold_compound_t *vc);    /* undo magic */++#ifdef  VRNA_BACKWARD_COMPAT++/* wrappers for old API compatibility */+PRIVATE void      wrap_array_export(int **f5_p,int **c_p,int **fML_p,int **fM1_p,int **fc_p,int **indx_p,char **ptype_p);+PRIVATE float     wrap_cofold(const char *string,char *structure,vrna_param_t *parameters,int is_constrained);+PRIVATE SOLUTION *wrap_zukersubopt( const char *string,vrna_param_t *parameters);++#endif++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_cofold(const char *seq,+            char *structure){++  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.min_loop_size = 0;  /* set min loop length to 0 */++  /* get compound structure */+  vc = vrna_fold_compound(seq, &md, 0);++  mfe = vrna_mfe_dimer(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;+}++PUBLIC float+vrna_mfe_dimer( vrna_fold_compound_t  *vc,+                char                  *structure){++  int     length, energy;+  char    *s;+  sect    bt_stack[MAXSECTORS]; /* stack of partial structures for backtracking */+  vrna_bp_stack_t   *bp;++  length = (int) vc->length;++  vc->sequence_encoding[0] = vc->sequence_encoding2[0]; /* store length at pos. 0 in S1 too */++  if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_MFE | VRNA_OPTION_HYBRID)){+    vrna_message_warning("vrna_mfe_dimer@cofold.c: Failed to prepare vrna_fold_compound");+    return (float)(INF/100.);+  }++  /* call user-defined recursion status callback function */+  if(vc->stat_cb)+    vc->stat_cb(VRNA_STATUS_MFE_PRE, vc->auxdata);++  energy = fill_arrays(vc, 0);++  /* call user-defined recursion status callback function */+  if(vc->stat_cb)+    vc->stat_cb(VRNA_STATUS_MFE_POST, vc->auxdata);++  if(structure && vc->params->model_details.backtrack){+    bp = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4*(1+length/2))); /* add a guess of how many G's may be involved in a G quadruplex */++    backtrack(bt_stack, bp, vc);++    s = vrna_db_from_bp_stack(bp, length);+    strncpy(structure, s, length + 1);+    free(s);+    free(bp);+  }++  if (vc->params->model_details.backtrack_type=='C')+    return (float) vc->matrices->c[vc->jindx[length]+1]/100.;+  else if (vc->params->model_details.backtrack_type=='M')+    return (float) vc->matrices->fML[vc->jindx[length]+1]/100.;+  else+    return (float) energy/100.;+}++PRIVATE int+fill_arrays(vrna_fold_compound_t  *vc,+            int                 zuker){++  /* fill "c", "fML" and "f5" arrays and return  optimal energy */++  unsigned int  *sn;+  int   i, j, length, energy;+  int   cp, uniq_ML;+  int   no_close, type, maxj, *indx;+  int   *my_f5, *my_c, *my_fML, *my_fM1, *my_fc;+  int   *cc, *cc1;  /* auxilary arrays for canonical structures     */+  int   *Fmi;       /* holds row i of fML (avoids jumps in memory)  */+  int   *DMLi;      /* DMLi[j] holds  MIN(fML[i,k]+fML[k+1,j])      */+  int   *DMLi1;     /*                MIN(fML[i+1,k]+fML[k+1,j])    */+  int   *DMLi2;     /*                MIN(fML[i+2,k]+fML[k+1,j])    */++  int   dangle_model, noGUclosure, noLP, hc_decompose, turn;+  char              *ptype, *hard_constraints;+  vrna_param_t      *P;+  vrna_mx_mfe_t     *matrices;+  vrna_hc_t         *hc;++  length            = (int)vc->length;+  ptype             = vc->ptype;+  indx              = vc->jindx;+  P                 = vc->params;+  dangle_model      = P->model_details.dangles;+  noGUclosure       = P->model_details.noGUclosure;+  noLP              = P->model_details.noLP;+  uniq_ML           = P->model_details.uniq_ML;+  sn                = vc->strand_number;+  hc                = vc->hc;+  hard_constraints  = hc->matrix;+  matrices          = vc->matrices;+  my_f5             = matrices->f5;+  my_c              = matrices->c;+  my_fML            = matrices->fML;+  my_fM1            = matrices->fM1;+  my_fc             = matrices->fc;+  cp                = vc->cutpoint;+  turn              = P->model_details.min_loop_size;++  /* allocate memory for all helper arrays */+  cc    = (int *) vrna_alloc(sizeof(int)*(length + 2));+  cc1   = (int *) vrna_alloc(sizeof(int)*(length + 2));+  Fmi   = (int *) vrna_alloc(sizeof(int)*(length + 1));+  DMLi  = (int *) vrna_alloc(sizeof(int)*(length + 1));+  DMLi1 = (int *) vrna_alloc(sizeof(int)*(length + 1));+  DMLi2 = (int *) vrna_alloc(sizeof(int)*(length + 1));+++  /* hard code min_loop_size to 0, since we can not be sure yet that this is already the case */+  turn = 0;++  for (j=1; j<=length; j++) {+    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;+    my_fc[j]=0;+  }++  for (j = 1; j<=length; j++)+    for (i=1; i<=j; i++) {+      my_c[indx[j]+i] = my_fML[indx[j]+i] = INF;+      if (uniq_ML) my_fM1[indx[j]+i] = INF;+    }++  for (i = length-turn-1; i >= 1; i--) { /* i,j in [1..length] */++    maxj=(zuker)? (MIN2(i+cp-1,length)):length;+    for (j = i+turn+1; j <= maxj; j++) {+      int ij;+      ij            = indx[j]+i;+      type          = (unsigned char)ptype[ij];+      hc_decompose  = hard_constraints[ij];+      energy        = INF;++      no_close = (((type==3)||(type==4))&&noGUclosure);++      if (hc_decompose) {   /* we have a pair */+        int new_c = INF;++        if(!no_close){+          /* check for hairpin loop */+          energy  = vrna_E_hp_loop(vc, i, j);+          new_c   = MIN2(new_c, energy);++          /* check for multibranch loops */+          energy  = vrna_E_mb_loop_fast(vc, i, j, DMLi1, DMLi2);+          new_c   = MIN2(new_c, energy);+        }++        if (dangle_model==3) { /* coaxial stacking */+          energy  = E_mb_loop_stack(i, j, vc);+          new_c   = MIN2(new_c, energy);+        }++        /* check for interior loops */+        energy = vrna_E_int_loop(vc, i, j);+        new_c = MIN2(new_c, energy);++        /* remember stack energy for --noLP option */+        if(noLP){+          if ((sn[i] == sn[i + 1]) && (sn[j - 1] == sn[j])) {+            int stackEnergy = vrna_E_stack(vc, i, j);+            new_c = MIN2(new_c, cc1[j-1]+stackEnergy);+            my_c[ij] = cc1[j-1]+stackEnergy;+          } else { /* currently we don't allow stacking over the cut point */+            my_c[ij] = FORBIDDEN;+          }+          cc[j] = new_c;+        } else {+          my_c[ij] = new_c;+        }+      } /* end >> if (pair) << */++      else my_c[ij] = INF;++      /* done with c[i,j], now compute fML[i,j] */+      /* free ends ? -----------------------------------------*/++      my_fML[ij] = vrna_E_ml_stems_fast(vc, i, j, Fmi, DMLi);++      if(uniq_ML){  /* compute fM1 for unique decomposition */+        my_fM1[ij] = E_ml_rightmost_stem(i, j, vc);+      }++    }++    if (i==cp)+      for (j=i; j<=maxj; j++)+        free_end(my_fc, j, cp, vc);+    if (i<cp)+      free_end(my_fc,i,cp-1, vc);+++    {+      int *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=1; j<=maxj; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+    }+  }++  /* calculate energies of 5' and 3' fragments */++  for (i=1; i<=length; i++)+    free_end(my_f5, i, 1, vc);++  if (cp>0) {+    mfe1  = my_f5[cp-1];+    mfe2  = my_fc[length];+    /* add DuplexInit, check whether duplex*/+    for (i=cp; i<=length; i++) {+      my_f5[i] = MIN2(my_f5[i]+P->DuplexInit, my_fc[i]+my_fc[1]);+    }+  }++  energy = my_f5[length];+  if (cp<1) mfe1=mfe2=energy;++  /* clean up memory */+  free(cc);+  free(cc1);+  free(Fmi);+  free(DMLi);+  free(DMLi1);+  free(DMLi2);++  return energy;+}++PRIVATE void+backtrack_co( sect bt_stack[],+              vrna_bp_stack_t *bp_list,+              int s,+              int b, /* b=0: start new structure, b \ne 0: add to existing structure */+              vrna_fold_compound_t *vc) {++  /*------------------------------------------------------------------+    trace back through the "c", "fc", "f5" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This is fast, since only few structure elements are recalculated.+    ------------------------------------------------------------------*/++  int   i, j, ij, k, length, energy, en, new, ml0, ml5, ml3, ml53, no_close, type, type_2, tt;+  char  *string         = vc->sequence;+  vrna_param_t  *P      = vc->params;+  int     *indx         = vc->jindx;+  char    *ptype        = vc->ptype;++  short *S1             = vc->sequence_encoding;+  short *S              = vc->sequence_encoding2;+  int   dangle_model    = P->model_details.dangles;+  int   noLP            = P->model_details.noLP;+  int   noGUclosure     = P->model_details.noGUclosure;+  int   with_gquad      = P->model_details.gquad;+  int   turn            = P->model_details.min_loop_size;+  int   *rtype          = &(P->model_details.rtype[0]);+  char  backtrack_type  = P->model_details.backtrack_type;+  int   cp              = vc->cutpoint;+  vrna_hc_t  *hc        = vc->hc;+  vrna_sc_t  *sc        = vc->sc;+  char      *hard_constraints  = hc->matrix;++  /* the folding matrices */+  int   *my_f5, *my_c, *my_fML, *my_fc, *my_ggg;++  length  = vc->length;+  my_f5   = vc->matrices->f5;+  my_c    = vc->matrices->c;+  my_fML  = vc->matrices->fML;+  my_fc   = vc->matrices->fc;+  my_ggg  = vc->matrices->ggg;++  /* int   b=0;*/++  /* hard code min_loop_size to 0, since we can not be sure yet that this is already the case */+  turn = 0;++  length = strlen(string);+  if (s==0) {+    bt_stack[++s].i = 1;+    bt_stack[s].j   = length;+    bt_stack[s].ml  = (backtrack_type=='M') ? 1 : ((backtrack_type=='C')?2:0);+  }+  while (s>0) {+    int ml, fij, fi, cij, traced, i1, j1, mm, p, q, jj=0, gq=0;+    int canonical = 1;     /* (i,j) closes a canonical structure */++    /* pop one element from stack */+    i  = bt_stack[s].i;+    j  = bt_stack[s].j;+    ml = bt_stack[s--].ml;++    switch(ml){+      /* backtrack in f5 */+      case 0: {+                int p, q;+                if(vrna_BT_ext_loop_f5(vc, &j, &p, &q, bp_list, &b)){+                  if(j > 0){+                    bt_stack[++s].i = 1;+                    bt_stack[s].j   = j;+                    bt_stack[s].ml  = 0;+                  }+                  if(p > 0){+                    i = p;+                    j = q;+                    goto repeat1;+                  }++                  continue;+                } else {+                  vrna_message_error("backtrack failed in f5\n%s", string);+                }+              }+              break;++      /* true multi-loop backtrack in fML */+      case 1: {+                int p, q, comp1, comp2;+                if(vrna_BT_mb_loop_split(vc, &i, &j, &p, &q, &comp1, &comp2, bp_list, &b)){+                  if(i > 0){+                    bt_stack[++s].i = i;+                    bt_stack[s].j   = j;+                    bt_stack[s].ml  = comp1;+                  }+                  if(p > 0){+                    bt_stack[++s].i = p;+                    bt_stack[s].j   = q;+                    bt_stack[s].ml  = comp2;+                  }++                  continue;+                } else {+                  vrna_message_error("backtrack failed in fML\n%s", string);+                }+              }+              break;++      case 2: bp_list[++b].i = i;+              bp_list[b].j   = j;+              goto repeat1;++      /* backtrack fake-multi loop parts */+      case 3: case 4:+              {+                int lower, k, p, q;+                p = i;+                q = j;+                lower = (i < cp) ? 1 : 0;++                if(vrna_BT_mb_loop_fake(vc, &k, &i, &j, bp_list, &b)){+                  if(k > 0){+                    bt_stack[++s].i = (lower) ? k : p;+                    bt_stack[s].j   = (lower) ? q : k;+                    bt_stack[s].ml  = ml;+                  }+                  if(i > 0){+                    goto repeat1;+                  }++                  continue;+                } else {+                  vrna_message_error("backtrack failed in fc\n%s", string);+                }+              }+              break;+    } /* end of switch(ml) */++  repeat1:++    /*----- begin of "repeat:" -----*/+    ij = indx[j]+i;++    if (canonical)+      cij = my_c[ij];++    type = ptype[ij];++    if (noLP)+      if(vrna_BT_stack(vc, &i, &j, &cij, bp_list, &b)){+        canonical = 0;+        goto repeat1;+    }++    canonical = 1;++    no_close = (((type==3)||(type==4))&&noGUclosure);+    if (no_close) {+      if (cij == FORBIDDEN) continue;+    } else {+      if(vrna_BT_hp_loop(vc, i, j, cij, bp_list, &b))+        continue;+    }++    if(vrna_BT_int_loop(vc, &i, &j, cij, bp_list, &b)){+      if(i < 0)+        continue;+      else+        goto repeat1;+    }++    /* (i.j) must close a fake or true multi-loop */+    int comp1, comp2;++    if(vrna_BT_mb_loop(vc, &i, &j, &k, cij, &comp1, &comp2)){+      bt_stack[++s].i = i;+      bt_stack[s].j   = k;+      bt_stack[s].ml  = comp1;+      bt_stack[++s].i = k + 1;+      bt_stack[s].j   = j;+      bt_stack[s].ml  = comp2;+    } else {+      vrna_message_error("backtracking failed in repeat");+    }++    /* end of repeat: --------------------------------------------------*/++  } /* end >> while (s>0) << */++  bp_list[0].i = b;    /* save the total number of base pairs */+}++PRIVATE void+free_end( int *array,+          int i,+          int start,+          vrna_fold_compound_t *vc){++  unsigned int  *sn;+  int inc, type, energy, en, length, j, left, right, cp, dangle_model, with_gquad, *indx, *c, *ggg, turn;+  vrna_param_t  *P;+  short         *S1;+  char          *ptype, *hard_constraints;+  vrna_mx_mfe_t *matrices;+  vrna_hc_t     *hc;+  vrna_sc_t     *sc;++  cp            = vc->cutpoint;+  P             = vc->params;+  dangle_model  = P->model_details.dangles;+  with_gquad    = P->model_details.gquad;+  turn          = P->model_details.min_loop_size;+  inc           = (i>start)? 1:-1;+  length        = (int)vc->length;+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype;+  indx          = vc->jindx;+  sn            = vc->strand_number;+  matrices      = vc->matrices;+  c             = matrices->c;+  ggg           = matrices->ggg;+  hc            = vc->hc;+  sc            = vc->sc;+  hard_constraints  = hc->matrix;++  if(hc->up_ext[i]){+    if (i==start) array[i]=0;+    else array[i] = array[i-inc];+    if(sc){+      if(sc->energy_up)+        array[i] += sc->energy_up[i][1];+    }+  } else+    array[i] = INF;++  if (inc>0) {+    left = start; right=i;+  } else {+    left = i; right = start;+  }++  /* hard code min_loop_size to 0, since we can not be sure yet that this is already the case */+  turn = 0;++  for (j=start; inc*(i-j)>turn; j+=inc) {+    int ii, jj;+    short si, sj;+    if (i>j) { ii = j; jj = i;} /* inc>0 */+    else     { ii = i; jj = j;} /* inc<0 */+    type = ptype[indx[jj]+ii];+    if(hard_constraints[indx[jj]+ii] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){++      if(type == 0)+        type = 7;++      si = ((ii > 1) && (sn[ii - 1] == sn[ii])) ? S1[ii - 1] : -1;+      sj = ((jj < length) && (sn[jj] == sn[jj + 1])) ? S1[jj + 1] : -1;+      energy = c[indx[jj]+ii];+      if(energy != INF){+        switch(dangle_model){+          case 0:   if(array[j-inc] != INF){+                      en = array[j-inc] + energy + E_ExtLoop(type, -1, -1, P);+                      array[i] = MIN2(array[i], en);+                    }+                    break;+          case 2:   if(array[j-inc] != INF){+                      en = array[j-inc] + energy + E_ExtLoop(type, si, sj, P);+                      array[i] = MIN2(array[i], en);+                    }+                    break;+          default:  if(array[j-inc] != INF){+                      en = array[j-inc] + energy + E_ExtLoop(type, -1, -1, P);+                      array[i] = MIN2(array[i], en);+                    }+                    if(inc > 0){+                      if(j > left){+                        if(hc->up_ext[ii-1]){+                          if(array[j-2] != INF){+                            en = array[j-2] + energy + E_ExtLoop(type, si, -1, P);+                            if(sc)+                              if(sc->energy_up)+                                en += sc->energy_up[ii-1][1];++                            array[i] = MIN2(array[i], en);+                          }+                        }+                      }+                    } else if(j < right){+                      if(hc->up_ext[jj+1]){+                        if(array[j+2] != INF){+                          en = array[j+2] + energy + E_ExtLoop(type, -1, sj, P);+                          if(sc)+                            if(sc->energy_up)+                              en += sc->energy_up[jj+1][1];++                          array[i] = MIN2(array[i], en);+                        }+                      }+                    }+                    break;+        }+      }+    }++    if(with_gquad){+      if (sn[ii] == sn[jj])+        if(array[j-inc] != INF)+          array[i] = MIN2(array[i], array[j-inc] + ggg[indx[jj]+ii]);+    }++    if (dangle_model%2==1) {+      /* interval ends in a dangle (i.e. i-inc is paired) */+      if (i>j) { ii = j; jj = i-1;} /* inc>0 */+      else     { ii = i+1; jj = j;} /* inc<0 */++      if (!(hard_constraints[indx[jj]+ii] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP))+        continue;++      type = ptype[indx[jj]+ii];++      if(type == 0)+        type = 7;++      si = (ii > left)  && (sn[ii - 1] == sn[ii]) ? S1[ii - 1] : -1;+      sj = (jj < right) && (sn[jj] == sn[jj + 1]) ? S1[jj + 1] : -1;+      energy = c[indx[jj]+ii];+      if(energy != INF){+        if(inc>0){+          if(hc->up_ext[jj-1]){+            if(array[j-inc] != INF){+              en = array[j - inc] + energy + E_ExtLoop(type, -1, sj, P);+              if(sc)+                if(sc->energy_up)+                  en += sc->energy_up[jj+1][1];++              array[i] = MIN2(array[i], en);+            }+          }+        } else {+          if(hc->up_ext[ii-1]){+            if(array[j - inc] != INF){+              en = array[j - inc] + energy + E_ExtLoop(type, si, -1, P);+              if(sc)+                if(sc->energy_up)+                  en += sc->energy_up[ii-1][1];++              array[i] = MIN2(array[i], en);+            }+          }+        }+        if(j!= start){ /* dangle_model on both sides */+          if(hc->up_ext[jj-1] && hc->up_ext[ii-1]){+            if(array[j-2*inc] != INF){+              en = array[j-2*inc] + energy + E_ExtLoop(type, si, sj, P);+              if(sc)+                if(sc->energy_up)+                  en += sc->energy_up[ii-1][1] + sc->energy_up[jj+1][1];++              array[i] = MIN2(array[i], en);+            }+          }+        }+      }+    }+  }+}++PRIVATE void+backtrack(sect bt_stack[],+          vrna_bp_stack_t *bp_list,+          vrna_fold_compound_t *vc){++  /*routine to call backtrack_co from 1 to n, backtrack type??*/+  backtrack_co(bt_stack, bp_list, 0,0, vc);+}++PRIVATE void+doubleseq(vrna_fold_compound_t *vc){++  unsigned int  length, i, s;++  length  = vc->length;++  /* do some magic to re-use cofold code */+  vc->sequence  = vrna_realloc(vc->sequence, sizeof(char)*(2*length+2));+  memcpy(vc->sequence+length, vc->sequence, sizeof(char) * length);+  vc->sequence[2*length] = '\0';+  vc->length    = (unsigned int)strlen(vc->sequence);+  vc->cutpoint  = length+1;++  free(vc->strand_number);+  vc->strand_number = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (vc->length + 1));+  for (s = i = 0; i <= vc->length; i++) {+    if (i == length + 1)+      s++;+    vc->strand_number[i] = s;+  }++  vc->sequence_encoding = vrna_realloc(vc->sequence_encoding, sizeof(short)*(vc->length + 2));+  memcpy(vc->sequence_encoding+length+1, vc->sequence_encoding+1, sizeof(short)*length);+  vc->sequence_encoding[0] = vc->sequence_encoding[vc->length];+  vc->sequence_encoding[vc->length+1] = vc->sequence_encoding[1];++  vc->sequence_encoding2 = vrna_realloc(vc->sequence_encoding2, sizeof(short)*(vc->length + 2));+  memcpy(vc->sequence_encoding2 + length + 1, vc->sequence_encoding2 + 1, sizeof(short)*length);+  vc->sequence_encoding2[0] = vc->length;+  vc->sequence_encoding2[vc->length+1] = 0;++  free(vc->ptype);+  vc->ptype = vrna_ptypes(vc->sequence_encoding2, &(vc->params->model_details));+  free(vc->iindx);+  vc->iindx = vrna_idx_row_wise(vc->length);+  free(vc->jindx);+  vc->jindx = vrna_idx_col_wise(vc->length);++  vrna_hc_init(vc);++  /* add DP matrices */+  vrna_mx_mfe_add(vc, VRNA_MX_DEFAULT, 0);+}++PRIVATE void+halfseq(vrna_fold_compound_t *vc){++  unsigned int halflength;++  halflength = vc->length/2;++  vc->sequence = vrna_realloc(vc->sequence, sizeof(char)*(halflength + 1));+  vc->sequence[halflength] = '\0';+  vc->length = (unsigned int)strlen(vc->sequence);+  vc->cutpoint = -1;+  vc->strand_number = (unsigned int *)vrna_realloc(vc->strand_number, sizeof(unsigned int) * (vc->length + 1));++  vc->sequence_encoding = vrna_realloc(vc->sequence_encoding, sizeof(short)*(vc->length + 2));+  vc->sequence_encoding[0] = vc->sequence_encoding[vc->length];+  vc->sequence_encoding[vc->length+1] = vc->sequence_encoding[1];++  vc->sequence_encoding2 = vrna_realloc(vc->sequence_encoding2, sizeof(short)*(vc->length + 2));+  vc->sequence_encoding2[0] = vc->length;+  vc->sequence_encoding2[vc->length+1] = 0;++  free(vc->ptype);+  vc->ptype = vrna_ptypes(vc->sequence_encoding2, &(vc->params->model_details));+  free(vc->iindx);+  vc->iindx = vrna_idx_row_wise(vc->length);+  free(vc->jindx);+  vc->jindx = vrna_idx_col_wise(vc->length);++  vrna_hc_init(vc);++  /* add DP matrices */+  vrna_mx_mfe_add(vc, VRNA_MX_DEFAULT, 0);+}++typedef struct{+  int i;+  int j;+  int e;+  int idxj;+} zuker_pair;++PRIVATE int comp_pair(const void *A, const void *B) {+  zuker_pair *x,*y;+  int ex, ey;+  x = (zuker_pair *) A;+  y = (zuker_pair *) B;+  ex = x->e;+  ey = y->e;+  if (ex>ey) return 1;+  if (ex<ey) return -1;+  return (x->idxj + x->i - y->idxj + y->i);+}++PUBLIC SOLUTION *+vrna_subopt_zuker(vrna_fold_compound_t *vc){++/* Compute zuker suboptimal. Here, we're abusing the cofold() code+   "double" sequence, compute dimerarray entries, track back every base pair.+   This is slightly wasteful compared to the normal solution */++  char          *structure, *mfestructure, **todo, *ptype;+  int           i, j, counter, num_pairs, psize, p, *indx, *c, turn;+  unsigned int  length, doublelength;+  float         energy;+  SOLUTION      *zukresults;+  vrna_bp_stack_t         *bp_list;+  zuker_pair              *pairlist;+  sect          bt_stack[MAXSECTORS]; /* stack of partial structures for backtracking */+  vrna_mx_mfe_t *matrices;+  vrna_md_t     *md;++  md                = &(vc->params->model_details);+  turn              = md->min_loop_size;++  /* do some magic to re-use cofold code although vc is single sequence */+  md->min_loop_size = 0;+  doubleseq(vc);++  if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_MFE | VRNA_OPTION_HYBRID)){+    vrna_message_warning("vrna_subopt_zuker@cofold.c: Failed to prepare vrna_fold_compound");+    return NULL;+  }++++  doublelength    = vc->length;+  length          = doublelength/2;+  indx            = vc->jindx;+  ptype           = vc->ptype;+  matrices        = vc->matrices;+  c               = matrices->c;+  num_pairs       = counter = 0;+  mfestructure    = (char *) vrna_alloc((unsigned) doublelength+1);+  structure       = (char *) vrna_alloc((unsigned) doublelength+1);+  zukresults      = (SOLUTION *)vrna_alloc(((length*(length-1))/2)*sizeof(SOLUTION));+  mfestructure[0] = '\0';++  /* store length at pos. 0 */+  vc->sequence_encoding[0] = vc->sequence_encoding2[0];++  /* get mfe and do forward recursion */+  (void)fill_arrays(vc, 1);++  psize     = length;+  pairlist  = (zuker_pair *) vrna_alloc(sizeof(zuker_pair)*(psize+1));+  bp_list   = (vrna_bp_stack_t *) vrna_alloc(sizeof(vrna_bp_stack_t) * (1 + length/2));+  todo      = (char **) vrna_alloc(sizeof(char *)*(length+1));+  for (i=1; i<length; i++) {+    todo[i] = (char *) vrna_alloc(sizeof(char)*(length+1));+  }++  /* Make a list of all base pairs */+  for (i=1; i<length; i++) {+    for (j=i+turn+1/*??*/; j<=length; j++) {+      if (ptype[indx[j]+i]==0) continue;+      if (num_pairs>=psize) {+        psize = 1.2*psize + 32;+        pairlist = vrna_realloc(pairlist, sizeof(zuker_pair)*(psize+1));+      }+      pairlist[num_pairs].i       = i;+      pairlist[num_pairs].j       = j;+      pairlist[num_pairs].e       = c[indx[j]+i]+c[indx[i+length]+j];+      pairlist[num_pairs++].idxj  = indx[j];++      todo[i][j]=1;+    }+  }++  qsort(pairlist, num_pairs, sizeof(zuker_pair), comp_pair);++  for (p=0; p<num_pairs; p++) {+    i=pairlist[p].i;+    j=pairlist[p].j;+    if (todo[i][j]) {+      int   k;+      char  *sz;+      bt_stack[1].i   = i;+      bt_stack[1].j   = j;+      bt_stack[1].ml  = 2;+      backtrack_co(bt_stack, bp_list, 1,0, vc);+      bt_stack[1].i   = j;+      bt_stack[1].j   = i + length;+      bt_stack[1].ml  = 2;+      backtrack_co(bt_stack, bp_list, 1,bp_list[0].i, vc);+      energy = pairlist[p].e;+      sz = vrna_db_from_bp_stack(bp_list, length);+      zukresults[counter].energy      = energy/100.;+      zukresults[counter++].structure = sz;+      for (k = 1; k <= bp_list[0].i; k++) { /* mark all pairs in structure as done */+        int x,y;+        x=bp_list[k].i;+        y=bp_list[k].j;+        if (x>length) x-=length;+        if (y>length) y-=length;+        if (x>y) {+          int temp;+          temp=x; x=y; y=temp;+        }+        todo[x][y] = 0;+      }+    }+  }++  /* clean up */+  free(pairlist);+  for (i=1; i<length; i++)+    free(todo[i]);+  free(todo);+  free(structure);+  free(mfestructure);+  free(bp_list);++  /* undo magic */+  halfseq(vc);+  md->min_loop_size = turn;++  return zukresults;+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++#ifdef  VRNA_BACKWARD_COMPAT++PRIVATE void+wrap_array_export(int **f5_p,+                  int **c_p,+                  int **fML_p,+                  int **fM1_p,+                  int **fc_p,+                  int **indx_p,+                  char **ptype_p){++  /* make the DP arrays available to routines such as subopt() */+  if(backward_compat_compound){+    *f5_p     = backward_compat_compound->matrices->f5;+    *c_p      = backward_compat_compound->matrices->c;+    *fML_p    = backward_compat_compound->matrices->fML;+    *fM1_p    = backward_compat_compound->matrices->fM1;+    *fc_p     = backward_compat_compound->matrices->fc;+    *indx_p   = backward_compat_compound->jindx;+    *ptype_p  = backward_compat_compound->ptype;+  }+}++/*--------------------------------------------------------------------------*/++PRIVATE float+wrap_cofold(const char *string,+            char *structure,+            vrna_param_t *parameters,+            int is_constrained){++  unsigned int        length;+  char                *seq;+  vrna_fold_compound_t  *vc;+  vrna_param_t        *P;+  float               mfe;++  vc      = NULL;+  length  = strlen(string);++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++  /* we need the parameter structure for hard constraints */+  if(parameters)+    P = vrna_params_copy(parameters);+  else{+    vrna_md_t md;+    set_model_details(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }+  P->model_details.min_loop_size = 0;  /* set min loop length to 0 */++  /* dirty hack to reinsert the '&' according to the global variable 'cut_point' */+  seq = vrna_cut_point_insert(string, cut_point);++  /* get compound structure */+  vc = vrna_fold_compound(seq, &(P->model_details), 0);++  if(parameters){ /* replace params if necessary */+    free(vc->params);+    vc->params = P;+  } else {+    free(P);+  }++  /* handle hard constraints in pseudo dot-bracket format if passed via simple interface */+  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK+                          | VRNA_CONSTRAINT_DB_INTRAMOL+                          | VRNA_CONSTRAINT_DB_INTERMOL;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;++  /* cleanup */+  free(seq);++  /* call mfe_dimer without backtracing */+  mfe = vrna_mfe_dimer(vc, NULL);++  /* now we backtrace in a backward compatible way */+  if(structure && vc->params->model_details.backtrack){+    char            *s;+    sect            bt_stack[MAXSECTORS];+    vrna_bp_stack_t *bp;++    bp = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4*(1+length/2))); /* add a guess of how many G's may be involved in a G quadruplex */++    backtrack(bt_stack, bp, vc);++    s = vrna_db_from_bp_stack(bp, length);+    strncpy(structure, s, length + 1);+    free(s);++    if(base_pair)+      free(base_pair);+    base_pair = bp;+  }++  return mfe;+}++PRIVATE SOLUTION *+wrap_zukersubopt( const char *string,+                  vrna_param_t *parameters){++  vrna_fold_compound_t  *vc;+  vrna_param_t        *P;++  vc      = NULL;++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++  /* we need the parameter structure for hard constraints */+  if(parameters)+    P = vrna_params_copy(parameters);+  else{+    vrna_md_t md;+    set_model_details(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }++  /* get compound structure */+  vc = vrna_fold_compound(string, &(P->model_details), VRNA_OPTION_DEFAULT);++  if(parameters){ /* replace params if necessary */+    free(vc->params);+    vc->params = P;+  } else {+    free(P);+  }++  if(backward_compat_compound)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;++  return vrna_subopt_zuker(vc);+}++PUBLIC void+initialize_cofold(int length){ /* DO NOTHING */ }++PUBLIC void+free_co_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound  = NULL;+    backward_compat           = 0;+  }+}+++/*--------------------------------------------------------------------------*/++PUBLIC void+export_cofold_arrays_gq(int **f5_p,+                        int **c_p,+                        int **fML_p,+                        int **fM1_p,+                        int **fc_p,+                        int **ggg_p,+                        int **indx_p,+                        char **ptype_p){++  /* make the DP arrays available to routines such as subopt() */+  wrap_array_export(f5_p, c_p, fML_p, fM1_p, fc_p, indx_p, ptype_p);+  if(backward_compat_compound){+    *ggg_p = backward_compat_compound->matrices->ggg;+  }+}++PUBLIC void+export_cofold_arrays( int **f5_p,+                      int **c_p,+                      int **fML_p,+                      int **fM1_p,+                      int **fc_p,+                      int **indx_p,+                      char **ptype_p){++  wrap_array_export(f5_p, c_p, fML_p, fM1_p, fc_p, indx_p, ptype_p);+}++PUBLIC float+cofold( const char *string,+        char *structure){++  return wrap_cofold(string, structure, NULL, fold_constrained);+}++PUBLIC float+cofold_par( const char *string,+            char *structure,+            vrna_param_t *parameters,+            int is_constrained){++  return wrap_cofold(string, structure, parameters, is_constrained);+}++PUBLIC SOLUTION *+zukersubopt(const char *string) {++  return wrap_zukersubopt(string, NULL);+}++PUBLIC SOLUTION *+zukersubopt_par(const char *string,+                vrna_param_t *parameters){++  return wrap_zukersubopt(string, parameters);+}++PUBLIC void+update_cofold_params(void){++  vrna_fold_compound_t *v;+  +  if(backward_compat_compound && backward_compat){+    vrna_md_t md;+    v = backward_compat_compound;++    if(v->params)+      free(v->params);++    set_model_details(&md);+    v->params = vrna_params(&md);+  }+}++PUBLIC void+update_cofold_params_par(vrna_param_t *parameters){++  vrna_fold_compound_t *v;+  +  if(backward_compat_compound && backward_compat){+    v = backward_compat_compound;++    if(v->params)+      free(v->params);++    if(parameters){+      v->params = vrna_params_copy(parameters);+    } else {+      vrna_md_t md;+      set_model_details(&md);+      md.temperature = temperature;+      v->params = vrna_params(&md);+    }+  }+}++PUBLIC void get_monomere_mfes(float *e1, float *e2) {+  /*exports monomere free energies*/+  *e1 = mfe1;+  *e2 = mfe2;+}++#endif
+ C/ViennaRNA/cofold.h view
@@ -0,0 +1,202 @@+#ifndef VIENNA_RNA_PACKAGE_COFOLD_H+#define VIENNA_RNA_PACKAGE_COFOLD_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/mfe.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     cofold.h+ *  @ingroup  cofold+ *  @brief    MFE implementations for RNA-RNA interaction+ */++/**+ *  @addtogroup mfe_cofold+ *  @brief MFE version of cofolding routines+ *  This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to+ *  MFE Cofolding...+ *  This also includes the Zuker suboptimals calculations, since they are implemented using the cofold+ *  routines.+ *+ *  @{+ *  @ingroup mfe_cofold+ */++/**+ *  @brief Compute Minimum Free Energy (MFE), and a corresponding secondary structure for two dimerized RNA sequences+ *+ *  This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for+ *  two RNA sequences upon dimerization using default options. Memory required for dynamic programming+ *  (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of this function, the+ *  recursively filled matrices are not available any more for any post-processing, e.g. suboptimal+ *  backtracking, etc.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_mfe_dimer(), vrna_fold_compound(), #vrna_fold_compound_t, vrna_cut_point_insert()+ *+ *  @param sequence   two RNA sequences separated by the '&' character+ *  @param structure  A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_cofold(const char *sequence,+            char *structure);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Compute the minimum free energy of two interacting RNA molecules+ *+ *  The code is analog to the fold() function. If #cut_point ==-1 results+ *  should be the same as with fold().+ *+ *  @ingroup mfe_cofold+ *+ *  @deprecated use vrna_mfe_dimer() instead+ *+ *  @param    sequence  The two sequences concatenated+ *  @param    structure Will hold the barcket dot structure of the dimer molecule+ *  @return   minimum free energy of the structure+ */+DEPRECATED(float+cofold( const char *sequence,+        char *structure));++/**+ *  @brief Compute the minimum free energy of two interacting RNA molecules+ *+ *  @deprecated use vrna_mfe_dimer() instead+ *+ */+DEPRECATED(float+cofold_par( const char *string,+            char *structure,+            vrna_param_t *parameters,+            int is_constrained));++/**+ *  @brief Free memory occupied by cofold()+ *+ *  @deprecated This function will only free memory allocated by a prior call of cofold() or cofold_par().+ *  See vrna_mfe_dimer() for how to use the new API+ *+ *  @note folding matrices now reside in the fold compound, and should be free'd there+ *  @see  vrna_fc_destroy(), vrna_mfe_dimer()+ */+DEPRECATED(void free_co_arrays(void));++/**+ *  @brief Recalculate parameters+ *  @deprecated See vrna_params_subst() for an alternative using the new API+ */+DEPRECATED(void update_cofold_params(void));++/**+ *  @brief Recalculate parameters+ *  @deprecated See vrna_params_subst() for an alternative using the new API+ */+DEPRECATED(void update_cofold_params_par(vrna_param_t *parameters));+++/**+ *  @brief Export the arrays of partition function cofold (with gquadruplex support)+ *+ *  Export the cofold arrays for use e.g. in the concentration+ *  Computations or suboptimal secondary structure backtracking+ *+ *  @deprecated folding matrices now reside within the fold compound. Thus, this function will+ *  only work in conjunction with a prior call to cofold() or cofold_par()+ *+ *  @see vrna_mfe_dimer() for the new API+ *+ *  @param  f5_p    A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]+ *  @param  c_p     A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j+ *  @param  fML_p   A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem+ *  @param  fM1_p   A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem+ *  @param  fc_p    A pointer to the 'fc' array, i.e. array ...+ *  @param  ggg_p   A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]+ *  @param  indx_p  A pointer to the indexing array used for accessing the energy matrices+ *  @param  ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)+ */+DEPRECATED(void export_cofold_arrays_gq(int **f5_p,+                                        int **c_p,+                                        int **fML_p,+                                        int **fM1_p,+                                        int **fc_p,+                                        int **ggg_p,+                                        int **indx_p,+                                        char **ptype_p));++/**+ *  @brief Export the arrays of partition function cofold+ *+ *  Export the cofold arrays for use e.g. in the concentration+ *  Computations or suboptimal secondary structure backtracking+ *+ *  @deprecated folding matrices now reside within the #vrna_fold_compound_t. Thus, this function will+ *  only work in conjunction with a prior call to the deprecated functions cofold() or cofold_par()+ *+ *  @see vrna_mfe_dimer() for the new API+ *+ *  @param  f5_p    A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]+ *  @param  c_p     A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j+ *  @param  fML_p   A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem+ *  @param  fM1_p   A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem+ *  @param  fc_p    A pointer to the 'fc' array, i.e. array ...+ *  @param  indx_p  A pointer to the indexing array used for accessing the energy matrices+ *  @param  ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)+ */+DEPRECATED(void export_cofold_arrays( int **f5_p,+                                      int **c_p,+                                      int **fML_p,+                                      int **fM1_p,+                                      int **fc_p,+                                      int **indx_p,+                                      char **ptype_p));++++/**+ *  @brief get_monomer_free_energies+ *+ *  Export monomer free energies out of cofold arrays+ *  @deprecated{This function is obsolete and will be removed soon!}+ *+ *  @param e1 A pointer to a variable where the energy of molecule A will be written to+ *  @param e2 A pointer to a variable where the energy of molecule B will be written to+ */+DEPRECATED(void get_monomere_mfes( float *e1, float *e2));+++/**+ *  allocate arrays for folding+ *  @deprecated{This function is obsolete and will be removed soon!}+ */+DEPRECATED(void initialize_cofold(int length));++#endif++/**+ *  @}+ */+++#endif
+ C/ViennaRNA/color_output.inc view
@@ -0,0 +1,338 @@++/* deactivate ANSI colors in TTY output if we compile for windows */+#ifndef WITHOUT_TTY_COLORS+# ifdef _WIN32+#   define WITHOUT_TTY_COLORS+# endif+#endif++#ifndef WITHOUT_TTY_COLORS++#define ANSI_COLOR_BRIGHT     "\x1b[1m"+#define ANSI_COLOR_UNDERLINE  "\x1b[4m"+#define ANSI_COLOR_RED        "\x1b[31m"+#define ANSI_COLOR_GREEN      "\x1b[32m"+#define ANSI_COLOR_YELLOW     "\x1b[33m"+#define ANSI_COLOR_BLUE       "\x1b[34m"+#define ANSI_COLOR_MAGENTA    "\x1b[35m"+#define ANSI_COLOR_CYAN       "\x1b[36m"+#define ANSI_COLOR_RED_B      "\x1b[1;31m"+#define ANSI_COLOR_GREEN_B    "\x1b[1;32m"+#define ANSI_COLOR_YELLOW_B   "\x1b[1;33m"+#define ANSI_COLOR_BLUE_B     "\x1b[1;34m"+#define ANSI_COLOR_MAGENTA_B  "\x1b[1;35m"+#define ANSI_COLOR_CYAN_B     "\x1b[1;36m"+#define ANSI_COLOR_RESET      "\x1b[0m"++static void+print_fasta_header( FILE *fp,+                    const char *head){++  if(head){+    if(isatty(fileno(fp))){+      fprintf(fp, ANSI_COLOR_YELLOW ">%s" ANSI_COLOR_RESET "\n", head);+    } else {+      fprintf(fp, ">%s\n", head);+    }+  }+}++static void+print_structure(FILE *fp,+                const char *structure,+                const char *data){++  if(structure){+    if(data){+      if(isatty(fileno(fp))){+        fprintf(fp, "%s" ANSI_COLOR_GREEN "%s" ANSI_COLOR_RESET "\n", structure, data);+      } else {+        fprintf(fp, "%s%s\n", structure, data);+      }+    } else {+      fprintf(fp, "%s\n", structure);+    }+  } else {+    if(data){+      if(isatty(fileno(fp))){+        fprintf(fp, ANSI_COLOR_GREEN "%s" ANSI_COLOR_RESET "\n", data);+      } else {+        fprintf(fp, "%s\n", data);+      }+    }+  }+}+++static void+print_eval_ext_loop(FILE  *fp,+                    int   energy){++  if(isatty(fileno(fp))){+    fprintf(fp, ANSI_COLOR_CYAN "External loop" ANSI_COLOR_RESET+                "                           : "+                ANSI_COLOR_GREEN "%5d" ANSI_COLOR_RESET "\n", energy);+  } else {+    fprintf(fp, "External loop"+                "                           : "+                "%5d\n", energy);+  }+}++static void+print_eval_hp_loop( FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   energy){++  if(isatty(fileno(fp))){+    fprintf(fp, ANSI_COLOR_CYAN "Hairpin  loop" ANSI_COLOR_RESET+                " (%3d,%3d) "+                ANSI_COLOR_BRIGHT "%c%c" ANSI_COLOR_RESET+                "              : "+                ANSI_COLOR_GREEN "%5d" ANSI_COLOR_RESET "\n",+                i, j,+                si, sj,+                energy);+  } else {+    fprintf(fp, "Hairpin  loop"+                " (%3d,%3d) %c%c              : "+                "%5d\n",+                i, j,+                si, sj,+                energy);+  }+}+++static void+print_eval_int_loop(FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   k,+                    int   l,+                    char  sk,+                    char  sl,+                    int   energy){++  if(isatty(fileno(fp))){+    fprintf(fp, ANSI_COLOR_CYAN "Interior loop" ANSI_COLOR_RESET+                " (%3d,%3d) "+                ANSI_COLOR_BRIGHT "%c%c" ANSI_COLOR_RESET+                "; (%3d,%3d) "+                ANSI_COLOR_BRIGHT "%c%c" ANSI_COLOR_RESET+                ": "+                ANSI_COLOR_GREEN "%5d" ANSI_COLOR_RESET "\n",+                i, j,+                si, sj,+                k, l,+                sk, sl,+                energy);+  } else {+    fprintf(fp, "Interior loop"+                " (%3d,%3d) "+                "%c%c"+                "; (%3d,%3d) "+                "%c%c"+                ": "+                "%5d\n",+                i, j,+                si, sj,+                k, l,+                sk, sl,+                energy);+  }+}+++static void+print_eval_mb_loop( FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   energy){++  if(isatty(fileno(fp))){+    fprintf(fp, ANSI_COLOR_CYAN "Multi    loop" ANSI_COLOR_RESET+                " (%3d,%3d) "+                ANSI_COLOR_BRIGHT "%c%c" ANSI_COLOR_RESET+                "              : "+                ANSI_COLOR_GREEN "%5d" ANSI_COLOR_RESET "\n",+                i, j,+                si, sj,+                energy);+  } else {+    fprintf(fp, "Multi    loop"+                " (%3d,%3d) %c%c              : "+                "%5d\n",+                i, j,+                si, sj,+                energy);+  }+}+++static void+print_table(FILE *fp,+            const char *head,+            const char *line){++  if(head){+    if(isatty(fileno(fp))){+      fprintf(fp, ANSI_COLOR_UNDERLINE ANSI_COLOR_BRIGHT "%s" ANSI_COLOR_RESET "\n", head);+    } else {+      fprintf(fp, "%s\n", head);+    }+  }+  if(line){+    if(isatty(fileno(fp))){+      fprintf(fp, ANSI_COLOR_GREEN "%s" ANSI_COLOR_RESET "\n", line);+    } else {+      fprintf(fp, "%s\n", line);+    }+  }+}++static void+print_comment(FILE *fp,+              const char *line){++  if(line){+    if(isatty(fileno(fp))){+      fprintf(fp, ANSI_COLOR_CYAN "%s" ANSI_COLOR_RESET "\n", line);+    } else {+      fprintf(fp, "%s\n", line);+    }+  }+}++#else++static void+print_fasta_header( FILE *fp,+                    const char *head){++  if(head){+    fprintf(fp, ">%s\n", head);+  }+}++static void+print_structure(FILE *fp,+                const char *structure,+                const char *data){++  if(structure){+    if(data){+      fprintf(fp, "%s%s\n", structure, data);+    } else {+      fprintf(fp, "%s\n", structure);+    }+  } else {+    if(data){+      fprintf(fp, "%s\n", data);+    }+  }+}+++static void+print_eval_ext_loop(FILE  *fp,+                    int   energy){++  fprintf(fp, "External loop"+              "                           : "+              "%5d\n", energy);+}+++static void+print_eval_hp_loop( FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   energy){++  fprintf(fp, "Hairpin  loop"+              " (%3d,%3d) %c%c              : "+              "%5d\n",+              i, j,+              si, sj,+              energy);+}+++static void+print_eval_int_loop(FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   k,+                    int   l,+                    char  sk,+                    char  sl,+                    int   energy){++  fprintf(fp, "Interior loop"+              " (%3d,%3d) "+              "%c%c"+              "; (%3d,%3d) "+              "%c%c"+              ": "+              "%5d\n",+              i, j,+              si, sj,+              k, l,+              sk, sl,+              energy);+}+++static void+print_eval_mb_loop( FILE  *fp,+                    int   i,+                    int   j,+                    char  si,+                    char  sj,+                    int   energy){++  fprintf(fp, "Multi    loop"+              " (%3d,%3d) %c%c              : "+              "%5d\n",+              i, j,+              si, sj,+              energy);+}+++static void+print_table(FILE *fp,+            const char *head,+            const char *line){++  if(head){+    fprintf(fp, "%s\n", head);+  }+  if(line){+    fprintf(fp, "%s\n", line);+  }+}++static void+print_comment(FILE *fp,+              const char *line){++  if(line){+    fprintf(fp, "%s\n", line);+  }+}++#endif+
+ C/ViennaRNA/commands.c view
@@ -0,0 +1,776 @@+/*+    commands.c++    Various functions dealing with parsing and application of commands++    (c) 2016 Ronny Lorenz++    ViennaRNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <ctype.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/commands.h"+++typedef void *(command_parser_function)(const char *line);++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE vrna_cmd_t parse_command(const char *line, int line_number, const char *filename);++PRIVATE void *parse_ud_command( const char *line);++PRIVATE void *parse_constraint_force(const char *line);+PRIVATE void *parse_constraint_prohibit(const char *line);+PRIVATE void *parse_constraint_con(const char *line);+PRIVATE void *parse_constraint_allow(const char *line);+PRIVATE void *parse_constraint_energy(const char *line);+PRIVATE void *parse_constraint(const char *line, char command);++PRIVATE int parse_constraints_line( const char *line,+                                    char command,+                                    int *i,+                                    int *j,+                                    int *k,+                                    int *l,+                                    char *loop,+                                    char *orientation,+                                    float *e);+++PRIVATE int apply_hard_constraint(vrna_fold_compound_t *vc,+                                  void *constraint);++PRIVATE int apply_soft_constraint(vrna_fold_compound_t *vc,+                                  void *constraint);++PRIVATE int apply_ud(vrna_fold_compound_t *vc, void *data);++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++typedef struct {+  char                    cmd[3];+  vrna_command_e          type;+  command_parser_function *parser;+} parsable;+++/* number of commands we currently know and are able to interpret */+#define NUM_COMMANDS  7++/* set of known parsable commands */+parsable known_commands[NUM_COMMANDS] = {+  /* cmd , type , parser */+  { "UD", VRNA_CMD_UD, parse_ud_command },          /* unstructured domain */+  { "SD", VRNA_CMD_SD, NULL },                      /* structured domain */+  { "P",  VRNA_CMD_HC, parse_constraint_prohibit }, /* prohibit base pairing */+  { "F",  VRNA_CMD_HC, parse_constraint_force },    /* force base pairing */+  { "C",  VRNA_CMD_HC, parse_constraint_con },      /* remove conflicting pairs/force nucleotide in loop context */+  { "A",  VRNA_CMD_HC, parse_constraint_allow },    /* allow (non-canonical) pairs */+  { "E",  VRNA_CMD_SC, parse_constraint_energy }    /* soft constraint */+};++typedef struct {+  int   i;+  int   j;+  int   k;+  int   l;+  int   size;+  char  loop;+  char  orientation;+  float e;+  char  command;+} constraint_struct;+++typedef struct {+  char          *motif;+  float         motif_en;+  unsigned int  loop_type;+} ud_struct;++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC int+vrna_file_commands_apply( vrna_fold_compound_t *vc,+                          const char *filename,+                          unsigned int options){++  /** [Applying commands from file] */+  int         r;+  vrna_cmd_t  *cmds;++  cmds  = vrna_file_commands_read(filename, options);+  r     = vrna_commands_apply(vc, cmds, options);++  vrna_commands_free(cmds);++  return r;+  /** [Applying commands from file] */+}++PUBLIC vrna_cmd_t *+vrna_file_commands_read(const char *filename,+                        unsigned int options){+  FILE        *fp;+  char        *line;+  int         num_commands, max_commands, line_number, valid;+  vrna_cmd_t  cmd, *output;++  line_number   = 0;+  num_commands  = 0;+  max_commands  = 15;+  line          = NULL;++  if(!(fp = fopen(filename, "r"))){+    vrna_message_warning("Command File could not be opened!");+    return NULL;+  }++  output = (vrna_cmd_t *)vrna_alloc(sizeof(vrna_cmd_t) * max_commands);++  /* let's go through the file line by line and parse the commands */+  while((line=vrna_read_line(fp))){+    line_number++;+    switch(*line){+      /* skip comment lines */+      case '#': case '%': case ';': case '/': case '*': case ' ': case '\0':+        free(line);+        continue;+      default:+        cmd = parse_command((const char *)line, line_number, filename);+        break;+    }++    free(line);++    if(cmd.type == VRNA_CMD_LAST){ /* end of command list */+      break;+    } else { /* check whether command is valid in user-defined context */+      valid = 0;+      switch(cmd.type){+        case VRNA_CMD_HC: valid = options & VRNA_CMD_PARSE_HC;+                          break;++        case VRNA_CMD_SC: valid = options & VRNA_CMD_PARSE_SC;+                          break;++        case VRNA_CMD_UD: valid = options & VRNA_CMD_PARSE_UD;+                          break;++        case VRNA_CMD_SD: valid = options & VRNA_CMD_PARSE_SD;+                          break;++        default:          break;+      }+      +      if(valid){ /* add command to list */+        output[num_commands++] = cmd;++        /* increase length of command list if necessary */+        if(num_commands == max_commands){+          max_commands *= 1.2;+          output = (vrna_cmd_t *)vrna_realloc(output, sizeof(vrna_cmd_t) * max_commands);+        }+      }+    }+  }++  /* mark end of command list */+  output = (vrna_cmd_t *)vrna_realloc(output, sizeof(vrna_cmd_t) * (num_commands + 1));+  output[num_commands].type = VRNA_CMD_LAST;+  output[num_commands].data = NULL;++  /* cleanup */+  free(line);++  return output;+}+++PUBLIC int+vrna_commands_apply(vrna_fold_compound_t *vc,+                    vrna_cmd_t *commands,+                    unsigned int options){++  int         r = 0;+  vrna_cmd_t  *ptr;++  if(vc && commands){+    for(ptr = commands; ptr->type != VRNA_CMD_LAST; ptr++){+      switch(ptr->type){+        case VRNA_CMD_HC:   if(options & VRNA_CMD_PARSE_HC)+                              r += apply_hard_constraint(vc, ptr->data);+                            break;++        case VRNA_CMD_SC:   if(options & VRNA_CMD_PARSE_SC)+                              r += apply_soft_constraint(vc, ptr->data);+                            break;++        case VRNA_CMD_UD:   if(options & VRNA_CMD_PARSE_UD)+                              r += apply_ud(vc, ptr->data);+                            break;++        default:            /* do nothing */+                            break;+      }+    }+  }+  +  return r;+}++PUBLIC void+vrna_commands_free( vrna_cmd_t *commands){++  vrna_cmd_t *ptr;++  if(commands){+    for(ptr = commands; ptr->type != VRNA_CMD_LAST; ptr++){+      switch(ptr->type){+        case VRNA_CMD_UD: {+                            ud_struct *d = (ud_struct *)ptr->data;+                            free(d->motif);+                            free(ptr->data);+                          }+                          break;++        default:          free(ptr->data);+                          break;+      }+    }+    free(commands);+  }+}+++PRIVATE int+apply_ud(vrna_fold_compound_t *vc, void *data){+++  ud_struct *d = (ud_struct *)data;+  vrna_ud_add_motif(vc, d->motif, d->motif_en, d->loop_type);+  +  return 1;+}+++PRIVATE int+apply_hard_constraint(vrna_fold_compound_t *vc,+                      void *data){++  int               i, j, k, l, h, cnt1, cnt2, cnt3;+  int               num_hc_up, max_hc_up;+  vrna_hc_up_t      *hc_up;+  char              t, orientation;+  constraint_struct *constraint = (constraint_struct *)data;++  i           = constraint->i;+  j           = constraint->j;+  k           = constraint->k;+  l           = constraint->l;+  t           = constraint->loop;+  orientation = constraint->orientation;+  h           = constraint->size;++  /* actually apply constraints */+  if(h == 0){ /* range mode (prohibit pairs only) */+    for(cnt1 = i; cnt1 <= j; cnt1++)+      for(cnt2 = MAX2(cnt1 + 1, k); cnt2 <= l; cnt2++){+        vrna_hc_add_bp(vc, cnt1, cnt2, t);+      }+  } else {++    /* we'll collect hard constraints for unpairedness */+    num_hc_up = 0;+    max_hc_up = 15;+    hc_up     = vrna_alloc(sizeof(vrna_hc_up_t) * max_hc_up);++    for(cnt1 = i; cnt1 <= j; cnt1++)+      for(cnt2 = k; cnt2 <= l; cnt2++)+        for(cnt3 = h; cnt3 != 0; cnt3--){+          if(cnt2 == 0){  /* enforce unpairedness of nucleotide */+            /* just store this constraint, we'll apply it later */+            hc_up[num_hc_up].position = cnt1 + (cnt3 - 1);+            hc_up[num_hc_up].options  = t;+            num_hc_up++;+            if(num_hc_up == max_hc_up){ /* increase size of hc_up if necessary */+              max_hc_up  = 1.2 * max_hc_up;+              hc_up      = (vrna_hc_up_t *)vrna_realloc(hc_up, sizeof(vrna_hc_up_t) * max_hc_up);+            }+          } else if((i == j) && (j == k) && (k == l)){  /* enforce pairedness of nucleotide */+            int d = 0;+            if(orientation != '\0')+              d = (orientation == 'U') ? -1 : 1;+            vrna_hc_add_bp_nonspecific(vc, cnt1 + (cnt3 - 1), d, t);+          } else {  /* enforce / prohibit base pair */+            vrna_hc_add_bp(vc, cnt1 + (cnt3 - 1), cnt2 - (cnt3 - 1), t);+          }+        }++    /* add hard constraints for unpairedness */+    if(num_hc_up > 0){+      hc_up[num_hc_up].position = 0; /* mark end of list */+      vrna_hc_add_up_batch(vc, hc_up);+    }+    free(hc_up);++  }++  return 1;+}+++PRIVATE int+apply_soft_constraint(vrna_fold_compound_t *vc,+                      void *data){++  int               i, j, k, l, h, cnt1, cnt2, cnt3;+  float             e;+  constraint_struct *constraint = (constraint_struct *)data;++  i           = constraint->i;+  j           = constraint->j;+  k           = constraint->k;+  l           = constraint->l;+  h           = constraint->size;+  e           = constraint->e;++  for(cnt1 = i; cnt1 <= j; cnt1++)+    for(cnt2 = k; cnt2 <= l; cnt2++)+      for(cnt3 = h; cnt3 != 0; cnt3--){+        if((cnt2 == 0) || ((i == j) && (j == k) && (k == l))){  /* enforce nucleotide constraint */+          vrna_sc_add_up(vc, cnt1 + (cnt3 - 1), e, VRNA_OPTION_DEFAULT);+        } else {  /* enforce base pair constraint */+          vrna_sc_add_bp(vc, cnt1 + (cnt3 - 1), cnt2 - (cnt3 - 1), e, VRNA_OPTION_DEFAULT);+        }+      }++  return 1;+}+++PRIVATE vrna_cmd_t+parse_command(const char *line, int line_number, const char *filename){++  vrna_cmd_t cmd;+  int i, r;+  char command[3];++  command[0] = '\0';+  i = NUM_COMMANDS;++  r = sscanf(line, "%2c", command);+  if(r == 1){+    command[2] = '\0'; /* just a precaution */+    for(i = 0; i < NUM_COMMANDS; i++){+      if(!strncmp(known_commands[i].cmd, command, strlen(known_commands[i].cmd)))+        break;+    }+  }++  if(i < NUM_COMMANDS){ /* command is known, so lets try to process it */+    cmd.data = (known_commands[i].parser) ? known_commands[i].parser(line) : NULL;+    if(cmd.data)+      cmd.type = known_commands[i].type;+    else {+      vrna_message_warning("Ignoring invalid command in file \"%s\":\nline %d: %s", filename, line_number, line);+      cmd.type = VRNA_CMD_ERROR;+    }+  } else {+    vrna_message_warning("Ignoring unknown command in file \"%s\":\nline %d: %s", filename, line_number, line);+    cmd.type = VRNA_CMD_ERROR;+    cmd.data = NULL;+  }++  return cmd;+}+++PRIVATE void *+parse_ud_command( const char *line){++  int           ret, entries_seen, max_entries, pos, pp;+  char          *ptr, *buffer;+  float         e;+  unsigned int  loop_type;+  ud_struct     *data;++  buffer        = (char *)vrna_alloc(sizeof(char) * (strlen(line) + 1));+  data          = (ud_struct *)vrna_alloc(sizeof(ud_struct));+  data->motif   = NULL;+  ret           = 0;  /* error indicator */+  entries_seen  = 0;  /* entries seen so far */+  max_entries   = 3;  /* expected number of entries */+  pos           = 2;  /* position relative to start of line */+  pp            = 0;++  while(!ret && (entries_seen < max_entries) && (sscanf(line+pos,"%s%n", buffer, &pp) == 1)){+    pos += pp;+    switch(entries_seen){+      case 0:       /* motif in IUPAC format */+                    data->motif = strdup(buffer);+                    break;++      case 1:       /* motif energy in kcal/mol */+                    if(sscanf(buffer, "%g", &e) == 1){+                      data->motif_en = e;+                    } else {+                      ret = 1;+                    }+                    break;++      case 2:       /* motif loop type */+                    loop_type = 0;+                    for(ptr=buffer; *ptr != '\0'; ptr++){+                      switch(*ptr){+                        case 'A'  : loop_type |= VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS;+                                    break;+                        case 'E'  : loop_type |= VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP;+                                    break;+                        case 'H'  : loop_type |= VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP;+                                    break;+                        case 'I'  : loop_type |= VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP;+                                    break;+                        case 'M'  : loop_type |= VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP;+                                    break;+                        default:    ret = 1;+                                    break;+                      }+                      if(ret)+                        break;+                    }+                    data->loop_type = loop_type;+                    break;+    }+    entries_seen++;+  }++  free(buffer);++  if(ret){+    free(data->motif);+    free(data);+    return NULL;+  }++  if(data->loop_type == 0){+    data->loop_type = VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS;+    vrna_message_warning("");+  }+  return (void *)data;+}++PRIVATE void *+parse_constraint_force(const char *line){++  return parse_constraint(line, 'F');+}++PRIVATE void *+parse_constraint_prohibit(const char *line){++  return parse_constraint(line, 'P');+}++PRIVATE void *+parse_constraint_con(const char *line){++  return parse_constraint(line, 'C');+}++PRIVATE void *+parse_constraint_allow(const char *line){++  return parse_constraint(line, 'A');+}++PRIVATE void *+parse_constraint_energy(const char *line){++  return parse_constraint(line, 'E');+}+++PRIVATE void *+parse_constraint( const char *line,+                  char command){++  int               ret, i, j, k, l, h, valid;+  char              loop, orientation;+  float             e;+  constraint_struct *output;++  output = NULL;++  i = j = k = l = -1;+  orientation = '\0'; /* no orientation */+  e = 0.;++  ret = parse_constraints_line(line + 1, command, &i, &j, &k, &l, &loop, &orientation, &e);++  if(ret == 0){++    /* do something with the constraint we've just read */++    h = 1; /* helix length for pairs, or number of unpaired nucleotides */++    /* check indices */+    valid = 0;+    if(i > 0){+      if(j == -1){ /* i and range [k:l] */+        if((k > 0) && (l > 0)){+          if((k < l) && (i < k) && (orientation == '\0')){+            j     = i;+            valid = 1;+          }+        }+      } else if(k <= 0){ /* range [i:j] and l */+        if((i < j) && (j < l) && (orientation == '\0')){+          k     = l;+          valid = 1;+        }+      } else if(l <= 0){ /* helix of size k starting with pair (i,j), or segment [i:i+k-1] */+        if(i != j){+          if((j == 0) || (((j - i + 1) > 2*k) && (orientation == '\0'))){+            h     = k;+            k = l = j;+            j     = i;+            valid = 1;+          }+        }+      } else if((i < j) && (k < l) && (i <= k) && (j <= l) && (orientation == '\0')){  /* range [i:j] and [k:l] */+        if(command == 'P'){ /* we only allow this for 'prohibit pairing between two ranges' */+          h     = 0;+          valid = 1;+        }+      }+    }++    if(valid){+      /* nucleotide constraint? */+      if((k == 0) && (l == 0) && (i == j) && (h > 0)){+        /* set correct loop type context */+        switch(command){+          case 'P': break;+          case 'A': /* this case allows particular nucleotides to form non-canonical pairs */+                    loop |= VRNA_CONSTRAINT_CONTEXT_NO_REMOVE; /* do not remove possibility to stay unpaired */+                    /* fall through */+          case 'F': /* set i == j == k == l */+                    k = l = i;+                    break;+          case 'E': loop = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS; /* soft constraints are always applied for all loops */+                    break;+          case 'C': loop |= VRNA_CONSTRAINT_CONTEXT_ENFORCE;  /* enforce context dependency */+                    break;+          default:  break;+        }+      } else { /* base pair constraint */+        /* set correct loop type context */+        switch(command){+          case 'P': loop = ~loop; /* prohibit */+                    loop &= VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+                    loop |= VRNA_CONSTRAINT_CONTEXT_NO_REMOVE;  /* since we prohibit pairs, we do not want to remove incompatible pairs */+                    break;+          case 'F': loop |= VRNA_CONSTRAINT_CONTEXT_ENFORCE;  /* enforce */+                    break;+          case 'E': loop = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;  /* soft constraints are always applied for all loops */+                    break;+          case 'C': break;  /* remove conflicting pairs only */+          case 'A': loop |= VRNA_CONSTRAINT_CONTEXT_NO_REMOVE; /* since we allow pairs, we do not want to remove incompatible pairs */+                    break;+          default:  break;+        }+      }++      output = (constraint_struct *)vrna_alloc(sizeof(constraint_struct));+      output->command     = command;+      output->i           = i;+      output->j           = j;+      output->k           = k;+      output->l           = l;+      output->size        = h;+      output->loop        = loop;+      output->orientation = orientation;+      output->e           = e;+    }+  }++  return (void *)output;+}++PRIVATE int+parse_constraints_line( const char *line,+                        char command,+                        int *i,+                        int *j,+                        int *k,+                        int *l,+                        char *loop,+                        char *orientation,+                        float *e){++  int v1, v2;+  int ret = 0;+  int range_mode = 0;+  int pos = 0;+  int max_entries = 5;+  int entries_seen = 0;+  int pp;+  float energy;+  char buf[256], buf2[10], *c, tmp_loop;++  switch(command){+    case 'A':   /* fall through */+    case 'F':   /* fall through */+    case 'P':   max_entries = 5;+                break;+    case 'C':   /* fall through */+    case 'E':   max_entries = 4;+                break;+    default:    ret = 1;  /* error */+                break;+  }++  /* default to all loop types */+  *loop     = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+  tmp_loop  = (char)0;++  /* now lets scan the entire line for content */+  while(!ret && (entries_seen < max_entries) && (sscanf(line+pos,"%15s%n", &buf[0], &pp) == 1)){+    pos += pp;+    switch(entries_seen){+      case 0: /* must be i, or range */+              if(sscanf(buf, "%d-%d%n", &v1, &v2, &pp) == 2){+                if(pp == strlen(buf)){+                  *i = v1;+                  *j = v2;+                  range_mode = 1;+                  --max_entries; /* no orientation allowed now */+                  break;+                }+              } else if(sscanf(buf, "%d%n", &v1, &pp) == 1){+                if(pp == strlen(buf)){+                  *i = v1;+                  break;+                }+              }+              ret = 1;+              break;+      case 1: /* must be j, or range */+              if(sscanf(buf, "%d-%d%n", &v1, &v2, &pp) == 2){+                if(pp == strlen(buf)){+                  *k = v1;+                  *l = v2;+                  if(!range_mode)+                    --max_entries; /* no orientation allowed now */+                  range_mode = 1;+                  break;+                }+              } else if(range_mode){+                if(sscanf(buf, "%d%n", &v1, &pp) == 1){+                  if(pp == strlen(buf)){+                    *l = v1;+                    break;+                  }+                }+              } else if(sscanf(buf, "%d%n", &v1, &pp) == 1){+                if(pp == strlen(buf)){+                  *j = v1;+                  break;+                }+              }+              ret = 1;+              break;+      case 2: /* skip if in range_mode */+              if(!range_mode){+                /* must be k */+                if(sscanf(buf, "%d%n", &v1, &pp) == 1){+                  if(pp == strlen(buf)){+                    *k = v1;+                    break;+                  }+                }+                ret = 1;+                break;+              } else {+                --max_entries;+                /* fall through */+              }+      case 3: +              if(command == 'E'){ /* must be pseudo energy */+                if(sscanf(buf, "%g%n", &energy, &pp) == 1){+                  if(pp == strlen(buf)){+                    *e = energy;+                    break;+                  }+                }+              } else { /*  must be loop type, or orientation */+                if(sscanf(buf, "%8s%n", &buf2[0], &pp) == 1){+                  buf2[8] = '\0';+                  if(pp == strlen(buf)){+                    for(c = &(buf2[0]); (*c != '\0') && (!ret); c++){+                      switch(*c){+                        case 'E': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_EXT_LOOP;+                                  break;+                        case 'H': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_HP_LOOP;+                                  break;+                        case 'I': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_INT_LOOP;+                                  break;+                        case 'i': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;+                                  break;+                        case 'M': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_MB_LOOP;+                                  break;+                        case 'm': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC;+                                  break;+                        case 'A': tmp_loop |= VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+                                  break;+                        case 'U': case 'D':+                                  *orientation = *c;+                                  break;+                        default:  ret = 1;+                      }+                    }+                    if(tmp_loop)+                      *loop = tmp_loop;++                    break;+                  }+                }+              }+              ret = 1;+              break;+      case 4: /* must be orientation */+              if(!(sscanf(buf, "%c", orientation) == 1)){+                ret = 1;+              }+              break;+    }+    ++entries_seen;+  }++  return ret;+}
+ C/ViennaRNA/commands.h view
@@ -0,0 +1,131 @@+#ifndef VIENNA_RNA_PACKAGE_COMMANDS_H+#define VIENNA_RNA_PACKAGE_COMMANDS_H++/**+ *  @file     commands.h+ *  @ingroup  file_utils+ *  @brief    Parse and apply different commands that alter the behavior of+ *  secondary structure prediction and evaluation+ */++/**+ *  @{+ *  @ingroup  file_utils+ */++/** @brief Typename for the command repesenting data structure #vrna_command_s */+typedef struct vrna_command_s vrna_cmd_t;+++#include <ViennaRNA/data_structures.h>++/**+ * @brief Command parse/apply flag indicating hard constraints+ * @see   #vrna_command_s, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()+ */+#define VRNA_CMD_PARSE_HC      1U+/**+ * @brief Command parse/apply flag indicating soft constraints+ * @see   #vrna_command_s, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()+ */+#define VRNA_CMD_PARSE_SC      2U+/**+ * @brief Command parse/apply flag indicating unstructured domains+ * @see   #vrna_command_s, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()+ */+#define VRNA_CMD_PARSE_UD      4U+/**+ * @brief Command parse/apply flag indicating structured domains+ * @see   #vrna_command_s, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()+ */+#define VRNA_CMD_PARSE_SD      8U+/**+ * @brief Command parse/apply flag indicating default set of commands+ * @see   #vrna_command_s, vrna_file_commands_read(), vrna_file_commands_apply(), vrna_commands_apply()+ */+#define VRNA_CMD_PARSE_DEFAULTS (   VRNA_CMD_PARSE_HC \+                                  | VRNA_CMD_PARSE_SC \+                                  | VRNA_CMD_PARSE_UD \+                                  | VRNA_CMD_PARSE_SD \+                                )++/**+ *  @brief Types of commands within a list of #vrna_command_s structures+ */+typedef enum {+  VRNA_CMD_ERROR=-1,+  VRNA_CMD_LAST=0,+  VRNA_CMD_HC,+  VRNA_CMD_SC,+  VRNA_CMD_MOTIF,+  VRNA_CMD_UD,+  VRNA_CMD_SD+} vrna_command_e;++/**+ *  @brief List element for commands ready for application to a #vrna_fold_compound_t+ *  @see vrna_file_commands_read(), vrna_commands_apply(), vrna_commands_free()+ */+struct vrna_command_s {+  vrna_command_e  type;+  void *data;+};++/**+ *  @brief Extract a list of commands from a command file+ *+ *  Read a list of commands specified in the input file+ *  and return them as list of abstract commands+ *+ *  @see  vrna_commands_apply(), vrna_file_commands_apply(),+ *        vrna_commands_free()+ *+ *  @param    filename  The filename+ *  @param    options   Options to limit the type of commands read from the file+ *  @return             A list of abstract commands+ */+vrna_cmd_t *vrna_file_commands_read(const char *filename,+                                    unsigned int options);++/**+ *  @brief Apply a list of commands from a command file+ *+ *  This function is a shortcut to directly parse a commands file+ *  and apply all successfully parsed commands to a #vrna_fold_compound_t+ *  data structure. It is the same as:+ *  @snippet commands.c Applying commands from file+ *+ *  @param    vc        The #vrna_fold_compound_t the command list will be applied to+ *  @param    filename  The filename+ *  @param    options   Options to limit the type of commands read from the file+ *  @return             The number of commands successfully applied+ */+int vrna_file_commands_apply( vrna_fold_compound_t *vc,+                              const char *filename,+                              unsigned int options);++/**+ *  @brief Apply a list of commands to a #vrna_fold_compound_t+ *+ *  @param    vc        The #vrna_fold_compound_t the command list will be applied to+ *  @param    commands  The list of commands to apply+ *  @param    options   Options to limit the type of commands read from the file+ *  @return             The number of commands successfully applied+ */+int vrna_commands_apply(vrna_fold_compound_t *vc,+                        vrna_cmd_t *commands,+                        unsigned int options);++/**+ *  @brief Free memory occupied by a list of commands+ *+ *  Release memory occupied by a list of commands+ *  @param  commands  A pointer to a list of commands+ */+void vrna_commands_free( vrna_cmd_t *commands);++/**+ * @}+ */++#endif
+ C/ViennaRNA/constraints.c view
@@ -0,0 +1,59 @@+/* constraints handling */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <assert.h>+#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/file_formats.h"+#include "ViennaRNA/commands.h"+#include "ViennaRNA/constraints.h"+++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC  void+vrna_constraints_add( vrna_fold_compound_t *vc,+                      const char *constraint,+                      unsigned int options){++  if(vc){+    if(!vc->hc)+      vrna_hc_init(vc);++    if(options & VRNA_CONSTRAINT_DB){ /* apply hard constraints from dot-bracket notation */+      vrna_hc_add_from_db(vc, constraint, options);+    } else { /* constraints from file is the default */+      vrna_file_commands_apply(vc, constraint, VRNA_CMD_PARSE_HC | VRNA_CMD_PARSE_SC);+    }+  }+}
+ C/ViennaRNA/constraints.h view
@@ -0,0 +1,370 @@+#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H+#define VIENNA_RNA_PACKAGE_CONSTRAINTS_H++#include <ViennaRNA/data_structures.h>++/* include all structure constraint related headers */+#include <ViennaRNA/constraints_hard.h>+#include <ViennaRNA/constraints_soft.h>+#include <ViennaRNA/constraints_SHAPE.h>+#include <ViennaRNA/perturbation_fold.h>+#include <ViennaRNA/constraints_ligand.h>++/**+ *  @file     constraints.h+ *  @brief    Functions and data structures for constraining secondary structure predictions and evaluation+ *  @ingroup  constraints+ */++/**+ *  @brief  Flag for vrna_constraints_add() to indicate that constraints are present in a text file+ *+ *  @see vrna_constraints_add()+ *  @deprecated   Use 0 instead!+ *  @ingroup  constraints+ *+ */+#define VRNA_CONSTRAINT_FILE      0++/**+ *  @brief  Indicate generation of constraints for MFE folding+ *  @deprecated   This flag has no meaning anymore, since constraints are now always stored!+ *  @ingroup  constraints+ *+ */+#define VRNA_CONSTRAINT_SOFT_MFE  0++/**+ *  @brief  Indicate generation of constraints for partition function computation+ *  @deprecated   Use #VRNA_OPTION_PF instead!+ *  @ingroup  constraints+ *+ */+#define VRNA_CONSTRAINT_SOFT_PF   VRNA_OPTION_PF++/**+ *  @brief  Flag passed to generic softt constraints callback to indicate hairpin loop decomposition step+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a hairpin loop enclosed by the base pair @f$(i,j)@f$.+ *+ *  @image html   decomp_hp.svg+ *  @image latex  decomp_hp.eps+ *+ */+#define VRNA_DECOMP_PAIR_HP     1++/**+ *  @brief  Indicator for interior loop decomposition step+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an interior loop enclosed by the base pair @f$(i,j)@f$,+ *  and enclosing the base pair @f$(k,l)@f$.+ *+ *  @image html   decomp_il.svg+ *  @image latex  decomp_il.eps+ *+ */+#define VRNA_DECOMP_PAIR_IL     2++/**+ *  @brief  Indicator for multibranch loop decomposition step+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop enclosed by the base pair @f$(i,j)@f$,+ *  and consisting of some enclosed multi loop content from k to l.+ *+ *  @image html   decomp_ml.svg+ *  @image latex  decomp_ml.eps+ *+ */+#define VRNA_DECOMP_PAIR_ML     3++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into two multibranch loop parts @f$[i:k]@f$, and @f$[l:j]@f$.+ *+ *  @image html   decomp_ml_ml_ml.svg+ *  @image latex  decomp_ml_ml_ml.eps+ *+ */+#define VRNA_DECOMP_ML_ML_ML    5++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  which will be considered a single stem branching off with base pair @f$(k,l)@f$.+ *+ *  @image html   decomp_ml_stem.svg+ *  @image latex  decomp_ml_stem.eps+ *+ */+#define VRNA_DECOMP_ML_STEM     4++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into a (usually) smaller multibranch loop part @f$[k:l]@f$.+ *+ *  @image html   decomp_ml_ml.svg+ *  @image latex  decomp_ml_ml.eps+ *+ */+#define VRNA_DECOMP_ML_ML       6++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  which will be considered a multibranch loop part that only consists of unpaired+ *  nucleotides.+ *+ *  @image html   decomp_ml_up.svg+ *  @image latex  decomp_ml_up.eps+ *+ */+#define VRNA_DECOMP_ML_UP       11++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  which will decomposed into a multibranch loop part @f$[i:k]@f$, and a stem with+ *  enclosing base pair @f$(l,j)@f$.+ *+ *  @image html   decomp_ml_ml_stem.svg+ *  @image latex  decomp_ml_ml_stem.eps+ *+ */+#define VRNA_DECOMP_ML_ML_STEM 20++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  where two stems with enclosing pairs @f$(i,k)@f$ and @f$(l,j)@f$ are coaxially stacking+ *  onto each other.+ *+ *  @image html   decomp_ml_coaxial.svg+ *  @image latex  decomp_ml_coaxial.eps+ *+ */+#define VRNA_DECOMP_ML_COAXIAL  13++/**+ *  @brief  Indicator for decomposition of multibranch loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates a multibranch loop part in the interval @f$[i:j]@f$,+ *  where two stems with enclosing pairs @f$(i,k)@f$ and @f$(l,j)@f$ are coaxially stacking+ *  onto each other.+ *+ *  @image html   decomp_ml_coaxial.svg+ *  @image latex  decomp_ml_coaxial.eps+ *+ */+#define VRNA_DECOMP_ML_COAXIAL_ENC  22++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @def VRNA_DECOMP_EXT_EXT+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into a (usually) smaller exterior loop part @f$[k:l]@f$.+ *+ *  @image html   decomp_ext_ext.svg+ *  @image latex  decomp_ext_ext.eps+ *+ */+#define VRNA_DECOMP_EXT_EXT     9++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be considered as an exterior loop component consisting of only unpaired+ *  nucleotides.+ *+ *  @image html   decomp_ext_up.svg+ *  @image latex  decomp_ext_up.eps+ *+ */+#define VRNA_DECOMP_EXT_UP      8++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be considered a stem with enclosing pair @f$(k,l)@f$.+ *+ *  @image html   decomp_ext_stem.svg+ *  @image latex  decomp_ext_stem.eps+ *+ */+#define VRNA_DECOMP_EXT_STEM 14++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into two exterior loop parts @f$[i:k]@f$ and @f$[l:j]@f$.+ *+ *  @image html   decomp_ext_ext_ext.svg+ *  @image latex  decomp_ext_ext_ext.eps+ *+ */+#define VRNA_DECOMP_EXT_EXT_EXT 15++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into a stem branching off with base pair @f$(i,k)@f$, and+ *  an exterior loop part @f$[l:j]@f$.+ *+ *  @image html   decomp_ext_stem_ext.svg+ *  @image latex  decomp_ext_stem_ext.eps+ *+ */+#define VRNA_DECOMP_EXT_STEM_EXT 16++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ */+#define VRNA_DECOMP_EXT_STEM_OUTSIDE 17++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into an exterior loop part @f$[i:k]@f$, and a stem+ *  branching off with base pair @f$(l,j)@f$.+ *+ *  @image html   decomp_ext_ext_stem.svg+ *  @image latex  decomp_ext_ext_stem.eps+ *+ */+#define VRNA_DECOMP_EXT_EXT_STEM 18++/**+ *  @brief  Indicator for decomposition of exterior loop part+ *+ *  @ingroup  constraints+ *+ *  @def VRNA_DECOMP_EXT_EXT_STEM1+ *  @details This flag notifies the soft or hard constraint callback function that the current+ *  decomposition step evaluates an exterior loop part in the interval @f$[i:j]@f$,+ *  which will be decomposed into an exterior loop part @f$[i:k]@f$, and a stem+ *  branching off with base pair @f$(l,j-1)@f$.+ *+ *  @image html   decomp_ext_ext_stem1.svg+ *  @image latex  decomp_ext_ext_stem1.eps++ */+#define VRNA_DECOMP_EXT_EXT_STEM1 19+++#define VRNA_DECOMP_EXT_L         20+++#define VRNA_DECOMP_EXT_EXT_L     21++/**+ *  @brief  Add constraints to a #vrna_fold_compound_t data structure+ *+ *  Use this function to add/update the hard/soft constraints+ *  The function allows for passing a string 'constraint' that can either be a+ *  filename that points to a constraints definition file or it may be a+ *  pseudo dot-bracket notation indicating hard constraints. For the latter, the+ *  user has to pass the #VRNA_CONSTRAINT_DB option. Also, the+ *  user has to specify, which characters are allowed to be interpreted as+ *  constraints by passing the corresponding options via the third parameter.+ *+ *  @see      vrna_hc_init(), vrna_hc_add_up(), vrna_hc_add_up_batch(), vrna_hc_add_bp(),+ *            vrna_sc_init(), vrna_sc_set_up(), vrna_sc_set_bp(), + *            vrna_sc_add_SHAPE_deigan(),  vrna_sc_add_SHAPE_zarringhalam(),+ *            vrna_hc_free(), vrna_sc_free(),+ *            #VRNA_CONSTRAINT_DB, #VRNA_CONSTRAINT_DB_DEFAULT, #VRNA_CONSTRAINT_DB_PIPE,+ *            #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X, #VRNA_CONSTRAINT_DB_ANG_BRACK,+ *            #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTRAMOL,+ *            #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_GQUAD+ *+ *  @ingroup  constraints+ *+ *  The following is an example for adding hard constraints given in+ *  pseudo dot-bracket notation. Here, @p vc is the #vrna_fold_compound_t object,+ *  @p structure is a char array with the hard constraint in dot-bracket notation,+ *  and @p enforceConstraints is a flag indicating whether or not constraints for+ *  base pairs should be enforced instead of just doing a removal of base pair that+ *  conflict with the constraint.+ *+ *  @snippet RNAfold.c Adding hard constraints from pseudo dot-bracket+ *+ *  In constrat to the above, constraints may also be read from file:+ *+ *  @snippet RNAfold.c Adding hard constraints from file+ *+ *  @see  vrna_hc_add_from_db(), vrna_hc_add_up(), vrna_hc_add_up_batch()+ *        vrna_hc_add_bp_unspecific(), vrna_hc_add_bp()+ *+ *  @param  vc            The fold compound+ *  @param  constraint    A string with either the filename of the constraint definitions+ *                        or a pseudo dot-bracket notation of the hard constraint. May be NULL.+ *  @param  options       The option flags+ */+void vrna_constraints_add(vrna_fold_compound_t *vc,+                          const char *constraint,+                          unsigned int options);++#endif
+ C/ViennaRNA/constraints_SHAPE.c view
@@ -0,0 +1,575 @@+/* SHAPE reactivity data handling */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <assert.h>+#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/energy_const.h" /* defines MINPSCORE */+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/file_formats.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/constraints_SHAPE.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void+sc_parse_parameters(const char *string,+                    char c1,+                    char c2,+                    float *v1,+                    float *v2);++PRIVATE void+sc_add_stack_en_mfe(vrna_fold_compound_t *vc,+                    const FLT_OR_DBL *constraints,+                    unsigned int options);++PRIVATE void+prepare_Boltzmann_weights_stack(vrna_fold_compound_t *vc);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC void+vrna_constraints_add_SHAPE( vrna_fold_compound_t *vc,+                            const char *shape_file,+                            const char *shape_method,+                            const char *shape_conversion,+                            int verbose,+                            unsigned int constraint_type){++  float p1, p2;+  char method;+  char *sequence;+  double *values;+  int i, length = vc->length;++  if(!vrna_sc_SHAPE_parse_method(shape_method, &method, &p1, &p2)){+    vrna_message_warning("Method for SHAPE reactivity data conversion not recognized!");+    return;+  }++  if(verbose){+    if(method != 'W'){+      if(method == 'Z')+        vrna_message_info(stderr, "Using SHAPE method '%c' with parameter p1=%f", method, p1);+      else+        vrna_message_info(stderr, "Using SHAPE method '%c' with parameters p1=%f and p2=%f", method, p1, p2);+    }+  }++  sequence = vrna_alloc(sizeof(char) * (length + 1));+  values = vrna_alloc(sizeof(double) * (length + 1));+  vrna_file_SHAPE_read(shape_file, length, method == 'W' ? 0 : -1, sequence, values);++  if(method == 'D'){+    (void)vrna_sc_add_SHAPE_deigan(vc, (const double *)values, p1, p2, constraint_type);+  }+  else if(method == 'Z'){+    (void)vrna_sc_add_SHAPE_zarringhalam(vc, (const double *)values, p1, 0.5, shape_conversion, constraint_type);+  } else {+    assert(method == 'W');+    FLT_OR_DBL *v = vrna_alloc(sizeof(FLT_OR_DBL) * (length + 1));+    for(i = 0; i < length; i++)+      v[i] = values[i];++    vrna_sc_set_up(vc, v, constraint_type);++    free(v);+  }++  free(values);+  free(sequence);+}+++PUBLIC void+vrna_constraints_add_SHAPE_ali( vrna_fold_compound_t *vc,+                      const char *shape_method,+                      const char **shape_files,+                      const int  *shape_file_association,+                      int verbose,+                      unsigned int constraint_type){++  float p1, p2;+  char method;++  if(!vrna_sc_SHAPE_parse_method(shape_method, &method, &p1, &p2)){+    vrna_message_warning("Method for SHAPE reactivity data conversion not recognized!");+    return;+  }++  if(verbose){+    if(method != 'W'){+      if(method == 'Z')+        vrna_message_info( stderr,+                                  "Using SHAPE method '%c' with parameter p1=%f",+                                  method, p1);+      else+        vrna_message_info( stderr,+                                  "Using SHAPE method '%c' with parameters p1=%f and p2=%f",+                                  method, p1, p2);+    }+  }++  if(method == 'D'){+    vrna_sc_add_SHAPE_deigan_ali(vc, shape_files, shape_file_association, p1, p2, constraint_type);+    return;+  }+}+++PUBLIC int+vrna_sc_SHAPE_to_pr(const char *shape_conversion,+                    double *values,+                    int length,+                    double default_value){++  int *indices;+  int i, j;+  int index;+  int ret = 1;++  if(!shape_conversion || !(*shape_conversion) || length <= 0)+    return 0;++  if(*shape_conversion == 'S')+    return 1;++  indices = vrna_alloc(sizeof(int) * (length + 1));+  for (i = 1, j = 0; i <= length; ++i){+    if(values[i] < 0)+      values[i] = default_value;+    else+      indices[j++] = i;+  }++  if(*shape_conversion == 'M'){+    double max;+    double map_info[4][2] = {{0.25, 0.35},+                           {0.30, 0.55},+                           {0.70, 0.85},+                           {0, 1}};++    max = values[1];+    for(i = 2; i <= length; ++i)+      max = MAX2(max, values[i]);+    map_info[3][0] = max;++    for(i = 0; indices[i]; ++i){+      double lower_source = 0;+      double lower_target = 0;++      index = indices[i];++      if(values[index] == 0)+        continue;++      for(j = 0; j < 4; ++j){+        if(values[index] > lower_source && values[index] <= map_info[j][0]){+          double diff_source = map_info[j][0] - lower_source;+          double diff_target = map_info[j][1] - lower_target;+          values[index] = (values[index] - lower_source) / diff_source * diff_target + lower_target;+          break;+        }++        lower_source = map_info[j][0];+        lower_target = map_info[j][1];+      }+    }+  }+  else if (*shape_conversion == 'C'){+    float cutoff = 0.25;+    int i;++    sscanf(shape_conversion + 1, "%f", &cutoff);++    for(i = 0; indices[i]; ++i){+      index = indices[i];+      values[index] = values[index] < cutoff ? 0 : 1;+    }+  }+  else if (*shape_conversion == 'L' || *shape_conversion == 'O'){+    int i;+    float slope = (*shape_conversion == 'L') ? 0.68 : 1.6;+    float intercept = (*shape_conversion == 'L') ? 0.2 : -2.29;++    sc_parse_parameters(shape_conversion + 1, 's', 'i', &slope, &intercept);++    for(i = 0; indices[i]; ++i){+      double v;+      index = indices[i];++      v = (*shape_conversion == 'L') ? values[index] : log(values[index]);+      values[index] = MAX2(MIN2((v - intercept) / slope, 1),0);+    }+  }+  else+    ret = 0;++  free(indices);++  return ret;+}++PUBLIC  int+vrna_sc_add_SHAPE_zarringhalam( vrna_fold_compound_t *vc,+                                const double *reactivities,+                                double b,+                                double default_value,+                                const char *shape_conversion,+                                unsigned int options){++  int       i, j, n, ret;+  double        *pr;+  FLT_OR_DBL    *up, **bp;+  vrna_md_t *md;++  ret = 0; /* error */++  if(vc && reactivities && (vc->type == VRNA_FC_TYPE_SINGLE)){+    n   = vc->length;+    md  = &(vc->params->model_details);++    /* first we copy over the reactivities to convert them into probabilities later on */+    pr = (double *)vrna_alloc(sizeof(double) * (n + 1));+    for(i=0; i<=n; i++)+      pr[i] = reactivities[i];++    if(vrna_sc_SHAPE_to_pr(shape_conversion, pr, n, default_value)){++      /*  now, convert them into pseudo free energies for unpaired, and+          paired nucleotides+      */+      up = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+      bp = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 1));+      for(i = 1; i <= n; ++i){+        up[i] = b * fabs(pr[i] - 1);+        bp[i] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+        for(j = i + md->min_loop_size + 1; j <= n; ++j)+          bp[i][j] = b * (pr[i] + pr[j]);+      }++      /* add the pseudo energies as soft constraints */+      vrna_sc_set_up(vc, (const FLT_OR_DBL *)up, options);+      vrna_sc_set_bp(vc, (const FLT_OR_DBL **)bp, options);++      /* clean up memory */+      for(i = 1; i <= n; ++i)+        free(bp[i]);+      free(bp);+      free(up);++      ret = 1; /* success */+    }++    free(pr);++  }++  return ret;+}+++PUBLIC int+vrna_sc_add_SHAPE_deigan( vrna_fold_compound_t *vc,+                          const double *reactivities,+                          double m,+                          double b,+                          unsigned int options){++  int     i;+  FLT_OR_DBL  *values;++  if(vc && (vc->type == VRNA_FC_TYPE_SINGLE)){+    if(reactivities){++      values = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (vc->length + 1));++      /* first convert the values according to provided slope and intercept values */+      for (i = 1; i <= vc->length; ++i){+        values[i] = reactivities[i] < 0 ? 0. : (FLT_OR_DBL)(m * log(reactivities[i] + 1) + b);+      }++      /* always store soft constraints in plain format */+      sc_add_stack_en_mfe(vc, (const FLT_OR_DBL *)values, options);+      free(values);+    }++    if(options & VRNA_OPTION_PF)+      prepare_Boltzmann_weights_stack(vc);++    return 1; /* success */+  }+  return 0; /* error */+}++PUBLIC int+vrna_sc_add_SHAPE_deigan_ali( vrna_fold_compound_t *vc,+                              const char **shape_files,+                              const int *shape_file_association,+                              double m,+                              double b,+                              unsigned int options){++  float           reactivity, *reactivities, e1;+  char            *line, nucleotide, *sequence;+  int             s, i, p, r, position, *pseudo_energies, n_seq;+  unsigned short  **a2s;++  if(vc && (vc->type == VRNA_FC_TYPE_COMPARATIVE)){+    n_seq = vc->n_seq;+    a2s   = vc->a2s;++    vrna_sc_init(vc);++    for(s = 0; shape_file_association[s] != -1; s++){+      int ss = shape_file_association[s]; /* actual sequence number in alignment */++      if(ss >= n_seq){+        vrna_message_warning("SHAPE file association exceeds sequence number in alignment");+        continue;+      }++      /* read the shape file */+      FILE *fp;+      if(!(fp = fopen(shape_files[s], "r"))){+        vrna_message_warning("SHAPE data file %d could not be opened. No shape data will be used.", s);+      } else {++        reactivities  = (float *)vrna_alloc(sizeof(float) * (vc->length + 1));+        sequence      = (char *)vrna_alloc(sizeof(char) * (vc->length + 1));++        /* initialize reactivities with missing data for entire alignment length */+        for(i = 1; i <= vc->length; i++)+          reactivities[i] = -1.;++        while((line=vrna_read_line(fp))){+          r = sscanf(line, "%d %c %f", &position, &nucleotide, &reactivity);+          if(r){+            if((position <= 0) || (position > vc->length))+              vrna_message_error("provided shape data outside of sequence scope");++            switch(r){+              case 1:   nucleotide = 'N';+                        /* fall through */+              case 2:   reactivity = -1.;+                        /* fall through */+              default:  sequence[position-1]    = nucleotide;+                        reactivities[position]  = reactivity;+                        break;+            }+          }+          free(line);+        }+        fclose(fp);++        sequence[vc->length] = '\0';++        /* double check information by comparing the sequence read from */+        char *tmp_seq = get_ungapped_sequence(vc->sequences[shape_file_association[s]]);+        if(strcmp(tmp_seq, sequence)){+          vrna_message_warning("Input sequence %d differs from sequence provided via SHAPE file!\n", shape_file_association[s]);+        }+        free(tmp_seq);++        /* convert reactivities to pseudo energies */+        for(i = 1; i <= vc->length; i++){+          if(reactivities[i] < 0)+            reactivities[i] = 0.;+          else+            reactivities[i] = m * log(reactivities[i] + 1.) + b; /* this should be a value in kcal/mol */+        }++        /*  begin actual storage of the pseudo energies */+        /*  beware of the fact that energy_stack will be accessed through a2s[s] array,+            hence pseudo_energy might be gap-free (default)+        */+        /* ALWAYS store soft constraints in plain format */+        int energy, cnt, gaps, is_gap;+        pseudo_energies = (int *)vrna_alloc(sizeof(int) * (vc->length + 1));+        for(gaps = cnt = 0, i = 1; i<=vc->length; i++){+          is_gap  = (vc->sequences[ss][i-1] == '-') ? 1 : 0;+          energy  = ((i - gaps > 0) && !(is_gap)) ? (int)roundf(reactivities[i - gaps] * 100.) : 0;++          if(vc->params->model_details.oldAliEn){+            pseudo_energies[i] = energy;+            cnt++;+          } else if(!is_gap){ /* store gap-free */+            pseudo_energies[a2s[ss][i]] = energy;+            cnt++;+          }++          gaps += is_gap;+        }++        /* resize to actual number of entries */+        pseudo_energies = vrna_realloc(pseudo_energies, sizeof(int) * (cnt + 2));+        vc->scs[ss]->energy_stack = pseudo_energies;++        if(options & VRNA_OPTION_PF){+          FLT_OR_DBL *exp_pe = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (vc->length + 1));+          for(i=0;i<=vc->length;i++)+            exp_pe[i] = 1.;++          for(p = 0, i = 1; i<=vc->length; i++){+            e1 = (i - p > 0) ? reactivities[i - p] : 0.;+            if(vc->sequences[ss][i-1] == '-'){+              p++; e1 = 0.;+            }+            exp_pe[i] = (FLT_OR_DBL)exp(-(e1 * 1000.) / vc->exp_params->kT );+          }+          vc->scs[ss]->exp_energy_stack = exp_pe;+        }+        +        free(reactivities);+      }+    }++    return 1; /* success */+  } else {+    return 0; /* error */+  }+}++PUBLIC  int+vrna_sc_SHAPE_parse_method( const char *method_string,+                            char *method,+                            float *param_1,+                            float *param_2){++  const char *params = method_string + 1;++  *param_1 = 0;+  *param_2 = 0;++  if (!method_string || !method_string[0])+    return 0;++  *method = method_string[0];++  switch(method_string[0]){+    case 'Z':   *param_1 = 0.89;+                sc_parse_parameters(params, 'b', '\0', param_1, NULL);+                break;++    case 'D':   *param_1 = 1.8;+                *param_2 = -0.6;+                sc_parse_parameters(params, 'm', 'b', param_1, param_2);+                break;++    case 'W':   break;++    default:    *method = 0;+                return 0;+  }++  return 1;+}++PRIVATE void+sc_parse_parameters( const char *string,+                        char c1,+                        char c2,+                        float *v1,+                        float *v2){++  char fmt[8];+  const char warning[] = "SHAPE method parameters not recognized! Using default parameters!";+  int r;++  assert(c1);+  assert(v1);++  if(!string || !(*string))+    return;++  if(c2 == 0 || v2 == NULL){+    sprintf(fmt, "%c%%f", c1);+    r = sscanf(string, fmt, v1);++    if(!r)+      vrna_message_warning(warning);++    return;+  }++  sprintf(fmt, "%c%%f%c%%f", c1, c2);+  r = sscanf(string, fmt, v1, v2);++  if(r!=2){+    sprintf(fmt, "%c%%f", c1);+    r = sscanf(string, fmt, v1);++    if(!r){+      sprintf(fmt, "%c%%f", c2);+      r = sscanf(string, fmt, v2);++      if(!r)+        vrna_message_warning(warning);+    }+  }+}++PRIVATE void+sc_add_stack_en_mfe(vrna_fold_compound_t *vc,+                    const FLT_OR_DBL *constraints,+                    unsigned int options){+  int i;++  if(!vc->sc)+    vrna_sc_init(vc);++  if(!vc->sc->energy_stack)+    vc->sc->energy_stack = (int *)vrna_alloc(sizeof(int) * (vc->length + 1));++  for(i = 1; i <= vc->length; ++i)+    vc->sc->energy_stack[i] = (int)roundf(constraints[i] * 100.);+}++PRIVATE void+prepare_Boltzmann_weights_stack(vrna_fold_compound_t *vc){+  int i;+  vrna_sc_t *sc = vc->sc;++  if(sc->energy_stack){+    if(!sc->exp_energy_stack){+      sc->exp_energy_stack = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (vc->length + 1));+      for(i = 0; i <= vc->length; ++i)+        sc->exp_energy_stack[i] = 1.;+    }++    for(i = 1; i <= vc->length; ++i)+      sc->exp_energy_stack[i] = (FLT_OR_DBL)exp(-(sc->energy_stack[i] * 10.)/ vc->exp_params->kT);+  }+}+
+ C/ViennaRNA/constraints_SHAPE.h view
@@ -0,0 +1,142 @@+#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H+#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H++#include <ViennaRNA/data_structures.h>++/**+ *  @file constraints_SHAPE.h+ *  @brief This module provides function to incorporate SHAPE reactivity data+ *  into the folding recursions by means of soft constraints+ *+ *  @ingroup SHAPE_reactivities+ */++void vrna_constraints_add_SHAPE(vrna_fold_compound_t *vc,+                                const char *shape_file,+                                const char *shape_method,+                                const char *shape_conversion,+                                int verbose,+                                unsigned int constraint_type);++void vrna_constraints_add_SHAPE_ali(vrna_fold_compound_t *vc,+                                    const char *shape_method,+                                    const char **shape_files,+                                    const int  *shape_file_association,+                                    int verbose,+                                    unsigned int constraint_type);+/**+ *  @brief  Add SHAPE reactivity data as soft constraints (Deigan et al. method)+ *+ *  This approach of SHAPE directed RNA folding uses the simple linear ansatz+ *  @f[ \Delta G_{\text{SHAPE}}(i) = m \ln(\text{SHAPE reactivity}(i)+1)+ b @f]+ *  to convert SHAPE reactivity values to pseudo energies whenever a+ *  nucleotide @f$ i @f$ contributes to a stacked pair. A positive slope @f$ m @f$+ *  penalizes high reactivities in paired regions, while a negative intercept @f$ b @f$+ *  results in a confirmatory ``bonus'' free energy for correctly predicted base pairs.+ *  Since the energy evaluation of a base pair stack involves two pairs, the pseudo+ *  energies are added for all four contributing nucleotides. Consequently, the+ *  energy term is applied twice for pairs inside a helix and only once for pairs+ *  adjacent to other structures. For all other loop types the energy model remains+ *  unchanged even when the experimental data highly disagrees with a certain motif.+ *+ *  @see  For further details, we refer to @cite deigan:2009.+ *  @see  vrna_sc_remove(), vrna_sc_add_SHAPE_zarringhalam(), vrna_sc_minimize_pertubation()+ *  @ingroup SHAPE_reactivities+ *  @param  vc            The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  reactivities  A vector of normalized SHAPE reactivities+ *  @param  m             The slope of the conversion function+ *  @param  b             The intercept of the conversion function+ *  @param  options       The options flag indicating how/where to store the soft constraints+ *  @return               1 on successful extraction of the method, 0 on errors+ */+int vrna_sc_add_SHAPE_deigan( vrna_fold_compound_t *vc,+                              const double *reactivities,+                              double m,+                              double b,+                              unsigned int options);++/**+ *  @brief  Add SHAPE reactivity data from files as soft constraints for consensus structure prediction (Deigan et al. method)+ *+ *  @ingroup SHAPE_reactivities+ *  @param  vc            The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  shape_files   A set of filenames that contain normalized SHAPE reactivity data+ *  @param  shape_file_association  An array of integers that associate the files with sequences in the alignment+ *  @param  m             The slope of the conversion function+ *  @param  b             The intercept of the conversion function+ *  @param  options       The options flag indicating how/where to store the soft constraints+ *  @return               1 on successful extraction of the method, 0 on errors+ */+int vrna_sc_add_SHAPE_deigan_ali( vrna_fold_compound_t *vc,+                                  const char **shape_files,+                                  const int *shape_file_association,+                                  double m,+                                  double b,+                                  unsigned int options);++/**+ *  @brief  Add SHAPE reactivity data as soft constraints (Zarringhalam et al. method)+ *+ *  This method first converts the observed SHAPE reactivity of nucleotide @f$ i @f$ into a+ *  probability @f$ q_i @f$ that position @f$ i @f$ is unpaired by means of a non-linear map.+ *  Then pseudo-energies of the form @f[ \Delta G_{\text{SHAPE}}(x,i) = \beta\ |x_i - q_i| @f]+ *  are computed, where @f$ x_i=0 @f$ if position @f$ i @f$ is unpaired and @f$ x_i=1 @f$+ *  if @f$ i @f$ is paired in a given secondary structure. The parameter @f$ \beta @f$ serves as+ *  scaling factor. The magnitude of discrepancy between prediction and experimental observation+ *  is represented by @f$ |x_i - q_i| @f$.+ *+ *  @see For further details, we refer to @cite zarringhalam:2012+ *  @see  vrna_sc_remove(), vrna_sc_add_SHAPE_deigan(), vrna_sc_minimize_pertubation()+ *  @ingroup SHAPE_reactivities+ *  @param  vc                The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  reactivities      A vector of normalized SHAPE reactivities+ *  @param  b                 The scaling factor @f$ \beta @f$ of the conversion function+ *  @param  default_value     The default value for a nucleotide where reactivity data is missing for+ *  @param  shape_conversion  A flag that specifies how to convert reactivities to probabilities+ *  @param  options           The options flag indicating how/where to store the soft constraints+ *  @return                   1 on successful extraction of the method, 0 on errors+ */+int vrna_sc_add_SHAPE_zarringhalam( vrna_fold_compound_t *vc,+                                    const double *reactivities,+                                    double b,+                                    double default_value,+                                    const char *shape_conversion,+                                    unsigned int options);++/**+ *  @brief  Parse a character string and extract the encoded SHAPE reactivity conversion+ *          method and possibly the parameters for conversion into pseudo free energies+ *+ *  @ingroup soft_cosntraints+ *+ *  @param  method_string   The string that contains the encoded SHAPE reactivity conversion method+ *  @param  method          A pointer to the memory location where the method character will be stored+ *  @param  param_1         A pointer to the memory location where the first parameter of the corresponding method will be stored+ *  @param  param_2         A pointer to the memory location where the second parameter of the corresponding method will be stored+ *  @return                 1 on successful extraction of the method, 0 on errors+ */+int vrna_sc_SHAPE_parse_method( const char *method_string,+                                char *method,+                                float *param_1,+                                float *param_2);++/**+ *  @brief Convert SHAPE reactivity values to probabilities for being unpaired+ *+ *  This function parses the informations from a given file and stores the result+ *  in the preallocated string sequence and the #FLT_OR_DBL array values.+ *+ *  @ingroup SHAPE_reactivities+ *+ *  @see vrna_file_SHAPE_read()+ *  @param shape_conversion String definining the method used for the conversion process+ *  @param values           Pointer to an array of SHAPE reactivities+ *  @param length           Length of the array of SHAPE reactivities+ *  @param default_value    Result used for position with invalid/missing reactivity values+ */+int vrna_sc_SHAPE_to_pr(const char *shape_conversion,+                        double *values,+                        int length,+                        double default_value);++#endif
+ C/ViennaRNA/constraints_hard.c view
@@ -0,0 +1,1056 @@+/* constraints handling */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <assert.h>+#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/energy_const.h" /* defines MINPSCORE */+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/file_formats.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/constraints_hard.h"+++#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void+hc_add_up(vrna_fold_compound_t *vc,+          int i,+          char option);++PRIVATE INLINE  void+hc_cant_pair( unsigned int i,+              char c_option,+              char *hc,+              unsigned int length,+              unsigned int min_loop_size,+              int *index);++PRIVATE INLINE  void+hc_must_pair( unsigned int i,+              char c_option,+              char *hc,+              int *index);++PRIVATE INLINE  void+hc_pairs_upstream(unsigned int i,+                  char c_option,+                  char *hc,+                  unsigned int length,+                  int *index);++PRIVATE INLINE  void+hc_pairs_downstream(unsigned int i,+                    char c_option,+                    char *hc,+                    unsigned int length,+                    int *index);++PRIVATE INLINE  void+hc_allow_pair(unsigned int i,+              unsigned int j,+              char c_option,+              char *hc,+              int *index);++PRIVATE INLINE  void+hc_weak_enforce_pair( unsigned int i,+                      unsigned int j,+                      char c_option,+                      char *hc,+                      unsigned int length,+                      unsigned int min_loop_size,+                      int *index);++PRIVATE INLINE  void+hc_enforce_pair(unsigned int i,+                unsigned int j,+                char c_option,+                char *hc,+                unsigned int length,+                unsigned int min_loop_size,+                int *index);++PRIVATE INLINE  void+hc_intramolecular_only( unsigned int i,+                        char c_option,+                        char *hc,+                        unsigned int length,+                        unsigned int min_loop_size,+                        int cut,+                        int *index);++PRIVATE INLINE  void+hc_intermolecular_only( unsigned int i,+                        char c_option,+                        char *hc,+                        unsigned int length,+                        unsigned int min_loop_size,+                        int cut,+                        int *index);++PRIVATE void+apply_DB_constraint(const char *constraint,+                    char *ptype,+                    unsigned int length,+                    unsigned int min_loop_size,+                    int cut,+                    unsigned int options);++PRIVATE void+hc_reset_to_default(vrna_fold_compound_t *vc);++PRIVATE void+hc_update_up(vrna_fold_compound_t *vc);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC  void+vrna_message_constraint_options_all(void){++  vrna_message_constraint_options(  VRNA_CONSTRAINT_DB_PIPE+                                  | VRNA_CONSTRAINT_DB_DOT+                                  | VRNA_CONSTRAINT_DB_X+                                  | VRNA_CONSTRAINT_DB_ANG_BRACK+                                  | VRNA_CONSTRAINT_DB_RND_BRACK);+}++PUBLIC  void+vrna_message_constraint_options(unsigned int option){++  printf("Input structure constraints using the following notation:\n");+  if(option & VRNA_CONSTRAINT_DB_PIPE)       printf("| : paired with another base\n");+  if(option & VRNA_CONSTRAINT_DB_DOT)        printf(". : no constraint at all\n");+  if(option & VRNA_CONSTRAINT_DB_X)          printf("x : base must not pair\n");+  if(option & VRNA_CONSTRAINT_DB_ANG_BRACK)  printf("< : base i is paired with a base j<i\n> : base i is paired with a base j>i\n");+  if(option & VRNA_CONSTRAINT_DB_RND_BRACK)  printf("matching brackets ( ): base i pairs base j\n");+}++PUBLIC  void+vrna_hc_init(vrna_fold_compound_t *vc){++  unsigned int  n;+  vrna_hc_t     *hc;++  n           = vc->length;++  /* free previous hard constraints */+  vrna_hc_free(vc->hc);++  /* allocate memory new hard constraints data structure */+  hc          = (vrna_hc_t *)vrna_alloc(sizeof(vrna_hc_t));+  hc->matrix  = (char *)vrna_alloc(sizeof(char)*((n*(n+1))/2+2));+  hc->up_ext  = (int *)vrna_alloc(sizeof(int)*(n+2));+  hc->up_hp   = (int *)vrna_alloc(sizeof(int)*(n+2));+  hc->up_int  = (int *)vrna_alloc(sizeof(int)*(n+2));+  hc->up_ml   = (int *)vrna_alloc(sizeof(int)*(n+2));++  /* set new hard constraints */+  vc->hc = hc;++  /* prefill default values  */+  hc_reset_to_default(vc);++  /* add null pointers for the generalized hard constraint feature */+  hc->f           = NULL;+  hc->data        = NULL;+  hc->free_data   = NULL;++  /* update */+  hc_update_up(vc);+}++PUBLIC void+vrna_hc_add_up( vrna_fold_compound_t *vc,+                int i,+                char option){++  int j;++  if(vc)+    if(vc->hc){+      if((i <= 0) || (i > vc->length)){+        vrna_message_warning("vrna_hc_add_up: position out of range, not doing anything");+        return;+      }++      hc_add_up(vc, i, option);++      hc_update_up(vc);+    }+}++PUBLIC int+vrna_hc_add_up_batch( vrna_fold_compound_t *vc,+                      vrna_hc_up_t *constraints){++  int i, ret;++  ret = 0; /* failure */++  if(vc)+    if(vc->hc && constraints){+      for(i = 0; constraints[i].position != 0; i++){+        int pos       = constraints[i].position;+        char options  = constraints[i].options;+        if((pos <= 0) || (pos > vc->length)){+          vrna_message_warning("vrna_hc_add_up_batch: position out of range, application of hard constraints stops here!");+          return ret;+        }+        hc_add_up(vc, pos, options);+      }++      hc_update_up(vc);+      ret = 1; /* success */+    }++  return ret;+}++PRIVATE void+hc_add_up(vrna_fold_compound_t *vc,+          int i,+          char option){++  int   j;+  char  type = (char)0;++  if(option & VRNA_CONSTRAINT_CONTEXT_ENFORCE){ /* force nucleotide to appear unpaired within a certain type of loop */+    /* do not allow i to be paired with any other nucleotide */+    if(!(option & VRNA_CONSTRAINT_CONTEXT_NO_REMOVE)){+      for(j = 1; j < i; j++)+        vc->hc->matrix[vc->jindx[i] + j] = (char)0;+      for(j = i+1; j <= vc->length; j++)+        vc->hc->matrix[vc->jindx[j] + i] = (char)0;+    }++    type = option & (char)( VRNA_CONSTRAINT_CONTEXT_EXT_LOOP+                            | VRNA_CONSTRAINT_CONTEXT_HP_LOOP+                            | VRNA_CONSTRAINT_CONTEXT_INT_LOOP+                            | VRNA_CONSTRAINT_CONTEXT_MB_LOOP);++    vc->hc->matrix[vc->jindx[i] + i] = type;+  } else {+    type = option & VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;++    /* do not allow i to be paired with any other nucleotide (in context type) */+    if(!(option & VRNA_CONSTRAINT_CONTEXT_NO_REMOVE)){+      for(j = 1; j < i; j++)+        vc->hc->matrix[vc->jindx[i] + j] &= ~type;+      for(j = i+1; j <= vc->length; j++)+        vc->hc->matrix[vc->jindx[j] + i] &= ~type;+    }++    vc->hc->matrix[vc->jindx[i] + i] = (char)(  VRNA_CONSTRAINT_CONTEXT_EXT_LOOP+                                              | VRNA_CONSTRAINT_CONTEXT_HP_LOOP+                                              | VRNA_CONSTRAINT_CONTEXT_INT_LOOP+                                              | VRNA_CONSTRAINT_CONTEXT_MB_LOOP);+  }+}++PUBLIC void+vrna_hc_add_bp_nonspecific( vrna_fold_compound_t *vc,+                            int i,+                            int d,+                            char option){+  int   p;+  char  type, t1, t2;++  if(vc)+    if(vc->hc){+      if((i <= 0) || (i > vc->length)){+        vrna_message_warning("vrna_hc_add_bp_nonspecific: position out of range, not doing anything");+        return;+      }++      /* position i may pair in provided contexts */+      type  = option & VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+      /* acknowledge pairing direction */+      t1    = (d <= 0) ? type : (char)0;+      t2    = (d >= 0) ? type : (char)0;++      if(option & VRNA_CONSTRAINT_CONTEXT_NO_REMOVE){+        /* only allow for possibly non-canonical pairs, do not enforce them */+        for(p = 1; p < i; p++)+          vc->hc->matrix[vc->jindx[i] + p] |= t1;+        for(p = i+1; p <= vc->length; p++)+          vc->hc->matrix[vc->jindx[p] + i] |= t2;+      } else {+        /* force pairing direction */+        for(p = 1; p < i; p++)+          vc->hc->matrix[vc->jindx[i] + p] &= t1;+        for(p = i+1; p <= vc->length; p++)+          vc->hc->matrix[vc->jindx[p] + i] &= t2;+        /* nucleotide mustn't be unpaired */+        vc->hc->matrix[vc->jindx[i] + i] = (char)0;+      }++      hc_update_up(vc);+    }++}++PUBLIC void+vrna_hc_add_bp( vrna_fold_compound_t *vc,+                int i,+                int j,+                char option){++  int   k, l;+  char  type;++  if(vc)+    if(vc->hc){+      if((i <= 0) || (j <= i) || (j > vc->length)){+        vrna_message_warning("vrna_hc_add_bp: position out of range, not doing anything");+        return;+      }++      /* reset ptype in case (i,j) is a non-canonical pair */+      if(option & VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS){+        if(vc->hc->matrix[vc->jindx[j] + i])+          if(vc->ptype[vc->jindx[j] + i] == 0)+            vc->ptype[vc->jindx[j] + i] = 7;+      }++      vc->hc->matrix[vc->jindx[j] + i] = option & VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;++      if(!(option & VRNA_CONSTRAINT_CONTEXT_NO_REMOVE)){+        /*+          remove all conflicting base pairs, i.e. do not allow i,j to pair+          with any other nucleotide k+        */+        for(k = 1; k < i; k++){+          vc->hc->matrix[vc->jindx[i] + k] = (char)0;+          vc->hc->matrix[vc->jindx[j] + k] = (char)0;+          for(l = i+1; l < j; l++)+            vc->hc->matrix[vc->jindx[l] + k] = (char)0;+        }+        for(k = i+1; k < j; k++){+          vc->hc->matrix[vc->jindx[k] + i] = (char)0;+          vc->hc->matrix[vc->jindx[j] + k] = (char)0;+          for(l = j + 1; l <= vc->length; l++)+            vc->hc->matrix[vc->jindx[l] + k] = (char)0;+        }+        for(k = j+1; k <= vc->length; k++){+          vc->hc->matrix[vc->jindx[k] + i] = (char)0;+          vc->hc->matrix[vc->jindx[k] + j] = (char)0;+        }+      }++      if(option & VRNA_CONSTRAINT_CONTEXT_ENFORCE){++        /* do not allow i,j to be unpaired */+        vc->hc->matrix[vc->jindx[i] + i] = (char)0;+        vc->hc->matrix[vc->jindx[j] + j] = (char)0;++        hc_update_up(vc);+      }+    }+}++PUBLIC void+vrna_hc_free(vrna_hc_t *hc){++  if(hc){+    free(hc->matrix);+    free(hc->up_ext);+    free(hc->up_hp);+    free(hc->up_int);+    free(hc->up_ml);++    if(hc->free_data)+      hc->free_data(hc->data);++    free(hc);+  }+}+++PUBLIC void+vrna_hc_add_f(vrna_fold_compound_t *vc,+              vrna_callback_hc_evaluate *f)+{+  if (vc && f) {+    if (vc->type == VRNA_FC_TYPE_SINGLE) {+      if (!vc->hc)+        vrna_hc_init(vc);++      vc->hc->f = f;+    }+  }+}+++PUBLIC void+vrna_hc_add_data( vrna_fold_compound_t *vc,+                  void *data,+                  vrna_callback_free_auxdata *f)+{+  if (vc && data) {+    if (vc->type == VRNA_FC_TYPE_SINGLE) {+      if (!vc->hc)+        vrna_hc_init(vc);++      vc->hc->data        = data;+      vc->hc->free_data   = f;+    }+  }+}+++PUBLIC  int+vrna_hc_add_from_db(vrna_fold_compound_t *vc,+                    const char *constraint,+                    unsigned int options){++  int         i, d, ret;+  vrna_md_t   *md;++  ret = 0; /* Failure */++  if(vc){+    if(vc->params)+      md = &(vc->params->model_details);+    else if(vc->exp_params)+      md = &(vc->exp_params->model_details);+    else+      return ret;++    if(!vc->hc)+      vrna_hc_init(vc);++    /* apply hard constraints from dot-bracket notation */+    apply_DB_constraint(constraint,+                        vc->hc->matrix,+                        vc->length,+                        md->min_loop_size,+                        -1,+                        options);+    hc_update_up(vc);+    ret = 1; /* Success */+  }++  return ret;+}+++PRIVATE void+apply_DB_constraint(const char *constraint,+                    char *hc,+                    unsigned int length,+                    unsigned int min_loop_size,+                    int cut,+                    unsigned int options){++  int n,i,j;+  int hx, *stack;+  int *index;+  char c_option;++  if(constraint == NULL) return;++  n         = (int)strlen(constraint);+  stack     = (int *) vrna_alloc(sizeof(int)*(n+1));+  index     = vrna_idx_col_wise(length);+  c_option  =   VRNA_CONSTRAINT_CONTEXT_EXT_LOOP+              | VRNA_CONSTRAINT_CONTEXT_HP_LOOP+              | VRNA_CONSTRAINT_CONTEXT_INT_LOOP+              | VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC+              | VRNA_CONSTRAINT_CONTEXT_MB_LOOP+              | VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC;++  for(hx=0, j=1; j<=n; j++) {+    switch (constraint[j-1]) {+       /* can't pair */+       case 'x':  if(options & VRNA_CONSTRAINT_DB_X){+                    hc_cant_pair(j, c_option, hc, length, min_loop_size, index);+                  }+                  break;++      /* must pair, i.e. may not be unpaired */+      case '|':   if(options & VRNA_CONSTRAINT_DB_PIPE){+                    if(options & VRNA_CONSTRAINT_DB_ENFORCE_BP)+                      hc_must_pair(j, c_option, hc, index);+                  }+                  break;++      /* weak enforced pair 'open' */+      case '(':   if(options & VRNA_CONSTRAINT_DB_RND_BRACK){+                    stack[hx++]=j;+                  }+                  break;++      /* weak enforced pair 'close' */+      case ')':   if(options & VRNA_CONSTRAINT_DB_RND_BRACK){+                    if (hx<=0) {+                      vrna_message_error("%s\nunbalanced brackets in constraints", constraint);+                    }+                    i = stack[--hx];+                    if(options & VRNA_CONSTRAINT_DB_ENFORCE_BP)+                      hc_enforce_pair(i, j, c_option, hc, length, min_loop_size, index);+                    else+                      hc_weak_enforce_pair(i, j, c_option, hc, length, min_loop_size, index);+                  }+                  break;++      /* pairs upstream */+      case '<':   if(options & VRNA_CONSTRAINT_DB_ANG_BRACK){+                    hc_pairs_downstream(j, c_option, hc, length, index);+                    if(options & VRNA_CONSTRAINT_DB_ENFORCE_BP)+                      hc_must_pair(j, c_option, hc, index);+                  }+                  break;++      /* pairs downstream */+      case '>':   if(options & VRNA_CONSTRAINT_DB_ANG_BRACK){+                    hc_pairs_upstream(j, c_option, hc, length, index);+                    if(options & VRNA_CONSTRAINT_DB_ENFORCE_BP)+                      hc_must_pair(j, c_option, hc, index);+                  }+                  break;++      /* only intramolecular basepairing */+      case 'l':   if(options & VRNA_CONSTRAINT_DB_INTRAMOL){+                    hc_intramolecular_only(j, c_option, hc, length, min_loop_size, cut, index);+                  }+                  break;++      /* only intermolecular bp */+      case 'e':   if(options & VRNA_CONSTRAINT_DB_INTERMOL){+                    hc_intermolecular_only(j, c_option, hc, length, min_loop_size, cut, index);+                  }+                  break;++      case '.':   break;++      default:    vrna_message_warning("Unrecognized character '%c' in pseudo dot-bracket notation constraint string",+                                              constraint[j-1]);+                  break;+    }+  }++  if (hx!=0) {+    vrna_message_error("%s\nunbalanced brackets in constraint string", constraint);+  }+  /* clean up */+  free(index);+  free(stack);+}++PRIVATE INLINE  void+hc_intramolecular_only( unsigned int i,+                        char c_option,+                        char *hc,+                        unsigned int length,+                        unsigned int min_loop_size,+                        int cut,+                        int *index){++  unsigned int l;++  if(cut > 1){+    if(i < cut)+      for(l = MAX2(i+min_loop_size, cut); l <= length; l++)+        hc[index[l] + i] &= ~c_option;+    else+      for(l = 1; l < MIN2(cut, i-min_loop_size); l++)+        hc[index[i] + l] &= ~c_option;+  }+}++PRIVATE INLINE  void+hc_intermolecular_only( unsigned int i,+                        char c_option,+                        char *hc,+                        unsigned int length,+                        unsigned int min_loop_size,+                        int cut,+                        int *index){++  unsigned int l;++  if(cut > 1){+    if(i < cut){+      for(l = 1; l < i; l++)+        hc[index[i] + l] &= ~c_option;+      for(l = i + 1; l < cut; l++)+        hc[index[l] + i] &= ~c_option;+    } else {+      for(l = cut; l < i; l++)+        hc[index[i] + l] &= ~c_option;+      for(l = i + 1; l <= length; l++)+        hc[index[l] + i] &= ~c_option;+    }+  }+}++PRIVATE INLINE  void+hc_cant_pair( unsigned int i,+              char c_option,+              char *hc,+              unsigned int length,+              unsigned int min_loop_size,+              int *index){++  hc_pairs_upstream(i, c_option, hc, length, index);+  hc_pairs_downstream(i, c_option, hc, length, index);+}++PRIVATE INLINE  void+hc_must_pair( unsigned int i,+              char c_option,+              char *hc,+              int *index){++  hc[index[i]+i] &= ~c_option;+}++PRIVATE INLINE  void+hc_pairs_upstream(unsigned int i,+                  char c_option,+                  char *hc,+                  unsigned int length,+                  int *index){++  unsigned int l;++  /* prohibit downstream pairs */+  for(l = length; l > i; l--)+    hc[index[l] + i] = (char)0;+  /* allow upstream pairs of given type */+  for(l = i - 1; l >= 1; l--)+    hc[index[i] + l] &= c_option;+}++PRIVATE INLINE  void+hc_pairs_downstream(unsigned int i,+                    char c_option,+                    char *hc,+                    unsigned int length,+                    int *index){++  unsigned int l;+  /* allow downstream pairs of given type */+  for(l = length; l > i; l--)+    hc[index[l] + i] &= c_option;+  /* forbid upstream pairs */+  for(l = i - 1; l >= 1; l--)+    hc[index[i] + l] = (char)0;+}++PRIVATE INLINE  void+hc_allow_pair(unsigned int i,+              unsigned int j,+              char c_option,+              char *hc,+              int *index){++  hc[index[j] + i] |= c_option;+}++PRIVATE INLINE  void+hc_weak_enforce_pair( unsigned int i,+                      unsigned int j,+                      char c_option,+                      char *hc,+                      unsigned int length,+                      unsigned int min_loop_size,+                      int *index){++  unsigned int k, l;++  /* don't allow pairs (k,i) 1 <= k < i */+  /* don't allow pairs (i,k) i < k <= n */ +  hc_pairs_upstream(i, (char)0, hc, length, index);+  /* don't allow pairs (k,j) 1 <= k < j */+  /* don't allow pairs (j,k) j < k <= n */ +  hc_pairs_upstream(j, (char)0, hc, length, index);++  /* don't allow pairs i < k < j < l */+  for(k = i+1; k < j; k++)+    for(l = j+1; l <= length; l++){+      hc[index[l] + k] = 0;+    }+  /* don't allow pairs k<i<l<j */+  for(k = 1; k < i; k++)+    for(l = i+1; l < j; l++){+      hc[index[l] + k] = 0;+    }+  /* allow base pair (i,j) */+  hc[index[j] + i] |= c_option;+}++PRIVATE INLINE  void+hc_enforce_pair(unsigned int i,+                unsigned int j,+                char c_option,+                char *hc,+                unsigned int length,+                unsigned int min_loop_size,+                int *index){++  hc_weak_enforce_pair( i,+                        j,+                        c_option,+                        hc,+                        length,+                        min_loop_size,+                        index);++  /* forbid i and j to be unpaired */+  hc[index[i] + i] = 0;+  hc[index[j] + j] = 0;+}++PRIVATE void+hc_reset_to_default(vrna_fold_compound_t *vc){++  unsigned int      i, j, ij, min_loop_size, n;+  int               max_span, *idx;+  vrna_md_t         *md;+  vrna_hc_t         *hc;+  short             *S;++  md  = NULL;+  n   = vc->length;+  hc  = vc->hc;+  idx = vc->jindx;+  S   = vc->sequence_encoding;++  if(vc->params)+    md  = &(vc->params->model_details);+  else if(vc->exp_params)+    md  = &(vc->exp_params->model_details);+  else+    vrna_message_error("missing model_details in fold_compound");++  min_loop_size = md->min_loop_size;+  max_span      = md->max_bp_span;++  if((max_span < 5) || (max_span > n))+    max_span  = n;++  /* ######################### */+  /* fill with default values  */+  /* ######################### */++  /* 1. unpaired nucleotides are allowed in all contexts */+  for(i = 1; i <= n; i++)+    hc->matrix[idx[i] + i]  =   VRNA_CONSTRAINT_CONTEXT_EXT_LOOP+                              | VRNA_CONSTRAINT_CONTEXT_HP_LOOP+                              | VRNA_CONSTRAINT_CONTEXT_INT_LOOP+                              | VRNA_CONSTRAINT_CONTEXT_MB_LOOP;++  /* 2. all base pairs with pscore above threshold are allowed in all contexts */+  switch(vc->type){+    case VRNA_FC_TYPE_COMPARATIVE:  for(j = n; j > min_loop_size + 1; j--){+                                    ij = idx[j]+1;+                                    for(i=1; i < j - min_loop_size; i++, ij++){+                                      char opt = (char)0;+                                      if((j-i+1) <= max_span){+                                        if(vc->pscore[idx[j]+i] >= md->cv_fact*MINPSCORE)+                                          opt = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+                                      }+                                      hc->matrix[ij] = opt;+                                    }+                                  }+                                  break;++    case VRNA_FC_TYPE_SINGLE:     for(j = n; j > min_loop_size + 1; j--){+                                    ij = idx[j]+1;+                                    for(i=1; i < j - min_loop_size; i++, ij++){+                                      char opt = (char)0;+                                      if((j-i+1) <= max_span){+                                        int t = md->pair[S[i]][S[j]];+                                        switch(t){+                                          case 0:   break;+                                          case 3:   /* fallthrough */+                                          case 4:   if(md->noGU){+                                                      break;+                                                    } else if(md->noGUclosure){+                                                      opt = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+                                                      opt &= ~(VRNA_CONSTRAINT_CONTEXT_HP_LOOP | VRNA_CONSTRAINT_CONTEXT_MB_LOOP);+                                                      break;+                                                    } /* else fallthrough */+                                          default:  opt = VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS;+                                                    break;+                                        }+                                      }+                                      hc->matrix[ij] = opt;+                                    }+                                  }++                                  /* correct for no lonely pairs (assuming that ptypes already incorporate noLP status) */+                                  /* this should be fixed such that ij loses its hard constraint type if it does not+                                     allow for enclosing an interior loop, etc.+                                  */+                                  /*  ???????+                                      Is this necessary? We could leave the noLP option somewhere else, i.e. do not enforce it+                                      on the level of ptype/constraints, but an the level of recursions...+                                      ???????+                                  */+                                  if(md->noLP){+                                    if(!vc->ptype)+                                      vc->ptype = vrna_ptypes(vc->sequence_encoding2, md);+                                    for(i = 1; i < n; i++)+                                      for(j = i + min_loop_size + 1; j <= n; j++){+                                        if(hc->matrix[idx[j] +i]){+                                          if(!vc->ptype[idx[j] + i]){+                                            hc->matrix[idx[j] + i] = (char)0;+                                          }+                                        }+                                      }+                                  }+                                  break;++    default:                      break;+  }++  /* should we reset the generalized hard constraint feature here? */+  if(hc->f || hc->data){+    if(hc->free_data)+      hc->free_data(hc->data);++    hc->f           = NULL;+    hc->data        = NULL;+    hc->free_data   = NULL;+  }++}++PRIVATE void+hc_update_up(vrna_fold_compound_t *vc){++  unsigned int      i, n;+  int               *idx;+  vrna_hc_t         *hc;++  n   = vc->length;+  idx = vc->jindx;+  hc  = vc->hc;++  for(hc->up_ext[n+1] = 0, i = n; i > 0; i--) /* unpaired stretch in exterior loop */+    hc->up_ext[i] = (hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) ? 1 + hc->up_ext[i+1] : 0;++  for(hc->up_hp[n+1] = 0, i = n; i > 0; i--)  /* unpaired stretch in hairpin loop */+    hc->up_hp[i] = (hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP) ? 1 + hc->up_hp[i+1] : 0;++  for(hc->up_int[n+1] = 0, i = n; i > 0; i--) /* unpaired stretch in interior loop */+    hc->up_int[i] = (hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) ? 1 + hc->up_int[i+1] : 0;++  for(hc->up_ml[n+1] = 0, i = n; i > 0; i--)  /* unpaired stretch in multibranch loop */+    hc->up_ml[i] = (hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP) ? 1 + hc->up_ml[i+1] : 0;++  /*+   *  loop arround once more until we find a nucleotide that mustn't+   *  be unpaired (needed for circular folding)+   */++  if(hc->matrix[idx[1]+1] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+    hc->up_ext[n+1] = hc->up_ext[1];+    for(i = n; i > 0; i--){+      if(hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+        hc->up_ext[i] = MIN2(n, 1 + hc->up_ext[i+1]);+      } else+        break;+    }+  }++  if(hc->matrix[idx[1]+1] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){+    hc->up_hp[n+1] = hc->up_hp[1];+    for(i = n; i > 0; i--){+      if(hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){+        hc->up_hp[i] = MIN2(n, 1 + hc->up_hp[i+1]);+      } else+        break;+    }+  }++  if(hc->matrix[idx[1]+1] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+    hc->up_int[n+1] = hc->up_int[1];+    for(i = n; i > 0; i--){+      if(hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+        hc->up_int[i] = MIN2(n, 1 + hc->up_int[i+1]);+      } else+        break;+    }+  }++  if(hc->matrix[idx[1]+1] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+    hc->up_ml[n+1] = hc->up_ml[1];+    for(i = n; i > 0; i--){+      if(hc->matrix[idx[i]+i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+        hc->up_ml[i] = MIN2(n, 1 + hc->up_ml[i+1]);+      } else+        break;+    }+  }++}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC  void+print_tty_constraint_full(void){++  vrna_message_constraint_options_all();+}++PUBLIC  void+print_tty_constraint(unsigned int option){++  vrna_message_constraint_options(option);+}++PUBLIC void+constrain_ptypes( const char *constraint,+                  unsigned int length,+                  char *ptype,+                  int *BP,+                  int min_loop_size,+                  unsigned int idx_type){++  int n,i,j,k,l;+  int hx, *stack;+  char type;+  int *index;++  if(constraint == NULL) return;++  n = (int)strlen(constraint);++  stack = vrna_alloc(sizeof(int)*(n+1));++  if(!idx_type){ /* index allows access in energy matrices at pos (i,j) via index[j]+i */+    index = vrna_idx_col_wise(length);++    for(hx=0, j=1; j<=n; j++){+      switch(constraint[j-1]){+        case '|':   if(BP) BP[j] = -1;+                    break;+        case 'x':   /* can't pair */+                    for (l=1; l<j-min_loop_size; l++)+                      ptype[index[j]+l] = 0;+                    for (l=j+min_loop_size+1; l<=(int)length; l++)+                      ptype[index[l]+j] = 0;+                    break;+        case '(':   stack[hx++]=j;+                    /* fallthrough */+        case '<':   /* pairs upstream */+                    for (l=1; l<j-min_loop_size; l++)+                      ptype[index[j]+l] = 0;+                    break;+        case ')':   if (hx<=0) {+                      vrna_message_error("%s\nunbalanced brackets in constraint", constraint);+                    }+                    i = stack[--hx];+                    type = ptype[index[j]+i];+                    for (k=i+1; k<=(int)length; k++)+                      ptype[index[k]+i] = 0;+                    /* don't allow pairs i<k<j<l */+                    for (l=j; l<=(int)length; l++)+                      for (k=i+1; k<=j; k++)+                        ptype[index[l]+k] = 0;+                    /* don't allow pairs k<i<l<j */+                    for (l=i; l<=j; l++)+                      for (k=1; k<=i; k++)+                        ptype[index[l]+k] = 0;+                    for (k=1; k<j; k++)+                      ptype[index[j]+k] = 0;+                    ptype[index[j]+i] = (type==0) ? 7 : type;+                    /* fallthrough */+        case '>':   /* pairs downstream */+                    for (l=j+min_loop_size+1; l<=(int)length; l++)+                      ptype[index[l]+j] = 0;+                    break;+      }+    }+  }+  else{ /* index allows access in energy matrices at pos (i,j) via index[i]-j */+    index = vrna_idx_row_wise(length);++    for(hx=0, j=1; j<=n; j++) {+      switch (constraint[j-1]) {+        case 'x':   /* can't pair */+                    for (l=1; l<j-min_loop_size; l++)+                      ptype[index[l]-j] = 0;+                    for (l=j+min_loop_size+1; l<=(int)length; l++)+                      ptype[index[j]-l] = 0;+                    break;+        case '(':   stack[hx++]=j;+                    /* fallthrough */+        case '<':   /* pairs upstream */+                    for (l=1; l<j-min_loop_size; l++)+                      ptype[index[l]-j] = 0;+                    break;+        case ')':   if (hx<=0) {+                      vrna_message_error("%s\nunbalanced brackets in constraints", constraint);+                    }+                    i = stack[--hx];+                    type = ptype[index[i]-j];+                    /* don't allow pairs i<k<j<l */+                    for (k=i; k<=j; k++)+                      for (l=j; l<=(int)length; l++)+                        ptype[index[k]-l] = 0;+                    /* don't allow pairs k<i<l<j */+                    for (k=1; k<=i; k++)+                      for (l=i; l<=j; l++)+                        ptype[index[k]-l] = 0;+                    ptype[index[i]-j] = (type==0) ? 7 : type;+                    /* fallthrough */+        case '>':   /* pairs downstream */+                    for (l=j+min_loop_size+1; l<=(int)length; l++)+                      ptype[index[j]-l] = 0;+                    break;+      }+    }+  }+  if (hx!=0) {+    vrna_message_error("%s\nunbalanced brackets in constraint string", constraint);+  }+  free(index);+  free(stack);+}++#endif
+ C/ViennaRNA/constraints_hard.h view
@@ -0,0 +1,575 @@+#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H+#define VIENNA_RNA_PACKAGE_CONSTRAINTS_HARD_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif+++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file       constraints_hard.h+ *  @ingroup    hard_constraints+ *  @brief      Functions and data structures for handling of secondary structure hard constraints+ */+#include <ViennaRNA/data_structures.h>++/**+ *  @addtogroup hard_constraints+ *+ *  @brief  This module covers all functionality for hard constraints in secondary+ *          structure prediction+ */++/**+ *  @brief Typename for the hard constraints data structure #vrna_hc_s+ *  @ingroup  hard_constraints+ */+typedef struct  vrna_hc_s vrna_hc_t;++/**+ *  @brief Typename for the single nucleotide hard constraint data structure #vrna_hc_up_s+ *  @ingroup  hard_constraints+ */+typedef struct vrna_hc_up_s vrna_hc_up_t;++/**+ * @brief Callback to evaluate whether or not a particular decomposition step is contributing to the solution space+ *+ * @ingroup hard_constraints+ *+ * This is the prototype for callback functions used by the folding recursions to evaluate generic+ * hard constraints. The first four parameters passed indicate the delimiting nucleotide positions+ * of the decomposition, and the parameter @p denotes the decomposition step. The last parameter+ * @p data is the auxiliary data structure associated to the hard constraints via vrna_hc_add_data(),+ * or NULL if no auxiliary data was added.+ *+ * @see #VRNA_DECOMP_PAIR_HP, #VRNA_DECOMP_PAIR_IL, #VRNA_DECOMP_PAIR_ML, #VRNA_DECOMP_ML_ML_ML,+ *      #VRNA_DECOMP_ML_STEM, #VRNA_DECOMP_ML_ML, #VRNA_DECOMP_ML_UP, #VRNA_DECOMP_ML_ML_STEM,+ *      #VRNA_DECOMP_ML_COAXIAL, #VRNA_DECOMP_EXT_EXT, #VRNA_DECOMP_EXT_UP, #VRNA_DECOMP_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_EXT, #VRNA_DECOMP_EXT_STEM_EXT, #VRNA_DECOMP_EXT_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_STEM1, vrna_hc_add_f(), vrna_hc_add_data()+ *+ * @param i         Left (5') delimiter position of substructure+ * @param j         Right (3') delimiter position of substructure+ * @param k         Left delimiter of decomposition+ * @param l         Right delimiter of decomposition+ * @param d         Decomposition step indicator+ * @param data      Auxiliary data+ * @return          Pseudo energy contribution in deka-kalories per mol+ */+typedef char (vrna_callback_hc_evaluate)(int i, int j, int k, int l, char d, void *data);++/**+ *  @brief  do not print the header information line+ *  @deprecated   This mode is not supported anymore!+ *+ */+#define VRNA_CONSTRAINT_NO_HEADER         0++/**+ *  @brief  Flag for vrna_constraints_add() to indicate that constraint is passed in pseudo dot-bracket notation+ *+ *  @see vrna_constraints_add(), vrna_message_constraint_options(), vrna_message_constraint_options_all()+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_DB                16384U++/**+ *  @brief Switch for dot-bracket structure constraint to enforce base pairs+ *+ *  This flag should be used to really enforce base pairs given in dot-bracket constraint rather than+ *  just weakly-enforcing them.+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_ENFORCE_BP           32768U++/**+ *  @brief  Flag that is used to indicate the pipe '|' sign in pseudo dot-bracket+ *  notation of hard constraints.+ *+ *  Use this definition to indicate the pipe sign '|' (paired with another base)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_PIPE              65536U++/**+ *  @brief  dot '.' switch for structure constraints (no constraint at all)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_DOT               131072U+/**+ *  @brief  'x' switch for structure constraint (base must not pair)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_X                 262144U+/**+ *  @brief  angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_ANG_BRACK         524288U+/**+ *  @brief  round brackets '(',')' switch for structure constraint (base i pairs base j)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_RND_BRACK         1048576U++/**+ *  @brief  Flag that is used to indicate the character 'l' in pseudo dot-bracket+ *  notation of hard constraints.+ *+ *  Use this definition to indicate the usage of 'l' character (intramolecular pairs only)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_INTRAMOL    2097152U++/**+ *  @brief  Flag that is used to indicate the character 'e' in pseudo dot-bracket+ *  notation of hard constraints.+ *+ *  Use this definition to indicate the usage of 'e' character (intermolecular pairs only)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_INTERMOL    4194304U++/**+ *  @brief '+' switch for structure constraint (base is involved in a gquad)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ *+ *  @warning  This flag is for future purposes only! No implementation recognizes it yet.+ */+#define VRNA_CONSTRAINT_DB_GQUAD                8388608U++/**+ *  @brief Switch for dot-bracket structure constraint with default symbols+ *+ *  This flag conveniently combines all possible symbols in dot-bracket notation+ *  for hard constraints and #VRNA_CONSTRAINT_DB+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_from_db(), vrna_constraints_add(), vrna_message_constraint_options(),+ *        vrna_message_constraint_options_all()+ */+#define VRNA_CONSTRAINT_DB_DEFAULT \+    (   VRNA_CONSTRAINT_DB \+      | VRNA_CONSTRAINT_DB_PIPE \+      | VRNA_CONSTRAINT_DB_DOT \+      | VRNA_CONSTRAINT_DB_X \+      | VRNA_CONSTRAINT_DB_ANG_BRACK \+      | VRNA_CONSTRAINT_DB_RND_BRACK \+      | VRNA_CONSTRAINT_DB_INTRAMOL \+      | VRNA_CONSTRAINT_DB_INTERMOL \+      | VRNA_CONSTRAINT_DB_GQUAD \+    )++/**+ *  @brief  Hard constraints flag, base pair in the exterior loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_EXT_LOOP      (char)0x01++/**+ *  @brief  Hard constraints flag, base pair encloses hairpin loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_HP_LOOP       (char)0x02++/**+ *  @brief  Hard constraints flag, base pair encloses an interior loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP      (char)0x04++/**+ *  @brief  Hard constraints flag, base pair encloses a multi branch loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC  (char)0x08++/**+ *  @brief  Hard constraints flag, base pair is enclosed in an interior loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP       (char)0x10++/**+ *  @brief  Hard constraints flag, base pair is enclosed in a multi branch loop+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC   (char)0x20++/**+ *  @brief  Hard constraint flag to indicate enforcement of constraints+ */+#define VRNA_CONSTRAINT_CONTEXT_ENFORCE       (char)0x40++/**+ *  @brief  Hard constraint flag to indicate not to remove base pairs that conflict with a given constraint+ */+#define VRNA_CONSTRAINT_CONTEXT_NO_REMOVE     (char)0x80++/**+ * @brief  Hard constraints flag, shortcut for all base pairs+ *+ *  @ingroup  hard_constraints+ *+ */+#define VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS     (char)(   VRNA_CONSTRAINT_CONTEXT_EXT_LOOP \+                                                      | VRNA_CONSTRAINT_CONTEXT_HP_LOOP \+                                                      | VRNA_CONSTRAINT_CONTEXT_INT_LOOP \+                                                      | VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC \+                                                      | VRNA_CONSTRAINT_CONTEXT_MB_LOOP \+                                                      | VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)++/**+ *  @brief  The hard constraints data structure+ *+ *  The content of this data structure determines the decomposition pattern+ *  used in the folding recursions. Attribute 'matrix' is used as source for+ *  the branching pattern of the decompositions during all folding recursions.+ *  Any entry in matrix[i,j] consists of the 6 LSB that allows one to distinguish the+ *  following types of base pairs:+ *  - in the exterior loop (#VRNA_CONSTRAINT_CONTEXT_EXT_LOOP)+ *  - enclosing a hairpin (#VRNA_CONSTRAINT_CONTEXT_HP_LOOP)+ *  - enclosing an interior loop (#VRNA_CONSTRAINT_CONTEXT_INT_LOOP)  + *  - enclosed by an exterior loop (#VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC)+ *  - enclosing a multi branch loop (#VRNA_CONSTRAINT_CONTEXT_MB_LOOP)+ *  - enclosed by a multi branch loop (#VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)+ *+ *  The four linear arrays 'up_xxx' provide the number of available unpaired+ *  nucleotides (including position i) 3' of each position in the sequence.+ *+ *  @see  vrna_hc_init(), vrna_hc_free(), #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_HP_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC+ *+ *  @ingroup hard_constraints+ */+struct vrna_hc_s {+  char    *matrix;  /**<  @brief  Upper triangular matrix that encodes where a+                                  base pair or unpaired nucleotide is allowed+                    */+  int     *up_ext;  /**<  @brief  A linear array that holds the number of allowed+                                  unpaired nucleotides in an exterior loop+                    */+  int     *up_hp;   /**<  @brief  A linear array that holds the number of allowed+                                  unpaired nucleotides in a hairpin loop+                    */+  int     *up_int;  /**<  @brief  A linear array that holds the number of allowed+                                  unpaired nucleotides in an interior loop+                    */+  int     *up_ml;   /**<  @brief  A linear array that holds the number of allowed+                                  unpaired nucleotides in a multi branched loop+                    */++  vrna_callback_hc_evaluate *f; /**<  @brief  A function pointer that returns whether or+                                              not a certain decomposition may be evaluated+                                */++  void *data;                         /**<  @brief  A pointer to some structure where the user+                                                    may store necessary data to evaluate its+                                                    generic hard constraint function+                                      */++  vrna_callback_free_auxdata *free_data;  /**<  @brief  A pointer to a function to free memory+                                                        occupied by auxiliary data++                                                The function this pointer is pointing to will be+                                                called upon destruction of the #vrna_hc_s, and+                                                provided with the vrna_hc_s.data pointer that+                                                may hold auxiliary data. Hence, to avoid leaking+                                                memory, the user may use this pointer to free+                                                memory occupied by auxiliary data.+                                          */+};++/**+ *  @brief  A single hard constraint for a single nucleotide+ *+ *  @ingroup hard_constraints+ */+struct vrna_hc_up_s {+  int   position; /**<  @brief The sequence position (1-based)  */+  char  options;  /**<  @brief The hard constraint option       */+};++/**+ *  @brief Print a help message for pseudo dot-bracket structure constraint characters to stdout.+ *  (constraint support is specified by option parameter)+ *+ *  Currently available options are:\n+ *  #VRNA_CONSTRAINT_DB_PIPE (paired with another base)\n+ *  #VRNA_CONSTRAINT_DB_DOT (no constraint at all)\n+ *  #VRNA_CONSTRAINT_DB_X (base must not pair)\n+ *  #VRNA_CONSTRAINT_DB_ANG_BRACK (paired downstream/upstream)\n+ *  #VRNA_CONSTRAINT_DB_RND_BRACK (base i pairs base j)\n+ *+ *  pass a collection of options as one value like this:+ *  @verbatim vrna_message_constraints(option_1 | option_2 | option_n) @endverbatim+ *+ *  @ingroup  constraints+ *+ *  @see  vrna_message_constraint_options_all(), vrna_constraints_add(), #VRNA_CONSTRAINT_DB,+ *        #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X, #VRNA_CONSTRAINT_DB_ANG_BRACK,+ *        #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_INTRAMOL+ *+ *  @param option Option switch that tells which constraint help will be printed+ */+void vrna_message_constraint_options(unsigned int option);++/**+ *  @brief Print structure constraint characters to stdout+ *  (full constraint support)+ *+ *  @ingroup  constraints+ *+ *  @see  vrna_message_constraint_options(), vrna_constraints_add(), #VRNA_CONSTRAINT_DB,+ *        #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X, #VRNA_CONSTRAINT_DB_ANG_BRACK,+ *        #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_INTRAMOL+ */+void vrna_message_constraint_options_all(void);++/**+ *  @brief  Initialize/Reset hard constraints to default values+ *+ *  This function resets the hard constraints to their default values, i.e.+ *  all positions may be unpaired in all contexts, and base pairs are+ *  allowed in all contexts, if they resemble canonical pairs.+ *  Previously set hard constraints will be removed vefore initialization.+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_add_up()+ *+ *  @param  vc  The fold compound+ */+void vrna_hc_init(vrna_fold_compound_t *vc);++/**+ *  @brief  Make a certain nucleotide unpaired+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_bp(), vrna_hc_add_bp_nonspecific(), vrna_hc_init(),+ *        #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS+ *+ *  @param  vc      The #vrna_fold_compound_t the hard constraints are associated with+ *  @param  i       The position that needs to stay unpaired (1-based)+ *  @param  option  The options flag indicating how/where to store the hard constraints+ */+void vrna_hc_add_up(vrna_fold_compound_t *vc,+                    int i,+                    char option);++/**+ *  @brief Apply a list of hard constraints for single nucleotides+ *+ *  @ingroup  hard_constraints+ *+ *  @param  vc          The #vrna_fold_compound_t the hard constraints are associated with+ *  @param  constraints The list off constraints to apply, last entry must have position+ *                      attribute set to 0+ */+int+vrna_hc_add_up_batch( vrna_fold_compound_t *vc,+                      vrna_hc_up_t *constraints);++/**+ *  @brief  Favorize/Enforce  a certain base pair (i,j)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_bp_nonspecific(), vrna_hc_add_up(), vrna_hc_init(),+ *        #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC,+ *        #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC,+ *        #VRNA_CONSTRAINT_CONTEXT_ENFORCE, #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS+ *+ *  @param  vc      The #vrna_fold_compound_t the hard constraints are associated with+ *  @param  i       The 5' located nucleotide position of the base pair (1-based)+ *  @param  j       The 3' located nucleotide position of the base pair (1-based)+ *  @param  option  The options flag indicating how/where to store the hard constraints+ */+void vrna_hc_add_bp(vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    char option);++/**+ *  @brief  Enforce a nucleotide to be paired (upstream/downstream)+ *+ *  @ingroup  hard_constraints+ *+ *  @see  vrna_hc_add_bp(), vrna_hc_add_up(), vrna_hc_init(),+ *        #VRNA_CONSTRAINT_CONTEXT_EXT_LOOP, #VRNA_CONSTRAINT_CONTEXT_HP_LOOP,+ *        #VRNA_CONSTRAINT_CONTEXT_INT_LOOP, #VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC,+ *        #VRNA_CONSTRAINT_CONTEXT_MB_LOOP, #VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC,+ *        #VRNA_CONSTRAINT_CONTEXT_ALL_LOOPS+ *+ *  @param  vc      The #vrna_fold_compound_t the hard constraints are associated with+ *  @param  i       The position that needs to stay unpaired (1-based)+ *  @param  d       The direction of base pairing (@f$ d < 0 @f$: pairs upstream,+ *                  @f$ d > 0 @f$: pairs downstream, @f$ d == 0 @f$: no direction)+ *  @param  option  The options flag indicating in which loop type context the pairs may appear+ */+void vrna_hc_add_bp_nonspecific(vrna_fold_compound_t *vc,+                                int i,+                                int d,+                                char option);++/**+ *  @brief  Free the memory allocated by a #vrna_hc_t data structure+ *+ *  Use this function to free all memory that was allocated for a data structure+ *  of type #vrna_hc_t .+ *+ *  @see get_hard_constraints(), #vrna_hc_t+ *+ *  @ingroup  hard_constraints+ *+ */+void vrna_hc_free(vrna_hc_t *hc);+++/**+ *  @brief  Add a function pointer pointer for the generic hard constraint+ *          feature+ */+void vrna_hc_add_f( vrna_fold_compound_t *vc,+                    vrna_callback_hc_evaluate *f);++/**+ *  @brief Add an auxiliary data structure for the generic hard constraints callback function+ *+ *  @ingroup generic_hc+ *+ *  @see vrna_hc_add_f()+ *+ *  @param  vc        The fold compound the generic hard constraint function should be bound to+ *  @param  data      A pointer to the data structure that holds required data for function 'f'+ *  @param  free_data A pointer to a function that free's the memory occupied by @data (Maybe NULL)+ */+void vrna_hc_add_data(vrna_fold_compound_t *vc,+                      void *data,+                      vrna_callback_free_auxdata *f);+++/**+ *  @brief Add hard constraints from pseudo dot-bracket notation+ *+ *  This function allows one to apply hard constraints from a pseudo dot-bracket+ *  notation. The @p options parameter controls, which characters are recognized+ *  by the parser. Use the #VRNA_CONSTRAINT_DB_DEFAULT convenience macro, if you+ *  want to allow all known characters+ *+ *  @ingroup  hard_constraints+ *+ *  @see  #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X,+ *        #VRNA_CONSTRAINT_DB_ANG_BRACK, #VRNA_CONSTRAINT_DB_RND_BRACK, #VRNA_CONSTRAINT_DB_INTRAMOL,+ *        #VRNA_CONSTRAINT_DB_INTERMOL, #VRNA_CONSTRAINT_DB_GQUAD+ *+ *  @param  vc            The fold compound+ *  @param  constraint    A pseudo dot-bracket notation of the hard constraint.+ *  @param  options       The option flags+ */+int+vrna_hc_add_from_db(vrna_fold_compound_t *vc,+                    const char *constraint,+                    unsigned int options);+++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief Print structure constraint characters to stdout.+ *  (constraint support is specified by option parameter)+ *+ *  @deprecated Use vrna_message_constraints() instead!+ *  @param option Option switch that tells which constraint help will be printed+ */+DEPRECATED(void print_tty_constraint(unsigned int option));++/**+ *  @brief Print structure constraint characters to stdout+ *  (full constraint support)+ *+ *  @deprecated Use vrna_message_constraint_options_all() instead!+ */+DEPRECATED(void print_tty_constraint_full(void));++/**+ *  @brief Insert constraining pair types according to constraint structure string+ *+ *  @deprecated   Do not use this function anymore! Structure constraints are now handled through #vrna_hc_t and related functions.+ *+ *  @param constraint     The structure constraint string+ *  @param length         The actual length of the sequence (constraint may be shorter)+ *  @param ptype          A pointer to the basepair type array+ *  @param BP             (not used anymore)+ *  @param min_loop_size  The minimal loop size (usually #TURN )+ *  @param idx_type       Define the access type for base pair type array (0 = indx, 1 = iindx)+ */+DEPRECATED(void constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type));++#endif++#endif
+ C/ViennaRNA/constraints_ligand.c view
@@ -0,0 +1,761 @@+/*+ * Reference implementation for including ligand binding to hairpins, or+ * interior loops, with known sequence and/or structure motif, and+ * binding free energy utilizing generic soft constraint feature+ *+ * (c) 2015 Ronny Lorenz - ViennaRNA Package+ */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdlib.h>+#include <stdio.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/model.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/eval.h"+#include "ViennaRNA/constraints_ligand.h"+++/*+#################################+# PRIVATE DATA STRUCTURES       #+#################################+*/++typedef struct{+  int i;+  int j;+  int k;+  int l;+} quadruple_position;++typedef struct{+  char  *seq_motif_5;+  char  *seq_motif_3;+  char  *struct_motif_5;+  char  *struct_motif_3;+  int   energy;+  int   energy_alt;+  int   pair_count;+  vrna_basepair_t *pairs;++  quadruple_position *positions;+} ligand_data;++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++static void+split_sequence( const char *string,+                      char **seq1,+                      char **seq2,+                      int cp);++static void+correctMotifContribution( const char *seq,+                          const char *struct_motif,+                          const char *struct_motif_alt,+                          int *contribution,+                          int *contribution_alt,+                          vrna_md_t *md);++static void+delete_ligand_data(void *data);++static int+AptamerContrib(int i, int j, int k, int l, char d, void *data);++static int+AptamerContribHairpin(int i, int j, int k, int l, char d, void *data);++static FLT_OR_DBL+expAptamerContrib(int i, int j, int k, int l, char d, void *data);++static FLT_OR_DBL+expAptamerContribHairpin(int i, int j, int k, int l, char d, void *data);++static vrna_basepair_t *+backtrack_int_motif(int i, int j, int k, int l, char d, void *data);++static vrna_basepair_t *+backtrack_hp_motif(int i, int j, int k, int l, char d, void *data);++static quadruple_position *+scanForMotif( const char *seq,+              const char *motif1,+              const char *motif2);++static vrna_basepair_t *+scanForPairs( const char  *motif5,+              const char  *motif3,+              int         *pair_count);++static int+vrna_sc_detect_hi_motif(vrna_fold_compound_t *vc,+                        const char *structure,+                        int *i,+                        int *j,+                        int *k,+                        int *l);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC vrna_sc_motif_t *+vrna_sc_ligand_detect_motifs( vrna_fold_compound_t *vc,+                              const char *structure){++  int             a, b, c, d, motif_count, motif_list_size;+  vrna_sc_motif_t *motif_list;+  +  motif_list = NULL;+  +  if(vc && structure){+    a               = 1;+    motif_count     = 0;+    motif_list_size = 10;++    motif_list = (vrna_sc_motif_t *)vrna_alloc(sizeof(vrna_sc_motif_t) * motif_list_size);++    while(vrna_sc_detect_hi_motif(vc, structure, &a, &b, &c, &d)){+      if(motif_count == motif_list_size){+        motif_list_size *= 1.2;+        motif_list = (vrna_sc_motif_t *)vrna_realloc(motif_list, sizeof(vrna_sc_motif_t) * motif_list_size);+      }++      motif_list[motif_count].number  = 0;++      if(c != 0){ /* interior loop motif */+        motif_list[motif_count].i = a;+        motif_list[motif_count].j = b;+        motif_list[motif_count].k = c;+        motif_list[motif_count].l = d;+        a = c;+      } else { /* hairpin loop motif */+        motif_list[motif_count].i = a;+        motif_list[motif_count].j = b;+        motif_list[motif_count].k = a;+        motif_list[motif_count].l = b;+        a = b;+      }+      motif_count++;+    }++    motif_list = (vrna_sc_motif_t *)vrna_realloc(motif_list, sizeof(vrna_sc_motif_t) * (motif_count + 1));+    motif_list[motif_count].i       = 0;+    motif_list[motif_count].j       = 0;+    motif_list[motif_count].k       = 0;+    motif_list[motif_count].l       = 0;+  }++  return motif_list;+}++PRIVATE int+vrna_sc_detect_hi_motif(vrna_fold_compound_t *vc,+                        const char *structure,+                        int *i,+                        int *j,+                        int *k,+                        int *l){++  int p, q, n;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(vc && vc->sc && vc->sc->data){+    n = vc->length;+    ldata = (ligand_data *)vc->sc->data;++    for(p = *i; p < n; p++){+      for(pos = ldata->positions; pos->i; pos++){+        if(pos->i == p){+          /* check whether we find the motif in the provided structure */+          int i_m, j_m, k_m, l_m;+          i_m = pos->i;+          j_m = pos->j;+          k_m = pos->k;+          l_m = pos->l;+          for(q = 0; q < strlen(ldata->struct_motif_5); q++){+            if(ldata->struct_motif_5[q] != structure[i_m+q-1])+              break;+          }+          if(q == strlen(ldata->struct_motif_5)){ /* 5' motif detected */+            if(k_m > 0){+              for(q = 0; q < strlen(ldata->struct_motif_3); q++){+                if(ldata->struct_motif_3[q] != structure[l_m+q-1])+                  break;+              }+              if(q == strlen(ldata->struct_motif_3)){ /* 3' motif detected */+                *i = i_m;+                *j = j_m;+                *k = k_m;+                *l = l_m;+                return 1;+              }+            } else {+                *i = i_m;+                *j = j_m;+                *k = k_m;+                *l = l_m;+                return 1;+            }+          }+        }+      }+    }+      +  }+  return 0;+}++PUBLIC int+vrna_sc_get_hi_motif( vrna_fold_compound_t *vc,+                      int *i,+                      int *j,+                      int *k,+                      int *l){++  int p, n;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(vc && vc->sc && vc->sc->data){+    n = vc->length;+    ldata = (ligand_data *)vc->sc->data;++    for(p = *i; p < n; p++){+      for(pos = ldata->positions; pos->i; pos++){+        if(pos->i == p){+          *i = pos->i;+          *j = pos->j;+          *k = pos->k;+          *l = pos->l;+          return 1;+        }+      }+    }+  }+  return 0;+}++PUBLIC int+vrna_sc_add_hi_motif( vrna_fold_compound_t *vc,+                      const char *seq,+                      const char *structure,+                      FLT_OR_DBL energy,+                      unsigned int options){++    int                   i, cp, cp2;+    char                  *sequence, *motif, *motif_alt;+    vrna_md_t             *md_p;+    ligand_data           *ldata;++    sequence              = NULL;+    motif                 = NULL;+    motif_alt             = NULL;+    ldata                 = NULL;+    md_p                  = NULL;++    sequence  = vrna_cut_point_remove(seq, &cp);                /* ligand sequence motif  */+    motif     = vrna_cut_point_remove(structure, &cp2);         /* ligand structure motif */++    /* check for obvious inconsistencies in input sequence/structure motif */+    if(cp != cp2){+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: Cutpoint in sequence and structure motif differ!");+      goto hi_motif_error;+    } else if(strlen(seq) != strlen(structure)){+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: length of sequence and structure motif differ!");+      goto hi_motif_error;+    }++    /* create auxiliary soft constraints data structure */+    ldata                 = vrna_alloc(sizeof(ligand_data));+    ldata->seq_motif_5    = NULL;+    ldata->seq_motif_3    = NULL;+    ldata->struct_motif_5 = NULL;+    ldata->struct_motif_3 = NULL;+    ldata->positions      = NULL;+    ldata->energy         = (int)(energy * 100.);++    split_sequence(sequence, &(ldata->seq_motif_5), &(ldata->seq_motif_3), cp);+    split_sequence(motif, &(ldata->struct_motif_5), &(ldata->struct_motif_3), cp);++    motif_alt = vrna_alloc(sizeof(char) * (strlen(motif) + 1)); /* alternative structure motif */+    memset(motif_alt, '.', strlen(motif) - 1);++    if(cp > 0){+      if((motif[0] != '(') || (motif[strlen(motif) - 1] != ')') || (motif[cp-2] != '(') || (motif[cp-1] != ')')){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: No closing and/or enclosed pair in interior loop motif!");+        goto hi_motif_error;+      }+      /* construct corresponding alternative interior loop motif (....(&)...) */+      motif_alt[0] = '(';+      motif_alt[cp-2] = '(';+      motif_alt[cp-1] = ')';+      motif_alt[strlen(motif) - 1] = ')';+      motif_alt[strlen(motif)] = '\0';++      vrna_sc_add_bt(vc, &backtrack_int_motif);+      vrna_sc_add_f(vc, &AptamerContrib);+      vrna_sc_add_exp_f(vc, &expAptamerContrib);++    } else {+      if((motif[0] != '(') || (motif[strlen(motif) - 1] != ')')){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: No closing pair in hairpin motif!");+        goto hi_motif_error;+      }++      /* construct corresponding alternative hairpin motif (....) */+      motif_alt[0] = '(';+      motif_alt[strlen(motif) - 1] = ')';+      motif_alt[strlen(motif)] = '\0';++      vrna_sc_add_bt(vc, &backtrack_hp_motif);+      vrna_sc_add_f(vc, &AptamerContribHairpin);+      vrna_sc_add_exp_f(vc, &expAptamerContribHairpin);+    }++    /* correct motif contributions */+    if(vc->params)+      md_p = &(vc->params->model_details);+    else+      md_p = &(vc->exp_params->model_details);++    correctMotifContribution(seq, motif, motif_alt, &(ldata->energy), &(ldata->energy_alt), md_p);++    /* scan for sequence motif positions */+    ldata->positions = scanForMotif(vc->sequence, ldata->seq_motif_5, ldata->seq_motif_3);++    /* scan for additional base pairs in the structure motif */+    int pair_count = 0;+    vrna_basepair_t *pairs = scanForPairs(ldata->struct_motif_5, ldata->struct_motif_3, &pair_count);+    if((pair_count > 0) && (pairs == NULL)){ /* error while parsing structure motif */+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: Error while parsing additional pairs in structure motif");+      goto hi_motif_error;+    }++    ldata->pairs      = pairs;+    ldata->pair_count = pair_count;++    /* add generalized soft-constraint data structure and corresponding 'delete' function */+    vrna_sc_add_data(vc, (void *)ldata, &delete_ligand_data);++    free(sequence);+    free(motif);+    free(motif_alt);++    return 1; /* success */++/* exit with error */+hi_motif_error:++    free(sequence);+    free(motif);+    free(motif_alt);+    delete_ligand_data(ldata);++    return 0;+}++static void+split_sequence( const char *string,+                      char **seq1,+                      char **seq2,+                      int cp){++  int l = (int)strlen(string);+  *seq1 = NULL;+  *seq2 = NULL;++  if(cp > 0){+    if(cp < l){+      *seq1 = vrna_alloc(sizeof(char) * cp);+      strncpy(*seq1, string, cp - 1);+      (*seq1)[cp - 1] = '\0';+      *seq2 = vrna_alloc(sizeof(char) * (l - cp + 2));+      strncpy(*seq2, string + cp - 1, (l - cp + 1));+      (*seq2)[l - cp + 1] = '\0';+    }+  } else {+    *seq1 = vrna_alloc(sizeof(char) * (l+1));+    strncpy(*seq1, string, l);+    (*seq1)[l] = '\0';+  }+}++static void+correctMotifContribution( const char *seq,+                          const char *struct_motif,+                          const char *struct_motif_alt,+                          int *contribution,+                          int *contribution_alt,+                          vrna_md_t *md){++  float                 alt, corr, energy;+  vrna_fold_compound_t  *tmp_vc;++  tmp_vc  = vrna_fold_compound(seq, md, VRNA_OPTION_EVAL_ONLY);+  alt     = vrna_eval_structure(tmp_vc, struct_motif_alt);+  corr    = vrna_eval_structure(tmp_vc, struct_motif);+  energy  = corr - alt;++  *contribution     += (int)(energy * 100.);+  *contribution_alt  = (int)(alt    * 100.);++  vrna_fold_compound_free(tmp_vc);+}++static void+delete_ligand_data(void *data){++  ligand_data *ldata = (ligand_data *)data;++  free(ldata->seq_motif_5);+  free(ldata->seq_motif_3);+  free(ldata->struct_motif_5);+  free(ldata->struct_motif_3);+  free(ldata->positions);+  free(ldata->pairs);++  free(data);+}++static int+AptamerContrib(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    for(pos = ((ligand_data *)data)->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        return ldata->energy;+      }+    }+  }++  return 0;+}++static int+AptamerContribHairpin(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    for(pos = ((ligand_data *)data)->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        return ldata->energy;+      }+    }+  }++  return 0;+}++static FLT_OR_DBL+expAptamerContrib(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;+  FLT_OR_DBL          exp_e;+  double              kT;++  exp_e = 1.;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    kT    = (37. + K0) * GASCONST;++    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        exp_e =   (FLT_OR_DBL)exp((double) (-ldata->energy) * 10./kT);+        exp_e +=  (FLT_OR_DBL)exp((double) (-ldata->energy_alt) * 10./kT); /* add alternative, i.e. unbound ligand */+        break;+      }+    }+  }++  return exp_e;+}++static FLT_OR_DBL+expAptamerContribHairpin(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;+  FLT_OR_DBL          exp_e;+  double              kT;++  exp_e = 1.;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    kT    = (37. + K0) * GASCONST;++    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        exp_e =   (FLT_OR_DBL)exp((double) (-ldata->energy) * 10./kT);+        exp_e +=  (FLT_OR_DBL)exp((double) (-ldata->energy_alt) * 10./kT); /* add alternative, i.e. unbound ligand */+        break;+      }+    }+  }++  return exp_e;+}++static vrna_basepair_t *+backtrack_int_motif(int i, int j, int k, int l, char d, void *data){++  int                 bp_size = 15;+  vrna_basepair_t     *pairs = NULL;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        /* found motif in our list, lets create pairs */+        char  *ptr;+#if 0+        int   actual_size = 0;+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * bp_size);++        for(ptr=ldata->struct_motif_5; *ptr != '\0'; ptr++, i++){+          if(*ptr == '.'){+            pairs[actual_size].i = pairs[actual_size].j = i;+            actual_size++;+            if(actual_size == bp_size){+              bp_size *= 2;+              pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * bp_size);+            }+          }+        }+        for(ptr=ldata->struct_motif_3; *ptr != '\0'; ptr++, l++){+          if(*ptr == '.'){+            pairs[actual_size].i = pairs[actual_size].j = l;+            actual_size++;+            if(actual_size == bp_size){+              bp_size *= 2;+              pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * bp_size);+            }+          }+        }+        pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * (actual_size + 1));+        pairs[actual_size].i = pairs[actual_size].j = -1;+#else+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * (ldata->pair_count + 1));+        vrna_basepair_t *pptr;+        int             count;+        for(count = 0,pptr = ldata->pairs; pptr && (pptr->i != 0); pptr++, count++){+          pairs[count].i = (pptr->i < 0) ? j + pptr->i : i + pptr->i - 1;+          pairs[count].j = (pptr->j < 0) ? j + pptr->j : i + pptr->j - 1;+        }+        pairs[count].i = pairs[count].j = 0;+#endif++        return pairs;+      }+    }+  }++  return pairs;+}++static vrna_basepair_t *+backtrack_hp_motif(int i, int j, int k, int l, char d, void *data){++  int                 count;+  vrna_basepair_t     *pairs = NULL;+  quadruple_position  *pos;+  ligand_data         *ldata;+  vrna_basepair_t     *pptr;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        /* found motif in our list, lets create pairs */+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * (ldata->pair_count + 1));+        for(count = 0,pptr = ldata->pairs; pptr && (pptr->i != 0); pptr++, count++){+          pairs[count].i = i + pptr->i - 1;+          pairs[count].j = i + pptr->j - 1;+        }+        pairs[count].i = pairs[count].j = 0;+        return pairs;+      }+    }+  }++  return pairs;+}++static quadruple_position *+scanForMotif( const char *seq,+              const char *motif1,+              const char *motif2){++  int   i, j, k, l, l1, l2, n, cnt, cnt2;+  char  *ptr;+  quadruple_position *pos;+  +  n     = (int) strlen(seq);+  l1    = (int) strlen(motif1);+  l2    = (motif2) ? (int) strlen(motif2) : 0;+  cnt   = 0;+  cnt2  = 5; /* initial guess how many matching motifs we might encounter */++  pos = (quadruple_position *)vrna_alloc(sizeof(quadruple_position) * cnt2);++  for(i = 0; i <= n - l1 - l2; i++){+    if(seq[i] == motif1[0]){+      for(j = i+1; j < i + l1; j++){+        if(seq[j] == motif1[j-i]){+          continue;+        }+        else goto next_i;+      }+      /* found 5' motif */+      if(motif2){+        for(k = j + 1; k <= n - l2; k++){+          if(seq[k] == motif2[0]){+            for(l = k + 1; l < k + l2; l++){+              if(seq[l] == motif2[l-k]){+                continue;+              }+              else goto next_k;+            }+            /* we found a quadruple, so store it */+            pos[cnt].i   = i + 1;+            pos[cnt].j   = l;+            pos[cnt].k   = j;+            pos[cnt++].l = k + 1;++            /* allocate more memory if necessary */+            if(cnt == cnt2){+              cnt2 *= 2;+              pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * cnt2);+            }+          }+/* early exit from l loop */+next_k: continue;+        }+      } else { /* hairpin loop motif */+        /* store it */+        pos[cnt].i   = i + 1;+        pos[cnt].j   = j;+        pos[cnt].k   = 0;+        pos[cnt++].l = 0;++        /* allocate more memory if necessary */+        if(cnt == cnt2){+          cnt2 *= 2;+          pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * cnt2);+        }+      }+    }+/* early exit from j loop */+next_i: continue;+  }++  /* reallocate to actual size */+  pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * (cnt + 1));++  /* set end marker */+  pos[cnt].i = pos[cnt].j = pos[cnt].k = pos[cnt].l = 0;++  return pos;+}++static vrna_basepair_t *+scanForPairs( const char  *motif5,+              const char  *motif3,+              int         *pair_count){++  int             i, l5, l3, stack_size, stack_count, *stack;+  vrna_basepair_t *pairs;++  l5          = (motif5) ? strlen(motif5) : 0;+  l3          = (motif3) ? strlen(motif3) : 0;+  stack_count = 0;+  stack_size  = l5 + l3 + 1;+  *pair_count = 0;+  stack       = vrna_alloc(sizeof(int)              * stack_size);+  pairs       = vrna_alloc(sizeof(vrna_basepair_t)  * stack_size);++  /* go through 5' side of structure motif */+  for(i = 2; i < l5; i++){+    if(motif5[i - 1] == '('){+      stack[stack_count++] = i;+    } else if(motif5[i - 1] == ')'){+      pairs[*pair_count].i = stack[--stack_count];+      pairs[*pair_count].j = i;+      /* printf("5' p[%d, %d]\n", pairs[*pair_count].i, pairs[*pair_count].j); */+      (*pair_count)++;+      if(stack_count < 0){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: 5' structure motif contains unbalanced brackets");+        free(stack);+        free(pairs);+        return NULL;+      }+    }+  }++  if(motif3){+    for(i = 2; i < l3; i++){ /* go through 3' side of motif */+      if(motif3[i-1] == '('){+        stack[stack_count++] = -(l3 - i);+      } else if(motif3[i-1] == ')'){+        pairs[*pair_count].i = stack[--stack_count];+        pairs[*pair_count].j = -(l3 - i);+        /* printf("3' p[%d, %d]\n", pairs[*pair_count].i, pairs[*pair_count].j); */+        (*pair_count)++;+        if(stack_count < 0){+          vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: 3' structure motif contains unbalanced brackets");+          free(stack);+          free(pairs);+          return NULL;+        }+      }+    }+  }++  if(stack_count != 0){+    vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: structure motif contains unbalanced brackets");+    (*pair_count)++;+    free(stack);+    free(pairs);+    return NULL;+  }++  if(*pair_count > 0){+    pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * (*pair_count + 1));+    pairs[*pair_count].i = pairs[*pair_count].j = 0;+  } else {+    free(pairs);+    pairs = NULL;+  }++  free(stack);++  return pairs;+}+
+ C/ViennaRNA/constraints_ligand.h view
@@ -0,0 +1,53 @@+#ifndef VIENNA_RNA_PACKAGE_LIGAND_H+#define VIENNA_RNA_PACKAGE_LIGAND_H++/**+ *  @file     constraints_ligand.h+ *  @ingroup  ligand_binding+ *  @brief    Functions for incorporation of ligands binding to hairpin and interior loop motifs using the soft constraints framework+ */+typedef struct vrna_sc_motif_s  vrna_sc_motif_t;++#include <ViennaRNA/data_structures.h>++struct vrna_sc_motif_s {+  int i;+  int j;+  int k;+  int l;+  int number;+};+++/**+ *  @brief  Add soft constraints for hairpin or interior loop binding motif+ *+ *  @ingroup  constraints_ligand+ *+ *  @param  vc        The #vrna_fold_compound_t the motif is applied to+ *  @param  seq       The sequence motif (may be interspaced by '&' character+ *  @param  structure The structure motif (may be interspaced by '&' character+ *  @param  energy    The free energy of the motif (e.g. binding free energy)+ *  @param  options   Options+ *  @return           non-zero value if application of the motif using soft constraints was successful+ *  + */+int+vrna_sc_add_hi_motif( vrna_fold_compound_t *vc,+                      const char *seq,+                      const char *structure,+                      FLT_OR_DBL energy,+                      unsigned int options);++vrna_sc_motif_t *+vrna_sc_ligand_detect_motifs( vrna_fold_compound_t *vc,+                              const char *structure);++int+vrna_sc_get_hi_motif( vrna_fold_compound_t *vc,+                      int *i,+                      int *j,+                      int *k,+                      int *l);++#endif
+ C/ViennaRNA/constraints_soft.c view
@@ -0,0 +1,520 @@+/* constraints handling */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <assert.h>+#include <config.h>+#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/energy_const.h" /* defines MINPSCORE */+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/file_formats.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints_soft.h"+++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void+sc_add_up(vrna_fold_compound_t *vc,+          const FLT_OR_DBL *constraints);++PRIVATE void+sc_add_bp(vrna_fold_compound_t *vc,+          const FLT_OR_DBL **constraints);++PRIVATE void+sc_really_add_up( vrna_fold_compound_t *vc,+                  int i,+                  FLT_OR_DBL energy);++PRIVATE void+sc_really_add_bp( vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  FLT_OR_DBL energy);++PRIVATE void+prepare_Boltzmann_weights_up( vrna_fold_compound_t *vc);++PRIVATE void+prepare_Boltzmann_weights_bp(vrna_fold_compound_t *vc);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC void+vrna_sc_init(vrna_fold_compound_t *vc){++  unsigned int s;+  vrna_sc_t    *sc;++  if(vc){+    vrna_sc_remove(vc);++    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     sc                    = (vrna_sc_t *)vrna_alloc(sizeof(vrna_sc_t));+                                    sc->energy_up         = NULL;+                                    sc->energy_bp         = NULL;+                                    sc->energy_stack      = NULL;+                                    sc->exp_energy_stack  = NULL;+                                    sc->exp_energy_up     = NULL;+                                    sc->exp_energy_bp     = NULL;+                                    sc->f                 = NULL;+                                    sc->exp_f             = NULL;+                                    sc->data              = NULL;+                                    sc->free_data         = NULL;++                                    vc->sc  = sc;+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  vc->scs = (vrna_sc_t **)vrna_alloc(sizeof(vrna_sc_t*) * (vc->n_seq + 1));+                                    for(s = 0; s < vc->n_seq; s++){+                                      sc                    = (vrna_sc_t *)vrna_alloc(sizeof(vrna_sc_t));+                                      sc->energy_up         = NULL;+                                      sc->energy_bp         = NULL;+                                      sc->energy_stack      = NULL;+                                      sc->exp_energy_stack  = NULL;+                                      sc->exp_energy_up     = NULL;+                                      sc->exp_energy_bp     = NULL;+                                      sc->f                 = NULL;+                                      sc->exp_f             = NULL;+                                      sc->data              = NULL;+                                      sc->free_data         = NULL;++                                      vc->scs[s]  = sc;+                                    }+                                    break;+      default:                      /* do nothing */+                                    break;+    }+  }+}++PUBLIC void+vrna_sc_remove(vrna_fold_compound_t *vc){++  int s;++  if(vc){+    switch(vc->type){+      case  VRNA_FC_TYPE_SINGLE:    vrna_sc_free(vc->sc);+                                    vc->sc = NULL;+                                    break;+      case  VRNA_FC_TYPE_COMPARATIVE: if(vc->scs){+                                      for(s = 0; s < vc->n_seq; s++)+                                        vrna_sc_free(vc->scs[s]);+                                      free(vc->scs);+                                    }+                                    vc->scs = NULL;+                                    break;+      default:                      /* do nothing */+                                    break;+    }+  }+}++PUBLIC void+vrna_sc_free(vrna_sc_t *sc){++  int i;+  if(sc){+    if(sc->energy_up){+      for(i = 0; sc->energy_up[i]; free(sc->energy_up[i++]));+      free(sc->energy_up);+    }+    if(sc->exp_energy_up){+      for(i = 0; sc->exp_energy_up[i]; free(sc->exp_energy_up[i++]));+      free(sc->exp_energy_up);+    }+    +    free(sc->energy_bp);+    free(sc->exp_energy_bp);+    free(sc->energy_stack);+    free(sc->exp_energy_stack);++    if(sc->free_data)+      sc->free_data(sc->data);++    free(sc);+  }+}++PUBLIC void+vrna_sc_set_bp( vrna_fold_compound_t *vc,+                const FLT_OR_DBL **constraints,+                unsigned int options){++  if(vc && (vc->type == VRNA_FC_TYPE_SINGLE)){+    if(constraints){+      /* always add (pure) soft constraints */+      sc_add_bp(vc, constraints);+    }++    if(options & VRNA_OPTION_PF) /* prepare Boltzmann factors for the BP soft constraints */+      prepare_Boltzmann_weights_bp(vc);+  }+}++PUBLIC void+vrna_sc_add_bp(vrna_fold_compound_t *vc,+                      int i,+                      int j,+                      FLT_OR_DBL energy,+                      unsigned int options){++  if(vc && (vc->type == VRNA_FC_TYPE_SINGLE)){+    sc_really_add_bp(vc, i, j, energy);++    if(options & VRNA_OPTION_PF) /* prepare Boltzmann factors for the BP soft constraints */+      prepare_Boltzmann_weights_bp(vc);+  }+}++PUBLIC void+vrna_sc_set_up( vrna_fold_compound_t *vc,+                const FLT_OR_DBL *constraints,+                unsigned int options){++  if(vc && (vc->type == VRNA_FC_TYPE_SINGLE)){+    if(constraints){+      /* always add (pure) soft constraints */+      sc_add_up(vc, constraints);+    }++    if(options & VRNA_OPTION_PF)+      prepare_Boltzmann_weights_up(vc);+  }+}++PUBLIC void+vrna_sc_add_up(vrna_fold_compound_t *vc,+                      int i,+                      FLT_OR_DBL energy,+                      unsigned int options){++  if(vc && (vc->type == VRNA_FC_TYPE_SINGLE)){+    if((i < 1) || (i > vc->length)){+      vrna_message_warning( "vrna_sc_add_up(): Nucleotide position %d out of range!"+                            " (Sequence length: %d)",+                            i, vc->length);+    } else {+      sc_really_add_up(vc, i, energy);++      if(options & VRNA_OPTION_PF)+        prepare_Boltzmann_weights_up(vc);+    }+  }+}++PUBLIC void+vrna_sc_add_data( vrna_fold_compound_t *vc,+                  void *data,+                  vrna_callback_free_auxdata *free_data){++  if(vc){+    if(vc->type == VRNA_FC_TYPE_SINGLE){+      if(!vc->sc)+        vrna_sc_init(vc);++      vc->sc->data        = data;+      vc->sc->free_data   = free_data;+    }+  }+}++PUBLIC void+vrna_sc_add_f(vrna_fold_compound_t *vc,+              vrna_callback_sc_energy *f){++  if(vc && f){+    if(vc->type == VRNA_FC_TYPE_SINGLE){+      if(!vc->sc)+        vrna_sc_init(vc);++      vc->sc->f       = f;+    }+  }+}++PUBLIC void+vrna_sc_add_bt( vrna_fold_compound_t *vc,+                vrna_callback_sc_backtrack *f){++  if(vc && f){+    if(vc->type == VRNA_FC_TYPE_SINGLE){+      if(!vc->sc)+        vrna_sc_init(vc);++      vc->sc->bt      = f;+    }+  }+}++PUBLIC void+vrna_sc_add_exp_f(vrna_fold_compound_t *vc,+                  vrna_callback_sc_exp_energy *exp_f){++  if(vc && exp_f){+    if(vc->type == VRNA_FC_TYPE_SINGLE){+      if(!vc->sc)+        vrna_sc_init(vc);++      vc->sc->exp_f   = exp_f;+    }+  }+}++PRIVATE void+sc_add_bp(vrna_fold_compound_t *vc,+          const FLT_OR_DBL **constraints){++  unsigned int  i, j, n;+  vrna_sc_t     *sc;+  int           *idx;++  n   = vc->length;++  if(!vc->sc)+    vrna_sc_init(vc);++  sc              = vc->sc;++  if(sc->energy_bp)+    free(sc->energy_bp);++  sc->energy_bp = (int *)vrna_alloc(sizeof(int) * (((n + 1) * (n + 2)) / 2));++  idx = vc->jindx;+  for(i = 1; i < n; i++)+    for(j=i+1; j<=n; j++)+      sc->energy_bp[idx[j]+i] = (int)roundf(constraints[i][j] * 100.);++}++PRIVATE void+sc_really_add_bp( vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  FLT_OR_DBL energy){++  unsigned int  n;+  vrna_sc_t     *sc;+  int           *idx;++  n   = vc->length;++  if(!vc->sc)+    vrna_sc_init(vc);++  sc              = vc->sc;++  if(!sc->energy_bp)+    sc->energy_bp = (int *)vrna_alloc(sizeof(int) * (((n + 1) * (n + 2)) / 2));++  idx = vc->jindx;+  sc->energy_bp[idx[j]+i] += (int)roundf(energy * 100.);+}+++PRIVATE void+sc_add_up(vrna_fold_compound_t *vc,+          const FLT_OR_DBL *constraints){++  unsigned int  i, j, n;+  vrna_sc_t     *sc;++  if(vc && constraints){+    n   = vc->length;++    if(!vc->sc)+      vrna_sc_init(vc);++    sc  = vc->sc;+    /*  allocate memory such that we can access the soft constraint+        energies of a subsequence of length j starting at position i+        via sc->energy_up[i][j]+    */+    if(sc->energy_up){+      for(i = 0; i <= n; i++)+        if(sc->energy_up[i])+          free(sc->energy_up[i]);+      free(sc->energy_up);+    }++    sc->energy_up = (int **)vrna_alloc(sizeof(int *) * (n + 2));+    for(i = 0; i <= n; i++)+      sc->energy_up[i] = (int *)vrna_alloc(sizeof(int) * (n - i + 2));++    sc->energy_up[n+1] = NULL;++    for(i = 1; i <= n; i++){+      for(j = 1; j <= (n - i + 1); j++){+        sc->energy_up[i][j] =   sc->energy_up[i][j-1]+                                  + (int)roundf(constraints[i+j-1] * 100.); /* convert to 10kal/mol */+      }+    }+  }+}++PRIVATE void+sc_really_add_up( vrna_fold_compound_t *vc,+                  int i,+                  FLT_OR_DBL energy){++  unsigned int  j, u, n;+  vrna_sc_t     *sc;++  n   = vc->length;++  if(!vc->sc)+    vrna_sc_init(vc);++  sc  = vc->sc;+  /*+      Prepare memory:+      allocate memory such that we can access the soft constraint+      energies of a subsequence of length j starting at position i+      via sc->energy_up[i][j]+  */+  if(!(sc->energy_up)){+    sc->energy_up = (int **)vrna_alloc(sizeof(int *) * (n + 2));+  }++  for(j = 0; j <= n; j++){+    if(!(sc->energy_up[j]))+      sc->energy_up[j] = (int *)vrna_alloc(sizeof(int) * (n - j + 2));+  }++  sc->energy_up[n+1] = NULL;++  /* update soft constraints for subsequences starting at some position */+  for(j = 1; j <= i; j++){+    int u_max   = n - j + 1;+    int u_start = i - j + 1;++    sc->energy_up[j][u_start] += (int)roundf(energy * 100.); /* convert to 10kal/mol */++    for(u = u_start + 1; u <= u_max; u++){+      sc->energy_up[j][u] = sc->energy_up[j][u-1]+                            + sc->energy_up[j + u - 1][1];+    }+  }+}+++/* compute Boltzmann factors for BP soft constraints from stored free energies */+PRIVATE void+prepare_Boltzmann_weights_bp(vrna_fold_compound_t *vc){++  unsigned int  i, j, n;+  vrna_sc_t     *sc;+  int           *idx, *jidx;++  if(vc->sc && vc->sc->energy_bp){+    n   = vc->length;+    sc  = vc->sc;++    vrna_exp_param_t  *exp_params = vc->exp_params;+    double            GT          = 0.;+    double            temperature = exp_params->temperature;+    double            kT          = exp_params->kT;+    double            TT          = (temperature+K0)/(Tmeasure);++    if(sc->exp_energy_bp)+      free(sc->exp_energy_bp);+    sc->exp_energy_bp     = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (((n + 1) * (n + 2)) / 2));++    idx   = vc->iindx;+    jidx  = vc->jindx;++    for(i = 1; i < n; i++)+      for(j = i + 1; j <= n; j++){+        GT = sc->energy_bp[jidx[j] + i] * 10.;+        sc->exp_energy_bp[idx[i]-j] = (FLT_OR_DBL)exp( -GT / kT);+      }+  }+}++PRIVATE void+prepare_Boltzmann_weights_up(vrna_fold_compound_t *vc){++  unsigned int  i, j, n;+  vrna_sc_t     *sc;++  n   = vc->length;++  sc  = vc->sc;++  vrna_exp_param_t   *exp_params = vc->exp_params;+  double             GT          = 0.;+  double             temperature = exp_params->temperature;+  double             kT          = exp_params->kT;+  double             TT          = (temperature+K0)/(Tmeasure);++  /* #################################### */+  /* # single nucleotide contributions  # */+  /* #################################### */++  if(sc && sc->energy_up){+    /*  allocate memory such that we can access the soft constraint+        energies of a subsequence of length j starting at position i+        via sc->exp_energy_up[i][j]+    */++    /* free previous unpaired nucleotide constraints */+    if(sc->exp_energy_up){+      for(i = 0; i <= n; i++)+        if(sc->exp_energy_up[i])+          free(sc->exp_energy_up[i]);+      free(sc->exp_energy_up);+    }++    /* allocate memory and create Boltzmann factors from stored contributions */+    sc->exp_energy_up = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 2));+    sc->exp_energy_up[0] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+    for(j = 0; j <= (n + 1); j++)+        sc->exp_energy_up[0][j] = 1.;++    for(i = 1; i <= n; i++){+      sc->exp_energy_up[i] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n - i + 2));++      sc->exp_energy_up[i][0] = 1.;++      for(j = 1; j <= (n - i + 1); j++){+        GT  = (double)sc->energy_up[i][j] * 10.; /* convert to cal/mol */+        sc->exp_energy_up[i][j] = (FLT_OR_DBL)exp( -GT / kT);+      }+    }++    sc->exp_energy_up[n+1] = NULL;+  }+}
+ C/ViennaRNA/constraints_soft.h view
@@ -0,0 +1,317 @@+#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H+#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H++#include <ViennaRNA/data_structures.h>++/**+ *  @file     constraints_soft.h+ *  @brief    Functions and data structures for secondary structure soft constraints+ *  @ingroup  soft_constraints+ */+++/** @brief Typename for the soft constraints data structure #vrna_sc_s+ *  @ingroup  soft_constraints+ */+typedef struct  vrna_sc_s vrna_sc_t;++/**+ * @brief Callback to retrieve pseudo energy contribution for soft constraint feature+ *+ * @ingroup soft_constraints+ *+ * This is the prototype for callback functions used by the folding recursions to evaluate generic+ * soft constraints. The first four parameters passed indicate the delimiting nucleotide positions+ * of the decomposition, and the parameter @p denotes the decomposition step. The last parameter+ * @p data is the auxiliary data structure associated to the hard constraints via vrna_sc_add_data(),+ * or NULL if no auxiliary data was added.+ *+ * @see #VRNA_DECOMP_PAIR_HP, #VRNA_DECOMP_PAIR_IL, #VRNA_DECOMP_PAIR_ML, #VRNA_DECOMP_ML_ML_ML,+ *      #VRNA_DECOMP_ML_STEM, #VRNA_DECOMP_ML_ML, #VRNA_DECOMP_ML_UP, #VRNA_DECOMP_ML_ML_STEM,+ *      #VRNA_DECOMP_ML_COAXIAL, #VRNA_DECOMP_EXT_EXT, #VRNA_DECOMP_EXT_UP, #VRNA_DECOMP_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_EXT, #VRNA_DECOMP_EXT_STEM_EXT, #VRNA_DECOMP_EXT_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_bt(),+ *      vrna_sc_add_data()+ *+ * @param i         Left (5') delimiter position of substructure+ * @param j         Right (3') delimiter position of substructure+ * @param k         Left delimiter of decomposition+ * @param l         Right delimiter of decomposition+ * @param d         Decomposition step indicator+ * @param data      Auxiliary data+ * @return          Pseudo energy contribution in deka-kalories per mol+ */+typedef int (vrna_callback_sc_energy)(int i, int j, int k, int l, char d, void *data);++/**+ * @brief Callback to retrieve pseudo energy contribution as Boltzmann Factors for soft constraint feature+ *+ * @ingroup soft_constraints+ *+ * This is the prototype for callback functions used by the partition function recursions to evaluate generic+ * soft constraints. The first four parameters passed indicate the delimiting nucleotide positions+ * of the decomposition, and the parameter @p denotes the decomposition step. The last parameter+ * @p data is the auxiliary data structure associated to the hard constraints via vrna_sc_add_data(),+ * or NULL if no auxiliary data was added.+ *+ * @see #VRNA_DECOMP_PAIR_HP, #VRNA_DECOMP_PAIR_IL, #VRNA_DECOMP_PAIR_ML, #VRNA_DECOMP_ML_ML_ML,+ *      #VRNA_DECOMP_ML_STEM, #VRNA_DECOMP_ML_ML, #VRNA_DECOMP_ML_UP, #VRNA_DECOMP_ML_ML_STEM,+ *      #VRNA_DECOMP_ML_COAXIAL, #VRNA_DECOMP_EXT_EXT, #VRNA_DECOMP_EXT_UP, #VRNA_DECOMP_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_EXT, #VRNA_DECOMP_EXT_STEM_EXT, #VRNA_DECOMP_EXT_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_exp_f(), vrna_sc_add_f(), vrna_sc_add_bt(),+ *      vrna_sc_add_data()+ *+ * @param i         Left (5') delimiter position of substructure+ * @param j         Right (3') delimiter position of substructure+ * @param k         Left delimiter of decomposition+ * @param l         Right delimiter of decomposition+ * @param d         Decomposition step indicator+ * @param data      Auxiliary data+ * @return          Pseudo energy contribution in deka-kalories per mol+ */+typedef FLT_OR_DBL (vrna_callback_sc_exp_energy)(int i, int j, int k, int l, char d, void *data);++/**+ * @brief Callback to retrieve auxiliary base pairs for soft constraint feature+ *+ * @ingroup soft_constraints+ *+ * @see #VRNA_DECOMP_PAIR_HP, #VRNA_DECOMP_PAIR_IL, #VRNA_DECOMP_PAIR_ML, #VRNA_DECOMP_ML_ML_ML,+ *      #VRNA_DECOMP_ML_STEM, #VRNA_DECOMP_ML_ML, #VRNA_DECOMP_ML_UP, #VRNA_DECOMP_ML_ML_STEM,+ *      #VRNA_DECOMP_ML_COAXIAL, #VRNA_DECOMP_EXT_EXT, #VRNA_DECOMP_EXT_UP, #VRNA_DECOMP_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_EXT, #VRNA_DECOMP_EXT_STEM_EXT, #VRNA_DECOMP_EXT_EXT_STEM,+ *      #VRNA_DECOMP_EXT_EXT_STEM1, vrna_sc_add_bt(), vrna_sc_add_f(), vrna_sc_add_exp_f(),+ *      vrna_sc_add_data()+ *+ * @param i         Left (5') delimiter position of substructure+ * @param j         Right (3') delimiter position of substructure+ * @param k         Left delimiter of decomposition+ * @param l         Right delimiter of decomposition+ * @param d         Decomposition step indicator+ * @param data      Auxiliary data+ * @return          List of additional base pairs+ */+typedef vrna_basepair_t *(vrna_callback_sc_backtrack)(int i, int j, int k, int l, char d, void *data);++/**+ *  @brief  The soft constraints data structure+ *+ *  @ingroup soft_constraints+ */+struct vrna_sc_s {+  int         **energy_up;            /**<  @brief Energy contribution for stretches of unpaired nucleotides */+  int         *energy_bp;             /**<  @brief Energy contribution for base pairs */+  FLT_OR_DBL  **exp_energy_up;        /**<  @brief Boltzmann Factors of the energy contributions for unpaired sequence stretches */+  FLT_OR_DBL  *exp_energy_bp;         /**<  @brief Boltzmann Factors of the energy contribution for base pairs */++  int         *energy_stack;          /**<  @brief Pseudo Energy contribution per base pair involved in a stack */+  FLT_OR_DBL  *exp_energy_stack;      /**<  @brief Boltzmann weighted pseudo energy contribution per nucleotide involved in a stack */++  /* generic soft contraints below */+  vrna_callback_sc_energy *f;         /**<  @brief  A function pointer used for pseudo+                                                    energy contribution in MFE calculations+                                            @see    vrna_sc_add_f()+                                      */++  vrna_callback_sc_backtrack *bt;     /**<  @brief  A function pointer used to obtain backtraced+                                                    base pairs in loop regions that were altered+                                                    by soft constrained pseudo energy contributions+                                            @see    vrna_sc_add_bt()+                                      */++  vrna_callback_sc_exp_energy *exp_f; /**<  @brief  A function pointer used for pseudo energy+                                                    contribution boltzmann factors in PF+                                                    calculations+                                            @see    vrna_sc_add_exp_f()+                                      */++  void *data;                         /**<  @brief  A pointer to the data object provided for+                                                    for pseudo energy contribution functions of the+                                                    generic soft constraints feature+                                      */+  vrna_callback_free_auxdata *free_data;+};++/**+ *  @brief Initialize an empty soft constraints data structure within a #vrna_fold_compound_t+ *+ *  This function adds a proper soft constraints data structure+ *  to the #vrna_fold_compound_t data structure.+ *  If soft constraints already exist within the fold compound, they are removed.+ *+ *  \note Accepts vrna_fold_compound_t of type #VRNA_FC_TYPE_SINGLE and #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @ingroup  soft_constraints+ *+ *  @see  vrna_sc_set_bp(), vrna_sc_set_up(), vrna_sc_add_SHAPE_deigan(),+ *        vrna_sc_add_SHAPE_zarringhalam(), vrna_sc_remove(), vrna_sc_add_f(),+ *        vrna_sc_add_exp_f(), vrna_sc_add_pre(), vrna_sc_add_post()+ *  @param  vc  The #vrna_fold_compound_t where an empty soft constraint feature is to be added to+ */+void vrna_sc_init(vrna_fold_compound_t *vc);++/**+ *  @brief  Set soft constraints for paired nucleotides+ *+ *  @note     This function replaces any pre-exisitng soft constraints with the ones supplied+ *            in @p constraints.+ *+ *  @ingroup  soft_constraints+ *+ *  @see      vrna_sc_add_bp(), vrna_sc_set_up(), vrna_sc_add_up()+ *+ *  @param  vc          The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  constraints A two-dimensional array of pseudo free energies in @f$ kcal / mol @f$+ *  @param  options     The options flag indicating how/where to store the soft constraints+ */+void vrna_sc_set_bp(vrna_fold_compound_t *vc,+                    const FLT_OR_DBL **constraints,+                    unsigned int options);++/**+ *  @brief  Add soft constraints for paired nucleotides+ *+ *  @ingroup  soft_constraints+ *+ *  @see      vrna_sc_set_bp(), vrna_sc_set_up(), vrna_sc_add_up()+ *+ *  @param  vc          The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  i           The 5' position of the base pair the soft constraint is added for+ *  @param  j           The 3' position of the base pair the soft constraint is added for+ *  @param  energy      The free energy (soft-constraint) in @f$ kcal / mol @f$+ *  @param  options     The options flag indicating how/where to store the soft constraints+ */+void vrna_sc_add_bp(vrna_fold_compound_t *vc,+                   int i,+                   int j,+                   FLT_OR_DBL energy,+                   unsigned int options);++/**+ *  @brief  Set soft constraints for unpaired nucleotides+ *+ *  @note     This function replaces any pre-exisitng soft constraints with the ones supplied+ *            in @p constraints.+ *+ *  @ingroup  soft_constraints+ *+ *  @see      vrna_sc_add_up(), vrna_sc_set_bp(), vrna_sc_add_bp()+ *+ *  @param  vc          The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  constraints A vector of pseudo free energies in @f$ kcal / mol @f$+ *  @param  options     The options flag indicating how/where to store the soft constraints+ */+void vrna_sc_set_up(vrna_fold_compound_t *vc,+                    const FLT_OR_DBL *constraints,+                    unsigned int options);++/**+ *  @brief  Add soft constraints for unpaired nucleotides+ *+ *  @ingroup  soft_constraints+ *+ *  @see      vrna_sc_set_up(), vrna_sc_add_bp(), vrna_sc_set_bp()+ *+ *  @param  vc          The #vrna_fold_compound_t the soft constraints are associated with+ *  @param  i           The nucleotide position the soft constraint is added for+ *  @param  energy      The free energy (soft-constraint) in @f$ kcal / mol @f$+ *  @param  options     The options flag indicating how/where to store the soft constraints+ */+void vrna_sc_add_up( vrna_fold_compound_t *vc,+                            int i,+                            FLT_OR_DBL energy,+                            unsigned int options);++/**+ *  @brief  Remove soft constraints from #vrna_fold_compound_t+ *+ *  \note Accepts vrna_fold_compound_t of type #VRNA_FC_TYPE_SINGLE and #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @ingroup  soft_constraints+ *+ *  @param  vc  The #vrna_fold_compound_t possibly containing soft constraints+ */+void vrna_sc_remove(vrna_fold_compound_t *vc);++/**+ *  @brief  Free memory occupied by a #vrna_sc_t data structure+ *+ *  @ingroup  soft_constraints+ *+ *  @param  sc  The data structure to free from memory+ */+void vrna_sc_free(vrna_sc_t *sc);++/**+ *  @brief Add an auxiliary data structure for the generic soft constraints callback function+ *+ *  @ingroup soft_constraints+ *+ *  @see vrna_sc_add_f(), vrna_sc_add_exp_f(), vrna_sc_add_bt()+ *+ *  @param  vc        The fold compound the generic soft constraint function should be bound to+ *  @param  data      A pointer to the data structure that holds required data for function 'f'+ *  @param  free_data A pointer to a function that free's the memory occupied by @p data (Maybe NULL)+ */+void vrna_sc_add_data(vrna_fold_compound_t *vc,+                      void *data,+                      vrna_callback_free_auxdata *free_data);++/**+ *  @brief  Bind a function pointer for generic soft constraint feature (MFE version)+ *+ *  This function allows one to easily bind a function pointer and corresponding data structure+ *  to the soft constraint part #vrna_sc_t of the #vrna_fold_compound_t.+ *  The function for evaluating the generic soft constraint feature has to return+ *  a pseudo free energy @f$ \hat{E} @f$ in @f$ dacal/mol @f$, where @f$ 1 dacal/mol = 10 cal/mol @f$.+ *+ *  @ingroup soft_constraints+ *+ *  @see vrna_sc_add_data(), vrna_sc_add_bt(), vrna_sc_add_exp_f()+ *+ *  @param  vc    The fold compound the generic soft constraint function should be bound to+ *  @param  f     A pointer to the function that evaluates the generic soft constraint feature+ */+void vrna_sc_add_f( vrna_fold_compound_t *vc,+                    vrna_callback_sc_energy *f);++/**+ *  @brief  Bind a backtracking function pointer for generic soft constraint feature+ *+ *  This function allows one to easily bind a function pointer to the soft constraint part+ *  #vrna_sc_t of the #vrna_fold_compound_t.+ *  The provided function should be used for backtracking purposes in loop regions+ *  that were altered via the generic soft constraint feature. It has to return+ *  an array of #vrna_basepair_t data structures, were the last element in the list is indicated+ *  by a value of -1 in it's i position.+ *+ *  @ingroup soft_constraints+ *+ *  @see vrna_sc_add_data(), vrna_sc_add_f(), vrna_sc_add_exp_f()+ *+ *  @param  vc    The fold compound the generic soft constraint function should be bound to+ *  @param  f     A pointer to the function that returns additional base pairs+ */+void vrna_sc_add_bt(vrna_fold_compound_t *vc,+                    vrna_callback_sc_backtrack *f);++/**+ *  @brief  Bind a function pointer for generic soft constraint feature (PF version)+ *+ *  This function allows one to easily bind a function pointer and corresponding data structure+ *  to the soft constraint part #vrna_sc_t of the #vrna_fold_compound_t.+ *  The function for evaluating the generic soft constraint feature has to return+ *  a pseudo free energy @f$ \hat{E} @f$ as Boltzmann factor, i.e. @f$ exp(- \hat{E} / kT) @f$.+ *  The required unit for @f$ E @f$ is @f$ cal/mol @f$.+ *+ *  @ingroup soft_constraints+ *+ *  @see vrna_sc_add_bt(), vrna_sc_add_f(), vrna_sc_add_data()+ *+ *  @param  vc    The fold compound the generic soft constraint function should be bound to+ *  @param  exp_f A pointer to the function that evaluates the generic soft constraint feature+ */+void vrna_sc_add_exp_f( vrna_fold_compound_t *vc,+                        vrna_callback_sc_exp_energy *exp_f);++#endif
+ C/ViennaRNA/convert_epars.c view
@@ -0,0 +1,954 @@+/*+###################################+# convert energy parameter files  #+# from ViennaRNAPackage 1.8.4 to  #+# 2.0 format                      #+#                                 #+# Ronny Lorenz                    #+###################################+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/read_epars.h"+#include "ViennaRNA/pair_mat.h"++#include "1.8.4_epars.h"+#include "1.8.4_intloops.h"++#include "ViennaRNA/convert_epars.h"++enum parset_184 {UNKNOWN_184= -1, QUIT_184, S_184, SH_184, HP_184, B_184, IL_184, MMI_184, MMH_184, MMM_184, MM_H_184,+             DE5_184, DE3_184, DE5_H_184, DE3_H_184, ML_184, TL_184, TRI_184, TE_184, NIN_184, MISC_184,+             INT11_184, INT11_H_184, INT21_184, INT21_H_184, INT22_184, INT22_H_184};+++PRIVATE unsigned int  read_old_parameter_file(FILE *ifile, int skip_header);+PRIVATE void          write_new_parameter_file(FILE *ofile, unsigned int options);+PRIVATE void          rd_stacks(int stack[NBPAIRS+1][NBPAIRS+1], FILE *fp);+PRIVATE void          rd_loop(int looparray[31], FILE *fp);+PRIVATE void          rd_mismatch(int mismatch[NBPAIRS+1][5][5], FILE *fp);+PRIVATE void          rd_int11(int int11[NBPAIRS+1][NBPAIRS+1][5][5], FILE *fp);+PRIVATE void          rd_int21(int int21[NBPAIRS+1][NBPAIRS+1][5][5][5], FILE *fp);+PRIVATE void          rd_int22(int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5], FILE *fp);+PRIVATE void          rd_dangle(int dangles[NBPAIRS+1][5], FILE *fp);+PRIVATE void          rd_MLparams(FILE *fp);+PRIVATE void          rd_misc(FILE *fp);+PRIVATE void          rd_ninio(FILE *fp);+PRIVATE void          rd_Tetra_loop(FILE *fp);+PRIVATE void          rd_Tri_loop(FILE *fp);+PRIVATE void          check_symmetry(void);+PRIVATE enum          parset_184 gettype_184(char ident[]);+PRIVATE char          *get_array1(int *arr, int size, FILE *fp);+PRIVATE void          ignore_comment(char *line);+PRIVATE void          display_array(int *p, int size, int line, FILE *fp);+++PUBLIC void convert_parameter_file(const char *iname, const char *oname, unsigned int options){+  FILE          *ifile, *ofile;+  unsigned int  old_options = 0;+  int           skip_input_header = 0;++  if(options & VRNA_CONVERT_OUTPUT_DUMP){+    if(oname == NULL) oname = iname;+    skip_input_header = 1;+  }+  else{+    if(iname == NULL){+      ifile = stdin;+      skip_input_header = 1;+    }+    else if(!(ifile=fopen(iname,"r"))){+      vrna_message_warning("convert_epars: can't open file %s", iname);+      return;+    }+    /* read old (1.8.4 format) parameter file */+    old_options = read_old_parameter_file(ifile, skip_input_header);+    if(ifile != stdin) fclose(ifile);+    check_symmetry();+  }++  if(options & VRNA_CONVERT_OUTPUT_VANILLA)+    options = old_options;++  if(oname == NULL) ofile = stdout;+  else if(!(ofile=fopen(oname,"a+"))){+    vrna_message_warning("convert_epars: can't open file %s for writing", oname);+    return;+  }+  write_new_parameter_file(ofile, options);+  if(ofile != stdout) fclose(ofile);+}+++/*------------------------------------------------------------*/+PRIVATE unsigned int read_old_parameter_file(FILE *ifile, int skip_header){+  char                  *line, ident[32];+  enum      parset_184  type;+  int                   r, last;+  unsigned  int         read_successfully = 0;++  if (!(line = vrna_read_line(ifile))) {+    vrna_message_warning("convert_epars: can't read input parameter file");+    return 0;+  }+  if(!skip_header){+    if (strncmp(line,"## RNAfold parameter file",25)!=0){+      vrna_message_warning("convert_epars: Missing header line in input parameter file.\n"+                "May be this file has incorrect format?");+      free(line);+      return 0;+    }+    free(line);+    line = vrna_read_line(ifile);+  }+  last = 0;+  do{+    r = sscanf(line, "# %31s", ident);+    if (r==1){+      type = gettype_184(ident);+      switch (type){+        case QUIT_184:    if(ifile == stdin){+                            vrna_message_info(stderr, "press ENTER to continue...");+                            fflush(stderr);+                          }+                          last = 1;+                          break;+        case SH_184:      rd_stacks(enthalpies_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_STACK;+                          break;+        case S_184:       rd_stacks(stack37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_STACK;+                          break;+        case HP_184:      rd_loop(hairpin37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_HP;+                          break;+        case B_184:       rd_loop(bulge37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_BULGE;+                          break;+        case IL_184:      rd_loop(internal_loop37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT;+                          break;+        case MMH_184:     rd_mismatch(mismatchH37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_MM_HP;+                          break;+        case MMI_184:     rd_mismatch(mismatchI37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_MM_INT+                                              |VRNA_CONVERT_OUTPUT_MM_INT_1N  /* since 1:n-interior loop mismatches are treated seperately in 2.0 */+                                              |VRNA_CONVERT_OUTPUT_MM_INT_23; /* since 2:3-interior loop mismatches are treated seperately in 2.0 */+                          break;+        case MMM_184:     rd_mismatch(mismatchM37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_MM_MULTI;+                          break;+        case MM_H_184:    rd_mismatch(mism_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_MM_HP      /* since hairpin mismatches are treated seperately in 2.0 */+                                              |VRNA_CONVERT_OUTPUT_MM_INT     /* since interior loop  mismatches are treated seperately in 2.0 */+                                              |VRNA_CONVERT_OUTPUT_MM_INT_1N  /* since 1:n-interior loop mismatches are treated seperately in 2.0 */+                                              |VRNA_CONVERT_OUTPUT_MM_INT_23  /* since 2:3-interior loop mismatches are treated seperately in 2.0 */+                                              |VRNA_CONVERT_OUTPUT_MM_MULTI;  /* since multi loop mismatches are treated seperately in 2.0 */+                          break;+        case INT11_184:   rd_int11(int11_37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_11;+                          break;+        case INT11_H_184: rd_int11(int11_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_11;+                          break;+        case INT21_184:   rd_int21(int21_37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_21;+                          break;+        case INT21_H_184: rd_int21(int21_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_21;+                          break;+        case INT22_184:   rd_int22(int22_37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_22;+                          break;+        case INT22_H_184: rd_int22(int22_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_INT_22;+                          break;+        case DE5_184:     rd_dangle(dangle5_37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_DANGLE5+                                              |VRNA_CONVERT_OUTPUT_MM_MULTI /* since multi loop mismatches were treated as dangle contribution */+                                              |VRNA_CONVERT_OUTPUT_MM_EXT;  /* since exterior loop mismatches were treated as dangle contribution */+                          break;+        case DE5_H_184:   rd_dangle(dangle5_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_DANGLE5+                                              |VRNA_CONVERT_OUTPUT_MM_MULTI /* since multi loop mismatches were treated as dangle contribution */+                                              |VRNA_CONVERT_OUTPUT_MM_EXT;  /* since exterior loop mismatches were treated as dangle contribution */+                          break;+        case DE3_184:     rd_dangle(dangle3_37_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_DANGLE3+                                              |VRNA_CONVERT_OUTPUT_MM_MULTI /* since multi loop mismatches were treated as dangle contribution */+                                              |VRNA_CONVERT_OUTPUT_MM_EXT;  /* since exterior loop mismatches were treated as dangle contribution */+                          break;+        case DE3_H_184:   rd_dangle(dangle3_H_184, ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_DANGLE3+                                              |VRNA_CONVERT_OUTPUT_MM_MULTI /* since multi loop mismatches were treated as dangle contribution */+                                              |VRNA_CONVERT_OUTPUT_MM_EXT;  /* since exterior loop mismatches were treated as dangle contribution */+                          break;+        case ML_184:      rd_MLparams(ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_ML+                                              |VRNA_CONVERT_OUTPUT_MISC;    /* since TerminalAU went to "misc" section */+                          break;+        case NIN_184:     rd_ninio(ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_NINIO;+                          break;+        case TL_184:      rd_Tetra_loop(ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_SPECIAL_HP;+                          break;+        case TRI_184:     rd_Tri_loop(ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_SPECIAL_HP;+                          break;+        case MISC_184:    rd_misc(ifile);+                          read_successfully |= VRNA_CONVERT_OUTPUT_MISC;+                          break;+        default:          /* do nothing but complain */+                          vrna_message_warning("convert_parameter_file: Unknown field identifier in `%s'", line);+      }+    } /* else ignore line */+    free(line);+  } while((line=vrna_read_line(ifile)) && !last);+  return read_successfully;+}++PRIVATE void display_array(int *p, int size, int nl, FILE *fp){+  int i;+  for (i=1; i<=size; i++, p++) {+    switch(*p){+      case  INF: fprintf(fp,"   INF");    break;+      case -INF: fprintf(fp,"  -INf");    break;+      case  DEF: fprintf(fp,"   DEF");    break;+      default:   fprintf(fp,"%6d",  *p);  break;+    }+    if ((i%nl)==0) fprintf(fp,"\n");+  }+  if (size%nl) fprintf(fp,"\n");+  return;+}++PRIVATE char *get_array1(int *arr, int size, FILE *fp){+  int    i, p, pos, pp, r, last;+  char  *line, buf[16];+  i = last = 0;+  while( i<size ) {+    line = vrna_read_line(fp);+    if (!line) vrna_message_error("convert_epars: unexpected end of file in get_array1");+    ignore_comment(line);+    pos=0;+    while ((i<size)&&(sscanf(line+pos,"%15s%n", buf, &pp)==1)) {+      pos += pp;+      if (buf[0]=='*') {i++; continue;}+      else if (buf[0]=='x') { /* should only be used for loop parameters */+        if (i==0) vrna_message_error("convert_epars: can't extrapolate first value");+        p = arr[last] + (int) (0.5+ lxc37_184*log(((double) i)/(double)(last)));+      }+      else if (strcmp(buf,"DEF") == 0) p = DEF;+      else if (strcmp(buf,"INF") == 0) p = INF;+      else if (strcmp(buf,"NST") == 0) p = NST;+      else {+        r=sscanf(buf,"%d", &p);+        if (r!=1) {+          return line+pos;+          vrna_message_error("convert_epars: can't interpret `%s' in get_array1", buf);+          exit(1);+        }+        last = i;+      }+      arr[i++]=p;+    }+    free(line);+  }++  return NULL;+}+/*------------------------------------------------------------*/++PRIVATE void  rd_stacks(int stacks[NBPAIRS+1][NBPAIRS+1], FILE *fp)+{+  int    i;+  char  *cp;+  for (i=1; i<=NBPAIRS; i++) {+    cp = get_array1(stacks[i]+1,NBPAIRS, fp);+    if (cp) {+      vrna_message_error("convert_epars: \nrd_stacks: %s", cp);+      exit(1);+    }+  }+  return;+}+/*------------------------------------------------------------*/++PRIVATE void rd_loop(int loop[31], FILE *fp)+{+  char *cp;++  cp   = get_array1(loop, 31, fp);++  if (cp) {+    vrna_message_error("convert_epars: \nrd_loop: %s", cp);+    exit(1);+  }+  return;+}+/*------------------------------------------------------------*/++PRIVATE void rd_mismatch(int mismatch[NBPAIRS+1][5][5], FILE *fp)+{+  char  *cp;+  int    i;++  for (i=1; i<NBPAIRS+1; i++) {+    cp = get_array1(mismatch[i][0],5*5, fp);+    if (cp) {+      vrna_message_error("convert_epars: rd_mismatch: in field mismatch[%d]\n\t%s", i, cp);+      exit(1);+    }+  }+  return;+}++/*------------------------------------------------------------*/+PRIVATE void rd_int11(int int11[NBPAIRS+1][NBPAIRS+1][5][5], FILE *fp)+{+  char  *cp;+  int    i, j;++  for (i=1; i<NBPAIRS+1; i++) {+    for (j=1; j<NBPAIRS+1; j++) {+      cp = get_array1(int11[i][j][0],5*5, fp);+      if (cp) {+        vrna_message_error("convert_epars: rd_int11: in field int11[%d][%d]\n\t%s", i, j, cp);+        exit(1);+      }+    }+  }+  return;+}++/*------------------------------------------------------------*/+PRIVATE void rd_int21(int int21[NBPAIRS+1][NBPAIRS+1][5][5][5], FILE *fp)+{+  char  *cp;+  int    i, j, k;++  for (i=1; i<NBPAIRS+1; i++) {+    for (j=1; j<NBPAIRS+1; j++) {+      for (k=0; k<5; k++) {+        cp = get_array1(int21[i][j][k][0],5*5, fp);+        if (cp) {+          vrna_message_error("convert_epars: rd_int21: in field int21[%d][%d][%d]\n\t%s",+                                    i, j, k, cp);+          exit(1);+        }+      }+    }+  }+  return;+}++/*------------------------------------------------------------*/+PRIVATE void rd_int22(int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5], FILE *fp)+{+  char  *cp;+  int    i, j, k, l, m;++  for (i=1; i<NBPAIRS+1; i++)+    for (j=1; j<NBPAIRS+1; j++)+      for (k=1; k<5; k++)+        for (l=1; l<5; l++)+          for (m=1; m<5; m++) {+            cp = get_array1(int22[i][j][k][l][m]+1,4, fp);+            if (cp) {+              vrna_message_error("convert_epars: rd_int22: in field "+                                        "int22[%d][%d][%d][%d][%d]\n\t%s",+                                        i, j, k, l, m, cp);+              exit(1);+            }+          }++  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_dangle(int dangle[NBPAIRS+1][5], FILE *fp)+{+  int   i;+  char *cp;++  for (i=0; i< NBPAIRS+1; i++) {+    cp = get_array1(dangle[i],5, fp);+    if (cp) {+      vrna_message_error("convert_epars: \nrd_dangle: %s", cp);+      exit(1);+    }+  }+  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_MLparams(FILE *fp)+{+  char *cp;+  int values[4];++  cp   = get_array1(values,4, fp);+  if (cp) {+    vrna_message_error("convert_epars: rd_MLparams: %s", cp);+    exit(1);+  }++  ML_BASE37_184     = values[0];+  ML_closing37_184  = values[1];+  ML_intern37_184   = values[2];+  TerminalAU_184    = values[3];++  return;+}++/*------------------------------------------------------------*/++PRIVATE void  rd_misc(FILE *fp)+{+  char *cp;+  int values[1]; /* so far just one */++  cp   = get_array1(values,1, fp);+  if (cp) {+    vrna_message_error("convert_epars: rd_misc: %s", cp);+    exit(1);+  }++  DuplexInit_184 = values[0];++  return;+}++/*------------------------------------------------------------*/++PRIVATE void  rd_ninio(FILE *fp)+{+  char  *cp;+  int temp[2];++  cp = get_array1(temp, 2, fp);++  if (cp) {+    vrna_message_error("convert_epars: rd_F_ninio: %s", cp);+    exit(1);+  }+  F_ninio37_184[2] = temp[0];+  MAX_NINIO_184  = temp[1];+  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_Tetra_loop(FILE *fp)+{+  int    i, r;+  char   *buf;++  i=0;+  memset(&Tetraloops_184, 0, 1400);+  memset(&TETRA_ENERGY37_184, 0, sizeof(int)*200);+  do {+    buf = vrna_read_line(fp);+    if (buf==NULL) break;+    r = sscanf(buf,"%6s %d", &Tetraloops_184[7*i], &TETRA_ENERGY37_184[i]);+    strcat(Tetraloops_184, " ");+    free(buf);+    i++;+  } while((r==2)&&(i<200));+  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_Tri_loop(FILE *fp)+{+  int    i, r;+  char   *buf;++  i=0;+  memset(&Triloops_184, 0, 241);+  memset(&Triloop_E37_184, 0, sizeof(int)*40);+  do {+    buf = vrna_read_line(fp);+    if (buf==NULL) break;+    r = sscanf(buf,"%5s %d", &Triloops_184[6*i], &Triloop_E37_184[i]);+    Triloops_184[6*i+5]=' ';+    free(buf);+    i++;+  } while((r==2)&&(i<40));+  return;+}++/*------------------------------------------------------------*/+++PRIVATE void ignore_comment(char * line)+{+  /* excise C style comments */+  /* only one comment per line, no multiline comments */+  char *cp1, *cp2;++  if ((cp1=strstr(line, "/*"))) {+    cp2 = strstr(cp1, "*/");+    if (cp2==NULL)+      vrna_message_error("convert_epars: unclosed comment in parameter file");+    /* can't use strcpy for overlapping strings */+    for (cp2+=2; *cp2!='\0'; cp2++, cp1++)+      *cp1 = *cp2;+    *cp1 = '\0';+  }++  return;+}++PRIVATE enum parset_184 gettype_184(char ident[]){+  if (strcmp(ident,"stack_enthalpies") == 0)          return SH_184;+  else if (strcmp(ident,"stack_energies") == 0)       return S_184;+  else if (strcmp(ident,"hairpin" ) == 0)             return HP_184;+  else if (strcmp(ident,"bulge") == 0)                return B_184;+  else if (strcmp(ident,"internal_loop") == 0)        return IL_184;+  else if (strcmp(ident,"mismatch_hairpin") == 0)     return MMH_184;+  else if (strcmp(ident,"mismatch_interior") == 0)    return MMI_184;+  else if (strcmp(ident,"mismatch_multi") == 0)       return MMM_184;+  else if (strcmp(ident,"mismatch_enthalpies") == 0)  return MM_H_184;+  else if (strcmp(ident,"int11_energies") == 0)       return INT11_184;+  else if (strcmp(ident,"int11_enthalpies") == 0)     return INT11_H_184;+  else if (strcmp(ident,"int21_energies") == 0)       return INT21_184;+  else if (strcmp(ident,"int21_enthalpies") == 0)     return INT21_H_184;+  else if (strcmp(ident,"int22_energies") == 0)       return INT22_184;+  else if (strcmp(ident,"int22_enthalpies") == 0)     return INT22_H_184;+  else if (strcmp(ident,"dangle5")== 0)               return DE5_184;+  else if (strcmp(ident,"dangle3")== 0)               return DE3_184;+  else if (strcmp(ident,"dangle5_enthalpies")== 0)    return DE5_H_184;+  else if (strcmp(ident,"dangle3_enthalpies")== 0)    return DE3_H_184;+  else if (strcmp(ident,"ML_params")== 0)             return ML_184;+  else if (strcmp(ident,"NINIO") == 0)                return NIN_184;+  else if (strcmp(ident,"Tetraloops") == 0)           return TL_184;+  else if (strcmp(ident,"Triloops") == 0)             return TRI_184;+  else if (strcmp(ident,"END") == 0)                  return QUIT_184;+  else return UNKNOWN_184;+}++PRIVATE void write_new_parameter_file(FILE *ofile, unsigned int option_bits){+  int           c;+  char          *pnames[] = {"NP", "CG", "GC", "GU", "UG", "AU", "UA", " @"};+  char          bnames[]  = "@ACGU";+  unsigned  int options   = 0;++  options = (option_bits & VRNA_CONVERT_OUTPUT_ALL) ?+              VRNA_CONVERT_OUTPUT_HP+            | VRNA_CONVERT_OUTPUT_STACK+            | VRNA_CONVERT_OUTPUT_MM_HP+            | VRNA_CONVERT_OUTPUT_MM_INT+            | VRNA_CONVERT_OUTPUT_MM_INT_1N+            | VRNA_CONVERT_OUTPUT_MM_INT_23+            | VRNA_CONVERT_OUTPUT_MM_MULTI+            | VRNA_CONVERT_OUTPUT_MM_EXT+            | VRNA_CONVERT_OUTPUT_DANGLE5+            | VRNA_CONVERT_OUTPUT_DANGLE3+            | VRNA_CONVERT_OUTPUT_INT_11+            | VRNA_CONVERT_OUTPUT_INT_21+            | VRNA_CONVERT_OUTPUT_INT_22+            | VRNA_CONVERT_OUTPUT_BULGE+            | VRNA_CONVERT_OUTPUT_INT+            | VRNA_CONVERT_OUTPUT_ML+            | VRNA_CONVERT_OUTPUT_MISC+            | VRNA_CONVERT_OUTPUT_SPECIAL_HP+            | VRNA_CONVERT_OUTPUT_NINIO+            :+              option_bits;++  make_pair_matrix(); /* needed for special loop energy contributions */++  fprintf(ofile,"## RNAfold parameter file v2.0\n");++  if(options & VRNA_CONVERT_OUTPUT_STACK){+    fprintf(ofile,"\n# %s\n", settype(S));+    fprintf(ofile,"/*  CG    GC    GU    UG    AU    UA    @  */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(stack37_184[c]+1,NBPAIRS,NBPAIRS, ofile);+    fprintf(ofile,"\n# %s\n", settype(S_H));+    fprintf(ofile,"/*  CG    GC    GU    UG    AU    UA    @  */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(enthalpies_184[c]+1,NBPAIRS,NBPAIRS, ofile);+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_HP){+    fprintf(ofile,"\n# %s\n", settype(MMH));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mismatchH37_184[k][i],5,5, ofile);+    }+    fprintf(ofile,"\n# %s\n", settype(MMH_H));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mism_H_184[k][i],5,5, ofile);+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_INT){+    fprintf(ofile,"\n# %s\n", settype(MMI));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mismatchI37_184[k][i],5,5, ofile);+    }+    fprintf(ofile,"\n# %s\n", settype(MMI_H));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mism_H_184[k][i],5,5, ofile);+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_INT_1N){+    fprintf(ofile,"\n# %s\n", settype(MMI1N));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mismatchI37_184[k][i],5,5, ofile);+    }+    fprintf(ofile,"\n# %s\n", settype(MMI1N_H));+    { int i,k;+    for (k=1; k<NBPAIRS+1; k++)+      for (i=0; i<5; i++)+        display_array(mism_H_184[k][i],5,5, ofile);+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_INT_23){+    fprintf(ofile,"\n# %s\n", settype(MMI23));+    { int i,k;+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++)+          display_array(mismatchI37_184[k][i],5,5, ofile);+    }+    fprintf(ofile,"\n# %s\n", settype(MMI23_H));+    { int i,k;+    for (k=1; k<NBPAIRS+1; k++)+      for (i=0; i<5; i++)+        display_array(mism_H_184[k][i],5,5, ofile);+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_MULTI){+    fprintf(ofile,"\n# %s\n", settype(MMM));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    { int i,j,k;+      int bla[5];+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++){+          for(j=0;j<5; j++)+            bla[j] = ((dangle5_37_184[k][i] == INF) ? 0 : dangle5_37_184[k][i]) + ((dangle3_37_184[k][j] == INF) ? 0 : dangle3_37_184[k][j]);+          display_array(bla,5,5, ofile);+        }+    }+    fprintf(ofile,"\n# %s\n", settype(MMM_H));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    { int i,j,k,bla[5];+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++){+          for(j=0;j<5; j++)+            bla[j] = ((dangle5_H_184[k][i] == INF) ? 0 : dangle5_H_184[k][i]) + ((dangle3_H_184[k][j] == INF) ? 0 : dangle3_H_184[k][j]);+          display_array(bla,5,5, ofile);+        }+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_MM_EXT){+    fprintf(ofile,"\n# %s\n", settype(MME));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    { int i,j,k;+      int bla[5];+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++){+          for(j=0;j<5; j++)+            bla[j] = ((dangle5_37_184[k][i] == INF) ? 0 : dangle5_37_184[k][i]) + ((dangle3_37_184[k][j] == INF) ? 0 : dangle3_37_184[k][j]);+          display_array(bla,5,5, ofile);+        }+    }+    fprintf(ofile,"\n# %s\n", settype(MME_H));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    { int i,j,k,bla[5];+      for (k=1; k<NBPAIRS+1; k++)+        for (i=0; i<5; i++){+          for(j=0;j<5; j++)+            bla[j] = ((dangle5_37_184[k][i] == INF) ? 0 : dangle5_H_184[k][i]) + ((dangle3_H_184[k][j] == INF) ? 0 : dangle3_H_184[k][j]);+          display_array(bla,5,5, ofile);+        }+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_DANGLE5){+    fprintf(ofile,"\n# %s\n", settype(D5));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(dangle5_37_184[c], 5, 5, ofile);+    fprintf(ofile,"\n# %s\n", settype(D5_H));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(dangle5_H_184[c], 5, 5, ofile);+  }++  if(options & VRNA_CONVERT_OUTPUT_DANGLE3){+    fprintf(ofile,"\n# %s\n", settype(D3));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(dangle3_37_184[c], 5, 5, ofile);+    fprintf(ofile,"\n# %s\n", settype(D3_H));+    fprintf(ofile,"/*  @     A     C     G     U   */\n");+    for (c=1; c<NBPAIRS+1; c++)+      display_array(dangle3_H_184[c], 5, 5, ofile);+  }++  if(options & VRNA_CONVERT_OUTPUT_INT_11){+    /* don't print "no pair" entries for interior loop arrays */+    fprintf(ofile,"\n# %s\n", settype(INT11));+    { int i,k,l;+      for (k=1; k<NBPAIRS+1; k++)+        for (l=1; l<NBPAIRS+1; l++){+          fprintf(ofile, "/* %2s..%2s */\n", pnames[k], pnames[l]);+          for (i=0; i<5; i++)+            display_array(int11_37_184[k][l][i], 5, 5, ofile);+        }+    }+    fprintf(ofile,"\n# %s\n", settype(INT11_H));+    { int i,k,l;+      for (k=1; k<NBPAIRS+1; k++)+        for (l=1; l<NBPAIRS+1; l++){+          fprintf(ofile, "/* %2s..%2s */\n", pnames[k], pnames[l]);+          for (i=0; i<5; i++)+            display_array(int11_H_184[k][l][i],5,5, ofile);+        }+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_INT_21){+    fprintf(ofile,"\n# %s\n", settype(INT21));+    { int p1, p2, i, j;+      for (p1=1; p1<NBPAIRS+1; p1++)+        for (p2=1; p2<NBPAIRS+1; p2++)+          for (i=0; i<5; i++){+            fprintf(ofile, "/* %2s.%c..%2s */\n", pnames[p1], bnames[i], pnames[p2]);+            for (j=0; j<5; j++)+              display_array(int21_37_184[p1][p2][i][j],5,5, ofile);+          }+    }+    fprintf(ofile,"\n# %s\n", settype(INT21_H));+    { int p1, p2, i, j;+      for (p1=1; p1<NBPAIRS+1; p1++)+        for (p2=1; p2<NBPAIRS+1; p2++)+          for (i=0; i<5; i++){+            fprintf(ofile, "/* %2s.%c..%2s */\n", pnames[p1], bnames[i], pnames[p2]);+            for (j=0; j<5; j++)+              display_array(int21_H_184[p1][p2][i][j],5,5, ofile);+          }+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_INT_22){+    fprintf(ofile,"\n# %s\n", settype(INT22));+    { int p1, p2, i, j, k;+      for (p1=1; p1<NBPAIRS; p1++)+        for (p2=1; p2<NBPAIRS; p2++)+          for (i=1; i<5; i++)+            for (j=1; j<5; j++){+              fprintf(ofile, "/* %2s.%c%c..%2s */\n", pnames[p1], bnames[i], bnames[j], pnames[p2]);+              for (k=1; k<5; k++)+                display_array(int22_37_184[p1][p2][i][j][k]+1,4,5, ofile);+            }+    }+    fprintf(ofile,"\n# %s\n", settype(INT22_H));+    { int p1, p2, i, j, k;+      for (p1=1; p1<NBPAIRS; p1++)+        for (p2=1; p2<NBPAIRS; p2++)+          for (i=1; i<5; i++)+            for (j=1; j<5; j++){+              fprintf(ofile, "/* %2s.%c%c..%2s */\n", pnames[p1], bnames[i], bnames[j], pnames[p2]);+              for (k=1; k<5; k++)+                display_array(int22_H_184[p1][p2][i][j][k]+1,4,5, ofile);+            }+    }+  }++  if(options & VRNA_CONVERT_OUTPUT_HP){+    fprintf(ofile,"\n# %s\n", settype(HP));+    display_array(hairpin37_184, 31, 10, ofile);+    /* we had no hairpin enthalpies before, so+    *  we just pretend to have had some with value 0+    */+    fprintf(ofile,"\n# %s\n", settype(HP_H));+    {+      fprintf(ofile, "   INF   INF   INF");+      for(c=4;c<=31; c++){+        fprintf(ofile, "%6d", 0);+        if(c%10 == 0) fprintf(ofile, "\n");+      }+    }+    fprintf(ofile,"\n");+  }++  if(options & VRNA_CONVERT_OUTPUT_BULGE){+    fprintf(ofile,"\n# %s\n", settype(B));+    display_array(bulge37_184, 31, 10, ofile);++    /* we had no bulge enthalpies before, so+    *  we just pretend to have had some with value 0+    */+    fprintf(ofile,"\n# %s\n", settype(B_H));+    {+      fprintf(ofile, "   INF");+      for(c=2;c<=31; c++){+        fprintf(ofile, "%6d", 0);+        if(c%10 == 0) fprintf(ofile, "\n");+      }+    }+    fprintf(ofile,"\n");+  }++  if(options & VRNA_CONVERT_OUTPUT_INT){+    fprintf(ofile,"\n# %s\n", settype(IL));+    display_array(internal_loop37_184, 31, 10, ofile);++    /* we had no internal_loop enthalpies before, so+    *  we just pretend to have had some with value 0+    */+    fprintf(ofile,"\n# %s\n", settype(IL_H));+    {+      fprintf(ofile, "   INF   INF   INF   INF");+      for(c=5;c<=31; c++){+        fprintf(ofile, "%6d", 0);+        if(c%10 == 0) fprintf(ofile, "\n");+      }+    }+    fprintf(ofile,"\n");+    fprintf(ofile,"\n# %s\n"+                  "/* Ninio = MIN(max, m*|n1-n2| */\n"+                  "/*\t    m\t  m_dH     max  */\n"+                  "\t%6d\t%6d\t%6d\n", settype(NIN), F_ninio37_184[2], 0, MAX_NINIO_184);+  }++  if(options & VRNA_CONVERT_OUTPUT_ML){+    fprintf(ofile,"\n# %s\n", settype(ML));+    fprintf(ofile,"/* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */\n");+    fprintf(ofile,"/*\t    cu\t cu_dH\t    cc\t cc_dH\t    ci\t ci_dH  */\n");+    fprintf(ofile,"\t%6d\t%6d\t%6d\t%6d\t%6d\t%6d\n", ML_BASE37_184, 0, ML_closing37_184, 0, ML_intern37_184, 0);+  }++  if(options & VRNA_CONVERT_OUTPUT_MISC){+    fprintf(ofile,"\n# %s\n", settype(MISC));+    fprintf(ofile,"/* all parameters are pairs of 'energy enthalpy' */\n");+    fprintf(ofile,"/*    DuplexInit     TerminalAU   LXC  */\n");+    fprintf(ofile,"   %6d %6d %6d %6d   %3.6f %6d\n", DuplexInit_184, 0, TerminalAU_184, 0, lxc37_184, 0);+  }++  if(options & VRNA_CONVERT_OUTPUT_SPECIAL_HP){+    fprintf(ofile,"\n# %s\n", settype(TRI));+    {+      int base_en = hairpin37_184[3];+      int base_dH = TETRA_ENTH37_184;+      for (c=0; c< (int)strlen(Triloops_184)/6; c++){+        int en = base_en;+        char bla[5];+        strncpy(bla, Triloops_184+c*6, 5);+        int type = pair[(short)encode_char(toupper(bla[0]))][(short)encode_char(toupper(bla[4]))];+        if(type > 2) en += TerminalAU_184;+        fprintf(ofile,"\t%.5s %6d %6d\n", Triloops_184+c*6, Triloop_E37_184[c] + en, base_dH);+      }+    }++    /* since the old hairpin loop function treated the tabulated tetraloop energy as bonus+    *  and the new one takes this tabulated energy as a total energy, we have to compute some+    *  things now...+    */+    fprintf(ofile,"\n# %s\n", settype(TL));+    {+      int base_en = hairpin37_184[4];+      int base_dH = TETRA_ENTH37_184;+      for (c=0; c< (int)strlen(Tetraloops_184)/7; c++){+        char bla[6];+        int en = base_en;+        int dH = base_dH;+        strncpy(bla, Tetraloops_184+c*7, 6);+        short si  = (short)encode_char(toupper(bla[1]));+        short sj  = (short)encode_char(toupper(bla[4]));+        int type  = pair[(short)encode_char(toupper(bla[0]))][(short)encode_char(toupper(bla[5]))];+        en   += mismatchH37_184[type][si][sj];+        dH   += mism_H_184[type][si][sj];+        fprintf(ofile,"\t%.6s %6d %6d\n", Tetraloops_184+c*7, en + TETRA_ENERGY37_184[c], dH);+      }+    }+    fprintf(ofile,"\n# %s\n", settype(HEX));+    {+      fprintf(ofile, "\n");+    }+  }++  fprintf(ofile, "\n# %s\n", settype(QUIT));+}++PRIVATE void check_symmetry(void) {+  int i,j,k,l;++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      if (stack37_184[i][j] != stack37_184[j][i])+        vrna_message_warning("stacking energies not symmetric");++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      if (enthalpies_184[i][j] != enthalpies_184[j][i])+        vrna_message_warning("stacking enthalpies not symmetric");+++  /* interior 1x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++)+          if (int11_37_184[i][j][k][l] != int11_37_184[j][i][l][k])+            vrna_message_warning("int11 energies not symmetric");++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++)+          if (int11_H_184[i][j][k][l] != int11_H_184[j][i][l][k])+            vrna_message_warning("int11 enthalpies not symmetric");++  /* interior 2x2 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++)+              if (int22_37_184[i][j][k][l][m][n] != int22_37_184[j][i][m][n][k][l])+                vrna_message_warning("int22 energies not symmetric");+        }++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++)+              if (int22_H_184[i][j][k][l][m][n] != int22_H_184[j][i][m][n][k][l])+                vrna_message_warning("int22 enthalpies not symmetric: %d %d %d %d %d %d", i,j,k,l,m,n);+        }+}
+ C/ViennaRNA/convert_epars.h view
@@ -0,0 +1,96 @@+#ifndef VIENNA_RNA_PACKAGE_CONVERT_EPARS_H+#define VIENNA_RNA_PACKAGE_CONVERT_EPARS_H++/**+ *  @file convert_epars.h+ *  @ingroup energy_parameters+ *  @brief Functions and definitions for energy parameter file format conversion+ */++/**+ *  @addtogroup energy_parameters_convert+ *  @brief      Convert energy parameter files into the latest format+ *+ *  To preserve some backward compatibility the RNAlib also provides+ *  functions to convert energy parameter files from the format used+ *  in version 1.4-1.8 into the new format used since version 2.0+ *+ *  @{+ *  @ingroup energy_parameters_convert+ */++/** Flag to indicate printing of a complete parameter set */+#define VRNA_CONVERT_OUTPUT_ALL           1U+/** Flag to indicate printing of hairpin contributions */+#define VRNA_CONVERT_OUTPUT_HP            2U+/** Flag to indicate printing of base pair stack contributions */+#define VRNA_CONVERT_OUTPUT_STACK         4U+/** Flag to indicate printing of  hairpin mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_HP         8U+/** Flag to indicate printing of  interior loop mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_INT        16U+/** Flag to indicate printing of  1:n interior loop mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_INT_1N     32U+/** Flag to indicate printing of  2:3 interior loop mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_INT_23     64U+/** Flag to indicate printing of  multi loop mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_MULTI      128U+/** Flag to indicate printing of  exterior loop mismatch contribution  */+#define VRNA_CONVERT_OUTPUT_MM_EXT        256U+/** Flag to indicate printing of  5' dangle conctribution  */+#define VRNA_CONVERT_OUTPUT_DANGLE5       512U+/** Flag to indicate printing of  3' dangle contribution  */+#define VRNA_CONVERT_OUTPUT_DANGLE3       1024U+/** Flag to indicate printing of  1:1 interior loop contribution  */+#define VRNA_CONVERT_OUTPUT_INT_11        2048U+/** Flag to indicate printing of  2:1 interior loop contribution */+#define VRNA_CONVERT_OUTPUT_INT_21        4096U+/** Flag to indicate printing of  2:2 interior loop contribution  */+#define VRNA_CONVERT_OUTPUT_INT_22        8192U+/** Flag to indicate printing of  bulge loop contribution  */+#define VRNA_CONVERT_OUTPUT_BULGE         16384U+/** Flag to indicate printing of  interior loop contribution  */+#define VRNA_CONVERT_OUTPUT_INT           32768U+/** Flag to indicate printing of  multi loop contribution  */+#define VRNA_CONVERT_OUTPUT_ML            65536U+/** Flag to indicate printing of  misc contributions (such as terminalAU)  */+#define VRNA_CONVERT_OUTPUT_MISC          131072U+/** Flag to indicate printing of  special hairpin contributions (tri-, tetra-, hexa-loops)  */+#define VRNA_CONVERT_OUTPUT_SPECIAL_HP    262144U+/** Flag to indicate printing of  given parameters only\n\note This option overrides all other output options, except #VRNA_CONVERT_OUTPUT_DUMP ! */+#define VRNA_CONVERT_OUTPUT_VANILLA       524288U+/** Flag to indicate printing of  interior loop asymmetry contribution  */+#define VRNA_CONVERT_OUTPUT_NINIO         1048576U+/** Flag to indicate dumping the energy contributions from the library instead of an input file  */+#define VRNA_CONVERT_OUTPUT_DUMP          2097152U++/**+ *  Convert/dump a Vienna 1.8.4 formatted energy parameter file+ * + *  The options argument allows one to control the different output modes.\n+ *  Currently available options are:\n+ *  #VRNA_CONVERT_OUTPUT_ALL, #VRNA_CONVERT_OUTPUT_HP, #VRNA_CONVERT_OUTPUT_STACK\n+ *  #VRNA_CONVERT_OUTPUT_MM_HP, #VRNA_CONVERT_OUTPUT_MM_INT, #VRNA_CONVERT_OUTPUT_MM_INT_1N\n+ *  #VRNA_CONVERT_OUTPUT_MM_INT_23, #VRNA_CONVERT_OUTPUT_MM_MULTI, #VRNA_CONVERT_OUTPUT_MM_EXT\n+ *  #VRNA_CONVERT_OUTPUT_DANGLE5, #VRNA_CONVERT_OUTPUT_DANGLE3, #VRNA_CONVERT_OUTPUT_INT_11\n+ *  #VRNA_CONVERT_OUTPUT_INT_21, #VRNA_CONVERT_OUTPUT_INT_22, #VRNA_CONVERT_OUTPUT_BULGE\n+ *  #VRNA_CONVERT_OUTPUT_INT, #VRNA_CONVERT_OUTPUT_ML, #VRNA_CONVERT_OUTPUT_MISC\n+ *  #VRNA_CONVERT_OUTPUT_SPECIAL_HP, #VRNA_CONVERT_OUTPUT_VANILLA, #VRNA_CONVERT_OUTPUT_NINIO\n+ *  #VRNA_CONVERT_OUTPUT_DUMP+ * + *  The defined options are fine for bitwise compare- and assignment-operations,+ *  e. g.: pass a collection of options as a single value like this:+ *  @verbatim convert_parameter_file(ifile, ofile, option_1 | option_2 | option_n) @endverbatim+ * + *  @param iname    The input file name (If NULL input is read from stdin)+ *  @param oname    The output file name (If NULL output is written to stdout)+ *  @param options  The options (as described above)+ */+void convert_parameter_file(const char *iname,+                            const char *oname,+                            unsigned int options);++/**+ *  @}+ */+#endif
+ C/ViennaRNA/data_structures.c view
@@ -0,0 +1,787 @@+/** \file data_structures.c **/++/*+                  Data structure creation/destruction++                  This file contains everything which is necessary to+                  obtain and destroy datastructures used in the folding+                  recurrences throughout the VienneRNA paclage++                  c Ronny Lorenx++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/structure_utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/ribo.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/cofold.h"+#include "ViennaRNA/mm.h"++#ifdef _OPENMP+#include <omp.h>+#endif++/*+#################################+# PRIVATE MACROS                #+#################################+*/++#define WITH_PTYPE          1L    /* passed to set_fold_compound() to indicate that we need to set vc->ptype */+#define WITH_PTYPE_COMPAT   2L    /* passed to set_fold_compound() to indicate that we need to set vc->ptype_compat */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  set_fold_compound(vrna_fold_compound_t *vc, vrna_md_t *md_p, unsigned int options, unsigned int aux);+PRIVATE void  make_pscores(vrna_fold_compound_t *vc);+PRIVATE void  add_params(vrna_fold_compound_t *vc, vrna_md_t *md_p, unsigned int options);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC  void+vrna_fold_compound_free(vrna_fold_compound_t *vc){++  int s;++  if(vc){++    /* first destroy common attributes */+    vrna_mx_mfe_free(vc);+    vrna_mx_pf_free(vc);+    free(vc->iindx);+    free(vc->jindx);+    free(vc->params);+    free(vc->exp_params);+    free(vc->strand_number);+    vrna_hc_free(vc->hc);+    vrna_ud_remove(vc);++    /* now distinguish the vc type */+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     free(vc->sequence);+                                    free(vc->sequence_encoding);+                                    free(vc->sequence_encoding2);+                                    free(vc->ptype);+                                    free(vc->ptype_pf_compat);+                                    vrna_sc_free(vc->sc);+                                    break;+      case VRNA_FC_TYPE_COMPARATIVE:  for(s=0;s<vc->n_seq;s++){+                                      free(vc->sequences[s]);+                                      free(vc->S[s]);+                                      free(vc->S5[s]);+                                      free(vc->S3[s]);+                                      free(vc->Ss[s]);+                                      free(vc->a2s[s]);+                                    }+                                    free(vc->sequences);+                                    free(vc->cons_seq);+                                    free(vc->S_cons);+                                    free(vc->S);+                                    free(vc->S5);+                                    free(vc->S3);+                                    free(vc->Ss);+                                    free(vc->a2s);+                                    free(vc->pscore);+                                    free(vc->pscore_pf_compat);+                                    if(vc->scs){+                                      for(s=0;s<vc->n_seq;s++)+                                        vrna_sc_free(vc->scs[s]);+                                      free(vc->scs);+                                    }+                                    break;+      default:                      /* do nothing */+                                    break;+    }++    /* free Distance Class Partitioning stuff (should be NULL if not used) */+    free(vc->reference_pt1);+    free(vc->reference_pt2);+    free(vc->referenceBPs1);+    free(vc->referenceBPs2);+    free(vc->bpdist);+    free(vc->mm1);+    free(vc->mm2);++    /* free local folding related stuff (should be NULL if not used) */+    if(vc->ptype_local){+      for (s=0; (s < vc->window_size + 5) && (s <= vc->length); s++){+        free(vc->ptype_local[s]);+      }+      free(vc->ptype_local);+    }++    if(vc->free_auxdata)+      vc->free_auxdata(vc->auxdata);++    free(vc);+  }+}+++PUBLIC vrna_fold_compound_t *+vrna_fold_compound( const char *sequence,+                    vrna_md_t *md_p,+                    unsigned int options){++  int i;+  unsigned int        length, aux_options;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  if(sequence == NULL) return NULL;++  /* sanity check */+  length = strlen(sequence);+  if(length == 0)+    vrna_message_error("vrna_fold_compound@data_structures.c: sequence length must be greater 0");++  if(length > vrna_sequence_length_max(options))+    vrna_message_error("vrna_fold_compound@data_structures.c: sequence length of %d exceeds addressable range", length);++  vc            = vrna_alloc(sizeof(vrna_fold_compound_t));+  vc->type      = VRNA_FC_TYPE_SINGLE;+  vc->length    = length;+  vc->sequence  = strdup(sequence);+  aux_options   = 0L;+++  /* get a copy of the model details */+  if(md_p)+    md = *md_p;+  else+    vrna_md_set_default(&md);++  if(options & VRNA_OPTION_WINDOW){ /* sliding window structure prediction */+    if(md.window_size <= 0)+      md.window_size = (int)vc->length;+    else if(md.window_size > (int)vc->length)+      md.window_size = (int)vc->length;++    vc->window_size = md.window_size;++    if((md.max_bp_span <= 0) || (md.max_bp_span > md.window_size))+      md.max_bp_span = md.window_size;++    set_fold_compound(vc, &md, options, aux_options);++    vc->ptype_local = vrna_alloc(sizeof(char *)*(vc->length+1));+    for (i = (int)vc->length; ( i > (int)vc->length - vc->window_size - 5) && (i >= 0); i--){+      vc->ptype_local[i] = vrna_alloc(sizeof(char)*(vc->window_size+5));+    }++    if(!(options & VRNA_OPTION_EVAL_ONLY)){+      /* add default hard constraints */+      /* vrna_hc_init(vc); */ /* no hard constraints in Lfold, yet! */++      /* add DP matrices */+      vrna_mx_add(vc, VRNA_MX_WINDOW, options);+    }+  } else { /* regular global structure prediction */++    /* set window size to entire sequence */+    md.window_size = (int)vc->length;++    aux_options |= WITH_PTYPE;++    if(options & VRNA_OPTION_PF)+      aux_options |= WITH_PTYPE_COMPAT;++    set_fold_compound(vc, &md, options, aux_options);++    if(!(options & VRNA_OPTION_EVAL_ONLY)){+      /* add default hard constraints */+      vrna_hc_init(vc);++      /* add DP matrices (if required) */+      vrna_mx_add(vc, VRNA_MX_DEFAULT, options);+    }+  }++  return vc;+}++PUBLIC vrna_fold_compound_t *+vrna_fold_compound_comparative( const char **sequences,+                                vrna_md_t *md_p,+                                unsigned int options){++  int s, n_seq, length;+  vrna_fold_compound_t *vc;+  vrna_md_t           md;+  unsigned int        aux_options;++  aux_options = 0U;+ +  if(sequences == NULL) return NULL;++  for(s=0;sequences[s];s++); /* count the sequences */++  n_seq = s;++  length = strlen(sequences[0]);+  /* sanity check */+  if(length == 0)+    vrna_message_error("vrna_fold_compound_comparative@data_structures.c: sequence length must be greater 0");+  else if(length > vrna_sequence_length_max(options))+    vrna_message_error("vrna_fold_compound_comparative@data_structures.c: sequence length of %d exceeds addressable range", length);++  for(s = 0; s < n_seq; s++)+    if(strlen(sequences[s]) != length)+      vrna_message_error("vrna_fold_compound_comparative@data_structures.c: uneqal sequence lengths in alignment");++  vc            = vrna_alloc(sizeof(vrna_fold_compound_t));+  vc->type      = VRNA_FC_TYPE_COMPARATIVE;++  vc->n_seq     = n_seq;+  vc->length    = length;+  vc->sequences = vrna_alloc(sizeof(char *) * (vc->n_seq + 1));+  for(s = 0; sequences[s]; s++)+    vc->sequences[s] = strdup(sequences[s]);++  /* get a copy of the model details */+  if(md_p)+    md = *md_p;+  else /* this fallback relies on global parameters and thus is not threadsafe */+    vrna_md_set_default(&md);+++  aux_options |= WITH_PTYPE;++  if(options & VRNA_OPTION_PF)+    aux_options |= WITH_PTYPE_COMPAT;++  set_fold_compound(vc, &md, options, aux_options);++  make_pscores(vc);++  if(!(options & VRNA_OPTION_EVAL_ONLY)){+    /* add default hard constraints */+    vrna_hc_init(vc);++    /* add DP matrices (if required) */+    vrna_mx_add(vc, VRNA_MX_DEFAULT, options);+  }++  return vc;+}++PUBLIC vrna_fold_compound_t *+vrna_fold_compound_TwoD(const char *sequence,+                      const char *s1,+                      const char *s2,+                      vrna_md_t *md_p,+                      unsigned int options){++  int                 length, l, turn;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;+++  if(sequence == NULL) return NULL;++  /* sanity check */+  length = strlen(sequence);+  if(length == 0)+    vrna_message_error("vrna_fold_compound_TwoD: sequence length must be greater 0");+  else if(length > vrna_sequence_length_max(options))+    vrna_message_error("vrna_fold_compound_TwoD@data_structures.c: sequence length of %d exceeds addressable range", length);++  l = strlen(s1);+  if(l != length)+    vrna_message_error("vrna_fold_compound_TwoD: sequence and s1 differ in length");++  l = strlen(s2);+  if(l != length)+    vrna_message_error("vrna_fold_compound_TwoD: sequence and s2 differ in length");++  vc                = vrna_alloc(sizeof(vrna_fold_compound_t));+  vc->type          = VRNA_FC_TYPE_SINGLE;+  vc->length        = length;+  vc->sequence      = strdup(sequence);++  /* get a copy of the model details */+  if(md_p)+    md = *md_p;+  else /* this fallback relies on global parameters and thus is not threadsafe */+    vrna_md_set_default(&md);++  /* always make uniq ML decomposition ! */+  md.uniq_ML      = 1;+  md.compute_bpp  = 0;++  set_fold_compound(vc, &md, options, WITH_PTYPE | WITH_PTYPE_COMPAT);++  if(!(options & VRNA_OPTION_EVAL_ONLY)){+    vrna_hc_init(vc); /* add default hard constraints */++    /* add DP matrices */+    vrna_mx_add(vc, VRNA_MX_2DFOLD, options);+  }++  /* set all fields that are unique to Distance class partitioning... */+  turn  = vc->params->model_details.min_loop_size;+  vc->reference_pt1 = vrna_ptable(s1);+  vc->reference_pt2 = vrna_ptable(s2);+  vc->referenceBPs1 = vrna_refBPcnt_matrix(vc->reference_pt1, turn);+  vc->referenceBPs2 = vrna_refBPcnt_matrix(vc->reference_pt2, turn);+  vc->bpdist        = vrna_refBPdist_matrix(vc->reference_pt1, vc->reference_pt2, turn);+  /* compute maximum matching with reference structure 1 disallowed */+  vc->mm1           = maximumMatchingConstraint(vc->sequence, vc->reference_pt1);+  /* compute maximum matching with reference structure 2 disallowed */+  vc->mm2           = maximumMatchingConstraint(vc->sequence, vc->reference_pt2);++  vc->maxD1         = vc->mm1[vc->iindx[1]-length] + vc->referenceBPs1[vc->iindx[1]-length];+  vc->maxD2         = vc->mm2[vc->iindx[1]-length] + vc->referenceBPs2[vc->iindx[1]-length];++  return vc;+}++PUBLIC void+vrna_fold_compound_add_auxdata( vrna_fold_compound_t *vc,+                                void *data,+                                vrna_callback_free_auxdata *f){++  if(vc && data){++    if(vc->free_auxdata) /* free pre-existing auxdata */+      vc->free_auxdata(vc->auxdata);++    vc->auxdata       = data;+    vc->free_auxdata  = f;+  }+}++PUBLIC void+vrna_fold_compound_add_callback(vrna_fold_compound_t *vc,+                                vrna_callback_recursion_status *f){++  if(vc && f){+    vc->stat_cb       = f;+  }+}++PUBLIC int+vrna_fold_compound_prepare( vrna_fold_compound_t *vc,+                            unsigned int options){+  int ret = 1; /* success */++  /* check maximum sequence length restrictions */+  if(vc->length > vrna_sequence_length_max(options)){+    vrna_message_warning("vrna_fold_compound_prepare@data_structures.c: sequence length of %d exceeds addressable range", vc->length);+    return 0;+  }++  if(options & VRNA_OPTION_MFE){   /* prepare for MFE computation */+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     if(!vc->ptype)+                                      if(!(options & VRNA_OPTION_WINDOW))+                                        vc->ptype = vrna_ptypes(vc->sequence_encoding2,+                                                                &(vc->params->model_details));+                                    break;+      case VRNA_FC_TYPE_COMPARATIVE:  break;+      default:                      break;+    }+++  }++  if(options & VRNA_OPTION_PF){   /* prepare for partition function computation */++    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* get pre-computed Boltzmann factors if not present*/+                                    if(!vc->exp_params)+                                      vc->exp_params      = vrna_exp_params(&(vc->params->model_details));++                                    if(!vc->ptype)+                                      vc->ptype           = vrna_ptypes(vc->sequence_encoding2, &(vc->exp_params->model_details));+#ifdef VRNA_BACKWARD_COMPAT+                                    /* backward compatibility ptypes */+                                    if(!vc->ptype_pf_compat)+                                      vc->ptype_pf_compat = get_ptypes(vc->sequence_encoding2, &(vc->exp_params->model_details), 1);+#endif+                                    /* get precomputed Boltzmann factors for soft-constraints (if any) */+                                    if(vc->sc){+                                      if(!vc->sc->exp_energy_up)+                                        vrna_sc_set_up(vc, NULL, VRNA_OPTION_PF);+                                      if(!vc->sc->exp_energy_bp)+                                        vrna_sc_set_bp(vc, NULL, VRNA_OPTION_PF);+                                      if(!vc->sc->exp_energy_stack)+                                        vrna_sc_add_SHAPE_deigan(vc, NULL, 0, 0, VRNA_OPTION_PF);+                                    }++                                    if(vc->domains_up) /* turn on unique ML decomposition with qm1 array */+                                      vc->exp_params->model_details.uniq_ML = 1;++                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  /* get pre-computed Boltzmann factors if not present*/+                                    if(!vc->exp_params)+                                      vc->exp_params  = vrna_exp_params_comparative(vc->n_seq, &(vc->params->model_details));+                                    break;++      default:                      break;+    }+  }++  /* Add DP matrices, if not they are not present or do not fit current settings */+  vrna_mx_prepare(vc, options);++  return ret;+}+++#ifndef VRNA_DISABLE_C11_FEATURES+PUBLIC void+vrna_C11_features(void){++  __asm("nop");+}+#endif++/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/++PRIVATE void+add_params( vrna_fold_compound_t *vc,+            vrna_md_t *md_p,+            unsigned int options){++  /* ALWAYS add regular energy parameters */+  vc->params = vrna_params(md_p);++  if(options & VRNA_OPTION_PF){+    vc->exp_params  = (vc->type == VRNA_FC_TYPE_SINGLE) ? \+                        vrna_exp_params(md_p) : \+                        vrna_exp_params_comparative(vc->n_seq, md_p);+  }++}++PRIVATE void+set_fold_compound(vrna_fold_compound_t *vc,+                  vrna_md_t *md_p,+                  unsigned int options,+                  unsigned int aux){+++  char *sequence, **sequences;+  unsigned int        length, s, i;+  int                 cp;                     /* cut point for cofold */+  char                *seq, *seq2;++  sequence          = NULL;+  sequences         = NULL;+  cp                = -1;++  /* some default init values */+  vc->params        = NULL;+  vc->exp_params    = NULL;+  vc->matrices      = NULL;+  vc->exp_matrices  = NULL;+  vc->hc            = NULL;+  vc->auxdata       = NULL;+  vc->free_auxdata  = NULL;++  vc->strand_number = NULL;+  vc->domains_struc = NULL;+  vc->domains_up    = NULL;+  vc->aux_grammar   = NULL;++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     sequence  = vc->sequence;++                                  seq2 = strdup(sequence);+                                  seq = vrna_cut_point_remove(seq2, &cp); /*  splice out the '&' if concatenated sequences and+                                                                        reset cp... this should also be safe for+                                                                        single sequences */+                                  vc->cutpoint            = cp;++                                  if((cp > 0) && (md_p->min_loop_size == TURN))+                                    md_p->min_loop_size = 0;  /* is it safe to set this here? */++                                  free(vc->sequence);+                                  vc->sequence            = seq;+                                  vc->length              = length = strlen(seq);+                                  vc->sequence_encoding   = vrna_seq_encode(seq, md_p);+                                  vc->sequence_encoding2  = vrna_seq_encode_simple(seq, md_p);++                                  vc->strand_number       = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (vc->length + 1));+                                  if (cp > 0)+                                    for (s = i = 0; i <= vc->length; i++) {+                                      if (i == vc->cutpoint)+                                        s++;+                                      vc->strand_number[i] = s;+                                    }++                                  if(!(options & VRNA_OPTION_EVAL_ONLY)){+                                    vc->ptype               = (aux & WITH_PTYPE) ? vrna_ptypes(vc->sequence_encoding2, md_p) : NULL;+                                    /* backward compatibility ptypes */+                                    vc->ptype_pf_compat     = (aux & WITH_PTYPE_COMPAT) ? get_ptypes(vc->sequence_encoding2, md_p, 1) : NULL;+                                  } else {+                                    vc->ptype           = NULL;+                                    vc->ptype_pf_compat = NULL;+                                  }+                                  vc->sc                  = NULL;+                                  free(seq2);+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  sequences     = vc->sequences;++                                  vc->length    = length = vc->length;++                                  vc->strand_number       = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (vc->length + 1));++                                  vc->cons_seq  = consensus((const char **)sequences);+                                  vc->S_cons    = vrna_seq_encode_simple(vc->cons_seq, md_p);++                                  vc->pscore    = vrna_alloc(sizeof(int)*((length*(length+1))/2+2));+                                  /* backward compatibility ptypes */+                                  vc->pscore_pf_compat = (aux & WITH_PTYPE_COMPAT) ? vrna_alloc(sizeof(int)*((length*(length+1))/2+2)) : NULL;++                                  oldAliEn = vc->oldAliEn  = md_p->oldAliEn;++                                  vc->S   = vrna_alloc((vc->n_seq+1) * sizeof(short *));+                                  vc->S5  = vrna_alloc((vc->n_seq+1) * sizeof(short *));+                                  vc->S3  = vrna_alloc((vc->n_seq+1) * sizeof(short *));+                                  vc->a2s = vrna_alloc((vc->n_seq+1) * sizeof(unsigned short *));+                                  vc->Ss  = vrna_alloc((vc->n_seq+1) * sizeof(char *));++                                  for (s = 0; s < vc->n_seq; s++) {+                                    vrna_aln_encode(vc->sequences[s],+                                                    &(vc->S[s]),+                                                    &(vc->S5[s]),+                                                    &(vc->S3[s]),+                                                    &(vc->Ss[s]),+                                                    &(vc->a2s[s]),+                                                    md_p);+                                  }+                                  vc->S5[vc->n_seq]  = NULL;+                                  vc->S3[vc->n_seq]  = NULL;+                                  vc->a2s[vc->n_seq] = NULL;+                                  vc->Ss[vc->n_seq]  = NULL;+                                  vc->S[vc->n_seq]   = NULL;++                                  vc->scs       = NULL;+                                  break;++    default:                      /* do nothing ? */+                                  break;+  }++  if(vc->length <= vrna_sequence_length_max(options)){+    vc->iindx = vrna_idx_row_wise(vc->length);+    vc->jindx = vrna_idx_col_wise(vc->length);+  } else {+    vc->iindx = NULL;+    vc->jindx = NULL;+  }++  /* now come the energy parameters */+  add_params(vc, md_p, options);++}++PRIVATE void+make_pscores(vrna_fold_compound_t *vc){++  /* calculate co-variance bonus for each pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */++#define NONE -10000 /* score for forbidden pairs */++  char *structure = NULL;+  int i,j,k,l,s, max_span, turn;+  float **dm;+  int olddm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                  {0,0,2,2,1,2,2} /* CG */,+                  {0,2,0,1,2,2,2} /* GC */,+                  {0,2,1,0,2,1,2} /* GU */,+                  {0,1,2,2,0,2,1} /* UG */,+                  {0,2,2,1,2,0,2} /* AU */,+                  {0,2,2,2,1,2,0} /* UA */};++  short           **S         = vc->S;+  char            **AS        = vc->sequences;+  int             n_seq       = vc->n_seq;+  vrna_md_t       *md         = (vc->params) ? &(vc->params->model_details) : &(vc->exp_params->model_details);+  int             *pscore     = vc->pscore;     /* precomputed array of pair types */             +  int             *indx       = vc->jindx;                                             +  int             *my_iindx   = vc->iindx;                                             +  int             n           = vc->length;                                            ++  turn    = md->min_loop_size;++  if (md->ribo) {+    if (RibosumFile !=NULL) dm=readribosum(RibosumFile);+    else dm=get_ribosum((const char **)AS, n_seq, n);+  }+  else { /*use usual matrix*/+    dm = vrna_alloc(7*sizeof(float*));+    for (i=0; i<7;i++) {+      dm[i] = vrna_alloc(7*sizeof(float));+      for (j=0; j<7; j++)+        dm[i][j] = (float) olddm[i][j];+    }+  }++  max_span = md->max_bp_span;+  if((max_span < turn+2) || (max_span > n))+    max_span = n;+  for (i=1; i<n; i++) {+    for (j=i+1; (j<i+turn+1) && (j<=n); j++)+      pscore[indx[j]+i] = NONE;+    for (j=i+turn+1; j<=n; j++) {+      int pfreq[8]={0,0,0,0,0,0,0,0};+      double score;+      for (s=0; s<n_seq; s++) {+        int type;+        if (S[s][i]==0 && S[s][j]==0) type = 7; /* gap-gap  */+        else {+          if ((AS[s][i] == '~')||(AS[s][j] == '~')) type = 7;+          else type = md->pair[S[s][i]][S[s][j]];+        }+        pfreq[type]++;+      }+      if (pfreq[0]*2+pfreq[7]>n_seq) { pscore[indx[j]+i] = NONE; continue;}+      for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+        for (l=k; l<=6; l++)+          score += pfreq[k]*pfreq[l]*dm[k][l];+      /* counter examples score -1, gap-gap scores -0.25   */+      pscore[indx[j]+i] = md->cv_fact *+        ((UNIT*score)/n_seq - md->nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));++      if((j - i + 1) > max_span){+        pscore[indx[j]+i] = NONE;+      }+    }+  }++  if (md->noLP) /* remove unwanted pairs */+    for (k=1; k<n-turn-1; k++)+      for (l=1; l<=2; l++) {+        int type,ntype=0,otype=0;+        i=k; j = i+turn+l;+        type = pscore[indx[j]+i];+        while ((i>=1)&&(j<=n)) {+          if ((i>1)&&(j<n)) ntype = pscore[indx[j+1]+i-1];+          if ((otype<md->cv_fact*MINPSCORE)&&(ntype<md->cv_fact*MINPSCORE))  /* too many counterexamples */+            pscore[indx[j]+i] = NONE; /* i.j can only form isolated pairs */+          otype =  type;+          type  = ntype;+          i--; j++;+        }+      }+++  if (fold_constrained&&(structure!=NULL)) {+    int psij, hx, hx2, *stack, *stack2;+    stack = vrna_alloc(sizeof(int)*(n+1));+    stack2 = vrna_alloc(sizeof(int)*(n+1));++    for(hx=hx2=0, j=1; j<=n; j++) {+      switch (structure[j-1]) {+      case 'x': /* can't pair */+        for (l=1; l<j-turn; l++) pscore[indx[j]+l] = NONE;+        for (l=j+turn+1; l<=n; l++) pscore[indx[l]+j] = NONE;+        break;+      case '(':+        stack[hx++]=j;+        /* fallthrough */+      case '[':+        stack2[hx2++]=j;+        /* fallthrough */+      case '<': /* pairs upstream */+        for (l=1; l<j-turn; l++) pscore[indx[j]+l] = NONE;+        break;+      case ']':+        if (hx2<=0) {+          vrna_message_error("unbalanced brackets in constraints\n%s", structure);+        }+        i = stack2[--hx2];+        pscore[indx[j]+i]=NONE;+        break;+      case ')':+        if (hx<=0) {+          vrna_message_error("unbalanced brackets in constraints\n%s", structure);+        }+        i = stack[--hx];+        psij = pscore[indx[j]+i]; /* store for later */+        for (k=j; k<=n; k++)+          for (l=i; l<=j; l++)+            pscore[indx[k]+l] = NONE;+        for (l=i; l<=j; l++)+          for (k=1; k<=i; k++)+            pscore[indx[l]+k] = NONE;+        for (k=i+1; k<j; k++)+          pscore[indx[k]+i] = pscore[indx[j]+k] = NONE;+        pscore[indx[j]+i] = (psij>0) ? psij : 0;+        /* fallthrough */+      case '>': /* pairs downstream */+        for (l=j+turn+1; l<=n; l++) pscore[indx[l]+j] = NONE;+        break;+      }+    }+    if (hx!=0) {+      vrna_message_error("unbalanced brackets in constraint string\n%s", structure);+    }+    free(stack); free(stack2);+  }+  /*free dm */+  for (i=0; i<7;i++) {+    free(dm[i]);+  }+  free(dm);++  /* copy over pscores for backward compatibility */+  if(vc->pscore_pf_compat){+    for(i = 1; i < n; i++)+      for(j = i; j <= n; j++){+        vc->pscore_pf_compat[my_iindx[i] - j] = (short)pscore[indx[j] + i];+      }+  }++}
+ C/ViennaRNA/data_structures.h view
@@ -0,0 +1,850 @@+#ifndef VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H+#define VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H++/**+ *  @file     data_structures.h+ *  @ingroup  data_structures+ *  @brief    Various data structures and pre-processor macros+ */++/**+ *  @addtogroup   data_structures+ *  @brief All datastructures and typedefs shared among the Vienna RNA Package can be found here+ *+ *  @{+ *  @ingroup data_structures+ */++/* below are several convenience typedef's we use throughout the ViennaRNA library */++/** @brief Typename for the fold_compound data structure #vrna_fc_s+ *  @ingroup fold_compound+ */+typedef struct vrna_fc_s        vrna_fold_compound_t;++/** @brief Typename for the base pair repesenting data structure #vrna_basepair_s */+typedef struct vrna_basepair_s  vrna_basepair_t;++/** @brief Typename for the base pair list repesenting data structure #vrna_plist_s */+typedef struct vrna_plist_s     vrna_plist_t;++/** @brief Typename for the base pair stack repesenting data structure #vrna_bp_stack_s */+typedef struct vrna_bp_stack_s  vrna_bp_stack_t;++/** @brief Typename for data structure #vrna_cpair_s */+typedef struct vrna_cpair_s  vrna_cpair_t;++/** @brief Typename for stack of partial structures #vrna_sect_s */+typedef struct vrna_sect_s  vrna_sect_t;++typedef struct vrna_data_linear_s vrna_data_lin_t;++typedef struct vrna_color_s vrna_color_t;++/** @brief Typename for floating point number in partition function computations */+#ifdef  USE_FLOAT_PF+typedef float FLT_OR_DBL;+#else+typedef double  FLT_OR_DBL;+#endif++/**+ *  @brief Callback to free memory allocated for auxiliary user-provided data+ *+ *  @ingroup fold_compound+ *  This type of user-implemented function usually deletes auxiliary data structures.+ *  The user must take care to free all the memory occupied by the data structure passed.+ * + *  @param data    The data that needs to be free'd+ */+typedef void (vrna_callback_free_auxdata)(void *data);++/**+ *  @brief Callback to perform specific user-defined actions before, or after recursive computations+ *+ *  @ingroup fold_compound+ *  @see #VRNA_STATUS_MFE_PRE, #VRNA_STATUS_MFE_POST, #VRNA_STATUS_PF_PRE, #VRNA_STATUS_PF_POST+ *  @param status   The status indicator+ *  @param data     The data structure that was assigned with vrna_fold_compound_add_auxdata()+ *  @param status   The status indicator+ */+typedef void (vrna_callback_recursion_status)(unsigned char status, void *data);++/**+ *  @brief  Status message indicating that MFE computations are about to begin+ *+ *  @ingroup fold_compound+ *  @see  #vrna_fold_compound_t.stat_cb, vrna_callback_recursion_status(), vrna_mfe(), vrna_fold(), vrna_circfold(),+ *        vrna_alifold(), vrna_circalifold(), vrna_cofold()+ */+#define VRNA_STATUS_MFE_PRE     (unsigned char)1++/**+ *  @brief  Status message indicating that MFE computations are finished+ *+ *  @ingroup fold_compound+ *  @see  #vrna_fold_compound_t.stat_cb, vrna_callback_recursion_status(), vrna_mfe(), vrna_fold(), vrna_circfold(),+ *        vrna_alifold(), vrna_circalifold(), vrna_cofold()+ */+#define VRNA_STATUS_MFE_POST    (unsigned char)2++/**+ *  @brief  Status message indicating that Partition function computations are about to begin+ *+ *  @ingroup fold_compound+ *  @see  #vrna_fold_compound_t.stat_cb, vrna_callback_recursion_status(), vrna_pf()+ */+#define VRNA_STATUS_PF_PRE      (unsigned char)3++/**+ *  @brief  Status message indicating that Partition function computations are finished+ *+ *  @ingroup fold_compound+ *  @see  #vrna_fold_compound_t.stat_cb, vrna_callback_recursion_status(), vrna_pf()+ */+#define VRNA_STATUS_PF_POST     (unsigned char)4+++#define VRNA_PLIST_TYPE_BASEPAIR      0+#define VRNA_PLIST_TYPE_GQUAD         1+#define VRNA_PLIST_TYPE_H_MOTIF       2+#define VRNA_PLIST_TYPE_I_MOTIF       3+#define VRNA_PLIST_TYPE_UD_MOTIF      4+++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT+++#ifdef VRNA_BACKWARD_COMPAT++/* the following typedefs are for backward compatibility only */++/**+ *  @brief Old typename of #vrna_basepair_s+ *  @deprecated Use #vrna_basepair_t instead!+ */+typedef struct vrna_basepair_s  PAIR;++/**+ *  @brief Old typename of #vrna_plist_s+ *  @deprecated Use #vrna_plist_t instead!+ */+typedef struct vrna_plist_s     plist;++/**+ *  @brief Old typename of #vrna_cpair_s+ *  @deprecated Use #vrna_cpair_t instead!+ */+typedef struct vrna_cpair_s     cpair;++/**+ *  @brief Old typename of #vrna_sect_s+ *  @deprecated Use #vrna_sect_t instead!+ */+typedef struct vrna_sect_s      sect;++/**+ *  @brief Old typename of #vrna_bp_stack_s+ *  @deprecated Use #vrna_bp_stack_t instead!+ */+typedef struct vrna_bp_stack_s  bondT;++#endif++#include <ViennaRNA/energy_const.h>+#include <ViennaRNA/model.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/dp_matrices.h>+#include <ViennaRNA/constraints.h>+#include <ViennaRNA/grammar.h>+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"++/*+* ############################################################+* Here are the type definitions of various datastructures+* shared among the Vienna RNA Package+* ############################################################+*/++/**+ *  @brief  Base pair data structure used in subopt.c+ */+struct vrna_basepair_s {+  int i;+  int j;+};++/**+ *  @brief this datastructure is used as input parameter in functions of PS_dot.h and others+ */+struct vrna_plist_s {+  int i;+  int j;+  float p;+  int type;+};++/**+ *  @brief this datastructure is used as input parameter in functions of PS_dot.c+ */+struct vrna_cpair_s {+  int i,j,mfe;+  float p, hue, sat;+};++struct vrna_color_s {+  float hue;+  float sat;+  float bri;+};++struct vrna_data_linear_s {+  unsigned int  position;+  float         value;+  vrna_color_t  color;+};+++/**+ *  @brief  Stack of partial structures for backtracking+ */+struct vrna_sect_s {+  int  i;+  int  j;+  int ml;+};++/**+ *  @brief  Base pair stack element+ */+struct vrna_bp_stack_s {+   unsigned int i;+   unsigned int j;+};+++/*+* ############################################################+* RNAup data structures+* ############################################################+*/++/**+ *  @brief contributions to p_u+ */+typedef struct pu_contrib {+  double **H; /**<  @brief  hairpin loops */+  double **I; /**<  @brief  interior loops */+  double **M; /**<  @brief  multi loops */+  double **E; /**<  @brief  exterior loop */+  int length; /**<  @brief  length of the input sequence */+  int w;      /**<  @brief  longest unpaired region */+} pu_contrib;++/**+ *  @brief  interaction data structure for RNAup+ */+typedef struct interact {+  double *Pi;       /**<  @brief  probabilities of interaction */+  double *Gi;       /**<  @brief  free energies of interaction */+  double Gikjl;     /**<  @brief  full free energy for interaction between [k,i] k<i+                                  in longer seq and [j,l] j<l in shorter seq */+  double Gikjl_wo;  /**<  @brief  Gikjl without contributions for prob_unpaired */+  int i;            /**<  @brief  k<i in longer seq */+  int k;            /**<  @brief  k<i in longer seq */+  int j;            /**<  @brief  j<l in shorter seq */+  int l;            /**<  @brief  j<l in shorter seq */+  int length;       /**<  @brief  length of longer sequence */+} interact;++/**+ *  @brief  Collection of all free_energy of beeing unpaired values for output+ */+typedef struct pu_out {+  int len;            /**<  @brief  sequence length */+  int u_vals;         /**<  @brief  number of different -u values */+  int contribs;       /**<  @brief  [-c "SHIME"] */+  char **header;      /**<  @brief  header line */+  double **u_values;  /**<  @brief  (the -u values * [-c "SHIME"]) * seq len */+} pu_out;++/**+ *  @brief  constraints for cofolding+ */+typedef struct constrain{+  int *indx;+  char *ptype;+} constrain;++/*+* ############################################################+* RNAduplex data structures+* ############################################################+*/++/**+ *  @brief  Data structure for RNAduplex+ */+typedef struct {+  int i;+  int j;+  int end;+  char *structure;+  double energy;+  double energy_backtrack;+  double opening_backtrack_x;+  double opening_backtrack_y;+  int offset;+  double dG1;+  double dG2;+  double ddG;+  int tb;+  int te;+  int qb;+  int qe;+} duplexT;++/*+* ############################################################+* RNAsnoop data structures+* ############################################################+*/++/**+ *  @brief  Data structure for RNAsnoop (fold energy list)+ */+typedef struct node {+  int k;+  int energy;+  struct node *next;+} folden;++/**+ *  @brief  Data structure for RNAsnoop+ */+typedef struct {+  int i;+  int j;+  int u;+  char *structure;+  float energy;+  float Duplex_El;+  float Duplex_Er;+  float Loop_E;+  float Loop_D;+  float pscd;+  float psct;+  float pscg;+  float Duplex_Ol;+  float Duplex_Or;+  float Duplex_Ot;+  float fullStemEnergy;+} snoopT;+++/*+* ############################################################+* PKplex data structures+* ############################################################+*/++/**+ *  @brief  Data structure used in RNApkplex+ */+typedef struct dupVar{+  int i;+  int j;+  int end;+  char *pk_helix;+  char *structure;+  double energy;+  int offset;+  double dG1;+  double dG2;+  double ddG;+  int tb;+  int te;+  int qb;+  int qe;+  int inactive;+  int processed;+} dupVar;++/**+ *  @brief  Dummy symbol to check whether the library was build using C11/C++11 features+ *+ *  By default, several data structures of our new v3.0 API use C11/C++11 features, such+ *  as unnamed unions, unnamed structs. However, these features can be deactivated at+ *  compile time to allow building the library and executables with compilers that do not+ *  support these features.+ *+ *  Now, the problem arises that once our static library is compiled and a third-party+ *  application is supposed to link against it, it needs to know, at compile time, how to+ *  correctly address particular data structures. This is usually implicitely taken care of+ *  through the API exposed in our header files. Unfortunately, we had some preprocessor directives+ *  in our header files that changed the API depending on the capabilities of the compiler+ *  the third-party application is build with. This in turn prohibited the use of an RNAlib+ *  compiled without C11/C++11 support in a program that compiles/links with enabled C11/C++11+ *  support and vice-versa.+ *+ *  Therefore, we introduce this dummy symbol which can be used to check, whether the+ *  static library was build with C11/C++11 features.+ *+ *  @note If the symbol is present, the library was build with enabled C11/C++11 features support+ *  and no action is required. However, if the symbol is missing in RNAlib >= 2.2.9, programs+ *  that link to RNAlib must define a pre-processor identifier @em VRNA_DISABLE_C11_FEATURES before+ *  including any ViennaRNA Package header file, for instance by adding a @em CPPFLAG+ *  @code+CPPFLAGS+=-DVRNA_DISABLE_C11_FEATURES+ *  @endcode+ *+ *  @since v2.2.9+ */+#ifndef VRNA_DISABLE_C11_FEATURES+void vrna_C11_features(void);+#endif++/**+ * @}+ */+++/*+* ############################################################+* VRNA fold compound related functions+* ############################################################+*/++/**+ *  @addtogroup   fold_compound   The Fold Compound+ *  @{+ *+ *  @brief  This module provides interfaces that deal with the most basic data structure used+ *          in structure predicting and energy evaluating function of the RNAlib.+ *+ *          Throughout the entire RNAlib, the #vrna_fold_compound_t, is used to group+ *          information and data that is required for structure prediction and energy evaluation.+ *          Here, you'll find interface functions to create, modify, and delete #vrna_fold_compound_t+ *          data structures.+ */++/**+ *  @brief  An enumerator that is used to specify the type of a #vrna_fold_compound_t+ */+typedef enum {+  VRNA_FC_TYPE_SINGLE,      /**< Type is suitable for single, and hybridizing sequences */+  VRNA_FC_TYPE_COMPARATIVE  /**< Type is suitable for sequence alignments (consensus structure prediction) */+} vrna_fc_type_e;+++/**+ *  @brief  The most basic data structure required by many functions throughout the RNAlib+ *+ *  @note   Please read the documentation of this data structure carefully! Some attributes are only available for+ *  specific types this data structure can adopt.+ *+ *  @warning  Reading/Writing from/to attributes that are not within the scope of the current type usually result+ *  in undefined behavior!+ *+ *  @see  #vrna_fold_compound_t.type, vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_fold_compound_free(),+ *        #VRNA_FC_TYPE_SINGLE, #VRNA_FC_TYPE_COMPARATIVE+ */+struct vrna_fc_s{++  /**+      @name Common data fields+      @{+   */+  vrna_fc_type_e    type;           /**<  @brief  The type of the #vrna_fold_compound_t.+                                      @details Currently possible values are #VRNA_FC_TYPE_SINGLE, and #VRNA_FC_TYPE_COMPARATIVE+                                      @warning Do not edit this attribute, it will be automagically set by+                                            the corresponding get() methods for the #vrna_fold_compound_t.+                                            The value specified in this attribute dictates the set of other+                                            attributes to use within this data structure.+                                    */+  unsigned int      length;         /**<  @brief  The length of the sequence (or sequence alignment) */+  int               cutpoint;       /**<  @brief  The position of the (cofold) cutpoint within the provided sequence.+                                      If there is no cutpoint, this field will be set to -1+                                    */++  unsigned int      *strand_number; /**<  @brief  The strand number a particular nucleotide is associated with */++  vrna_hc_t         *hc;            /**<  @brief  The hard constraints data structure used for structure prediction */++  vrna_mx_mfe_t     *matrices;      /**<  @brief  The MFE DP matrices */+  vrna_mx_pf_t      *exp_matrices;  /**<  @brief  The PF DP matrices  */++  vrna_param_t      *params;        /**<  @brief  The precomputed free energy contributions for each type of loop */+  vrna_exp_param_t  *exp_params;    /**<  @brief  The precomputed free energy contributions as Boltzmann factors  */++  int               *iindx;         /**<  @brief  DP matrix accessor  */+  int               *jindx;         /**<  @brief  DP matrix accessor  */++  /**+      @}++      @name User-defined data fields+      @{+   */+  vrna_callback_recursion_status *stat_cb;  /**<  @brief  Recursion status callback (usually called just before, and+                                                          after recursive computations in the library+                                                  @see    vrna_callback_recursion_status(), vrna_fold_compound_add_callback()+                                            */++  void              *auxdata;               /**<  @brief  A pointer to auxiliary, user-defined data+                                                  @see vrna_fold_compound_add_auxdata(), #vrna_fold_compound_t.free_auxdata+                                            */++  vrna_callback_free_auxdata *free_auxdata; /**<  @brief A callback to free auxiliary user data whenever the fold_compound itself is free'd+                                                  @see  #vrna_fold_compound_t.auxdata, vrna_callback_free_auxdata()+                                            */++  /**+      @}++      @name Secondary Structure Decomposition (grammar) related data fields+      @{+   */++  /* data structure to adjust additional structural domains, such as G-quadruplexes */+  vrna_sd_t         *domains_struc;         /**<  @brief  Additional structured domains */++  /* data structure to adjust additional contributions to unpaired stretches, e.g. due to protein binding */+  vrna_ud_t         *domains_up;            /**<  @brief  Additional unstructured domains */++  /* auxiliary (user-defined) extension to the folding grammar */+  vrna_gr_aux_t     *aux_grammar;++  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+  union {+    struct {+#endif++  /**+      @name Data fields available for single/hybrid structure prediction+      @{+   */+      char  *sequence;              /**<  @brief  The input sequence string+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_SINGLE @endverbatim+                                    */+      short *sequence_encoding;     /**<  @brief  Numerical encoding of the input sequence+                                          @see    vrna_sequence_encode()+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_SINGLE @endverbatim+                                    */+      short *sequence_encoding2;+      char  *ptype;                 /**<  @brief  Pair type array+                                     +                                          Contains the numerical encoding of the pair type for each pair (i,j) used+                                          in MFE, Partition function and Evaluation computations.+                                          @note This array is always indexed via jindx, in contrast to previously+                                          different indexing between mfe and pf variants!+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_SINGLE @endverbatim+                                          @see    vrna_idx_col_wise(), vrna_ptypes()+                                    */+      char  *ptype_pf_compat;       /**<  @brief  ptype array indexed via iindx+                                          @deprecated  This attribute will vanish in the future!+                                          It's meant for backward compatibility only!+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_SINGLE @endverbatim+                                    */+      vrna_sc_t *sc;                /**<  @brief  The soft constraints for usage in structure prediction and evaluation+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_SINGLE @endverbatim+                                    */++  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+    struct {+#endif++  /**+      @name Data fields for consensus structure prediction+      @{+   */+      char  **sequences;            /**<  @brief  The aligned sequences+                                          @note   The end of the alignment is indicated by a NULL pointer in the second dimension+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      unsigned int    n_seq;        /**<  @brief  The number of sequences in the alignment+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      char            *cons_seq;    /**<  @brief  The consensus sequence of the aligned sequences+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      short           *S_cons;      /**<  @brief  Numerical encoding of the consensus sequence+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      short           **S;          /**<  @brief  Numerical encoding of the sequences in the alignment+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      short           **S5;         /**<  @brief    S5[s][i] holds next base 5' of i in sequence s+                                          @warning  Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      short           **S3;         /**<  @brief    Sl[s][i] holds next base 3' of i in sequence s+                                          @warning  Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      char            **Ss;+      unsigned short  **a2s;+      int             *pscore;      /**<  @brief  Precomputed array of pair types expressed as pairing scores+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      short           *pscore_pf_compat;  /**<  @brief  Precomputed array of pair types expressed as pairing scores indexed via iindx+                                                @deprecated  This attribute will vanish in the future!+                                                @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      vrna_sc_t       **scs;        /**<  @brief  A set of soft constraints (for each sequence in the alignment)+                                          @warning   Only available if @verbatim type==VRNA_FC_TYPE_COMPARATIVE @endverbatim+                                    */+      int             oldAliEn;++  /**+      @}+   */+#ifndef VRNA_DISABLE_C11_FEATURES+    };+  };+#endif++  /**+   *  @name Additional data fields for Distance Class Partitioning+   *+   *  These data fields are typically populated with meaningful data only if used in the context of Distance Class Partitioning+   *  @{+   */+  unsigned int    maxD1;          /**<  @brief  Maximum allowed base pair distance to first reference */+  unsigned int    maxD2;          /**<  @brief  Maximum allowed base pair distance to second reference */+  short           *reference_pt1; /**<  @brief  A pairtable of the first reference structure */+  short           *reference_pt2; /**<  @brief  A pairtable of the second reference structure */++  unsigned int    *referenceBPs1; /**<  @brief  Matrix containing number of basepairs of reference structure1 in interval [i,j] */+  unsigned int    *referenceBPs2; /**<  @brief  Matrix containing number of basepairs of reference structure2 in interval [i,j] */+  unsigned int    *bpdist;        /**<  @brief  Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */++  unsigned int    *mm1;           /**<  @brief  Maximum matching matrix, reference struct 1 disallowed */+  unsigned int    *mm2;           /**<  @brief  Maximum matching matrix, reference struct 2 disallowed */+  +  /**+      @}+   */++  /**+   *  @name Additional data fields for local folding+   *+   *  These data fields are typically populated with meaningful data only if used in the context of local folding+   *  @{+   */+  int             window_size;    /**<  @brief  window size for local folding sliding window approach */+  char            **ptype_local;  /**<  @brief  Pair type array (for local folding) */+  /**+      @}+   */++};+++/* the definitions below should be used for functions that return/receive/destroy fold compound data structures */++/**+ *  @brief  Option flag to specify default settings/requirements+ */+#define VRNA_OPTION_DEFAULT         0U++/**+ *  @brief  Option flag to specify requirement of Minimum Free Energy (MFE) DP matrices+ *          and corresponding set of energy parameters+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), #VRNA_OPTION_EVAL_ONLY+ */+#define VRNA_OPTION_MFE             1U++/**+ *  @brief  Option flag to specify requirement of Partition Function (PF) DP matrices+ *          and corresponding set of Boltzmann factors+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), #VRNA_OPTION_EVAL_ONLY+ */+#define VRNA_OPTION_PF              2U++/**+ *  @brief  Option flag to specify requirement of dimer DP matrices+ */+#define VRNA_OPTION_HYBRID          4U++/**+ *  @brief  Option flag to specify that neither MFE, nor PF DP matrices are required+ *+ *  Use this flag in conjuntion with #VRNA_OPTION_MFE, and #VRNA_OPTION_PF to save+ *  memory for a #vrna_fold_compound_t obtained from vrna_fold_compound(), or vrna_fold_compound_comparative()+ *  in cases where only energy evaluation but no structure prediction is required.+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_eval_structure()+ */+#define VRNA_OPTION_EVAL_ONLY       8U++/**+ *  @brief  Option flag to specify requirement of DP matrices for local folding approaches+ */+#define VRNA_OPTION_WINDOW          16U++/**+ *  @brief  Retrieve a #vrna_fold_compound_t data structure for single sequences and hybridizing sequences+ *+ *  This function provides an easy interface to obtain a prefilled #vrna_fold_compound_t by passing a single+ *  sequence, or two contatenated sequences as input. For the latter, sequences need to be seperated by+ *  an '&' character like this: @verbatim char *sequence = "GGGG&CCCC"; @endverbatim+ *+ *  The optional parameter @p md_p can be used to specify the model details for successive computations+ *  based on the content of the generated #vrna_fold_compound_t. Passing NULL will instruct the function+ *  to use default model details.+ *  The third parameter @p options may be used to specify dynamic programming (DP) matrix requirements.+ *  Use the macros:+ *+ *  - #VRNA_OPTION_MFE+ *  - #VRNA_OPTION_PF+ *  - #VRNA_OPTION_WINDOW+ *  - #VRNA_OPTION_EVAL_ONLY+ *  - #VRNA_OPTION_DEFAULT+ *+ *  to specify the required type of computations that will be performed with the #vrna_fold_compound_t.+ *+ *  If you just need the folding compound serving as a container for your data, you can simply pass+ *  #VRNA_OPTION_DEFAULT to the @p option parameter. This creates a #vrna_fold_compound_t without DP+ *  matrices, thus saving memory. Subsequent calls of any structure prediction function will then take+ *  care of allocating the memory required for the DP matrices.+ *  If you only intend to evaluate structures instead of actually predicting them, you may use the+ *  #VRNA_OPTION_EVAL_ONLY macro. This will seriously speedup the creation of the #vrna_fold_compound_t.+ *+ *  @note The sequence string must be uppercase, and should contain only RNA (resp. DNA) alphabet depending+ *        on what energy parameter set is used+ *+ *  @see  vrna_fold_compound_free(), vrna_fold_compound_comparative(), #vrna_md_t, #VRNA_OPTION_MFE,+ *        #VRNA_OPTION_PF, #VRNA_OPTION_EVAL_ONLY, #VRNA_OPTION_WINDOW+ *+ *  @param    sequence    A single sequence, or two concatenated sequences seperated by an '&' character+ *  @param    md_p        An optional set of model details+ *  @param    options     The options for DP matrices memory allocation+ *  @return               A prefilled vrna_fold_compound_t that can be readily used for computations+ */+vrna_fold_compound_t *+vrna_fold_compound( const char *sequence,+                    vrna_md_t *md_p,+                    unsigned int options);++/**+ *  @brief  Retrieve a #vrna_fold_compound_t data structure for sequence alignments+ *+ *  This function provides an easy interface to obtain a prefilled #vrna_fold_compound_t by passing an+ *  alignment of sequences.+ *+ *  The optional parameter @p md_p can be used to specify the model details for successive computations+ *  based on the content of the generated #vrna_fold_compound_t. Passing NULL will instruct the function+ *  to use default model details.+ *  The third parameter @p options may be used to specify dynamic programming (DP) matrix requirements.+ *  Use the macros:+ *+ *  - #VRNA_OPTION_MFE+ *  - #VRNA_OPTION_PF+ *  - #VRNA_OPTION_EVAL_ONLY+ *  - #VRNA_OPTION_DEFAULT+ *+ *  to specify the required type of computations that will be performed with the #vrna_fold_compound_t.+ *+ *  If you just need the folding compound serving as a container for your data, you can simply pass+ *  #VRNA_OPTION_DEFAULT to the @p option parameter. This creates a #vrna_fold_compound_t without DP+ *  matrices, thus saving memory. Subsequent calls of any structure prediction function will then take+ *  care of allocating the memory required for the DP matrices.+ *  If you only intend to evaluate structures instead of actually predicting them, you may use the+ *  #VRNA_OPTION_EVAL_ONLY macro. This will seriously speedup the creation of the #vrna_fold_compound_t.+ *+ *  @note The sequence strings must be uppercase, and should contain only RNA (resp. DNA) alphabet including+ *        gap characters depending on what energy parameter set is used.+ *+ *  @see  vrna_fold_compound_free(), vrna_fold_compound(), #vrna_md_t, #VRNA_OPTION_MFE, #VRNA_OPTION_PF,+ *        #VRNA_OPTION_EVAL_ONLY, read_clustal()+ *+ *  @param    sequences   A sequence alignment including 'gap' characters+ *  @param    md_p        An optional set of model details+ *  @param    options     The options for DP matrices memory allocation+ *  @return               A prefilled vrna_fold_compound_t that can be readily used for computations+ */+vrna_fold_compound_t *+vrna_fold_compound_comparative( const char **sequences,+                                vrna_md_t *md_p,+                                unsigned int options);++vrna_fold_compound_t *+vrna_fold_compound_TwoD(const char *sequence,+                        const char *s1,+                        const char *s2,+                        vrna_md_t *md_p,+                        unsigned int options);++int+vrna_fold_compound_prepare( vrna_fold_compound_t *vc,+                            unsigned int options);++/**+ *  @brief  Free memory occupied by a #vrna_fold_compound_t+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_mx_mfe_free(), vrna_mx_pf_free()+ *+ *  @param  vc  The #vrna_fold_compound_t that is to be erased from memory+ */+void+vrna_fold_compound_free(vrna_fold_compound_t *vc);++/**+ *  @brief  Add auxiliary data to the #vrna_fold_compound_t+ *+ *  This function allows one to bind arbitrary data to a #vrna_fold_compound_t which may later on be used+ *  by one of the callback functions, e.g. vrna_callback_recursion_status(). To allow for proper cleanup+ *  of the memory occupied by this auxiliary data, the user may also provide a pointer to a cleanup function+ *  that free's the corresponding memory. This function will be called automatically when the #vrna_fold_compound_t+ *  is free'd with vrna_fold_compound_free().+ *+ *  @note Before attaching the arbitrary data pointer, this function will call the vrna_callback_free_auxdata()+ *        on any pre-existing data that is already attached.+ *+ *  @see vrna_callback_free_auxdata()+ *  @param  vc    The fold_compound the arbitrary data pointer should be associated with+ *  @param  data  A pointer to an arbitrary data structure+ *  @param  f     A pointer to function that free's memory occupied by the arbitrary data (May be NULL)+ */+void vrna_fold_compound_add_auxdata(vrna_fold_compound_t *vc,+                                    void *data,+                                    vrna_callback_free_auxdata *f);++/**+ *  @brief  Add a recursion status callback to the #vrna_fold_compound_t+ *+ *  Binding a recursion status callback function to a #vrna_fold_compound_t allows one to perform+ *  arbitrary operations just before, or after an actual recursive computations, e.g. MFE prediction,+ *  is performed by the RNAlib. The callback function will be provided with a pointer to its+ *  #vrna_fold_compound_t, and a status message. Hence, it has complete access to all variables that+ *  incluence the recursive computations.+ *+ *  @see  vrna_callback_recursion_status(), #vrna_fold_compound_t,+ *        #VRNA_STATUS_MFE_PRE, #VRNA_STATUS_MFE_POST, #VRNA_STATUS_PF_PRE, #VRNA_STATUS_PF_POST+ *+ *  @param  vc    The fold_compound the callback function should be attached to+ *  @param  f     The pointer to the recursion status callback function+ */+void vrna_fold_compound_add_callback( vrna_fold_compound_t *vc,+                                      vrna_callback_recursion_status *f);+++/**+ *  @}+ */++#endif
+ C/ViennaRNA/dist_vars.c view
@@ -0,0 +1,8 @@+/*             Global variables for Distance-Package */++int  edit_backtrack = 0;  /* calculate aligned representation */++char *aligned_line[4];    /* containes the aligned string representations */++int  cost_matrix = 0;     /* 0 for usual costs, 1 for Shapiro's costs */+
+ C/ViennaRNA/dist_vars.h view
@@ -0,0 +1,60 @@+#ifndef VIENNA_RNA_PACKAGE_DIST_VARS_H+#define VIENNA_RNA_PACKAGE_DIST_VARS_H++/**+ *  @file dist_vars.h+ *  @brief Global variables for Distance-Package+ */++/**+ *  @brief Produce an alignment of the two structures being compared by+ *  tracing the editing path giving the minimum distance.+ * + *  set to 1 if you want backtracking+ */+extern int   edit_backtrack;++/**+ *  @brief Contains the two aligned structures after a call to one of the distance+ *  functions with #edit_backtrack set to 1.+ */+extern char *aligned_line[4];++/**+ *  @brief Specify the cost matrix to be used for distance calculations+ * + *  if 0, use the default cost matrix (upper matrix in example), otherwise+ *  use Shapiro's costs (lower matrix).+ */+extern int  cost_matrix;++/*  Global type defs for Distance-Package */++/**+ *  @brief Postorder data structure+ */+typedef struct {+                 int  type;+                 int  weight;+                 int  father;+                 int  sons;+                 int  leftmostleaf;+               } Postorder_list;++/**+ *  @brief  Tree data structure+ */+typedef struct {+                 Postorder_list *postorder_list;+                 int            *keyroots;+               } Tree;++/**+ *  @brief  Some other data structure+ */+typedef struct {+                 int    type;+                 int    sign;+                 float  weight;+               } swString;+#endif
+ C/ViennaRNA/dp_matrices.c view
@@ -0,0 +1,1453 @@+/** \file dp_matrices.c **/++/*+                  Dynamic Programming matrix related functions++                  This file contains everything necessary to+                  obtain and destroy data structures representing+                  dynamic programming (DP) matrices used in the folding+                  recurrences throughout the VienneRNA paclage++                  c Ronny Lorenz++                  ViennaRNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdlib.h>+#include <math.h>++#include "data_structures.h"+#include "model.h"+#include "utils.h"+#include "gquad.h"+#include "dp_matrices.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++/* the definitions below indicate which arrays should be allocated upon retrieval of a matrices data structure */+#define ALLOC_NOTHING     0+#define ALLOC_F           1+#define ALLOC_F5          2+#define ALLOC_F3          4+#define ALLOC_FC          8+#define ALLOC_C           16+#define ALLOC_FML         32+#define ALLOC_PROBS       256+#define ALLOC_AUX         512++#define ALLOC_CIRC        1024+#define ALLOC_HYBRID      2048+#define ALLOC_UNIQ        4096+++#define ALLOC_MFE_DEFAULT         (ALLOC_F5 | ALLOC_C | ALLOC_FML)+#define ALLOC_MFE_LOCAL           (ALLOC_F3 | ALLOC_C | ALLOC_FML)++#define ALLOC_PF_WO_PROBS         (ALLOC_F | ALLOC_C | ALLOC_FML)+#define ALLOC_PF_DEFAULT          (ALLOC_PF_WO_PROBS | ALLOC_PROBS | ALLOC_AUX)++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE unsigned int    get_mx_alloc_vector(vrna_md_t *md_p, vrna_mx_type_e type, unsigned int options);+PRIVATE unsigned int    get_mx_mfe_alloc_vector_current(vrna_mx_mfe_t *mx, vrna_mx_type_e mx_type);+PRIVATE unsigned int    get_mx_pf_alloc_vector_current(vrna_mx_pf_t *mx, vrna_mx_type_e mx_type);+PRIVATE void            mfe_matrices_alloc_default(vrna_mx_mfe_t *vars, unsigned int m, unsigned int alloc_vector);+PRIVATE void            mfe_matrices_free_default(vrna_mx_mfe_t *self);+PRIVATE void            mfe_matrices_alloc_window(vrna_mx_mfe_t *vars, unsigned int m, unsigned int alloc_vector);+PRIVATE void            mfe_matrices_free_window(vrna_mx_mfe_t *self, unsigned int length, unsigned int window_size);+PRIVATE void            mfe_matrices_alloc_2Dfold(vrna_mx_mfe_t *vars, unsigned int m, unsigned int alloc_vector);+PRIVATE void            mfe_matrices_free_2Dfold( vrna_mx_mfe_t *self, unsigned int length, int *indx);+PRIVATE void            pf_matrices_alloc_default(vrna_mx_pf_t *vars, unsigned int m, unsigned int alloc_vector);+PRIVATE void            pf_matrices_free_default(vrna_mx_pf_t *self);+PRIVATE void            pf_matrices_alloc_2Dfold(vrna_mx_pf_t *vars, unsigned int m, unsigned int alloc_vector);+PRIVATE void            pf_matrices_free_2Dfold(vrna_mx_pf_t *self, unsigned int length, int *indx, int *jindx);+PRIVATE vrna_mx_mfe_t   *get_mfe_matrices_alloc(unsigned int n, unsigned int m, vrna_mx_type_e type, unsigned int alloc_vector);+PRIVATE vrna_mx_pf_t    *get_pf_matrices_alloc(unsigned int n, vrna_mx_type_e type, unsigned int alloc_vector);+PRIVATE void            add_pf_matrices( vrna_fold_compound_t *vc, vrna_mx_type_e type, unsigned int alloc_vector);+PRIVATE void            add_mfe_matrices(vrna_fold_compound_t *vc, vrna_mx_type_e type, unsigned int alloc_vector);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC void+vrna_mx_mfe_free(vrna_fold_compound_t *vc){++  if(vc){+    vrna_mx_mfe_t *self = vc->matrices;+    if(self){+      switch(self->type){+        case VRNA_MX_DEFAULT:   mfe_matrices_free_default(self);+                                break;++        case VRNA_MX_WINDOW:    mfe_matrices_free_window(self, vc->length, vc->window_size);+                                break;++        case VRNA_MX_2DFOLD:    mfe_matrices_free_2Dfold(self, vc->length, vc->iindx);+                                break;++        default:                /* do nothing */+                                break;+      }+      free(self);+      vc->matrices = NULL;+    }+  }+}++PUBLIC void+vrna_mx_pf_free(vrna_fold_compound_t *vc){++  if(vc){+    vrna_mx_pf_t  *self = vc->exp_matrices;+    if(self){+      switch(self->type){+        case VRNA_MX_DEFAULT:   pf_matrices_free_default(self);+                                break;++        case VRNA_MX_2DFOLD:    pf_matrices_free_2Dfold(self, vc->length, vc->iindx, vc->jindx);+                                break;++        default:                /* do nothing */+                                break;+      }++      free(self->expMLbase);+      free(self->scale);++      free(self);+      vc->exp_matrices = NULL;+    }+  }+}++PUBLIC int+vrna_mx_add(vrna_fold_compound_t *vc,+            vrna_mx_type_e mx_type,+            unsigned int options){++  int ret;++  ret = 1;++  if(options & VRNA_OPTION_MFE){+    ret &= vrna_mx_mfe_add(vc, mx_type, options);+  }++  if(options & VRNA_OPTION_PF){+    ret &= vrna_mx_pf_add(vc, mx_type, options);+  }++  return ret;+}++PUBLIC int+vrna_mx_mfe_add(vrna_fold_compound_t *vc,+                vrna_mx_type_e mx_type,+                unsigned int options){++  unsigned int mx_alloc_vector;++  if(vc->params){+    options |= VRNA_OPTION_MFE;+    if(vc->cutpoint > 0)+      options |= VRNA_OPTION_HYBRID;++    mx_alloc_vector = get_mx_alloc_vector(&(vc->params->model_details), mx_type, options);+    vrna_mx_mfe_free(vc);+    add_mfe_matrices(vc, mx_type, mx_alloc_vector);+  } else {+    return 0;+  }++  return 1;+}++PUBLIC int+vrna_mx_pf_add( vrna_fold_compound_t *vc,+                vrna_mx_type_e mx_type,+                unsigned int options){++  unsigned int mx_alloc_vector;+  if(vc->exp_params){+    mx_alloc_vector = get_mx_alloc_vector(&(vc->exp_params->model_details), mx_type, options | VRNA_OPTION_PF);+    vrna_mx_pf_free(vc);+    add_pf_matrices(vc, mx_type, mx_alloc_vector);+  } else {+    return 0;+  }++  return 1;+}++PUBLIC int+vrna_mx_prepare(vrna_fold_compound_t *vc,+                unsigned int options){++  int             ret, realloc;+  unsigned int    mx_alloc_vector, mx_alloc_vector_current;+  vrna_mx_type_e  mx_type;++  ret = 1;++  if(vc){+    /*  check whether we have the correct DP matrices attached, and if there is+        enough memory allocated+    */+    if(options & VRNA_OPTION_MFE){  /* prepare for MFE computation */+      if(options & VRNA_OPTION_WINDOW){ /* Windowing approach, a.k.a. locally optimal */+        mx_type = VRNA_MX_WINDOW;+      } else {                          /* default is regular MFE */+        mx_type = VRNA_MX_DEFAULT;+      }++      if(vc->cutpoint > 0)+        options |= VRNA_OPTION_HYBRID;++      realloc = 0;++      if(!vc->matrices || (vc->matrices->type != mx_type) || (vc->matrices->length < vc->length)){+        realloc = 1;+      } else {+        mx_alloc_vector         = get_mx_alloc_vector(&(vc->params->model_details), mx_type, options);+        mx_alloc_vector_current = get_mx_mfe_alloc_vector_current(vc->matrices, mx_type);+        if((mx_alloc_vector & mx_alloc_vector_current) != mx_alloc_vector)+          realloc = 1;+      }++      if(realloc) /* Add DP matrices, if not they are not present */+        ret &= vrna_mx_mfe_add(vc, mx_type, options);++    }++    if(options & VRNA_OPTION_PF){   /* prepare for partition function computations */+      if(!vc->exp_params) /* return failure if exp_params data is not present */+        return 0;++      mx_type = VRNA_MX_DEFAULT;  /* for now, we only check default matrices */++      if(vc->cutpoint > 0)+        options |= VRNA_OPTION_HYBRID;++      realloc = 0;++      /*  Add DP matrices, if not they are not present */+      if(!vc->exp_matrices || (vc->exp_matrices->type != mx_type) || (vc->exp_matrices->length < vc->length)){+        realloc = 1;+      } else {+        mx_alloc_vector         = get_mx_alloc_vector(&(vc->exp_params->model_details), mx_type, options);+        mx_alloc_vector_current = get_mx_pf_alloc_vector_current(vc->exp_matrices, mx_type);+        if((mx_alloc_vector & mx_alloc_vector_current) != mx_alloc_vector)+          realloc = 1;+      }+      +      if(realloc){ /* Add DP matrices, if not they are not present */+        ret &= vrna_mx_pf_add(vc, mx_type, options);+      }+#ifdef VRNA_BACKWARD_COMPAT+      else { /* re-compute pf_scale and MLbase contributions (for RNAup)*/+        vrna_exp_params_rescale(vc, NULL);+      }+#endif+  +    }+  } else {+    ret = 0;+  }++  return ret;+}+/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/+PRIVATE unsigned int+get_mx_mfe_alloc_vector_current(vrna_mx_mfe_t *mx,+                                vrna_mx_type_e mx_type){++  unsigned int mx_alloc_vector = ALLOC_NOTHING;++  if(mx){+    switch(mx_type){+      case VRNA_MX_DEFAULT: if(mx->f5)+                              mx_alloc_vector |= ALLOC_F5;+                            if(mx->f3)+                              mx_alloc_vector |= ALLOC_F3;+                            if(mx->fc)+                              mx_alloc_vector |= ALLOC_HYBRID;+                            if(mx->c)+                              mx_alloc_vector |= ALLOC_C;+                            if(mx->fML)+                              mx_alloc_vector |= ALLOC_FML;+                            if(mx->fM1)+                              mx_alloc_vector |= ALLOC_UNIQ;+                            if(mx->fM2)+                              mx_alloc_vector |= ALLOC_CIRC;+                            break;++      default:              break;+    }+  }+  +  return mx_alloc_vector;+}++PRIVATE unsigned int+get_mx_pf_alloc_vector_current( vrna_mx_pf_t *mx,+                                vrna_mx_type_e mx_type){++  unsigned int mx_alloc_vector = ALLOC_NOTHING;++  if(mx){+    switch(mx_type){+      case VRNA_MX_DEFAULT: if(mx->q)+                              mx_alloc_vector |= ALLOC_F;+                            if(mx->qb)+                              mx_alloc_vector |= ALLOC_C;+                            if(mx->qm)+                              mx_alloc_vector |= ALLOC_FML;+                            if(mx->qm1)+                              mx_alloc_vector |= ALLOC_UNIQ;+                            if(mx->qm2)+                              mx_alloc_vector |= ALLOC_CIRC;+                            if(mx->probs)+                              mx_alloc_vector |= ALLOC_PROBS;+                            if(mx->q1k && mx->qln)+                              mx_alloc_vector |= ALLOC_AUX;+                            break;++      default:              break;+    }+  }++  return mx_alloc_vector;+}+PRIVATE void+add_pf_matrices(vrna_fold_compound_t *vc,+                vrna_mx_type_e type,+                unsigned int alloc_vector){++  if(vc){+    vc->exp_matrices  = get_pf_matrices_alloc(vc->length, type, alloc_vector);+    if(vc->exp_params->model_details.gquad){+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:   vc->exp_matrices->G = NULL;+                                    /* can't do that here, since scale[] is not filled yet :( +                                      vc->exp_matrices->G = get_gquad_pf_matrix(vc->sequence_encoding2, vc->exp_matrices->scale, vc->exp_params);+                                    */+                                    break;+        default:                    /* do nothing */+                                    break;+      }+    }+    vrna_exp_params_rescale(vc, NULL);+  }+}++PRIVATE void+add_mfe_matrices( vrna_fold_compound_t *vc,+                  vrna_mx_type_e mx_type,+                  unsigned int alloc_vector){++  if(vc){+    switch(mx_type){+      case VRNA_MX_WINDOW:  vc->matrices = get_mfe_matrices_alloc(vc->length, vc->window_size, mx_type, alloc_vector);+                            break;+      default:              vc->matrices = get_mfe_matrices_alloc(vc->length, vc->length, mx_type, alloc_vector);+                            break;+    }++    if(vc->params->model_details.gquad){+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:     switch(mx_type){+                                        case VRNA_MX_WINDOW:  /* do nothing, since we handle memory somewhere else */+                                                              break;+                                        default:              vc->matrices->ggg = get_gquad_matrix(vc->sequence_encoding2, vc->params);+                                                              break;+                                      }+                                      break;+        case VRNA_FC_TYPE_COMPARATIVE:  vc->matrices->ggg = get_gquad_ali_matrix(vc->S_cons, vc->S, vc->n_seq,  vc->params);+                                      break;+        default:                      /* do nothing */+                                      break;+      }+    }+  }+}++PRIVATE vrna_mx_mfe_t  *+get_mfe_matrices_alloc( unsigned int n,+                        unsigned int m,+                        vrna_mx_type_e type,+                        unsigned int alloc_vector){++  vrna_mx_mfe_t *vars;++  if((int)(n * m) >= (int)INT_MAX)+    vrna_message_error("get_mfe_matrices_alloc@data_structures.c: sequence length exceeds addressable range");++  vars          = (vrna_mx_mfe_t *)vrna_alloc(sizeof(vrna_mx_mfe_t));+  vars->length  = n;+  vars->type    = type;++  switch(type){+    case VRNA_MX_DEFAULT:   mfe_matrices_alloc_default(vars, m, alloc_vector);+                            break;++    case VRNA_MX_WINDOW:    mfe_matrices_alloc_window(vars, m, alloc_vector);+                            break;++    case VRNA_MX_2DFOLD:    mfe_matrices_alloc_2Dfold(vars, m, alloc_vector);+                            break;++    default:                /* do nothing */+                            break;+  }++  return vars;+}++PRIVATE vrna_mx_pf_t  *+get_pf_matrices_alloc(unsigned int n,+                      vrna_mx_type_e type,+                      unsigned int alloc_vector){++  unsigned int  lin_size;+  vrna_mx_pf_t  *vars;++  if(n >= (unsigned int)sqrt((double)INT_MAX))+    vrna_message_error("get_pf_matrices_alloc@data_structures.c: sequence length exceeds addressable range");++  lin_size      = n + 2;+  vars          = (vrna_mx_pf_t *)vrna_alloc(sizeof(vrna_mx_pf_t));+  vars->length  = n;+  vars->type    = type;+++  switch(type){+    case VRNA_MX_DEFAULT:   pf_matrices_alloc_default(vars, n, alloc_vector);+                            break;++    case VRNA_MX_2DFOLD:    pf_matrices_alloc_2Dfold(vars, n, alloc_vector);+                            break;++    default:                /* do nothing */+                            break;+  }++  /*+      always alloc the helper arrays for unpaired nucleotides in multi-+      branch loops and scaling+  */+  vars->scale     = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * lin_size);+  vars->expMLbase = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * lin_size);++  return vars;+}++PRIVATE unsigned int+get_mx_alloc_vector(vrna_md_t *md_p,+                    vrna_mx_type_e mx_type,+                    unsigned int options){++  unsigned int  v;++  v = ALLOC_NOTHING;++  /* default MFE matrices ? */+  if(options & VRNA_OPTION_MFE)+    v |= (mx_type == VRNA_MX_WINDOW) ? ALLOC_MFE_LOCAL : ALLOC_MFE_DEFAULT;++  /* default PF matrices ? */+  if(options & VRNA_OPTION_PF)+    v |= (md_p->compute_bpp) ? ALLOC_PF_DEFAULT : ALLOC_PF_WO_PROBS;++  if(options & VRNA_OPTION_HYBRID)+    v |= ALLOC_HYBRID;++  /* matrices for circular folding ? */+  if(md_p->circ){+    md_p->uniq_ML = 1; /* we need unique ML arrays for circular folding */+    v |= ALLOC_CIRC;+  }++  /* unique ML decomposition ? */+  if(md_p->uniq_ML)+    v |= ALLOC_UNIQ;++  return v;+}+++PRIVATE void+mfe_matrices_alloc_default( vrna_mx_mfe_t *vars,+                            unsigned int m,+                            unsigned int alloc_vector){++  unsigned int  n, size, lin_size;++  n             = vars->length;+  size          = ((n + 1) * (m + 2)) / 2;+  lin_size      = n + 2;++  vars->f5  = NULL;+  vars->f3  = NULL;+  vars->fc  = NULL;+  vars->c   = NULL;+  vars->fML = NULL;+  vars->fM1 = NULL;+  vars->fM2 = NULL;+  vars->ggg = NULL;++  if(alloc_vector & ALLOC_F5)+    vars->f5  = (int *) vrna_alloc(sizeof(int) * lin_size);++  if(alloc_vector & ALLOC_F3)+    vars->f3  = (int *) vrna_alloc(sizeof(int) * lin_size);++  if(alloc_vector & ALLOC_HYBRID)+    vars->fc  = (int *) vrna_alloc(sizeof(int) * lin_size);++  if(alloc_vector & ALLOC_C)+    vars->c   = (int *) vrna_alloc(sizeof(int) * size);++  if(alloc_vector & ALLOC_FML)+    vars->fML = (int *) vrna_alloc(sizeof(int) * size);++  if(alloc_vector & ALLOC_UNIQ)+    vars->fM1 = (int *) vrna_alloc(sizeof(int) * size);++  if(alloc_vector & ALLOC_CIRC)+    vars->fM2 = (int *) vrna_alloc(sizeof(int) * lin_size);++  /* setting exterior loop energies for circular case to INF is always safe */+  vars->FcH = vars->FcI = vars->FcM = vars->Fc = INF;++}++PRIVATE void+mfe_matrices_free_default(vrna_mx_mfe_t *self){++  free(self->f5);+  free(self->f3);+  free(self->fc);+  free(self->c);+  free(self->fML);+  free(self->fM1);+  free(self->fM2);+  free(self->ggg);+}++PRIVATE void+mfe_matrices_alloc_window(vrna_mx_mfe_t *vars,+                          unsigned int m,+                          unsigned int alloc_vector){++  int i;+  unsigned int  n, lin_size;++  n             = vars->length;+  lin_size      = n + 2;++  vars->f3_local = NULL;+  vars->c_local = NULL;+  vars->fML_local = NULL;+  vars->ggg_local = NULL;++  if(alloc_vector & ALLOC_F3)+    vars->f3_local = (int *) vrna_alloc(sizeof(int) * lin_size);++  if(alloc_vector & ALLOC_C){+    vars->c_local = (int **) vrna_alloc(sizeof(int *) * lin_size);+    for (i = (int)n; ( i > ((int)n - (int)m - 5)) && (i>=0); i--){+      vars->c_local[i] = (int *) vrna_alloc(sizeof(int)*(m + 5));+    }+  }++  if(alloc_vector & ALLOC_FML){+    vars->fML_local = (int **) vrna_alloc(sizeof(int *) * lin_size);+    for (i = (int)n; ( i > ((int)n - (int)m - 5)) && (i>=0); i--){+      vars->fML_local[i] = (int *) vrna_alloc(sizeof(int)*(m + 5));+    }+  }+}++PRIVATE void+mfe_matrices_free_window( vrna_mx_mfe_t *self,+                          unsigned int length,+                          unsigned int window_size){++  unsigned int  i;++  if(self->c_local)+    for (i=0; (i < window_size + 5) && (i <= length); i++){+      free(self->c_local[i]);+    }+  free(self->c_local);++  if(self->fML_local)+    for (i=0; (i < window_size + 5) && (i <= length); i++){+      free(self->fML_local[i]);+    }+  free(self->fML_local);++  if(self->ggg_local)+    for (i=0; (i < window_size + 5) && (i <= length); i++){+      free(self->ggg_local[i]);+    }+  free(self->ggg_local);++  free(self->f3_local);+}++PRIVATE void+mfe_matrices_alloc_2Dfold(vrna_mx_mfe_t *vars,+                          unsigned int m,+                          unsigned int alloc_vector){++  unsigned int  n, i, size, lin_size;++  n               = vars->length;+  size            = ((n + 1) * (m + 2)) / 2;+  lin_size        = n + 2;++  vars->E_F5      = NULL;+  vars->l_min_F5  = NULL;+  vars->l_max_F5  = NULL;+  vars->k_min_F5  = NULL;+  vars->k_max_F5  = NULL;+  vars->E_F5_rem  = NULL;++  vars->E_F3      = NULL;+  vars->l_min_F3  = NULL;+  vars->l_max_F3  = NULL;+  vars->k_min_F3  = NULL;+  vars->k_max_F3  = NULL;+  vars->E_F3_rem  = NULL;++  vars->E_C       = NULL;+  vars->l_min_C   = NULL;+  vars->l_max_C   = NULL;+  vars->k_min_C   = NULL;+  vars->k_max_C   = NULL;+  vars->E_C_rem   = NULL;++  vars->E_M       = NULL;+  vars->l_min_M   = NULL;+  vars->l_max_M   = NULL;+  vars->k_min_M   = NULL;+  vars->k_max_M   = NULL;+  vars->E_M_rem   = NULL;++  vars->E_M1      = NULL;+  vars->l_min_M1  = NULL;+  vars->l_max_M1  = NULL;+  vars->k_min_M1  = NULL;+  vars->k_max_M1  = NULL;+  vars->E_M1_rem  = NULL;++  vars->E_M2      = NULL;+  vars->l_min_M2  = NULL;+  vars->l_max_M2  = NULL;+  vars->k_min_M2  = NULL;+  vars->k_max_M2  = NULL;+  vars->E_M2_rem  = NULL;++  /* setting exterior loop energies for circular case to INF is always safe */+  vars->E_Fc      = NULL;+  vars->E_FcH     = NULL;+  vars->E_FcI     = NULL;+  vars->E_FcM     = NULL;+  vars->E_Fc_rem  = INF;+  vars->E_FcH_rem = INF;+  vars->E_FcI_rem = INF;+  vars->E_FcM_rem = INF;++  if(alloc_vector & ALLOC_F5){+    vars->E_F5      = (int ***) vrna_alloc(sizeof(int **) * lin_size);+    vars->l_min_F5  = (int **)  vrna_alloc(sizeof(int *)  * lin_size);+    vars->l_max_F5  = (int **)  vrna_alloc(sizeof(int *)  * lin_size);+    vars->k_min_F5  = (int *)   vrna_alloc(sizeof(int)    * lin_size);+    vars->k_max_F5  = (int *)   vrna_alloc(sizeof(int)    * lin_size);+    vars->E_F5_rem  = (int *)   vrna_alloc(sizeof(int)    * lin_size);+    for(i = 0; i <= n; i++)+      vars->E_F5_rem[i] = INF;+  }++  if(alloc_vector & ALLOC_F3){+    vars->E_F3      = (int ***) vrna_alloc(sizeof(int **)  * lin_size);+    vars->l_min_F3  = (int **)  vrna_alloc(sizeof(int *)   * lin_size);+    vars->l_max_F3  = (int **)  vrna_alloc(sizeof(int *)   * lin_size);+    vars->k_min_F3  = (int *)   vrna_alloc(sizeof(int)     * lin_size);+    vars->k_max_F3  = (int *)   vrna_alloc(sizeof(int)     * lin_size);+    vars->E_F3_rem  = (int *)   vrna_alloc(sizeof(int)    * lin_size);+    for(i = 0; i <= n; i++)+      vars->E_F3_rem[i] = INF;+  }++  if(alloc_vector & ALLOC_C){+    vars->E_C     = (int ***) vrna_alloc(sizeof(int **) * size);+    vars->l_min_C = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->l_max_C = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->k_min_C = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->k_max_C = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->E_C_rem = (int *)   vrna_alloc(sizeof(int)    * size);+    for(i = 0; i < size; i++)+      vars->E_C_rem[i] = INF;+  }++  if(alloc_vector & ALLOC_FML){+    vars->E_M     = (int ***) vrna_alloc(sizeof(int **) * size);+    vars->l_min_M = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->l_max_M = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->k_min_M = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->k_max_M = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->E_M_rem = (int *)   vrna_alloc(sizeof(int)    * size);+    for(i = 0; i < size; i++)+      vars->E_M_rem[i] = INF;+  }++  if(alloc_vector & ALLOC_UNIQ){+    vars->E_M1      = (int ***) vrna_alloc(sizeof(int **) * size);+    vars->l_min_M1  = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->l_max_M1  = (int **)  vrna_alloc(sizeof(int *)  * size);+    vars->k_min_M1  = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->k_max_M1  = (int *)   vrna_alloc(sizeof(int)    * size);+    vars->E_M1_rem  = (int *)   vrna_alloc(sizeof(int)    * size);+    for(i = 0; i < size; i++)+      vars->E_M1_rem[i] = INF;+  }++  if(alloc_vector & ALLOC_CIRC){+    vars->E_M2      = (int ***) vrna_alloc(sizeof(int **)  * lin_size);+    vars->l_min_M2  = (int **)  vrna_alloc(sizeof(int *)   * lin_size);+    vars->l_max_M2  = (int **)  vrna_alloc(sizeof(int *)   * lin_size);+    vars->k_min_M2  = (int *)   vrna_alloc(sizeof(int)     * lin_size);+    vars->k_max_M2  = (int *)   vrna_alloc(sizeof(int)     * lin_size);+    vars->E_M2_rem  = (int *)   vrna_alloc(sizeof(int)     * lin_size);+    for(i = 0; i <= n; i++)+      vars->E_M2_rem[i] = INF;+  }++#ifdef COUNT_STATES+  vars->N_C   = (unsigned long ***) vrna_alloc(sizeof(unsigned long **)  * size);+  vars->N_F5  = (unsigned long ***) vrna_alloc(sizeof(unsigned long **)  * lin_size);+  vars->N_M   = (unsigned long ***) vrna_alloc(sizeof(unsigned long **)  * size);+  vars->N_M1  = (unsigned long ***) vrna_alloc(sizeof(unsigned long **)  * size);+#endif+}++PRIVATE void+mfe_matrices_free_2Dfold( vrna_mx_mfe_t *self,+                          unsigned int length,+                          int *indx){++  unsigned int  i, j, ij;+  int           cnt1;++  /* This will be some fun... */+#ifdef COUNT_STATES+  if(self->N_F5 != NULL){+    for(i = 1; i <= length; i++){+      if(!self->N_F5[i]) continue;+      for(cnt1 = self->k_min_F5[i]; cnt1 <= vars->k_max_F5[i]; cnt1++)+        if(vars->l_min_F5[i][cnt1] < INF){+          vars->N_F5[i][cnt1] += vars->l_min_F5[i][cnt1]/2;+          free(vars->N_F5[i][cnt1]);+        }+      if(vars->k_min_F5[i] < INF){+        vars->N_F5[i] += vars->k_min_F5[i];+        free(vars->N_F5[i]);+      }+    }+    free(vars->N_F5);+  }+#endif++  if(self->E_F5 != NULL){+    for(i = 1; i <= length; i++){+      if(!self->E_F5[i]) continue;+      for(cnt1 = self->k_min_F5[i]; cnt1 <= self->k_max_F5[i]; cnt1++)+        if(self->l_min_F5[i][cnt1] < INF){+          self->E_F5[i][cnt1] += self->l_min_F5[i][cnt1]/2;+          free(self->E_F5[i][cnt1]);+        }+      if(self->k_min_F5[i] < INF){+        self->E_F5[i] += self->k_min_F5[i];+        free(self->E_F5[i]);+        self->l_min_F5[i] += self->k_min_F5[i];+        self->l_max_F5[i] += self->k_min_F5[i];+        free(self->l_min_F5[i]);+        free(self->l_max_F5[i]);+      }+    }+    free(self->E_F5);+    free(self->l_min_F5);+    free(self->l_max_F5);+    free(self->k_min_F5);+    free(self->k_max_F5);+  }++  if(self->E_F3 != NULL){+    for(i = 1; i <= length; i++){+      if(!self->E_F3[i]) continue;+      for(cnt1 = self->k_min_F3[i]; cnt1 <= self->k_max_F3[i]; cnt1++)+        if(self->l_min_F3[i][cnt1] < INF){+          self->E_F3[i][cnt1] += self->l_min_F3[i][cnt1]/2;+          free(self->E_F3[i][cnt1]);+        }+      if(self->k_min_F3[i] < INF){+        self->E_F3[i] += self->k_min_F3[i];+        free(self->E_F3[i]);+        self->l_min_F3[i] += self->k_min_F3[i];+        self->l_max_F3[i] += self->k_min_F3[i];+        free(self->l_min_F3[i]);+        free(self->l_max_F3[i]);+      }+    }+    free(self->E_F3);+    free(self->l_min_F3);+    free(self->l_max_F3);+    free(self->k_min_F3);+    free(self->k_max_F3);+  }++#ifdef COUNT_STATES+  if(self->N_C != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->N_C[ij]) continue;+        for(cnt1 = self->k_min_C[ij]; cnt1 <= self->k_max_C[ij]; cnt1++)+          if(self->l_min_C[ij][cnt1] < INF){+            self->N_C[ij][cnt1] += self->l_min_C[ij][cnt1]/2;+            free(self->N_C[ij][cnt1]);+          }+        if(self->k_min_C[ij] < INF){+          self->N_C[ij] += self->k_min_C[ij];+          free(self->N_C[ij]);+        }+      }+    }+    free(self->N_C);+  }+#endif++  if(self->E_C != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->E_C[ij]) continue;+        for(cnt1 = self->k_min_C[ij]; cnt1 <= self->k_max_C[ij]; cnt1++)+          if(self->l_min_C[ij][cnt1] < INF){+            self->E_C[ij][cnt1] += self->l_min_C[ij][cnt1]/2;+            free(self->E_C[ij][cnt1]);+          }+        if(self->k_min_C[ij] < INF){+          self->E_C[ij] += self->k_min_C[ij];+          free(self->E_C[ij]);+          self->l_min_C[ij] += self->k_min_C[ij];+          self->l_max_C[ij] += self->k_min_C[ij];+          free(self->l_min_C[ij]);+          free(self->l_max_C[ij]);+        }+      }+    }+    free(self->E_C);+    free(self->l_min_C);+    free(self->l_max_C);+    free(self->k_min_C);+    free(self->k_max_C);+  }++#ifdef COUNT_STATES+  if(self->N_M != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->N_M[ij]) continue;+        for(cnt1 = self->k_min_M[ij]; cnt1 <= self->k_max_M[ij]; cnt1++)+          if(self->l_min_M[ij][cnt1] < INF){+            self->N_M[ij][cnt1] += self->l_min_M[ij][cnt1]/2;+            free(self->N_M[ij][cnt1]);+          }+        if(self->k_min_M[ij] < INF){+          self->N_M[ij] += self->k_min_M[ij];+          free(self->N_M[ij]);+        }+      }+    }+    free(self->N_M);+  }+#endif++  if(self->E_M != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->E_M[ij]) continue;+        for(cnt1 = self->k_min_M[ij]; cnt1 <= self->k_max_M[ij]; cnt1++)+          if(self->l_min_M[ij][cnt1] < INF){+            self->E_M[ij][cnt1] += self->l_min_M[ij][cnt1]/2;+            free(self->E_M[ij][cnt1]);+          }+        if(self->k_min_M[ij] < INF){+          self->E_M[ij] += self->k_min_M[ij];+          free(self->E_M[ij]);+          self->l_min_M[ij] += self->k_min_M[ij];+          self->l_max_M[ij] += self->k_min_M[ij];+          free(self->l_min_M[ij]);+          free(self->l_max_M[ij]);+        }+      }+    }+    free(self->E_M);+    free(self->l_min_M);+    free(self->l_max_M);+    free(self->k_min_M);+    free(self->k_max_M);+  }++#ifdef COUNT_STATES+  if(self->N_M1 != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->N_M1[ij]) continue;+        for(cnt1 = self->k_min_M1[ij]; cnt1 <= self->k_max_M1[ij]; cnt1++)+          if(self->l_min_M1[ij][cnt1] < INF){+            self->N_M1[ij][cnt1] += self->l_min_M1[ij][cnt1]/2;+            free(self->N_M1[ij][cnt1]);+          }+        if(self->k_min_M1[ij] < INF){+          self->N_M1[ij] += self->k_min_M1[ij];+          free(self->N_M1[ij]);+        }+      }+    }+    free(self->N_M1);+  }+#endif++  if(self->E_M1 != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->E_M1[ij]) continue;+        for(cnt1 = self->k_min_M1[ij]; cnt1 <= self->k_max_M1[ij]; cnt1++)+          if(self->l_min_M1[ij][cnt1] < INF){+            self->E_M1[ij][cnt1] += self->l_min_M1[ij][cnt1]/2;+            free(self->E_M1[ij][cnt1]);+          }+        if(self->k_min_M1[ij] < INF){+          self->E_M1[ij] += self->k_min_M1[ij];+          free(self->E_M1[ij]);+          self->l_min_M1[ij] += self->k_min_M1[ij];+          self->l_max_M1[ij] += self->k_min_M1[ij];+          free(self->l_min_M1[ij]);+          free(self->l_max_M1[ij]);+        }+      }+    }+    free(self->E_M1);+    free(self->l_min_M1);+    free(self->l_max_M1);+    free(self->k_min_M1);+    free(self->k_max_M1);+  }++  if(self->E_M2 != NULL){+    for(i = 1; i < length-TURN-1; i++){+      if(!self->E_M2[i]) continue;+      for(cnt1 = self->k_min_M2[i]; cnt1 <= self->k_max_M2[i]; cnt1++)+        if(self->l_min_M2[i][cnt1] < INF){+          self->E_M2[i][cnt1] += self->l_min_M2[i][cnt1]/2;+          free(self->E_M2[i][cnt1]);+        }+      if(self->k_min_M2[i] < INF){+        self->E_M2[i] += self->k_min_M2[i];+        free(self->E_M2[i]);+        self->l_min_M2[i] += self->k_min_M2[i];+        self->l_max_M2[i] += self->k_min_M2[i];+        free(self->l_min_M2[i]);+        free(self->l_max_M2[i]);+      }+    }+    free(self->E_M2);+    free(self->l_min_M2);+    free(self->l_max_M2);+    free(self->k_min_M2);+    free(self->k_max_M2);+  }++  if(self->E_Fc != NULL){+    for(cnt1 = self->k_min_Fc; cnt1 <= self->k_max_Fc; cnt1++)+      if(self->l_min_Fc[cnt1] < INF){+        self->E_Fc[cnt1] += self->l_min_Fc[cnt1]/2;+        free(self->E_Fc[cnt1]);+      }+    if(self->k_min_Fc < INF){+      self->E_Fc += self->k_min_Fc;+      free(self->E_Fc);+      self->l_min_Fc += self->k_min_Fc;+      self->l_max_Fc += self->k_min_Fc;+      free(self->l_min_Fc);+      free(self->l_max_Fc);+    }+  }++  if(self->E_FcI != NULL){+    for(cnt1 = self->k_min_FcI; cnt1 <= self->k_max_FcI; cnt1++)+      if(self->l_min_FcI[cnt1] < INF){+        self->E_FcI[cnt1] += self->l_min_FcI[cnt1]/2;+        free(self->E_FcI[cnt1]);+      }+    if(self->k_min_FcI < INF){+      self->E_FcI += self->k_min_FcI;+      free(self->E_FcI);+      self->l_min_FcI += self->k_min_FcI;+      self->l_max_FcI += self->k_min_FcI;+      free(self->l_min_FcI);+      free(self->l_max_FcI);+    }+  }++  if(self->E_FcH != NULL){+    for(cnt1 = self->k_min_FcH; cnt1 <= self->k_max_FcH; cnt1++)+      if(self->l_min_FcH[cnt1] < INF){+        self->E_FcH[cnt1] += self->l_min_FcH[cnt1]/2;+        free(self->E_FcH[cnt1]);+      }+    if(self->k_min_FcH < INF){+      self->E_FcH += self->k_min_FcH;+      free(self->E_FcH);+      self->l_min_FcH += self->k_min_FcH;+      self->l_max_FcH += self->k_min_FcH;+      free(self->l_min_FcH);+      free(self->l_max_FcH);+    }+  }++  if(self->E_FcM != NULL){+    for(cnt1 = self->k_min_FcM; cnt1 <= self->k_max_FcM; cnt1++)+      if(self->l_min_FcM[cnt1] < INF){+        self->E_FcM[cnt1] += self->l_min_FcM[cnt1]/2;+        free(self->E_FcM[cnt1]);+      }+    if(self->k_min_FcM < INF){+      self->E_FcM += self->k_min_FcM;+      free(self->E_FcM);+      self->l_min_FcM += self->k_min_FcM;+      self->l_max_FcM += self->k_min_FcM;+      free(self->l_min_FcM);+      free(self->l_max_FcM);+    }+  }++  free(self->E_F5_rem);+  free(self->E_F3_rem);+  free(self->E_C_rem);+  free(self->E_M_rem);+  free(self->E_M1_rem);+  free(self->E_M2_rem);+}++PRIVATE void+pf_matrices_alloc_default(vrna_mx_pf_t *vars,+                          unsigned int m,+                          unsigned int alloc_vector){++  unsigned int  n, size, lin_size;++  n             = vars->length;+  size          = ((n + 1) * (n + 2)) / 2;+  lin_size      = n + 2;++  vars->q       = NULL;+  vars->qb      = NULL;+  vars->qm      = NULL;+  vars->qm1     = NULL;+  vars->qm2     = NULL;+  vars->probs   = NULL;+  vars->q1k     = NULL;+  vars->qln     = NULL;++  if(alloc_vector & ALLOC_F)+    vars->q     = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * size);++  if(alloc_vector & ALLOC_C)+    vars->qb    = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * size);++  if(alloc_vector & ALLOC_FML)+    vars->qm    = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * size);++  if(alloc_vector & ALLOC_UNIQ)+    vars->qm1   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * size);++  if(alloc_vector & ALLOC_CIRC)+    vars->qm2   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * lin_size);++  if(alloc_vector & ALLOC_PROBS)+    vars->probs = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * size);++  if(alloc_vector & ALLOC_AUX){+    vars->q1k   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * lin_size);+    vars->qln   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * lin_size);+  }+}++PRIVATE void+pf_matrices_free_default( vrna_mx_pf_t *self){++  free(self->q);+  free(self->qb);+  free(self->qm);+  free(self->qm1);+  free(self->qm2);+  free(self->probs);+  free(self->G);+  free(self->q1k);+  free(self->qln);+}++PRIVATE void+pf_matrices_alloc_2Dfold( vrna_mx_pf_t *vars,+                          unsigned int m,+                          unsigned int alloc_vector){++  unsigned int  n, size, lin_size;++  n             = vars->length;+  size          = ((n + 1) * (n + 2)) / 2;+  lin_size      = n + 2;++  vars->Q           = NULL;+  vars->l_min_Q     = NULL;+  vars->l_max_Q     = NULL;+  vars->k_min_Q     = NULL;+  vars->k_max_Q     = NULL;+  vars->Q_rem       = NULL;++  vars->Q_B         = NULL;+  vars->l_min_Q_B   = NULL;+  vars->l_max_Q_B   = NULL;+  vars->k_min_Q_B   = NULL;+  vars->k_max_Q_B   = NULL;+  vars->Q_B_rem     = NULL;++  vars->Q_M         = NULL;+  vars->l_min_Q_M   = NULL;+  vars->l_max_Q_M   = NULL;+  vars->k_min_Q_M   = NULL;+  vars->k_max_Q_M   = NULL;+  vars->Q_M_rem     = NULL;++  vars->Q_M1        = NULL;+  vars->l_min_Q_M1  = NULL;+  vars->l_max_Q_M1  = NULL;+  vars->k_min_Q_M1  = NULL;+  vars->k_max_Q_M1  = NULL;+  vars->Q_M1_rem    = NULL;++  vars->Q_M2        = NULL;+  vars->l_min_Q_M2  = NULL;+  vars->l_max_Q_M2  = NULL;+  vars->k_min_Q_M2  = NULL;+  vars->k_max_Q_M2  = NULL;+  vars->Q_M2_rem    = NULL;++  vars->Q_c         = NULL;+  vars->Q_cH        = NULL;+  vars->Q_cI        = NULL;+  vars->Q_cM        = NULL;+  vars->Q_c_rem     = 0.;+  vars->Q_cH_rem    = 0.;+  vars->Q_cI_rem    = 0.;+  vars->Q_cM_rem    = 0.;++  if(alloc_vector & ALLOC_F){+    vars->Q       = (FLT_OR_DBL ***)vrna_alloc(sizeof(FLT_OR_DBL **)  * size);+    vars->l_min_Q = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->l_max_Q = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->k_min_Q = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->k_max_Q = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->Q_rem   = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)     * size);+  }++  if(alloc_vector & ALLOC_C){+    vars->Q_B       = (FLT_OR_DBL ***)vrna_alloc(sizeof(FLT_OR_DBL **)  * size);+    vars->l_min_Q_B = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->l_max_Q_B = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->k_min_Q_B = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->k_max_Q_B = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->Q_B_rem   = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)     * size);+  }++  if(alloc_vector & ALLOC_FML){+    vars->Q_M       = (FLT_OR_DBL ***)vrna_alloc(sizeof(FLT_OR_DBL **)  * size);+    vars->l_min_Q_M = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->l_max_Q_M = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->k_min_Q_M = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->k_max_Q_M = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->Q_M_rem   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)      * size);+  }++  if(alloc_vector & ALLOC_UNIQ){+    vars->Q_M1        = (FLT_OR_DBL ***)vrna_alloc(sizeof(FLT_OR_DBL **)  * size);+    vars->l_min_Q_M1  = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->l_max_Q_M1  = (int **)        vrna_alloc(sizeof(int *)          * size);+    vars->k_min_Q_M1  = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->k_max_Q_M1  = (int *)         vrna_alloc(sizeof(int)            * size);+    vars->Q_M1_rem    = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)     * size);+  }++  if(alloc_vector & ALLOC_CIRC){+    vars->Q_M2        = (FLT_OR_DBL ***)vrna_alloc(sizeof(FLT_OR_DBL **)  * lin_size);+    vars->l_min_Q_M2  = (int **)        vrna_alloc(sizeof(int *)          * lin_size);+    vars->l_max_Q_M2  = (int **)        vrna_alloc(sizeof(int *)          * lin_size);+    vars->k_min_Q_M2  = (int *)         vrna_alloc(sizeof(int)            * lin_size);+    vars->k_max_Q_M2  = (int *)         vrna_alloc(sizeof(int)            * lin_size);+    vars->Q_M2_rem    = (FLT_OR_DBL *)  vrna_alloc(sizeof(FLT_OR_DBL)     * lin_size);+  }+}++PRIVATE void+pf_matrices_free_2Dfold(vrna_mx_pf_t *self,+                        unsigned int length,+                        int *indx,+                        int *jindx){++  unsigned int  i, j, ij;+  int           cnt1;++  /* This will be some fun... */+  if(self->Q != NULL){+    for(i = 1; i <= length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->Q[ij]) continue;+        for(cnt1 = self->k_min_Q[ij]; cnt1 <= self->k_max_Q[ij]; cnt1++)+          if(self->l_min_Q[ij][cnt1] < INF){+            self->Q[ij][cnt1] += self->l_min_Q[ij][cnt1]/2;+            free(self->Q[ij][cnt1]);+          }+        if(self->k_min_Q[ij] < INF){+          self->Q[ij] += self->k_min_Q[ij];+          free(self->Q[ij]);+          self->l_min_Q[ij] += self->k_min_Q[ij];+          self->l_max_Q[ij] += self->k_min_Q[ij];+          free(self->l_min_Q[ij]);+          free(self->l_max_Q[ij]);+        }+      }+    }+  }+  free(self->Q);+  free(self->l_min_Q);+  free(self->l_max_Q);+  free(self->k_min_Q);+  free(self->k_max_Q);++  if(self->Q_B != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->Q_B[ij]) continue;+        for(cnt1 = self->k_min_Q_B[ij]; cnt1 <= self->k_max_Q_B[ij]; cnt1++)+          if(self->l_min_Q_B[ij][cnt1] < INF){+            self->Q_B[ij][cnt1] += self->l_min_Q_B[ij][cnt1]/2;+            free(self->Q_B[ij][cnt1]);+          }+        if(self->k_min_Q_B[ij] < INF){+          self->Q_B[ij] += self->k_min_Q_B[ij];+          free(self->Q_B[ij]);+          self->l_min_Q_B[ij] += self->k_min_Q_B[ij];+          self->l_max_Q_B[ij] += self->k_min_Q_B[ij];+          free(self->l_min_Q_B[ij]);+          free(self->l_max_Q_B[ij]);+        }+      }+    }+  }+  free(self->Q_B);+  free(self->l_min_Q_B);+  free(self->l_max_Q_B);+  free(self->k_min_Q_B);+  free(self->k_max_Q_B);++  if(self->Q_M != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = indx[i] - j;+        if(!self->Q_M[ij]) continue;+        for(cnt1 = self->k_min_Q_M[ij]; cnt1 <= self->k_max_Q_M[ij]; cnt1++)+          if(self->l_min_Q_M[ij][cnt1] < INF){+            self->Q_M[ij][cnt1] += self->l_min_Q_M[ij][cnt1]/2;+            free(self->Q_M[ij][cnt1]);+          }+        if(self->k_min_Q_M[ij] < INF){+          self->Q_M[ij] += self->k_min_Q_M[ij];+          free(self->Q_M[ij]);+          self->l_min_Q_M[ij] += self->k_min_Q_M[ij];+          self->l_max_Q_M[ij] += self->k_min_Q_M[ij];+          free(self->l_min_Q_M[ij]);+          free(self->l_max_Q_M[ij]);+        }+      }+    }+  }+  free(self->Q_M);+  free(self->l_min_Q_M);+  free(self->l_max_Q_M);+  free(self->k_min_Q_M);+  free(self->k_max_Q_M);++  if(self->Q_M1 != NULL){+    for(i = 1; i < length; i++){+      for(j = i; j <= length; j++){+        ij = jindx[j] + i;+        if(!self->Q_M1[ij]) continue;+        for(cnt1 = self->k_min_Q_M1[ij]; cnt1 <= self->k_max_Q_M1[ij]; cnt1++)+          if(self->l_min_Q_M1[ij][cnt1] < INF){+            self->Q_M1[ij][cnt1] += self->l_min_Q_M1[ij][cnt1]/2;+            free(self->Q_M1[ij][cnt1]);+          }+        if(self->k_min_Q_M1[ij] < INF){+          self->Q_M1[ij] += self->k_min_Q_M1[ij];+          free(self->Q_M1[ij]);+          self->l_min_Q_M1[ij] += self->k_min_Q_M1[ij];+          self->l_max_Q_M1[ij] += self->k_min_Q_M1[ij];+          free(self->l_min_Q_M1[ij]);+          free(self->l_max_Q_M1[ij]);+        }+      }+    }+  }+  free(self->Q_M1);+  free(self->l_min_Q_M1);+  free(self->l_max_Q_M1);+  free(self->k_min_Q_M1);+  free(self->k_max_Q_M1);++  if(self->Q_M2 != NULL){+    for(i = 1; i < length-TURN-1; i++){+      if(!self->Q_M2[i]) continue;+      for(cnt1 = self->k_min_Q_M2[i]; cnt1 <= self->k_max_Q_M2[i]; cnt1++)+        if(self->l_min_Q_M2[i][cnt1] < INF){+          self->Q_M2[i][cnt1] += self->l_min_Q_M2[i][cnt1]/2;+          free(self->Q_M2[i][cnt1]);+        }+      if(self->k_min_Q_M2[i] < INF){+        self->Q_M2[i] += self->k_min_Q_M2[i];+        free(self->Q_M2[i]);+        self->l_min_Q_M2[i] += self->k_min_Q_M2[i];+        self->l_max_Q_M2[i] += self->k_min_Q_M2[i];+        free(self->l_min_Q_M2[i]);+        free(self->l_max_Q_M2[i]);+      }+    }+  }+  free(self->Q_M2);+  free(self->l_min_Q_M2);+  free(self->l_max_Q_M2);+  free(self->k_min_Q_M2);+  free(self->k_max_Q_M2);++  if(self->Q_c != NULL){+    for(cnt1 = self->k_min_Q_c; cnt1 <= self->k_max_Q_c; cnt1++)+      if(self->l_min_Q_c[cnt1] < INF){+        self->Q_c[cnt1] += self->l_min_Q_c[cnt1]/2;+        free(self->Q_c[cnt1]);+      }+    if(self->k_min_Q_c < INF){+      self->Q_c += self->k_min_Q_c;+      free(self->Q_c);+      self->l_min_Q_c += self->k_min_Q_c;+      self->l_max_Q_c += self->k_min_Q_c;+      free(self->l_min_Q_c);+      free(self->l_max_Q_c);+    }+  }++  if(self->Q_cI != NULL){+    for(cnt1 = self->k_min_Q_cI; cnt1 <= self->k_max_Q_cI; cnt1++)+      if(self->l_min_Q_cI[cnt1] < INF){+        self->Q_cI[cnt1] += self->l_min_Q_cI[cnt1]/2;+        free(self->Q_cI[cnt1]);+      }+    if(self->k_min_Q_cI < INF){+      self->Q_cI += self->k_min_Q_cI;+      free(self->Q_cI);+      self->l_min_Q_cI += self->k_min_Q_cI;+      self->l_max_Q_cI += self->k_min_Q_cI;+      free(self->l_min_Q_cI);+      free(self->l_max_Q_cI);+    }+  }++  if(self->Q_cH != NULL){+    for(cnt1 = self->k_min_Q_cH; cnt1 <= self->k_max_Q_cH; cnt1++)+      if(self->l_min_Q_cH[cnt1] < INF){+        self->Q_cH[cnt1] += self->l_min_Q_cH[cnt1]/2;+        free(self->Q_cH[cnt1]);+      }+    if(self->k_min_Q_cH < INF){+      self->Q_cH += self->k_min_Q_cH;+      free(self->Q_cH);+      self->l_min_Q_cH += self->k_min_Q_cH;+      self->l_max_Q_cH += self->k_min_Q_cH;+      free(self->l_min_Q_cH);+      free(self->l_max_Q_cH);+    }+  }++  if(self->Q_cM != NULL){+    for(cnt1 = self->k_min_Q_cM; cnt1 <= self->k_max_Q_cM; cnt1++)+      if(self->l_min_Q_cM[cnt1] < INF){+        self->Q_cM[cnt1] += self->l_min_Q_cM[cnt1]/2;+        free(self->Q_cM[cnt1]);+      }+    if(self->k_min_Q_cM < INF){+      self->Q_cM += self->k_min_Q_cM;+      free(self->Q_cM);+      self->l_min_Q_cM += self->k_min_Q_cM;+      self->l_max_Q_cM += self->k_min_Q_cM;+      free(self->l_min_Q_cM);+      free(self->l_max_Q_cM);+    }+  }++  free(self->Q_rem);+  free(self->Q_B_rem);+  free(self->Q_M_rem);+  free(self->Q_M1_rem);+  free(self->Q_M2_rem);+}+
+ C/ViennaRNA/dp_matrices.h view
@@ -0,0 +1,407 @@+#ifndef VIENNA_RNA_PACKAGE_DP_MATRICES_H+#define VIENNA_RNA_PACKAGE_DP_MATRICES_H++/**+ *  @file     dp_matrices.h+ *  @ingroup  data_structures+ *  @brief    Functions to deal with standard dynamic programming (DP) matrices+ */++/**+ *  @addtogroup dp_matrices   The Dynamic Programming Matrices+ *  @brief  This module provides interfaces that deal with creation and destruction of+ *          dynamic programming matrices used within the RNAlib.+ *+ *  @{+ *  @ingroup  dp_matrices+ */++/** @brief Typename for the Minimum Free Energy (MFE) DP matrices data structure #vrna_mx_mfe_s */+typedef struct  vrna_mx_mfe_s vrna_mx_mfe_t;+/** @brief Typename for the Partition Function (PF) DP matrices data structure #vrna_mx_pf_s */+typedef struct  vrna_mx_pf_s  vrna_mx_pf_t;++#include <ViennaRNA/data_structures.h>++/**+ *  @brief  An enumerator that is used to specify the type of a polymorphic Dynamic Programming (DP)+ *  matrix data structure+ *  @see #vrna_mx_mfe_t, #vrna_mx_pf_t+ */+typedef enum {+  VRNA_MX_DEFAULT,  /**<  @brief  Default DP matrices */+  VRNA_MX_WINDOW,   /**<  @brief  DP matrices suitable for local structure prediction using+                          window approach.+                          @see    vrna_mfe_window(), vrna_mfe_window_zscore(), pfl_fold()+                    */+  VRNA_MX_2DFOLD    /**<  @brief  DP matrices suitable for distance class partitioned structure prediction+                          @see  vrna_mfe_TwoD(), vrna_pf_TwoD()+                    */+} vrna_mx_type_e;++/**+ *  @brief  Minimum Free Energy (MFE) Dynamic Programming (DP) matrices data structure required within the #vrna_fold_compound_t+ */+struct vrna_mx_mfe_s {+  /** @name Common fields for MFE matrices+      @{+   */+  vrna_mx_type_e     type;+  unsigned int  length;    /**<  @brief  Length of the sequence, therefore an indicator of the size of the DP matrices */+  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+  union {+    struct {+#endif+      /** @name Default DP matrices+          @note These data fields are available if+                @code vrna_mx_mfe_t.type == VRNA_MX_DEFAULT @endcode+        @{+       */+      int     *c;   /**<  @brief  Energy array, given that i-j pair */+      int     *f5;  /**<  @brief  Energy of 5' end */+      int     *f3;  /**<  @brief  Energy of 3' end */+      int     *fc;  /**<  @brief  Energy from i to cutpoint (and vice versa if i>cut) */+      int     *fML; /**<  @brief  Multi-loop auxiliary energy array */+      int     *fM1; /**<  @brief  Second ML array, only for unique multibrnach loop decomposition */+      int     *fM2; /**<  @brief  Energy for a multibranch loop region with exactly two stems, extending to 3' end */+      int     *ggg; /**<  @brief  Energies of g-quadruplexes */+      int     Fc;   /**<  @brief  Minimum Free Energy of entire circular RNA */+      int     FcH;+      int     FcI;+      int     FcM;+      /**+        @}+       */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+    struct {+#endif+      /** @name Local Folding DP matrices using window approach+          @note These data fields are available if+                @code vrna_mx_mfe_t.type == VRNA_MX_WINDOW @endcode+        @{+       */+      int     **c_local;    /**<  @brief  Energy array, given that i-j pair */+      int     *f3_local;    /**<  @brief  Energy of 5' end */+      int     **fML_local;  /**<  @brief  Multi-loop auxiliary energy array */+      int     **ggg_local;  /**<  @brief  Energies of g-quadruplexes */+      /**+        @}+       */+#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+    struct {+#endif++      /** @name Distance Class DP matrices+          @note These data fields are available if+                @code vrna_mx_mfe_t.type == VRNA_MX_2DFOLD @endcode+        @{+      */+      int             ***E_F5;+      int             **l_min_F5;+      int             **l_max_F5;+      int             *k_min_F5;+      int             *k_max_F5;++      int             ***E_F3;+      int             **l_min_F3;+      int             **l_max_F3;+      int             *k_min_F3;+      int             *k_max_F3;++      int             ***E_C;+      int             **l_min_C;+      int             **l_max_C;+      int             *k_min_C;+      int             *k_max_C;++      int             ***E_M;+      int             **l_min_M;+      int             **l_max_M;+      int             *k_min_M;+      int             *k_max_M;++      int             ***E_M1;+      int             **l_min_M1;+      int             **l_max_M1;+      int             *k_min_M1;+      int             *k_max_M1;++      int             ***E_M2;+      int             **l_min_M2;+      int             **l_max_M2;+      int             *k_min_M2;+      int             *k_max_M2;++      int             **E_Fc;+      int             *l_min_Fc;+      int             *l_max_Fc;+      int             k_min_Fc;+      int             k_max_Fc;++      int             **E_FcH;+      int             *l_min_FcH;+      int             *l_max_FcH;+      int             k_min_FcH;+      int             k_max_FcH;++      int             **E_FcI;+      int             *l_min_FcI;+      int             *l_max_FcI;+      int             k_min_FcI;+      int             k_max_FcI;++      int             **E_FcM;+      int             *l_min_FcM;+      int             *l_max_FcM;+      int             k_min_FcM;+      int             k_max_FcM;++      /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */+      int             *E_F5_rem;+      int             *E_F3_rem;+      int             *E_C_rem;+      int             *E_M_rem;+      int             *E_M1_rem;+      int             *E_M2_rem;++      int             E_Fc_rem;+      int             E_FcH_rem;+      int             E_FcI_rem;+      int             E_FcM_rem;++#ifdef COUNT_STATES+      unsigned long   ***N_F5;+      unsigned long   ***N_C;+      unsigned long   ***N_M;+      unsigned long   ***N_M1;+#endif++      /**+        @}+       */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+  };+#endif+};++/**+ *  @brief  Partition function (PF) Dynamic Programming (DP) matrices data structure required within the #vrna_fold_compound_t+ */+struct vrna_mx_pf_s {+  /** @name Common fields for DP matrices+      @{+   */+  vrna_mx_type_e  type;+  unsigned int    length;+  FLT_OR_DBL      *scale;+  FLT_OR_DBL      *expMLbase;+++  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+  union {+    struct {+#endif++  /** @name Default PF matrices+      @note These data fields are available if+            @code vrna_mx_pf_t.type == VRNA_MX_DEFAULT @endcode+      @{+   */+      FLT_OR_DBL  *q;+      FLT_OR_DBL  *qb;+      FLT_OR_DBL  *qm;+      FLT_OR_DBL  *qm1;+      FLT_OR_DBL  *probs;+      FLT_OR_DBL  *q1k;+      FLT_OR_DBL  *qln;+      FLT_OR_DBL  *G;++      FLT_OR_DBL  qo;+      FLT_OR_DBL  *qm2;+      FLT_OR_DBL  qho;+      FLT_OR_DBL  qio;+      FLT_OR_DBL  qmo;++  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+    struct {+#endif++  /** @name Distance Class DP matrices+      @note These data fields are available if+            @code vrna_mx_pf_t.type == VRNA_MX_2DFOLD @endcode+      @{+   */+      FLT_OR_DBL      ***Q;+      int             **l_min_Q;+      int             **l_max_Q;+      int             *k_min_Q;+      int             *k_max_Q;+++      FLT_OR_DBL      ***Q_B;+      int             **l_min_Q_B;+      int             **l_max_Q_B;+      int             *k_min_Q_B;+      int             *k_max_Q_B;++      FLT_OR_DBL      ***Q_M;+      int             **l_min_Q_M;+      int             **l_max_Q_M;+      int             *k_min_Q_M;+      int             *k_max_Q_M;++      FLT_OR_DBL      ***Q_M1;+      int             **l_min_Q_M1;+      int             **l_max_Q_M1;+      int             *k_min_Q_M1;+      int             *k_max_Q_M1;++      FLT_OR_DBL      ***Q_M2;+      int             **l_min_Q_M2;+      int             **l_max_Q_M2;+      int             *k_min_Q_M2;+      int             *k_max_Q_M2;++      FLT_OR_DBL      **Q_c;+      int             *l_min_Q_c;+      int             *l_max_Q_c;+      int             k_min_Q_c;+      int             k_max_Q_c;++      FLT_OR_DBL      **Q_cH;+      int             *l_min_Q_cH;+      int             *l_max_Q_cH;+      int             k_min_Q_cH;+      int             k_max_Q_cH;++      FLT_OR_DBL      **Q_cI;+      int             *l_min_Q_cI;+      int             *l_max_Q_cI;+      int             k_min_Q_cI;+      int             k_max_Q_cI;++      FLT_OR_DBL      **Q_cM;+      int             *l_min_Q_cM;+      int             *l_max_Q_cM;+      int             k_min_Q_cM;+      int             k_max_Q_cM;++      /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */+      FLT_OR_DBL      *Q_rem;+      FLT_OR_DBL      *Q_B_rem;+      FLT_OR_DBL      *Q_M_rem;+      FLT_OR_DBL      *Q_M1_rem;+      FLT_OR_DBL      *Q_M2_rem;++      FLT_OR_DBL      Q_c_rem;+      FLT_OR_DBL      Q_cH_rem;+      FLT_OR_DBL      Q_cI_rem;+      FLT_OR_DBL      Q_cM_rem;+  /**+      @}+   */++#ifndef VRNA_DISABLE_C11_FEATURES+    /* C11 support for unnamed unions/structs */+    };+  };+#endif+};++/**+ *  @brief  Add Dynamic Programming (DP) matrices (allocate memory)+ *+ *  This function adds DP matrices of a specific type to the provided+ *  #vrna_fold_compound_t, such that successive DP recursion can be applied.+ *  The function caller has to specify which type of DP matrix is requested,+ *  see #vrna_mx_type_e, and what kind of recursive algorithm will be applied+ *  later on, using the parameters type, and options, respectively. For the+ *  latter, Minimum free energy (MFE), and Partition function (PF)+ *  computations are distinguished. A third option that may be passed+ *  is #VRNA_OPTION_HYBRID, indicating that auxiliary DP arrays are+ *  required for RNA-RNA interaction prediction.+ *+ *  @note Usually, there is no need to call this function, since+ *  the constructors of #vrna_fold_compound_t are handling all the DP+ *  matrix memory allocation.+ *+ *  @see vrna_mx_mfe_add(), vrna_mx_pf_add(), vrna_fold_compound(),+ *  vrna_fold_compound_comparative(), vrna_fold_compound_free(),+ *  vrna_mx_pf_free(), vrna_mx_mfe_free(), #vrna_mx_type_e,+ *  #VRNA_OPTION_MFE, #VRNA_OPTION_PF, #VRNA_OPTION_HYBRID, #VRNA_OPTION_EVAL_ONLY+ *+ *  @param  vc      The #vrna_fold_compound_t that holds pointers to the DP matrices+ *  @param  type    The type of DP matrices requested+ *  @param  options Option flags that specify the kind of DP matrices, such+ *                  as MFE or PF arrays, and auxiliary requirements+ *  @returns        1 if DP matrices were properly allocated and attached,+ *                  0 otherwise+ */+int+vrna_mx_add(vrna_fold_compound_t *vc,+            vrna_mx_type_e type,+            unsigned int options);++int+vrna_mx_mfe_add(vrna_fold_compound_t *vc,+                vrna_mx_type_e mx_type,+                unsigned int options);++int+vrna_mx_pf_add( vrna_fold_compound_t *vc,+                vrna_mx_type_e mx_type,+                unsigned int options);++int+vrna_mx_prepare(vrna_fold_compound_t *vc,+                unsigned int options);++/**+ *  @brief  Free memory occupied by the Minimum Free Energy (MFE) Dynamic Programming (DP) matrices+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_fold_compound_free(), vrna_mx_pf_free()+ *+ *  @param  vc  The #vrna_fold_compound_t storing the MFE DP matrices that are to be erased from memory+ */+void+vrna_mx_mfe_free(vrna_fold_compound_t *vc);++/**+ *  @brief  Free memory occupied by the Partition Function (PF) Dynamic Programming (DP) matrices+ *+ *  @see vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_fold_compound_free(), vrna_mx_mfe_free()+ *+ *  @param  vc  The #vrna_fold_compound_t storing the PF DP matrices that are to be erased from memory+ */+void+vrna_mx_pf_free(vrna_fold_compound_t *vc);++/**+ *  @}+ */++#endif
+ C/ViennaRNA/duplex.c view
@@ -0,0 +1,564 @@+/*+           compute the duplex structure of two RNA strands,+                allowing only inter-strand base pairs.+         see cofold() for computing hybrid structures without+                             restriction.++                             Ivo Hofacker+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/alifold.h"+#include "ViennaRNA/subopt.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/duplex.h"++#ifdef _OPENMP+#include <omp.h>+#endif++#define STACK_BULGE1  1     /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1     /* new asymetry penalty */+#define MAXSECTORS    500   /* dimension for a backtrack array */+#define LOCALITY      0.    /* locality parameter for base-pairs */+#define UNIT 100+#define MINPSCORE -2 * UNIT+#define NONE -10000         /* score for forbidden pairs */++++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE vrna_param_t  *P  = NULL;+PRIVATE int     **c = NULL;                  /* energy array, given that i-j pair */+PRIVATE short   *S1 = NULL, *SS1 = NULL, *S2 = NULL, *SS2 = NULL;+PRIVATE int     n1,n2;                /* sequence lengths */++#ifdef _OPENMP++/* NOTE: all variables are assumed to be uninitialized if they are declared as threadprivate+*/+#pragma omp threadprivate(P, c, S1, SS1, S2, SS2, n1, n2)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE duplexT duplexfold_cu(const char *s1, const char *s2, int clean_up);+PRIVATE duplexT aliduplexfold_cu(const char *s1[], const char *s2[], int clean_up);+PRIVATE char    *backtrack(int i, int j);+PRIVATE char    *alibacktrack(int i, int j, const short **S1, const short **S2);+PRIVATE int     compare(const void *sub1, const void *sub2);+PRIVATE int     covscore(const int *types, int n_seq);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC duplexT duplexfold(const char *s1, const char *s2){+  return duplexfold_cu(s1, s2, 1);+}++PRIVATE duplexT duplexfold_cu(const char *s1, const char *s2, int clean_up){+  int i, j, Emin=INF, i_min=0, j_min=0;+  char *struc;+  duplexT mfe;+  vrna_md_t md;++  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=1; i<=n1; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));++  S1  = encode_sequence(s1, 0);+  S2  = encode_sequence(s2, 0);+  SS1 = encode_sequence(s1, 1);+  SS2 = encode_sequence(s2, 1);++  for (i=1; i<=n1; i++) {+    for (j=n2; j>0; j--) {+      int type, type2, E, k,l;+      type = pair[S1[i]][S2[j]];+      c[i][j] = type ? P->DuplexInit : INF;+      if (!type) continue;+      c[i][j] += E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, P);+      for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+        for (l=j+1; l<=n2; l++) {+          if (i-k+l-j-2>MAXLOOP) break;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          E = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                            SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1], P);+          c[i][j] = MIN2(c[i][j], c[k][l]+E);+        }+      }+      E = c[i][j];+      E += E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      }+    }+  }++  struc = backtrack(i_min, j_min);+  if (i_min<n1) i_min++;+  if (j_min>1 ) j_min--;++  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (float) Emin/100.;+  mfe.structure = struc;+  if(clean_up) {+    for (i=1; i<=n1; i++) free(c[i]);+    free(c);+    free(S1);+    free(S2);+    free(SS1);+    free(SS2);+  }+  return mfe;+}++PUBLIC duplexT *duplex_subopt(const char *s1, const char *s2, int delta, int w) {+  int i,j, n1, n2, thresh, E, n_subopt=0, n_max;+  char *struc;+  duplexT mfe;+  duplexT *subopt;++  n_max=16;+  subopt = (duplexT *) vrna_alloc(n_max*sizeof(duplexT));+  mfe = duplexfold_cu(s1, s2, 0);+  free(mfe.structure);++  thresh = (int) mfe.energy*100+0.1 + delta;+  n1 = strlen(s1); n2=strlen(s2);+  for (i=n1; i>0; i--) {+    for (j=1; j<=n2; j++) {+      int type, ii,jj, Ed;+      type = pair[S2[j]][S1[i]];+      if (!type) continue;+      E = Ed = c[i][j];+      Ed += E_ExtLoop(type, (j>1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+      if (Ed>thresh) continue;+      /* too keep output small, remove hits that are dominated by a+         better one close (w) by. For simplicity we do test without+         adding dangles, which is slightly inaccurate.+      */+      for (ii=MAX2(i-w,1); (ii<=MIN2(i+w,n1)) && type; ii++) {+        for (jj=MAX2(j-w,1); jj<=MIN2(j+w,n2); jj++)+          if (c[ii][jj]<E) {type=0; break;}+      }+      if (!type) continue;++      struc = backtrack(i,j);+      vrna_message_info(stderr, "%d %d %d", i,j,E);+      if (n_subopt+1>=n_max) {+        n_max *= 2;+        subopt = (duplexT *) vrna_realloc(subopt, n_max*sizeof(duplexT));+      }+      subopt[n_subopt].i = MIN2(i+1,n1);+      subopt[n_subopt].j = MAX2(j-1,1);+      subopt[n_subopt].energy = Ed * 0.01;+      subopt[n_subopt++].structure = struc;+    }+  }+  /* free all static globals */+  for (i=1; i<=n1; i++) free(c[i]);+  free(c);+  free(S1); free(S2); free(SS1); free(SS2);++  if (subopt_sorted) qsort(subopt, n_subopt, sizeof(duplexT), compare);+  subopt[n_subopt].i =0;+  subopt[n_subopt].j =0;+  subopt[n_subopt].structure = NULL;+  return subopt;+}++PRIVATE char *backtrack(int i, int j) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;++  st1 = (char *) vrna_alloc(sizeof(char)*(n1+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n2+1));++  i0=MIN2(i+1,n1); j0=MAX2(j-1,1);++  while (i>0 && j<=n2) {+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    type = pair[S1[i]][S2[j]];+    if (!type) vrna_message_error("backtrack failed in fold duplex");+    for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+      for (l=j+1; l<=n2; l++) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        type2 = pair[S1[k]][S2[l]];+        if (!type2) continue;+        LE = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                       SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1], P);+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      E -= E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, P);+      if (E != P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex");+      } else break;+    }+  }+  if (i>1)  i--;+  if (j<n2) j++;++  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&");+  strcat(struc, st2+j0-1);++  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2);++  return struc;+}++/*------------------------------------------------------------------------*/++PRIVATE int compare(const void *sub1, const void *sub2) {+  int d;+  if (((duplexT *) sub1)->energy > ((duplexT *) sub2)->energy)+    return 1;+  if (((duplexT *) sub1)->energy < ((duplexT *) sub2)->energy)+    return -1;+  d = ((duplexT *) sub1)->i - ((duplexT *) sub2)->i;+  if (d!=0) return d;+  return  ((duplexT *) sub1)->j - ((duplexT *) sub2)->j;+}++/*---------------------------------------------------------------------------*/++PUBLIC duplexT aliduplexfold(const char *s1[], const char *s2[]){+  return aliduplexfold_cu(s1, s2, 1);+}++PRIVATE duplexT aliduplexfold_cu(const char *s1[], const char *s2[], int clean_up) {+  int i, j, s, n_seq, Emin=INF, i_min=0, j_min=0;+  char *struc;+  duplexT mfe;+  short **S1, **S2;+  int *type;+  vrna_md_t md;+  n1 = (int) strlen(s1[0]);+  n2 = (int) strlen(s2[0]);++  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; s2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in aliduplexfold()\n");++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=1; i<=n1; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));++  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_sequence(s1[s], 0);+    S2[s] = encode_sequence(s2[s], 0);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  for (i=1; i<=n1; i++) {+    for (j=n2; j>0; j--) {+      int k,l,E,psc;+      for (s=0; s<n_seq; s++) {+        type[s] = pair[S1[s][i]][S2[s][j]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      c[i][j] = (psc>=MINPSCORE) ? (n_seq*P->DuplexInit) : INF;+      if (psc<MINPSCORE) continue;+      for(s=0; s<n_seq;s++){+        c[i][j] += E_ExtLoop(type[s], (i>1) ? S1[s][i-1] : -1, (j<n2) ? S2[s][j+1] : -1, P);+      }+      for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+        for (l=j+1; l<=n2; l++) {+          int type2;+          if (i-k+l-j-2>MAXLOOP) break;+          if (c[k][l]>INF/2) continue;+          for (E=s=0; s<n_seq; s++) {+            type2 = pair[S1[s][k]][S2[s][l]];+            if (type2==0) type2=7;+            E += E_IntLoop(i-k-1, l-j-1, type2, rtype[type[s]],+                           S1[s][k+1], S2[s][l-1], S1[s][i-1], S2[s][j+1], P);+          }+          c[i][j] = MIN2(c[i][j], c[k][l]+E);+        }+      }+      c[i][j] -= psc;+      E = c[i][j];+      for (s=0; s<n_seq; s++) {+        E += E_ExtLoop(rtype[type[s]], (j>1) ? S2[s][j-1] : -1, (i<n1) ? S1[s][i+1] : -1, P);+      }+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      }+    }+  }++  struc = alibacktrack(i_min, j_min, (const short **)S1,(const short **)S2);+  if (i_min<n1) i_min++;+  if (j_min>1 ) j_min--;++  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (float) (Emin/(100.*n_seq));+  mfe.structure = struc;+  if (clean_up){+    for (i=1; i<=n1; i++) free(c[i]);+    free(c);+  }+  for (s=0; s<n_seq; s++) {+    free(S1[s]); free(S2[s]);+  }+  free(S1);+  free(S2);+  free(type);+  return mfe;+}++PUBLIC duplexT *aliduplex_subopt(const char *s1[], const char *s2[], int delta, int w) {+  int i,j, n1, n2, thresh, E, n_subopt=0, n_max, s, n_seq, *type;+  char *struc;+  duplexT mfe;+  duplexT *subopt;+  short **S1, **S2;++  n_max=16;+  subopt = (duplexT *) vrna_alloc(n_max*sizeof(duplexT));+  mfe = aliduplexfold_cu(s1, s2, 0);+  free(mfe.structure);++  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;++  thresh =  (int) ((mfe.energy*100. + delta)*n_seq +0.1);+  n1 = strlen(s1[0]); n2=strlen(s2[0]);+  S1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  S2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if (strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    S1[s] = encode_sequence(s1[s], 0);+    S2[s] = encode_sequence(s2[s], 0);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  for (i=n1; i>0; i--) {+    for (j=1; j<=n2; j++) {+      int ii, jj, skip, Ed, psc;++      for (s=0; s<n_seq; s++) {+        type[s] = pair[S2[s][j]][S1[s][i]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      if (psc<MINPSCORE) continue;+      E = Ed = c[i][j];+      for  (s=0; s<n_seq; s++) {+        Ed += E_ExtLoop(type[s], (j>1) ? S2[s][j-1] : -1, (i<n1) ? S1[s][i+1] : -1, P);+      }+      if (Ed>thresh) continue;+      /* too keep output small, skip hits that are dominated by a+         better one close (w) by. For simplicity we don't take dangels+         into account here, thus the heuristic is somewhat inaccurate.+      */+      for (skip=0, ii=MAX2(i-w,1); (ii<=MIN2(i+w,n1)) && type; ii++) {+        for (jj=MAX2(j-w,1); jj<=MIN2(j+w,n2); jj++)+          if (c[ii][jj]<E) {skip=1; break;}+      }+      if (skip) continue;+      struc = alibacktrack(i,j,(const short **)S1, (const short **)S2);+      vrna_message_info(stderr, "%d %d %d", i,j,E);+      if (n_subopt+1>=n_max) {+        n_max *= 2;+        subopt = (duplexT *) vrna_realloc(subopt, n_max*sizeof(duplexT));+      }+      subopt[n_subopt].i = MIN2(i+1,n1);+      subopt[n_subopt].j = MAX2(j-1,1);+      subopt[n_subopt].energy = Ed * 0.01/n_seq;+      subopt[n_subopt++].structure = struc;+    }+  }++  for (i=1; i<=n1; i++) free(c[i]);+  free(c);+  for (s=0; s<n_seq; s++) {+    free(S1[s]); free(S2[s]);+  }+  free(S1); free(S2); free(type);++  if (subopt_sorted) qsort(subopt, n_subopt, sizeof(duplexT), compare);+  subopt[n_subopt].i =0;+  subopt[n_subopt].j =0;+  subopt[n_subopt].structure = NULL;+  return subopt;+}++PRIVATE char *alibacktrack(int i, int j, const short **S1, const short **S2) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, *type, type2, E, traced, i0, j0, s, n_seq;+  char *st1, *st2, *struc;++  n1 = (int) S1[0][0];+  n2 = (int) S2[0][0];++  for (s=0; S1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; S2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in alibacktrack()\n");++  st1 = (char *) vrna_alloc(sizeof(char)*(n1+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n2+1));+  type = (int *) vrna_alloc(n_seq*sizeof(int));++  i0=MIN2(i+1,n1); j0=MAX2(j-1,1);++  while (i>0 && j<=n2) {+    int psc;+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    for (s=0; s<n_seq; s++) {+      type[s] = pair[S1[s][i]][S2[s][j]];+    }+    psc = covscore(type, n_seq);+    for (s=0; s<n_seq; s++) if (type[s]==0) type[s] = 7;+    E += psc;+    for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+      for (l=j+1; l<=n2; l++) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        if (c[k][l]>INF/2) continue;+        for (s=LE=0; s<n_seq; s++) {+          type2 = pair[S1[s][k]][S2[s][l]];+          if (type2==0) type2=7;+          LE += E_IntLoop(i-k-1, l-j-1, type2, rtype[type[s]],+                           S1[s][k+1], S2[s][l-1], S1[s][i-1], S2[s][j+1], P);+        }+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      for (s=0; s<n_seq; s++) {+        E -= E_ExtLoop(type[s], (i>1) ? S1[s][i-1] : -1, (j<n2) ? S2[s][j+1] : -1, P);+      }+      if (E != n_seq*P->DuplexInit) {+        vrna_message_error("backtrack failed in aliduplex");+      } else break;+    }+  }+  if (i>1)  i--;+  if (j<n2) j++;++  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&");+  strcat(struc, st2+j0-1);++  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2); free(type);++  return struc;+}+++PRIVATE int covscore(const int *types, int n_seq) {+  /* calculate co-variance bonus for a pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */+  int k,l,s,score, pscore;+  int dm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                {0,0,2,2,1,2,2} /* CG */,+                {0,2,0,1,2,2,2} /* GC */,+                {0,2,1,0,2,1,2} /* GU */,+                {0,1,2,2,0,2,1} /* UG */,+                {0,2,2,1,2,0,2} /* AU */,+                {0,2,2,2,1,2,0} /* UA */};++  int pfreq[8]={0,0,0,0,0,0,0,0};+  for (s=0; s<n_seq; s++)+    pfreq[types[s]]++;++  if (pfreq[0]*2>n_seq) return NONE;+  for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+    for (l=k+1; l<=6; l++)+      /* scores for replacements between pairtypes    */+      /* consistent or compensatory mutations score 1 or 2  */+      score += pfreq[k]*pfreq[l]*dm[k][l];++  /* counter examples score -1, gap-gap scores -0.25   */+  pscore = cv_fact *+    ((UNIT*score)/n_seq - nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));+  return pscore;+}
+ C/ViennaRNA/duplex.h view
@@ -0,0 +1,29 @@+#ifndef VIENNA_RNA_PACKAGE_DUPLEX_H+#define VIENNA_RNA_PACKAGE_DUPLEX_H++#include <ViennaRNA/data_structures.h>++/**+ *  @file     duplex.h+ *  @ingroup  cofold+ *  @brief    Functions for simple RNA-RNA duplex interactions+ */+++duplexT duplexfold( const char *s1,+                    const char *s2);++duplexT *duplex_subopt( const char *s1,+                        const char *s2,+                        int delta,+                        int w);++duplexT aliduplexfold(const char *s1[],+                      const char *s2[]);++duplexT *aliduplex_subopt(const char *s1[],+                          const char *s2[],+                          int delta,+                          int w);++#endif
+ C/ViennaRNA/edit_cost.h view
@@ -0,0 +1,53 @@+/**+ *  \file edit_cost.h+ *  \brief global variables for Edit Costs included by treedist.c and stringdist.c+ */++#define PRIVATE static++PRIVATE char   sep    = ':';+PRIVATE char  *coding = "Null:U:P:H:B:I:M:S:E:R";++#define DIST_INF 10000  /* infinity */++typedef int CostMatrix[10][10];++PRIVATE CostMatrix *EditCost;  /* will point to UsualCost or ShapiroCost */++PRIVATE CostMatrix  UsualCost =+{++/*    Null,       U,        P,        H,        B,        I,        M,        S,        E,        R     */++   {        0,        1,        2,        2,        2,        2,        2,        1,        1, DIST_INF},   /* Null replaced */+   {        1,        0,        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* U    replaced */+   {        2,        1,        0, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* P    replaced */+   {        2, DIST_INF, DIST_INF,        0,        2,        2,        2, DIST_INF, DIST_INF, DIST_INF},   /* H    replaced */+   {        2, DIST_INF, DIST_INF,        2,        0,        1,        2, DIST_INF, DIST_INF, DIST_INF},   /* B    replaced */+   {        2, DIST_INF, DIST_INF,        2,        1,        0,        2, DIST_INF, DIST_INF, DIST_INF},   /* I    replaced */+   {        2, DIST_INF, DIST_INF,        2,        2,        2,        0, DIST_INF, DIST_INF, DIST_INF},   /* M    replaced */+   {        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF, DIST_INF},   /* S    replaced */+   {        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF},   /* E    replaced */+   { DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0},   /* R    replaced */++};+++PRIVATE CostMatrix ShapiroCost =+{++/*    Null,       U,        P,        H,        B,        I,        M,        S,        E,        R     */++   {        0,        1,        2,      100,        5,        5,       75,        5,        5, DIST_INF},   /* Null replaced */+   {        1,        0,        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* U    replaced */+   {        2,        1,        0, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* P    replaced */+   {      100, DIST_INF, DIST_INF,        0,        8,        8,        8, DIST_INF, DIST_INF, DIST_INF},   /* H    replaced */+   {        5, DIST_INF, DIST_INF,        8,        0,        3,        8, DIST_INF, DIST_INF, DIST_INF},   /* B    replaced */+   {        5, DIST_INF, DIST_INF,        8,        3,        0,        8, DIST_INF, DIST_INF, DIST_INF},   /* I    replaced */+   {       75, DIST_INF, DIST_INF,        8,        8,        8,        0, DIST_INF, DIST_INF, DIST_INF},   /* M    replaced */+   {        5, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF, DIST_INF},   /* S    replaced */+   {        5, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF},   /* E    replaced */+   { DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0},   /* R    replaced */++};+
+ C/ViennaRNA/energy_const.h view
@@ -0,0 +1,39 @@+#ifndef VIENNA_RNA_PACKAGE_ENERGY_CONST_H+#define VIENNA_RNA_PACKAGE_ENERGY_CONST_H++#include <limits.h>++/**+ *  @file     energy_const.h+ *  @ingroup  energy_parameters+ *  @brief    Energy parameter constants+ */++/** The gas constant */+#define GASCONST 1.98717  /* in [cal/K] */+/** 0 deg Celsius in Kelvin */+#define K0  273.15+/** Infinity as used in minimization routines */+#define INF 10000000 /* (INT_MAX/10) */++#define EMAX (INF/10)+/** forbidden */+#define FORBIDDEN 9999+/** bonus contribution */+#define BONUS 10000+/** The number of distinguishable base pairs */+#define NBPAIRS 7+/** The minimum loop length */+#define TURN 3+/** The maximum loop length */+#define MAXLOOP 30++#define UNIT 100++#define MINPSCORE -2 * UNIT+++#define   VRNA_GQUAD_MISMATCH_PENALTY   300   /* penalty for incompatible nucleotides in an alignment that destruct a gquad layer */+#define   VRNA_GQUAD_MISMATCH_NUM_ALI   1   /* maximum number of mismatching sequences in the alignment when gquad should be formed */++#endif
+ C/ViennaRNA/energy_par.c view
@@ -0,0 +1,843 @@+++/*+    Automatically generated using the TurnerParser+    TurnerParser (c) 2008,2009,2010+      Christian Hoener zu Siederdissen, TBI Vienna+      choener (at) tbi.univie.ac.at++    The library enabling this can be found at:+    http://hackage.haskell.org/package/BiobaseVienna+    the program can be found at:+    (sorry, not yet)+    install using cabal: cabal install (sorry, not yet)+*/++/*+     Current free energy parameters are summarized in:++     D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner+     "Expanded sequence dependence of thermodynamic parameters improves+     prediction of RNA secondary structure"+     JMB, 288, pp 911-940, 1999++     Enthalpies taken from:++     A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker+     "Coaxial stacking of helices enhances binding of oligoribonucleotides.."+     PNAS, 91, pp 9218-9222, 1994++     D.H. Turner, N. Sugimoto, and S.M. Freier.+     "RNA Structure Prediction",+     Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.++     John A.Jaeger, Douglas H.Turner, and Michael Zuker.+     "Improved predictions of secondary structures for RNA",+     PNAS, 86, 7706-7710, October 1989.++     L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner+     "Nearest-Neighbor Parameters for GU Mismatches...."+     Biochemistry 1991, 30 11124-11132++     A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner+     "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."+     Biochemistry 1991, 30, 6428--6435+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include "ViennaRNA/energy_const.h"++#define NST 0     /* Energy for nonstandard stacked pairs */+#define DEF -50   /* Default terminal mismatch, used for I */+                  /* and any non_pairing bases */+#define NSM 0     /* terminal mismatch for non standard pairs */++#define PUBLIC++PUBLIC double Tmeasure = 37+K0;  /* temperature of param measurements */+++/* PUBLIC double lxc37=107.9; */+PUBLIC double lxc37=107.856;+PUBLIC int ML_intern37=-90;+PUBLIC int ML_interndH=-220;+PUBLIC int ML_closing37=930;+PUBLIC int ML_closingdH=3000;+PUBLIC int ML_BASE37=0;+PUBLIC int ML_BASEdH=0;+PUBLIC int MAX_NINIO=300;+PUBLIC int ninio37=60;+PUBLIC int niniodH=320;+PUBLIC int TerminalAU37=50;+PUBLIC int TerminalAUdH=370;+PUBLIC int DuplexInit37=410;+PUBLIC int DuplexInitdH=360;+PUBLIC int TripleC37=100;+PUBLIC int TripleCdH=1860;+PUBLIC int MultipleCA37=30;+PUBLIC int MultipleCAdH=340;+PUBLIC int MultipleCB37=160;+PUBLIC int MultipleCBdH=760;++PUBLIC int GQuadAlpha37 = -1800;+PUBLIC int GQuadAlphadH = -11934;+PUBLIC int GQuadBeta37 = 1200;+PUBLIC int GQuadBetadH = 0;++PUBLIC int stack37[NBPAIRS+1][NBPAIRS+1] =+{{   INF,   INF,   INF,   INF,   INF,   INF,   INF,   INF}+,{   INF,  -240,  -330,  -210,  -140,  -210,  -210,  -140}+,{   INF,  -330,  -340,  -250,  -150,  -220,  -240,  -150}+,{   INF,  -210,  -250,   130,   -50,  -140,  -130,   130}+,{   INF,  -140,  -150,   -50,    30,   -60,  -100,    30}+,{   INF,  -210,  -220,  -140,   -60,  -110,   -90,   -60}+,{   INF,  -210,  -240,  -130,  -100,   -90,  -130,   -90}+,{   INF,  -140,  -150,   130,    30,   -60,   -90,   130}};+PUBLIC int stackdH[NBPAIRS+1][NBPAIRS+1] =+{{   INF,   INF,   INF,   INF,   INF,   INF,   INF,   INF}+,{   INF, -1060, -1340, -1210,  -560, -1050, -1040,  -560}+,{   INF, -1340, -1490, -1260,  -830, -1140, -1240,  -830}+,{   INF, -1210, -1260, -1460, -1350,  -880, -1280,  -880}+,{   INF,  -560,  -830, -1350,  -930,  -320,  -700,  -320}+,{   INF, -1050, -1140,  -880,  -320,  -940,  -680,  -320}+,{   INF, -1040, -1240, -1280,  -700,  -680,  -770,  -680}+,{   INF,  -560,  -830,  -880,  -320,  -320,  -680,  -320}};++PUBLIC int hairpin37[31] = {   INF,   INF,   INF,   540,   560,   570,   540,   600,   550,   640,   650,   660,   670,   680,   690,   690,   700,   710,   710,   720,   720,   730,   730,   740,   740,   750,   750,   750,   760,   760,   770};+PUBLIC int hairpindH[31] = {   INF,   INF,   INF,   130,   480,   360,  -290,   130,  -290,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500};+PUBLIC int bulge37[31] = {   INF,   380,   280,   320,   360,   400,   440,   460,   470,   480,   490,   500,   510,   520,   530,   540,   540,   550,   550,   560,   570,   570,   580,   580,   580,   590,   590,   600,   600,   600,   610};+PUBLIC int bulgedH[31] = {   INF,  1060,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710};+PUBLIC int internal_loop37[31] = {   INF,   INF,   100,   100,   110,   200,   200,   210,   230,   240,   250,   260,   270,   280,   290,   290,   300,   310,   310,   320,   330,   330,   340,   340,   350,   350,   350,   360,   360,   370,   370};+PUBLIC int internal_loopdH[31] = {   INF,   INF,   -720,   -720,  -720,  -680,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130};++PUBLIC int mismatchI37[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,   -80,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,  -100,     0,  -100,     0}+ ,{     0,     0,     0,     0,   -60}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,   -80,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,  -100,     0,  -100,     0}+ ,{     0,     0,     0,     0,   -60}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,   -10,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -30,    70,   -30,    70}+ ,{    70,    70,    70,    70,    10}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,   -10,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -30,    70,   -30,    70}+ ,{    70,    70,    70,    70,    10}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,   -10,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -30,    70,   -30,    70}+ ,{    70,    70,    70,    70,    10}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,   -10,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -30,    70,   -30,    70}+ ,{    70,    70,    70,    70,    10}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,   -10,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -30,    70,   -30,    70}+ ,{    70,    70,    70,    70,    10}+ }};+PUBLIC int mismatchIdH[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{   280,     0,     0,   280,     0}+ ,{     0,     0,     0,  -340,     0}+ ,{     0,     0,     0,     0,     0}+ ,{   280,  -760,     0,   280,     0}+ ,{     0,     0,     0,     0,  -580}+ }+,{{   280,     0,     0,   280,     0}+ ,{     0,     0,     0,  -340,     0}+ ,{     0,     0,     0,     0,     0}+ ,{   280,  -760,     0,   280,     0}+ ,{     0,     0,     0,     0,  -580}+ }+,{{   790,   500,   500,   790,   500}+ ,{   500,   500,   500,   170,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   790,  -260,   500,   790,   500}+ ,{   500,   500,   500,   500,   -80}+ }+,{{   790,   500,   500,   790,   500}+ ,{   500,   500,   500,   170,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   790,  -260,   500,   790,   500}+ ,{   500,   500,   500,   500,   -80}+ }+,{{   790,   500,   500,   790,   500}+ ,{   500,   500,   500,   170,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   790,  -260,   500,   790,   500}+ ,{   500,   500,   500,   500,   -80}+ }+,{{   790,   500,   500,   790,   500}+ ,{   500,   500,   500,   170,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   790,  -260,   500,   790,   500}+ ,{   500,   500,   500,   500,   -80}+ }+,{{   790,   500,   500,   790,   500}+ ,{   500,   500,   500,   170,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   790,  -260,   500,   790,   500}+ ,{   500,   500,   500,   500,   -80}+ }};++PUBLIC int mismatchH37[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{   -80,  -100,  -110,  -100,   -80}+ ,{  -140,  -150,  -150,  -140,  -150}+ ,{   -80,  -100,  -110,  -100,   -80}+ ,{  -150,  -230,  -150,  -240,  -150}+ ,{  -100,  -100,  -140,  -100,  -210}+ }+,{{   -50,  -110,   -70,  -110,   -50}+ ,{  -110,  -110,  -150,  -130,  -150}+ ,{   -50,  -110,   -70,  -110,   -50}+ ,{  -150,  -250,  -150,  -220,  -150}+ ,{  -100,  -110,  -100,  -110,  -160}+ }+,{{    20,    20,   -20,   -10,   -20}+ ,{    20,    20,   -50,   -30,   -50}+ ,{   -10,   -10,   -20,   -10,   -20}+ ,{   -50,  -100,   -50,  -110,   -50}+ ,{   -10,   -10,   -30,   -10,  -100}+ }+,{{     0,   -20,   -10,   -20,     0}+ ,{   -30,   -50,   -30,   -60,   -30}+ ,{     0,   -20,   -10,   -20,     0}+ ,{   -30,   -90,   -30,  -110,   -30}+ ,{   -10,   -20,   -10,   -20,   -90}+ }+,{{   -10,   -10,   -20,   -10,   -20}+ ,{   -30,   -30,   -50,   -30,   -50}+ ,{   -10,   -10,   -20,   -10,   -20}+ ,{   -50,  -120,   -50,  -110,   -50}+ ,{   -10,   -10,   -30,   -10,  -120}+ }+,{{     0,   -20,   -10,   -20,     0}+ ,{   -30,   -50,   -30,   -50,   -30}+ ,{     0,   -20,   -10,   -20,     0}+ ,{   -30,  -150,   -30,  -150,   -30}+ ,{   -10,   -20,   -10,   -20,   -90}+ }+,{{    20,    20,   -10,   -10,     0}+ ,{    20,    20,   -30,   -30,   -30}+ ,{     0,   -10,   -10,   -10,     0}+ ,{   -30,   -90,   -30,  -110,   -30}+ ,{   -10,   -10,   -10,   -10,   -90}+ }};+PUBLIC int mismatchHdH[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{   560,  -570,   560,  -560,  -270}+ ,{  -560,  -910,  -560,  -560,  -560}+ ,{  -270,  -570,  -340,  -570,  -270}+ ,{   560, -1400,   560,  -920,  -560}+ ,{  -530,  -570,  -530,  -570, -1440}+ }+,{{    50,  -520,    50,  -560,  -400}+ ,{  -400,  -520,  -400,  -560,  -400}+ ,{    50,  -720,    50,  -720,  -420}+ ,{  -400, -1290,  -400,  -620,  -400}+ ,{   -30,  -720,   -30,  -720, -1080}+ }+,{{   970,   140,   970,   140,   570}+ ,{   570,    30,   570,    20,   570}+ ,{   970,   140,   970,   140,   340}+ ,{   570,  -270,   570,    20,   570}+ ,{   830,   140,   830,   140,   -50}+ }+,{{   230,   100,   230,   220,   190}+ ,{  -110,  -110,  -260,  -520,  -260}+ ,{   190,   -60,  -140,   -60,   190}+ ,{   220,   100,  -260,   220,  -260}+ ,{   230,   -60,   230,   -60,   -70}+ }+,{{   970,   140,   970,   140,   570}+ ,{   570,   -20,   570,    20,   570}+ ,{   970,   140,   970,   140,   340}+ ,{   570,  -520,   570,    20,   570}+ ,{   830,   140,   830,   140,  -380}+ }+,{{   230,   -30,   230,   -60,   190}+ ,{   -30,   -30,  -260,  -520,  -260}+ ,{   190,   -60,  -140,   -60,   190}+ ,{  -260,  -590,  -260,  -520,  -260}+ ,{   230,   -60,   230,   -60,   -70}+ }+,{{   970,   140,   970,   220,   570}+ ,{   570,    30,   570,    20,   570}+ ,{   970,   140,   970,   140,   340}+ ,{   570,   100,   570,   220,   570}+ ,{   830,   140,   830,   140,   -50}+ }};++/* mismatch_multi */+PUBLIC int mismatchM37[NBPAIRS+1][5][5] =+{{ /* NP.. */+  {   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ },+ { /* CG.. */+  {   -50,  -110,   -50,  -140,   -70}+ ,{  -110,  -110,  -110,  -160,  -110}+ ,{   -70,  -150,   -70,  -150,  -100}+ ,{  -110,  -130,  -110,  -140,  -110}+ ,{   -50,  -150,   -50,  -150,   -70}+ },+ { /* GC.. */+  {   -80,  -140,   -80,  -140,  -100}+ ,{  -100,  -150,  -100,  -140,  -100}+ ,{  -110,  -150,  -110,  -150,  -140}+ ,{  -100,  -140,  -100,  -160,  -100}+ ,{   -80,  -150,   -80,  -150,  -120}+ },+ { /* GU.. */+  {   -50,   -80,   -50,   -50,   -50}+ ,{   -50,  -100,   -70,   -50,   -70}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -110,   -70,   -80,   -70}+ ,{   -50,   -80,   -50,   -80,   -50}+ },+ { /* UG.. */+  {   -30,   -30,   -60,   -60,   -60}+ ,{   -30,   -30,   -60,   -60,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -60,  -100,   -70,  -100,   -60}+ },+ { /* AU.. */+  {   -50,   -80,   -50,   -80,   -50}+ ,{   -70,  -100,   -70,  -110,   -70}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -110,   -70,  -120,   -70}+ ,{   -50,   -80,   -50,   -80,   -50}+ },+ { /* UA.. */+  {   -60,   -80,   -60,   -80,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ },+ { /* NN.. */+  {   -30,   -30,   -50,   -50,   -50}+ ,{   -30,   -30,   -60,   -50,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -50,   -80,   -50,   -80,   -50}+ }};++/* mismatch_multi_enthalpies */+PUBLIC int mismatchMdH[NBPAIRS+1][5][5] =+{{ /* NP.. */+  {   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ },+ { /* CG.. */+  {    50,  -400,    50,  -400,   -30}+ ,{  -520,  -520,  -720,  -710,  -720}+ ,{    50,  -400,    50,  -400,   -30}+ ,{  -560,  -560,  -720,  -620,  -720}+ ,{  -400,  -400,  -420,  -400,  -500}+ },+ { /* GC.. */+  {  -270,  -560,  -270,  -560,  -530}+ ,{  -570,  -910,  -570,  -820,  -570}+ ,{  -340,  -560,  -340,  -560,  -530}+ ,{  -560,  -560,  -570,  -920,  -570}+ ,{  -270,  -560,  -270,  -560,  -860}+ },+ { /* GU.. */+  {   310,  -480,  -180,   310,   140}+ ,{   310,  -480,  -430,   310,  -430}+ ,{  -140,  -630,  -510,  -630,  -140}+ ,{  -150,  -890,  -430,  -150,  -430}+ ,{   140,  -630,  -180,  -630,   140}+ },+ { /* UG.. */+  {   600,   200,   600,   200,   460}+ ,{   -60,  -340,  -230,   -60,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -230,  -350,  -230,  -350,  -230}+ ,{   200,   200,   -30,   200,   160}+ },+ { /* AU.. */+  {   140,  -400,  -180,  -380,   140}+ ,{  -380,  -400,  -430,  -380,  -430}+ ,{  -140,  -630,  -510,  -630,  -140}+ ,{  -430,  -890,  -430,  -890,  -430}+ ,{   140,  -630,  -180,  -630,   140}+ },+ { /* UA.. */+  {   600,   200,   600,   200,   460}+ ,{  -230,  -390,  -230,  -310,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -230,  -350,  -230,  -350,  -230}+ ,{   200,   200,   -30,   200,  -170}+ },+ { /* NN.. */+  {   600,   200,   600,   310,   460}+ ,{   310,  -340,  -230,   310,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -150,  -350,  -230,  -150,  -230}+ ,{   200,   200,   -30,   200,   160}+ }};++PUBLIC int mismatch1nI37[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ }};+PUBLIC int mismatch1nIdH[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ }};++PUBLIC int mismatch23I37[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,   -50,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,  -110,     0,   -70,     0}+ ,{     0,     0,     0,     0,   -30}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,  -120,     0,   -70,     0}+ ,{     0,     0,     0,     0,   -30}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -40,    70,     0,    70}+ ,{    70,    70,    70,    70,    40}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    20,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -40,    70,     0,    70}+ ,{    70,    70,    70,    70,    40}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -40,    70,     0,    70}+ ,{    70,    70,    70,    70,    40}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    20,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -40,    70,     0,    70}+ ,{    70,    70,    70,    70,    40}+ }+,{{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,    70,    70,    70,    70}+ ,{    70,   -40,    70,     0,    70}+ ,{    70,    70,    70,    70,    40}+ }};+PUBLIC int mismatch23IdH[NBPAIRS+1][5][5] =+{{{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,  -570,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,  -860,     0,  -900,     0}+ ,{     0,     0,     0,     0,  -640}+ }+,{{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0,     0,     0,     0,     0}+ ,{     0, -1090,     0,  -900,     0}+ ,{     0,     0,     0,     0,  -640}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,  -580,   500,  -400,   500}+ ,{   500,   500,   500,   500,  -140}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   -60,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,  -360,   500,  -400,   500}+ ,{   500,   500,   500,   500,  -140}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,  -580,   500,  -400,   500}+ ,{   500,   500,   500,   500,  -140}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   -60,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,  -360,   500,  -400,   500}+ ,{   500,   500,   500,   500,  -140}+ }+,{{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,   500,   500,   500,   500}+ ,{   500,  -360,   500,  -400,   500}+ ,{   500,   500,   500,   500,  -140}+ }};++/* mismatch_exterior */+PUBLIC int mismatchExt37[NBPAIRS+1][5][5] =+{{ /* NP.. */+  {   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ },+ { /* CG.. */+  {   -50,  -110,   -50,  -140,   -70}+ ,{  -110,  -110,  -110,  -160,  -110}+ ,{   -70,  -150,   -70,  -150,  -100}+ ,{  -110,  -130,  -110,  -140,  -110}+ ,{   -50,  -150,   -50,  -150,   -70}+ },+ { /* GC.. */+  {   -80,  -140,   -80,  -140,  -100}+ ,{  -100,  -150,  -100,  -140,  -100}+ ,{  -110,  -150,  -110,  -150,  -140}+ ,{  -100,  -140,  -100,  -160,  -100}+ ,{   -80,  -150,   -80,  -150,  -120}+ },+ { /* GU.. */+  {   -50,   -80,   -50,   -50,   -50}+ ,{   -50,  -100,   -70,   -50,   -70}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -110,   -70,   -80,   -70}+ ,{   -50,   -80,   -50,   -80,   -50}+ },+ { /* UG.. */+  {   -30,   -30,   -60,   -60,   -60}+ ,{   -30,   -30,   -60,   -60,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -60,  -100,   -70,  -100,   -60}+ },+ { /* AU.. */+  {   -50,   -80,   -50,   -80,   -50}+ ,{   -70,  -100,   -70,  -110,   -70}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -110,   -70,  -120,   -70}+ ,{   -50,   -80,   -50,   -80,   -50}+ },+ { /* UA.. */+  {   -60,   -80,   -60,   -80,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -70,  -100,   -70,  -100,   -80}+ },+ { /* NN.. */+  {   -30,   -30,   -50,   -50,   -50}+ ,{   -30,   -30,   -60,   -50,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -60,   -80,   -60,   -80,   -60}+ ,{   -50,   -80,   -50,   -80,   -50}+ }};++/* mismatch_exterior_enthalpies */+PUBLIC int mismatchExtdH[NBPAIRS+1][5][5] =+{{ /* NP.. */+  {   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ ,{   INF,   INF,   INF,   INF,   INF}+ },+ { /* CG.. */+  {    50,  -400,    50,  -400,   -30}+ ,{  -520,  -520,  -720,  -710,  -720}+ ,{    50,  -400,    50,  -400,   -30}+ ,{  -560,  -560,  -720,  -620,  -720}+ ,{  -400,  -400,  -420,  -400,  -500}+ },+ { /* GC.. */+  {  -270,  -560,  -270,  -560,  -530}+ ,{  -570,  -910,  -570,  -820,  -570}+ ,{  -340,  -560,  -340,  -560,  -530}+ ,{  -560,  -560,  -570,  -920,  -570}+ ,{  -270,  -560,  -270,  -560,  -860}+ },+ { /* GU.. */+  {   310,  -480,  -180,   310,   140}+ ,{   310,  -480,  -430,   310,  -430}+ ,{  -140,  -630,  -510,  -630,  -140}+ ,{  -150,  -890,  -430,  -150,  -430}+ ,{   140,  -630,  -180,  -630,   140}+ },+ { /* UG.. */+  {   600,   200,   600,   200,   460}+ ,{   -60,  -340,  -230,   -60,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -230,  -350,  -230,  -350,  -230}+ ,{   200,   200,   -30,   200,   160}+ },+ { /* AU.. */+  {   140,  -400,  -180,  -380,   140}+ ,{  -380,  -400,  -430,  -380,  -430}+ ,{  -140,  -630,  -510,  -630,  -140}+ ,{  -430,  -890,  -430,  -890,  -430}+ ,{   140,  -630,  -180,  -630,   140}+ },+ { /* UA.. */+  {   600,   200,   600,   200,   460}+ ,{  -230,  -390,  -230,  -310,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -230,  -350,  -230,  -350,  -230}+ ,{   200,   200,   -30,   200,  -170}+ },+ { /* NN.. */+  {   600,   200,   600,   310,   460}+ ,{   310,  -340,  -230,   310,  -230}+ ,{   600,   200,   600,   200,   460}+ ,{  -150,  -350,  -230,  -150,  -230}+ ,{   200,   200,   -30,   200,   160}+ }};++/* dangle5 */+PUBLIC int dangle5_37[NBPAIRS+1][5] =+{ /*           N      A      C      G      U */+/* NP */ {   INF,   INF,   INF,   INF,   INF},+/* CG */ {   -10,   -50,   -30,   -20,   -10},+/* GC */ {    -0,   -20,   -30,    -0,    -0},+/* GU */ {   -20,   -30,   -30,   -40,   -20},+/* UG */ {   -10,   -30,   -10,   -20,   -20},+/* AU */ {   -20,   -30,   -30,   -40,   -20},+/* UA */ {   -10,   -30,   -10,   -20,   -20},+/* NN */ {    -0,   -20,   -10,    -0,    -0}+};++/* dangle3 */+PUBLIC int dangle3_37[NBPAIRS+1][5] =+{ /*           N      A      C      G      U */+/* NP */ {   INF,   INF,   INF,   INF,   INF},+/* CG */ {   -40,  -110,   -40,  -130,   -60},+/* GC */ {   -80,  -170,   -80,  -170,  -120},+/* GU */ {   -10,   -70,   -10,   -70,   -10},+/* UG */ {   -50,   -80,   -50,   -80,   -60},+/* AU */ {   -10,   -70,   -10,   -70,   -10},+/* UA */ {   -50,   -80,   -50,   -80,   -60},+/* NN */ {   -10,   -70,   -10,   -70,   -10}+};++/* dangle5_enthalpies */+PUBLIC int dangle5_dH[NBPAIRS+1][5] =+{ /*           N      A      C      G      U */+/* NP */ {   INF,   INF,   INF,   INF,   INF},+/* CG */ {   330,  -240,   330,    80,  -140},+/* GC */ {    70,  -160,    70,  -460,   -40},+/* GU */ {   310,   160,   220,    70,   310},+/* UG */ {   690,   -50,   690,    60,    60},+/* AU */ {   310,   160,   220,    70,   310},+/* UA */ {   690,   -50,   690,    60,    60},+/* NN */ {   690,   160,   690,    80,   310}+};++/* dangle3_enthalpies */+PUBLIC int dangle3_dH[NBPAIRS+1][5] =+{ /*           N      A      C      G      U */+/* NP */ {   INF,   INF,   INF,   INF,   INF},+/* CG */ {  -280,  -740,  -280,  -640,  -360},+/* GC */ {  -410,  -900,  -410,  -860,  -750},+/* GU */ {   -70,  -570,   -70,  -580,  -220},+/* UG */ {   -90,  -490,   -90,  -550,  -230},+/* AU */ {   -70,  -570,   -70,  -580,  -220},+/* UA */ {   -90,  -490,   -90,  -550,  -230},+/* NN */ {   -70,  -490,   -70,  -550,  -220}+};++PUBLIC char Triloops[241] =+  "CAACG "+  "GUUAC "+;+PUBLIC int Triloop37[40] = {   680,   690};+PUBLIC int TriloopdH[40] = {  2370,  1080};++PUBLIC char Tetraloops[281] =+  "CAACGG "+  "CCAAGG "+  "CCACGG "+  "CCCAGG "+  "CCGAGG "+  "CCGCGG "+  "CCUAGG "+  "CCUCGG "+  "CUAAGG "+  "CUACGG "+  "CUCAGG "+  "CUCCGG "+  "CUGCGG "+  "CUUAGG "+  "CUUCGG "+  "CUUUGG "+;+PUBLIC int Tetraloop37[40] = {   550,   330,   370,   340,   350,   360,   370,   250,   360,   280,   370,   270,   280,   350,   370,   370};+PUBLIC int TetraloopdH[40] = {   690, -1030,  -330,  -890,  -660,  -750,  -350, -1390,  -760, -1070,  -660, -1290, -1070,  -620, -1530,  -680};++PUBLIC char Hexaloops[361] =+  "ACAGUACU "+  "ACAGUGAU "+  "ACAGUGCU "+  "ACAGUGUU "+;+PUBLIC int Hexaloop37[40] = {   280,   360,   290,   180};+PUBLIC int HexaloopdH[40] = { -1680, -1140, -1280, -1540};++#include "intl11.h"+#include "intl11dH.h"+#include "intl21.h"+#include "intl21dH.h"+#include "intl22.h"+#include "intl22dH.h"+
+ C/ViennaRNA/energy_par.h view
@@ -0,0 +1,100 @@+/*+   prototypes for energy_par.c+*/++#ifndef VIENNA_RNA_PACKAGE_ENERGY_PAR_H+#define VIENNA_RNA_PACKAGE_ENERGY_PAR_H++#include <ViennaRNA/energy_const.h>++#define PUBLIC+++extern double lxc37;   /* parameter for logarithmic loop+			  energy extrapolation            */++extern int stack37[NBPAIRS+1][NBPAIRS+1];+extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */+extern int entropies[NBPAIRS+1][NBPAIRS+1];  /* not used anymore */++extern int hairpin37[31];+extern int hairpindH[31];+extern int bulge37[31];+extern int bulgedH[31];+extern int internal_loop37[31];+extern int internal_loopdH[31];+extern int internal2_energy;+extern int old_mismatch_37[NBPAIRS+1][5][5];+extern int mismatchI37[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatchIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatch1nI37[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatch23I37[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatch1nIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatch23IdH[NBPAIRS+1][5][5];  /* interior loop mismatches */+extern int mismatchH37[NBPAIRS+1][5][5];  /* same for hairpins */+extern int mismatchM37[NBPAIRS+1][5][5];  /* same for multiloops */+extern int mismatchHdH[NBPAIRS+1][5][5];  /* same for hairpins */+extern int mismatchMdH[NBPAIRS+1][5][5];  /* same for multiloops */+extern int mismatchExt37[NBPAIRS+1][5][5];+extern int mismatchExtdH[NBPAIRS+1][5][5];++extern int dangle5_37[NBPAIRS+1][5];      /* 5' dangle exterior of pair */+extern int dangle3_37[NBPAIRS+1][5];      /* 3' dangle */+extern int dangle3_dH[NBPAIRS+1][5];       /* corresponding enthalpies */+extern int dangle5_dH[NBPAIRS+1][5];++extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */+extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];++extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */+extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];++extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */+extern int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5];++/* constants for linearly destabilizing contributions for multi-loops+   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */+extern int ML_BASE37;+extern int ML_BASEdH;+extern int ML_closing37;+extern int ML_closingdH;+extern int ML_intern37;+extern int ML_interndH;++extern int TripleC37;+extern int TripleCdH;+extern int MultipleCA37;+extern int MultipleCAdH;+extern int MultipleCB37;+extern int MultipleCBdH;++/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */+/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */+extern int  MAX_NINIO;                   /* maximum correction */+extern int ninio37;+extern int niniodH;+/* penalty for helices terminated by AU (actually not GC) */+extern int TerminalAU37;+extern int TerminalAUdH;+/* penalty for forming bi-molecular duplex */+extern int DuplexInit37;+extern int DuplexInitdH;+/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */+extern char Tetraloops[];  /* string containing the special tetraloops */+extern int  Tetraloop37[];  /* Bonus energy for special tetraloops */+extern int  TetraloopdH[];+extern char Triloops[];    /* string containing the special triloops */+extern int  Triloop37[]; /* Bonus energy for special Triloops */+extern int  TriloopdH[]; /* Bonus energy for special Triloops */+extern char Hexaloops[];    /* string containing the special triloops */+extern int  Hexaloop37[]; /* Bonus energy for special Triloops */+extern int  HexaloopdH[]; /* Bonus energy for special Triloops */++extern int GQuadAlpha37;+extern int GQuadAlphadH;+extern int GQuadBeta37;+extern int GQuadBetadH;++extern double Tmeasure;       /* temperature of param measurements */++#endif
+ C/ViennaRNA/equilibrium_probs.c view
@@ -0,0 +1,2775 @@+/*+                  partiton function for RNA secondary structures++                  Ivo L Hofacker + Ronny Lorenz+                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/mfe.h"+#include "ViennaRNA/part_func.h"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  pf_create_bppm(vrna_fold_compound_t *vc, char *structure);+PRIVATE void  alipf_create_bppm(vrna_fold_compound_t *vc, char *structure);+PRIVATE INLINE void bppm_circ(vrna_fold_compound_t *vc);++PRIVATE INLINE void ud_outside_ext_loops(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_hp_loops(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_int_loops(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_mb_loops(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_hp_loops2(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_int_loops2(vrna_fold_compound_t *vc);+PRIVATE INLINE void ud_outside_mb_loops2(vrna_fold_compound_t *vc);+++PRIVATE FLT_OR_DBL  numerator_single(vrna_fold_compound_t *vc, int i, int j);+PRIVATE FLT_OR_DBL  numerator_comparative(vrna_fold_compound_t *vc, int i, int j);+++PRIVATE double+wrap_mean_bp_distance(FLT_OR_DBL *p,+                      int length,+                      int *index,+                      int turn);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++void+vrna_pairing_probs( vrna_fold_compound_t *vc,+                    char *structure){++  if(vc){+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     pf_create_bppm(vc, structure);+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  alipf_create_bppm(vc, structure);+                                    break;++      default:                      vrna_message_warning("vrna_pf@part_func.c: Unrecognized fold compound type");+                                    break;+    }+  }+}++/* calculate base pairing probs */+PRIVATE void+pf_create_bppm( vrna_fold_compound_t *vc,+                char *structure){++  int n, i,j,k,l, ij, kl, ii, u, u1, u2, cnt, ov=0;+  unsigned char type, type_2, tt;+  FLT_OR_DBL  temp, Qmax=0, prm_MLb;+  FLT_OR_DBL  prmt, prmt1;+  FLT_OR_DBL  *tmp;+  FLT_OR_DBL  tmp2, tmp_ud;+  FLT_OR_DBL  expMLclosing;+  FLT_OR_DBL  *qb, *qm, *G, *probs, *scale, *expMLbase;+  FLT_OR_DBL  *q1k, *qln;++  char              *ptype;++  double            max_real;+  int               *rtype, with_gquad;+  short             *S, *S1;+  vrna_hc_t         *hc;+  vrna_sc_t         *sc;+  int               *my_iindx, *jindx;+  int               circular, turn, with_ud, with_ud_outside;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  vrna_md_t         *md;+  vrna_ud_t         *domains_up;++  n                 = vc->length;+  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  S                 = vc->sequence_encoding2;+  S1                = vc->sequence_encoding;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  ptype             = vc->ptype;++  circular          = md->circ;+  with_gquad        = md->gquad;+  turn              = md->min_loop_size;++  hc                = vc->hc;+  sc                = vc->sc;++  domains_up        = vc->domains_up;+  matrices          = vc->exp_matrices;++  qb                = matrices->qb;+  qm                = matrices->qm;+  G                 = matrices->G;+  probs             = matrices->probs;+  q1k               = matrices->q1k;+  qln               = matrices->qln;+  scale             = matrices->scale;+  expMLbase         = matrices->expMLbase;++  with_ud           = (domains_up && domains_up->exp_energy_cb) ? 1 : 0;+  with_ud_outside   = (with_ud && domains_up->probs_add) ? 1 : 0;++  FLT_OR_DBL  expMLstem         = (with_gquad) ? exp_E_MLstem(0, -1, -1, pf_params) : 0;+  char        *hard_constraints = hc->matrix;+  int         *hc_up_int        = hc->up_int;++  int           corr_size       = 5;+  int           corr_cnt        = 0;+  vrna_plist_t  *bp_correction  = vrna_alloc(sizeof(vrna_plist_t) * corr_size);++  max_real      = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  /*+    the following is a crude check whether the partition function forward recursion+    has already been taken place+  */+  if(qb && probs && ( circular ? matrices->qm2 != NULL : (q1k != NULL && qln != NULL))){++    expMLclosing  = pf_params->expMLclosing;+    with_gquad    = pf_params->model_details.gquad;+    rtype         = &(pf_params->model_details.rtype[0]);++    /*+      The hc_local array provides row-wise access to hc->matrix, i.e.+      my_iindx. Using this in the cubic order loop for multiloops below+      results in way faster computation due to fewer cache misses. Also,+      it introduces only little memory overhead, e.g. ~450MB for+      sequences of length 30,000+    */+    char *hc_local = (char *)vrna_alloc(sizeof(char) * (((n + 1) * (n + 2)) /2 + 2));+    for(i = 1; i <= n; i++)+      for(j = i; j <= n; j++)+        hc_local[my_iindx[i] - j] = hard_constraints[jindx[j] + i];++    FLT_OR_DBL *prm_l  = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+    FLT_OR_DBL *prm_l1 = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+    FLT_OR_DBL *prml   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));++    int         ud_max_size = 0;+    FLT_OR_DBL  **pmlu      = NULL;+    FLT_OR_DBL  *prm_MLbu   = NULL;++    if(with_ud){+      /* find out maximum size of any unstructured domain */+      for(u = 0; u < domains_up->uniq_motif_count; u++)+        if(ud_max_size < domains_up->uniq_motif_size[u])+          ud_max_size = domains_up->uniq_motif_size[u];++      pmlu  = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *) * (ud_max_size + 1)); /* maximum motif size */++      for(u = 0; u <= ud_max_size; u++)+        pmlu[u] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));++      prm_MLbu = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (ud_max_size + 1));+    }++    Qmax=0;++    /* 1. exterior pair i,j and initialization of pr array */+    if(circular){+      bppm_circ(vc);+    } else {+      for (i=1; i<=n; i++) {+        for (j=i; j<=MIN2(i+turn,n); j++)+          probs[my_iindx[i]-j] = 0.;++        for (j=i+turn+1; j<=n; j++) {+          ij = my_iindx[i]-j;+          if((hc_local[ij] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) && (qb[ij] > 0.)){+            type      = (unsigned char)ptype[jindx[j] + i];++            if(type == 0)+              type = 7;++            probs[ij] = q1k[i-1]*qln[j+1]/q1k[n];+            probs[ij] *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);+            if(sc){+              if(sc->exp_f){+                probs[ij] *= sc->exp_f(1, n, i, j, VRNA_DECOMP_EXT_STEM_OUTSIDE, sc->data);+              }+            }+          } else+            probs[ij] = 0.;+        }+      }+    } /* end if(!circular)  */++    for (l = n; l > turn + 1; l--) {++      /* 2. bonding k,l as substem of 2:loop enclosed by i,j */+      for(k = 1; k < l - turn; k++){+        kl      = my_iindx[k]-l;+        type_2  = (unsigned char)ptype[jindx[l] + k];+        type_2  = rtype[type_2];++        if(type_2 == 0)+          type_2 = 7;++        if (qb[kl]==0.) continue;++        if(hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC){+          for(i = MAX2(1, k - MAXLOOP - 1); i <= k - 1; i++){+            u1 = k - i - 1;+            if(hc_up_int[i+1] < u1) continue;++            for(j = l + 1; j <= MIN2(l + MAXLOOP - k + i + 2, n); j++){+              u2 = j-l-1;+              if(hc_up_int[l+1] < u2) break;++              ij = my_iindx[i] - j;+              if(hc_local[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+                type = (unsigned char)ptype[jindx[j] + i];++                if(type == 0)+                  type = 7;++                if(probs[ij] > 0){+                  tmp2 =  probs[ij]+                          * scale[u1 + u2 + 2]+                          * exp_E_IntLoop(u1, u2, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params);++                  if(sc){+                    if(sc->exp_energy_up)+                      tmp2 *=   sc->exp_energy_up[i+1][u1]+                              * sc->exp_energy_up[l+1][u2];++                    if(sc->exp_energy_bp)+                      tmp2 *=   sc->exp_energy_bp[ij];++                    if(sc->exp_energy_stack){+                      if((i+1 == k) && (j-1 == l)){+                        tmp2 *=   sc->exp_energy_stack[i]+                                * sc->exp_energy_stack[k]+                                * sc->exp_energy_stack[l]+                                * sc->exp_energy_stack[j];+                      }+                    }++                    if(sc->exp_f)+                      tmp2 *= sc->exp_f(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);+                  }++                  if(with_ud){+                    FLT_OR_DBL qql, qqr;++                    qql = qqr = 0.;++                    if(u1 > 0)+                      qql = domains_up->exp_energy_cb(vc,+                                                      i+1, k-1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                      domains_up->data);+                    if(u2 > 0)+                      qqr = domains_up->exp_energy_cb(vc,+                                                      l+1, j-1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                      domains_up->data);+                    temp  = tmp2;+                    tmp2 += temp * qql;+                    tmp2 += temp * qqr;+                    tmp2 += temp * qql * qqr;+                  }++                  if(sc && sc->exp_f && sc->bt){ /* store probability correction for auxiliary pairs in interior loop motif */+                    vrna_basepair_t *ptr, *aux_bps;+                    aux_bps = sc->bt(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);+                    for(ptr = aux_bps; ptr && ptr->i != 0; ptr++){+                      bp_correction[corr_cnt].i = ptr->i;+                      bp_correction[corr_cnt].j = ptr->j;+                      bp_correction[corr_cnt++].p = tmp2 * qb[kl];+                      if(corr_cnt == corr_size){+                        corr_size += 5;+                        bp_correction = vrna_realloc(bp_correction, sizeof(vrna_plist_t) * corr_size);+                      }+                    }+                    free(aux_bps);+                  }++                  probs[kl] += tmp2;+                }+              }+            }+          }+        }+      }++      if(with_gquad){+        /* 2.5. bonding k,l as gquad enclosed by i,j */+        double *expintern = &(pf_params->expinternal[0]);+        FLT_OR_DBL qe;++        if(l < n - 3){+          for(k = 2; k <= l - VRNA_GQUAD_MIN_BOX_SIZE; k++){+            kl = my_iindx[k]-l;+            if (G[kl]==0.) continue;+            tmp2 = 0.;+            i = k - 1;+            for(j = MIN2(l + MAXLOOP + 1, n); j > l + 3; j--){+              ij = my_iindx[i] - j;+              type = (unsigned char)ptype[jindx[j] + i];+              if(!type) continue;+              qe = (type > 2) ? pf_params->expTermAU : 1.;+              tmp2 +=   probs[ij]+                      * qe+                      * (FLT_OR_DBL)expintern[j-l-1]+                      * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]]+                      * scale[2];+            }+            probs[kl] += tmp2 * G[kl];+          }+        }++        if (l < n - 1){+          for (k=3; k<=l-VRNA_GQUAD_MIN_BOX_SIZE; k++) {+            kl = my_iindx[k]-l;+            if (G[kl]==0.) continue;+            tmp2 = 0.;+            for (i=MAX2(1,k-MAXLOOP-1); i<=k-2; i++){+              u1 = k - i - 1;+              for (j=l+2; j<=MIN2(l + MAXLOOP - u1 + 1,n); j++) {+                ij = my_iindx[i] - j;+                type = (unsigned char)ptype[jindx[j] + i];+                if(!type) continue;+                qe = (type > 2) ? pf_params->expTermAU : 1.;+                tmp2 +=   probs[ij]+                        * qe+                        * (FLT_OR_DBL)expintern[u1+j-l-1]+                        * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]]+                        * scale[2];+              }+            }+            probs[kl] += tmp2 * G[kl];+          }+        }++        if(l < n){+          for(k = 4; k <= l - VRNA_GQUAD_MIN_BOX_SIZE; k++){+            kl = my_iindx[k]-l;+            if (G[kl]==0.) continue;+            tmp2 = 0.;+            j = l + 1;+            for (i=MAX2(1,k-MAXLOOP-1); i < k - 3; i++){+              ij = my_iindx[i] - j;+              type = (unsigned char)ptype[jindx[j] + i];+              if(!type) continue;+              qe = (type > 2) ? pf_params->expTermAU : 1.;+              tmp2 +=   probs[ij]+                      * qe+                      * (FLT_OR_DBL)expintern[k - i - 1]+                      * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]]+                      * scale[2];+            }+            probs[kl] += tmp2 * G[kl];+          }+        }+      }++      /* 3. bonding k,l as substem of multi-loop enclosed by i,j */+      prm_MLb = 0.;++      if(with_ud){+        for(u = 0; u <= ud_max_size; u++)+          prm_MLbu[u] = 0.;+      }++      if (l<n)+        for (k = 2; k < l - turn; k++) {+          kl    = my_iindx[k] - l;+          i     = k - 1;+          prmt  = prmt1 = 0.0;++          int lj;+          short s3;+          FLT_OR_DBL ppp;+          ij = my_iindx[i] - (l+2);+          lj = my_iindx[l+1]-(l+1);+          s3 = S1[i+1];+          for (j = l + 2; j<=n; j++, ij--, lj--){+            if(hc_local[ij] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+              tt = (unsigned char)md->pair[S1[j]][S1[i]];++              if(tt == 0)+                tt = 7;++              /* which decomposition is covered here? =>+                i + 1 = k < l < j:+                (i,j)       -> enclosing pair+                (k, l)      -> enclosed pair+                (l+1, j-1)  -> multiloop part with at least one stem+                a.k.a. (k,l) is left-most stem in multiloop closed by (k-1, j)+              */+              ppp = probs[ij]+                    * exp_E_MLstem(tt, S1[j-1], s3, pf_params)+                    * qm[lj];++              if(sc){+                if(sc->exp_energy_bp)+                  ppp *= sc->exp_energy_bp[ij];+/*+                if(sc->exp_f)+                  ppp *= sc->exp_f(i, j, l+1, j-1, , sc->data);+*/+              }+              prmt += ppp;+            }+          }+          prmt *= expMLclosing;+++          prml[ i]  =   prmt;++          ii = my_iindx[i];     /* ii-j=[i,j]     */+          tt = (unsigned char)ptype[jindx[l+1] + i];+          tt = rtype[tt];+          if(hc_local[ii - (l + 1)] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){++            if(tt == 0)+              tt = 7;++            prmt1 = probs[ii-(l+1)]+                    * expMLclosing+                    * exp_E_MLstem(tt, S1[l], S1[i+1], pf_params);++            if(sc){+              /* which decompositions are covered here? => (i, l+1) -> enclosing pair */+              if(sc->exp_energy_bp)+                prmt1 *= sc->exp_energy_bp[ii - (l+1)];++/*+              if(sc->exp_f)+                prmt1 *= sc->exp_f(i, l+1, k, l, , sc->data);+*/+            }+          }++          /* l+1 is unpaired */+          if(hc->up_ml[l+1]){+            ppp = prm_l1[i] * expMLbase[1];+            if(sc){+              if(sc->exp_energy_up)+                ppp *= sc->exp_energy_up[l+1][1];++/*+              if(sc_exp_f)+                ppp *= sc->exp_f(, sc->data);+*/+            }++            /* add contributions of MB loops where any unstructured domain starts at l+1 */+            if(with_ud){+              int cnt;+              for(cnt = 0; cnt < domains_up->uniq_motif_count; cnt++){+                u = domains_up->uniq_motif_size[cnt];+                if(hc->up_ml[l+1] >= u){+                  if(l + u < n){+                    temp =    domains_up->exp_energy_cb(vc,+                                                        l+1, l+u,+                                                        VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                        domains_up->data)+                            * pmlu[u][i]+                            * expMLbase[u];++                    if(sc){+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[l+1][u];+                    }++                    ppp += temp;+                  }+                }+              }+              pmlu[0][i] = ppp + prmt1;+            }++            prm_l[i] = ppp + prmt1;+          } else { /* skip configuration where l+1 is unpaired */+            prm_l[i] = prmt1;++            if(with_ud)+              pmlu[0][i] = prmt1;+          }++          /* i is unpaired */+          if(hc->up_ml[i]){+            ppp = prm_MLb * expMLbase[1];+            if(sc){+              if(sc->exp_energy_up)+                ppp *= sc->exp_energy_up[i][1];++/*+              if(sc->exp_f)+                ppp *= sc->exp_f(, sc->data);+*/+            }++            if(with_ud){+              int cnt;+              for(cnt = 0; cnt < domains_up->uniq_motif_count; cnt++){+                u = domains_up->uniq_motif_size[cnt];+                if(hc->up_ml[i] >= u){+                  temp =    prm_MLbu[u]+                          * expMLbase[u]+                          * domains_up->exp_energy_cb(vc,+                                                      i, i+u,+                                                      VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                      domains_up->data);++                  if(sc){+                    if(sc->exp_energy_up)+                      temp *= sc->exp_energy_up[i][u];+                  }+                  ppp += temp;+                }+              }+              prm_MLbu[0] = ppp + prml[i];+            }++            prm_MLb = ppp + prml[i];+            /* same as:    prm_MLb = 0;+               for (i=1; i<=k-1; i++) prm_MLb += prml[i]*expMLbase[k-i-1]; */++          } else { /* skip all configurations where i is unpaired */+            prm_MLb = prml[i];++            if(with_ud)+              prm_MLbu[0] = prml[i];+          }++          prml[i] = prml[i] + prm_l[i];++          tt = ptype[jindx[l] + k];++          if(with_gquad){+            if ((!tt) && (G[kl] == 0.)) continue;+          } else {+            if (qb[kl] == 0.) continue;+          }++          if(hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){++            temp = prm_MLb;++            for (i=1;i<=k-2; i++)+              temp += prml[i]*qm[my_iindx[i+1] - (k-1)];++            if(with_gquad){+              if(tt)+                temp    *= exp_E_MLstem(tt, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params) * scale[2];+              else+                temp    *= G[kl] * expMLstem * scale[2];+            } else {++              if(tt == 0)+                tt = 7;++              temp    *= exp_E_MLstem(tt, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params) * scale[2];+            }++            probs[kl]  += temp;++            if (probs[kl]>Qmax) {+              Qmax = probs[kl];+              if (Qmax>max_real/10.)+                vrna_message_warning("P close to overflow: %d %d %g %g\n",+                                            k, l, probs[kl], qb[kl]);+            }+            if (probs[kl]>=max_real) {+              ov++;+              probs[kl]=FLT_MAX;+            }+          }++          /* rotate prm_MLbu entries required for unstructured domain feature */+          if(with_ud){+            for(u = ud_max_size; u > 0; u--)+              prm_MLbu[u] = prm_MLbu[u - 1];+          }+        } /* end for (k=..) */++      /* rotate prm_l and prm_l1 arrays */+      tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;++      /* rotate pmlu entries required for unstructured domain feature */+      if(with_ud){+        tmp = pmlu[ud_max_size];+        for(u = ud_max_size; u > 0; u--)+          pmlu[u] = pmlu[u - 1];+        pmlu[0] = tmp;+      }+    }  /* end for (l=..)   */++    if(with_ud_outside){+      /*+          The above recursions only deal with base pairs, and how they might be+          enclosed by other pairs. However, for unstructrued domains, we have+          unpaired stretches, and require information about how these are enclosed+          by base pairs.+      */++      /* 1. Exterior loops */+      ud_outside_ext_loops(vc);++      /* 2. Hairpin loops */+      ud_outside_hp_loops(vc);++      /* 3. Interior loops */+      ud_outside_int_loops(vc);++      /* 4. Multi branch loops */+      ud_outside_mb_loops(vc);+    }++    if(sc && sc->f && sc->bt){+      for (i=1; i<=n; i++)+        for (j=i+turn+1; j<=n; j++) {+          ij = my_iindx[i]-j;+          /*  search for possible auxiliary base pairs in hairpin loop motifs to store+              the corresponding probability corrections+          */ +          if(hc_local[ij] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){+            vrna_basepair_t *ptr, *aux_bps;+            aux_bps = sc->bt(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+            if(aux_bps){+              FLT_OR_DBL qhp = vrna_exp_E_hp_loop(vc, i, j);+              for(ptr = aux_bps; ptr && ptr->i != 0; ptr++){+                bp_correction[corr_cnt].i = ptr->i;+                bp_correction[corr_cnt].j = ptr->j;+                bp_correction[corr_cnt++].p = probs[ij] * qhp;+                if(corr_cnt == corr_size){+                  corr_size += 5;+                  bp_correction = vrna_realloc(bp_correction, sizeof(vrna_plist_t) * corr_size);+                }+              }+            }+            free(aux_bps);+          }+        }++      /*  correct pairing probabilities for auxiliary base pairs from hairpin-, or interior loop motifs+          as augmented by the generalized soft constraints feature+      */+      for(i = 0; i < corr_cnt; i++){+        ij = my_iindx[bp_correction[i].i] - bp_correction[i].j;+        /* printf("correcting pair %d, %d by %f\n", bp_correction[i].i, bp_correction[i].j, bp_correction[i].p); */+        probs[ij] += bp_correction[i].p / qb[ij];+      }+    }+    free(bp_correction);++    for (i=1; i<=n; i++)+      for (j=i+turn+1; j<=n; j++) {+        ij = my_iindx[i]-j;++        if(with_gquad){+          if (qb[ij] > 0.)+            probs[ij] *= qb[ij];++          if (G[ij] > 0.){+            probs[ij] += q1k[i-1] * G[ij] * qln[j+1]/q1k[n];+          }+        } else {+          if (qb[ij] > 0.)+            probs[ij] *= qb[ij];+        }+      }++    if (structure!=NULL){+      char *s = vrna_db_from_probs(probs, (unsigned int)n);+      memcpy(structure, s, n);+      structure[n] = '\0';+      free(s);+    }+    if(ov > 0)+      vrna_message_warning("%d overflows occurred while backtracking;\n"+                                  "you might try a smaller pf_scale than %g\n",+                                  ov, pf_params->pf_scale);++    /* clean up */+    free(prm_l);+    free(prm_l1);+    free(prml);++    if(with_ud){+      for(u = 0; u <= ud_max_size; u++)+        free(pmlu[u]);+      free(pmlu);+      free(prm_MLbu);+    }++    free(hc_local);+  } /* end if 'check for forward recursion' */+  else+    vrna_message_error("bppm calculations have to be done after calling forward recursion\n");++#if 0+  if(with_ud_outside){+    for(i = 1; i <= n; i++)+      for(j = i; j <= n; j++){+        FLT_OR_DBL p, pp;+        pp = 0.;+        p = domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP, 0, domains_up->data);+        if(p > 0.)+          printf("p_ext[0][%d,%d] = %g\n", i, j, p);+        pp += p;+        p = domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP, 0, domains_up->data);+        pp += p;+        if(p > 0.)+          printf("p_hp[0][%d,%d] = %g\n", i, j, p);+        p = domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP, 0, domains_up->data);+        pp += p;+        if(p > 0.)+          printf("p_int[0][%d,%d] = %g\n", i, j, p);+        p = domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP, 0, domains_up->data);+        pp += p;+        if(p > 0.)+          printf("p_ml[0][%d,%d] = %g\n", i, j, p);+        if(pp > 0.)+          printf("p[0][%d,%d] = %g\n", i, j, pp);+      }+  }+#endif++  return;+}+++PRIVATE INLINE void+ud_outside_ext_loops( vrna_fold_compound_t *vc){++  int         i, j, u, n, cnt, *motif_list, *hc_up;+  FLT_OR_DBL  *q1k, *qln, temp, *scale;+  vrna_sc_t   *sc;+  vrna_ud_t   *domains_up;++  n           = vc->length;+  q1k         = vc->exp_matrices->q1k;+  qln         = vc->exp_matrices->qln;+  scale       = vc->exp_matrices->scale;+  hc_up       = vc->hc->up_ext;+  domains_up  = vc->domains_up;+  sc          = vc->sc;++  for(i = 1; i <= n; i++){+    motif_list = vrna_ud_get_motif_size_at(vc, i, VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP);++    /* 1. Exterior loops */+    if(motif_list){+      cnt = 0;+      while(-1 != (u = motif_list[cnt])){+        j = i + u - 1;+        if(j <= n){+          if(hc_up[i] >= u){+            temp = q1k[i-1] * qln[j + 1]/q1k[n];+            temp *= domains_up->exp_energy_cb(vc,+                                              i, j,+                                              VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                              domains_up->data);++            if(sc){+              if(sc->exp_energy_up)+                temp *= sc->exp_energy_up[i][u];+            }+            temp *= scale[u];++            if(temp > 0.)+              domains_up->probs_add(vc,+                                    i, j,+                                    VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                    temp,+                                    domains_up->data);+          }+        }+        cnt++;+      }+    }+    free(motif_list);+  }+}++PRIVATE INLINE void+ud_outside_hp_loops( vrna_fold_compound_t *vc){+++  int         i, j, k, l, kl, *my_iindx, u, n, cnt, *motif_list, *hc_up;+  FLT_OR_DBL  *q1k, *qln, temp, *scale, outside, exp_motif_en, *probs, q1, q2;++  vrna_sc_t   *sc;+  vrna_ud_t   *domains_up, *ud_bak;++  n           = vc->length;+  my_iindx    = vc->iindx;+  q1k         = vc->exp_matrices->q1k;+  qln         = vc->exp_matrices->qln;+  probs       = vc->exp_matrices->probs;+  scale       = vc->exp_matrices->scale;+  hc_up       = vc->hc->up_hp;+  domains_up  = vc->domains_up;+  sc          = vc->sc;++  for(i = 1; i <= n; i++){+    motif_list = vrna_ud_get_motif_size_at(vc, i, VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP);++    /* 2. Hairpin loops */+    if(motif_list){+      cnt = 0;+      while(-1 != (u = motif_list[cnt])){+        outside = 0.;+        j       = i + u - 1;+        if(j < n){+          if(hc_up[i] >= u){+            exp_motif_en = domains_up->exp_energy_cb( vc,+                                                      i, j,+                                                      VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                      domains_up->data);++            /*+              compute the contribution of all hairpins with+              bound motif+            */+            for(k = 1; k < i; k++)+              for(l = j + 1; l <= n; l++){+                kl = my_iindx[k] - l;+                if(probs[kl] > 0.){+                  ud_bak          = vc->domains_up;+                  vc->domains_up  = NULL;+                  temp            = vrna_exp_E_hp_loop(vc, k, l);+                  vc->domains_up  = ud_bak;++                  /* add contribution of motif */+                  if(temp > 0.){+                    temp *= exp_motif_en * probs[kl];++                    q1 = q2 = 0.;+                    /* add contributions of other motifs in remaining unpaired segments */+                    if((i - k - 1) > 0)+                      q1 = domains_up->exp_energy_cb( vc,+                                                      k + 1, i - 1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                                      domains_up->data);+                    if((l - j - 1) > 0)+                      q2 = domains_up->exp_energy_cb( vc,+                                                      j + 1, l - 1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                                      domains_up->data);++                    outside += temp;+                    outside += temp * q1;+                    outside += temp * q1 * q2;+                    outside += temp * q2;+                  }+                }+              }+          }+        }++        if(outside > 0.)+          domains_up->probs_add(vc,+                                i, j,+                                VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                outside,+                                domains_up->data);++        cnt++;+      }+    }+    free(motif_list);+  }++}++PRIVATE INLINE void+ud_outside_hp_loops2( vrna_fold_compound_t *vc){+++  int         i, j, k, l, kl, *my_iindx, u, u1, u2, n, cnt, *motif_list, *hc_up, turn, m;+  FLT_OR_DBL  *q1k, *qln, temp, *scale, outside, exp_motif_en, *probs, q1, q2, **qq_ud, **pp_ud;++  vrna_sc_t   *sc;+  vrna_ud_t   *domains_up, *ud_bak;++  n           = vc->length;+  my_iindx    = vc->iindx;+  q1k         = vc->exp_matrices->q1k;+  qln         = vc->exp_matrices->qln;+  probs       = vc->exp_matrices->probs;+  scale       = vc->exp_matrices->scale;+  hc_up       = vc->hc->up_hp;+  domains_up  = vc->domains_up;+  sc          = vc->sc;+  turn        = vc->exp_params->model_details.min_loop_size;++  qq_ud = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 1));+  for(k = 0; k < domains_up->uniq_motif_count; k++){+    qq_ud[k] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+    u = domains_up->uniq_motif_size[k];+    for(i = 1; i <= n - u + 1; i++){+      qq_ud[k][i] = domains_up->exp_energy_cb(vc,+                                              i, i + u - 1,+                                              VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                              domains_up->data);+    }+  }++  pp_ud = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 1));+  for(k = 0; k < domains_up->uniq_motif_count; k++){+    pp_ud[k] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  }++  for(k = 1; k < n; k++){+    for(l = k + turn + 1; l <= n; l++){+      kl = my_iindx[k] - l;+      if(probs[kl] > 0.){+        ud_bak          = vc->domains_up;+        vc->domains_up  = NULL;+        temp            = vrna_exp_E_hp_loop(vc, k, l);+        vc->domains_up  = ud_bak;+        temp           *= probs[kl];++        if(temp > 0.){+          for(m = 0; m < domains_up->uniq_motif_count; m++){+            u = domains_up->uniq_motif_size[m];+            for(u1 = 0, u2 = l - k - u - 1, i = k + 1, j = k + u; j < l; i++, j++, u1++, u2--){+              exp_motif_en = qq_ud[m][i];+              q1 = q2 = 1.;+              if(u1 > 0)+                q1 += domains_up->exp_energy_cb(vc,+                                                k + 1, i - 1,+                                                VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                                domains_up->data);+              if(u2 > 0)+                q2 += domains_up->exp_energy_cb(vc,+                                                j + 1, l - 1,+                                                VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                                domains_up->data);+              outside = temp * q1 * q2 * exp_motif_en;+              pp_ud[m][i] += outside;+            }+          }+        }+      }+    }+  }++  for(k = 0; k < domains_up->uniq_motif_count; k++){+    u = domains_up->uniq_motif_size[k];+    /* actually store the results */+    for(i = 1; i <= n - u + 1; i++){+      if(pp_ud[k][i] > 0.)+        domains_up->probs_add(vc,+                              i, i + u - 1,+                              VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                              pp_ud[k][i],+                              domains_up->data);+    }+    free(qq_ud[k]);+    free(pp_ud[k]);+  }+  free(qq_ud);+  free(pp_ud);+}+++PRIVATE INLINE void+ud_outside_int_loops( vrna_fold_compound_t *vc){++  int         i, j, k, l, p, q, pq, kl, u, n, cnt, *motif_list, *my_iindx,+              *hc_up, kmin, pmax, qmin, lmax, turn;+  FLT_OR_DBL  *q1k, *qln, temp, *scale, q1, q2, q3, exp_motif_en, outside,+              *probs, *qb;+  vrna_sc_t   *sc;+  vrna_ud_t   *domains_up, *ud_bak;++  n           = vc->length;+  my_iindx    = vc->iindx;+  q1k         = vc->exp_matrices->q1k;+  qln         = vc->exp_matrices->qln;+  qb          = vc->exp_matrices->qb;+  probs       = vc->exp_matrices->probs;+  scale       = vc->exp_matrices->scale;+  hc_up       = vc->hc->up_int;+  domains_up  = vc->domains_up;+  sc          = vc->sc;+  turn        = vc->exp_params->model_details.min_loop_size;++  for(i = 2; i <= n; i++){+    motif_list = vrna_ud_get_motif_size_at(vc, i, VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP);++    /* 3. Interior loops */+    if(motif_list){+      cnt = 0;+      while(-1 != (u = motif_list[cnt])){+        outside = 0.;+        j       = i + u - 1;++        if(j < n){+          if(hc_up[i] >= u){+            exp_motif_en = domains_up->exp_energy_cb( vc,+                                                      i, j,+                                                      VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                      domains_up->data);++            /* 3.1 motif is within 5' loop */+            kmin  = j - MAXLOOP - 1;+            kmin  = MAX2(kmin, 1);+            for(k = kmin; k < i; k++){+              pmax = k + MAXLOOP + 1;+              pmax = MIN2(pmax, n);+              for(p = j + 1; p < n; p++)+                for(q = p + turn + 1; q < n; q++){+                  pq    = my_iindx[p] - q;+                  if(qb[pq] == 0)+                    continue;+                  lmax  =  k + MAXLOOP + q - p + 2;+                  lmax  = MIN2(lmax, n);+                  for(l = q + 1; l <= lmax; l++){+                    kl = my_iindx[k] - l;+                    if(probs[kl] > 0.){+                      ud_bak          = vc->domains_up;+                      vc->domains_up  = NULL;+                      temp            = vrna_exp_E_interior_loop(vc, k, l, p, q);+                      vc->domains_up  = ud_bak;++                      if(temp > 0.){+                        temp *= probs[kl] * qb[pq] * exp_motif_en;++                        q1 = q2 = q3 = 0.;+                        if((l - q - 1) > 0)+                          q1 = domains_up->exp_energy_cb( vc,+                                                          q + 1, l - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);+                        if((i - k - 1) > 0)+                          q2 = domains_up->exp_energy_cb( vc,+                                                          k + 1, i - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);+                        if((p - j - 1) > 0)+                          q3 = domains_up->exp_energy_cb( vc,+                                                          j + 1, p - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);++                        outside += temp;+                        outside += temp * q1;+                        outside += temp * q1 * q2;+                        outside += temp * q1 * q2 * q3;+                        outside += temp * q2;+                        outside += temp * q2 * q3;+                        outside += temp * q3;+                      }+                    }+                  }+                }+            }++            /* 3.2 motif is within 3' loop */+            for(k = 1; k < i - turn - 2; k++){+              pmax = k + i + MAXLOOP - j;+              pmax = MIN2(pmax, n);+              for(p = k + 1; p <= pmax; p++){+                qmin = p + j - k - MAXLOOP - 1;+                qmin = MAX2(qmin, p + turn + 1);+                for(q = i - 1; q >= qmin; q--){+                  pq    = my_iindx[p] - q;+                  if(qb[pq] == 0.)+                    continue;+                  lmax  = k + q - p + MAXLOOP + 2;+                  lmax  = MIN2(lmax, n);+                  for(l = j + 1; l < lmax; l++){+                    kl = my_iindx[k] - l;+                    if(probs[kl] > 0.){+                      ud_bak          = vc->domains_up;+                      vc->domains_up  = NULL;+                      temp            = vrna_exp_E_interior_loop(vc, k, l, p, q);+                      vc->domains_up  = ud_bak;++                      if(temp > 0.){+                        FLT_OR_DBL q1, q2, q3;+                        temp *= probs[kl] * qb[pq] * exp_motif_en;++                        q1 = q2 = q3 = 0.;+                        if((l - j - 1) > 0)+                          q1 = domains_up->exp_energy_cb( vc,+                                                          j + 1, l - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);+                        if((i - q - 1) > 0)+                          q2 = domains_up->exp_energy_cb( vc,+                                                          q + 1,+                                                          i - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);+                        if((p - k - 1) > 0)+                          q3 = domains_up->exp_energy_cb( vc,+                                                          k + 1,+                                                          p - 1,+                                                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                          domains_up->data);++                        outside += temp;+                        outside += temp * q1;+                        outside += temp * q1 * q2;+                        outside += temp * q1 * q2 * q3;+                        outside += temp * q2;+                        outside += temp * q2 * q3;+                        outside += temp * q3;+                      }+                    }+                  }+                }+              }+            }++          }+        }++        if(outside > 0.)+          domains_up->probs_add(vc,+                                i, j,+                                VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                outside,+                                domains_up->data);++        cnt++;+      }+    }+    free(motif_list);+  }+}++PRIVATE INLINE void+ud_outside_int_loops2( vrna_fold_compound_t *vc){++  char        *hard_constraints, *hc_local;+  int         i, j, k, l, p, q, pq, kl, u, n, cnt, *motif_list, *my_iindx,+              *hc_up, kmin, pmax, qmin, lmax, turn, *jindx, u1, u2, uu1, uu2,+              u2_max, m;+  FLT_OR_DBL  *q1k, *qln, temp, *scale, q1, q2, q5, q3, exp_motif_en, outside,+              *probs, *qb, qq1, qq2, *qqk, *qql, *qqp, **qq_ud, **pp_ud, temp5,+              temp3;+  vrna_sc_t   *sc;+  vrna_ud_t   *domains_up, *ud_bak;++  n           = vc->length;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  q1k         = vc->exp_matrices->q1k;+  qln         = vc->exp_matrices->qln;+  qb          = vc->exp_matrices->qb;+  probs       = vc->exp_matrices->probs;+  scale       = vc->exp_matrices->scale;+  hc_up       = vc->hc->up_int;+  hard_constraints = vc->hc->matrix;+  domains_up  = vc->domains_up;+  sc          = vc->sc;+  turn        = vc->exp_params->model_details.min_loop_size;++  hc_local = (char *)vrna_alloc(sizeof(char) * (((n + 1) * (n + 2)) /2 + 2));+  for(i = 1; i <= n; i++)+    for(j = i; j <= n; j++)+      hc_local[my_iindx[i] - j] = hard_constraints[jindx[j] + i];++  qqk = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  qql = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  qqp = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));++  qq_ud = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 1));+  for(k = 0; k < domains_up->uniq_motif_count; k++){+    qq_ud[k] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+    u = domains_up->uniq_motif_size[k];+    for(i = 1; i <= n - u + 1; i++){+      qq_ud[k][i] = domains_up->exp_energy_cb(vc,+                                              i, i + u - 1,+                                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                              domains_up->data);+    }+  }++  pp_ud = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (n + 1));+  for(k = 0; k < domains_up->uniq_motif_count; k++){+    pp_ud[k] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  }++  for(k = 1; k < n; k++){+    for(l = k + 1; l <= MIN2(k + MAXLOOP, n); l++){+      qqk[l] = domains_up->exp_energy_cb(vc,+                                         k + 1, l,+                                         VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                        domains_up->data);+    }+    for(l = k + turn + 1 + 3; l <= n; l++){+      kl = my_iindx[k] - l;+      if(probs[kl] == 0.)+        continue;+      if(hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){++        for(i = l - 1; i > MAX2(k, l - MAXLOOP - 1); i--){+          qql[i] = domains_up->exp_energy_cb( vc,+                                              i, l - 1,+                                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                              domains_up->data);+        }++        pmax = k + MAXLOOP + 1;+        pmax = MIN2(pmax, l - turn);+        for(p = k + 1; p < pmax; p++){+          u1      = p - k - 1;+          u2_max  = MAXLOOP - u1;+          qmin    = l - 1 - u2_max;+          qmin    = MAX2(qmin, p + turn + 1);+          for(i = p - 1; i > k; i--){+            qqp[i] = domains_up->exp_energy_cb( vc,+                                                i, p - 1,+                                                VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                domains_up->data);+          }++          q5 = 1.;+          if(u1 > 0)+            q5 += qqk[p - 1];++          for(q = qmin; q < l; q++){+            pq = my_iindx[p] - q;++            if(hc_local[pq] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC){+              u2 = l - q - 1;+              ud_bak          = vc->domains_up;+              vc->domains_up  = NULL;+              temp            = vrna_exp_E_interior_loop(vc, k, l, p, q);+              vc->domains_up  = ud_bak;+              temp           *= probs[kl] * qb[pq];++              q3 = 1.;+              if(u2 > 0)+                q3 += qql[q+1];++              temp5           = temp * q3;+              temp3           = temp * q5;++              /* loop over all available motifs */+              for(m = 0; m < domains_up->uniq_motif_count; m++){+                u = domains_up->uniq_motif_size[m];+                for(i = k + 1, j = k + u; j < p; i++, j++){ /* ud in 5' loop */+                  exp_motif_en = qq_ud[m][i];+                  uu1 = i - k - 1;+                  uu2 = p - j - 1;+                  qq1 = 1.;+                  qq2 = 1.;+                  if(uu1 > 0)+                    qq1 += qqk[i - 1];+                  if(uu2 > 0)+                    qq2 += qqp[j + 1];++                  outside = temp5 * qq1 * qq2 * exp_motif_en;+                  pp_ud[m][i] += outside;+                }++                for(i = q + 1, j = q + u; j < l; i++, j++){ /* ud in 3' loop */+                  exp_motif_en = qq_ud[m][i];+                  uu1 = i - q - 1;+                  uu2 = l - j - 1;+                  qq1 = 1.;+                  qq2 = 1.;+                  if(uu1 > 0)+                    qq1 += domains_up->exp_energy_cb( vc,+                                                      q + 1, i - 1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                                      domains_up->data);+                  if(uu2 > 0)+                    qq2 += qql[j + 1];++                  outside = temp3 * qq1 * qq2 * exp_motif_en;+                  pp_ud[m][i] += outside;+                }+              }+            }+          }+        }+      }+    }+  }++  free(hc_local);+  free(qqk);+  free(qql);+  free(qqp);+  for(k = 0; k < domains_up->uniq_motif_count; k++){+    u = domains_up->uniq_motif_size[k];+    /* actually store the results */+    for(i = 1; i <= n - u + 1; i++){+      if(pp_ud[k][i] > 0.)+        domains_up->probs_add(vc,+                              i, i + u - 1,+                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                              pp_ud[k][i],+                              domains_up->data);+    }+    free(qq_ud[k]);+    free(pp_ud[k]);+  }+  free(qq_ud);+  free(pp_ud);+}++PRIVATE INLINE void+ud_outside_mb_loops(vrna_fold_compound_t *vc){+++  char              *hc, *ptype;+  short             *S;+  int               i, j, k, l, kl, jkl, *my_iindx, u, n, cnt, *motif_list,+                    *hc_up, turn, tt, *jindx, *rtype, up, ud_max_size;+  FLT_OR_DBL        *q1k, *qln, temp, *scale, outside, exp_motif_en, *probs,+                    *qb, *qm, q1, q2, expMLclosing, *expMLbase, *qmli,+                    exp_motif_ml_left, exp_motif_ml_right;+  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  vrna_sc_t         *sc;+  vrna_ud_t         *domains_up, *ud_bak;++  n             = vc->length;+  S             = vc->sequence_encoding;+  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  ptype         = vc->ptype;+  pf_params     = vc->exp_params;+  md            = &(vc->exp_params->model_details);+  q1k           = vc->exp_matrices->q1k;+  qln           = vc->exp_matrices->qln;+  qb            = vc->exp_matrices->qb;+  qm            = vc->exp_matrices->qm;+  probs         = vc->exp_matrices->probs;+  scale         = vc->exp_matrices->scale;+  hc_up         = vc->hc->up_ml;+  hc            = vc->hc->matrix;+  domains_up    = vc->domains_up;+  sc            = vc->sc;+  turn          = md->min_loop_size;+  rtype         = &(md->rtype[0]);+  expMLbase     = vc->exp_matrices->expMLbase;+  expMLclosing  = pf_params->expMLclosing;++  for(ud_max_size = u = 0; u < domains_up->uniq_motif_count; u++)+    if(ud_max_size < domains_up->uniq_motif_size[u])+      ud_max_size = domains_up->uniq_motif_size[u];++  for(i = 1; i <= n; i++){+    motif_list = vrna_ud_get_motif_size_at(vc, i, VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP);++    /* 4. Multibranch loops */+    if(motif_list){+      cnt = 0;+      while(-1 != (u = motif_list[cnt])){+        outside = 0.;+        j       = i + u - 1;+        if(j < n){+          if(hc_up[i] >= u){+            exp_motif_en = domains_up->exp_energy_cb( vc,+                                                      i, j,+                                                      VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                      domains_up->data);++            exp_motif_en *= expMLbase[u];++            if(sc){+              if(sc->exp_energy_up)+                exp_motif_en *= sc->exp_energy_up[i][u];+            }++            temp = 0;++            /* 4.1 Motif [i:j] is somewhere in between branching stems */+            for(l = j + turn + 1; l <= n; l++){+              for(k = i - turn - 1; k > 0; k--){+                kl = my_iindx[k] - l;+                if(probs[kl] > 0.){+                  jkl = jindx[l] + k;+                  if(hc[jkl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){ /* respect hard constraints */+                    FLT_OR_DBL qqq;+                    tt = ptype[jkl];+                    tt = rtype[tt];+                    qqq =   probs[kl]+                          * qm[my_iindx[k+1] - (i - 1)]+                          * qm[my_iindx[j+1] - (l - 1)]+                          * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                          * expMLclosing+                          * scale[2];++                    if(sc){+                      if(sc->exp_energy_bp)+                        qqq *= sc->exp_energy_bp[kl];+                    }++                    temp += qqq;+                  }+                }+              }+            }++            outside +=    temp+                        * exp_motif_en;++            /* 4.2 Motif is in left-most unpaired stretch of multiloop */+            FLT_OR_DBL **qm1ui = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (ud_max_size + 1));++            for(l = 0; l <= ud_max_size; l++)+              qm1ui[l] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));++            exp_motif_ml_left = 0.;+            for(l = j + turn + 1; l <= n; l++){+              FLT_OR_DBL lqq = 0.;+              FLT_OR_DBL rqq = 0.;+              for(k = i - 1; k > 0; k--){+                up = i - k - 1;+                kl = my_iindx[k] - l;+                if((hc[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP) && (probs[kl] > 0.) && (hc_up[k+1] >= up)){+                  tt = ptype[jindx[l] + k];+                  tt = rtype[tt];+                  temp =    probs[kl]+                          * expMLbase[up]+                          * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                          * expMLclosing+                          * scale[2];+                  if(sc){+                    if(sc->exp_energy_bp)+                      temp *= sc->exp_energy_bp[kl];+                    if(sc->exp_energy_up)+                      temp *= sc->exp_energy_up[k+1][up];+                  }++                  lqq +=  temp;+                  lqq +=    temp+                          * domains_up->exp_energy_cb(vc,+                                                      k + 1, i - 1,+                                                      VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                                      domains_up->data);+                }+              }++              for(u = j + turn + 1; u < l - turn; u++){++                /* 1st, l-1 is unpaired */+                if(hc_up[l - 1]){+                  temp = qm1ui[1][u] * expMLbase[1];+                  if(sc){+                    if(sc->exp_energy_up)+                      temp *= sc->exp_energy_up[l - 1][1];+                  }+                  qm1ui[0][u] = temp;+                } else {+                  qm1ui[0][u] = 0.;+                }++                /* 2nd, l-1 is the final position of another motif [p:l-1] */+                for(cnt = 0; cnt < domains_up->uniq_motif_count; cnt++){+                  int size = domains_up->uniq_motif_size[cnt];+                  if((u < l - size) && (hc_up[l - size] >= size)){+                    temp  =   qm1ui[size][u]+                            * expMLbase[size]+                            * domains_up->exp_energy_cb(vc,+                                                        l - size, l - 1,+                                                        VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                        domains_up->data);+                    if(sc){+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[l - size][size];+                    }+                    qm1ui[0][u] += temp;+                  }+                }++                /* 3rd, l - 1 pairs with u */+                if(hc[jindx[l - 1] + u] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+                  tt    = ptype[jindx[l - 1] + u];+                  temp  =   qb[my_iindx[u] - (l - 1)]+                          * exp_E_MLstem(tt, S[u - 1], S[l], pf_params);++                  qm1ui[0][u] += temp;+                }++                rqq += qm[my_iindx[j+1] - (u - 1)] * qm1ui[0][u];+              }++              /* finally, compose contribution */+              exp_motif_ml_left += lqq * rqq;++              /* rotate auxiliary arrays */+              FLT_OR_DBL *tmp = qm1ui[ud_max_size];+              for(cnt = ud_max_size; cnt > 0; cnt--)+                qm1ui[cnt] = qm1ui[cnt - 1];+              qm1ui[0] = tmp;+            }++            /* cleanup memory */+            for(l = 0; l <= ud_max_size; l++)+              free(qm1ui[l]);+            free(qm1ui);++            outside +=    exp_motif_ml_left+                        * exp_motif_en;++            /* 4.3 Motif is in right-most unpaired stretch of multiloop */+            qmli = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * n);+            exp_motif_ml_right = 0.;+            for(k = i - turn - 1; k > 0; k--){+              FLT_OR_DBL lqq = 0.;+              FLT_OR_DBL rqq = 0;++              /* update qmli[k] = qm1[k,i-1] */+              for(qmli[k] = 0., u = k + turn + 1; u < i; u++){+                /* respect hard constraints */+                if(hc[jindx[u] + k] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+                  up = (i - 1) - (u + 1) + 1;+                  if(hc_up[u+1] >= up){+                    temp =    qb[my_iindx[k] - u]+                            * expMLbase[up];++                    /* add soft constraints */+                    if(sc){+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[u+1][up];+                    }+                    qmli[k] += temp;++                    /* add contributions of other motifs within [u+1:i-1] */+                    qmli[k] +=    temp+                                * domains_up->exp_energy_cb(vc,+                                                            u+1, i-1,+                                                            VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                                            domains_up->data);+                  }+                }+              }++              for(u = k + turn; u < i - turn; u++){+                lqq +=    qm[my_iindx[k+1] - (u - 1)]+                        * qmli[u];+              }++              for(l = j + 1; l <= n; l++){+                kl = my_iindx[k] - l;+                if(hc[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+                  int up;+                  tt = ptype[jindx[l] + k];+                  tt = rtype[tt];+                  up = l - j - 1;+                  if(hc_up[j + 1] >= up){+                    temp =    probs[kl]+                            * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                            * expMLclosing+                            * scale[2]+                            * expMLbase[up];++                    if(sc){+                      if(sc->exp_energy_bp)+                        temp *= sc->exp_energy_bp[kl];+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[j+1][up];+                    }++                    rqq += temp;++                    /* add contributions of other motifs within [j+1:l-1] */+                    rqq  +=   temp+                            * domains_up->exp_energy_cb(vc,+                                                        j+1, l-1,+                                                        VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                                        domains_up->data);+                  }+                }+              }+              exp_motif_ml_right += rqq * lqq;+            }+            free(qmli);+            qmli = NULL;++            outside +=    exp_motif_ml_right+                        * exp_motif_en;+          }+        }++        if(outside > 0.)+          domains_up->probs_add(vc,+                                i, j,+                                VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                outside,+                                domains_up->data);++        cnt++;+      }+    }+    free(motif_list);+  }++}++PRIVATE INLINE void+ud_outside_mb_loops2(vrna_fold_compound_t *vc){+++  char              *hc, *ptype, *hc_local;+  short             *S;+  int               i, j, k, l, kl, jkl, *my_iindx, u, n, cnt, *motif_list,+                    *hc_up, turn, tt, *jindx, *rtype, up, ud_max_size;+  FLT_OR_DBL        *q1k, *qln, temp, *scale, outside, exp_motif_en, *probs,+                    *qb, *qm, q1, q2, expMLclosing, *expMLbase, *qmli,+                    exp_motif_ml_left, exp_motif_ml_right, *qqi, *qqj,+                    *qqmi, *qqmj;+  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  vrna_sc_t         *sc;+  vrna_ud_t         *domains_up, *ud_bak;++  n             = vc->length;+  S             = vc->sequence_encoding;+  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  ptype         = vc->ptype;+  pf_params     = vc->exp_params;+  md            = &(vc->exp_params->model_details);+  q1k           = vc->exp_matrices->q1k;+  qln           = vc->exp_matrices->qln;+  qb            = vc->exp_matrices->qb;+  qm            = vc->exp_matrices->qm;+  probs         = vc->exp_matrices->probs;+  scale         = vc->exp_matrices->scale;+  hc_up         = vc->hc->up_ml;+  hc            = vc->hc->matrix;+  domains_up    = vc->domains_up;+  sc            = vc->sc;+  turn          = md->min_loop_size;+  rtype         = &(md->rtype[0]);+  expMLbase     = vc->exp_matrices->expMLbase;+  expMLclosing  = pf_params->expMLclosing;++  hc_local = (char *)vrna_alloc(sizeof(char) * (((n + 1) * (n + 2)) /2 + 2));+  for(i = 1; i <= n; i++)+    for(j = i; j <= n; j++)+      hc_local[my_iindx[i] - j] = hc[jindx[j] + i];++  for(ud_max_size = u = 0; u < domains_up->uniq_motif_count; u++)+    if(ud_max_size < domains_up->uniq_motif_size[u])+      ud_max_size = domains_up->uniq_motif_size[u];++  qqi = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  qqj = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  qqmi = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));+  qqmj = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 1));++  for(i = 1; i <= n; i++){+    motif_list = vrna_ud_get_motif_size_at(vc, i, VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP);++    /* 4. Multibranch loops */+    if(motif_list){+      cnt = 0;+      while(-1 != (u = motif_list[cnt])){+        outside = 0.;+        j       = i + u - 1;+        if(j < n){+          if(hc_up[i] >= u){+            exp_motif_en = domains_up->exp_energy_cb( vc,+                                                      i, j,+                                                      VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                      domains_up->data);+            for(k = 1; k < i; k++){+              qqi[k] = domains_up->exp_energy_cb( vc,+                                                  k, i - 1,+                                                  VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                                  domains_up->data);+              qqmi[k] = qm[my_iindx[k] - (i - 1)];+            }+            for(l = j + 1; l <= n; l++){+              qqj[l] = domains_up->exp_energy_cb( vc,+                                                  j + 1, l,+                                                  VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                                  domains_up->data);+              qqmj[k] = qm[my_iindx[j + 1] - l];+            }+            exp_motif_en *= expMLbase[u];++            if(sc){+              if(sc->exp_energy_up)+                exp_motif_en *= sc->exp_energy_up[i][u];+            }++            temp = 0;++            /* 4.1 Motif [i:j] is somewhere in between branching stems */+            for(l = j + turn + 1; l <= n; l++){+              for(k = i - turn - 1; k > 0; k--){+                kl = my_iindx[k] - l;+                if(probs[kl] > 0.){+                  jkl = jindx[l] + k;+                  if(hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){ /* respect hard constraints */+                    FLT_OR_DBL qqq;+                    tt = ptype[jkl];+                    tt = rtype[tt];+                    qqq =   probs[kl]+                          * qqmi[k + 1]+                          * qqmj[l - 1]+                          * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                          * expMLclosing+                          * scale[2];++                    if(sc){+                      if(sc->exp_energy_bp)+                        qqq *= sc->exp_energy_bp[kl];+                    }++                    temp += qqq;+                  }+                }+              }+            }++            outside +=    temp+                        * exp_motif_en;++            /* 4.2 Motif is in left-most unpaired stretch of multiloop */+            FLT_OR_DBL **qm1ui = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (ud_max_size + 1));++            for(l = 0; l <= ud_max_size; l++)+              qm1ui[l] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));++            exp_motif_ml_left = 0.;+            for(l = j + turn + 1; l <= n; l++){+              FLT_OR_DBL lqq = 0.;+              FLT_OR_DBL rqq = 0.;+              for(k = i - 1; k > 0; k--){+                up = i - k - 1;+                kl = my_iindx[k] - l;+                if((hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP) && (probs[kl] > 0.) && (hc_up[k+1] >= up)){+                  tt = ptype[jindx[l] + k];+                  tt = rtype[tt];+                  temp =    probs[kl]+                          * expMLbase[up]+                          * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                          * expMLclosing+                          * scale[2];+                  if(sc){+                    if(sc->exp_energy_bp)+                      temp *= sc->exp_energy_bp[kl];+                    if(sc->exp_energy_up)+                      temp *= sc->exp_energy_up[k+1][up];+                  }++                  lqq +=  temp;+                  lqq +=    temp+                          * qqi[k+1];+                }+              }++              for(u = j + turn + 1; u < l - turn; u++){++                /* 1st, l-1 is unpaired */+                if(hc_up[l - 1]){+                  temp = qm1ui[1][u] * expMLbase[1];+                  if(sc){+                    if(sc->exp_energy_up)+                      temp *= sc->exp_energy_up[l - 1][1];+                  }+                  qm1ui[0][u] = temp;+                } else {+                  qm1ui[0][u] = 0.;+                }++                /* 2nd, l-1 is the final position of another motif [p:l-1] */+                for(cnt = 0; cnt < domains_up->uniq_motif_count; cnt++){+                  int size = domains_up->uniq_motif_size[cnt];+                  if((u < l - size) && (hc_up[l - size] >= size)){+                    temp  =   qm1ui[size][u]+                            * expMLbase[size]+                            * domains_up->exp_energy_cb(vc,+                                                        l - size, l - 1,+                                                        VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                        domains_up->data);+                    if(sc){+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[l - size][size];+                    }+                    qm1ui[0][u] += temp;+                  }+                }++                /* 3rd, l - 1 pairs with u */+                int ul = my_iindx[u] - (l - 1);+                if(hc_local[ul] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+                  tt    = ptype[jindx[l - 1] + u];+                  temp  =   qb[ul]+                          * exp_E_MLstem(tt, S[u - 1], S[l], pf_params);++                  qm1ui[0][u] += temp;+                }++                rqq += qqmj[u - 1] * qm1ui[0][u];+              }++              /* finally, compose contribution */+              exp_motif_ml_left += lqq * rqq;++              /* rotate auxiliary arrays */+              FLT_OR_DBL *tmp = qm1ui[ud_max_size];+              for(cnt = ud_max_size; cnt > 0; cnt--)+                qm1ui[cnt] = qm1ui[cnt - 1];+              qm1ui[0] = tmp;+            }++            /* cleanup memory */+            for(l = 0; l <= ud_max_size; l++)+              free(qm1ui[l]);+            free(qm1ui);++            outside +=    exp_motif_ml_left+                        * exp_motif_en;++            /* 4.3 Motif is in right-most unpaired stretch of multiloop */+            qmli = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * n);+            exp_motif_ml_right = 0.;+            for(k = i - turn - 1; k > 0; k--){+              FLT_OR_DBL lqq = 0.;+              FLT_OR_DBL rqq = 0;++              /* update qmli[k] = qm1[k,i-1] */+              for(qmli[k] = 0., u = k + turn + 1; u < i; u++){+                int ku = my_iindx[k] - u;+                /* respect hard constraints */+                if(hc_local[ku] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+                  up = (i - 1) - (u + 1) + 1;+                  if(hc_up[u+1] >= up){+                    temp =    qb[ku]+                            * expMLbase[up];++                    /* add soft constraints */+                    if(sc){+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[u+1][up];+                    }+                    qmli[k] += temp;++                    /* add contributions of other motifs within [u+1:i-1] */+                    qmli[k] +=    temp+                                * qqi[u + 1];+                  }+                }+              }++              for(u = k + turn; u < i - turn; u++){+                lqq +=    qm[my_iindx[k+1] - (u - 1)]+                        * qmli[u];+              }++              for(l = j + 1; l <= n; l++){+                kl = my_iindx[k] - l;+                if(hc_local[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+                  int up;+                  tt = ptype[jindx[l] + k];+                  tt = rtype[tt];+                  up = l - j - 1;+                  if(hc_up[j + 1] >= up){+                    temp =    probs[kl]+                            * exp_E_MLstem(tt, S[l-1], S[k+1], pf_params)+                            * expMLclosing+                            * scale[2]+                            * expMLbase[up];++                    if(sc){+                      if(sc->exp_energy_bp)+                        temp *= sc->exp_energy_bp[kl];+                      if(sc->exp_energy_up)+                        temp *= sc->exp_energy_up[j+1][up];+                    }++                    rqq += temp;++                    /* add contributions of other motifs within [j+1:l-1] */+                    rqq  +=   temp+                            * qqj[l - 1];+                  }+                }+              }+              exp_motif_ml_right += rqq * lqq;+            }+            free(qmli);+            qmli = NULL;++            outside +=    exp_motif_ml_right+                        * exp_motif_en;+          }+        }++        if(outside > 0.)+          domains_up->probs_add(vc,+                                i, j,+                                VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                outside,+                                domains_up->data);++        cnt++;+      }+    }+    free(motif_list);+  }++  free(qqi);+  free(qqj);+  free(qqmi);+  free(qqmj);+  free(hc_local);+}+++PRIVATE FLT_OR_DBL+numerator_single( vrna_fold_compound_t *vc,+                  int i,+                  int j){++  return 1.;+}++PRIVATE FLT_OR_DBL+numerator_comparative(vrna_fold_compound_t *vc,+                      int i,+                      int j){++  int     *pscore = vc->pscore;             /* precomputed array of pair types */                      +  double  kTn     = vc->exp_params->kT/10.; /* kT in cal/mol  */+  int     *jindx  = vc->jindx;++  return exp(pscore[jindx[j]+i]/kTn);+}++/* calculate base pairing probs */+PRIVATE INLINE void+bppm_circ(vrna_fold_compound_t *vc){++  unsigned char     type;+  char              *ptype, *sequence;+  char              *hard_constraints;+  short             *S, *S1;+  int               n, i,j,k,l, ij, *rtype, *my_iindx, *jindx, turn;+  FLT_OR_DBL        tmp2, expMLclosing, *qb, *qm, *qm1, *probs, *scale, *expMLbase, qo;+  vrna_hc_t         *hc;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  vrna_md_t         *md;+  FLT_OR_DBL (*numerator_f)(vrna_fold_compound_t *vc, int i, int j);++  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  S                 = vc->sequence_encoding2;+  S1                = vc->sequence_encoding;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  ptype             = vc->ptype;+  turn              = md->min_loop_size;+  hc                = vc->hc;+  matrices          = vc->exp_matrices;+  qb                = matrices->qb;+  qm                = matrices->qm;+  qm1               = matrices->qm1;+  probs             = matrices->probs;+  scale             = matrices->scale;+  expMLbase         = matrices->expMLbase;+  qo                = matrices->qo;+  hard_constraints  = hc->matrix;+  sequence          = vc->sequence;+++  expMLclosing  = pf_params->expMLclosing;+  rtype         = &(pf_params->model_details.rtype[0]);+  n             = S[0];++  switch(vc->type){+    case  VRNA_FC_TYPE_SINGLE:    numerator_f = numerator_single;+                                  break;+    case  VRNA_FC_TYPE_COMPARATIVE: numerator_f = numerator_comparative;+                                  break;+    default:                      numerator_f = NULL;+                                  break;+  }++  /*+    The hc_local array provides row-wise access to hc->matrix, i.e.+    my_iindx. Using this in the cubic order loop for multiloops below+    results in way faster computation due to fewer cache misses. Also,+    it introduces only little memory overhead, e.g. ~450MB for+    sequences of length 30,000+  */+  char *hc_local = (char *)vrna_alloc(sizeof(char) * (((n + 1) * (n + 2)) /2 + 2));+  for(i = 1; i <= n; i++)+    for(j = i; j <= n; j++)+      hc_local[my_iindx[i] - j] = hard_constraints[jindx[j] + i];++  /* 1. exterior pair i,j */+  for (i=1; i<=n; i++) {+    for (j=i; j<=MIN2(i+turn,n); j++)+      probs[my_iindx[i]-j] = 0;+    for (j=i+turn+1; j<=n; j++) {+      ij = my_iindx[i]-j;+      if(qb[ij] > 0.){+        probs[ij] = numerator_f(vc, i, j)/qo;++        type = (unsigned char)ptype[jindx[j] + i];++        unsigned char rt = rtype[type];++        /* 1.1. Exterior Hairpin Contribution */+        tmp2 = vrna_exp_E_hp_loop(vc, j, i);++        /* 1.2. Exterior Interior Loop Contribution                     */+        /* 1.2.1. i,j  delimtis the "left" part of the interior loop    */+        /* (j,i) is "outer pair"                                        */+        for(k=1; k < i-turn-1; k++){+          int ln1, lstart;+          ln1 = k + n - j - 1;+          if(ln1>MAXLOOP) break;+          lstart = ln1+i-1-MAXLOOP;+          if(lstart<k+turn+1) lstart = k + turn + 1;+          for(l=lstart; l < i; l++){+            int ln2, type_2;+            type_2 = (unsigned char)ptype[jindx[l] + k];+            if (type_2==0) continue;+            ln2 = i - l - 1;+            if(ln1+ln2>MAXLOOP) continue;+            tmp2 += qb[my_iindx[k] - l]+                    * exp_E_IntLoop(ln1,+                                    ln2,+                                    rt,+                                    rtype[type_2],+                                    S1[j+1],+                                    S1[i-1],+                                    S1[k-1],+                                    S1[l+1],+                                    pf_params)+                    * scale[ln1 + ln2];+          }+        }+        /* 1.2.2. i,j  delimtis the "right" part of the interior loop  */+        for(k=j+1; k < n-turn; k++){+          int ln1, lstart;+          ln1 = k - j - 1;+          if((ln1 + i - 1)>MAXLOOP) break;+          lstart = ln1+i-1+n-MAXLOOP;+          if(lstart<k+turn+1) lstart = k + turn + 1;+          for(l=lstart; l <= n; l++){+            int ln2, type_2;+            type_2 = (unsigned char)ptype[jindx[l] + k];+            if (type_2==0) continue;+            ln2 = i - 1 + n - l;+            if(ln1+ln2>MAXLOOP) continue;+            tmp2 += qb[my_iindx[k] - l]+                    * exp_E_IntLoop(ln2,+                                    ln1,+                                    rtype[type_2],+                                    rt,+                                    S1[l+1],+                                    S1[k-1],+                                    S1[i-1],+                                    S1[j+1],+                                    pf_params)+                    * scale[ln1 + ln2];+          }+        }+        /* 1.3 Exterior multiloop decomposition */+        /* 1.3.1 Middle part                    */+        if((i>turn+2) && (j<n-turn-1))+          tmp2 += qm[my_iindx[1]-i+1]+                  * qm[my_iindx[j+1]-n]+                  * expMLclosing+                  * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);++        /* 1.3.2 Left part  */+        for(k=turn+2; k < i-turn-2; k++)+          tmp2 += qm[my_iindx[1]-k]+                  * qm1[jindx[i-1]+k+1]+                  * expMLbase[n-j]+                  * expMLclosing+                  * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);++        /* 1.3.3 Right part */+        for(k=j+turn+2; k < n-turn-1;k++)+          tmp2 += qm[my_iindx[j+1]-k]+                  * qm1[jindx[n]+k+1]+                  * expMLbase[i-1]+                  * expMLclosing+                  * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);++        /* all exterior loop decompositions for pair i,j done  */+        probs[ij] *= tmp2;++      }+      else probs[ij] = 0;+    }+  }+}++++PRIVATE double+wrap_mean_bp_distance(FLT_OR_DBL *p,+                      int length,+                      int *index,+                      int turn){++  int         i,j;+  double      d = 0.;++  /* compute the mean base pair distance in the thermodynamic ensemble */+  /* <d> = \sum_{a,b} p_a p_b d(S_a,S_b)+     this can be computed from the pair probs p_ij as+     <d> = \sum_{ij} p_{ij}(1-p_{ij}) */++  for (i=1; i<=length; i++)+    for (j=i+turn+1; j<=length; j++)+      d += p[index[i]-j] * (1-p[index[i]-j]);++  return 2*d;+}+++PUBLIC double+vrna_mean_bp_distance_pr( int length,+                          FLT_OR_DBL *p){++  int *index = vrna_idx_row_wise((unsigned int) length);+  double d;++  if (p==NULL)+    vrna_message_error("vrna_mean_bp_distance_pr: p==NULL. You need to supply a valid probability matrix");++  d = wrap_mean_bp_distance(p, length, index, TURN);++  free(index);+  return d;+}++PUBLIC double+vrna_mean_bp_distance(vrna_fold_compound_t *vc){++  if(!vc){+    vrna_message_error("vrna_mean_bp_distance: run vrna_pf_fold first!");+  } else if(!vc->exp_matrices){+    vrna_message_error("vrna_mean_bp_distance: exp_matrices==NULL!");+  } else if( !vc->exp_matrices->probs){+    vrna_message_error("vrna_mean_bp_distance: probs==NULL!");+  }++  return wrap_mean_bp_distance( vc->exp_matrices->probs,+                                vc->length,+                                vc->iindx,+                                vc->exp_params->model_details.min_loop_size);+}++PUBLIC vrna_plist_t *+vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff){++  vrna_plist_t             *pl;+  int               i, j, plsize, turn, length, *index, *jindx, *rtype, num;+  char              *ptype;+  FLT_OR_DBL        *qb, *probs, *scale, p;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;++  plsize  = 256;+  pl      = NULL;+  num     = 0;++  if(vc){+    pf_params = vc->exp_params;+    length    = vc->length;+    index     = vc->iindx;+    jindx     = vc->jindx;+    rtype     = &(pf_params->model_details.rtype[0]);+    ptype     = vc->ptype;+    matrices  = vc->exp_matrices;+    qb        = matrices->qb;+    probs     = matrices->probs;+    scale     = matrices->scale;+    turn      = pf_params->model_details.min_loop_size;++    pl        = (vrna_plist_t *) vrna_alloc(plsize*sizeof(vrna_plist_t));++    for (i=1; i<length; i++)+      for (j=i+turn+3; j<=length; j++) {+        if((p=probs[index[i]-j]) < cutoff) continue;+        if (qb[index[i+1]-(j-1)]<FLT_MIN) continue;+        p *= qb[index[i+1]-(j-1)]/qb[index[i]-j];+        p *= exp_E_IntLoop(0,0,(unsigned char)ptype[jindx[j]+i],rtype[(unsigned char)ptype[jindx[j-1] + i+1]],+                           0,0,0,0, pf_params)*scale[2];/* add *scale[u1+u2+2] */+        if (p>cutoff) {+          pl[num].i     = i;+          pl[num].j     = j;+          pl[num].type  = 0;+          pl[num++].p   = p;+          if (num>=plsize) {+            plsize *= 2;+            pl = vrna_realloc(pl, plsize*sizeof(vrna_plist_t));+          }+        }+      }+    pl[num].i=0;+  }++  return pl;+}+++PRIVATE void+alipf_create_bppm(vrna_fold_compound_t *vc,+                  char *structure){++  int s;+  int i,j,k,l, ij, kl, ii, ll, tt, *type, ov=0;+  FLT_OR_DBL temp, prm_MLb;+#ifdef USE_FLOAT_PF+  FLT_OR_DBL Qmax=0.;+#endif+  FLT_OR_DBL prmt,prmt1;+  FLT_OR_DBL qbt1, *tmp, tmp2, tmp3;++  int             n_seq         = vc->n_seq;+  int             n             = vc->length;+++  short             **S           = vc->S;                                                                   +  short             **S5          = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/            +  short             **S3          = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/            +  char              **Ss          = vc->Ss;+  unsigned short    **a2s         = vc->a2s;                                                                   +  vrna_exp_param_t  *pf_params    = vc->exp_params;+  vrna_mx_pf_t      *matrices     = vc->exp_matrices;+  vrna_md_t         *md           = &(pf_params->model_details);+  vrna_hc_t         *hc           = vc->hc;+  vrna_sc_t         **sc          = vc->scs;+  int               *my_iindx     = vc->iindx;+  int               *jindx        = vc->jindx;+  FLT_OR_DBL        *q            = matrices->q;+  FLT_OR_DBL        *qb           = matrices->qb;+  FLT_OR_DBL        *qm           = matrices->qm;+  FLT_OR_DBL        *qm1          = matrices->qm1;+  FLT_OR_DBL        qo            = matrices->qo;+  int               *pscore       = vc->pscore;     /* precomputed array of pair types */                      +  int               *rtype        = &(md->rtype[0]);+  int               circular      = md->circ;+  FLT_OR_DBL        *scale        = matrices->scale;+  FLT_OR_DBL        *expMLbase    = matrices->expMLbase;+  FLT_OR_DBL        expMLclosing  = pf_params->expMLclosing;+  FLT_OR_DBL        *probs        = matrices->probs;+  char              *hard_constraints = hc->matrix;++  double kTn;+  FLT_OR_DBL pp;++  FLT_OR_DBL *prm_l   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  FLT_OR_DBL *prm_l1  = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  FLT_OR_DBL *prml    = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  type                = (int *)vrna_alloc(sizeof(int) * n_seq);++  if((matrices->q1k == NULL) || (matrices->qln == NULL)){+    free(matrices->q1k);+    matrices->q1k = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+1));+    free(matrices->qln);+    matrices->qln = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  }++  FLT_OR_DBL *q1k    = matrices->q1k;+  FLT_OR_DBL *qln    = matrices->qln;++  for (k=1; k<=n; k++) {+    q1k[k] = q[my_iindx[1] - k];+    qln[k] = q[my_iindx[k] - n];+  }+  q1k[0] = 1.0;+  qln[n+1] = 1.0;+++  kTn = pf_params->kT/10.;   /* kT in cal/mol  */++  for (i=0; i<=n; i++)+    prm_l[i]=prm_l1[i]=prml[i]=0;++  /* 1. exterior pair i,j and initialization of pr array */+  if(circular){+    for (i=1; i<=n; i++) {+      for (j=i; j<=MIN2(i+TURN,n); j++) probs[my_iindx[i]-j] = 0;+      for (j=i+TURN+1; j<=n; j++) {+        ij = my_iindx[i]-j;+        if (qb[ij]>0.) {+          probs[ij] =  exp(pscore[jindx[j]+i]/kTn)/qo;++          /* get pair types  */+          for (s=0; s<n_seq; s++) {+            type[s] = md->pair[S[s][j]][S[s][i]];+            if (type[s]==0) type[s]=7;+          }++          tmp2 = 0.;++          /* 1.1. Exterior Hairpin Contribution */+          tmp2 += vrna_exp_E_hp_loop(vc, j, i);++          /* 1.2. Exterior Interior Loop Contribution */+          /* recycling of k and l... */+          if(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){++            /* 1.2.1. first we calc exterior loop energy with constraint, that i,j  */+            /* delimtis the "right" part of the interior loop                       */+            /* (l,k) is "outer pair"                                                */+            for(k=1; k < i-TURN-1; k++){+              /* so first, lets calc the length of loop between j and k */+              int ln1, lstart;+              ln1 = k + n - j - 1;+              if(ln1>MAXLOOP)+                break;+              if(hc->up_int[j+1] < ln1)+                break;++              lstart = ln1+i-1-MAXLOOP;+              if(lstart<k+TURN+1) lstart = k + TURN + 1;+              for(l=lstart; l < i; l++){+                int ln2,ln2a,ln1a, type_2;+                ln2 = i - l - 1;+                if(ln1+ln2>MAXLOOP)+                  continue;+                if(hc->up_int[l+1] < ln2)+                  continue;+                if(!(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP))+                  continue;+                +                FLT_OR_DBL qloop=1.;+                if(qb[my_iindx[k]-l]==0.){+                  qloop=0.;+                  continue;+                }++                for (s=0; s<n_seq; s++){+                  ln2a= a2s[s][i-1];+                  ln2a-=a2s[s][l];+                  ln1a= a2s[s][n]-a2s[s][j];+                  ln1a+=a2s[s][k-1];+                  type_2 = md->pair[S[s][l]][S[s][k]];+                  if (type_2 == 0) type_2 = 7;+                  qloop *= exp_E_IntLoop(ln1a, ln2a, type[s], type_2,+                              S[s][j+1],+                              S[s][i-1],+                              S[s][(k>1) ? k-1 : n],+                              S[s][l+1], pf_params);+                }+                if(sc)+                  for(s = 0; s < n_seq; s++){+                    if(sc[s]){+                      ln2a= a2s[s][i-1];+                      ln2a-=a2s[s][l];+                      ln1a= a2s[s][n]-a2s[s][j];+                      ln1a+=a2s[s][k-1];++                      if(sc[s]->exp_energy_up)+                        qloop *=    sc[s]->exp_energy_up[a2s[s][l]+1][ln2a]+                                  * ((j < n) ? sc[s]->exp_energy_up[a2s[s][j]+1][a2s[s][n] - a2s[s][j]] : 1.)+                                  * ((k > 1) ? sc[s]->exp_energy_up[1][a2s[s][k]-1] : 1.);++                      if((ln1a + ln2a == 0) && sc[s]->exp_energy_stack){+                        if(S[s][i] && S[s][j] && S[s][k] && S[s][l]){ /* don't allow gaps in stack */+                          qloop *=    sc[s]->exp_energy_stack[a2s[s][k]]+                                    * sc[s]->exp_energy_stack[a2s[s][l]]+                                    * sc[s]->exp_energy_stack[a2s[s][i]]+                                    * sc[s]->exp_energy_stack[a2s[s][j]];+                        }+                      }+                    }+                  }+                tmp2 += qb[my_iindx[k] - l] * qloop * scale[ln1+ln2];+              }+            }++            /* 1.2.2. second we calc exterior loop energy with constraint, that i,j */+            /* delimtis the "left" part of the interior loop                        */+            /* (j,i) is "outer pair"                                                */+            for(k=j+1; k < n-TURN; k++){+              /* so first, lets calc the length of loop between l and i */+              int ln1, lstart;+              ln1 = k - j - 1;+              if((ln1 + i - 1)>MAXLOOP)+                break;+              if(hc->up_int[j+1] < ln1)+                break;++              lstart = ln1+i-1+n-MAXLOOP;+              if(lstart<k+TURN+1) lstart = k + TURN + 1;+              for(l=lstart; l <= n; l++){+                int ln2, type_2;+                ln2 = i - 1 + n - l;+                if(ln1+ln2>MAXLOOP)+                  continue;+                if(hc->up_int[l+1] < ln2)+                  continue;+                if(!(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP))+                  continue;++                FLT_OR_DBL qloop=1.;+                if(qb[my_iindx[k]-l]==0.){+                  qloop=0.;+                  continue;+                }++                for (s=0; s<n_seq; s++){+                  ln1 = a2s[s][k] - a2s[s][j+1];+                  ln2 = a2s[s][i-1] + a2s[s][n] - a2s[s][l];+                  type_2 = md->pair[S[s][l]][S[s][k]];+                  if (type_2 == 0) type_2 = 7;+                  qloop *= exp_E_IntLoop(ln2, ln1, type_2, type[s],+                          S3[s][l],+                          S5[s][k],+                          S5[s][i],+                          S3[s][j], pf_params);+                }+                if(sc)+                  for(s = 0; s < n_seq; s++){+                    if(sc[s]){+                      ln1 = a2s[s][k] - a2s[s][j+1];+                      ln2 = a2s[s][i-1] + a2s[s][n] - a2s[s][l];++                      if(sc[s]->exp_energy_up)+                        qloop *=    sc[s]->exp_energy_up[a2s[s][j]+1][ln1]+                                  * ((l < n) ? sc[s]->exp_energy_up[a2s[s][l]+1][a2s[s][n] - a2s[s][l]] : 1.)+                                  * ((i > 1) ? sc[s]->exp_energy_up[1][a2s[s][i]-1] : 1.);++                      if((ln1 + ln2 == 0) && sc[s]->exp_energy_stack){+                        if(S[s][i] && S[s][j] && S[s][k] && S[s][l]){ /* don't allow gaps in stack */+                          qloop *=    sc[s]->exp_energy_stack[a2s[s][k]]+                                    * sc[s]->exp_energy_stack[a2s[s][l]]+                                    * sc[s]->exp_energy_stack[a2s[s][i]]+                                    * sc[s]->exp_energy_stack[a2s[s][j]];+                        }+                      }+                    }+                  }+                tmp2 += qb[my_iindx[k] - l] * qloop * scale[ln1+ln2];+              }+            }+          }+          /* 1.3 Exterior multiloop decomposition */+          if(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+            /* 1.3.1 Middle part                    */+            if((i>TURN+2) && (j<n-TURN-1)){++              for (tmp3=1, s=0; s<n_seq; s++){+                tmp3 *= exp_E_MLstem(rtype[type[s]], S5[s][i], S3[s][j], pf_params);+              }+              tmp2 += qm[my_iindx[1]-i+1] * qm[my_iindx[j+1]-n] * tmp3 * pow(expMLclosing,n_seq);+            }+            /* 1.3.2 Left part    */+            for(k=TURN+2; k < i-TURN-2; k++){+              if(hc->up_ml[j+1] < n-j)+                break;++              for (tmp3=1, s=0; s<n_seq; s++){+                tmp3 *= exp_E_MLstem(rtype[type[s]], S5[s][i], S3[s][j], pf_params);+              }++              if(sc)+                for(s = 0; s < n_seq; s++){+                  if(sc[s]){+                    if(sc[s]->exp_energy_bp)+                      tmp3 *= sc[s]->exp_energy_bp[jindx[j] + i];++                    if(sc[s]->exp_energy_up)+                      tmp3 *= sc[s]->exp_energy_up[a2s[s][j]+1][a2s[s][n]-a2s[s][j]];+                  }+                }++              tmp2 += qm[my_iindx[1]-k] * qm1[jindx[i-1]+k+1] * tmp3 * expMLbase[n-j] * pow(expMLclosing,n_seq);+            }+            /* 1.3.3 Right part    */+            for(k=j+TURN+2; k < n-TURN-1;k++){+              if(hc->up_ml[1] < i-1)+                break;++              for (tmp3=1, s=0; s<n_seq; s++){+                tmp3 *= exp_E_MLstem(rtype[type[s]], S5[s][i], S3[s][j], pf_params);+              }++              if(sc)+                for(s = 0; s < n_seq; s++){+                  if(sc[s]){+                    if(sc[s]->exp_energy_bp)+                      tmp3 *= sc[s]->exp_energy_bp[jindx[j] + i];++                    if(sc[s]->exp_energy_up)+                      tmp3 *= sc[s]->exp_energy_up[a2s[s][1]][a2s[s][i]-a2s[s][1]];+                  }+                }++              tmp2 += qm[my_iindx[j+1]-k] * qm1[jindx[n]+k+1] * tmp3 * expMLbase[i-1] * pow(expMLclosing,n_seq);+            }+          }+          probs[ij] *= tmp2;+        }+        else probs[ij] = 0;+      }  /* end for j=..*/+    }  /* end or i=...  */+  } /* end if(circular)  */+  else{+    for (i=1; i<=n; i++) {+      for (j=i; j<=MIN2(i+TURN,n); j++)+        probs[my_iindx[i]-j] = 0;++      for (j=i+TURN+1; j<=n; j++) {+        ij = my_iindx[i]-j;+        if ((qb[ij] > 0.) && (hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP)){+          probs[ij] = q1k[i-1] * qln[j+1]/q1k[n] * exp(pscore[jindx[j]+i]/kTn);+          for (s=0; s<n_seq; s++) {+            int typ;+            typ = md->pair[S[s][i]][S[s][j]]; if (typ==0) typ=7;+            probs[ij] *= exp_E_ExtLoop(typ, (i>1) ? S5[s][i] : -1, (j<n) ? S3[s][j] : -1, pf_params);+          }+        } else+          probs[ij] = 0;+      }+    }+  } /* end if(!circular)  */+  for (l=n; l>TURN+1; l--) {++    /* 2. bonding k,l as substem of 2:loop enclosed by i,j */+    for (k=1; k<l-TURN; k++) {+      pp = 0.;+      kl = my_iindx[k]-l;+      if (qb[kl] == 0.) continue;+      if(!(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC)) continue;++      for (s=0; s<n_seq; s++) {+        type[s] = md->pair[S[s][l]][S[s][k]];+        if (type[s]==0) type[s]=7;+      }++      for (i=MAX2(1,k-MAXLOOP-1); i<=k-1; i++){+        if(hc->up_int[i+1] < k - i - 1)+          continue;++        for (j=l+1; j<=MIN2(l+ MAXLOOP -k+i+2,n); j++) {+          FLT_OR_DBL qloop=1;+          ij = my_iindx[i] - j;++          if(probs[ij] == 0.) continue;+          if(!(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP)) continue;+          if(hc->up_int[l+1] < j - l - 1) break;++          for (s=0; s<n_seq; s++) {+            int typ, u1, u2;+            u1 = a2s[s][k-1] - a2s[s][i];+            u2 = a2s[s][j-1] - a2s[s][l];+            typ = md->pair[S[s][i]][S[s][j]]; if (typ==0) typ=7;+            qloop *=  exp_E_IntLoop(u1, u2, typ, type[s], S3[s][i], S5[s][j], S5[s][k], S3[s][l], pf_params);+          }++          if(sc){+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                int u1, u2;+                u1 = a2s[s][k-1] - a2s[s][i];+                u2 = a2s[s][j-1] - a2s[s][l];+/*+                u1 = k - i - 1;+                u2 = j - l - 1;+*/+                if(sc[s]->exp_energy_bp)+                  qloop *= sc[s]->exp_energy_bp[jindx[j] + i];++                if(sc[s]->exp_energy_up)+                  qloop *=    sc[s]->exp_energy_up[a2s[s][i]+1][u1]+                              * sc[s]->exp_energy_up[a2s[s][l]+1][u2];++                if(sc[s]->exp_energy_stack)+                  if(u1 + u2 == 0){+                    if(S[s][i] && S[s][j] && S[s][k] && S[s][l]){ /* don't allow gaps in stack */+                      qloop *=    sc[s]->exp_energy_stack[i]+                                * sc[s]->exp_energy_stack[k]+                                * sc[s]->exp_energy_stack[l]+                                * sc[s]->exp_energy_stack[j];+                    }+                  }+              }+            }+          }+          pp += probs[ij]*qloop*scale[k-i + j-l];+        }+      }+      probs[kl] += pp * exp(pscore[jindx[l]+k]/kTn);+    }+    /* 3. bonding k,l as substem of multi-loop enclosed by i,j */+    prm_MLb = 0.;+    if (l<n)+      for (k=2; k<l-TURN; k++) {+      i = k-1;+      prmt = prmt1 = 0.;++      if(1 /* hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC */){+        ii = my_iindx[i];     /* ii-j=[i,j]     */+        ll = my_iindx[l+1];   /* ll-j=[l+1,j-1] */+        if(hard_constraints[jindx[l+1] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+          prmt1 = probs[ii-(l+1)];+          for (s=0; s<n_seq; s++) {+            tt = md->pair[S[s][l+1]][S[s][i]]; if (tt==0) tt=7;+            prmt1 *= exp_E_MLstem(tt, S5[s][l+1], S3[s][i], pf_params) * expMLclosing;+          }++          if(sc)+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                if(sc[s]->exp_energy_bp)+                  prmt1 *= sc[s]->exp_energy_bp[jindx[l+1] + i];+              }+            }+        }++        for (j=l+2; j<=n; j++){+          pp = 1.;+          if(probs[ii-j]==0) continue;+          if(!(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP)) continue;++          for (s=0; s<n_seq; s++) {+            tt = md->pair[S[s][j]][S[s][i]]; if (tt==0) tt=7;+            pp *=  exp_E_MLstem(tt, S5[s][j], S3[s][i], pf_params) * expMLclosing;+          }++          if(sc)+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                if(sc[s]->exp_energy_bp)+                  pp *= sc[s]->exp_energy_bp[jindx[j] + i];+              }+            }++          prmt +=  probs[ii-j] * pp * qm[ll-(j-1)];+        }+        kl = my_iindx[k]-l;++        prml[ i] = prmt;++        pp = 0.;+        if(hc->up_ml[l+1]){+          pp = prm_l1[i] * expMLbase[1];+          if(sc)+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                if(sc[s]->exp_energy_up)+                  pp *= sc[s]->exp_energy_up[a2s[s][l+1]][1];+              }+            }+        }+        prm_l[i] = pp + prmt1; /* expMLbase[1]^n_seq */++        pp = 0.;+        if(hc->up_ml[i]){+          pp = prm_MLb * expMLbase[1];+          if(sc)+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                if(sc[s]->exp_energy_up)+                  pp *= sc[s]->exp_energy_up[a2s[s][i]][1];+              }+            }+        }+        prm_MLb = pp + prml[i];++        /* same as:    prm_MLb = 0;+           for (i=1; i<=k-1; i++) prm_MLb += prml[i]*expMLbase[k-i-1]; */++        prml[i] = prml[ i] + prm_l[i];++        if (qb[kl] == 0.) continue;++        temp = prm_MLb;++        for (i=1;i<=k-2; i++)+          temp += prml[i]*qm[my_iindx[i+1] - (k-1)];++        for (s=0; s<n_seq; s++) {+          tt=md->pair[S[s][k]][S[s][l]]; if (tt==0) tt=7;+          temp *= exp_E_MLstem(tt, S5[s][k], S3[s][l], pf_params);+        }+        probs[kl] += temp * scale[2] * exp(pscore[jindx[l]+k]/kTn);+      } else { /* (k,l) not allowed to be substem of multiloop closed by (i,j) */+        prml[i] = prm_l[i] = prm_l1[i] = 0.;+      }++#ifdef USE_FLOAT_PF+      if (probs[kl]>Qmax) {+        Qmax = probs[kl];+        if (Qmax>FLT_MAX/10.)+          vrna_message_warning("%d %d %g %g\n", i,j,probs[kl],qb[kl]);+      }+      if (probs[kl]>FLT_MAX) {+        ov++;+        probs[kl]=FLT_MAX;+      }+#endif+    } /* end for (k=2..) */+    tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;++  }  /* end for (l=..)   */++  for (i=1; i<=n; i++)+    for (j=i+TURN+1; j<=n; j++) {+      ij = my_iindx[i]-j;+      probs[ij] *= qb[ij] *exp(-pscore[jindx[j]+i]/kTn);+    }++  if (structure!=NULL){+    char *s = vrna_db_from_probs(probs, (unsigned int)n);+    memcpy(structure, s, n);+    structure[n] = '\0';+    free(s);+  }++  if(ov > 0)+    vrna_message_warning("%d overflows occurred while backtracking;\n"+                                "you might try a smaller pf_scale than %g\n",+                                ov, pf_params->pf_scale);++  free(type);+  free(prm_l);+  free(prm_l1);+  free(prml);+}+
+ C/ViennaRNA/equilibrium_probs.h view
@@ -0,0 +1,81 @@+#ifndef VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H+#define VIENNA_RNA_PACKAGE_EQUILIBRIUM_PROBS_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#include <ViennaRNA/data_structures.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     equilibrium_probs.h+ *  @ingroup  pf_fold+ *  @brief    Equilibrium Probability implementations+ * + *  This file includes various implementations for equilibrium+ *  probability computations based on the partition function+ *  of an RNA sequence, two concatenated sequences, or a sequence+ *  alignment.+ */++/*+#################################################+# BASE PAIR PROBABILITY RELATED FUNCTIONS       #+#################################################+*/++void  vrna_pairing_probs(vrna_fold_compound_t *vc, char *structure);++/**+ *  @brief Get the mean base pair distance in the thermodynamic ensemble from a probability matrix+ * + *  @f$<d> = \sum_{a,b} p_a p_b d(S_a,S_b)@f$\n+ *  this can be computed from the pair probs @f$p_ij@f$ as\n+ *  @f$<d> = \sum_{ij} p_{ij}(1-p_{ij})@f$+ * + *  @ingroup pf_fold+ *+ *  @param length The length of the sequence+ *  @param pr     The matrix containing the base pair probabilities+ *  @return       The mean pair distance of the structure ensemble+ */+double vrna_mean_bp_distance_pr(int length, FLT_OR_DBL *pr);++/**+ *  @brief Get the mean base pair distance in the thermodynamic ensemble+ * + *  @f$<d> = \sum_{a,b} p_a p_b d(S_a,S_b)@f$\n+ *  this can be computed from the pair probs @f$p_ij@f$ as\n+ *  @f$<d> = \sum_{ij} p_{ij}(1-p_{ij})@f$+ * + *  @ingroup pf_fold+ *+ *  @param vc     The fold compound data structure+ *  @return       The mean pair distance of the structure ensemble+ */+double vrna_mean_bp_distance(vrna_fold_compound_t *vc);++/**+ *  @brief  Compute stacking probabilities+ *+ *  For each possible base pair @f$(i,j)@f$, compute the probability of a stack+ *  @f$(i,j)@f$, @f$(i+1, j-1)@f$.+ *+ *  @ingroup pf_fold+ *+ *  @param  vc      The fold compound data structure with precomputed base pair probabilities+ *  @param  cutoff  A cutoff value that limits the output to stacks with @f$ p > \textrm{cutoff} @f$.+ *  @return         A list of stacks with enclosing base pair @f$(i,j)@f$ and probabiltiy @f$ p @f$+ */+vrna_plist_t *vrna_stack_prob(vrna_fold_compound_t *vc, double cutoff);++#endif
+ C/ViennaRNA/eval.c view
@@ -0,0 +1,2544 @@+/** \file eval.c */+++/*+                  Free energy evaluation++                  c Ivo Hofacker, Chrisoph Flamm+                  original implementation by+                  Walter Fontana++                  ViennaRNA Package >= v2.0 by Ronny Lorenz++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <unistd.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/structure_utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/model.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/cofold.h"+#include "ViennaRNA/eval.h"++#include "ViennaRNA/color_output.inc"++#define ON_SAME_STRAND(I,J,C)  (((I)>=(C))||((J)<(C)))++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+PUBLIC  int cut_point = -1; /* set to first pos of second seq for cofolding */+PUBLIC  int eos_debug = 0;  /* verbose info from energy_of_struct */++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;++PRIVATE int verbosity_default = 1;  /* default verbosity level */+PRIVATE int verbosity_quiet   = -1; /* verbosity level for quiet operations */++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE int+stack_energy( vrna_fold_compound_t *vc,+              int i,+              const short *pt,+              FILE *file,+              int verbostiy_level);++PRIVATE int+energy_of_extLoop_pt( vrna_fold_compound_t *vc,+                      int i,+                      const short *pt);++PRIVATE int+energy_of_ml_pt(vrna_fold_compound_t *vc,+                int i,+                const short *pt);++PRIVATE int+cut_in_loop(int i,+            const short *pt,+            int cp);++PRIVATE int+eval_pt(vrna_fold_compound_t *vc,+        const short *pt,+        FILE *file,+        int verbosity_level);++PRIVATE int+eval_circ_pt( vrna_fold_compound_t *vc,+              const short *pt,+              FILE *file,+              int verbosity_level);++PRIVATE int+en_corr_of_loop_gquad(vrna_fold_compound_t *vc,+                      int i,+                      int j,+                      const char *structure,+                      const short *pt);++PRIVATE vrna_param_t *+get_updated_params( vrna_param_t *parameters,+                    int compat);++PRIVATE float+wrap_eval_structure(vrna_fold_compound_t *vc,+                    const char *structure,+                    const short *pt,+                    FILE *file,+                    int verbosity);++PRIVATE int+wrap_eval_loop_pt(vrna_fold_compound_t *vc,+                  int i,+                  const short *pt,+                  int verbosity);++PRIVATE INLINE int+eval_int_loop(vrna_fold_compound_t *vc,+              int i,+              int j,+              int p,+              int q);++/* consensus structure variants below */+PRIVATE int+covar_energy_of_struct_pt(vrna_fold_compound_t *vc,+                          const short *pt);++PRIVATE int+stack_energy_covar_pt(vrna_fold_compound_t *vc,+                      int i,+                      const short *ptable);++PRIVATE int+en_corr_of_loop_gquad_ali(vrna_fold_compound_t *vc,+                          int i,+                          int j,+                          const char *structure,+                          const short *pt,+                          const int *loop_idx);++PRIVATE int+covar_en_corr_of_loop_gquad(vrna_fold_compound_t *vc,+                            int i,+                            int j,+                            const char *structure,+                            const short *pt,+                            const int *loop_idx);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+++PUBLIC float+vrna_eval_structure_simple( const char *string,+                            const char *structure){++  return vrna_eval_structure_simple_v(string, structure, verbosity_quiet, NULL);+}+++PUBLIC float+vrna_eval_structure_simple_verbose( const char *string,+                                    const char *structure,+                                    FILE *file){++  return vrna_eval_structure_simple_v(string, structure, verbosity_default, file);+}+++PUBLIC float+vrna_eval_structure_simple_v( const char *string,+                              const char *structure,+                              int verbosity_level,+                              FILE *file){++  float e;++  /* create fold_compound with default parameters and without DP matrices */+  vrna_fold_compound_t *vc = vrna_fold_compound(string, NULL, VRNA_OPTION_EVAL_ONLY);++  /* evaluate structure */+  e = vrna_eval_structure_v(vc, structure, verbosity_level, file);++  /* free fold_compound */+  vrna_fold_compound_free(vc);++  return e;+}+++PUBLIC int+vrna_eval_structure_pt_simple(const char *string,+                              const short *pt){++  return vrna_eval_structure_pt_simple_v(string, pt, verbosity_quiet, NULL);+}+++PUBLIC int+vrna_eval_structure_pt_simple_verbose(const char *string,+                                      const short *pt,+                                      FILE *file){++  return vrna_eval_structure_pt_simple_v(string, pt, verbosity_default, file);+}+++PUBLIC int+vrna_eval_structure_pt_simple_v(const char *string,+                                const short *pt,+                                int verbosity_level,+                                FILE *file){++  int e;++  /* create fold_compound with default parameters and without DP matrices */+  vrna_fold_compound_t *vc = vrna_fold_compound(string, NULL, VRNA_OPTION_EVAL_ONLY);++  /* evaluate structure */+  e = vrna_eval_structure_pt_v(vc, pt, verbosity_level, file);++  /* free fold_compound */+  vrna_fold_compound_free(vc);++  return e;++}+++PUBLIC int+vrna_eval_move_pt_simple( const char *string,+                          short *pt,+                          int m1,+                          int m2){++  int e;++  /* create fold_compound with default parameters and without DP matrices */+  vrna_fold_compound_t *vc = vrna_fold_compound(string, NULL, VRNA_OPTION_EVAL_ONLY);++  /* evaluate structure */+  e = vrna_eval_move_pt(vc, pt, m1, m2);++  /* free fold_compound */+  vrna_fold_compound_free(vc);++  return e;++}+++PUBLIC  float+vrna_eval_structure(vrna_fold_compound_t *vc,+                    const char *structure){++  return vrna_eval_structure_v(vc, structure, verbosity_quiet, NULL);+}+++PUBLIC float+vrna_eval_structure_verbose(vrna_fold_compound_t *vc,+                            const char *structure,+                            FILE *file){++  return vrna_eval_structure_v(vc, structure, verbosity_default, file);+}+++PUBLIC float+vrna_eval_structure_v(vrna_fold_compound_t *vc,+                      const char *structure,+                      int verbosity_level,+                      FILE *file){++  short *pt = vrna_ptable(structure);+  float en  = wrap_eval_structure(vc, structure, pt, file, verbosity_level);++  free(pt);+  return en;+}+++PUBLIC float+vrna_eval_covar_structure(vrna_fold_compound_t *vc,+                          const char *structure){++  int res, gq, *loop_idx;+  short *pt;++  pt                              = vrna_ptable(structure);+  res                             = 0;+  gq                              = vc->params->model_details.gquad;+  vc->params->model_details.gquad = 0;++  if(vc->type == VRNA_FC_TYPE_COMPARATIVE){+    res = (int)((float)covar_energy_of_struct_pt(vc, pt) / (float)vc->n_seq);++    vc->params->model_details.gquad = gq;++    if(gq){+      loop_idx  =   vrna_loopidx_from_ptable(pt);+      res       +=  (int)((float)covar_en_corr_of_loop_gquad(vc, 1, vc->length, structure, pt, (const int *)loop_idx) / (float)vc->n_seq);+      free(loop_idx);+    }+  }++  free(pt);++  return (float)res/100.;+}+++PUBLIC int+vrna_eval_structure_pt( vrna_fold_compound_t *vc,+                        const short *pt){++  return vrna_eval_structure_pt_v(vc, pt, verbosity_quiet, NULL);+}+++PUBLIC int+vrna_eval_structure_pt_verbose( vrna_fold_compound_t *vc,+                                const short *pt,+                                FILE *file){++  return vrna_eval_structure_pt_v(vc, pt, verbosity_default, file);+}+++PUBLIC int+vrna_eval_structure_pt_v( vrna_fold_compound_t *vc,+                          const short *pt,+                          int verbosity_level,+                          FILE *file){++  if(pt && vc){+    if(pt[0] != (short)vc->length)+      vrna_message_error("vrna_eval_structure_*: string and structure have unequal length");++    return eval_pt(vc, pt, file, verbosity_level);+  } else+    return INF;+}+++PUBLIC int+vrna_eval_loop_pt(vrna_fold_compound_t *vc,+                  int i,+                  const short *pt){++  return wrap_eval_loop_pt(vc, i, pt, verbosity_quiet);+}+++PUBLIC float+vrna_eval_move( vrna_fold_compound_t *vc,+                const char *structure,+                int m1,+                int m2){++  short   *pt;+  int     en;++  if (strlen(structure) != vc->length)+    vrna_message_error("vrna_eval_move: sequence and structure have unequal length");++  pt = vrna_ptable(structure);+  en = vrna_eval_move_pt(vc, pt, m1, m2);++  free(pt);++  return  (float)en/100.;+}+++PUBLIC int+vrna_eval_move_pt(vrna_fold_compound_t *vc,+                  short *pt,+                  int m1,+                  int m2){++  /*compute change in energy given by move (m1,m2)*/+  int en_post, en_pre, i,j,k,l, len, cp;+  vrna_param_t *P;+  +  len = vc->length;+  cp  = vc->cutpoint;+  P   = vc->params;++  k = (m1>0)?m1:-m1;+  l = (m2>0)?m2:-m2;+  /* first find the enclosing pair i<k<l<j */+  for (j=l+1; j<=len; j++) {+    if (pt[j]<=0) continue; /* unpaired */+    if (pt[j]<k) break;   /* found it */+    if (pt[j]>j) j=pt[j]; /* skip substructure */+    else {+      vrna_message_error( "illegal move or broken pair table in vrna_eval_move_pt()\n"+                          "%d %d %d %d ", m1, m2, j, pt[j]);+    }+  }+  i = (j<=len) ? pt[j] : 0;+  en_pre = vrna_eval_loop_pt(vc, i, (const short *)pt);+  en_post = 0;+  if (m1<0) { /*it's a delete move */+    en_pre += vrna_eval_loop_pt(vc, k, (const short *)pt);+    pt[k]=0;+    pt[l]=0;+  } else { /* insert move */+    pt[k]=l;+    pt[l]=k;+    en_post += vrna_eval_loop_pt(vc, k, (const short *)pt);+  }+  en_post += vrna_eval_loop_pt(vc, i, (const short *)pt);+  /*  restore pair table */+  if (m1<0) {+    pt[k]=l;+    pt[l]=k;+  } else {+    pt[k]=0;+    pt[l]=0;+  }++  /* Cofolding -- Check if move changes COFOLD-Penalty */+  if (!ON_SAME_STRAND(k, l, cp)) {+    int p, c; p=c=0;+    for (p=1; p < cp; ) { /* Count basepairs between two strands */+      if (pt[p] != 0) {+        if (ON_SAME_STRAND(p, pt[p], cp)) /* Skip stuff */+          p=pt[p];+        else if (++c > 1) break; /* Count a basepair, break if we have more than one */+      }+      p++;+    }+    if (m1<0 && c==1) /* First and only inserted basepair */+      return (en_post - en_pre - P->DuplexInit);+    else+      if (c==0) /* Must have been a delete move */+        return (en_post - en_pre + P->DuplexInit);+  }++  return (en_post - en_pre);+}++/*+#################################+# STATIC helper functions below #+#################################+*/++PRIVATE INLINE int+eval_int_loop(vrna_fold_compound_t *vc,+              int i,+              int j,+              int p,+              int q){++  int             ij, u1, u2, cp, *rtype, *indx;+  unsigned char   type, type_2;+  short           *S, si, sj, sp, sq;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_sc_t       *sc;++  cp      = vc->cutpoint;+  indx    = vc->jindx;+  P       = vc->params;+  md      = &(P->model_details);+  S       = vc->sequence_encoding;+  si      = S[i+1];+  sj      = S[j-1];+  sp      = S[p-1];+  sq      = S[q+1];+  ij      = indx[j] + i;+  rtype   = &(md->rtype[0]);+  type    = (unsigned char)md->pair[S[i]][S[j]];+  type_2  = rtype[(unsigned char)md->pair[S[p]][S[q]]];+  u1      = p - i - 1;+  u2      = j - q - 1;+  sc      = vc->sc;++  if(type == 0)+    type = 7;+  if(type_2 == 0)+    type_2 = 7;++  return ubf_eval_int_loop( i, j, p, q,+                            i + 1, j - 1, p - 1, q + 1,+                            si, sj, sp, sq,+                            type, type_2, rtype,+                            ij, cp,+                            P, sc);+}++PRIVATE INLINE int+eval_ext_int_loop(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  int p,+                  int q){++  int             e, u1, u2, length;+  unsigned int    s, n_seq;+  short           **SS, **S5, **S3;+  unsigned short  **a2s;+  unsigned char   type, type_2;+  short           *S, si, sj, sp, sq;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_sc_t       *sc, **scs;++  length  = vc->length;+  P       = vc->params;+  md      = &(P->model_details);+  S       = vc->sequence_encoding;+  e       = INF;++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     si      = S[j+1];+                                  sj      = S[i-1];+                                  sp      = S[p-1];+                                  sq      = S[q+1];+                                  type    = (unsigned char)md->pair[S[j]][S[i]];+                                  type_2  = (unsigned char)md->pair[S[q]][S[p]];+                                  sc      = vc->sc;++                                  if(type == 0)+                                    type = 7;+                                  if(type_2 == 0)+                                    type_2 = 7;++                                  e = ubf_eval_ext_int_loop(i, j, p, q,+                                                            i - 1, j + 1, p - 1, q + 1,+                                                            si, sj, sp, sq,+                                                            type, type_2,+                                                            length,+                                                            P, sc);+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  n_seq = vc->n_seq;+                                  SS      = vc->S;+                                  S5      = vc->S5; /* S5[s][i] holds next base 5' of i in sequence s */+                                  S3      = vc->S3; /* Sl[s][i] holds next base 3' of i in sequence s */+                                  a2s     = vc->a2s;+                                  n_seq   = vc->n_seq;+                                  scs     = vc->scs;++                                  for (e = 0, s = 0; s < n_seq; s++) {+                                    type    = (unsigned char)md->pair[SS[s][j]][SS[s][i]];+                                    if(type == 0)+                                      type = 7;+                                    type_2  = (unsigned char)md->pair[SS[s][q]][SS[s][p]]; /* q,p not p,q! */+                                    if(type_2 == 0)+                                      type_2 = 7;++                                    sc = (scs && scs[s]) ? scs[s] : NULL;++                                    e += ubf_eval_ext_int_loop(a2s[s][i], a2s[s][j], a2s[s][p], a2s[s][q],+                                                                    a2s[s][i - 1], a2s[s][j + 1], a2s[s][p - 1], a2s[s][q + 1],+                                                                    S3[s][j], S5[s][i], S5[s][p], S3[s][q],+                                                                    type, type_2,+                                                                    a2s[s][length],+                                                                    P, sc);+                                  }++                                  break;+  }++  return e;+}++PRIVATE  vrna_param_t *+get_updated_params(vrna_param_t *parameters, int compat){+  vrna_param_t *P = NULL;+  if(parameters){+    P = vrna_params_copy(parameters);+  } else {+    vrna_md_t md;+    if(compat)+      set_model_details(&md);+    else+      vrna_md_set_default(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }+  vrna_md_update(&(P->model_details));+  return P;+}++PRIVATE int+wrap_eval_loop_pt(vrna_fold_compound_t *vc,+                  int i,+                  const short *pt,+                  int verbosity){++  /* compute energy of a single loop closed by base pair (i,j) */+  int               j, type, p,q, energy, cp;+  short             *s;+  vrna_param_t      *P;++  P   = vc->params;+  cp  = vc->cutpoint;+  s   = vc->sequence_encoding2;++  if (i==0) { /* evaluate exterior loop */+    energy = energy_of_extLoop_pt(vc, 0, pt);+    return energy;+  }+  j = pt[i];+  if(j < i)+    vrna_message_error("i is unpaired in loop_energy()");+  type = P->model_details.pair[s[i]][s[j]];+  if (type==0) {+    type=7;+    if (verbosity > verbosity_quiet)+      vrna_message_warning( "bases %d and %d (%c%c) can't pair!",+                            i, j,+                            vrna_nucleotide_decode(s[i], &(P->model_details)),+                            vrna_nucleotide_decode(s[j], &(P->model_details)));+  }+  p=i; q=j;+++  while (pt[++p]==0);+  while (pt[--q]==0);+  if (p>q) { /* Hairpin */+    energy = vrna_eval_hp_loop(vc, i, j);+  }+  else if (pt[q]!=(short)p) { /* multi-loop */+    int ii;+    ii = cut_in_loop(i, (const short *)pt, cp);+    energy = (ii==0) ? energy_of_ml_pt(vc, i, (const short *)pt) : energy_of_extLoop_pt(vc, ii, (const short *)pt);+  }+  else { /* found interior loop */+    int type_2;+    type_2 = P->model_details.pair[s[q]][s[p]];+    if (type_2==0) {+      type_2=7;+      if (verbosity > verbosity_quiet)+        vrna_message_warning( "bases %d and %d (%c%c) can't pair!",+                              p, q,+                              vrna_nucleotide_decode(s[p], &(P->model_details)),+                              vrna_nucleotide_decode(s[q], &(P->model_details)));+    }++    energy = eval_int_loop(vc, i, j, p, q);++  }++  return energy;+}++PRIVATE float+wrap_eval_structure(vrna_fold_compound_t *vc,+                    const char *structure,+                    const short *pt,+                    FILE *file,+                    int verbosity){++  int res;+  int gq;++  res                             = INF;+  gq                              = vc->params->model_details.gquad;+  vc->params->model_details.gquad = 0;++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     if(vc->params->model_details.circ){+                                    res = eval_circ_pt(vc, pt, file, verbosity);+                                  } else {+                                    res = eval_pt(vc, pt, file, verbosity);+                                  }+                                  vc->params->model_details.gquad = gq;++                                  if(gq){+                                    res += en_corr_of_loop_gquad(vc, 1, vc->length, structure, pt);+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  if(vc->params->model_details.circ){+                                    res = (int)((float)eval_circ_pt(vc, pt, file, verbosity) / (float)vc->n_seq);+                                  } else {+                                    res = (int)((float)eval_pt(vc, pt, file, verbosity) / (float)vc->n_seq);+                                  }+                                  vc->params->model_details.gquad = gq;++                                  if(gq){+                                    int *loop_idx = vrna_loopidx_from_ptable(pt);+                                    res += (int)((float)en_corr_of_loop_gquad_ali(vc, 1, vc->length, structure, pt, (const int *)loop_idx) / (float)vc->n_seq);+                                    free(loop_idx);+                                  }+                                  break;++    default:                      /* do nothing */+                                  break;+  }+  return (float)res/100.;+}++PRIVATE int+eval_pt(vrna_fold_compound_t *vc,+        const short *pt,+        FILE *file,+        int verbosity_level){++  int   i, length, energy, cp;+  FILE  *out;++  out     = (file) ? file : stdout;+  length  = vc->length;+  cp      = vc->cutpoint;++  if(vc->params->model_details.gquad)+    vrna_message_warning( "vrna_eval_*_pt: No gquadruplex support!\n"+                          "Ignoring potential gquads in structure!\n"+                          "Use e.g. vrna_eval_structure() instead!");++  energy = vc->params->model_details.backtrack_type=='M' ? energy_of_ml_pt(vc, 0, pt) : energy_of_extLoop_pt(vc, 0, pt);++  if (verbosity_level>0)+    print_eval_ext_loop(out, energy);+  for (i=1; i<=length; i++) {+    if (pt[i]==0) continue;+    energy += stack_energy(vc, i, pt, out, verbosity_level);+    i=pt[i];+  }+  for (i=1; !ON_SAME_STRAND(i,length, cp); i++) {+    if (!ON_SAME_STRAND(i,pt[i], cp)) {+      energy += vc->params->DuplexInit;+      break;+    }+  }++  return energy;+}++PRIVATE int+eval_circ_pt( vrna_fold_compound_t *vc,+              const short *pt,+              FILE *file,+              int verbosity_level){++  unsigned int      s, n_seq;+  int               i, j, length, energy, en0, degree;+  unsigned short    **a2s;+  vrna_param_t      *P;+  vrna_sc_t         *sc, **scs;+  FILE              *out;++  energy        = 0;+  en0           = 0;+  degree        = 0;+  length        = vc->length;+  P             = vc->params;+  sc            = (vc->type == VRNA_FC_TYPE_SINGLE) ? vc->sc : NULL;+  scs           = (vc->type == VRNA_FC_TYPE_COMPARATIVE) ? vc->scs : NULL;+  out           = (file) ? file : stdout;++  if(P->model_details.gquad)+    vrna_message_warning( "vrna_eval_*_pt: No gquadruplex support!\n"+                          "Ignoring potential gquads in structure!\n"+                          "Use e.g. vrna_eval_structure() instead!");++  /* evaluate all stems in exterior loop */+  for (i=1; i<=length; i++) {+    if (pt[i]==0) continue;+    degree++;+    energy += stack_energy(vc, i, (const short *)pt, out, verbosity_level);+    i=pt[i];+  }++  /* find first stem */+  for (i=1; pt[i]==0; i++);+  j = pt[i];++  /* evaluate exterior loop itself */+  switch(degree){+    case 0:   /* unstructured */+              switch(vc->type){+                case VRNA_FC_TYPE_SINGLE:     if(sc){+                                                if(sc->energy_up)+                                                  en0 += sc->energy_up[1][length];+                                              }+                                              break;++                case VRNA_FC_TYPE_COMPARATIVE:  n_seq = vc->n_seq;+                                              a2s   = vc->a2s;+                                              if(scs)+                                                for(s = 0; s < n_seq; s++){+                                                  if(scs[s] && scs[s]->energy_up)+                                                    en0 += scs[s]->energy_up[1][a2s[s][length]];+                                                }+                                              break;+              }+              break;+    case 1:   /* hairpin loop */+              en0 = vrna_eval_ext_hp_loop(vc, i, j);+              break;++    case 2:   /* interior loop */+              {+                int p,q;+                /* seek to next pair */+                for (p=j+1; pt[p]==0; p++);+                q=pt[p];++                en0 = eval_ext_int_loop(vc, i, j, p, q);+              }+              break;++    default:  /* multibranch loop */+              en0 = energy_of_ml_pt(vc, 0, (const short *)pt);++              if(vc->type == VRNA_FC_TYPE_SINGLE)+                en0 -= E_MLstem(0, -1, -1, P); /* remove virtual closing pair */+              break;+  }++  if (verbosity_level>0)+    print_eval_ext_loop(out, en0);++  energy += en0;++  return energy;+}++++/*---------------------------------------------------------------------------*/+/*  returns a correction term that may be added to the energy retrieved+    from energy_of_struct_par() to correct misinterpreted loops. This+    correction is necessary since energy_of_struct_par() will forget+    about the existance of gquadruplexes and just treat them as unpaired+    regions.++    recursive variant+*/+PRIVATE int+en_corr_of_loop_gquad(vrna_fold_compound_t *vc,+                      int i,+                      int j,+                      const char *structure,+                      const short *pt){++  int               pos, energy, p, q, r, s, u, type, type2, L, l[3], *rtype, *loop_idx;+  int               num_elem, num_g, elem_i, elem_j, up_mis;+  short             *s1;+  vrna_param_t      *P;+  vrna_md_t         *md;++  loop_idx  = vrna_loopidx_from_ptable(pt);+  s1        = vc->sequence_encoding;+  P         = vc->params;+  md        = &(P->model_details);+  rtype     = &(md->rtype[0]);++  energy = 0;+  q = i;+  while((pos = parse_gquad(structure + q-1, &L, l)) > 0){+    q += pos-1;+    p = q - 4*L - l[0] - l[1] - l[2] + 1;+    if(q > j) break;+    /* we've found the first g-quadruplex at position [p,q] */+    energy += E_gquad(L, l, P);+    /* check if it's enclosed in a base pair */+    if(loop_idx[p] == 0){ q++; continue; /* g-quad in exterior loop */}+    else{+      energy += E_MLstem(0, -1, -1, P); /*  do not forget to remove this energy if+                                            the gquad is the only one surrounded by+                                            the enclosing pair+                                        */++      /*  find its enclosing pair */+      num_elem  = 0;+      num_g     = 1;+      r         = p - 1;+      up_mis    = q - p + 1;++      /* seek for first pairing base located 5' of the g-quad */+      for(r = p - 1; !pt[r] && (r >= i); r--);+      if(r < i)+        vrna_message_error("this should not happen");++      if(r < pt[r]){ /* found the enclosing pair */+        s = pt[r];+      } else {+        num_elem++;+        elem_i = pt[r];+        elem_j = r;+        r = pt[r]-1 ;+        /* seek for next pairing base 5' of r */+        for(; !pt[r] && (r >= i); r--);+        if(r < i)+          vrna_message_error("so nich");+        if(r < pt[r]){ /* found the enclosing pair */+          s = pt[r];+        } else {+          /* hop over stems and unpaired nucleotides */+          while((r > pt[r]) && (r >= i)){+            if(pt[r]){ r = pt[r]; num_elem++;}+            r--;+          }+          if(r < i)+            vrna_message_error("so nich");+          s = pt[r]; /* found the enclosing pair */+        }+      }+      /* now we have the enclosing pair (r,s) */++      u = q+1;+      /* we know everything about the 5' part of this loop so check the 3' part */+      while(u<s){+        if(structure[u-1] == '.') u++;+        else if (structure[u-1] == '+'){ /* found another gquad */+          pos = parse_gquad(structure + u - 1, &L, l);+          if(pos > 0){+            energy += E_gquad(L, l, P) + E_MLstem(0, -1, -1, P);+            up_mis += pos;+            u += pos;+            num_g++;+          }+        } else { /* we must have found a stem */+          if(!(u < pt[u]))+            vrna_message_error("wtf!");+          num_elem++; elem_i = u; elem_j = pt[u];+          energy += en_corr_of_loop_gquad(vc, u, pt[u], structure, pt);+          u = pt[u] + 1;+        }+      }+      if(u!=s)+        vrna_message_error("what the heck");+      else{ /* we are done since we've found no other 3' structure element */+        switch(num_elem){+          /* g-quad was misinterpreted as hairpin closed by (r,s) */+          case 0:   /* if(num_g == 1)+                      if((p-r-1 == 0) || (s-q-1 == 0))+                        vrna_message_error("too few unpaired bases");+                    */+                    type = md->pair[s1[r]][s1[s]];+                    if(dangles == 2)+                      energy += P->mismatchI[type][s1[r+1]][s1[s-1]];+                    if(type > 2)+                      energy += P->TerminalAU;+                    energy += P->internal_loop[s - r - 1 - up_mis];+                    energy -= E_MLstem(0, -1, -1, P);+                    energy -= vrna_eval_hp_loop(vc, r, s);++                    break;+          /* g-quad was misinterpreted as interior loop closed by (r,s) with enclosed pair (elem_i, elem_j) */+          case 1:   type = md->pair[s1[r]][s1[s]];+                    type2 = md->pair[s1[elem_i]][s1[elem_j]];+                    energy += P->MLclosing+                              + E_MLstem(rtype[type], s1[s-1], s1[r+1], P)+                              + (elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase+                              + E_MLstem(type2, s1[elem_i-1], s1[elem_j+1], P);+                    energy -= eval_int_loop(vc, r, s, elem_i, elem_j);++                    break;+          /* gquad was misinterpreted as unpaired nucleotides in a multiloop */+          default:  energy -= (up_mis) * P->MLbase;+                    break;+        }+      }+      q = s+1;+    }+  }++  free(loop_idx);+  return energy;+}++++PRIVATE int+stack_energy( vrna_fold_compound_t *vc,+              int i,+              const short *pt,+              FILE *file,+              int verbosity_level){++  /* recursively calculate energy of substructure enclosed by (i,j) */++  int               ee, energy, j, p, q, type, *rtype, *types, cp, ss, n_seq;+  char              *string, **Ss;+  short             *s, **S, **S5, **S3;+  unsigned short    **a2s;+  FILE              *out;+  vrna_param_t      *P;+  vrna_md_t         *md;++  cp      = vc->cutpoint;+  s       = vc->sequence_encoding2;+  P       = vc->params;+  md      = &(P->model_details);+  rtype   = &(md->rtype[0]);+  types   = NULL;+  energy  = 0;+  out     = (file) ? file : stdout;++  j = pt[i];++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     string  = vc->sequence;+                                  type    = md->pair[s[i]][s[j]];+                                  if(type == 0){+                                    type = 7;+                                    if(verbosity_level > verbosity_quiet)+                                      vrna_message_warning( "bases %d and %d (%c%c) can't pair!",+                                                            i, j,+                                                            string[i - 1],+                                                            string[j - 1]);+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  string  = vc->cons_seq;+                                  S       = vc->S;+                                  S5      = vc->S5; /* S5[s][i] holds next base 5' of i in sequence s */+                                  S3      = vc->S3; /* Sl[s][i] holds next base 3' of i in sequence s */+                                  Ss      = vc->Ss;+                                  a2s     = vc->a2s;+                                  n_seq   = vc->n_seq;+                                  types   = (int *)vrna_alloc(n_seq * sizeof(int));++                                  for(ss = 0; ss < n_seq; ss++){+                                    types[ss] = md->pair[S[ss][i]][S[ss][j]];+                                    if(types[ss] == 0){+                                      types[ss] = 7;+                                    }+                                  }+                                  break;++    default:                      return INF;+                                  break;+  }++  p = i;+  q = j;++  while(p < q){ /* process all stacks and interior loops */+    int type_2;+    while(pt[++p] == 0);+    while(pt[--q] == 0);+    if((pt[q] != (short)p) || (p > q))+      break;+    ee = 0;+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     type_2 = md->pair[s[q]][s[p]];+                                    if(type_2 == 0){+                                      type_2 = 7;+                                      if(verbosity_level > verbosity_quiet)+                                        vrna_message_warning( "bases %d and %d (%c%c) can't pair!",+                                                              p, q,+                                                              string[p - 1],+                                                              string[q - 1]);+                                    }+                                    ee = eval_int_loop(vc, i, j, p, q);++                                    type = rtype[type_2];+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  for(ss = 0; ss < n_seq; ss++){+                                      type_2 = md->pair[S[ss][q]][S[ss][p]];+                                      if(type_2 == 0){+                                        type_2 = 7;+                                      }+                                      ee += E_IntLoop(a2s[ss][p - 1] - a2s[ss][i],+                                                      a2s[ss][j - 1] - a2s[ss][q],+                                                      types[ss],+                                                      type_2,+                                                      S3[ss][i],+                                                      S5[ss][j],+                                                      S5[ss][p],+                                                      S3[ss][q],+                                                      P);+                                    }++                                    for(ss = 0; ss < n_seq; ss++){+                                      types[ss] = md->pair[S[ss][p]][S[ss][q]];+                                      if(types[ss] == 0)+                                        types[ss] = 7;+                                    }+                                    break;++      default:                      break; /* this should never happen */+    }++    if(verbosity_level > 0)+      print_eval_int_loop(out, i, j, string[i - 1], string[j - 1],+                               p, q, string[p - 1], string[q - 1],+                               ee);++    energy += ee;+    i = p;+    j = q;+  } /* end while */++  /* p,q don't pair must have found hairpin or multiloop */++  if(p > q){  /* hairpin */+    ee      = vrna_eval_hp_loop(vc, i, j);+    energy  += ee;++    if(verbosity_level > 0)+      print_eval_hp_loop(out, i, j, string[i - 1], string[j - 1], ee);++    free(types);++    return energy;+  }++  /* (i,j) is exterior pair of multiloop */+  while(p < j){+    /* add up the contributions of the substructures of the ML */+    energy += stack_energy(vc, p, pt, out, verbosity_level);+    p = pt[p];+    /* search for next base pair in multiloop */+    while(pt[++p] == 0);+  }+  +  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     {+                                    int ii = cut_in_loop(i, pt, cp);+                                    ee = (ii==0) ? energy_of_ml_pt(vc, i, pt) : energy_of_extLoop_pt(vc, ii, pt);+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  ee = energy_of_ml_pt(vc, i, pt);+                                  break;++    default:                      break; /* this should never happen */+  }++  energy += ee;+  if(verbosity_level > 0)+    print_eval_mb_loop(out, i, j, string[i - 1], string[j - 1], ee);++  free(types);++  return energy;+}++/*---------------------------------------------------------------------------*/++++/**+*** Calculate the energy contribution of+*** stabilizing dangling-ends/mismatches+*** for all stems branching off the exterior+*** loop+**/+PRIVATE int+energy_of_extLoop_pt( vrna_fold_compound_t *vc,+                      int i,+                      const short *pt){++  int               energy, mm5, mm3, bonus, p, q, q_prev, length, dangle_model, n_seq, cp, ss, u, start;+  short             *s, *s1, **S, **S5, **S3;+  unsigned short    **a2s;+  vrna_param_t      *P;+  vrna_md_t         *md;+  vrna_sc_t         *sc, **scs;+++  /* helper variables for dangles == 1 case */+  int E3_available;  /* energy of 5' part where 5' mismatch is available for current stem */+  int E3_occupied;   /* energy of 5' part where 5' mismatch is unavailable for current stem */+++  /* initialize vars */+  length        = vc->length;+  cp            = vc->cutpoint;+  P             = vc->params;+  md            = &(P->model_details);+  dangle_model  = md->dangles;++  energy        = 0;+  bonus         = 0;+  p = start     = (i==0) ? 1 : i;+  q_prev        = -1;++  if(dangle_model % 2 == 1){+    E3_available = INF;+    E3_occupied  = 0;+  }++  /* seek to opening base of first stem */+  while(p <= length && !pt[p]) p++;++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     s  = vc->sequence_encoding2;+                                  s1 = vc->sequence_encoding;+                                  sc = vc->sc;++                                  /* add soft constraints for first unpaired nucleotides */+                                  if(sc){+                                    if(sc->energy_up)+                                      bonus += sc->energy_up[start][p - start];+                                    /* how do we handle generalized soft constraints here ? */+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  S     = vc->S;+                                  S5    = vc->S5;     /* S5[s][i] holds next base 5' of i in sequence s */+                                  S3    = vc->S3;     /* Sl[s][i] holds next base 3' of i in sequence s */+                                  a2s   = vc->a2s;+                                  n_seq = vc->n_seq;+                                  scs   = vc->scs;++                                  /* add soft constraints for first unpaired nucleotides */+                                  if(scs){+                                    for(ss = 0; ss < n_seq; ss++){+                                      if(scs[ss]){+                                        if(scs[ss]->energy_up){+                                          u      = a2s[ss][p] - a2s[ss][start];+                                          bonus += scs[ss]->energy_up[a2s[ss][start]][u];+                                        }+                                        /* how do we handle generalized soft constraints here ? */+                                      }+                                    }+                                  }+                                  break;++    default:                      return INF;+                                  break;+  }++  while(p < length){+    int tt;+    /* p must have a pairing partner */+    q  = (int)pt[p];+    +    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* get type of base pair (p,q) */+                                    tt = md->pair[s[p]][s[q]];+                                    if(tt == 0)+                                      tt = 7;++                                    switch(dangle_model){+                                      /* no dangles */+                                      case 0:   energy += E_ExtLoop(tt, -1, -1, P);+                                                break;++                                      /* the beloved double dangles */+                                      case 2:   mm5 = ((ON_SAME_STRAND(p - 1, p, cp)) && (p>1))       ? s1[p-1] : -1;+                                                mm3 = ((ON_SAME_STRAND(q, q + 1, cp)) && (q<length))  ? s1[q+1] : -1;+                                                energy += E_ExtLoop(tt, mm5, mm3, P);+                                                break;++                                      default:  {+                                                  int tmp;+                                                  if(q_prev + 2 < p){+                                                    E3_available = MIN2(E3_available, E3_occupied);+                                                    E3_occupied  = E3_available;+                                                  }+                                                  mm5 = ((ON_SAME_STRAND(p - 1, p, cp)) && (p>1) && !pt[p-1])       ? s1[p-1] : -1;+                                                  mm3 = ((ON_SAME_STRAND(q, q + 1, cp)) && (q<length) && !pt[q+1])  ? s1[q+1] : -1;+                                                  tmp = MIN2(+                                                                                E3_occupied  + E_ExtLoop(tt, -1, mm3, P),+                                                                                E3_available + E_ExtLoop(tt, mm5, mm3, P)+                                                                              );+                                                  E3_available =       MIN2(+                                                                                E3_occupied  + E_ExtLoop(tt, -1, -1, P),+                                                                                E3_available + E_ExtLoop(tt, mm5, -1, P)+                                                                              );+                                                  E3_occupied = tmp;+                                                }+                                                break;++                                    } /* end switch dangle_model */+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  for(ss = 0; ss < n_seq; ss++){+                                      /* get type of base pair (p,q) */+                                      tt = md->pair[S[ss][p]][S[ss][q]];+                                      if(tt == 0)+                                        tt = 7;++                                      switch(dangle_model){+                                        case 0:   energy += E_ExtLoop(tt, -1, -1, P);+                                                  break;+                                        +                                        case 2:   mm5 = (a2s[ss][p] > 1) && (tt != 0) ? S5[ss][p] : -1;+                                                  mm3 = (a2s[ss][q] < a2s[ss][S[0][0]]) ? S3[ss][q] : -1; /* why S[0][0] ??? */+                                                  energy += E_ExtLoop(tt, mm5, mm3, P);+                                                  break;++                                        default:  break; /* odd dangles not implemented yet */+                                      }+                                    }+                                    break;++      default:                      break; /* this should never happen */+    }++    /* seek to the next stem */+    p = q + 1;+    q_prev = q;+    while (p <= length && !pt[p]) p++;++    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* add soft constraints for unpaired region */+                                    if(sc && (q_prev + 1 <= length)){+                                      if(sc->energy_up){+                                        bonus += sc->energy_up[q_prev + 1][p - q_prev - 1];+                                      }+                                      /* how do we handle generalized soft constraints here ? */+                                    }+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  if(scs){+                                      for(ss = 0; ss < n_seq; ss++){+                                        if(scs[ss]){+                                          if(scs[ss]->energy_up){+                                            u = a2s[ss][p] - a2s[ss][q_prev + 1];+                                            bonus += scs[ss]->energy_up[a2s[ss][q_prev + 1]][u];+                                          }+                                        }+                                      }+                                    }+                                    break;++      default:                      break; /* this should never happen */+    }++    if(p == i)+      break; /* cut was in loop */+  }++  if(dangle_model % 2 == 1)+    energy = MIN2(E3_occupied, E3_available);++  return energy + bonus;+}++/**+*** i is the 5'-base of the closing pair+***+*** since each helix can coaxially stack with at most one of its+*** neighbors we need an auxiliarry variable  cx_energy+*** which contains the best energy given that the last two pairs stack.+*** energy  holds the best energy given the previous two pairs do not+*** stack (i.e. the two current helices may stack)+*** We don't allow the last helix to stack with the first, thus we have to+*** walk around the Loop twice with two starting points and take the minimum+***/+PRIVATE int+energy_of_ml_pt(vrna_fold_compound_t *vc,+                int i,+                const short *pt){++  int               energy, cx_energy, tmp, tmp2, best_energy=INF, bonus, *idx, cp, dangle_model, logML, circular, *rtype, ss, n, n_seq;+  int               i1, j, p, q, q_prev, q_prev2, u, uu, x, type, count, mm5, mm3, tt, ld5, new_cx, dang5, dang3, dang;+  int               e_stem, e_stem5, e_stem3, e_stem53;+  int               mlintern[NBPAIRS+1];+  short             *s, *s1, **S, **S5, **S3;+  unsigned short    **a2s;+  vrna_param_t      *P;+  vrna_md_t         *md;+  vrna_sc_t         *sc, **scs;++  /* helper variables for dangles == 1|5 case */+  int E_mm5_available;  /* energy of 5' part where 5' mismatch of current stem is available */+  int E_mm5_occupied;   /* energy of 5' part where 5' mismatch of current stem is unavailable */+  int E2_mm5_available; /* energy of 5' part where 5' mismatch of current stem is available with possible 3' dangle for enclosing pair (i,j) */+  int E2_mm5_occupied;  /* energy of 5' part where 5' mismatch of current stem is unavailable with possible 3' dangle for enclosing pair (i,j) */++  n   = vc->length;+  cp  = vc->cutpoint;+  P   = vc->params;+  md  = &(P->model_details);+  idx = vc->jindx;++  circular      = md->circ;+  dangle_model  = md->dangles;+  logML         = md->logML;+  rtype         = &(md->rtype[0]);++  bonus = 0;++  if(i >= pt[i]){+    vrna_message_warning("energy_of_ml_pt: i is not 5' base of a closing pair!");+    return INF;+  }++  j = (i == 0) ? n + 1 : (int)pt[i];++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     s   = vc->sequence_encoding2;+                                  s1  = vc->sequence_encoding;+                                  sc  = vc->sc;++                                  if(i != 0){ /* (i,j) is closing pair of multibranch loop, add soft constraints */+                                    if(sc){+                                      if(sc->energy_bp)+                                        bonus += sc->energy_bp[idx[j] + i];+                                    }+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  S     = vc->S;+                                  S5    = vc->S5;+                                  S3    = vc->S3;+                                  a2s   = vc->a2s;+                                  n_seq = vc->n_seq;+                                  scs   = vc->scs;++                                  if((dangle_model % 2) || (dangle_model > 2) || (dangle_model < 0)){+                                    vrna_message_warning("consensus structure evaluation for odd dangle models not implemented (yet)!");+                                    return INF;+                                  }++                                  if(i != 0){ /* (i,j) is closing pair of multibranch loop, add soft constraints */+                                    if(scs){+                                      for(ss = 0; ss < n_seq; ss++){+                                        if(scs[ss] && scs[ss]->energy_bp)+                                          bonus += scs[ss]->energy_bp[idx[j] + i];+                                      }+                                    }+                                  }+                                  break;++    default:                      return INF;+                                  break;+  }++  /* init the variables */+  energy      = 0;+  u           = 0; /* the total number of unpaired nucleotides */+  p           = i+1;+  q_prev      = i-1;+  q_prev2     = i;+++  for (x = 0; x <= NBPAIRS; x++)+    mlintern[x] = P->MLintern[x];++  /* seek to opening base of first stem */+  while(p <= j && !pt[p])+    p++;++  /* add bonus energies for first stretch of unpaired nucleotides */+  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     u += p - i - 1;+                                  if(sc){+                                    if(sc->energy_up)+                                      bonus += sc->energy_up[i + 1][u];+                                  }+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  if(scs){+                                    for(ss = 0; ss < n_seq; ss++){+                                      uu = a2s[ss][p] - a2s[ss][i + 1];+                                      if(scs[ss] && scs[ss]->energy_up){+                                        bonus += scs[ss]->energy_up[a2s[ss][i + 1]][uu];+                                      }+                                      u += uu;+                                    }+                                  } else {+                                    for(ss = 0; ss < n_seq; ss++){+                                      u += a2s[ss][p] - a2s[ss][i + 1];+                                    }+                                  }+                                  break;++    default:                      break; /* this should never happen */+  }++  switch(dangle_model){+    case 0:   switch(vc->type){+                case VRNA_FC_TYPE_SINGLE:     while(p < j){+                                                /* p must have a pairing partner */+                                                q  = (int)pt[p];+                                                /* get type of base pair (p,q) */+                                                tt = md->pair[s[p]][s[q]];+                                                if(tt==0) tt=7;+                                                energy += E_MLstem(tt, -1, -1, P);++                                                /* seek to the next stem */+                                                p = q + 1;+                                                q_prev = q_prev2 = q;+                                                while (p <= j && !pt[p]) p++;+                                                u += p - q - 1; /* add unpaired nucleotides */++                                                if(sc){+                                                  if(sc->energy_up)+                                                    bonus += sc->energy_up[q+1][p-q-1];+                                                }+                                              }++                                              /* now lets get the energy of the enclosing stem */+                                              if(i > 0){  /* actual closing pair */+                                                tt = md->pair[s[j]][s[i]];+                                                if(tt == 0)+                                                  tt = 7;+                                                energy += E_MLstem(tt, -1, -1, P);++                                              } else {  /* virtual closing pair */+                                                energy += E_MLstem(0, -1, -1, P);+                                              }+                                              break;++                case VRNA_FC_TYPE_COMPARATIVE:  while(p < j){+                                                /* p must have a pairing partner */+                                                q  = (int)pt[p];+                                                for(ss = 0; ss < n_seq; ss++){+                                                  /* get type of base pair (p,q) */+                                                  tt = md->pair[S[ss][p]][S[ss][q]];+                                                  if(tt == 0)+                                                    tt = 7;+                                                  energy += E_MLstem(tt, -1, -1, P);+                                                }++                                                /* seek to the next stem */+                                                p = q + 1;+                                                q_prev = q_prev2 = q;+                                                while (p <= j && !pt[p]) p++;+                                                +                                                /* add unpaired nucleotides and possible soft constraints */+                                                if(scs){+                                                  for(ss = 0; ss < n_seq; ss++){+                                                    uu = a2s[ss][p] - a2s[ss][q + 1]; +                                                    if(scs[ss] && scs[ss]->energy_up){+                                                      bonus += sc->energy_up[a2s[ss][q + 1]][uu];+                                                    }+                                                    u += uu;+                                                  }+                                                } else {+                                                  for(ss = 0; ss < n_seq; ss++){+                                                    u += a2s[ss][p] - a2s[ss][q + 1];+                                                  }+                                                }+                                              }++                                              /* now lets get the energy of the enclosing stem */+                                              if(i > 0){  /* actual closing pair */+                                                for(ss = 0; ss < n_seq; ss++){+                                                  tt = md->pair[S[ss][j]][S[ss][i]];+                                                  if(tt == 0)+                                                    tt = 7;+                                                  energy += E_MLstem(tt, -1, -1, P);+                                                }+                                              }+                                              break;++                default:                      break; /* this should never happen */+              }+              break;++    case 2:   switch(vc->type){+                case VRNA_FC_TYPE_SINGLE:     while(p < j){+                                                /* p must have a pairing partner */+                                                q  = (int)pt[p];+                                                /* get type of base pair (p,q) */+                                                tt = md->pair[s[p]][s[q]];+                                                if(tt == 0)+                                                  tt = 7;+                                                mm5 = ON_SAME_STRAND(p - 1, p, cp) ? s1[p-1] : -1;+                                                mm3 = ON_SAME_STRAND(q, q + 1, cp) ? s1[q+1] : -1;+                                                energy += E_MLstem(tt, mm5, mm3, P);++                                                /* seek to the next stem */+                                                p = q + 1;+                                                q_prev = q_prev2 = q;+                                                while (p <= j && !pt[p]) p++;+                                                u += p - q - 1; /* add unpaired nucleotides */++                                                if(sc){+                                                  if(sc->energy_up)+                                                    bonus += sc->energy_up[q+1][p-q-1];+                                                }+                                              }+                                              if(i > 0){  /* actual closing pair */+                                                tt = md->pair[s[j]][s[i]];+                                                if(tt == 0)+                                                  tt = 7;+                                                mm5 = ON_SAME_STRAND(j - 1, j, cp) ? s1[j-1] : -1;+                                                mm3 = ON_SAME_STRAND(i, i + 1, cp) ? s1[i+1] : -1;+                                                energy += E_MLstem(tt, mm5, mm3, P);++                                              } else {  /* virtual closing pair */+                                                energy += E_MLstem(0, -1, -1, P);+                                              }+                                              break;++                case VRNA_FC_TYPE_COMPARATIVE:  while(p < j){+                                                /* p must have a pairing partner */+                                                q  = (int)pt[p];+                                                +                                                for(ss = 0; ss < n_seq; ss++){+                                                  /* get type of base pair (p,q) */+                                                  tt = md->pair[S[ss][p]][S[ss][q]];+                                                  if(tt == 0)+                                                    tt = 7;++                                                  mm5 = ((a2s[ss][p] > 1) || circular) ? S5[ss][p] : -1;+                                                  mm3 = ((a2s[ss][q] < a2s[ss][S[0][0]]) || circular) ? S3[ss][q] : -1;+                                                  energy += E_MLstem(tt, mm5, mm3, P);+                                                }++                                                /* seek to the next stem */+                                                p = q + 1;+                                                q_prev = q_prev2 = q;+                                                while (p <= j && !pt[p]) p++;++                                                /* add unpaired nucleotides and possible soft constraints */+                                                if(scs){+                                                  for(ss = 0; ss < n_seq; ss++){+                                                    uu = a2s[ss][p] - a2s[ss][q + 1]; +                                                    if(scs[ss] && scs[ss]->energy_up){+                                                      bonus += sc->energy_up[a2s[ss][q + 1]][uu];+                                                    }+                                                    u += uu;+                                                  }+                                                } else {+                                                  for(ss = 0; ss < n_seq; ss++){+                                                    u += a2s[ss][p] - a2s[ss][q + 1];+                                                  }+                                                }+                                              }++                                              if(i > 0){  /* actual closing pair */+                                                for(ss = 0; ss < n_seq; ss++){+                                                  tt = md->pair[S[ss][j]][S[ss][i]];+                                                  if(tt == 0)+                                                    tt = 7;++                                                  mm5 = S5[ss][j];+                                                  mm3 = S3[ss][i];+                                                  energy += E_MLstem(tt, mm5, mm3, P);+                                                }+                                              }+                                              break;++                default:                      break; /* this should never happen */+              }+              break;++    case 3:   /* we treat helix stacking different */+              for (count=0; count<2; count++) { /* do it twice */+                ld5 = 0; /* 5' dangle energy on prev pair (type) */+                if ( i==0 ) {+                  j = (unsigned int)pt[0]+1;+                  type = 0;  /* no pair */+                }+                else {+                  j = (unsigned int)pt[i];+                  type = P->model_details.pair[s[j]][s[i]]; if (type==0) type=7;+                  /* prime the ld5 variable */+                  if (ON_SAME_STRAND(j - 1, j, cp)) {+                    ld5 = P->dangle5[type][s1[j-1]];+                    if ((p=(unsigned int)pt[j-2]) && ON_SAME_STRAND(j - 2, j - 1, cp))+                    if (P->dangle3[P->model_details.pair[s[p]][s[j-2]]][s1[j-1]]<ld5) ld5 = 0;+                  }+                }+                i1=i; p = i+1; u=0;+                energy = 0; cx_energy=INF;+                do { /* walk around the multi-loop */+                  new_cx = INF;++                  /* hop over unpaired positions */+                  while (p <= (unsigned int)pt[0] && pt[p]==0) p++;++                  /* memorize number of unpaired positions */+                  u += p-i1-1;++                  if(sc){+                    if(sc->energy_up)+                      bonus += sc->energy_up[i1+1][p-i1-1];+                  }++                  /* get position of pairing partner */+                  if ( p == (unsigned int)pt[0]+1 ){+                    q = 0;tt = 0; /* virtual root pair */+                  } else {+                    q  = (unsigned int)pt[p];+                    /* get type of base pair P->q */+                    tt = P->model_details.pair[s[p]][s[q]]; if (tt==0) tt=7;+                  }++                  energy += mlintern[tt];+                  cx_energy += mlintern[tt];++                  dang5=dang3=0;+                  if ((ON_SAME_STRAND(p - 1, p, cp))&&(p>1))+                    dang5=P->dangle5[tt][s1[p-1]];      /* 5'dangle of pq pair */+                  if ((ON_SAME_STRAND(i1, i1 + 1, cp))&&(i1<(unsigned int)s[0]))+                    dang3 = P->dangle3[type][s1[i1+1]]; /* 3'dangle of previous pair */++                  switch (p-i1-1) {+                    case 0:   /* adjacent helices */+                              if (i1!=0){+                                if (ON_SAME_STRAND(i1, p, cp)) {+                                  new_cx = energy + P->stack[rtype[type]][rtype[tt]];+                                  /* subtract 5'dangle and TerminalAU penalty */+                                  new_cx += -ld5 - mlintern[tt]-mlintern[type]+2*mlintern[1];+                                }+                                ld5=0;+                                energy = MIN2(energy, cx_energy);+                              }+                              break;+                    case 1:   /* 1 unpaired base between helices */+                              dang = MIN2(dang3, dang5);+                              energy = energy +dang; ld5 = dang - dang3;+                              /* may be problem here: Suppose+                                cx_energy>energy, cx_energy+dang5<energy+                                and the following helices are also stacked (i.e.+                                we'll subtract the dang5 again */+                              if (cx_energy+dang5 < energy) {+                                energy = cx_energy+dang5;+                                ld5 = dang5;+                              }+                              new_cx = INF;  /* no coax stacking with mismatch for now */+                              break;+                    default:  /* many unpaired base between helices */+                              energy += dang5 +dang3;+                              energy = MIN2(energy, cx_energy + dang5);+                              new_cx = INF;  /* no coax stacking possible */+                              ld5 = dang5;+                              break;+                  }+                  type = tt;+                  cx_energy = new_cx;+                  i1 = q; p=q+1;+                } while (q!=i);+                best_energy = MIN2(energy, best_energy); /* don't use cx_energy here */+                /* skip a helix and start again */+                while (pt[p]==0) p++;+                if (i == (unsigned int)pt[p]) break;+                i = (unsigned int)pt[p];+              } /* end doing it twice */+              energy = best_energy;+              break;++    default:  E_mm5_available = E2_mm5_available  = INF;+              E_mm5_occupied  = E2_mm5_occupied   = 0;+              while(p < j){+                /* p must have a pairing partner */+                q  = (int)pt[p];+                /* get type of base pair (p,q) */+                tt = P->model_details.pair[s[p]][s[q]];+                if(tt==0) tt=7;+                if(q_prev + 2 < p){+                  E_mm5_available = MIN2(E_mm5_available, E_mm5_occupied);+                  E_mm5_occupied  = E_mm5_available;+                }+                if(q_prev2 + 2 < p){+                  E2_mm5_available  = MIN2(E2_mm5_available, E2_mm5_occupied);+                  E2_mm5_occupied   = E2_mm5_available;+                }+                mm5 = ((ON_SAME_STRAND(p - 1, p, cp)) && !pt[p-1])  ? s1[p-1] : -1;+                mm3 = ((ON_SAME_STRAND(q, q + 1, cp)) && !pt[q+1])  ? s1[q+1] : -1;+                e_stem    = E_MLstem(tt, -1, -1, P);+                e_stem5   = E_MLstem(tt, mm5, -1, P);+                e_stem3   = E_MLstem(tt, -1, mm3, P);+                e_stem53  = E_MLstem(tt, mm5, mm3, P);++                tmp   = E_mm5_occupied + e_stem3;+                tmp   = MIN2(tmp, E_mm5_available + e_stem53);+                tmp   = MIN2(tmp, E_mm5_available + e_stem3);+                tmp2  = E_mm5_occupied + e_stem;+                tmp2  = MIN2(tmp2, E_mm5_available + e_stem5);+                tmp2  = MIN2(tmp2, E_mm5_available + e_stem);++                E_mm5_occupied  = tmp;+                E_mm5_available = tmp2;++                tmp   = E2_mm5_occupied + e_stem3;+                tmp   = MIN2(tmp, E2_mm5_available + e_stem53);+                tmp   = MIN2(tmp, E2_mm5_available + e_stem3);+                tmp2  = E2_mm5_occupied + e_stem;+                tmp2  = MIN2(tmp2, E2_mm5_available + e_stem5);+                tmp2  = MIN2(tmp2, E2_mm5_available + e_stem);++                E2_mm5_occupied   = tmp;+                E2_mm5_available  = tmp2;++                /* seek to the next stem */+                p = q + 1;+                q_prev = q_prev2 = q;+                while (p <= j && !pt[p]) p++;+                u += p - q - 1; /* add unpaired nucleotides */++                if(sc){+                  if(sc->energy_up)+                    bonus += sc->energy_up[q+1][p-q-1];+                }+              }+              if(i > 0){  /* actual closing pair */+                type = P->model_details.pair[s[j]][s[i]]; if (type==0) type=7;+                mm5 = ((ON_SAME_STRAND(j - 1, j, cp)) && !pt[j-1])  ? s1[j-1] : -1;+                mm3 = ((ON_SAME_STRAND(i, i + 1, cp)) && !pt[i+1])  ? s1[i+1] : -1;+                if(q_prev + 2 < p){+                  E_mm5_available = MIN2(E_mm5_available, E_mm5_occupied);+                  E_mm5_occupied  = E_mm5_available;+                }+                if(q_prev2 + 2 < p){+                  E2_mm5_available  = MIN2(E2_mm5_available, E2_mm5_occupied);+                  E2_mm5_occupied   = E2_mm5_available;+                }+                e_stem    = E_MLstem(type, -1, -1, P);+                e_stem5   = E_MLstem(type, mm5, -1, P);+                e_stem3   = E_MLstem(type, -1, mm3, P);+                e_stem53  = E_MLstem(type, mm5, mm3, P);+              } else {  /* virtual closing pair */+                e_stem = e_stem5 = e_stem3 = e_stem53 = E_MLstem(0, -1, -1, P);+              }+              /* now lets see how we get the minimum including the enclosing stem */+              energy = E_mm5_occupied  + e_stem;+              energy = MIN2(energy, E_mm5_available   + e_stem5);+              energy = MIN2(energy, E_mm5_available   + e_stem);+              energy = MIN2(energy, E2_mm5_occupied   + e_stem3);+              energy = MIN2(energy, E2_mm5_occupied   + e_stem);+              energy = MIN2(energy, E2_mm5_available  + e_stem53);+              energy = MIN2(energy, E2_mm5_available  + e_stem3);+              energy = MIN2(energy, E2_mm5_available  + e_stem5);+              energy = MIN2(energy, E2_mm5_available  + e_stem);+              break;+  }/* end switch dangle_model */++  switch(vc->type){+    case VRNA_FC_TYPE_SINGLE:     energy += P->MLclosing;+                                  break;++    case VRNA_FC_TYPE_COMPARATIVE:  energy += P->MLclosing * n_seq;+                                  break;++    default:                      break;+  }++  /* logarithmic ML loop energy if logML */+  /* does this work for comparative predictions as well? */+  if(logML && (u>6))+    energy += 6*P->MLbase+(int)(P->lxc*log((double)u/6.));+  else+    energy += (u*P->MLbase);++  return energy + bonus;+}++++PRIVATE int+cut_in_loop(int i, const short *pt, int cp){++  /* walk around the loop;  return j pos of pair after cut if+     cut_point in loop else 0 */+  int  p, j;+  p = j = pt[i];+  do {+    i  = pt[p];  p = i+1;+    while ( pt[p]==0 ) p++;+  } while (p!=j && ON_SAME_STRAND(i, p, cp));+  return ON_SAME_STRAND(i, p, cp) ? 0 : j;+}++/* below are the consensus structure evaluation functions */++PRIVATE int+covar_energy_of_struct_pt(vrna_fold_compound_t *vc,+                              const short *pt){++  int e       = 0;+  int length  = vc->length;+  int i;++  for (i=1; i<=length; i++) {+    if (pt[i]==0) continue;+    e += stack_energy_covar_pt(vc, i, pt);+    i=pt[i];+  }++  return e;+}+++PRIVATE int+en_corr_of_loop_gquad_ali(vrna_fold_compound_t *vc,+                      int i,+                      int j,+                      const char *structure,+                      const short *pt,+                      const int *loop_idx){++  int pos, energy, p, q, r, s, u, type, type2, gq_en[2];+  int num_elem, num_g, elem_i, elem_j, up_mis;+  int L, l[3];++  short           **S           = vc->S;+  short           **S5          = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+  short           **S3          = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+  char            **Ss          = vc->Ss;+  unsigned short  **a2s         = vc->a2s;+  vrna_param_t    *P            = vc->params;+  vrna_md_t       *md           = &(P->model_details);+  int             n_seq         = vc->n_seq;+  int             dangle_model  = md->dangles;++  energy = 0;+  q = i;+  while((pos = parse_gquad(structure + q-1, &L, l)) > 0){+    q += pos-1;+    p = q - 4*L - l[0] - l[1] - l[2] + 1;+    if(q > j) break;+    /* we've found the first g-quadruplex at position [p,q] */+    E_gquad_ali_en(p, L, l, (const short **)S, n_seq, gq_en, P);+    energy    += gq_en[0];+    /* check if it's enclosed in a base pair */+    if(loop_idx[p] == 0){ q++; continue; /* g-quad in exterior loop */}+    else{+      energy += E_MLstem(0, -1, -1, P) * n_seq;+      /*  find its enclosing pair */+      num_elem  = 0;+      num_g     = 1;+      r         = p - 1;+      up_mis    = q - p + 1;++      /* seek for first pairing base located 5' of the g-quad */+      for(r = p - 1; !pt[r] && (r >= i); r--);+      if(r < i)+        vrna_message_error("this should not happen");++      if(r < pt[r]){ /* found the enclosing pair */+        s = pt[r];+      } else {+        num_elem++;+        elem_i = pt[r];+        elem_j = r;+        r = pt[r]-1 ;+        /* seek for next pairing base 5' of r */+        for(; !pt[r] && (r >= i); r--);+        if(r < i)+          vrna_message_error("so nich");+        if(r < pt[r]){ /* found the enclosing pair */+          s = pt[r];+        } else {+          /* hop over stems and unpaired nucleotides */+          while((r > pt[r]) && (r >= i)){+            if(pt[r]){ r = pt[r]; num_elem++;}+            r--;+          }+          if(r < i)+            vrna_message_error("so nich");+          s = pt[r]; /* found the enclosing pair */+        }+      }+      /* now we have the enclosing pair (r,s) */++      u = q+1;+      /* we know everything about the 5' part of this loop so check the 3' part */+      while(u<s){+        if(structure[u-1] == '.') u++;+        else if (structure[u-1] == '+'){ /* found another gquad */+          pos = parse_gquad(structure + u - 1, &L, l);+          if(pos > 0){+            E_gquad_ali_en(u, L, l, (const short **)S, n_seq, gq_en, P);+            energy += gq_en[0] + E_MLstem(0, -1, -1, P) * n_seq;+            up_mis += pos;+            u += pos;+            num_g++;+          }+        } else { /* we must have found a stem */+          if(!(u < pt[u]))+            vrna_message_error("wtf!");+          num_elem++;+          elem_i = u;+          elem_j = pt[u];+          energy += en_corr_of_loop_gquad_ali(vc,+                                u,+                                pt[u],+                                structure,+                                pt,+                                loop_idx);+          u = pt[u] + 1;+        }+      }+      if(u!=s)+        vrna_message_error("what the ...");+      else{ /* we are done since we've found no other 3' structure element */+        switch(num_elem){+          /* g-quad was misinterpreted as hairpin closed by (r,s) */+          case 0:   /*if(num_g == 1)+                      if((p-r-1 == 0) || (s-q-1 == 0))+                        vrna_message_error("too few unpaired bases");+                    */+                    {+                      int ee = 0;+                      int cnt;+                      for(cnt=0;cnt<n_seq;cnt++){+                        type = md->pair[S[cnt][r]][S[cnt][s]];+                        if(type == 0) type = 7;+                        if ((a2s[cnt][s-1]-a2s[cnt][r])<3) ee+=600;+                        else ee += E_Hairpin( a2s[cnt][s-1] - a2s[cnt][r],+                                              type,+                                              S3[cnt][r],+                                              S5[cnt][s],+                                              Ss[cnt] + a2s[cnt][r-1],+                                              P);+                      }+                      energy -= ee;+                      ee = 0;+                      for(cnt=0;cnt < n_seq; cnt++){+                        type = md->pair[S[cnt][r]][S[cnt][s]];+                        if(type == 0) type = 7;+                        if(dangle_model == 2)+                          ee += P->mismatchI[type][S3[cnt][r]][S5[cnt][s]];+                        if(type > 2)+                          ee += P->TerminalAU;+                      }+                      energy += ee;+                    }+                    energy += n_seq * P->internal_loop[s-r-1-up_mis];+                    break;+          /* g-quad was misinterpreted as interior loop closed by (r,s) with enclosed pair (elem_i, elem_j) */+          case 1:   {+                      int ee = 0;+                      int cnt;+                      for(cnt = 0; cnt<n_seq;cnt++){+                        type = md->pair[S[cnt][r]][S[cnt][s]];+                        if(type == 0) type = 7;+                        type2 = md->pair[S[cnt][elem_j]][S[cnt][elem_i]];+                        if(type2 == 0) type2 = 7;+                        ee += E_IntLoop(a2s[cnt][elem_i-1] - a2s[cnt][r],+                                        a2s[cnt][s-1] - a2s[cnt][elem_j],+                                        type,+                                        type2,+                                        S3[cnt][r],+                                        S5[cnt][s],+                                        S5[cnt][elem_i],+                                        S3[cnt][elem_j],+                                        P);+                      }+                      energy -= ee;+                      ee = 0;+                      for(cnt = 0; cnt < n_seq; cnt++){+                        type = md->pair[S[cnt][s]][S[cnt][r]];+                        if(type == 0) type = 7;+                        ee += E_MLstem(type, S5[cnt][s], S3[cnt][r], P);+                        type = md->pair[S[cnt][elem_i]][S[cnt][elem_j]];+                        if(type == 0) type = 7;+                        ee += E_MLstem(type, S5[cnt][elem_i], S3[cnt][elem_j], P);+                      }+                      energy += ee;+                    }+                    energy += (P->MLclosing + (elem_i-r-1+s-elem_j-1-up_mis) * P->MLbase) * n_seq;+                    break;+          /* gquad was misinterpreted as unpaired nucleotides in a multiloop */+          default:  energy -= (up_mis) * P->MLbase * n_seq;+                    break;+        }+      }+      q = s+1;+    }+  }++  return energy;++}++PRIVATE int+covar_en_corr_of_loop_gquad(vrna_fold_compound_t *vc,+                            int i,+                            int j,+                            const char *structure,+                            const short *pt,+                            const int *loop_idx){++  int pos, en_covar, p, q, r, s, u, gq_en[2];+  int num_elem, num_g, up_mis;+  int L, l[3];++  short           **S           = vc->S;+  vrna_param_t    *P            = vc->params;+  int             n_seq         = vc->n_seq;++  en_covar = 0;+  q = i;+  while((pos = parse_gquad(structure + q-1, &L, l)) > 0){+    q += pos-1;+    p = q - 4*L - l[0] - l[1] - l[2] + 1;+    if(q > j) break;+    /* we've found the first g-quadruplex at position [p,q] */+    E_gquad_ali_en(p, L, l, (const short **)S, n_seq, gq_en, P);+    en_covar  += gq_en[1];+    /* check if it's enclosed in a base pair */+    if(loop_idx[p] == 0){ q++; continue; /* g-quad in exterior loop */}+    else{+      /*  find its enclosing pair */+      num_elem  = 0;+      num_g     = 1;+      r         = p - 1;+      up_mis    = q - p + 1;++      /* seek for first pairing base located 5' of the g-quad */+      for(r = p - 1; !pt[r] && (r >= i); r--);+      if(r < i)+        vrna_message_error("this should not happen");++      if(r < pt[r]){ /* found the enclosing pair */+        s = pt[r];+      } else {+        num_elem++;+        r = pt[r]-1 ;+        /* seek for next pairing base 5' of r */+        for(; !pt[r] && (r >= i); r--);+        if(r < i)+          vrna_message_error("so nich");+        if(r < pt[r]){ /* found the enclosing pair */+          s = pt[r];+        } else {+          /* hop over stems and unpaired nucleotides */+          while((r > pt[r]) && (r >= i)){+            if(pt[r]){ r = pt[r]; num_elem++;}+            r--;+          }+          if(r < i)+            vrna_message_error("so nich");+          s = pt[r]; /* found the enclosing pair */+        }+      }+      /* now we have the enclosing pair (r,s) */++      u = q+1;+      /* we know everything about the 5' part of this loop so check the 3' part */+      while(u<s){+        if(structure[u-1] == '.') u++;+        else if (structure[u-1] == '+'){ /* found another gquad */+          pos = parse_gquad(structure + u - 1, &L, l);+          if(pos > 0){+            E_gquad_ali_en(u, L, l, (const short **)S, n_seq, gq_en, P);+            en_covar += gq_en[1];+            up_mis += pos;+            u += pos;+            num_g++;+          }+        } else { /* we must have found a stem */+          if(!(u < pt[u]))+            vrna_message_error("wtf!");+          num_elem++;+          en_covar += covar_en_corr_of_loop_gquad(vc,+                                u,+                                pt[u],+                                structure,+                                pt,+                                loop_idx);+          u = pt[u] + 1;+        }+      }+      if(u!=s)+        vrna_message_error("what the ...");+      else{+        /* we are done since we've found no other 3' structure element */+      }+      q = s+1;+    }+  }++  return en_covar;+}+++PRIVATE int+stack_energy_covar_pt(vrna_fold_compound_t *vc,+                      int i,+                      const short *pt){++  /* calculate energy of substructure enclosed by (i,j) */+  int             *indx       = vc->jindx;     /* index for moving in the triangle matrices c[] and fMl[]*/+  int             *pscore     = vc->pscore;     /* precomputed array of pair types */++  int energy = 0;+  int j, p, q;++  j = pt[i];+  p=i; q=j;+  while (p<q) { /* process all stacks and interior loops */+    while (pt[++p]==0);+    while (pt[--q]==0);+    if ((pt[q]!=(short)p)||(p>q)) break;+    energy += pscore[indx[j]+i];+    i=p; j=q;+  }  /* end while */++  /* p,q don't pair must have found hairpin or multiloop */++  if (p>q) { /* hairpin case */+    energy += pscore[indx[j]+i];+    return energy;+  }++  /* (i,j) is exterior pair of multiloop */+  energy += pscore[indx[j]+i];+  while (p<j) {+    /* add up the contributions of the substructures of the ML */+    energy += stack_energy_covar_pt(vc, p, pt);+    p = pt[p];+    /* search for next base pair in multiloop */+    while (pt[++p]==0);+  }++  return energy;+}+++/*+#################################+# DEPRECATED functions below    #+#################################+*/++PRIVATE vrna_fold_compound_t *+recycle_last_call(const char *string,+                  vrna_param_t *P){++  vrna_fold_compound_t  *vc;+  vrna_md_t           *md;+  int                 cleanup;+  char                *seq;++  vc      = NULL;+  cleanup = 0;++  if(P){+    md = &(P->model_details);+  } else {+    md = (vrna_md_t *)vrna_alloc(sizeof(vrna_md_t));+    set_model_details(md);+    cleanup = 1;+  }++  if(string){+    if(backward_compat_compound){+      if(!strcmp(string, backward_compat_compound->sequence)){ /* check if sequence is the same as before */+        md->window_size = (int)backward_compat_compound->length;+        if(!memcmp(md, &(backward_compat_compound->params->model_details), sizeof(vrna_md_t))){ /* check if model_details are the same as before */+          vc = backward_compat_compound; /* re-use previous vrna_fold_compound_t */+        }+      }+    }+  }++  /* prepare a new global vrna_fold_compound_t with current settings */+  if(!vc){+    vrna_fold_compound_free(backward_compat_compound);+    seq = vrna_cut_point_insert(string, cut_point);+    backward_compat_compound = vc = vrna_fold_compound(seq, md, VRNA_OPTION_EVAL_ONLY);+    if(P){+      free(vc->params);+      vc->params = get_updated_params(P, 1);+    }+    free(seq);+  }++  if(cleanup)+    free(md);++  return vc;+}+++PUBLIC float+energy_of_struct( const char *string,+                  const char *structure){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, NULL);++  if(eos_debug > 0)+    en = vrna_eval_structure_verbose(vc, structure, NULL);+  else+    en = vrna_eval_structure(vc, structure);++  return en;+}++PUBLIC int+energy_of_struct_pt(const char *string,+                    short *pt,+                    short *s,+                    short *s1){++  int                 en;+  vrna_fold_compound_t  *vc;++  if(pt && string){+    if(pt[0] != (short)strlen(string))+      vrna_message_error("energy_of_structure_pt: string and structure have unequal length");++    vc  = recycle_last_call(string, NULL);+    en  = eval_pt(vc, pt, NULL, eos_debug);++    return en;+  } else+    return INF;+}++PUBLIC float+energy_of_circ_struct(const char *string,+                      const char *structure){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, NULL);++  vc->params->model_details.circ = 1;++  if(eos_debug > 0)+    en = vrna_eval_structure_verbose(vc, structure, NULL);+  else+    en = vrna_eval_structure(vc, structure);++  return en;+}++PUBLIC  float+energy_of_structure(const char *string,+                    const char *structure,+                    int verbosity_level){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, NULL);++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}++PUBLIC float+energy_of_struct_par( const char *string,+                      const char *structure,+                      vrna_param_t *parameters,+                      int verbosity_level){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, parameters);++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}+++PUBLIC float+energy_of_gquad_structure(const char *string,+                          const char *structure,+                          int verbosity_level){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, NULL);++  vc->params->model_details.gquad = 1;++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}++PUBLIC float+energy_of_gquad_struct_par( const char *string,+                            const char *structure,+                            vrna_param_t *parameters,+                            int verbosity_level){+++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, parameters);++  vc->params->model_details.gquad = 1;++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}++PUBLIC int+energy_of_structure_pt( const char *string,+                        short *pt,+                        short *s,+                        short *s1,+                        int verbosity_level){++  int                 en;+  vrna_fold_compound_t  *vc;++  if(pt && string){+    if(pt[0] != (short)strlen(string))+      vrna_message_error("energy_of_structure_pt: string and structure have unequal length");++    vc  = recycle_last_call(string, NULL);+    en  = eval_pt(vc, pt, NULL, verbosity_level);++    return en;+  } else+    return INF;+}++PUBLIC int+energy_of_struct_pt_par(const char *string,+                        short *pt,+                        short *s,+                        short *s1,+                        vrna_param_t *parameters,+                        int verbosity_level){++  int en;+  vrna_fold_compound_t *vc;++  if(pt && string){+    if(pt[0] != (short)strlen(string))+      vrna_message_error("energy_of_structure_pt: string and structure have unequal length");++    vc  = recycle_last_call(string, parameters);+    en  = eval_pt(vc, pt, NULL, verbosity_level);++    return en;+  } else+    return INF;+}++PUBLIC float+energy_of_circ_structure( const char *string,+                          const char *structure,+                          int verbosity_level){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, NULL);++  vc->params->model_details.circ = 1;++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}++PUBLIC float+energy_of_circ_struct_par(const char *string,+                          const char *structure,+                          vrna_param_t *parameters,+                          int verbosity_level){++  float               en;+  vrna_fold_compound_t  *vc;++  vc = recycle_last_call(string, parameters);++  vc->params->model_details.circ = 1;++  return vrna_eval_structure_v(vc, structure, verbosity_level, NULL);+}++PUBLIC int+loop_energy(short *pt,+            short *s,+            short *s1,+            int i){++  int                 en, u;+  char                *seq;+  vrna_md_t           md;+  vrna_fold_compound_t  *vc;++  set_model_details(&md);++  /* convert encoded sequence back to actual string */+  seq = (char *)vrna_alloc(sizeof(char) * (s[0]+1));+  for(u = 1; u <= s[0]; u++){+    seq[u-1] = vrna_nucleotide_decode(s[u], &md);+  }+  seq[u-1] = '\0';++  vc  = recycle_last_call(seq, NULL);+  en  = wrap_eval_loop_pt(vc, i, pt, eos_debug);++  free(seq);++  return en;+}+++PUBLIC float+energy_of_move( const char *string,+                const char *structure,+                int m1,+                int m2){++  float               en;+  vrna_fold_compound_t  *vc;++  vc  = recycle_last_call(string, NULL);+  en  = vrna_eval_move(vc, structure, m1, m2);++  return en;+}++PUBLIC int+energy_of_move_pt(short *pt,+                  short *s,+                  short *s1,+                  int m1,+                  int m2){++  int                 en, u;+  char                *seq;+  vrna_md_t           md;+  vrna_fold_compound_t  *vc;++  set_model_details(&md);++  /* convert encoded sequence back to actual string */+  seq = (char *)vrna_alloc(sizeof(char) * (s[0]+1));+  for(u = 1; u <= s[0]; u++){+    seq[u-1] = vrna_nucleotide_decode(s[u], &md);+  }+  seq[u-1] = '\0';++  vc  = recycle_last_call(seq, NULL);+  en  = vrna_eval_move_pt(vc, pt, m1, m2);++  free(seq);++  return en;+}+
+ C/ViennaRNA/eval.h view
@@ -0,0 +1,663 @@+#ifndef VIENNA_RNA_PACKAGE_EVAL_H+#define VIENNA_RNA_PACKAGE_EVAL_H++#include <stdio.h>+#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>   /* for deprecated functions */++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     eval.h+ *  @ingroup  eval+ *  @brief    Functions and variables related to energy evaluation of sequence/structure pairs.+ */+++/**+ *  @addtogroup eval+ *  @brief Functions and variables related to free energy evaluation of sequence/structure pairs.+ *+ *  @{+ *  @ingroup  eval+ */++/** @brief set to first pos of second seq for cofolding  */+extern  int cut_point;++/**+ *  @brief verbose info from energy_of_struct+ */+extern  int eos_debug;++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function allows for energy evaluation of a given pair of structure+ *  and sequence (alignment).+ *  Model details, energy parameters, and possibly soft constraints are used as provided+ *  via the parameter 'vc'. The #vrna_fold_compound_t does not need to contain any DP matrices,+ *  but requires all most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @note Accepts vrna_fold_compound_t of type #VRNA_FC_TYPE_SINGLE and #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @see  vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),+ *        vrna_fold_compound(), vrna_fold_compound_comparative(), vrna_eval_covar_structure()+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param structure        Secondary structure in dot-bracket notation+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure(vrna_fold_compound_t *vc,+                          const char *structure);++/**+ *  @brief Calculate the pseudo energy derived by the covariance scores of a set of aligned sequences+ *+ *  Consensus structure prediction is driven by covariance scores of base pairs in rows of the+ *  provided alignment. This function allows one to retrieve the total amount of this covariance pseudo+ *  energy scores.+ *  The #vrna_fold_compound_t does not need to contain any DP matrices, but requires all most basic+ *  init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound_comparative(alignment, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @note Accepts vrna_fold_compound_t of type #VRNA_FC_TYPE_COMPARATIVE only!+ *+ *  @see  vrna_fold_compound_comparative(), vrna_eval_structure()+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param structure        Secondary (consensus) structure in dot-bracket notation+ *  @return                 The covariance pseudo energy score of the input structure given the input sequence alignment in kcal/mol+ */+float vrna_eval_covar_structure(vrna_fold_compound_t *vc,+                                const char *structure);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function allows for energy evaluation of a given sequence/structure pair.+ *  In contrast to vrna_eval_structure() this function assumes default model details+ *  and default energy parameters in order to evaluate the free energy of the secondary+ *  structure. Therefore, it serves as a simple interface function for energy evaluation+ *  for situations where no changes on the energy model are required.+ *+ *  @see vrna_eval_structure(), vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param structure        Secondary structure in dot-bracket notation+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure_simple( const char *string,+                                  const char *structure);++/**+ *  @brief Calculate the free energy of an already folded RNA and print contributions on a per-loop base.+ *+ *  This function is a simplyfied version of vrna_eval_structure_v() that uses the @em default+ *  verbosity level.+ (+ *  @see vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure_verbose(vrna_fold_compound_t *vc,+                                  const char *structure,+                                  FILE *file);++/**+ *  @brief Calculate the free energy of an already folded RNA and print contributions on a per-loop base.+ *+ *  This function allows for detailed energy evaluation of a given sequence/structure pair.+ *  In contrast to vrna_eval_structure() this function prints detailed energy contributions+ *  based on individual loops to a file handle. If NULL is passed as file handle, this function+ *  defaults to print to stdout. Any positive @p verbosity_level activates potential warning message+ *  of the energy evaluting functions, while values @f$ \ge 1 @f$ allow for detailed control of what+ *  data is printed. A negative parameter @p verbosity_level turns off printing all together.+ *+ *  Model details, energy parameters, and possibly soft constraints are used as provided+ *  via the parameter 'vc'. The fold_compound does not need to contain any DP matrices,+ *  but all the most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @see vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param verbosity_level  The level of verbosity of this function+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure_v(vrna_fold_compound_t *vc,+                            const char *structure,+                            int verbosity_level,+                            FILE *file);++/**+ *  @brief Calculate the free energy of an already folded RNA and print contributions per loop.+ *+ *  This function is a simplyfied version of vrna_eval_structure_simple_v() that uses the @em default+ *  verbosity level.+ *+ *  @see  vrna_eval_structure_simple_v(), vrna_eval_structure_verbose(), vrna_eval_structure_pt(),+ *        vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure_simple_verbose( const char *string,+                                          const char *structure,+                                          FILE *file);+++/**+ *  @brief Calculate the free energy of an already folded RNA and print contributions per loop.+ *+ *  This function allows for detailed energy evaluation of a given sequence/structure pair.+ *  In contrast to vrna_eval_structure() this function prints detailed energy contributions+ *  based on individual loops to a file handle. If NULL is passed as file handle, this function+ *  defaults to print to stdout. Any positive @p verbosity_level activates potential warning message+ *  of the energy evaluting functions, while values @f$ \ge 1 @f$ allow for detailed control of what+ *  data is printed. A negative parameter @p verbosity_level turns off printing all together.+ *+ *  In contrast to vrna_eval_structure_verbose() this function assumes default model details+ *  and default energy parameters in order to evaluate the free energy of the secondary+ *  structure. Threefore, it serves as a simple interface function for energy evaluation+ *  for situations where no changes on the energy model are required.+ *+ *  @see vrna_eval_structure_verbose(), vrna_eval_structure_pt(), vrna_eval_structure_verbose(), vrna_eval_structure_pt_verbose(),+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param verbosity_level  The level of verbosity of this function+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in kcal/mol+ */+float vrna_eval_structure_simple_v( const char *string,+                                    const char *structure,+                                    int verbosity_level,+                                    FILE *file);+++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function allows for energy evaluation of a given sequence/structure pair where+ *  the structure is provided in pair_table format as obtained from vrna_ptable().+ *  Model details, energy parameters, and possibly soft constraints are used as provided+ *  via the parameter 'vc'. The fold_compound does not need to contain any DP matrices,+ *  but all the most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @see vrna_ptable(), vrna_eval_structure(), vrna_eval_structure_pt_verbose()+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param pt               Secondary structure as pair_table+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt( vrna_fold_compound_t *vc,+                            const short *pt);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  In contrast to vrna_eval_structure_pt() this function assumes default model details+ *  and default energy parameters in order to evaluate the free energy of the secondary+ *  structure. Threefore, it serves as a simple interface function for energy evaluation+ *  for situations where no changes on the energy model are required.+ *+ *  @see vrna_ptable(), vrna_eval_structure_simple(), vrna_eval_structure_pt()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param pt               Secondary structure as pair_table+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt_simple(const char *string,+                                  const short *pt);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function is a simplyfied version of vrna_eval_structure_simple_v() that uses the @em default+ *  verbosity level.+ *+ *  @see vrna_eval_structure_pt_v(), vrna_ptable(), vrna_eval_structure_pt(), vrna_eval_structure_verbose()+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param pt               Secondary structure as pair_table+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt_verbose( vrna_fold_compound_t *vc,+                                    const short *pt,+                                    FILE *file);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function allows for energy evaluation of a given sequence/structure pair where+ *  the structure is provided in pair_table format as obtained from vrna_ptable().+ *  Model details, energy parameters, and possibly soft constraints are used as provided+ *  via the parameter 'vc'. The fold_compound does not need to contain any DP matrices,+ *  but all the most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *  In contrast to vrna_eval_structure_pt() this function prints detailed energy contributions+ *  based on individual loops to a file handle. If NULL is passed as file handle, this function+ *  defaults to print to stdout. Any positive @p verbosity_level activates potential warning message+ *  of the energy evaluting functions, while values @f$ \ge 1 @f$ allow for detailed control of what+ *  data is printed. A negative parameter @p verbosity_level turns off printing all together.+ *+ *  @see vrna_ptable(), vrna_eval_structure_pt(), vrna_eval_structure_verbose()+ *+ *  @param vc               A vrna_fold_compound_t containing the energy parameters and model details+ *  @param pt               Secondary structure as pair_table+ *  @param verbosity_level  The level of verbosity of this function+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt_v( vrna_fold_compound_t *vc,+                              const short *pt,+                              int verbosity_level,+                              FILE *file);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function is a simplyfied version of vrna_eval_structure_pt_simple_v() that uses the @em default+ *  verbosity level.+ *+ *  @see vrna_eval_structure_pt_simple_v(), vrna_ptable(), vrna_eval_structure_pt_verbose(), vrna_eval_structure_simple()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param pt               Secondary structure as pair_table+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt_simple_verbose(const char *string,+                                          const short *pt,+                                          FILE *file);++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  This function allows for energy evaluation of a given sequence/structure pair where+ *  the structure is provided in pair_table format as obtained from vrna_ptable().+ *  Model details, energy parameters, and possibly soft constraints are used as provided+ *  via the parameter 'vc'. The fold_compound does not need to contain any DP matrices,+ *  but all the most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *  In contrast to vrna_eval_structure_pt_verbose() this function assumes default model details+ *  and default energy parameters in order to evaluate the free energy of the secondary+ *  structure. Threefore, it serves as a simple interface function for energy evaluation+ *  for situations where no changes on the energy model are required.+ *+ *  @see vrna_ptable(), vrna_eval_structure_pt_v(), vrna_eval_structure_simple()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param pt               Secondary structure as pair_table+ *  @param verbosity_level  The level of verbosity of this function+ *  @param file             A file handle where this function should print to (may be NULL).+ *  @return                 The free energy of the input structure given the input sequence in 10cal/mol+ */+int vrna_eval_structure_pt_simple_v(const char *string,+                                    const short *pt,+                                    int verbosity_level,+                                    FILE *file);++/**+ * @brief Calculate energy of a loop+ *+ *  @param vc         A vrna_fold_compound_t containing the energy parameters and model details+ *  @param i          position of covering base pair+ *  @param pt         the pair table of the secondary structure+ *  @returns          free energy of the loop in 10cal/mol+ */+int vrna_eval_loop_pt(vrna_fold_compound_t *vc,+                      int i,+                      const short *pt);++/** + * @brief Calculate energy of a move (closing or opening of a base pair)+ *+ *  If the parameters m1 and m2 are negative, it is deletion (opening)+ *  of a base pair, otherwise it is insertion (opening).+ *+ *  @see              vrna_eval_move_pt()+ *  @param vc         A vrna_fold_compound_t containing the energy parameters and model details+ *  @param structure  secondary structure in dot-bracket notation+ *  @param m1         first coordinate of base pair+ *  @param m2         second coordinate of base pair+ *  @returns          energy change of the move in kcal/mol+ */+float vrna_eval_move( vrna_fold_compound_t *vc,+                      const char *structure,+                      int m1,+                      int m2);++/**+ * + * @brief Calculate energy of a move (closing or opening of a base pair)+ *+ *  If the parameters m1 and m2 are negative, it is deletion (opening)+ *  of a base pair, otherwise it is insertion (opening).+ *+ *  @see              vrna_eval_move()+ *  @param vc         A vrna_fold_compound_t containing the energy parameters and model details+ *  @param pt         the pair table of the secondary structure+ *  @param m1         first coordinate of base pair+ *  @param m2         second coordinate of base pair+ *  @returns          energy change of the move in 10cal/mol+ */+int vrna_eval_move_pt(vrna_fold_compound_t *vc,+                      short *pt,+                      int m1,+                      int m2);++int vrna_eval_move_pt_simple( const char *string,+                              short *pt,+                              int m1,+                              int m2);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Calculate the free energy of an already folded RNA using global model detail settings+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @note OpenMP: This function relies on several global model settings variables and thus is+ *        not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe+ *        implementation.+ *+ *  @deprecated Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!+ *+ *  @see vrna_eval_structure()+ *+ *  @param string     RNA sequence+ *  @param structure  secondary structure in dot-bracket notation+ *  @param verbosity_level a flag to turn verbose output on/off+ *  @return          the free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_structure(const char *string,+                          const char *structure,+                          int verbosity_level));++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @deprecated Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!+ *+ *  @see vrna_eval_structure()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param parameters       A data structure containing the prescaled energy contributions and the model details.+ *  @param verbosity_level  A flag to turn verbose output on/off+ *  @return                The free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_struct_par( const char *string,+                            const char *structure,+                            vrna_param_t *parameters,+                            int verbosity_level));++/**+ *  @brief Calculate the free energy of an already folded  circular RNA+ *+ *  @note OpenMP: This function relies on several global model settings variables and thus is+ *        not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe+ *        implementation.+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @deprecated Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!+ *+ *  @see vrna_eval_structure()+ *+ *  @param string           RNA sequence+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param verbosity_level  A flag to turn verbose output on/off+ *  @return                The free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_circ_structure( const char *string,+                                const char *structure,+                                int verbosity_level));++/**+ *  @brief Calculate the free energy of an already folded circular RNA+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @deprecated Use vrna_eval_structure() or vrna_eval_structure_verbose() instead!+ *+ *  @see vrna_eval_structure()+ *+ *  @param string           RNA sequence+ *  @param structure        Secondary structure in dot-bracket notation+ *  @param parameters       A data structure containing the prescaled energy contributions and the model details.+ *  @param verbosity_level  A flag to turn verbose output on/off+ *  @return                The free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_circ_struct_par(const char *string,+                                const char *structure,+                                vrna_param_t *parameters,+                                int verbosity_level));+++DEPRECATED(float energy_of_gquad_structure(const char *string,+                                const char *structure,+                                int verbosity_level));++DEPRECATED(float energy_of_gquad_struct_par( const char *string,+                                  const char *structure,+                                  vrna_param_t *parameters,+                                  int verbosity_level));+++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @note OpenMP: This function relies on several global model settings variables and thus is+ *        not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe+ *        implementation.+ *+ *  @deprecated Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!+ *+ *  @see vrna_eval_structure_pt()+ *+ *  @param string     RNA sequence+ *  @param ptable     the pair table of the secondary structure+ *  @param s          encoded RNA sequence+ *  @param s1         encoded RNA sequence+ *  @param verbosity_level a flag to turn verbose output on/off+ *  @return          the free energy of the input structure given the input sequence in 10kcal/mol+ */+DEPRECATED(int energy_of_structure_pt( const char *string,+                            short *ptable,+                            short *s,+                            short *s1,+                            int verbosity_level));++/**+ *  @brief Calculate the free energy of an already folded RNA+ *+ *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout+ *+ *  @deprecated Use vrna_eval_structure_pt() or vrna_eval_structure_pt_verbose() instead!+ *+ *  @see vrna_eval_structure_pt()+ *+ *  @param string           RNA sequence in uppercase letters+ *  @param ptable           The pair table of the secondary structure+ *  @param s                Encoded RNA sequence+ *  @param s1               Encoded RNA sequence+ *  @param parameters       A data structure containing the prescaled energy contributions and the model details.+ *  @param verbosity_level  A flag to turn verbose output on/off+ *  @return                The free energy of the input structure given the input sequence in 10kcal/mol+ */+DEPRECATED(int energy_of_struct_pt_par(const char *string,+                            short *ptable,+                            short *s,+                            short *s1,+                            vrna_param_t *parameters,+                            int verbosity_level));++++/** + * @brief Calculate energy of a move (closing or opening of a base pair)+ *+ *  If the parameters m1 and m2 are negative, it is deletion (opening)+ *  of a base pair, otherwise it is insertion (opening).+ *+ *  @deprecated Use vrna_eval_move() instead!+ *+ *  @see vrna_eval_move()+ *+ *  @param string     RNA sequence+ *  @param structure  secondary structure in dot-bracket notation+ *  @param m1         first coordinate of base pair+ *  @param m2         second coordinate of base pair+ *  @returns          energy change of the move in kcal/mol+ */+DEPRECATED(float energy_of_move( const char *string,+                      const char *structure,+                      int m1,+                      int m2));+++/**+ * + * @brief Calculate energy of a move (closing or opening of a base pair)+ *+ *  If the parameters m1 and m2 are negative, it is deletion (opening)+ *  of a base pair, otherwise it is insertion (opening).+ *+ *  @deprecated Use vrna_eval_move_pt() instead!+ *+ *  @see vrna_eval_move_pt()+ *+ *  @param pt         the pair table of the secondary structure+ *  @param s          encoded RNA sequence+ *  @param s1         encoded RNA sequence+ *  @param m1         first coordinate of base pair+ *  @param m2         second coordinate of base pair+ *  @returns          energy change of the move in 10cal/mol+ */+DEPRECATED(int energy_of_move_pt(short *pt,+                   short *s,+                   short *s1,+                   int m1,+                   int m2));++/**+ * @brief Calculate energy of a loop+ *+ *  @deprecated Use vrna_eval_loop_pt() instead!+ *+ *  @see vrna_eval_loop_pt()+ *+ *  @param ptable     the pair table of the secondary structure+ *  @param s          encoded RNA sequence+ *  @param s1         encoded RNA sequence+ *  @param i          position of covering base pair+ *  @returns          free energy of the loop in 10cal/mol+ */+DEPRECATED(int   loop_energy(short *ptable,+                  short *s,+                  short *s1,+                  int i));++/**+ *  Calculate the free energy of an already folded RNA+ * + *  @note This function is not entirely threadsafe! Depending on the state of the global+ *  variable @ref eos_debug it prints energy information to stdout or not...\n+ * + *  @deprecated This function is deprecated and should not be used in future programs!+ *  Use @ref energy_of_structure() instead!+ * + *  @see              energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt()+ *  @param string     RNA sequence+ *  @param structure  secondary structure in dot-bracket notation+ *  @return          the free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_struct(const char *string,+                                  const char *structure));++/**+ *  Calculate the free energy of an already folded RNA+ * + *  @note This function is not entirely threadsafe! Depending on the state of the global+ *  variable @ref eos_debug it prints energy information to stdout or not...\n+ * + *  @deprecated This function is deprecated and should not be used in future programs!+ *  Use @ref energy_of_structure_pt() instead!+ * + *  @see              make_pair_table(), energy_of_structure()+ *  @param string     RNA sequence+ *  @param ptable     the pair table of the secondary structure+ *  @param s          encoded RNA sequence+ *  @param s1         encoded RNA sequence+ *  @return          the free energy of the input structure given the input sequence in 10kcal/mol+ */+DEPRECATED(int energy_of_struct_pt( const char *string,+                                    short *ptable,+                                    short *s,+                                    short *s1));++/**+ *  Calculate the free energy of an already folded  circular RNA+ * + *  @note This function is not entirely threadsafe! Depending on the state of the global+ *  variable @ref eos_debug it prints energy information to stdout or not...\n+ * + *  @deprecated This function is deprecated and should not be used in future programs+ *  Use @ref energy_of_circ_structure() instead!+ * + *  @see              energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt()+ *  @param string     RNA sequence+ *  @param structure  secondary structure in dot-bracket notation+ *  @return          the free energy of the input structure given the input sequence in kcal/mol+ */+DEPRECATED(float energy_of_circ_struct( const char *string,+                                        const char *structure));++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/exterior_loops.c view
@@ -0,0 +1,1785 @@+#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"+#include "ViennaRNA/exterior_loops.h"++#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif++struct default_data {+  int                       *idx;+  char                      *mx;+  int                       cp;+  int                       *hc_up;+  void                      *hc_dat;+  vrna_callback_hc_evaluate *hc_f;+};+++/*+ #################################+ # PRIVATE FUNCTION DECLARATIONS #+ #################################+ */++PRIVATE FLT_OR_DBL+exp_E_ext_fast(vrna_fold_compound_t *vc,+               int                  i,+               int                  j,+               vrna_mx_pf_aux_el_t  *aux_mx);+++PRIVATE FLT_OR_DBL+exp_E_ext_fast_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j,+                           vrna_mx_pf_aux_el_t  *aux_mx);+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data);+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data);+++/*+ #################################+ # BEGIN OF FUNCTION DEFINITIONS #+ #################################+ */+PUBLIC int+E_ext_loop(int                  i,+           int                  j,+           vrna_fold_compound_t *vc)+{+  char                      *ptype, *hard_constraints;+  short                     *S;+  int                       ij, en, e, type, cp, *idx;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp                = vc->cutpoint;+  S                 = vc->sequence_encoding;+  idx               = vc->jindx;+  ptype             = vc->ptype;+  P                 = vc->params;+  md                = &(P->model_details);+  hard_constraints  = vc->hc->matrix;+  sc                = vc->sc;++  hc_dat_local.idx  = idx;+  hc_dat_local.mx   = hard_constraints;+  hc_dat_local.cp   = cp;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }+++  e     = INF;+  ij    = idx[j] + i;+  type  = ptype[ij];++  if ((cp < 0) || (((i) >= cp) || ((j) < cp))) {+    /* regular exterior loop */+    if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+      if (type == 0)+        type = 7;++      switch (md->dangles) {+        case 2:+          e = E_ExtLoop(type, S[i - 1], S[j + 1], P);+          break;++        case 0:+        /* fall through */++        default:+          e = E_ExtLoop(type, -1, -1, P);+          break;+      }+      if (sc)+        if (sc->f)+          e += sc->f(i, j, i, j, VRNA_DECOMP_EXT_STEM, sc->data);+    }++    if (md->dangles % 2) {+      ij = idx[j - 1] + i;+      if (evaluate(i, j, i, j - 1, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+        type = vc->ptype[ij];++        if (type == 0)+          type = 7;++        en = E_ExtLoop(type, -1, S[j], P);+        if (sc)+          if (sc->f)+            en += sc->f(i, j, i, j - 1, VRNA_DECOMP_EXT_STEM, sc->data);+        e = MIN2(e, en);+      }++      ij = idx[j] + i + 1;+      if (evaluate(i, j, i + 1, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+        type = vc->ptype[ij];++        if (type == 0)+          type = 7;++        en = E_ExtLoop(type, S[i], -1, P);+        if (sc)+          if (sc->f)+            en += sc->f(i, j, i + 1, j, VRNA_DECOMP_EXT_STEM, sc->data);+        e = MIN2(e, en);+      }+    }+  }++  return e;+}+++PUBLIC void+E_ext_loop_5(vrna_fold_compound_t *vc)+{+  char                      *ptype, *hc;+  short                     *S;+  int                       en, i, j, ij, type, length, *indx, *hc_up, *f5, *c, dangle_model,+                            *ggg, with_gquad, turn, k, u, with_ud;+  vrna_sc_t                 *sc;+  vrna_param_t              *P;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  length        = (int)vc->length;+  ptype         = vc->ptype;+  S             = vc->sequence_encoding;+  indx          = vc->jindx;+  hc            = vc->hc->matrix;+  hc_up         = vc->hc->up_ext;+  sc            = vc->sc;+  f5            = vc->matrices->f5;+  c             = vc->matrices->c;+  P             = vc->params;+  dangle_model  = P->model_details.dangles;+  ggg           = vc->matrices->ggg;+  with_gquad    = P->model_details.gquad;+  turn          = P->model_details.min_loop_size;+  domains_up    = vc->domains_up;+  with_ud       = (domains_up && domains_up->energy_cb) ? 1 : 0;++  hc_dat_local.idx    = indx;+  hc_dat_local.mx     = hc;+  hc_dat_local.hc_up  = hc_up;+  hc_dat_local.cp     = vc->cutpoint;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  f5[0] = 0;+  for (i = 1; i <= turn + 1; i++) {+    if (f5[i - 1] != INF) {+      if (evaluate(1, i, 1, i - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+        f5[i] = f5[i - 1];+        if (sc) {+          if (sc->energy_up)+            f5[i] += sc->energy_up[i][1];+          if (sc->f)+            f5[i] += sc->f(1, i, 1, i - 1, VRNA_DECOMP_EXT_EXT, sc->data);+        }+      } else {+        f5[i] = INF;+      }+    } else {+      f5[i] = INF;+    }+  }++  if (with_ud) {+    /* do we include ligand binding? */+    /*  construct all possible combinations of+     *  f[i-1] + L[i,j] with j <= turn + 1+     */+    for (i = 1; i <= turn + 1; i++) {+      if (f5[i - 1] != INF) {+        for (k = 0; k < domains_up->uniq_motif_count; k++) {+          u = domains_up->uniq_motif_size[k];+          j = i + u - 1;+          if (j <= turn + 1) {+            if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+              en = f5[i - 1]+                   + domains_up->energy_cb(vc,+                                           i, j,+                                           VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP,+                                           domains_up->data);+              if (sc) {+                if (sc->energy_up)+                  en += sc->energy_up[i][u];+                if (sc->f)+                  en += sc->f(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, sc->data);+              }+              f5[j] = MIN2(f5[j], en);+            }+          }+        }+      }+    }+  }++  /* duplicated code may be faster than conditions inside loop ;) */+  switch (dangle_model) {+    /* dont use dangling end and mismatch contributions at all */+    case 0:+      for (j = turn + 2; j <= length; j++) {+        /* initialize with INF */+        f5[j] = INF;++        /* check for 3' extension with one unpaired nucleotide */+        if (f5[j - 1] != INF) {+          if (evaluate(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+            f5[j] = f5[j - 1];+            if (sc) {+              if (sc->energy_up)+                f5[j] += sc->energy_up[j][1];+              if (sc->f)+                f5[j] += sc->f(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, sc->data);+            }+          }+        }++        if (with_ud) {+          for (k = 0; k < domains_up->uniq_motif_count; k++) {+            u = domains_up->uniq_motif_size[k];+            if ((j - u >= 0) && (f5[j - u] != INF)) {+              if (evaluate(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+                en = f5[j - u]+                     + domains_up->energy_cb(vc,+                                             j - u + 1, j,+                                             VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                             domains_up->data);+                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[j - u + 1][u];+                  if (sc->f)+                    en += sc->f(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, sc->data);+                }++                f5[j] = MIN2(f5[j], en);+              }+            }+          }+        }++        /* check for possible stems branching off the exterior loop */+        if (sc && sc->f) {+          for (i = j - turn - 1; i > 1; i--) {+            if (f5[i - 1] != INF) {+              ij = indx[j] + i;++              if (with_gquad)+                f5[j] = MIN2(f5[j], f5[i - 1] + ggg[ij]);++              if (c[ij] != INF) {+                if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                  type = ptype[ij];++                  if (type == 0)+                    type = 7;++                  en    = f5[i - 1] + c[ij] + E_ExtLoop(type, -1, -1, P);+                  en    += sc->f(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+                  f5[j] = MIN2(f5[j], en);+                }+              }+            }+          }+        } else {+          for (i = j - turn - 1; i > 1; i--) {+            if (f5[i - 1] != INF) {+              ij = indx[j] + i;++              if (with_gquad)+                f5[j] = MIN2(f5[j], f5[i - 1] + ggg[ij]);++              if (c[ij] != INF) {+                if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                  type = ptype[ij];++                  if (type == 0)+                    type = 7;++                  en    = f5[i - 1] + c[ij] + E_ExtLoop(type, -1, -1, P);+                  f5[j] = MIN2(f5[j], en);+                }+              }+            }+          }+        }+        ij = indx[j] + 1;++        if (with_gquad)+          f5[j] = MIN2(f5[j], ggg[ij]);++        if (c[ij] != INF) {+          if (evaluate(1, j, 1, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+            type = ptype[ij];++            if (type == 0)+              type = 7;++            en = c[ij] + E_ExtLoop(type, -1, -1, P);+            if (sc)+              if (sc->f)+                en += sc->f(1, j, 1, j, VRNA_DECOMP_EXT_STEM, sc->data);+            f5[j] = MIN2(f5[j], en);+          }+        }+      }+      break;++    /* always use dangles on both sides */+    case 2:+      for (j = turn + 2; j < length; j++) {+        f5[j] = INF;++        if (f5[j - 1] != INF) {+          if (evaluate(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+            f5[j] = f5[j - 1];+            if (sc) {+              if (sc->energy_up)+                f5[j] += sc->energy_up[j][1];+              if (sc->f)+                f5[j] += sc->f(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, sc->data);+            }+          }+        }++        if (with_ud) {+          for (k = 0; k < domains_up->uniq_motif_count; k++) {+            u = domains_up->uniq_motif_size[k];+            if ((j - u >= 0) && (f5[j - u] != INF)) {+              if (evaluate(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+                en = f5[j - u]+                     + domains_up->energy_cb(vc,+                                             j - u + 1, j,+                                             VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                             domains_up->data);+                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[j - u + 1][u];+                  if (sc->f)+                    en += sc->f(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, sc->data);+                }++                f5[j] = MIN2(f5[j], en);+              }+            }+          }+        }++        if (sc && sc->f) {+          for (i = j - turn - 1; i > 1; i--) {+            if (f5[i - 1] != INF) {+              ij = indx[j] + i;++              if (with_gquad)+                f5[j] = MIN2(f5[j], f5[i - 1] + ggg[ij]);++              if (c[ij] != INF) {+                if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                  type = ptype[ij];++                  if (type == 0)+                    type = 7;++                  en    = f5[i - 1] + c[ij] + E_ExtLoop(type, S[i - 1], S[j + 1], P);+                  en    += sc->f(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+                  f5[j] = MIN2(f5[j], en);+                }+              }+            }+          }+        } else {+          for (i = j - turn - 1; i > 1; i--) {+            if (f5[i - 1] != INF) {+              ij = indx[j] + i;++              if (with_gquad)+                f5[j] = MIN2(f5[j], f5[i - 1] + ggg[ij]);++              if (c[ij] != INF) {+                if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                  type = ptype[ij];++                  if (type == 0)+                    type = 7;++                  en    = f5[i - 1] + c[ij] + E_ExtLoop(type, S[i - 1], S[j + 1], P);+                  f5[j] = MIN2(f5[j], en);+                }+              }+            }+          }+        }+        ij = indx[j] + 1;++        if (with_gquad)+          f5[j] = MIN2(f5[j], ggg[ij]);++        if (c[ij] != INF) {+          if (evaluate(1, j, 1, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+            type = ptype[ij];++            if (type == 0)+              type = 7;++            en = c[ij] + E_ExtLoop(type, -1, S[j + 1], P);+            if (sc)+              if (sc->f)+                en += sc->f(1, j, 1, j, VRNA_DECOMP_EXT_STEM, sc->data);+            f5[j] = MIN2(f5[j], en);+          }+        }+      }++      f5[length] = INF;+      if (f5[length - 1] != INF) {+        if (evaluate(1, length, 1, length - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+          f5[length] = f5[length - 1];+          if (sc) {+            if (sc->energy_up)+              f5[length] += sc->energy_up[length][1];+            if (sc->f)+              f5[length] += sc->f(1, length, 1, length - 1, VRNA_DECOMP_EXT_EXT, sc->data);+          }+        }+      }++      if (with_ud) {+        for (k = 0; k < domains_up->uniq_motif_count; k++) {+          u = domains_up->uniq_motif_size[k];+          if ((length - u >= 0) && (f5[length - u] != INF)) {+            if (evaluate(1, length, 1, length - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+              en = f5[length - u]+                   + domains_up->energy_cb(vc,+                                           length - u + 1, length,+                                           VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                           domains_up->data);+              if (sc) {+                if (sc->energy_up)+                  en += sc->energy_up[length - u + 1][u];+                if (sc->f)+                  en += sc->f(1, length, 1, length - u, VRNA_DECOMP_EXT_EXT, sc->data);+              }++              f5[length] = MIN2(f5[length], en);+            }+          }+        }+      }++      if (sc && sc->f) {+        for (i = length - turn - 1; i > 1; i--) {+          if (f5[i - 1] != INF) {+            ij = indx[length] + i;++            if (with_gquad)+              f5[length] = MIN2(f5[length], f5[i - 1] + ggg[ij]);++            if (c[ij] != INF) {+              if (evaluate(1, length, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                type = ptype[ij];++                if (type == 0)+                  type = 7;++                en          = f5[i - 1] + c[ij] + E_ExtLoop(type, S[i - 1], -1, P);+                en          += sc->f(1, length, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+                f5[length]  = MIN2(f5[length], en);+              }+            }+          }+        }+      } else {+        for (i = length - turn - 1; i > 1; i--) {+          if (f5[i - 1] != INF) {+            ij = indx[length] + i;++            if (with_gquad)+              f5[length] = MIN2(f5[length], f5[i - 1] + ggg[ij]);++            if (c[ij] != INF) {+              if (evaluate(1, length, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                type = ptype[ij];++                if (type == 0)+                  type = 7;++                en          = f5[i - 1] + c[ij] + E_ExtLoop(type, S[i - 1], -1, P);+                f5[length]  = MIN2(f5[length], en);+              }+            }+          }+        }+      }+      ij = indx[length] + 1;++      if (with_gquad)+        f5[length] = MIN2(f5[length], ggg[ij]);++      if (c[ij] != INF) {+        if (evaluate(1, length, 1, length, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+          type = ptype[ij];++          if (type == 0)+            type = 7;++          en = c[ij] + E_ExtLoop(type, -1, -1, P);+          if (sc)+            if (sc->f)+              en += sc->f(1, length, 1, length, VRNA_DECOMP_EXT_STEM, sc->data);+          f5[length] = MIN2(f5[length], en);+        }+      }+      break;++    /* normal dangles, aka dangle_model = 1 || 3 */+    default:+      for (j = turn + 2; j <= length; j++) {+        f5[j] = INF;+        if (f5[j - 1] != INF) {+          if (evaluate(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+            f5[j] = f5[j - 1];+            if (sc) {+              if (sc->energy_up)+                f5[j] += sc->energy_up[j][1];+              if (sc->f)+                f5[j] += sc->f(1, j, 1, j - 1, VRNA_DECOMP_EXT_EXT, sc->data);+            }+          }+        }++        if (with_ud) {+          for (k = 0; k < domains_up->uniq_motif_count; k++) {+            u = domains_up->uniq_motif_size[k];+            if ((j - u >= 0) && (f5[j - u] != INF)) {+              if (evaluate(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+                en = f5[j - u]+                     + domains_up->energy_cb(vc,+                                             j - u + 1, j,+                                             VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                             domains_up->data);+                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[j - u + 1][u];+                  if (sc->f)+                    en += sc->f(1, j, 1, j - u, VRNA_DECOMP_EXT_EXT, sc->data);+                }++                f5[j] = MIN2(f5[j], en);+              }+            }+          }+        }++        for (i = j - turn - 1; i > 1; i--) {+          ij = indx[j] + i;+          if (f5[i - 1] != INF) {+            if (with_gquad)+              f5[j] = MIN2(f5[j], f5[i - 1] + ggg[ij]);++            if (c[ij] != INF) {+              if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+                type = ptype[ij];++                if (type == 0)+                  type = 7;++                en = f5[i - 1] + c[ij] + E_ExtLoop(type, -1, -1, P);+                if (sc)+                  if (sc->f)+                    en += sc->f(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+                f5[j] = MIN2(f5[j], en);+              }+            }+          }++          if ((f5[i - 2] != INF) && c[ij] != INF) {+            if (evaluate(1, j, i - 2, i, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+              type = ptype[ij];++              if (type == 0)+                type = 7;++              en = f5[i - 2] + c[ij] + E_ExtLoop(type, S[i - 1], -1, P);++              if (sc) {+                if (sc->energy_up)+                  en += sc->energy_up[i - 1][1];+                if (sc->f)+                  en += sc->f(1, j, i - 2, i, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+              }+              f5[j] = MIN2(f5[j], en);+            }+          }++          ij = indx[j - 1] + i;+          if (c[ij] != INF) {+            if (f5[i - 1] != INF) {+              if (evaluate(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM1, &hc_dat_local)) {+                type = ptype[ij];++                if (type == 0)+                  type = 7;++                en = f5[i - 1] + c[ij] + E_ExtLoop(type, -1, S[j], P);++                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[j][1];+                  if (sc->f)+                    en += sc->f(1, j, i - 1, i, VRNA_DECOMP_EXT_EXT_STEM1, sc->data);+                }+                f5[j] = MIN2(f5[j], en);+              }+            }++            if (f5[i - 2] != INF) {+              if (evaluate(1, j, i - 2, i, VRNA_DECOMP_EXT_EXT_STEM1, &hc_dat_local)) {+                type = ptype[ij];++                if (type == 0)+                  type = 7;++                en = f5[i - 2] + c[ij] + E_ExtLoop(type, S[i - 1], S[j], P);++                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[i - 1][1] + sc->energy_up[j][1];+                  if (sc->f)+                    en += sc->f(1, j, i - 2, i, VRNA_DECOMP_EXT_EXT_STEM1, sc->data);+                }+                f5[j] = MIN2(f5[j], en);+              }+            }+          }+        }++        ij = indx[j] + 1;++        if (with_gquad)+          f5[j] = MIN2(f5[j], ggg[ij]);++        if (c[ij] != INF) {+          if (evaluate(1, j, 1, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+            type = ptype[ij];++            if (type == 0)+              type = 7;++            en = c[ij] + E_ExtLoop(type, -1, -1, P);+            if (sc)+              if (sc->f)+                en += sc->f(1, j, 1, j, VRNA_DECOMP_EXT_STEM, sc->data);+            f5[j] = MIN2(f5[j], en);+          }+        }+        ij = indx[j - 1] + 1;+        if (c[ij] != INF) {+          if (evaluate(1, j, 1, j - 1, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+            type = ptype[ij];++            if (type == 0)+              type = 7;++            en = c[ij] + E_ExtLoop(type, -1, S[j], P);++            if (sc) {+              if (sc->energy_up)+                en += sc->energy_up[j][1];+              if (sc->f)+                en += sc->f(1, j, 1, j - 1, VRNA_DECOMP_EXT_STEM, sc->data);+            }+            f5[j] = MIN2(f5[j], en);+          }+        }+      }         /* end for j... */+      break;+  }+}+++PUBLIC int+E_Stem(int          type,+       int          si1,+       int          sj1,+       int          extLoop,+       vrna_param_t *P)+{+  int energy  = 0;+  int d5      = (si1 >= 0) ? P->dangle5[type][si1] : 0;+  int d3      = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;++  if (type > 2)+    energy += P->TerminalAU;++  if (si1 >= 0 && sj1 >= 0)+    energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];+  else+    energy += d5 + d3;++  if (!extLoop)+    energy += P->MLintern[type];++  return energy;+}+++PUBLIC int+E_ExtLoop(int           type,+          int           si1,+          int           sj1,+          vrna_param_t  *P)+{+  int energy = 0;++  if (si1 >= 0 && sj1 >= 0)+    energy += P->mismatchExt[type][si1][sj1];+  else if (si1 >= 0)+    energy += P->dangle5[type][si1];+  else if (sj1 >= 0)+    energy += P->dangle3[type][sj1];++  if (type > 2)+    energy += P->TerminalAU;++  return energy;+}+++PUBLIC FLT_OR_DBL+exp_E_Stem(int              type,+           int              si1,+           int              sj1,+           int              extLoop,+           vrna_exp_param_t *P)+{+  double  energy  = 1.0;+  double  d5      = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;+  double  d3      = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;++  if (si1 >= 0 && sj1 >= 0)+    energy = (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];+  else+    energy = d5 * d3;++  if (type > 2)+    energy *= P->expTermAU;++  if (!extLoop)+    energy *= P->expMLintern[type];++  return (FLT_OR_DBL)energy;+}+++PUBLIC FLT_OR_DBL+exp_E_ExtLoop(int               type,+              int               si1,+              int               sj1,+              vrna_exp_param_t  *P)+{+  double energy = 1.0;++  if (si1 >= 0 && sj1 >= 0)+    energy = P->expmismatchExt[type][si1][sj1];+  else if (si1 >= 0)+    energy = P->expdangle5[type][si1];+  else if (sj1 >= 0)+    energy = P->expdangle3[type][sj1];++  if (type > 2)+    energy *= P->expTermAU;++  return (FLT_OR_DBL)energy;+}+++PUBLIC int+vrna_BT_ext_loop_f5(vrna_fold_compound_t  *vc,+                    int                   *k,+                    int                   *i,+                    int                   *j,+                    vrna_bp_stack_t       *bp_stack,+                    int                   *stack_count)+{+  unsigned char             type;+  char                      *ptype;+  short                     mm5, mm3, *S1;+  unsigned int              *sn;+  int                       length, fij, fi, jj, u, en, e, *my_f5, *my_c, *my_ggg, *idx,+                            dangle_model, turn, with_gquad, cnt, ii, with_ud;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  length        = vc->length;+  P             = vc->params;+  md            = &(P->model_details);+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  my_f5         = vc->matrices->f5;+  my_c          = vc->matrices->c;+  my_ggg        = vc->matrices->ggg;+  domains_up    = vc->domains_up;+  idx           = vc->jindx;+  ptype         = vc->ptype;+  S1            = vc->sequence_encoding;+  dangle_model  = md->dangles;+  turn          = md->min_loop_size;+  with_gquad    = md->gquad;+  with_ud       = (domains_up && domains_up->energy_cb) ? 1 : 0;++  hc_dat_local.idx    = idx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ext;+  hc_dat_local.cp     = vc->cutpoint;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  jj = *k;++  /* nibble off unpaired 3' stretches harboring bound ligands (interspersed with unpaired nucleotides) */+  if (with_ud) {+    do {+      fij = my_f5[jj];+      fi  = INF;++      /* try nibble off one unpaired nucleotide first */+      if (evaluate(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+        fi = my_f5[jj - 1];++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[jj][1];+          if (sc->f)+            fi += sc->f(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_EXT, sc->data);+        }++        if (jj == 1) {+          /* no more pairs */+          *i  = *j = -1;+          *k  = 0;+          return 1;+        }++        if (fij == fi) {+          jj--;+          continue;+        }+      }++      /* next, try nibble off a ligand */+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u   = domains_up->uniq_motif_size[cnt];+        ii  = jj - u + 1;+        if ((ii > 0) && evaluate(1, jj, 1, jj - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+          en = domains_up->energy_cb(vc,+                                     ii, jj,+                                     VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                     domains_up->data);+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[ii][u];+            if (sc->f)+              en += sc->f(1, jj, 1, jj - u, VRNA_DECOMP_EXT_EXT, sc->data);+          }+          fi  = my_f5[ii - 1];+          fi  += en;++          if (fij == fi) {+            /* skip remaining motifs after first hit */+            jj = ii - 1;+            break;+          }+        }+      }++      if (jj == 0) {+        /* no more pairs */+        *i  = *j = -1;+        *k  = 0;+        return 1;+      }+    } while (fij == fi);+  } else {+    /* nibble off unpaired 3' bases */+    do {+      fij = my_f5[jj];+      fi  = INF;++      if (evaluate(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+        fi = my_f5[jj - 1];++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[jj][1];+          if (sc->f)+            fi += sc->f(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_EXT, sc->data);+        }+      }++      if (--jj == 0)+        break;+    } while (fij == fi);+    jj++;+  }++  if (jj < turn + 2) {+    /* no more pairs */+    *i  = *j = -1;+    *k  = 0;+    return 1;+  }++  /* must have found a decomposition */+  switch (dangle_model) {+    case 0:   /* j is paired. Find pairing partner */+      for (u = jj - turn - 1; u >= 1; u--) {+        if (with_gquad) {+          if (fij == my_f5[u - 1] + my_ggg[idx[jj] + u]) {+            *i  = *j = -1;+            *k  = u - 1;+            vrna_BT_gquad_mfe(vc, u, jj, bp_stack, stack_count);+            return 1;+          }+        }++        if (evaluate(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+          type = (unsigned char)ptype[idx[jj] + u];++          if (type == 0)+            type = 7;++          en = my_c[idx[jj] + u];+          if (sc)+            if (sc->f)+              en += sc->f(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+          if (sn[jj] != sn[u])+            en += P->DuplexInit;+          if (fij == E_ExtLoop(type, -1, -1, P) + en + my_f5[u - 1]) {+            *i                            = u;+            *j                            = jj;+            *k                            = u - 1;+            bp_stack[++(*stack_count)].i  = u;+            bp_stack[(*stack_count)].j    = jj;+            return 1;+          }+        }+      }+      break;++    case 2:+      mm3 = ((jj < length) && (sn[jj + 1] == sn[jj])) ? S1[jj + 1] : -1;+      for (u = jj - turn - 1; u >= 1; u--) {+        if (with_gquad) {+          if (fij == my_f5[u - 1] + my_ggg[idx[jj] + u]) {+            *i  = *j = -1;+            *k  = u - 1;+            vrna_BT_gquad_mfe(vc, u, jj, bp_stack, stack_count);+            return 1;+          }+        }++        if (evaluate(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+          mm5   = ((u > 1) && (sn[u] == sn[u - 1])) ? S1[u - 1] : -1;+          type  = (unsigned char)ptype[idx[jj] + u];++          if (type == 0)+            type = 7;++          en = my_c[idx[jj] + u];+          if (sc)+            if (sc->f)+              en += sc->f(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+          if (sn[jj] != sn[u])+            en += P->DuplexInit;+          if (fij == E_ExtLoop(type, mm5, mm3, P) + en + my_f5[u - 1]) {+            *i                            = u;+            *j                            = jj;+            *k                            = u - 1;+            bp_stack[++(*stack_count)].i  = u;+            bp_stack[(*stack_count)].j    = jj;+            return 1;+          }+        }+      }+      break;++    default:+      if (with_gquad) {+        if (fij == my_ggg[idx[jj] + 1]) {+          *i  = *j = -1;+          *k  = 0;+          vrna_BT_gquad_mfe(vc, 1, jj, bp_stack, stack_count);+          return 1;+        }+      }++      if (evaluate(1, jj, 1, jj, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+        type = (unsigned char)ptype[idx[jj] + 1];++        if (type == 0)+          type = 7;++        en = my_c[idx[jj] + 1];+        if (sc)+          if (sc->f)+            en += sc->f(1, jj, 1, jj, VRNA_DECOMP_EXT_STEM, sc->data);+        if (sn[jj] != sn[1])+          en += P->DuplexInit;+        if (fij == en + E_ExtLoop(type, -1, -1, P)) {+          *i                            = 1;+          *j                            = jj;+          *k                            = 0;+          bp_stack[++(*stack_count)].i  = 1;+          bp_stack[(*stack_count)].j    = jj;+          return 1;+        }+      }++      if (evaluate(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+        if (sn[jj] == sn[jj - 1]) {+          mm3   = S1[jj];+          type  = (unsigned char)ptype[idx[jj - 1] + 1];++          if (type == 0)+            type = 7;++          en = my_c[idx[jj - 1] + 1];+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[jj][1];+            if (sc->f)+              en += sc->f(1, jj, 1, jj - 1, VRNA_DECOMP_EXT_STEM, sc->data);+          }+          if (sn[jj - 1] != sn[1])+            en += P->DuplexInit;++          if (fij == en + E_ExtLoop(type, -1, mm3, P)) {+            *i                            = 1;+            *j                            = jj - 1;+            *k                            = 0;+            bp_stack[++(*stack_count)].i  = 1;+            bp_stack[(*stack_count)].j    = jj - 1;+            return 1;+          }+        }+      }++      for (u = jj - turn - 1; u > 1; u--) {+        if (with_gquad) {+          if (fij == my_f5[u - 1] + my_ggg[idx[jj] + u]) {+            *i  = *j = -1;+            *k  = u - 1;+            vrna_BT_gquad_mfe(vc, u, jj, bp_stack, stack_count);+            return 1;+          }+        }++        type = (unsigned char)ptype[idx[jj] + u];+        if (type == 0)+          type = 7;++        en = my_c[idx[jj] + u];+        if (sn[jj] != sn[u])+          en += P->DuplexInit;++        if (evaluate(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+          e = my_f5[u - 1] + en + E_ExtLoop(type, -1, -1, P);+          if (sc)+            if (sc->f)+              e += sc->f(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+          if (fij == e) {+            *i                            = u;+            *j                            = jj;+            *k                            = u - 1;+            bp_stack[++(*stack_count)].i  = u;+            bp_stack[(*stack_count)].j    = jj;+            return 1;+          }+        }++        if (evaluate(1, jj, u - 2, u, VRNA_DECOMP_EXT_EXT_STEM, &hc_dat_local)) {+          if (sn[u] == sn[u - 1]) {+            mm5 = S1[u - 1];+            e   = my_f5[u - 2] + en + E_ExtLoop(type, mm5, -1, P);+            if (sc) {+              if (sc->energy_up)+                e += sc->energy_up[u - 1][1];+              if (sc->f)+                e += sc->f(1, jj, u - 2, u, VRNA_DECOMP_EXT_EXT_STEM, sc->data);+            }+            if (fij == e) {+              *i                            = u;+              *j                            = jj;+              *k                            = u - 2;+              bp_stack[++(*stack_count)].i  = u;+              bp_stack[(*stack_count)].j    = jj;+              return 1;+            }+          }+        }++        type = (unsigned char)ptype[idx[jj - 1] + u];+        if (type == 0)+          type = 7;++        en = my_c[idx[jj - 1] + u];+        if (sn[jj - 1] != sn[u])+          en += P->DuplexInit;++        mm5 = (sn[u] == sn[u - 1]) ? S1[u - 1] : -1;+        mm3 = (sn[jj] == sn[jj - 1]) ? S1[jj] : -1;++        if (evaluate(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM1, &hc_dat_local)) {+          e = my_f5[u - 1] + en + E_ExtLoop(type, -1, mm3, P);++          if (sc) {+            if (sc->energy_up)+              e += sc->energy_up[jj][1];+            if (sc->f)+              e += sc->f(1, jj, u - 1, u, VRNA_DECOMP_EXT_EXT_STEM1, sc->data);+          }++          if (fij == e) {+            *i                            = u;+            *j                            = jj - 1;+            *k                            = u - 1;+            bp_stack[++(*stack_count)].i  = u;+            bp_stack[(*stack_count)].j    = jj - 1;+            return 1;+          }+        }++        if (evaluate(1, jj, u - 2, u, VRNA_DECOMP_EXT_EXT_STEM1, &hc_dat_local)) {+          e = my_f5[u - 2] + en + E_ExtLoop(type, mm5, mm3, P);+          if (sc) {+            if (sc->energy_up)+              e += sc->energy_up[jj][1]+                   + sc->energy_up[u - 1][1];+            if (sc->f)+              e += sc->f(1, jj, u - 2, u, VRNA_DECOMP_EXT_EXT_STEM1, sc->data);+          }+          if (fij == e) {+            *i                            = u;+            *j                            = jj - 1;+            *k                            = u - 2;+            bp_stack[++(*stack_count)].i  = u;+            bp_stack[(*stack_count)].j    = jj - 1;+            return 1;+          }+        }+      }+      break;+  }++  return 0;+}+++PUBLIC vrna_mx_pf_aux_el_t *+vrna_exp_E_ext_fast_init(vrna_fold_compound_t *vc)+{+  vrna_mx_pf_aux_el_t *aux_mx = NULL;++  if (vc) {+    char                      *hc;+    unsigned int              u, s;+    int                       i, j, d, n, turn, ij, *idx, *iidx, *hc_up;+    FLT_OR_DBL                *q, *scale;+    vrna_callback_hc_evaluate *evaluate;+    struct default_data       hc_dat_local;++    n     = (int)vc->length;+    idx   = vc->jindx;+    iidx  = vc->iindx;+    turn  = vc->exp_params->model_details.min_loop_size;+    q     = vc->exp_matrices->q;+    scale = vc->exp_matrices->scale;+    hc    = vc->hc->matrix;+    hc_up = vc->hc->up_ext;++    hc_dat_local.idx    = idx;+    hc_dat_local.mx     = hc;+    hc_dat_local.hc_up  = hc_up;+    hc_dat_local.cp     = vc->cutpoint;++    if (vc->hc->f) {+      evaluate            = &hc_default_user;+      hc_dat_local.hc_f   = vc->hc->f;+      hc_dat_local.hc_dat = vc->hc->data;+    } else {+      evaluate = &hc_default;+    }+++    /* allocate memory for helper arrays */+    aux_mx            = (vrna_mx_pf_aux_el_t *)vrna_alloc(sizeof(vrna_mx_pf_aux_el_t));+    aux_mx->qq        = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+    aux_mx->qq1       = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+    aux_mx->qqu_size  = 0;+    aux_mx->qqu       = NULL;++    if (vc->type == VRNA_FC_TYPE_SINGLE) {+      vrna_sc_t *sc         = vc->sc;+      vrna_ud_t *domains_up = vc->domains_up;+      int       with_ud     = (domains_up && domains_up->exp_energy_cb);++      /* pre-processing ligand binding production rule(s) and auxiliary memory */+      if (with_ud) {+        int ud_max_size = 0;+        for (u = 0; u < domains_up->uniq_motif_count; u++)+          if (ud_max_size < domains_up->uniq_motif_size[u])+            ud_max_size = domains_up->uniq_motif_size[u];++        aux_mx->qqu_size  = ud_max_size;+        aux_mx->qqu       = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (ud_max_size + 1));++        for (u = 0; u <= ud_max_size; u++)+          aux_mx->qqu[u] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+      }++      for (d = 0; d <= turn; d++)+        for (i = 1; i <= n - d; i++) {+          j   = i + d;+          ij  = iidx[i] - j;++          if (j > n)+            continue;++          if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_UP, &hc_dat_local)) {+            q[ij] = 1.0 * scale[d + 1];++            if (sc) {+              if (sc->exp_energy_up)+                q[ij] *= sc->exp_energy_up[i][d + 1];+              if (sc->exp_f)+                q[ij] *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_UP, sc->data);+            }++            if (with_ud) {+              q[ij] += q[ij] * domains_up->exp_energy_cb(vc,+                                                         i, j,+                                                         VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP,+                                                         domains_up->data);+            }+          } else {+            q[ij] = 0.;+          }+        }+    } else if (vc->type == VRNA_FC_TYPE_COMPARATIVE) {+      vrna_sc_t       **scs = vc->scs;+      unsigned short  **a2s = vc->a2s;+      for (d = 0; d <= turn; d++)+        for (i = 1; i <= n - d; i++) {+          j   = i + d;+          ij  = iidx[i] - j;+          if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_UP, &hc_dat_local)) {+            q[ij] = 1.0 * scale[d + 1];++            if (scs) {+              for (s = 0; s < vc->n_seq; s++)+                if (scs[s]) {+                  u = d + 1 /* a2s[s][j] - a2s[s][i] + 1 */;+                  if (scs[s]->exp_energy_up)+                    q[ij] *= scs[s]->exp_energy_up[a2s[s][i]][u];+                }+            }+          } else {+            q[ij] = 0.;+          }+        }+    }+  }++  return aux_mx;+}+++PUBLIC void+vrna_exp_E_ext_fast_rotate(vrna_fold_compound_t *vc,+                           vrna_mx_pf_aux_el_t  *aux_mx)+{+  if (vc && aux_mx) {+    int         u;+    FLT_OR_DBL  *tmp;++    tmp         = aux_mx->qq1;+    aux_mx->qq1 = aux_mx->qq;+    aux_mx->qq  = tmp;++    /* rotate auxiliary arrays for unstructured domains */+    if (aux_mx->qqu) {+      tmp = aux_mx->qqu[aux_mx->qqu_size];+      for (u = aux_mx->qqu_size; u > 0; u--)+        aux_mx->qqu[u] = aux_mx->qqu[u - 1];+      aux_mx->qqu[0] = tmp;+    }+  }+}+++PUBLIC void+vrna_exp_E_ext_fast_free(vrna_fold_compound_t *vc,+                         vrna_mx_pf_aux_el_t  *aux_mx)+{+  if (vc && aux_mx) {+    int u;++    free(aux_mx->qq);+    free(aux_mx->qq1);++    if (aux_mx->qqu) {+      for (u = 0; u <= aux_mx->qqu_size; u++)+        free(aux_mx->qqu[u]);++      free(aux_mx->qqu);+    }+    free(aux_mx);+  }+}+++PUBLIC FLT_OR_DBL+vrna_exp_E_ext_fast(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    vrna_mx_pf_aux_el_t   *aux_mx)+{+  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        return exp_E_ext_fast(vc, i, j, aux_mx);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        return exp_E_ext_fast_comparative(vc, i, j, aux_mx);+        break;++      default:+        vrna_message_warning("vrna_exp_E_ext_fast@exterior_loops.c: Unknown fold_compound type");+        return 0.;+        break;+    }+  } else {+    return 0.;+  }+}+++PRIVATE FLT_OR_DBL+exp_E_ext_fast(vrna_fold_compound_t *vc,+               int                  i,+               int                  j,+               vrna_mx_pf_aux_el_t  *aux_mx)+{+  short                     *S1;+  unsigned char             type;+  int                       n, *iidx, k, ij, kl, with_ud, u, circular, with_gquad;+  FLT_OR_DBL                qbt1, *q, *qb, *qq, *qq1, **qqu, q_temp, *scale, q_temp2, *G;+  vrna_md_t                 *md;+  vrna_exp_param_t          *pf_params;+  vrna_ud_t                 *domains_up;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  n                   = (int)vc->length;+  iidx                = vc->iindx;+  ij                  = iidx[i] - j;+  qq                  = aux_mx->qq;+  qq1                 = aux_mx->qq1;+  qqu                 = aux_mx->qqu;+  q                   = vc->exp_matrices->q;+  qb                  = vc->exp_matrices->qb;+  G                   = vc->exp_matrices->G;+  scale               = vc->exp_matrices->scale;+  pf_params           = vc->exp_params;+  md                  = &(pf_params->model_details);+  hc                  = vc->hc;+  sc                  = vc->sc;+  domains_up          = vc->domains_up;+  circular            = md->circ;+  with_gquad          = md->gquad;+  with_ud             = (domains_up && domains_up->exp_energy_cb);+  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ext;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  qbt1 = 0.;++  /* all exterior loop parts [i, j] with exactly one stem (i, u) i < u < j */+  if (evaluate(i, j, i, j - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+    q_temp = qq1[i] * scale[1];++    if (sc) {+      if (sc->exp_energy_up)+        q_temp *= sc->exp_energy_up[j][1];++      if (sc->exp_f)+        q_temp *= sc->exp_f(i, j, i, j - 1, VRNA_DECOMP_EXT_EXT, sc->data);+    }++    if (with_ud) {+      int cnt;+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u = domains_up->uniq_motif_size[cnt];+        if (j - u >= i) {+          if (evaluate(i, j, i, j - u, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+            q_temp2 = qqu[u][i]+                      * domains_up->exp_energy_cb(vc,+                                                  j - u + 1, j,+                                                  VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                  domains_up->data)+                      * scale[u];++            if (sc) {+              if (sc->exp_energy_up)+                q_temp2 *= sc->exp_energy_up[j - u + 1][u];+              if (sc->exp_f)+                q_temp2 *= sc->exp_f(i, j, i, j - u, VRNA_DECOMP_EXT_EXT, sc->data);+            }++            q_temp += q_temp2;+          }+        }+      }+    }++    qbt1 += q_temp;+  }++  /* exterior loop part with stem (i, j) */+  if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+    S1    = vc->sequence_encoding;+    type  = md->pair[S1[i]][S1[j]];+    if (type == 0)+      type = 7;++    q_temp = qb[ij]+             * exp_E_ExtLoop(type, ((i > 1) || circular) ? S1[i - 1] : -1, ((j < n) || circular) ? S1[j + 1] : -1, pf_params);++    if (sc)+      if (sc->exp_f)+        q_temp *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_STEM, sc->data);+    qbt1 += q_temp;+  }++  if (with_gquad)+    qbt1 += G[ij];++  qq[i] = qbt1;++  if (with_ud)+    qqu[0][i] = qbt1;++  /* the entire stretch [i,j] is unpaired */+  if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_UP, &hc_dat_local)) {+    u       = j - i + 1;+    q_temp  = 1.0 * scale[u];++    if (sc) {+      if (sc->exp_energy_up)+        q_temp *= sc->exp_energy_up[i][u];++      if (sc->exp_f)+        q_temp *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_UP, sc->data);+    }++    qbt1 += q_temp;++    if (with_ud) {+      qbt1 += q_temp * domains_up->exp_energy_cb(vc,+                                                 i, j,+                                                 VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP,+                                                 domains_up->data);+    }+  }++  kl = iidx[i] - j + 1;+  if (sc && sc->exp_f) {+    for (k = j; k > i; k--, kl++) {+      q_temp  = q[kl] * qq[k];+      q_temp  *= sc->exp_f(i, j, k - 1, k, VRNA_DECOMP_EXT_EXT_EXT, sc->data);+      qbt1    += q_temp;+    }+  } else {+    for (k = j; k > i; k--, kl++)+      qbt1 += q[kl] * qq[k];+  }++  return qbt1;+}+++PRIVATE FLT_OR_DBL+exp_E_ext_fast_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j,+                           vrna_mx_pf_aux_el_t  *aux_mx)+{+  int                       n, s, n_seq, *iidx, k, ij, kl, u, circular, type;+  unsigned short            **a2s;+  short                     **S, **S5, **S3;+  FLT_OR_DBL                qbt1, *q, *qb, *qq, *qq1, q_temp, *scale;+  vrna_md_t                 *md;+  vrna_exp_param_t          *pf_params;+  vrna_hc_t                 *hc;+  vrna_sc_t                 **scs;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  n                   = (int)vc->length;+  n_seq               = vc->n_seq;+  iidx                = vc->iindx;+  ij                  = iidx[i] - j;+  S                   = vc->S;+  S5                  = vc->S5;     /* S5[s][i] holds next base 5' of i in sequence s */+  S3                  = vc->S3;     /* Sl[s][i] holds next base 3' of i in sequence s */+  a2s                 = vc->a2s;+  qq                  = aux_mx->qq;+  qq1                 = aux_mx->qq1;+  q                   = vc->exp_matrices->q;+  qb                  = vc->exp_matrices->qb;+  scale               = vc->exp_matrices->scale;+  pf_params           = vc->exp_params;+  md                  = &(pf_params->model_details);+  hc                  = vc->hc;+  scs                 = vc->scs;+  circular            = md->circ;+  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ext;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  qbt1 = 0.;++  /* all exterior loop parts [i, j] with exactly one stem (i, u) i < u < j */+  if (evaluate(i, j, i, j - 1, VRNA_DECOMP_EXT_EXT, &hc_dat_local)) {+    q_temp = qq1[i] * scale[1];++    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->exp_energy_up)+            q_temp *= scs[s]->exp_energy_up[a2s[s][j]][1];+      }+    }++    qbt1 += q_temp;+  }++  /* exterior loop part with stem (i, j) */+  if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_STEM, &hc_dat_local)) {+    q_temp = qb[ij];++    for (s = 0; s < n_seq; s++) {+      type = md->pair[S[s][i]][S[s][j]];+      if (type == 0)+        type = 7;++      q_temp *= exp_E_ExtLoop(type, ((i > 1) || circular) ? S5[s][i] : -1, ((j < n) || circular) ? S3[s][j] : -1, pf_params);+    }++    qbt1 += q_temp;+  }++  qq[i] = qbt1;++  /* the entire stretch [i,j] is unpaired */+  if (evaluate(i, j, i, j, VRNA_DECOMP_EXT_UP, &hc_dat_local)) {+    u       = j - i + 1;+    q_temp  = 1.0 * scale[u];++    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->exp_energy_up)+            q_temp *= scs[s]->exp_energy_up[a2s[s][i]][a2s[s][j] - a2s[s][i] + 1];+      }+    }++    qbt1 += q_temp;+  }++  kl = iidx[i] - j + 1;+  for (k = j; k > i; k--, kl++)+    qbt1 += q[kl] * qq[k];++  return qbt1;+}+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data)+{+  int                 kl, di, dj;+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval  = (char)0;+  di    = k - i;+  dj    = j - l;+  switch (d) {+    case VRNA_DECOMP_EXT_EXT_STEM:+      kl = dat->idx[j] + l;+      if (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+        eval = (char)1;+        if (i != l) {+          /* otherwise, stem spans from i to j */+          di = l - k + 1;+          if ((di != 0) && (dat->hc_up[k + 1] < di))+            eval = (char)0;+        }+      }+      break;++    case VRNA_DECOMP_EXT_EXT_STEM1:+      kl = dat->idx[j - 1] + l;+      if (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+        eval = (char)1;+        if (i != l) {+          /* otherwise, stem spans from i to j - 1 */+          di = l - k + 1;+          if (dat->hc_up[j] == 0)+            eval = (char)0;+          if ((di != 0) && (dat->hc_up[k + 1] < di))+            eval = (char)0;+        }+      }+      break;++    case VRNA_DECOMP_EXT_STEM:+      kl = dat->idx[l] + k;+      if (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+        eval = (char)1;+        if ((di != 0) && (dat->hc_up[i] < di))+          eval = (char)0;+        if ((dj != 0) && (dat->hc_up[l + 1] < dj))+          eval = (char)0;+      }+      break;++    case VRNA_DECOMP_EXT_EXT:+      eval = (char)1;+      if ((di != 0) && (dat->hc_up[i] < di))+        eval = (char)0;+      if ((dj != 0) && (dat->hc_up[l + 1] < dj))+        eval = (char)0;+      break;++    case VRNA_DECOMP_EXT_UP:+      di    = j - i + 1;+      eval  = (dat->hc_up[i] >= di) ? (char)1 : (char)0;+      break;++    default:+      nrerror("wtf");+  }+  return eval;+}+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data)+{+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval  = hc_default(i, j, k, l, d, data);+  eval  = (dat->hc_f(i, j, k, l, d, dat->hc_dat)) ? eval : (char)0;++  return eval;+}
+ C/ViennaRNA/exterior_loops.h view
@@ -0,0 +1,175 @@+#ifndef VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H+#define VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++/**+ *  @file     exterior_loops.h+ *  @ingroup  loops+ *  @brief    Energy evaluation of exterior loops for MFE and partition function calculations+ */++/**+ *  @{+ *  @ingroup   loops+ *+ */++/**+ *  @brief  Auxiliary helper arrays for fast exterior loop computations+ *+ *  @see vrna_exp_E_ext_fast_init(), vrna_exp_E_ext_fast_rotate(),+ *  vrna_exp_E_ext_fast_free(), vrna_exp_E_ext_fast()+ */+typedef struct {+  FLT_OR_DBL  *qq;+  FLT_OR_DBL  *qq1;++  int         qqu_size;+  FLT_OR_DBL  **qqu;+} vrna_mx_pf_aux_el_t;+++/**+ *  <H2>Compute the Energy contribution of an Exterior loop stem</H2>+ *  This definition is a wrapper for the E_Stem() function.+ *  It is substituted by an E_Stem() function call with argument+ *  extLoop=1, so the energy contribution returned reflects a+ *  stem introduced in an exterior-loop.<BR>+ *  As for the parameters si1 and sj1 of the substituted+ *  E_Stem() function, you can inhibit to take 5'-, 3'-dangles+ *  or mismatch contributions to be taken into account by passing+ *  -1 to these parameters.+ * + *  @see    E_Stem()+ *  @param  type  The pair type of the stem-closing pair+ *  @param  si1   The 5'-mismatching nucleotide+ *  @param  sj1   The 3'-mismatching nucleotide+ *  @param  P     The data structure containing scaled energy parameters+ *  @return       The energy contribution of the introduced exterior-loop stem+ */+int E_ExtLoop(int type,+              int si1,+              int sj1,+              vrna_param_t *P);++/**+ *  This is the partition function variant of @ref E_ExtLoop()+ *  @see E_ExtLoop()+ *  @return The Boltzmann weighted energy contribution of the introduced exterior-loop stem+ */+FLT_OR_DBL exp_E_ExtLoop( int type,+                      int si1,+                      int sj1,+                      vrna_exp_param_t *P);++/**+ *  <H2>Compute the energy contribution of a stem branching off a loop-region</H2>+ *  This function computes the energy contribution of a stem that branches off+ *  a loop region. This can be the case in multiloops, when a stem branching off+ *  increases the degree of the loop but also <I>immediately interior base pairs</I>+ *  of an exterior loop contribute free energy.+ *  To switch the behavior of the function according to the evaluation of a multiloop-+ *  or exterior-loop-stem, you pass the flag 'extLoop'.+ *  The returned energy contribution consists of a TerminalAU penalty if the pair type+ *  is greater than 2, dangling end contributions of mismatching nucleotides adjacent to+ *  the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies+ *  if both mismatching nucleotides are positive values.+ *  Thus, to avoid incorporating dangling end or mismatch energies just pass a negative number,+ *  e.g. -1 to the mismatch argument.+ * + *  This is an illustration of how the energy contribution is assembled:+ *  <PRE>+ *        3'  5'+ *        |   |+ *        X - Y+ *  5'-si1     sj1-3'+ *  </PRE>+ * + *  Here, (X,Y) is the base pair that closes the stem that branches off a loop region.+ *  The nucleotides si1 and sj1 are the 5'- and 3'- mismatches, respectively. If the base pair+ *  type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be+ *  included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers,+ *  mismatch energies will also be included. If one of si1 or sj1 is a negative value, only+ *  5' or 3' dangling end contributions are taken into account. To prohibit any of these mismatch+ *  contributions to be incorporated, just pass a negative number to both, si1 and sj1.+ *  In case the argument extLoop is 0, the returned energy contribution also includes+ *  the <I>internal-loop-penalty</I> of a multiloop stem with closing pair type.+ * + *  @see    E_MLstem()+ *  @see    E_ExtLoop()+ *  @note   This function is threadsafe+ * + *  @param  type    The pair type of the first base pair un the stem+ *  @param  si1     The 5'-mismatching nucleotide+ *  @param  sj1     The 3'-mismatching nucleotide+ *  @param  extLoop A flag that indicates whether the contribution reflects the one of an exterior loop or not+ *  @param  P       The data structure containing scaled energy parameters+ *  @return         The Free energy of the branch off the loop in dcal/mol+ * + */+int E_Stem( int type,+            int si1,+            int sj1,+            int extLoop,+            vrna_param_t *P);++/**+ *  <H2>Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region</H2>+ *  This is the partition function variant of @ref E_Stem()+ *  @see E_Stem()+ *  @note This function is threadsafe+ * + *  @return The Boltzmann weighted energy contribution of the branch off the loop+ */+FLT_OR_DBL exp_E_Stem(int type,+                  int si1,+                  int sj1,+                  int extLoop,+                  vrna_exp_param_t *P);+++int+E_ext_loop( int i,+            int j,+            vrna_fold_compound_t *vc);++void+E_ext_loop_5( vrna_fold_compound_t *vc);++int+vrna_BT_ext_loop_f5(vrna_fold_compound_t *vc,+                    int *k,+                    int *i,+                    int *j,+                    vrna_bp_stack_t *bp_stack,+                    int *stack_count);+++vrna_mx_pf_aux_el_t *+vrna_exp_E_ext_fast_init(vrna_fold_compound_t *vc);+++void+vrna_exp_E_ext_fast_rotate( vrna_fold_compound_t  *vc,+                            vrna_mx_pf_aux_el_t   *aux_mx);+++void+vrna_exp_E_ext_fast_free( vrna_fold_compound_t  *vc,+                          vrna_mx_pf_aux_el_t   *aux_mx);+++FLT_OR_DBL+vrna_exp_E_ext_fast(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    vrna_mx_pf_aux_el_t   *aux_mx);++/**+ * @}+ */+++#endif
+ C/ViennaRNA/file_formats.c view
@@ -0,0 +1,593 @@+/*+    file_formats.c++    Various functions dealing with file formats for RNA sequences, structures, and alignments++    (c) 2014 Ronny Lorenz++    Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <ctype.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/file_utils.h"+#include "ViennaRNA/constraints.h"+#if WITH_JSON_SUPPORT+# include <json/json.h>+#endif+#include "ViennaRNA/file_formats.h"++#define DEBUG+/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++PRIVATE char          *inbuf  = NULL;+PRIVATE char          *inbuf2 = NULL;+PRIVATE unsigned int  typebuf = 0;++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE unsigned int+read_multiple_input_lines(char **string, FILE *file, unsigned int option);++PRIVATE void+elim_trailing_ws(char *string);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PRIVATE void+elim_trailing_ws(char *string){    /* eliminate whitespaces at the end of a character string */++  int i, l = strlen(string);++  for(i = l-1; i >= 0; i--){+    if      (string[i] == ' ')  continue;+    else if (string[i] == '\t') continue;+    else                        break;+  }+  string[(i >= 0) ? (i+1) : 0] = '\0';+}++PUBLIC void+vrna_file_helixlist(const char *seq,+                    const char *db,+                    float energy,+                    FILE *file){++  int         s;+  short       *pt;+  vrna_hx_t   *list;+  FILE *out;++  if(strlen(seq) != strlen(db))+    vrna_message_error("vrna_file_helixlist: sequence and structure have unequal length!");++  out   = (file) ? file : stdout;+  pt    = vrna_ptable(db);+  list  = vrna_hx_from_ptable(pt);++  fprintf(out, "%s\t%6.2f\n", seq, energy);+  for(s = 0; list[s].length > 0; s++){+    fprintf(out, "%d\t%d\t%d\n", list[s].start, list[s].end, list[s].length);+  }++  free(pt);+  free(list);+}++PUBLIC void+vrna_file_connect(const char *seq,+                  const char *db,+                  float energy,+                  const char *identifier,+                  FILE *file){++  int i, power_d;+  FILE *out = (file) ? file : stdout;++  if(strlen(seq) != strlen(db))+    vrna_message_error("vrna_file_connect: sequence and structure have unequal length!");++  short *pt = vrna_ptable(db);++  for(power_d=0;pow(10,power_d) <= (int)strlen(seq);power_d++);++  /*+    Connect table file format looks like this:++    300  ENERGY = 7.0  example+      1 G       0    2   22    1+      2 G       1    3   21    2++    where the headerline is followed by 6 columns with:+    1. Base number: index n+    2. Base (A, C, G, T, U, X)+    3. Index n-1  (0 if first nucleotide)+    4. Index n+1  (0 if last nucleotide)+    5. Number of the base to which n is paired. No pairing is indicated by 0 (zero).+    6. Natural numbering.+  */++  /* print header */+  fprintf(out, "%d  ENERGY = %6.2f", (int)strlen(seq), energy);+  if(identifier)+    fprintf(out, "  %s\n", identifier);++  /* print structure information except for last line */+  /* TODO: modify the structure information for cofold */+  for(i = 0; i < strlen(seq) - 1; i++){+    fprintf(out, "%*d %c %*d %*d %*d %*d\n",+                  power_d, i+1,           /* nucleotide index */+                  (char)toupper(seq[i]),  /* nucleotide char */+                  power_d, i,             /* nucleotide predecessor index */+                  power_d, i+2,           /* nucleotide successor index */+                  power_d, pt[i+1],       /* pairing partner index */+                  power_d, i+1);          /* nucleotide natural numbering */+  }+  /* print last line */+  fprintf(out, "%*d %c %*d %*d %*d %*d\n",+                power_d, i+1,+                (char)toupper(seq[i]),+                power_d, i,+                power_d, 0,+                power_d, pt[i+1],+                power_d, i+1);++  /* clean up */+  free(pt);+  fflush(out);+}++PUBLIC void+vrna_file_bpseq(const char *seq,+                const char *db,+                FILE *file){++  int i;+  FILE *out = (file) ? file : stdout;++  if(strlen(seq) != strlen(db))+    vrna_message_error("vrna_file_bpseq: sequence and structure have unequal length!");++  short *pt = vrna_ptable(db);++  for(i = 1; i <= pt[0]; i++){+    fprintf(out, "%d %c %d\n", i, (char)toupper(seq[i-1]), pt[i]);+  }++  /* clean up */+  free(pt);+  fflush(out);+}++#if WITH_JSON_SUPPORT++PUBLIC void+vrna_file_json( const char *seq,+                const char *db,+                double energy,+                const char *identifier,+                FILE *file){++  FILE *out = (file) ? file : stdout;++  JsonNode *data  = json_mkobject();+  JsonNode *value;++  if(identifier){+    value = json_mkstring(identifier);+    json_append_member(data, "id", value);+  }++  value = json_mkstring(seq);+  json_append_member(data, "sequence", value);++  value = json_mknumber(energy);+  json_append_member(data, "mfe", value);++  value = json_mkstring(db);+  json_append_member(data, "structure", value);++  +  fprintf(out, "%s\n", json_stringify(data, "\t"));++  fflush(out);+}++#endif++PRIVATE  unsigned int+read_multiple_input_lines(char **string,+                          FILE *file,+                          unsigned int option){++  char  *line;+  int   i, l;+  int   state = 0;+  int   str_length = 0;+  FILE  *in = (file) ? file : stdin;++  line = (inbuf2) ? inbuf2 : vrna_read_line(in);+  inbuf2 = NULL;+  do{++    /*+    * read lines until informative data appears or+    * report an error if anything goes wrong+    */+    if(!line) return VRNA_INPUT_ERROR;++    l = (int)strlen(line);++    /* eliminate whitespaces at the end of the line read */+    if(!(option & VRNA_INPUT_NO_TRUNCATION))+      elim_trailing_ws(line);++    l           = (int)strlen(line);+    str_length  = (*string) ? (int) strlen(*string) : 0;++    switch(*line){+      case  '@':    /* user abort */+                    if(state) inbuf2 = line;+                    else      free(line);+                    return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_QUIT;++      case  '\0':   /* empty line */+                    if(option & VRNA_INPUT_NOSKIP_BLANK_LINES){+                      if(state) inbuf2 = line;+                      else      free(line);+                      return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_BLANK_LINE;+                    }+                    break;++      case  '#': case  '%': case  ';': case  '/': case  '*': case ' ':+                    /* comments */+                    if(option & VRNA_INPUT_NOSKIP_COMMENTS){+                      if(state) inbuf2   = line;+                      else      *string = line;+                      return (state == 2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_COMMENT;+                    }+                    break;++      case  '>':    /* fasta header */+                    if(state) inbuf2   = line;+                    else      *string = line;+                    return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_FASTA_HEADER;++      case  'x': case 'e': case 'l': case '&':   /* seems to be a constraint or line starting with second sequence for dimer calculations */+                    i = 1;+                    /* lets see if this assumption holds for the complete line */+                    while((line[i] == 'x') || (line[i] == 'e') || (line[i] == 'l')) i++;+                    /* lines solely consisting of 'x's, 'e's or 'l's will be considered as structure constraint */+                    +                    if(+                            ((line[i]>64) && (line[i]<91))  /* A-Z */+                        ||  ((line[i]>96) && (line[i]<123)) /* a-z */+                      ){+                      if(option & VRNA_INPUT_FASTA_HEADER){+                        /* are we in structure mode? Then we remember this line for the next round */+                        if(state == 2){ inbuf2 = line; return VRNA_INPUT_CONSTRAINT;}+                        else{+                          *string = (char *)vrna_realloc(*string, sizeof(char) * (str_length + l + 1));+                          strcpy(*string + str_length, line);+                          state = 1;+                        }+                        break;+                      }+                      /* otherwise return line read */+                      else{ *string = line; return VRNA_INPUT_SEQUENCE;}+                    }+                    /* mmmh? it really seems to be a constraint */+                    /* fallthrough */+      case  '<': case  '.': case  '|': case  '(': case ')': case '[': case ']': case '{': case '}': case ',': case '+':+                    /* seems to be a structure or a constraint */+                    /* either we concatenate this line to one that we read previously */+                    if(option & VRNA_INPUT_FASTA_HEADER){+                      if(state == 1){+                        inbuf2 = line;+                        return VRNA_INPUT_SEQUENCE;+                      }+                      else{+                        *string = (char *)vrna_realloc(*string, sizeof(char) * (str_length + l + 1));+                        strcpy(*string + str_length, line);+                        state = 2;+                      }+                    }+                    /* or we return it as it is */+                    else{+                      *string = line;+                      return VRNA_INPUT_CONSTRAINT;+                    }+                    break;+      default:      if(option & VRNA_INPUT_FASTA_HEADER){+                      /* are we already in sequence mode? */+                      if(state == 2){+                        inbuf2 = line;+                        return VRNA_INPUT_CONSTRAINT;+                      }+                      else{+                        *string = (char *)vrna_realloc(*string, sizeof(char) * (str_length + l + 1));+                        strcpy(*string + str_length, line);+                        state = 1;+                      }+                    }+                    /* otherwise return line read */+                    else{+                      *string = line;+                      return VRNA_INPUT_SEQUENCE;+                    }+    }+    free(line);+    line = vrna_read_line(in);+  }while(line);++  return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_ERROR;+}++PUBLIC  unsigned int+vrna_file_fasta_read_record( char **header,+                        char **sequence,+                        char ***rest,+                        FILE *file,+                        unsigned int options){++  unsigned int  input_type, return_type, tmp_type;+  int           rest_count;+  char          *input_string;++  rest_count    = 0;+  return_type   = tmp_type = 0;+  input_string  = *header = *sequence = NULL;+  *rest         = (char **)vrna_alloc(sizeof(char *));++  /* remove unnecessary option flags from options variable... */+  options &= ~VRNA_INPUT_FASTA_HEADER;++  /* read first input or last buffered input */+  if(typebuf){+    input_type    = typebuf;+    input_string  = inbuf;+    typebuf       = 0;+    inbuf         = NULL;+  }+  else input_type  = read_multiple_input_lines(&input_string, file, options);++  if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;++  /* skip everything until we read either a fasta header or a sequence */+  while(input_type & (VRNA_INPUT_MISC | VRNA_INPUT_CONSTRAINT | VRNA_INPUT_BLANK_LINE)){+    free(input_string); input_string = NULL;+    input_type    = read_multiple_input_lines(&input_string, file, options);+    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;+  }++  if(input_type & VRNA_INPUT_FASTA_HEADER){+    return_type  |= VRNA_INPUT_FASTA_HEADER; /* remember that we've read a fasta header */+    *header       = input_string;+    input_string  = NULL;+    /* get next data-block with fasta support if not explicitely forbidden by VRNA_INPUT_NO_SPAN */+    input_type  = read_multiple_input_lines(+                    &input_string,+                    file,+                    ((options & VRNA_INPUT_NO_SPAN) ? 0 : VRNA_INPUT_FASTA_HEADER) | options+                  );+    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return (return_type | input_type);+  }++  if(input_type & VRNA_INPUT_SEQUENCE){+    return_type  |= VRNA_INPUT_SEQUENCE; /* remember that we've read a sequence */+    *sequence     = input_string;+    input_string  = NULL;+  } else vrna_message_error("sequence input missing");++  /* read the rest until we find user abort, EOF, new sequence or new fasta header */+  if(!(options & VRNA_INPUT_NO_REST)){+    options |= VRNA_INPUT_NOSKIP_COMMENTS; /* allow commetns to appear in rest output */+    tmp_type = VRNA_INPUT_QUIT | VRNA_INPUT_ERROR | VRNA_INPUT_SEQUENCE | VRNA_INPUT_FASTA_HEADER;+    if(options & VRNA_INPUT_NOSKIP_BLANK_LINES) tmp_type |= VRNA_INPUT_BLANK_LINE;+    while(!((input_type = read_multiple_input_lines(&input_string, file, options)) & tmp_type)){+      *rest = vrna_realloc(*rest, sizeof(char **)*(++rest_count + 1));+      (*rest)[rest_count-1] = input_string;+      input_string = NULL;+    }+    /*+    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;+    */++    /*  finished reading everything...+    *   we now put the last line into the buffer if necessary+    *   since it should belong to the next record+    */+    inbuf = input_string;+    typebuf = input_type;+  }+  (*rest)[rest_count] = NULL;+  return (return_type);+}++PUBLIC char *+vrna_extract_record_rest_structure( const char **lines,+                                    unsigned int length,+                                    unsigned int options){++  char *structure = NULL;+  int r, i, l, cl, stop;+  char *c;++  if(lines){+    for(r = i = stop = 0; lines[i]; i++){+      l   = (int)strlen(lines[i]);+      c   = (char *) vrna_alloc(sizeof(char) * (l+1));+      (void) sscanf(lines[i], "%s", c);+      cl  = (int)strlen(c);++      /* line commented out ? */+      if((*c == '#') || (*c == '%') || (*c == ';') || (*c == '/') || (*c == '*' || (*c == '\0'))){+        /* skip leading comments only, i.e. do not allow comments inside the constraint */+        if(!r)  continue;+        else    break;+      }++      /* append the structure part to the output */+      r += cl+1;+      structure = (char *)vrna_realloc(structure, r*sizeof(char));+      strcat(structure, c);+      free(c);+      /* stop if the assumed structure length has been reached */+      if((length > 0) && (r-1 == length)) break;+      /* stop if not allowed to read from multiple lines */+      if(!(options & VRNA_OPTION_MULTILINE)) break;+    }+  }+  return structure;+}++PUBLIC void+vrna_extract_record_rest_constraint(char **cstruc,+                                    const char **lines,+                                    unsigned int option){++  *cstruc = vrna_extract_record_rest_structure(lines, 0, option | (option & VRNA_CONSTRAINT_MULTILINE) ? VRNA_OPTION_MULTILINE : 0);+  +}++PUBLIC int+vrna_file_SHAPE_read( const char *file_name,+                      int length,+                      double default_value,+                      char *sequence,+                      double *values){++  FILE *fp;+  char *line;+  int i;+  int count = 0;++  if(!file_name)+    return 0;++  if(!(fp = fopen(file_name, "r"))){+    vrna_message_warning("SHAPE data file could not be opened");+    return 0;+  }++  for (i = 0; i < length; ++i)+  {+    sequence[i] = 'N';+    values[i + 1] = default_value;+  }++  sequence[length] = '\0';++  while((line=vrna_read_line(fp))){+    int position;+    unsigned char nucleotide = 'N';+    double reactivity = default_value;+    char *second_entry = 0;+    char *third_entry = 0;+    char *c;++    if(sscanf(line, "%d", &position) != 1)+    {+      free(line);+      continue;+    }++    if(position <= 0 || position > length)+    {+      vrna_message_warning("Provided SHAPE data outside of sequence scope");+      fclose(fp);+      free(line);+      return 0;+    }++    for(c = line + 1; *c; ++c){+      if(isspace(*(c-1)) && !isspace(*c)) {+        if(!second_entry){+          second_entry = c;+        }else{+          third_entry = c;+          break;+        }+      }+    }++    if(second_entry){+      if(third_entry){+        sscanf(second_entry, "%c", &nucleotide);+        sscanf(third_entry, "%lf", &reactivity);+      }else if(sscanf(second_entry, "%lf", &reactivity) != 1)+        sscanf(second_entry, "%c", &nucleotide);+    }++    sequence[position-1] = nucleotide;+    values[position] = reactivity;+    ++count;++    free(line);+  }++  fclose(fp);++  if(!count)+  {+      vrna_message_warning("SHAPE data file is empty");+      return 0;+  }++  return 1;+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC unsigned int+get_multi_input_line( char **string,+                      unsigned int option){++  return read_multiple_input_lines(string, NULL, option);+}++PUBLIC unsigned int+read_record(char **header,+            char **sequence,+            char  ***rest,+            unsigned int options){++  return vrna_file_fasta_read_record(header, sequence, rest, NULL, options);+}++PUBLIC char *+extract_record_rest_structure(const char **lines,+                              unsigned int length,+                              unsigned int options){++  return vrna_extract_record_rest_structure(lines, length, options);+}+++#endif
+ C/ViennaRNA/file_formats.h view
@@ -0,0 +1,278 @@+#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_H+#define VIENNA_RNA_PACKAGE_FILE_FORMATS_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     file_formats.h+ *  @ingroup  file_utils+ *  @brief    Read and write different file formats for RNA sequences, structures+ */++/**+ *  @{+ *  @ingroup  file_utils+ */++#include <stdio.h>++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/file_formats_msa.h>++/**+ *  @brief Print a secondary structure as helix list+ *+ *  @param  seq     The RNA sequence+ *  @param  db      The structure in dot-bracket format+ *  @param  energy  Free energy of the structure in kcal/mol+ *  @param  file    The file handle used to print to (print defaults to 'stdout' if(file == NULL) )+ */+void vrna_file_helixlist( const char *seq,+                          const char *db,+                          float energy,+                          FILE *file);++/**+ *  @brief Print a secondary structure as connect table+ *+ *  Connect table file format looks like this:+@verbatim+300  ENERGY = 7.0  example+  1 G       0    2   22    1+  2 G       1    3   21    2+@endverbatim+ *  where the headerline is followed by 6 columns with:+ *  1. Base number: index n+ *  2. Base (A, C, G, T, U, X)+ *  3. Index n-1  (0 if first nucleotide)+ *  4. Index n+1  (0 if last nucleotide)+ *  5. Number of the base to which n is paired. No pairing is indicated by 0 (zero).+ *  6. Natural numbering.+ *+ *  @param  seq         The RNA sequence+ *  @param  db          The structure in dot-bracket format+ *  @param  energy      The free energy of the structure+ *  @param  identifier  An optional identifier for the sequence+ *  @param  file  The file handle used to print to (print defaults to 'stdout' if(file == NULL) )+ */+void vrna_file_connect( const char *seq,+                        const char *db,+                        float energy,+                        const char *identifier,+                        FILE *file);++/**+ *  @brief Print a secondary structure in bpseq format+ *+ *  @param  seq         The RNA sequence+ *  @param  db          The structure in dot-bracket format+ *  @param  file  The file handle used to print to (print defaults to 'stdout' if(file == NULL) )+ */+void vrna_file_bpseq( const char *seq,+                      const char *db,+                      FILE *file);++#if WITH_JSON_SUPPORT++/**+ *  @brief Print a secondary structure in jsonformat+ *+ *  @param  seq         The RNA sequence+ *  @param  db          The structure in dot-bracket format+ *  @param  energy      The free energy+ *  @param  identifier  An identifier for the sequence+ *  @param  file  The file handle used to print to (print defaults to 'stdout' if(file == NULL) )+ */+void vrna_file_json(const char *seq,+                    const char *db,+                    double energy,+                    const char *identifier,+                    FILE *file);++#endif++/**+ *  @brief  Tell a function that an input is assumed to span several lines+ *+ *  If used as input-option a function might also be returning this state telling+ *  that it has read data from multiple lines.+ *+ *  @see vrna_extract_record_rest_structure(), vrna_file_fasta_read_record()+ *+ */+#define VRNA_OPTION_MULTILINE             32U+/**+ *  @brief parse multiline constraint+ *  @deprecated see vrna_extract_record_rest_structure()+ */+#define VRNA_CONSTRAINT_MULTILINE         32U++/**+ *  @brief  Get a (fasta) data set from a file or stdin+ * + *  This function may be used to obtain complete datasets from a filehandle or stdin.+ *  A dataset is always defined to contain at least a sequence. If data starts with a+ *  fasta header, i.e. a line like+ *  @verbatim >some header info @endverbatim+ *  then vrna_file_fasta_read_record() will assume that the sequence that follows the header may span+ *  over several lines. To disable this behavior and to assign a single line to the argument+ *  'sequence' one can pass #VRNA_INPUT_NO_SPAN in the 'options' argument.+ *  If no fasta header is read in the beginning of a data block, a sequence must not span over+ *  multiple lines!\n+ *  Unless the options #VRNA_INPUT_NOSKIP_COMMENTS or #VRNA_INPUT_NOSKIP_BLANK_LINES are passed,+ *  a sequence may be interrupted by lines starting with a comment character or empty lines.\n+ *  A sequence is regarded as completely read if it was either assumed to not span over multiple+ *  lines, a secondary structure or structure constraint follows the sequence on the next line,+ *  or a new header marks the beginning of a new sequence...\n+ *  All lines following the sequence (this includes comments) that do not initiate a new dataset+ *  according to the above definition are available through the line-array 'rest'.+ *  Here one can usually find the structure constraint or other information belonging to the+ *  current dataset. Filling of 'rest' may be prevented by passing #VRNA_INPUT_NO_REST to the+ *  options argument.\n+ * + *  @note This function will exit any program with an error message if no sequence could be read!+ *  @note This function is NOT threadsafe! It uses a global variable to store information about+ *  the next data block.+ * + *  The main purpose of this function is to be able to easily parse blocks of data+ *  in the header of a loop where all calculations for the appropriate data is done inside the+ *  loop. The loop may be then left on certain return values, e.g.:+ *  @code+char *id, *seq, **rest;+int  i;+id = seq = NULL;+rest = NULL;+while(!(vrna_file_fasta_read_record(&id, &seq, &rest, NULL, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){+  if(id) printf("%s\n", id);+  printf("%s\n", seq);+  if(rest)+    for(i=0;rest[i];i++){+      printf("%s\n", rest[i]);+      free(rest[i]);+    }+  free(rest);+  free(seq);+  free(id);+}+ *  @endcode+ *  In the example above, the while loop will be terminated when vrna_file_fasta_read_record() returns+ *  either an error, EOF, or a user initiated quit request.\n+ *  As long as data is read from stdin (we are passing NULL as the file pointer), the id is+ *  printed if it is available for the current block of data. The sequence will be printed in+ *  any case and if some more lines belong to the current block of data each line will be printed+ *  as well.+ * + *  @note Do not forget to free the memory occupied by header, sequence and rest!+ * + *  @param  header    A pointer which will be set such that it points to the header of the record+ *  @param  sequence  A pointer which will be set such that it points to the sequence of the record+ *  @param  rest      A pointer which will be set such that it points to an array of lines which also belong to the record+ *  @param  file      A file handle to read from (if NULL, this function reads from stdin)+ *  @param  options   Some options which may be passed to alter the behavior of the function, use 0 for no options+ *  @return           A flag with information about what the function actually did read+ */+unsigned int vrna_file_fasta_read_record(char **header,+                                    char **sequence,+                                    char  ***rest,+                                    FILE *file,+                                    unsigned int options);++/** @brief Extract a dot-bracket structure string from (multiline)character array+ *+ * This function extracts a dot-bracket structure string from the 'rest' array as+ * returned by vrna_file_fasta_read_record() and returns it. All occurences of comments within the+ * 'lines' array will be skipped as long as they do not break the structure string.+ * If no structure could be read, this function returns NULL.+ *+ * @pre      The argument 'lines' has to be a 2-dimensional character array as obtained+ *            by vrna_file_fasta_read_record()+ * @see vrna_file_fasta_read_record()+ *+ * @param lines   The (multiline) character array to be parsed+ * @param length  The assumed length of the dot-bracket string (passing a value < 1 results in no length limit)+ * @param option  Some options which may be passed to alter the behavior of the function, use 0 for no options+ * @return        The dot-bracket string read from lines or NULL+ */+char *vrna_extract_record_rest_structure( const char **lines,+                                          unsigned int length,+                                          unsigned int option);++/**+  * @brief Read data from a given SHAPE reactivity input file+  *+  * This function parses the informations from a given file and stores the result+  * in the preallocated string sequence and the double array values.+  *+  * @param file_name     Path to the constraints file+  * @param length        Length of the sequence (file entries exceeding this limit will cause an error)+  * @param default_value Value for missing indices+  * @param sequence      Pointer to an array used for storing the sequence obtained from the SHAPE reactivity file+  * @param values        Pointer to an array used for storing the values obtained from the SHAPE reactivity file+  */+int vrna_file_SHAPE_read( const char *file_name,+                          int length,+                          double default_value,+                          char *sequence,+                          double *values);+++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief  Extract a hard constraint encoded as pseudo dot-bracket string+ *+ *  @deprecated     Use vrna_extract_record_rest_structure() instead!+ *  @pre      The argument 'lines' has to be a 2-dimensional character array as obtained+ *            by vrna_file_fasta_read_record()+ *  @see      vrna_file_fasta_read_record(), #VRNA_CONSTRAINT_DB_PIPE, #VRNA_CONSTRAINT_DB_DOT, #VRNA_CONSTRAINT_DB_X+ *            #VRNA_CONSTRAINT_DB_ANG_BRACK, #VRNA_CONSTRAINT_DB_RND_BRACK+ *+ *  @param  cstruc  A pointer to a character array that is used as pseudo dot-bracket+ *                  output+ *  @param  lines   A 2-dimensional character array with the extension lines from the FASTA+ *                  input+ *  @param  option  The option flags that define the behavior and recognition pattern of+ *                  this function+ */+DEPRECATED(void vrna_extract_record_rest_constraint( char **cstruc, const char **lines, unsigned int option));++/** @brief Extract a dot-bracket structure string from (multiline)character array+ *+ * @deprecated This function is deprecated! Use \fn vrna_extract_record_rest_structure() as a replacment.+ */+DEPRECATED(char *extract_record_rest_structure( const char **lines,+                                                unsigned int length,+                                                unsigned int option));++/**+ *  @brief  Get a data record from stdin+ * + *  @deprecated This function is deprecated! Use vrna_file_fasta_read_record() as a replacment.+ *+ */+DEPRECATED(unsigned int read_record(char **header,+                                    char **sequence,+                                    char  ***rest,+                                    unsigned int options));+++DEPRECATED(unsigned int get_multi_input_line(char **string, unsigned int options));++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/file_formats_msa.c view
@@ -0,0 +1,897 @@+/*+    file_formats_msa.c++    Various functions dealing with file formats for Multiple Sequence Alignments (MSA)++    (c) 2016 Ronny Lorenz++    ViennaRNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <ctype.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/file_utils.h"+#include "ViennaRNA/file_formats.h"+#include "ViennaRNA/file_formats_msa.h"++/*+#################################+# STATIC DECLARATIONS           #+#################################+*/++typedef int (aln_parser_function)(FILE *fp, char ***names, char ***aln, char **id, char **structure, int verbosity);++typedef struct {+  unsigned int        code;+  aln_parser_function *parser;+  const char          *name;+} parsable;++PRIVATE aln_parser_function parse_aln_stockholm;++PRIVATE aln_parser_function parse_aln_clustal;++PRIVATE aln_parser_function parse_aln_fasta;++PRIVATE aln_parser_function parse_aln_maf;++PRIVATE int+parse_fasta_alignment(FILE *fp,+                      char ***names,+                      char ***aln,+                      int verbosity);++PRIVATE int+parse_clustal_alignment(FILE *clust,+                        char ***names,+                        char ***aln,+                        int verbosity);++PRIVATE int+parse_stockholm_alignment(FILE *fp,+                          char ***aln,+                          char ***names,+                          char  **id,+                          char  **structure,+                          int   verbosity);++PRIVATE int+parse_maf_alignment(FILE *fp,+                    char ***aln,+                    char ***names,+                    int   verbosity);++PRIVATE int+check_alignment(const char **names,+                const char **aln,+                int seq_num);++PRIVATE void+free_msa_record(char ***names,+                char ***aln,+                char **id,+                char **structure);++PRIVATE void+add_sequence( const char  *id,+              const char  *seq,+              char        ***names,+              char        ***aln,+              int         seq_num);++PRIVATE void+endmarker_msa_record( char ***names,+                      char ***aln,+                      int   seq_num);++/*+#################################+# STATIC VARIABLES              #+#################################+*/++/* number of known alignment parsers */+#define NUM_PARSERS 4++static parsable known_parsers[NUM_PARSERS] = {+  /* option, parser, name */+  { VRNA_FILE_FORMAT_MSA_STOCKHOLM, parse_aln_stockholm,  "Stockholm 1.0 format" },+  { VRNA_FILE_FORMAT_MSA_CLUSTAL,   parse_aln_clustal,    "ClustalW format" },+  { VRNA_FILE_FORMAT_MSA_FASTA,     parse_aln_fasta,      "FASTA format" },+  { VRNA_FILE_FORMAT_MSA_MAF,       parse_aln_maf,        "MAF format" }+};++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC unsigned int+vrna_file_msa_detect_format(const char *filename,+                            unsigned int options){++  FILE          *fp;+  char          **names, **aln;+  unsigned int  format;+  int           i, r;+  long int      fp_position;++  names     = NULL;+  aln       = NULL;+  format    = VRNA_FILE_FORMAT_MSA_UNKNOWN;++  /* if no alignment file format(s) were specified we probe for all of them */+  if(options == 0)+    options = VRNA_FILE_FORMAT_MSA_DEFAULT;++  if(!(fp = fopen(filename, "r"))){+    vrna_message_warning("Alignment file could not be opened!");+    return format;+  }++  r           = -1;+  fp_position = ftell(fp);++  for(i = 0; i < NUM_PARSERS; i++){+    if((options & known_parsers[i].code) && (known_parsers[i].parser)){+      /* go back to beginning of file */+      if(!fseek(fp, fp_position, SEEK_SET)){+        r = known_parsers[i].parser(fp, &names, &aln, NULL, NULL, -1);+        free_msa_record(&names, &aln, NULL, NULL);+        if(r > 0){+          format = known_parsers[i].code;+          break;+        }+      } else {+        vrna_message_error("Something unexpected happened while parsing the alignment file");+      }+    }+  }++  fclose(fp);++  return format;+}+++PUBLIC int+vrna_file_msa_read( const char *filename,+                    char ***names,+                    char ***aln,+                    char  **id,+                    char  **structure,+                    unsigned int options){++  FILE  *fp;+  char  *line = NULL;+  int   i, n, seq_num;+  seq_num   = 0;++  if(!(fp = fopen(filename, "r"))){+    vrna_message_warning("Alignment file could not be opened!");+    return seq_num;+  }++  if(names && aln){+    *names  = NULL;+    *aln    = NULL;+  } else {+    return seq_num;+  }++  if(id)+    *id = NULL;++  if(structure)+    *structure = NULL;++  /* if no alignment file format was specified, lets try to guess it */+  if(options == 0)+    options = VRNA_FILE_FORMAT_MSA_DEFAULT;++  int r = -1;+  long int fp_position = ftell(fp);++  for(i = 0; i < NUM_PARSERS; i++){+    if((options & known_parsers[i].code) && (known_parsers[i].parser)){+      /* go back to beginning of file */+      if(!fseek(fp, fp_position, SEEK_SET)){+        r = known_parsers[i].parser(fp, names, aln, id, structure, 0);+        if(r > 0)+          break;+      } else {+        vrna_message_error("Something unexpected happened while parsing the alignment file");+      }+    }+  }++  fclose(fp);++  if(r == -1){+    vrna_message_warning("Alignment file parser is unknown (or not specified?)");+  } else {+    seq_num = r;++    if((seq_num > 0) && (!(options & VRNA_FILE_FORMAT_MSA_NOCHECK))){+      if(!check_alignment((const char **)(*names), (const char **)(*aln), seq_num)){+        vrna_message_warning("Alignment did not pass sanity checks!");++        /* discard the data we've read! */+        free_msa_record(names, aln, id, structure);++        seq_num = 0;+      }+    }+  }++  return seq_num;+}+++PUBLIC int+vrna_file_msa_read_record(FILE *fp,+                          char ***names,+                          char ***aln,+                          char  **id,+                          char  **structure,+                          unsigned int options){++  const char          *parser_name;+  int                 i, r, n, seq_num;+  aln_parser_function *parser;++  seq_num     = 0;+  parser_name = NULL;+  parser      = NULL;++  if(!fp){+    vrna_message_warning("Can't read alignment from file pointer!");+    return seq_num;+  }++  if(names && aln){+    *names  = NULL;+    *aln    = NULL;+  } else {+    return seq_num;+  }++  if(id)+    *id = NULL;++  if(structure)+    *structure = NULL;++  for(r = i = 0; i < NUM_PARSERS; i++){+    if((options & known_parsers[i].code) && (known_parsers[i].parser)){+      if(!parser){+        parser      = known_parsers[i].parser;+        parser_name = known_parsers[i].name;+      }+      r++;+    }+  }++  if(r == 0){+    vrna_message_warning("Did not find parser for specified MSA format!");+  } else {+    if(r > 1) { +      vrna_message_warning("More than one MSA format parser specified!\n"+                                  "Using parser for %s", parser_name);+    }++    seq_num = parser(fp, names, aln, id, structure, 0);++    if((seq_num > 0) && (!(options & VRNA_FILE_FORMAT_MSA_NOCHECK))){+      if(!check_alignment((const char **)(*names), (const char **)(*aln), seq_num)){+        vrna_message_warning("Alignment did not pass sanity checks!");++        /* discard the data we've read! */+        free_msa_record(names, aln, id, structure);++        seq_num = -1;+      }+    }+  }++  return seq_num;+}+++PRIVATE int+parse_stockholm_alignment(FILE  *fp,+                          char  ***names,+                          char  ***aln,+                          char  **id,+                          char  **structure,+                          int   verbosity){++  char  *line = NULL;+  int   i, n, seq_num, seq_length, has_record;++  seq_num     = 0;+  seq_length  = 0;++  if(!fp){+    if(verbosity >= 0)+      vrna_message_warning("Can't read from filepointer while parsing Stockholm formatted sequence alignment!");+    return -1;+  }++  if(names && aln){+    *names  = NULL;+    *aln    = NULL;+  } else {+    return -1;+  }++  if(id)+    *id = NULL;++  if(structure)+    *structure = NULL;++  int inrecord = 0;+  while((line = vrna_read_line(fp))){+    if(strstr(line, "STOCKHOLM 1.0")){+      inrecord    = 1;+      has_record  = 1;+      free(line);+      break;+    }+    free(line);+  }++  if(inrecord){+    while((line = vrna_read_line(fp))){++      if(strncmp(line, "//", 2) == 0){+        /* end of alignment */+        free(line);+        line = NULL;+        break;+      }++      n = (int)strlen(line);++      switch(*line){+        /* we skip lines that start with whitespace */+        case ' ': case '\0':+          goto stockholm_next_line;++        /* Stockholm markup, or comment */+        case '#':+          if(strstr(line, "STOCKHOLM 1.0")){+            if(verbosity >= 0)+              vrna_message_warning("Malformatted Stockholm record, missing // ?");++            /* drop everything we've read so far and start new, blank record */+            free_msa_record(names, aln, id, structure);++            seq_num = 0;+          } else if(strncmp(line, "#=GF", 4) == 0){+            /* found feature markup */+            if((id != NULL) && (strncmp(line, "#=GF ID", 7) == 0)){+              *id = (char *)vrna_alloc(sizeof(char) * n);+              if(sscanf(line, "#=GF ID %s", *id) == 1){+                *id = (char *)vrna_realloc(*id, sizeof(char) * (strlen(*id) + 1));+              } else {+                free(*id);+                *id = NULL;+              }+            }+          } else if(strncmp(line, "#=GC", 4) == 0){+            /* found per-column annotation */+            if((structure != NULL) && (strncmp(line, "#=GC SS_cons", 12) == 0)){+              char *ss = (char *)vrna_alloc(sizeof(char) * n);+              if(sscanf(line, "#=GC SS_cons %s", ss) == 1){+                *structure = (char *)vrna_realloc(*structure, sizeof(char) * (strlen(ss) + 1));+                strcpy(*structure, ss);+              }+              free(ss);+            }+          } else if(strncmp(line, "#=GS", 4) == 0){+            /* found generic per-sequence annotation */+          } else if(strncmp(line, "#=GR", 4) == 0){+            /* found generic per-Residue annotation */+          } else {+            /* may be comment? */+          }+          break;++        /* should be sequence */+        default:+          {+            int tmp_l;+            char *tmp_name  = (char *)vrna_alloc(sizeof(char) * (n + 1));+            char *tmp_seq   = (char *)vrna_alloc(sizeof(char) * (n + 1));+            if(sscanf(line, "%s %s", tmp_name, tmp_seq) == 2){+              seq_num++;+              tmp_l = (int)strlen(tmp_seq);++              if(seq_num == 1){+                seq_length = tmp_l;+              } else {  /* check sequence length against first */+                if(seq_length != tmp_l){+                  if(verbosity >= 0)+                    vrna_message_warning("Discarding Stockholm record! Sequence lengths do not match.");++                  /* drop everything we've read so far and abort parsing */+                  free_msa_record(names, aln, id, structure);++                  seq_num = 0;++                  free(tmp_name);+                  free(tmp_seq);+                  free(line);+                  line = NULL;++                  goto stockholm_exit;+                }+              }++              add_sequence( tmp_name, tmp_seq,+                            names, aln,+                            seq_num);+            }+            free(tmp_name);+            free(tmp_seq);+          }+          break;+      }++stockholm_next_line:++      free(line);+    }+  } else {+    if(verbosity > 0)+      vrna_message_warning("Did not find any Stockholm 1.0 formatted record!");+    return -1;+  }++stockholm_exit:++  free(line);++  endmarker_msa_record(names, aln, seq_num);++  if((seq_num > 0) && (verbosity >= 0))+    vrna_message_info(stderr, "%d sequences; length of alignment %d.", seq_num, (int)strlen((*aln)[0]));++  return seq_num;+}+++PRIVATE int+parse_fasta_alignment(FILE *fp,+                      char ***names,+                      char ***aln,+                      int verbosity){++  unsigned int  read_opt, rec_type;+  int           seq_num;+  char          *rec_id, *rec_sequence, **rec_rest;++  rec_id        = NULL;+  rec_sequence  = NULL;+  rec_rest      = NULL;+  seq_num       = 0;+  read_opt      = VRNA_INPUT_NO_REST; /* read sequence and header information only */++  /* read until EOF or user abort */+  while(+    !((rec_type = vrna_file_fasta_read_record(&rec_id, &rec_sequence, &rec_rest, fp, read_opt))+        & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){++    if(rec_id){ /* valid FASTA entry */+      seq_num++;++      char *id = (char *)vrna_alloc(sizeof(char) * strlen(rec_id));+      (void) sscanf(rec_id, ">%s", id);+      vrna_seq_toupper(rec_sequence);++      add_sequence( id, rec_sequence,+                    names, aln,+                    seq_num);++      free(id);+    }++    free(rec_id);+    free(rec_sequence);+    free(rec_rest);+  }++  free(rec_id);+  free(rec_sequence);+  free(rec_rest);++  endmarker_msa_record(names, aln, seq_num);++  if((seq_num > 0) && (verbosity >= 0)){+    vrna_message_info(stderr, "%d sequences; length of alignment %d.", seq_num, (int)strlen((*aln)[0]));+  } else {+    if(verbosity > 0)+      vrna_message_warning("Did not find any FASTA formatted record!");+    return -1;+  }++  return seq_num;+}+++PRIVATE int+parse_clustal_alignment(FILE *clust,+                        char ***names,+                        char ***aln,+                        int verbosity){++  char *line, *name, *seq;+  int  n, r, nn=0, seq_num = 0, i;++  if((line = vrna_read_line(clust)) == NULL){+    return -1;+  }++  if(strncmp(line,"CLUSTAL", 7) != 0){+    if(verbosity > 0)+      vrna_message_warning("This doesn't look like a CLUSTALW file, sorry");++    free(line);+    return -1;+  }++  free(line);+  line = vrna_read_line(clust);++  while (line!=NULL) {+    n = strlen(line);++    if((n < 4) || isspace((int)line[0])) {+      /* skip non-sequence line */+      free(line);+      line = vrna_read_line(clust);+      nn    = 0;  /* reset sequence number */+      continue;+    }++    /* skip comments */+    if(line[0] == '#'){+      free(line);+      line = vrna_read_line(clust);+      continue;+    }++    seq   = (char *)vrna_alloc(sizeof(char) * (n + 1));+    name  = (char *)vrna_alloc(sizeof(char) * (n + 1));+    if(sscanf(line, "%s %s", name, seq) == 2){+      /* realloc to actual sizes */+      seq   = (char *)vrna_realloc(seq, sizeof(char) * (strlen(seq) + 1));+      name  = (char *)vrna_realloc(name, sizeof(char) * (strlen(name) + 1));+      for(i = 0; i < strlen(seq); i++){+        if(seq[i] == '.')+          seq[i] = '-'; /* replace '.' gaps with '-' */+      }++      /* convert sequence to uppercase letters */+      vrna_seq_toupper(seq);++      if(nn == seq_num){ /* first time */+            add_sequence( name, seq,+                          names, aln,+                          nn + 1);+      } else {+        if (strcmp(name, (*names)[nn]) != 0) {+          /* name doesn't match */+           vrna_message_warning("Sorry, your file is messed up (inconsitent seq-names)");+           free(line); free(seq);+           return 0;+        }+        (*aln)[nn] = (char *)vrna_realloc((*aln)[nn], strlen(seq) + strlen((*aln)[nn])+1);+        strcat((*aln)[nn], seq);+      }+      nn++;+      if(nn > seq_num)+        seq_num = nn;++      free(seq);+      free(name);+    }+    free(line);++    line = vrna_read_line(clust);+  }++  endmarker_msa_record(names, aln, seq_num);++  if((seq_num > 0) && (verbosity >= 0))+    vrna_message_info(stderr, "%d sequences; length of alignment %d.", seq_num, (int)strlen((*aln)[0]));++  return seq_num;+}+++PRIVATE int+parse_maf_alignment(FILE  *fp,+                    char  ***names,+                    char  ***aln,+                    int   verbosity){++  char  *line = NULL, *tmp_name, *tmp_sequence, strand;+  int   i, n, seq_num, seq_length, start, length, src_length;++  seq_num     = 0;+  seq_length  = 0;++  if(!fp){+    if(verbosity >= 0)+      vrna_message_warning("Can't read from filepointer while parsing MAF formatted sequence alignment!");+    return -1;+  }++  if(names && aln){+    *names  = NULL;+    *aln    = NULL;+  } else {+    return -1;+  }++  int inrecord = 0;+  while((line = vrna_read_line(fp))){+    if(*line == 'a'){+      if((line[1] == '\0') || isspace(line[1])){+        inrecord = 1;+        free(line);+        break;+      }+    }+    free(line);+  }++  if(inrecord){+    while((line = vrna_read_line(fp))){+      n = (int)strlen(line);++      switch(*line){+        case '#': /* comment */+          break;++        case 's': /* a sequence within the alignment block */+          tmp_name      = (char *)vrna_alloc(sizeof(char) * n);+          tmp_sequence  = (char *)vrna_alloc(sizeof(char) * n);+          if(sscanf(line, "s %s %d %d %c %d %s",+                tmp_name,+                &start,+                &length,+                &strand,+                &src_length,+                tmp_sequence) == 6){++            seq_num++;+            tmp_name      = (char *)vrna_realloc(tmp_name, sizeof(char) * (strlen(tmp_name) + 1));+            tmp_sequence  = (char *)vrna_realloc(tmp_sequence, sizeof(char) * (strlen(tmp_sequence) + 1));++            vrna_seq_toupper(tmp_sequence);++            add_sequence( tmp_name, tmp_sequence,+                          names, aln,+                          seq_num);++            free(tmp_name);+            free(tmp_sequence);+            break;+          }+          free(tmp_name);+          free(tmp_sequence);+          /* all through */++        default: /* something else that ends the block */+          free(line);+          goto maf_exit;+      }++      free(line);+    }+  } else {+    if(verbosity > 0)+      vrna_message_warning("Did not find any MAF formatted record!");+    return -1;+  }++maf_exit:++  endmarker_msa_record(names, aln, seq_num);++  if((seq_num > 0) && (verbosity >= 0))+    vrna_message_info(stderr, "%d sequences; length of alignment %d.", seq_num, (int)strlen((*aln)[0]));++  return seq_num;+}+++PRIVATE void+free_msa_record(char ***names,+                char ***aln,+                char **id,+                char **structure){++  int s, i;++  s = 0;+  if(aln && (*aln))+    for(; (*aln)[s]; s++);++  if(id != NULL){+    free(*id);+    *id = NULL;+  }++  if(structure != NULL){+    free(*structure);+    *structure = NULL;+  }++  for(i = 0; i < s; i++){+    free((*names)[i]);+    free((*aln)[i]);+  }++  if(names && (*names)){+    free(*names);+    *names = NULL;+  }++  if(aln && (*aln)){+    free(*aln);+    *aln = NULL;+  }+}+++PRIVATE int+parse_aln_stockholm(FILE *fp,+                    char ***names,+                    char ***aln,+                    char **id,+                    char **structure,+                    int  verbosity){++  return parse_stockholm_alignment(fp, names, aln, id, structure, verbosity);+}+++PRIVATE int+parse_aln_clustal(FILE *fp,+                  char ***names,+                  char ***aln,+                  char **id,+                  char **structure,+                  int  verbosity){++  /* clustal format doesn't contain id's or structure information */+  if(id)+    *id = NULL;+  if(structure)+    *structure = NULL;++  return parse_clustal_alignment(fp, names, aln, verbosity);+}+++PRIVATE int+parse_aln_fasta(FILE *fp,+                char ***names,+                char ***aln,+                char **id,+                char **structure,+                int  verbosity){++  /* fasta alignments do not contain an id, or structure information */+  if(id)+    *id = NULL;+  if(structure)+    *structure = NULL;++  return parse_fasta_alignment(fp, names, aln, verbosity);+}+++PRIVATE int+parse_aln_maf(FILE *fp,+              char ***names,+              char ***aln,+              char **id,+              char **structure,+              int  verbosity){++  /* MAF alignments do not contain an id, or structure information */+  if(id)+    *id = NULL;+  if(structure)+    *structure = NULL;++  return parse_maf_alignment(fp, names, aln, verbosity);+}+++PRIVATE void+add_sequence( const char  *id,+              const char  *seq,+              char        ***names,+              char        ***aln,+              int         seq_num){++  (*names)              = (char **)vrna_realloc(*names, sizeof(char *) * (seq_num));+  (*names)[seq_num - 1] = strdup(id);+  (*aln)                = (char **)vrna_realloc(*aln, sizeof(char *) * (seq_num));+  (*aln)[seq_num - 1]   = strdup(seq);+}+++PRIVATE void+append_sequence(char *seq,+                char  **aln,+                int   seq_num){+++}+++PRIVATE void+endmarker_msa_record( char ***names,+                      char ***aln,+                      int   seq_num){++  /*+    append additional entry in 'aln' and 'names' pointing to NULL (this may be+    used as an indication for the end of the sequence list)+  */+  if(seq_num > 0){+    (*aln)            = (char **)vrna_realloc(*aln, sizeof(char *) * (seq_num + 1));+    (*names)          = (char **)vrna_realloc(*names, sizeof(char *) * (seq_num + 1));+    (*aln)[seq_num]   = NULL;+    (*names)[seq_num] = NULL;+  }+}+++PRIVATE int+check_alignment(const char **names,+                const char **aln,+                int seq_num){++  int i, j, l, pass = 1;++  /* check for unique names */+  for(i = 0; i < seq_num; i++){+    for(j = i + 1; j < seq_num; j++){+      if(!strcmp(names[i], names[j])){+        vrna_message_warning("Sequence IDs in input alignment are not unique!");+        pass = 0;+      }+    }+  }++  /* check for equal lengths of sequences */+  l = (int)strlen(aln[0]);+  for(i = 1; i < seq_num; i++)+    if((int)strlen(aln[i]) != l){+      vrna_message_warning("Sequence lengths in input alignment do not match!");+      pass = 0;+    }++  return pass;+}
+ C/ViennaRNA/file_formats_msa.h view
@@ -0,0 +1,208 @@+#ifndef VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H+#define VIENNA_RNA_PACKAGE_FILE_FORMATS_MSA_H++/**+ *  @addtogroup   file_utils+ *+ *  @{+ *+ *  @file file_formats_msa.h+ *  @brief Functions dealing with file formats for Multiple Sequence Alignments (MSA)+ *+ */++#include <stdio.h>++/**+ *  @brief  Option flag indicating ClustalW formatted files+ *  @see vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_CLUSTAL      1U++/**+ *  @brief Option flag indicating Stockholm 1.0 formatted files+ *  @see vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_STOCKHOLM    2U++/**+ *  @brief Option flag indicating FASTA (Pearson) formatted files+ *  @see vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_FASTA        4U++/**+ *  @brief Option flag indicating MAF formatted files+ *  @see vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_MAF          8U++/**+ *  @brief Option flag indicating the set of default file formats+ *  @see vrna_file_msa_read(), vrna_file_msa_read_record(), vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_DEFAULT      ( \+                                              VRNA_FILE_FORMAT_MSA_CLUSTAL \+                                            | VRNA_FILE_FORMAT_MSA_STOCKHOLM \+                                            | VRNA_FILE_FORMAT_MSA_FASTA \+                                            | VRNA_FILE_FORMAT_MSA_MAF \+                                          )++/**+ *  @brief Option flag to disable validation of the alignment+ *  @see  vrna_file_msa_read(), vrna_file_msa_read_record()+ */+#define VRNA_FILE_FORMAT_MSA_NOCHECK      4096U++/**+ *  @brief Return flag of vrna_file_msa_detect_format() to indicate unknown or malformatted alignment+ *  @see vrna_file_msa_detect_format()+ */+#define VRNA_FILE_FORMAT_MSA_UNKNOWN      8192U++/**+ *  @brief Read a multiple sequence alignment from file+ *+ *  This function reads the (first) multiple sequence alignment from+ *  an input file. The read alignment is split into the sequence id/name+ *  part and the actual sequence information and stored in memory as+ *  arrays of ids/names and sequences. If the alignment file format+ *  allows for additional information, such as an ID of the entire alignment+ *  or consensus structure information, this data is retrieved as well+ *  and made available. The @p options parameter allows to specify the+ *  set of alignment file formats that should be used to retrieve the data.+ *  If 0 is passed as option, the list of alignment file formats defaults to+ *  #VRNA_FILE_FORMAT_MSA_DEFAULT.+ *+ *  Currently, the list of parsable multiple sequence alignment file formats+ *  consists of:+ *  - @ref msa-formats-clustal+ *  - @ref msa-formats-stockholm+ *  - @ref msa-formats-fasta+ *  - @ref msa-formats-maf+ *  .+ *+ *  @note After successfully reading an alignment, this function performs+ *        a validation of the data that includes uniqueness of the sequence+ *        identifiers, and equal sequence lengths. This check can be+ *        deactivated by passing #VRNA_FILE_FORMAT_MSA_NOCHECK in the+ *        @p options parameter.+ *+ *  @see  vrna_file_msa_read_record(), #VRNA_FILE_FORMAT_MSA_CLUSTAL,+ *        #VRNA_FILE_FORMAT_MSA_STOCKHOLM, #VRNA_FILE_FORMAT_MSA_FASTA,+ *        #VRNA_FILE_FORMAT_MSA_MAF, #VRNA_FILE_FORMAT_MSA_DEFAULT,+ *        #VRNA_FILE_FORMAT_MSA_NOCHECK+ *+ *  @param  filename    The name of input file that contains the alignment+ *  @param  names       An address to the pointer where sequence identifiers+ *                      should be written to+ *  @param  aln         An address to the pointer where aligned sequences should+ *                      be written to+ *  @param  id          An address to the pointer where the alignment ID should+ *                      be written to (Maybe NULL)+ *  @param  structure   An address to the pointer where consensus structure+ *                      information should be written to (Maybe NULL)+ *  @param  options     Options to manipulate the behavior of this function+ *  @return             The number of sequences in the alignment, or -1 if+ *                      no alignment record could be found+ */+int+vrna_file_msa_read( const char *filename,+                    char ***names,+                    char ***aln,+                    char  **id,+                    char  **structure,+                    unsigned int options);++/**+ *  @brief Read a multiple sequence alignment from file handle+ *+ *  Similar to vrna_file_msa_read(), this function reads a multiple+ *  sequence alignment from an input file handle. Since using a file+ *  handle, this function is not limited to the first alignment record,+ *  but allows for looping over all alignments within the input.+ *+ *  The read alignment is split into the sequence id/name+ *  part and the actual sequence information and stored in memory as+ *  arrays of ids/names and sequences. If the alignment file format+ *  allows for additional information, such as an ID of the entire alignment+ *  or consensus structure information, this data is retrieved as well+ *  and made available. The @p options parameter allows to specify the+ *  alignment file format used to retrieve the data. A single format+ *  must be specified here, see vrna_file_msa_detect_format() for helping+ *  to determine the correct MSA file format.+ *+ *  Currently, the list of parsable multiple sequence alignment file formats+ *  consists of:+ *  - @ref msa-formats-clustal+ *  - @ref msa-formats-stockholm+ *  - @ref msa-formats-fasta+ *  - @ref msa-formats-maf+ *  .+ *+ *  @note After successfully reading an alignment, this function performs+ *        a validation of the data that includes uniqueness of the sequence+ *        identifiers, and equal sequence lengths. This check can be+ *        deactivated by passing #VRNA_FILE_FORMAT_MSA_NOCHECK in the+ *        @p options parameter.+ *+ *  @see  vrna_file_msa_read(), vrna_file_msa_detect_format(),+ *        #VRNA_FILE_FORMAT_MSA_CLUSTAL, #VRNA_FILE_FORMAT_MSA_STOCKHOLM,+ *        #VRNA_FILE_FORMAT_MSA_FASTA, #VRNA_FILE_FORMAT_MSA_MAF,+ *        #VRNA_FILE_FORMAT_MSA_DEFAULT, #VRNA_FILE_FORMAT_MSA_NOCHECK+ *+ *  @param  fp          The file pointer the data will be retrieved from+ *  @param  names       An address to the pointer where sequence identifiers+ *                      should be written to+ *  @param  aln         An address to the pointer where aligned sequences should+ *                      be written to+ *  @param  id          An address to the pointer where the alignment ID should+ *                      be written to (Maybe NULL)+ *  @param  structure   An address to the pointer where consensus structure+ *                      information should be written to (Maybe NULL)+ *  @param  options     Options to manipulate the behavior of this function+ *  @return             The number of sequences in the alignment, or -1 if+ *                      no alignment record could be found+ */+int+vrna_file_msa_read_record(FILE *fp,+                          char ***names,+                          char ***aln,+                          char  **id,+                          char  **structure,+                          unsigned int options);++/**+ *  @brief Detect the format of a multiple sequence alignment file+ *+ *  This function attempts to determine the format of a file that+ *  supposedly contains a multiple sequence alignment (MSA). This is+ *  useful in cases where a MSA file contains more than a single record+ *  and therefore vrna_file_msa_read() can not be applied, since+ *  it only retrieves the first.+ *  Here, one can try to guess the correct file format using this+ *  function and then loop over the file, record by record using one+ *  of the low-level record retrieval functions for the corresponding+ *  MSA file format.+ *+ *  @note This function parses the entire first record within the+ *        specified file. As a result, it returns #VRNA_FILE_FORMAT_MSA_UNKNOWN+ *        not only if it can't detect the file's format, but also+ *        in cases where the file doesn't contain sequences!+ *+ *  @see  vrna_file_msa_read(), vrna_file_stockholm_read_record(),+ *        vrna_file_clustal_read_record(), vrna_file_fasta_read_record()+ *+ *  @param  filename  The name of input file that contains the alignment+ *  @param  options   Options to manipulate the behavior of this function+ *  @return           The MSA file format, or #VRNA_FILE_FORMAT_MSA_UNKNOWN+ */+unsigned int+vrna_file_msa_detect_format(const char *filename,+                            unsigned int options);++/**+ * @}+ */++#endif
+ C/ViennaRNA/file_utils.c view
@@ -0,0 +1,217 @@+/*+                               file_utils.c++                 c  Ronny Lorenz+                 Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <time.h>+#include <string.h>+#include <sys/types.h>+#include <sys/stat.h>+#include <stdint.h>+#include <stdarg.h>+#include <errno.h>+#include <libgen.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/file_utils.h"++#define PRIVATE  static+#define PUBLIC++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+#ifdef _WIN32+#ifdef __MINGW32__+#include <direct.h>+#endif+#define DIRSEPC '\\'+#define DIRSEPS "\\"+#else+#define DIRSEPC '/'+#define DIRSEPS "/"+#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE int is_absolute_path(const char *p);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC void+vrna_file_copy(FILE *from, FILE *to){++  int c;++  while ((c = getc(from)) != EOF) (void)putc(c, to);+}+++PUBLIC char *+vrna_read_line(FILE *fp){ /* reads lines of arbitrary length from fp */++  char s[512], *line, *cp;+  int len=0, size=0, l;+  line=NULL;+  do {+    if (fgets(s, 512, fp)==NULL) break;+    cp = strchr(s, '\n');+    if (cp != NULL) *cp = '\0';+    l = len + (int)strlen(s);+    if (l+1>size) {+      size = (int)((l+1)*1.2);+      line = (char *) vrna_realloc(line, size*sizeof(char));+    }+    strcat(line+len, s);+    len=l;+  } while(cp==NULL);++  return line;+}+++PUBLIC int+vrna_mkdir_p(const char *path){+  struct stat sb;+  char *slash, *ptr;+  int done = 0;++  if(!is_absolute_path(path))+    ptr = vrna_strdup_printf(".%c%s", DIRSEPC, path);+  else+    ptr = strdup(path);++  slash = ptr;++  while (!done) {+    slash += strspn(slash, DIRSEPS);+    slash += strcspn(slash, DIRSEPS);++    done = (*slash == '\0');+    *slash = '\0';++    if (stat(ptr, &sb)) {+#ifdef _WIN32+      if (errno != ENOENT || (_mkdir(ptr) &&+          errno != EEXIST)) {+#else+      if (errno != ENOENT || (mkdir(ptr, 0777) &&+          errno != EEXIST)) {+#endif+        vrna_message_warning("Can't create directory %s", ptr);+        free(ptr);+        return -1;+      }+    } else if (!S_ISDIR(sb.st_mode)) {+      vrna_message_warning("File exists but is not a directory %s: %s", ptr, strerror(ENOTDIR));+      free(ptr);+      return -1;+    }++    *slash = DIRSEPC;+  }++  free(ptr);+  return 0;+}+++PUBLIC char *+vrna_basename(const char *path){++  char  *name, *p, *ptr;+  int   pos;++  name = NULL;++  if(path){+    ptr = strrchr(path, DIRSEPC);++    if(ptr && (*(ptr + 1) != '\0'))+      name = strdup(ptr + 1);+    else if(!ptr)+      name = strdup(path);+  }++  return name;+}+++PUBLIC char *+vrna_dirname(const char *path){++  char  *name, *p, *ptr;+  int   pos;++  name = NULL;++  if(path){+    if(!is_absolute_path(path))+      ptr = vrna_strdup_printf(".%c%s", DIRSEPC, path);+    else+      ptr = strdup(path);++    pos = (int)strlen(ptr);+    p   = ptr + pos;++    do{ /* remove part after last separator */+      *p = '\0';+    } while((--p > ptr) && (*p != DIRSEPC));++    if(p > ptr)+      name = ptr;+  }++  return name;+}+++#ifdef _WIN32+PRIVATE int+is_drive_char(const char c){++  if((c >= 'a' && c <= 'z') || (c >= 'A' && c <= 'Z'))+    return 1;+  return 0;+}+#endif+++PRIVATE int+is_absolute_path(const char *p){++  if(*p == DIRSEPC)+    return 1;+#ifdef _WIN32+  if(is_drive_char((const char)*p) && (strlen(p) > 3))+    if((*(p + 1) == ':') && ((*(p + 2) == '\\') || (*(p + 2) == '/')))+      return 1;+#endif+  return 0;+}
+ C/ViennaRNA/file_utils.h view
@@ -0,0 +1,54 @@+#ifndef VIENNA_RNA_PACKAGE_FILE_UTILS_H+#define VIENNA_RNA_PACKAGE_FILE_UTILS_H++/**+ *  @file     file_utils.h+ *  @ingroup  file_utils+ *  @brief    Several utilities for file handling+ */++/**+ *  @addtogroup file_utils+ *  @brief      Functions dealing with file formats for RNA sequences, structures, and alignments+ *+ *  @{+ *  @ingroup  file_utils+ */++/**+ *  @brief Inefficient `cp'+ */+void vrna_file_copy(FILE *from, FILE *to);++/**+ *  @brief Read a line of arbitrary length from a stream+ *+ *  Returns a pointer to the resulting string. The necessary memory is+ *  allocated and should be released using @e free() when the string is+ *  no longer needed.+ *+ *  @param  fp  A file pointer to the stream where the function should read from+ *  @return     A pointer to the resulting string+ */+char  *vrna_read_line(FILE *fp);++/**+ *  @brief  Recursivly create a directory tree+ */+int vrna_mkdir_p(const char *path);++/**+ *  @brief  Extract the filename from a file path+ */+char *vrna_basename(const char *path);++/**+ *  @brief  Extract the directory part of a file path+ */+char *vrna_dirname(const char *path);++/**+ *  @}+ */++#endif
+ C/ViennaRNA/findpath.c view
@@ -0,0 +1,557 @@+/* gcc -fopenmp -g3 -DTEST_FINDPATH findpath.c -o FINDpath -lRNA -lm -I ../H/ -L ./ */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/findpath.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/model.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/cofold.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/structure_utils.h"++#ifdef _OPENMP+#include <omp.h>+#endif++#define LOOP_EN++/**+ *  @brief+ */+typedef struct move {+  int i;  /* i,j>0 insert; i,j<0 delete */+  int j;+  int when;  /* 0 if still available, else resulting distance from start */+  int E;+} move_t;++/**+ *  @brief+ */+typedef struct intermediate {+  short *pt;      /**<  @brief  pair table */+  int Sen;        /**<  @brief  saddle energy so far */+  int curr_en;    /**<  @brief  current energy */+  move_t *moves;  /**<  @brief  remaining moves to target */+} intermediate_t;++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE int         BP_dist;+PRIVATE move_t      *path=NULL;+PRIVATE int         path_fwd; /* 1: struc1->struc2, else struc2 -> struc1 */++PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;++#ifdef _OPENMP++/* NOTE: all variables are assumed to be uninitialized if they are declared as threadprivate+*/+#pragma omp threadprivate(BP_dist, path, path_fwd, backward_compat_compound)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE move_t  *copy_moves(move_t *mvs);+PRIVATE int     compare_ptable(const void *A, const void *B);+PRIVATE int     compare_energy(const void *A, const void *B);+PRIVATE int     compare_moves_when(const void *A, const void *B);+PRIVATE void    free_intermediate(intermediate_t *i);++#ifdef TEST_FINDPATH++/* TEST_FINDPATH, COFOLD */+PRIVATE void  usage(void);++#endif++PRIVATE int     find_path_once(vrna_fold_compound_t *vc, const char *struc1, const char *struc2, int maxE, int maxl);+PRIVATE int     try_moves(vrna_fold_compound_t *vc, intermediate_t c, int maxE, intermediate_t *next, int dist);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC void free_path(vrna_path_t *path){+  vrna_path_t *tmp = path;+  if(tmp){+    while(tmp->s){ free(tmp->s); tmp++;}+    free(path);+  }+}++PUBLIC int+find_saddle(const char *seq,+            const char *struc1,+            const char *struc2,+            int max){++  int                 maxE;+  char                *sequence;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  vc = NULL;+  set_model_details(&md);++  if(backward_compat_compound){+    if(!strcmp(seq, backward_compat_compound->sequence)){ /* check if sequence is the same as before */+      md.window_size = backward_compat_compound->length;+      if(!memcmp(&md, &(backward_compat_compound->params->model_details), sizeof(vrna_md_t))){ /* check if model_details are the same as before */+        vc = backward_compat_compound; /* re-use previous vrna_fold_compound_t */+      }+    }+  }++  if(!vc){+    vrna_fold_compound_free(backward_compat_compound);++    sequence = vrna_cut_point_insert(seq, cut_point);++    backward_compat_compound = vc = vrna_fold_compound(sequence, &md, VRNA_OPTION_EVAL_ONLY);++    free(sequence);+  }++  maxE = vrna_path_findpath_saddle(vc, struc1, struc2, max);++  return maxE;+}++PUBLIC int+vrna_path_findpath_saddle( vrna_fold_compound_t *vc,+                  const char *struc1,+                  const char *struc2,+                  int max) {++  int         maxl, maxE;+  const char  *tmp;+  move_t      *bestpath=NULL;+  int         dir;++  path_fwd  = 0;+  maxE      = INT_MAX - 1;++  maxl = 1;+  do {+    int saddleE;+    path_fwd = !path_fwd;+    if (maxl>max) maxl=max;+    if(path) free(path);+    saddleE  = find_path_once(vc, struc1, struc2, maxE, maxl);+    if (saddleE<maxE) {+      maxE = saddleE;+      if (bestpath) free(bestpath);+      bestpath = path;+      path = NULL;+      dir = path_fwd;+    } else{+      free(path);path=NULL;+    }+    tmp=struc1;+    struc1=struc2;+    struc2=tmp;+    maxl *=2;+  } while (maxl<2*max);++  /* (re)set some globals */+  path=bestpath;+  path_fwd = dir;++  return maxE;+}++PUBLIC vrna_path_t *+get_path( const char *seq,+          const char *s1,+          const char* s2,+          int maxkeep){++  vrna_path_t              *route    = NULL;+  char                *sequence = NULL;+  vrna_fold_compound_t  *vc       = NULL;+  vrna_md_t           md;++  set_model_details(&md);++  if(backward_compat_compound){+    if(!strcmp(seq, backward_compat_compound->sequence)){ /* check if sequence is the same as before */+      if(!memcmp(&md, &(backward_compat_compound->params->model_details), sizeof(vrna_md_t))){ /* check if model_details are the same as before */+        vc = backward_compat_compound; /* re-use previous vrna_fold_compound_t */+      }+    }+  }++  if(!vc){+    vrna_fold_compound_free(backward_compat_compound);++    sequence = vrna_cut_point_insert(seq, cut_point);++    backward_compat_compound = vc = vrna_fold_compound(sequence, &md, VRNA_OPTION_EVAL_ONLY);++    free(sequence);+  }++  route = vrna_path_findpath(vc, s1, s2, maxkeep);++  return (route);+}++PUBLIC vrna_path_t *+vrna_path_findpath(vrna_fold_compound_t *vc,+              const char *s1,+              const char* s2,+              int maxkeep){++  int E, d;+  vrna_path_t *route=NULL;++  E = vrna_path_findpath_saddle(vc, s1, s2, maxkeep);++  route = (vrna_path_t *)vrna_alloc((BP_dist+2)*sizeof(vrna_path_t));++  qsort(path, BP_dist, sizeof(move_t), compare_moves_when);++  if (path_fwd) {+    /* memorize start of path */+    route[0].s  = strdup(s1);+    route[0].en = vrna_eval_structure(vc, s1);++    for (d=0; d<BP_dist; d++) {+      int i,j;+      route[d+1].s = strdup(route[d].s);+      i = path[d].i; j=path[d].j;+      if (i<0) { /* delete */+        route[d+1].s[(-i)-1] = route[d+1].s[(-j)-1] = '.';+      } else {+        route[d+1].s[i-1] = '('; route[d+1].s[j-1] = ')';+      }+      route[d+1].en = path[d].E/100.0;+    }+  }+  else {+    /* memorize start of path */++    route[BP_dist].s  = strdup(s2);+    route[BP_dist].en = vrna_eval_structure(vc, s2);++    for (d=0; d<BP_dist; d++) {+      int i,j;+      route[BP_dist-d-1].s = strdup(route[BP_dist-d].s);+      i = path[d].i;+      j = path[d].j;+      if (i<0) { /* delete */+        route[BP_dist-d-1].s[(-i)-1] = route[BP_dist-d-1].s[(-j)-1] = '.';+      } else {+        route[BP_dist-d-1].s[i-1] = '('; route[BP_dist-d-1].s[j-1] = ')';+      }+      route[BP_dist-d-1].en = path[d].E/100.0;+    }+  }++#if _DEBUG_FINDPATH_+  fprintf(stderr, "\n%s\n%s\n%s\n\n", seq, s1, s2);+  for (d=0; d<=BP_dist; d++)+    fprintf(stderr, "%s %6.2f\n", route[d].s, route[d].en);+  fprintf(stderr, "%d\n", *num_entry);+#endif++  free(path);path=NULL;+  return (route);+}++PRIVATE int+try_moves(vrna_fold_compound_t *vc,+          intermediate_t c,+          int maxE,+          intermediate_t *next,+          int dist){++  int *loopidx, len, num_next=0, en, oldE;+  move_t *mv;+  short *pt;++  len = c.pt[0];+  loopidx = vrna_loopidx_from_ptable(c.pt);+  oldE = c.Sen;+  for (mv=c.moves; mv->i!=0; mv++) {+    int i,j;+    if (mv->when>0) continue;+    i = mv->i; j = mv->j;+    pt = (short *) vrna_alloc(sizeof(short)*(len+1));+    memcpy(pt, c.pt,(len+1)*sizeof(short));+    if (j<0) { /*it's a delete move */+      pt[-i]=0;+      pt[-j]=0;+    } else { /* insert move */+      if ((loopidx[i] == loopidx[j]) && /* i and j belong to same loop */+          (pt[i] == 0) && (pt[j]==0)     /* ... and are unpaired */+          ) {+        pt[i]=j;+        pt[j]=i;+      } else {+        free(pt);+        continue; /* llegal move, try next; */+      }+    }+#ifdef LOOP_EN+    en = c.curr_en + vrna_eval_move_pt(vc, c.pt, i, j);+#else+    en = vrna_eval_structure_pt(vc, pt);+#endif+    if (en<maxE) {+      next[num_next].Sen = (en>oldE)?en:oldE;+      next[num_next].curr_en = en;+      next[num_next].pt = pt;+      mv->when=dist;+      mv->E = en;+      next[num_next++].moves = copy_moves(c.moves);+      mv->when=0;+    }+    else free(pt);+  }+  free(loopidx);+  return num_next;+}++PRIVATE int find_path_once(vrna_fold_compound_t *vc, const char *struc1, const char *struc2, int maxE, int maxl) {+  short *pt1, *pt2;+  move_t *mlist;+  int i, len, d, dist=0, result;+  intermediate_t *current, *next;++  pt1 = vrna_ptable(struc1);+  pt2 = vrna_ptable(struc2);+  len = (int) strlen(struc1);++  mlist = (move_t *) vrna_alloc(sizeof(move_t)*len); /* bp_dist < n */++  for (i=1; i<=len; i++) {+    if (pt1[i] != pt2[i]) {+      if (i<pt1[i]) { /* need to delete this pair */+        mlist[dist].i = -i;+        mlist[dist].j = -pt1[i];+        mlist[dist++].when = 0;+      }+      if (i<pt2[i]) { /* need to insert this pair */+        mlist[dist].i = i;+        mlist[dist].j = pt2[i];+        mlist[dist++].when = 0;+      }+    }+  }+  free(pt2);+  BP_dist = dist;+  current = (intermediate_t *) vrna_alloc(sizeof(intermediate_t)*(maxl+1));+  current[0].pt = pt1;+  current[0].Sen = current[0].curr_en = vrna_eval_structure_pt(vc, pt1);+  current[0].moves = mlist;+  next = (intermediate_t *) vrna_alloc(sizeof(intermediate_t)*(dist*maxl+1));++  for (d=1; d<=dist; d++) { /* go through the distance classes */+    int c, u, num_next=0;+    intermediate_t *cc;++    for (c=0; current[c].pt != NULL; c++) {+      num_next += try_moves(vc, current[c], maxE, next+num_next, d);+    }+    if (num_next==0) {+      for (cc=current; cc->pt != NULL; cc++) free_intermediate(cc);+      current[0].Sen=INT_MAX;+      break;+    }+    /* remove duplicates via sort|uniq+       if this becomes a bottleneck we can use a hash instead */+    qsort(next, num_next, sizeof(intermediate_t),compare_ptable);+    for (u=0,c=1; c<num_next; c++) {+      if (memcmp(next[u].pt,next[c].pt,sizeof(short)*len)!=0) {+        next[++u] = next[c];+      } else {+        free_intermediate(next+c);+      }+    }+    num_next = u+1;+    qsort(next, num_next, sizeof(intermediate_t),compare_energy);+    /* free the old stuff */+    for (cc=current; cc->pt != NULL; cc++) free_intermediate(cc);+    for (u=0; u<maxl && u<num_next; u++) {+      current[u] = next[u];+    }+    for (; u<num_next; u++)+      free_intermediate(next+u);+    num_next=0;+  }+  free(next);+  path = current[0].moves;+  result = current[0].Sen;+  free(current[0].pt); free(current);+  return(result);+}++PRIVATE void free_intermediate(intermediate_t *i) {+   free(i->pt);+   free(i->moves);+   i->pt = NULL;+   i->moves = NULL;+   i->Sen = INT_MAX;+ }++PRIVATE int compare_ptable(const void *A, const void *B) {+  intermediate_t *a, *b;+  int c;+  a = (intermediate_t *) A;+  b = (intermediate_t *) B;++  c = memcmp(a->pt, b->pt, a->pt[0]*sizeof(short));+  if (c!=0) return c;+  if ((a->Sen - b->Sen) != 0) return (a->Sen - b->Sen);+  return (a->curr_en - b->curr_en);+}++PRIVATE int compare_energy(const void *A, const void *B) {+  intermediate_t *a, *b;+  a = (intermediate_t *) A;+  b = (intermediate_t *) B;++  if ((a->Sen - b->Sen) != 0) return (a->Sen - b->Sen);+  return (a->curr_en - b->curr_en);+}++PRIVATE int compare_moves_when(const void *A, const void *B) {+  move_t *a, *b;+  a = (move_t *) A;+  b = (move_t *) B;++  return(a->when - b->when);+}++PRIVATE move_t* copy_moves(move_t *mvs) {+  move_t *new;+  new = (move_t *) vrna_alloc(sizeof(move_t)*(BP_dist+1));+  memcpy(new,mvs,sizeof(move_t)*(BP_dist+1));+  return new;+}++#ifdef TEST_FINDPATH++PUBLIC void print_path(const char *seq, const char *struc) {+  int d;+  char *s;+  s = strdup(struc);+  if (cut_point == -1)+    printf("%s\n%s\n", seq, s);+    /* printf("%s\n%s %6.2f\n", seq, s, vrna_eval_structure_simple(seq,s)); */+  else {+    char *pstruct, *pseq;+    pstruct = vrna_cut_point_insert(s, cut_point);+    pseq = vrna_cut_point_insert(seq, cut_point);+    printf("%s\n%s\n", pseq, pstruct);+    /* printf("%s\n%s %6.2f\n", pseq, pstruct, vrna_eval_structure_simple(seq,s)); */+    free(pstruct);+    free(pseq);+  }+  qsort(path, BP_dist, sizeof(move_t), compare_moves_when);+  for (d=0; d<BP_dist; d++) {+    int i,j;+    i = path[d].i; j=path[d].j;+    if (i<0) { /* delete */+      s[(-i)-1] = s[(-j)-1] = '.';+    } else {+      s[i-1] = '('; s[j-1] = ')';+    }+    /* printf("%s %6.2f - %6.2f\n", s, vrna_eval_structure_simple(seq,s), path[d].E/100.0); */+  }+  free(s);+}++int main(int argc, char *argv[]) {+  char *line, *seq, *s1, *s2;+  int E, maxkeep=1000;+  int verbose=0, i;+  vrna_path_t *route, *r;++  for (i=1; i<argc; i++) {+    switch ( argv[i][1] ) {+      case 'm': if (strcmp(argv[i],"-m")==0)+                  sscanf(argv[++i], "%d", &maxkeep);+                break;+      case 'v': verbose = !strcmp(argv[i],"-v");+                break;+      case 'd': if (strcmp(argv[i],"-d")==0){+                  sscanf(argv[++i], "%d", &dangles);+                  md.dangles = dangles;+                }+                break;+      default: usage();+    }+  }++  cut_point = -1;+  line = vrna_read_line(stdin);+  seq = vrna_cut_point_remove(line, &cut_point);+  free(line);   +  line = vrna_read_line(stdin);+  s1 = vrna_cut_point_remove(line, &cut_point);+  free(line);+  line = vrna_read_line(stdin);+  s2 = vrna_cut_point_remove(line, &cut_point);+  free(line);++  E = find_saddle(seq, s1, s2, maxkeep);+  printf("saddle_energy = %6.2f\n", E/100.);+  if (verbose) {+      if (path_fwd)+          print_path(seq,s1);+      else+          print_path(seq,s2);+      free(path);+      path = NULL;+      route = get_path(seq, s1, s2, maxkeep);+      for (r=route; r->s; r++) {+          if (cut_point == -1) {+              printf("%s %6.2f\n", r->s, r->en);+              /* printf("%s %6.2f - %6.2f\n", r->s, vrna_eval_structure_simple(seq,r->s), r->en); */+          } else {+              char *pstruct;+              pstruct = vrna_cut_point_insert(r->s, cut_point);+              printf("%s %6.2f\n", pstruct, r->en);+              /* printf("%s %6.2f - %6.2f\n", pstruct, vrna_eval_structure_simple(seq,r->s), r->en); */+              free(pstruct);+          }+          free(r->s);+      }+      free(route);+  }+  free(seq); free(s1); free(s2);+  return(EXIT_SUCCESS);+}++static void usage(void){+  vrna_message_error("usage: findpath.c  [-m depth] [-d[0|1|2]] [-v]");+}++#endif
+ C/ViennaRNA/findpath.h view
@@ -0,0 +1,155 @@+#ifndef VIENNA_RNA_PACKAGE_FIND_PATH_H+#define VIENNA_RNA_PACKAGE_FIND_PATH_H++/**+ *  @file     findpath.h+ *  @ingroup  paths+ *  @brief    A breadth-first search heuristic for optimal direct folding paths+ */++/**+ *  @addtogroup   direct_paths+ *  @brief Heuristics to explore direct, optimal (re-)folding paths between two secondary structures+ *+ *  @{+ *  @ingroup  direct_paths+ */++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/* below are several convenience typedef's we use throughout the ViennaRNA library */++/**+ *  @brief Typename for the refolding path data structure #vrna_path_s+ */+typedef struct vrna_path_s  vrna_path_t;+++#ifdef VRNA_BACKWARD_COMPAT++/* the following typedefs are for backward compatibility only */++/**+ *  @brief Old typename of #vrna_path_s+ *  @deprecated Use #vrna_path_t instead!+*/+typedef struct vrna_path_s path_t;++#endif++#include <ViennaRNA/data_structures.h>++/**+ *  @brief  An element of a refolding path list+ *  @see    vrna_path_findpath()+ */+struct vrna_path_s {+  double en;  /**<  @brief  Free energy of current structure */+  char *s;    /**<  @brief  Secondary structure in dot-bracket notation */+};+++/**+ *  \brief Find energy of a saddle point between 2 structures+ *  (search only direct path)+ *+ *  This function uses an inplementation of the @em findpath algorithm @cite flamm:2001+ *  for near-optimal direct refolding path prediction.+ *+ *  Model details, and energy parameters are used as provided via the parameter 'vc'.+ *  The #vrna_fold_compound_t does not require memory for any DP matrices,+ *  but requires all most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @see vrna_fold_compound(), #vrna_fold_compound_t, vrna_path_findpath()+ *+ *  @param vc     The #vrna_fold_compound_t with precomputed sequence encoding and model details+ *  @param struc1 The start structure in dot-brakcet notation+ *  @param struc2 The target structure in dot-bracket notation+ *  @param max    A number specifying how many strutures are being kept at each step during the search+ *  @returns      The saddle energy in 10cal/mol+ */+int vrna_path_findpath_saddle(vrna_fold_compound_t *vc,+                              const char *struc1,+                              const char *struc2,+                              int max);++/**+ *  @brief Find refolding path between 2 structures+ *  (search only direct path)+ *+ *  This function uses an inplementation of the @em findpath algorithm @cite flamm:2001+ *  for near-optimal direct refolding path prediction.+ *+ *  Model details, and energy parameters are used as provided via the parameter 'vc'.+ *  The #vrna_fold_compound_t does not require memory for any DP matrices,+ *  but requires all most basic init values as one would get from a call like this:+ *  @code{.c}+ vc = vrna_fold_compound(sequence, NULL, VRNA_OPTION_EVAL_ONLY);+    @endcode+ *+ *  @see vrna_fold_compound(), #vrna_fold_compound_t, vrna_path_findpath_saddle()+ *+ *  @param vc       The #vrna_fold_compound_t with precomputed sequence encoding and model details+ *  @param s1       The start structure in dot-brakcet notation+ *  @param s2       The target structure in dot-bracket notation+ *  @param maxkeep  A number specifying how many strutures are being kept at each step during the search+ *  @returns        The saddle energy in 10cal/mol+ */+vrna_path_t *vrna_path_findpath(vrna_fold_compound_t *vc,+                                const char *s1,+                                const char* s2,+                                int maxkeep);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  \brief Find energy of a saddle point between 2 structures+ *  (search only direct path)+ *+ *  \param seq RNA sequence+ *  \param struc1 A pointer to the character array where the first+ *         secondary structure in dot-bracket notation will be written to+ *  \param struc2 A pointer to the character array where the second+ *         secondary structure in dot-bracket notation will be written to+ *  \param max integer how many strutures are being kept during the search+ *  \returns the saddle energy in 10cal/mol+ */+int find_saddle(const char *seq,+                const char *struc1,+                const char *struc2,+                int max);+/**+ *  \brief Free memory allocated by get_path() function+ *+ *  \param path pointer to memory to be freed+ */+void    free_path(vrna_path_t *path);++/**+ *  \brief Find refolding path between 2 structures+ *  (search only direct path)+ *+ *  \param seq RNA sequence+ *  \param s1 A pointer to the character array where the first+ *         secondary structure in dot-bracket notation will be written to+ *  \param s2 A pointer to the character array where the second+ *         secondary structure in dot-bracket notation will be written to+ *  \param maxkeep integer how many strutures are being kept during the search+ *  \returns direct refolding path between two structures+ */+vrna_path_t *get_path(const char *seq,+                      const char *s1,+                      const char* s2,+                      int maxkeep);++#endif++/**+ *  @}+ */++#endif
+ C/ViennaRNA/fold.c view
@@ -0,0 +1,569 @@+/** \file **/++/*+                  minimum free energy+                  RNA secondary structure prediction++                  c Ivo Hofacker, Chrisoph Flamm+                  original implementation by+                  Walter Fontana+                  g-quadruplex support and threadsafety+                  by Ronny Lorenz++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/fold.h"++#ifdef  VRNA_BACKWARD_COMPAT++#ifdef _OPENMP+#include <omp.h>+#endif++#endif++#define MAXSECTORS        500     /* dimension for a backtrack array */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++/* some backward compatibility stuff */+PRIVATE int                 backward_compat           = 0;+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++/* wrappers for old API compatibility */+PRIVATE float wrap_fold( const char *string, char *structure, vrna_param_t *parameters, int is_constrained, int is_circular);+PRIVATE void  wrap_array_export(int **f5_p, int **c_p, int **fML_p, int **fM1_p, int **indx_p, char **ptype_p);+PRIVATE void  wrap_array_export_circ( int *Fc_p, int *FcH_p, int *FcI_p, int *FcM_p, int **fM2_p);++#endif++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_fold(const char *string,+          char *structure){++  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  vc  = vrna_fold_compound(string, &md, 0);+  mfe = vrna_mfe(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;+}++PUBLIC float+vrna_circfold(const char *string,+              char *structure){++  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.circ = 1;+  vc      = vrna_fold_compound(string, &md, 0);+  mfe     = vrna_mfe(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;++}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++#ifdef  VRNA_BACKWARD_COMPAT++PRIVATE void+wrap_array_export(int **f5_p,+                  int **c_p,+                  int **fML_p,+                  int **fM1_p,+                  int **indx_p,+                  char **ptype_p){++  /* make the DP arrays available to routines such as subopt() */+  if(backward_compat_compound){+    *f5_p     = backward_compat_compound->matrices->f5;+    *c_p      = backward_compat_compound->matrices->c;+    *fML_p    = backward_compat_compound->matrices->fML;+    *fM1_p    = backward_compat_compound->matrices->fM1;+    *indx_p   = backward_compat_compound->jindx;+    *ptype_p  = backward_compat_compound->ptype;+  }+}++PRIVATE void+wrap_array_export_circ( int *Fc_p,+                        int *FcH_p,+                        int *FcI_p,+                        int *FcM_p,+                        int **fM2_p){++  /* make the DP arrays available to routines such as subopt() */+  if(backward_compat_compound){+    *Fc_p   = backward_compat_compound->matrices->Fc;+    *FcH_p  = backward_compat_compound->matrices->FcH;+    *FcI_p  = backward_compat_compound->matrices->FcI;+    *FcM_p  = backward_compat_compound->matrices->FcM;+    *fM2_p  = backward_compat_compound->matrices->fM2;+  }+}++PRIVATE float+wrap_fold( const char *string,+          char *structure,+          vrna_param_t *parameters,+          int is_constrained,+          int is_circular){++  vrna_fold_compound_t  *vc;+  vrna_param_t          *P;+  float                 mfe;++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++  /* we need the parameter structure for hard constraints */+  if(parameters){+    P = vrna_params_copy(parameters);+  } else {+    vrna_md_t md;+    set_model_details(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }+  P->model_details.circ = is_circular;++  vc = vrna_fold_compound(string, &(P->model_details), VRNA_OPTION_DEFAULT);++  if(parameters){ /* replace params if necessary */+    free(vc->params);+    vc->params = P;+  } else {+    free(P);+  }++  /* handle hard constraints in pseudo dot-bracket format if passed via simple interface */+  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound && backward_compat)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;++  /* call mfe() function without backtracking */+  mfe = vrna_mfe(vc, NULL);++  /* backtrack structure */+  if(structure && vc->params->model_details.backtrack){+    char            *ss;+    int             length;+    sect            bt_stack[MAXSECTORS];+    vrna_bp_stack_t *bp;++    length  = vc->length;+    bp      = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4*(1+length/2))); /* add a guess of how many G's may be involved in a G quadruplex */++    vrna_backtrack_from_intervals(vc, bp, bt_stack, 0);++    ss = vrna_db_from_bp_stack(bp, length);+    strncpy(structure, ss, length + 1);+    free(ss);++    if(base_pair)+      free(base_pair);+    base_pair = bp;+  }++  return mfe;+}++PUBLIC void+free_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound = NULL;+    backward_compat          = 0;+  }+}++PUBLIC float+fold_par( const char *string,+          char *structure,+          vrna_param_t *parameters,+          int is_constrained,+          int is_circular){++  return wrap_fold(string, structure, parameters, is_constrained, is_circular);++}++PUBLIC float+fold( const char *string,+      char *structure){++  return wrap_fold(string, structure, NULL, fold_constrained, 0);+}++PUBLIC float+circfold( const char *string,+          char *structure){++  return wrap_fold(string, structure, NULL, fold_constrained, 1);+}++PUBLIC void+initialize_fold(int length){++  /* DO NOTHING */+}++PUBLIC void+update_fold_params(void){++  vrna_md_t           md;++  if(backward_compat_compound && backward_compat){+    set_model_details(&md);+    vrna_params_reset(backward_compat_compound, &md);+  }+}++PUBLIC void+update_fold_params_par(vrna_param_t *parameters){++  vrna_md_t           md;++  if(backward_compat_compound && backward_compat){+    if(parameters)+      vrna_params_subst(backward_compat_compound, parameters);+    else{+      set_model_details(&md);+      vrna_params_reset(backward_compat_compound, &md);+    }+  }+}++PUBLIC void+export_fold_arrays( int **f5_p,+                    int **c_p,+                    int **fML_p,+                    int **fM1_p,+                    int **indx_p,+                    char **ptype_p){++  wrap_array_export(f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);+}++PUBLIC void+export_fold_arrays_par( int **f5_p,+                        int **c_p,+                        int **fML_p,+                        int **fM1_p,+                        int **indx_p,+                        char **ptype_p,+                        vrna_param_t **P_p){++  wrap_array_export(f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);+  if(backward_compat_compound) *P_p  = backward_compat_compound->params;+}++PUBLIC void+export_circfold_arrays( int *Fc_p,+                        int *FcH_p,+                        int *FcI_p,+                        int *FcM_p,+                        int **fM2_p,+                        int **f5_p,+                        int **c_p,+                        int **fML_p,+                        int **fM1_p,+                        int **indx_p,+                        char **ptype_p){++  wrap_array_export(f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);+  wrap_array_export_circ(Fc_p,FcH_p,FcI_p,FcM_p,fM2_p);+}++PUBLIC void+export_circfold_arrays_par( int *Fc_p,+                            int *FcH_p,+                            int *FcI_p,+                            int *FcM_p,+                            int **fM2_p,+                            int **f5_p,+                            int **c_p,+                            int **fML_p,+                            int **fM1_p,+                            int **indx_p,+                            char **ptype_p,+                            vrna_param_t **P_p){++  wrap_array_export(f5_p,c_p,fML_p,fM1_p,indx_p,ptype_p);+  wrap_array_export_circ(Fc_p,FcH_p,FcI_p,FcM_p,fM2_p);+  if(backward_compat_compound) *P_p  = backward_compat_compound->params;+}++PUBLIC char *+backtrack_fold_from_pair( char *sequence,+                          int i,+                          int j){++  char          *structure  = NULL;+  unsigned int  length      = 0;+  vrna_bp_stack_t         *bp         = NULL;+  sect          bt_stack[MAXSECTORS]; /* stack of partial structures for backtracking */++  if(sequence){+    length = strlen(sequence);+    bp = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (1+length/2));+  } else {+    vrna_message_error("backtrack_fold_from_pair@fold.c: no sequence given");+  }++  bt_stack[1].i  = i;+  bt_stack[1].j  = j;+  bt_stack[1].ml = 2;++  bp[0].i = 0; /* ??? this is set by backtrack anyway... */++  vrna_backtrack_from_intervals(backward_compat_compound, bp, bt_stack, 1);+  structure = vrna_db_from_bp_stack(bp, length);++  /* backward compatibitlity stuff */+  if(base_pair) free(base_pair);+  base_pair = bp;++  return structure;+}++#define STACK_BULGE1      1       /* stacking energies for bulges of size 1 */+#define NEW_NINIO         1       /* new asymetry penalty */++PUBLIC int HairpinE(int size, int type, int si1, int sj1, const char *string) {+  vrna_param_t  *P  = backward_compat_compound->params;+  int energy;++  energy = (size <= 30) ? P->hairpin[size] :+    P->hairpin[30]+(int)(P->lxc*log((size)/30.));++  if (tetra_loop){+    if (size == 4) { /* check for tetraloop bonus */+      char tl[7]={0}, *ts;+      strncpy(tl, string, 6);+      if ((ts=strstr(P->Tetraloops, tl)))+        return (P->Tetraloop_E[(ts - P->Tetraloops)/7]);+    }+    if (size == 6) {+      char tl[9]={0}, *ts;+      strncpy(tl, string, 8);+      if ((ts=strstr(P->Hexaloops, tl)))+        return (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);+    }+    if (size == 3) {+      char tl[6]={0,0,0,0,0,0}, *ts;+      strncpy(tl, string, 5);+      if ((ts=strstr(P->Triloops, tl))) {+        return (P->Triloop_E[(ts - P->Triloops)/6]);+      }+      if (type>2)  /* neither CG nor GC */+        energy += P->TerminalAU; /* penalty for closing AU GU pair IVOO??+                                    sind dass jetzt beaunuesse oder mahlnuesse (vorzeichen?)*/+      return energy;+    }+   }+   energy += P->mismatchH[type][si1][sj1];++  return energy;+}++/*---------------------------------------------------------------------------*/++PUBLIC int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2) {++  vrna_param_t  *P  = backward_compat_compound->params;+  short   *S1 = backward_compat_compound->sequence_encoding;++  /* compute energy of degree 2 loop (stack bulge or interior) */+  int n1, n2, m, energy;+  n1 = p-i-1;+  n2 = j-q-1;++  if (n1>n2) { m=n1; n1=n2; n2=m; } /* so that n2>=n1 */++  if (n2 == 0)+    energy = P->stack[type][type_2];   /* stack */++  else if (n1==0) {                  /* bulge */+    energy = (n2<=MAXLOOP)?P->bulge[n2]:+      (P->bulge[30]+(int)(P->lxc*log(n2/30.)));++#if STACK_BULGE1+    if (n2==1) energy+=P->stack[type][type_2];+#endif+  } else {                           /* interior loop */++    if ((n1+n2==2)&&(james_rule))+      /* special case for loop size 2 */+      energy = P->int11[type][type_2][S1[i+1]][S1[j-1]];+    else {+      energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]):+        (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));++#if NEW_NINIO+      energy += MIN2(MAX_NINIO, (n2-n1)*P->ninio[2]);+#else+      m       = MIN2(4, n1);+      energy += MIN2(MAX_NINIO,((n2-n1)*P->ninio[m]));+#endif+      energy += P->mismatchI[type][S1[i+1]][S1[j-1]]++        P->mismatchI[type_2][S1[q+1]][S1[p-1]];+    }+  }+  return energy;+}++/*--------------------------------------------------------------------------*/++PUBLIC int LoopEnergy(int n1, int n2, int type, int type_2,+                      int si1, int sj1, int sp1, int sq1) {++  vrna_param_t  *P  = backward_compat_compound->params;+  /* compute energy of degree 2 loop (stack bulge or interior) */+  int nl, ns, energy;++  if (n1>n2) { nl=n1; ns=n2;}+  else {nl=n2; ns=n1;}++  if (nl == 0)+    return P->stack[type][type_2];    /* stack */++  if (ns==0) {                       /* bulge */+    energy = (nl<=MAXLOOP)?P->bulge[nl]:+      (P->bulge[30]+(int)(P->lxc*log(nl/30.)));+    if (nl==1) energy += P->stack[type][type_2];+    else {+      if (type>2) energy += P->TerminalAU;+      if (type_2>2) energy += P->TerminalAU;+    }+    return energy;+  }+  else {                             /* interior loop */+    if (ns==1) {+      if (nl==1)                     /* 1x1 loop */+        return P->int11[type][type_2][si1][sj1];+      if (nl==2) {                   /* 2x1 loop */+        if (n1==1)+          energy = P->int21[type][type_2][si1][sq1][sj1];+        else+          energy = P->int21[type_2][type][sq1][si1][sp1];+        return energy;+      }+        else {  /* 1xn loop */+        energy = (nl+1<=MAXLOOP)?(P->internal_loop[nl+1]):+        (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));+        energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);+        energy += P->mismatch1nI[type][si1][sj1]++        P->mismatch1nI[type_2][sq1][sp1];+        return energy;+        }+    }+    else if (ns==2) {+      if(nl==2)      {   /* 2x2 loop */+        return P->int22[type][type_2][si1][sp1][sq1][sj1];}+      else if (nl==3)  { /* 2x3 loop */+        energy = P->internal_loop[5]+P->ninio[2];+        energy += P->mismatch23I[type][si1][sj1]++          P->mismatch23I[type_2][sq1][sp1];+        return energy;+      }++    }+    { /* generic interior loop (no else here!)*/+      energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]):+        (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));++      energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);++      energy += P->mismatchI[type][si1][sj1]++        P->mismatchI[type_2][sq1][sp1];+    }+  }+  return energy;+}++#endif
+ C/ViennaRNA/fold.h view
@@ -0,0 +1,320 @@+#ifndef VIENNA_RNA_PACKAGE_FOLD_H+#define VIENNA_RNA_PACKAGE_FOLD_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/mfe.h>+#include <ViennaRNA/eval.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file fold.h+ *  @ingroup  mfe_fold+ *  @brief MFE calculations for single RNA sequences+ */++/**+ *  @addtogroup mfe_fold_single+ *  @brief This module contains all functions and variables related to the calculation+ *  of global minimum free energy structures for single sequences.+ *+ *  The library provides a fast dynamic programming minimum free energy+ *  folding algorithm as described by "Zuker & Stiegler (1981)" @cite zuker:1981.+ *+ *  @{+ *  @ingroup  mfe_fold_single+ */++/**+ *  @brief Compute Minimum Free Energy (MFE), and a corresponding secondary structure for an RNA sequence+ *+ *  This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for an+ *  RNA sequence using default options. Memory required for dynamic programming (DP) matrices will+ *  be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled+ *  matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_circfold(), vrna_mfe(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequence   RNA sequence+ *  @param structure  A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_fold(const char *sequence,+          char *structure);++/**+ *  @brief Compute Minimum Free Energy (MFE), and a corresponding secondary structure for a circular RNA sequence+ *+ *  This simplified interface to vrna_mfe() computes the MFE and, if required, a secondary structure for a+ *  circular RNA sequence using default options. Memory required for dynamic programming (DP) matrices will+ *  be allocated and free'd on-the-fly. Hence, after return of this function, the recursively filled+ *  matrices are not available any more for any post-processing, e.g. suboptimal backtracking, etc.+ *+ *  Folding of circular RNA sequences is handled as a post-processing step of the forward+ *  recursions. See @cite hofacker:2006 for further details.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_mfe(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_fold(), vrna_mfe(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequence   RNA sequence+ *  @param structure  A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_circfold(const char *sequence,+              char *structure);++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief Compute minimum free energy and an appropriate secondary+ *  structure of an RNA sequence+ *+ *  The first parameter given, the RNA sequence, must be @a uppercase and should only contain+ *  an alphabet @f$\Sigma@f$ that is understood by the RNAlib\n+ *  (e.g. @f$ \Sigma = \{A,U,C,G\} @f$)\n+ *+ *  The second parameter, @a structure, must always point to an allocated+ *  block of memory with a size of at least @f$\mathrm{strlen}(\mathrm{sequence})+1@f$+ *+ *  If the third parameter is NULL, global model detail settings are assumed for the folding+ *  recursions. Otherwise, the provided parameters are used.+ *+ *  The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket+ *  notation is passed through the structure parameter or not. If so, the characters " | x < > " are+ *  recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively.+ *  Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases.+ *+ *  To indicate that the RNA sequence is circular and thus has to be post-processed, set the last+ *  parameter to non-zero+ *+ *  After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation)+ *  that exhibits the minimum of free energy will be written to the memory @a structure is pointing to.+ *  The function returns the minimum of free energy for any fold of the sequence given.+ *+ *  @note OpenMP: Passing NULL to the 'parameters' argument involves access to several global model+ *        detail variables and thus is not to be considered threadsafe+ *+ *  @deprecated use vrna_mfe() instead!+ *+ *  @see vrna_mfe(), fold(), circfold(), #vrna_md_t, set_energy_model(), get_scaled_parameters()+ *+ *  @param sequence       RNA sequence+ *  @param structure      A pointer to the character array where the+ *                        secondary structure in dot-bracket notation will be written to+ *  @param parameters     A data structure containing the pre-scaled energy contributions+ *                        and the model details. (NULL may be passed, see OpenMP notes above)+ *  @param is_constrained Switch to indicate that a structure constraint is passed via the structure argument (0==off)+ *  @param is_circular    Switch to (de-)activate post-processing steps in case RNA sequence is circular (0==off)+ *+ *  @return the minimum free energy (MFE) in kcal/mol+ */+DEPRECATED(float+fold_par( const char *sequence,+          char *structure,+          vrna_param_t *parameters,+          int is_constrained,+          int is_circular));++/**+ *  @brief Compute minimum free energy and an appropriate secondary structure of an RNA sequence+ *+ *  This function essentially does the same thing as fold_par(). However, it takes its model details,+ *  i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs+ *  from the current global settings within the library+ *+ *  @deprecated use vrna_fold(), or vrna_mfe() instead!+ *+ *  @see fold_par(), circfold()+ *+ *  @param sequence RNA sequence+ *  @param structure A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+DEPRECATED(float fold( const char *sequence, char *structure));++/**+ *  @brief Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence+ *+ *  This function essentially does the same thing as fold_par(). However, it takes its model details,+ *  i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs+ *  from the current global settings within the library+ *+ *  @deprecated Use vrna_circfold(), or vrna_mfe() instead!+ *+ *  @see fold_par(), circfold()+ *+ *  @param sequence RNA sequence+ *  @param structure A pointer to the character array where the+ *         secondary structure in dot-bracket notation will be written to+ *  @return the minimum free energy (MFE) in kcal/mol+ */+DEPRECATED(float circfold( const char *sequence, char *structure));+++/**+ *  @brief Free arrays for mfe folding+ *+ *  @deprecated See vrna_fold(), vrna_circfold(), or vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void free_arrays(void));++++/**+ *  @brief Recalculate energy parameters+ *+ *  @deprecated For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!+ *+ */+DEPRECATED(void update_fold_params(void));++/**+ *  @brief Recalculate energy parameters+ *+ *  @deprecated For non-default model settings use the new API with vrna_params_subst() and vrna_mfe() instead!+ *+ */+DEPRECATED(void update_fold_params_par(vrna_param_t *parameters));++/**+ *+ *  @deprecated See vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void+export_fold_arrays( int **f5_p,+                    int **c_p,+                    int **fML_p,+                    int **fM1_p,+                    int **indx_p,+                    char **ptype_p));++/**+ *+ *  @deprecated See vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void+export_fold_arrays_par( int **f5_p,+                        int **c_p,+                        int **fML_p,+                        int **fM1_p,+                        int **indx_p,+                        char **ptype_p,+                        vrna_param_t **P_p));++/**+ *+ *  @deprecated See vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void+export_circfold_arrays( int *Fc_p,+                        int *FcH_p,+                        int *FcI_p,+                        int *FcM_p,+                        int **fM2_p,+                        int **f5_p,+                        int **c_p,+                        int **fML_p,+                        int **fM1_p,+                        int **indx_p,+                        char **ptype_p));++/**+ *+ *  @deprecated See vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void+export_circfold_arrays_par( int *Fc_p,+                            int *FcH_p,+                            int *FcI_p,+                            int *FcM_p,+                            int **fM2_p,+                            int **f5_p,+                            int **c_p,+                            int **fML_p,+                            int **fM1_p,+                            int **indx_p,+                            char **ptype_p,+                            vrna_param_t **P_p));++++/* finally moved the loop energy function declarations to this header...  */+/* BUT: The functions only exist for backward compatibility reasons!      */+/* You better include "loop_energies.h" and call the functions:           */+/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get  */+/* a pointer to the energy parameter data structure as additional argument */++/**+ *  @deprecated {This function is deprecated and will be removed soon.+ *  Use @ref E_IntLoop() instead!}+ */+DEPRECATED(int LoopEnergy(int n1,+                          int n2,+                          int type,+                          int type_2,+                          int si1,+                          int sj1,+                          int sp1,+                          int sq1));++/**+ *  @deprecated {This function is deprecated and will be removed soon.+ *  Use @ref E_Hairpin() instead!}+ */+DEPRECATED(int HairpinE(int size,+                        int type,+                        int si1,+                        int sj1,+                        const char *string));++/**+ *  Allocate arrays for folding\n+ *  @deprecated See vrna_mfe() and #vrna_fold_compound_t for the usage of the new API!+ *+ */+DEPRECATED(void initialize_fold(int length));++/**+ *+ */+DEPRECATED(char *backtrack_fold_from_pair(char *sequence,+                                          int i,+                                          int j));+++#endif++/**+ *  @}+ */++#endif
+ C/ViennaRNA/fold_vars.h view
@@ -0,0 +1,93 @@+#ifndef VIENNA_RNA_PACKAGE_FOLD_VARS_H+#define VIENNA_RNA_PACKAGE_FOLD_VARS_H++#include <ViennaRNA/data_structures.h>+/*  For now, we include model.h by default to provide backwards compatibility+    However, this will most likely change, since fold_vars.h is scheduled to+    vanish from the sources at latest in ViennaRNA Package v3+*/+#include <ViennaRNA/model.h>+++/**+ *  \file fold_vars.h+ *  \brief Here all all declarations of the global variables used throughout RNAlib+ */++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  \brief Global switch to activate/deactivate folding with structure constraints+ */+extern int    fold_constrained;++/**+ *  \brief generate comma seperated output+ */+extern int  csv;++/**+ *  warning this variable will vanish in the future+ *  ribosums will be compiled in instead+ */+extern char *RibosumFile;   ++/**+ *  interior loops of size 2 get energy 0.8Kcal and+ *  no mismatches, default 1+ */+extern int  james_rule;++/**+ *  use logarithmic multiloop energy function+ */+extern int  logML;++/**+ *  \brief Marks the position (starting from 1) of the first+ *  nucleotide of the second molecule within the concatenated sequence.+ * + *  To evaluate the energy of a duplex structure (a structure formed by two+ *  strands), concatenate the to sequences and set it to the+ *  first base of the second strand in the concatenated sequence.+ *  The default value of -1 stands for single molecule folding. The+ *  cut_point variable is also used by vrna_file_PS_rnaplot() and+ *  PS_dot_plot() to mark the chain break in postscript plots.+ */+extern int  cut_point;++/**+ *  \brief Contains a list of base pairs after a call to fold().+ * + *  base_pair[0].i contains the total number of pairs.+ *  \deprecated Do not use this variable anymore!+ */+extern bondT  *base_pair;++/**+ *  \brief A pointer to the base pair probability matrix+ * + *  \deprecated Do not use this variable anymore!+ */+extern FLT_OR_DBL *pr;++/**+ *  \brief index array to move through pr.+ * + *  The probability for base i and j to form a pair is in pr[iindx[i]-j].+ *  \deprecated Do not use this variable anymore!+ */+extern int   *iindx;+++++#endif
+ C/ViennaRNA/gquad.c view
@@ -0,0 +1,1086 @@+/*+  gquad.c++  Ronny Lorenz 2012++  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <string.h>++#include "fold_vars.h"+#include "data_structures.h"+#include "energy_const.h"+#include "utils.h"+#include "aln_util.h"+#include "gquad.h"++#ifndef INLINE+#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif+#endif++/**+ *  Use this macro to loop over each G-quadruplex+ *  delimited by a and b within the subsequence [c,d]+ */+#define FOR_EACH_GQUAD(a, b, c, d)  \+          for((a) = (d) - VRNA_GQUAD_MIN_BOX_SIZE + 1; (a) >= (c); (a)--)\+            for((b) = (a) + VRNA_GQUAD_MIN_BOX_SIZE - 1;\+                (b) <= MIN2((d), (a) + VRNA_GQUAD_MAX_BOX_SIZE - 1);\+                (b)++)++/**+ *  This macro does almost the same as FOR_EACH_GQUAD() but keeps+ *  the 5' delimiter fixed. 'b' is the 3' delimiter of the gquad,+ *  for gquads within subsequence [a,c] that have 5' delimiter 'a'+ */+#define FOR_EACH_GQUAD_AT(a, b, c)  \+          for((b) = (a) + VRNA_GQUAD_MIN_BOX_SIZE - 1;\+              (b) <= MIN2((c), (a) + VRNA_GQUAD_MAX_BOX_SIZE - 1);\+              (b)++)+++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE INLINE+int *+get_g_islands(short *S);++PRIVATE INLINE+int *+get_g_islands_sub(short *S, int i, int j);++/**+ *  IMPORTANT:+ *  If you don't know how to use this function, DONT'T USE IT!+ *+ *  The function pointer this function takes as argument is+ *  used for individual calculations with each g-quadruplex+ *  delimited by [i,j].+ *  The function it points to always receives as first 3 arguments+ *  position i, the stack size L and an array l[3] containing the+ *  individual linker sizes.+ *  The remaining 4 (void *) pointers of the callback function receive+ *  the parameters 'data', 'P', 'aux1' and 'aux2' and thus may be+ *  used to pass whatever data you like to.+ *  As the names of those parameters suggest the convention is that+ *  'data' should be used as a pointer where data is stored into,+ *  e.g the MFE or PF and the 'P' parameter should actually be a+ *  'vrna_param_t *' or 'vrna_exp_param_t *' type.+ *  However, what you actually pass obviously depends on the+ *  function the pointer is pointing to.+ *+ *  Although all of this may look like an overkill, it is found+ *  to be almost as fast as implementing g-quadruplex enumeration+ *  in each individual scenario, i.e. code duplication.+ *  Using this function, however, ensures that all g-quadruplex+ *  enumerations are absolutely identical.+ */+PRIVATE+void+process_gquad_enumeration(int *gg,+                          int i,+                          int j,+                          void (*f)(int, int, int *,+                                    void *, void *, void *, void *),+                          void *data,+                          void *P,+                          void *aux1,+                          void *aux2);++/**+ *  MFE callback for process_gquad_enumeration()+ */+PRIVATE+void+gquad_mfe(int i,+          int L,+          int *l,+          void *data,+          void *P,+          void *NA,+          void *NA2);++PRIVATE+void+gquad_mfe_pos(int i,+              int L,+              int *l,+              void *data,+              void *P,+              void *Lmfe,+              void *lmfe);++PRIVATE+void+gquad_pos_exhaustive( int i,+                      int L,+                      int *l,+                      void *data,+                      void *P,+                      void *Lex,+                      void *lex);++/**+ * Partition function callback for process_gquad_enumeration()+ */+PRIVATE+void+gquad_pf( int i,+          int L,+          int *l,+          void *data,+          void *P,+          void *NA,+          void *NA2);++/**+ * Partition function callback for process_gquad_enumeration()+ * in contrast to gquad_pf() it stores the stack size L and+ * the linker lengths l[3] of the g-quadruplex that dominates+ * the interval [i,j]+ * (FLT_OR_DBL *)data must be 0. on entry+ */+PRIVATE+void+gquad_pf_pos( int i,+              int L,+              int *l,+              void *data,+              void *pf,+              void *Lmax,+              void *lmax);++/**+ * MFE (alifold) callback for process_gquad_enumeration()+ */+PRIVATE+void+gquad_mfe_ali(int i,+              int L,+              int *l,+              void *data,+              void *P,+              void *S,+              void *n_seq);++/**+ * MFE (alifold) callback for process_gquad_enumeration()+ * with seperation of free energy and penalty contribution+ */+PRIVATE+void+gquad_mfe_ali_en( int i,+                  int L,+                  int *l,+                  void *data,+                  void *P,+                  void *S,+                  void *n_seq);++PRIVATE+void+gquad_interact( int i,+                int L,+                int *l,+                void *data,+                void *pf,+                void *index,+                void *NA2);++PRIVATE+void+gquad_count(int i,+            int L,+            int *l,+            void *data,+            void *NA,+            void *NA2,+            void *NA3);++PRIVATE+void+gquad_count_layers( int i,+                    int L,+                    int *l,+                    void *data,+                    void *NA,+                    void *NA2,+                    void *NA3);++/* other useful static functions */++PRIVATE+int+gquad_ali_penalty(int i,+                  int L,+                  int l[3],+                  const short **S,+                  vrna_param_t *P);++PRIVATE int **+create_L_matrix(short *S,+                int start,+                int maxdist,+                int n,+                int **g,+                vrna_param_t *P);++/*+#########################################+# BEGIN OF PUBLIC FUNCTION DEFINITIONS  #+#      (all available in RNAlib)        #+#########################################+*/++/********************************+  Here are the G-quadruplex energy+  contribution functions+*********************************/++PUBLIC int E_gquad( int L,+                    int l[3],+                    vrna_param_t *P){++  int i, c = INF;++  for(i=0;i<3;i++){+    if(l[i] > VRNA_GQUAD_MAX_LINKER_LENGTH) return c;+    if(l[i] < VRNA_GQUAD_MIN_LINKER_LENGTH) return c;+  }+  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return c;+  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return c;+  +  gquad_mfe(0, L, l,+            (void *)(&c),+            (void *)P,+            NULL,+            NULL);+  return c;+}++PUBLIC FLT_OR_DBL exp_E_gquad(int L,+                              int l[3],+                              vrna_exp_param_t *pf){++  int i;+  FLT_OR_DBL q = 0.;++  for(i=0;i<3;i++){+    if(l[i] > VRNA_GQUAD_MAX_LINKER_LENGTH) return q;+    if(l[i] < VRNA_GQUAD_MIN_LINKER_LENGTH) return q;+  }+  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return q;+  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return q;++  gquad_pf( 0, L, l,+            (void *)(&q),+            (void *)pf,+            NULL,+            NULL);+  return q;+}++PUBLIC int E_gquad_ali( int i,+                        int L,+                        int l[3],+                        const short **S,+                        int n_seq,+                        vrna_param_t *P){++  int en[2];+  E_gquad_ali_en(i, L, l, S, n_seq, en, P);+  return en[0] + en[1];+}+++PUBLIC void E_gquad_ali_en( int i,+                            int L,+                            int l[3],+                            const short **S,+                            int n_seq,+                            int en[2],+                            vrna_param_t *P){++  int j;+  en[0] = en[1] = INF;++  for(j=0;j<3;j++){+    if(l[j] > VRNA_GQUAD_MAX_LINKER_LENGTH) return;+    if(l[j] < VRNA_GQUAD_MIN_LINKER_LENGTH) return;+  }+  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return;+  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return;++  gquad_mfe_ali_en( i, L, l,+                    (void *)(&(en[0])),+                    (void *)P,+                    (void *)S,+                    (void *)(&n_seq));+}++/********************************+  Now, the triangular matrix+  generators for the G-quadruplex+  contributions are following+*********************************/++PUBLIC int *get_gquad_matrix(short *S, vrna_param_t *P){++  int n, size, i, j, *gg, *my_index, *data;++  n         = S[0];+  my_index  = vrna_idx_col_wise(n);+  gg        = get_g_islands(S);+  size      = (n * (n+1))/2 + 2;+  data      = (int *)vrna_alloc(sizeof(int) * size);++  /* prefill the upper triangular matrix with INF */+  for(i = 0; i < size; i++) data[i] = INF;++  FOR_EACH_GQUAD(i, j, 1, n){+    process_gquad_enumeration(gg, i, j,+                              &gquad_mfe,+                              (void *)(&(data[my_index[j]+i])),+                              (void *)P,+                              NULL,+                              NULL);+  }++  free(my_index);+  free(gg);+  return data;+}++PUBLIC FLT_OR_DBL *get_gquad_pf_matrix( short *S,+                                        FLT_OR_DBL *scale,+                                        vrna_exp_param_t *pf){++  int n, size, *gg, i, j, *my_index;+  FLT_OR_DBL *data;+++  n         = S[0];+  size      = (n * (n+1))/2 + 2;+  data      = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * size);+  gg        = get_g_islands(S);+  my_index  = vrna_idx_row_wise(n);++  FOR_EACH_GQUAD(i, j, 1, n){+    process_gquad_enumeration(gg, i, j,+                              &gquad_pf,+                              (void *)(&(data[my_index[i]-j])),+                              (void *)pf,+                              NULL,+                              NULL);+    data[my_index[i]-j] *= scale[j-i+1];+  }++  free(my_index);+  free(gg);+  return data;+}++PUBLIC int *get_gquad_ali_matrix( short *S_cons,+                                  short **S,+                                  int n_seq,+                                  vrna_param_t *P){++  int n, size, *data, *gg;+  int i, j, *my_index;+++  n         = S[0][0];+  size      = (n * (n+1))/2 + 2;+  data      = (int *)vrna_alloc(sizeof(int) * size);+  gg        = get_g_islands(S_cons);+  my_index  = vrna_idx_col_wise(n);++  /* prefill the upper triangular matrix with INF */+  for(i=0;i<size;i++) data[i] = INF;++  FOR_EACH_GQUAD(i, j, 1, n){+    process_gquad_enumeration(gg, i, j,+                              &gquad_mfe_ali,+                              (void *)(&(data[my_index[j]+i])),+                              (void *)P,+                              (void *)S,+                              (void *)(&n_seq));+  }++  free(my_index);+  free(gg);+  return data;+}++PUBLIC int **get_gquad_L_matrix(short *S,+                                int start,+                                int maxdist,+                                int n,+                                int **g,+                                vrna_param_t *P){++  return create_L_matrix(S, start, maxdist, n, g, P);+}++PUBLIC void+vrna_gquad_mx_local_update( vrna_fold_compound_t *vc,+                            int start){++  vc->matrices->ggg_local = create_L_matrix(+                              vc->sequence_encoding,+                              start,+                              vc->window_size,+                              vc->length,+                              vc->matrices->ggg_local,+                              vc->params);+}++PRIVATE int **+create_L_matrix(short *S,+                int start,+                int maxdist,+                int n,+                int **g,+                vrna_param_t *P){++  int **data;+  int i, j, k, *gg;++  gg  = get_g_islands_sub(S, start, MIN2(n, start + maxdist + 4));++  if(g){ /* we just update the gquadruplex contribution for the current+            start and rotate the rest */+    data = g;+    /* we re-use the memory allocated previously */+    data[start] = data[start + maxdist + 5];+    data[start + maxdist + 5] = NULL;++    /* prefill with INF */+    for(i = 0; i < maxdist + 5; i++)+      data[start][i] = INF;++    /*  now we compute contributions for all gquads with 5' delimiter at+        position 'start'+    */+    FOR_EACH_GQUAD_AT(start, j, start + maxdist + 4){+      process_gquad_enumeration(gg, start, j,+                                &gquad_mfe,+                                (void *)(&(data[start][j-start])),+                                (void *)P,+                                NULL,+                                NULL);+    }++  } else { /* create a new matrix from scratch since this is the first+              call to this function */++    /* allocate memory and prefill with INF */+    data = (int **) vrna_alloc(sizeof(int *) * (n+1));+    for(k = n; (k>n-maxdist-5) && (k>=0); k--){+      data[k] = (int *) vrna_alloc(sizeof(int)*(maxdist+5));+      for(i = 0; i < maxdist+5; i++) data[k][i] = INF;+    }+    +    /* compute all contributions for the gquads in this interval */+    FOR_EACH_GQUAD(i, j, n - maxdist - 4, n){+      process_gquad_enumeration(gg, i, j,+                                &gquad_mfe,+                                (void *)(&(data[i][j-i])),+                                (void *)P,+                                NULL,+                                NULL);+    }+  }++  gg += start - 1;+  free(gg);+  return data;+}++PUBLIC plist *get_plist_gquad_from_db(const char *structure, float pr){+  int x, size, actual_size, L, n, ge, ee, gb, l[3];+  plist *pl;++  actual_size = 0;+  ge          = 0;+  n           = 2;+  size        = strlen(structure);+  pl          = (plist *)vrna_alloc(n*size*sizeof(plist));++  while((ee = parse_gquad(structure + ge, &L, l)) > 0){+    ge += ee;+    gb = ge - L*4 - l[0] - l[1] - l[2] + 1;+    /* add pseudo-base pair encloding gquad */+    for(x = 0; x < L; x++){+      if (actual_size >= n * size - 5){+        n *= 2;+        pl = (plist *)vrna_realloc(pl, n * size * sizeof(plist));+      }+      pl[actual_size].i = gb + x;+      pl[actual_size].j = ge + x - L + 1;+      pl[actual_size].p = pr;+      pl[actual_size++].type = 0;++      pl[actual_size].i = gb + x;+      pl[actual_size].j = gb + x + l[0] + L;+      pl[actual_size].p = pr;+      pl[actual_size++].type = 0;++      pl[actual_size].i = gb + x + l[0] + L;+      pl[actual_size].j = ge + x - 2*L - l[2] + 1;+      pl[actual_size].p = pr;+      pl[actual_size++].type = 0;++      pl[actual_size].i = ge + x - 2*L - l[2] + 1;+      pl[actual_size].j = ge + x - L + 1;+      pl[actual_size].p = pr;+      pl[actual_size++].type = 0;+    }+  } ++  pl[actual_size].i = pl[actual_size].j = 0;+  pl[actual_size++].p = 0;+  pl = (plist *)vrna_realloc(pl, actual_size * sizeof(plist));+  return pl;+}++PUBLIC void get_gquad_pattern_mfe(short *S,+                                  int i,+                                  int j,+                                  vrna_param_t *P,+                                  int *L,+                                  int l[3]){++  int *gg = get_g_islands_sub(S, i, j);+  int c = INF;++  process_gquad_enumeration(gg, i, j,+                            &gquad_mfe_pos,+                            (void *)(&c),+                            (void *)P,+                            (void *)L,+                            (void *)l);++  gg += i - 1;+  free(gg);+}++PUBLIC void+get_gquad_pattern_exhaustive( short *S,+                              int i,+                              int j,+                              vrna_param_t *P,+                              int *L,+                              int *l,+                              int threshold){++  int *gg = get_g_islands_sub(S, i, j);++  process_gquad_enumeration(gg, i, j,+                            &gquad_pos_exhaustive,+                            (void *)(&threshold),+                            (void *)P,+                            (void *)L,+                            (void *)l);++  gg += i - 1;+  free(gg);+}++PUBLIC void get_gquad_pattern_pf( short *S,+                                  int i,+                                  int j,+                                  vrna_exp_param_t *pf,+                                  int *L,+                                  int l[3]){++  int *gg = get_g_islands_sub(S, i, j);+  FLT_OR_DBL q = 0.;++  process_gquad_enumeration(gg, i, j,+                            &gquad_pf_pos,+                            (void *)(&q),+                            (void *)pf,+                            (void *)L,+                            (void *)l);++  gg += i - 1;+  free(gg);+}++PUBLIC plist *get_plist_gquad_from_pr(short *S,+                                      int gi,+                                      int gj,+                                      FLT_OR_DBL *G,+                                      FLT_OR_DBL *probs,+                                      FLT_OR_DBL *scale,+                                      vrna_exp_param_t *pf){++  int L, l[3];+  return  get_plist_gquad_from_pr_max(S, gi, gj, G, probs, scale, &L, l, pf);+}+++PUBLIC plist *get_plist_gquad_from_pr_max(short *S,+                                      int gi,+                                      int gj,+                                      FLT_OR_DBL *G,+                                      FLT_OR_DBL *probs,+                                      FLT_OR_DBL *scale,+                                      int *Lmax,+                                      int lmax[3],+                                      vrna_exp_param_t *pf){ ++  int n, size, *gg, counter, i, j, *my_index;+  FLT_OR_DBL pp, *tempprobs;+  plist *pl;+  +  n         = S[0];+  size      = (n * (n + 1))/2 + 2;+  tempprobs = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * size);+  pl        = (plist *)vrna_alloc((S[0]*S[0])*sizeof(plist));+  gg        = get_g_islands_sub(S, gi, gj);+  counter   = 0;+  my_index  = vrna_idx_row_wise(n);++  process_gquad_enumeration(gg, gi, gj,+                            &gquad_interact,+                            (void *)tempprobs,+                            (void *)pf,+                            (void *)my_index,+                            NULL);++  pp = 0.;+  process_gquad_enumeration(gg, gi, gj,+                            &gquad_pf_pos,+                            (void *)(&pp),+                            (void *)pf,+                            (void *)Lmax,+                            (void *)lmax);++  pp = probs[my_index[gi]-gj] * scale[gj-gi+1] / G[my_index[gi]-gj];+  for (i=gi;i<gj; i++) {+    for (j=i; j<=gj; j++) {+      if (tempprobs[my_index[i]-j]>0.) {+        pl[counter].i=i;+        pl[counter].j=j;+        pl[counter++].p = pp * tempprobs[my_index[i]-j];+      }+    }+  }+  pl[counter].i = pl[counter].j = 0;+  pl[counter++].p = 0.;+  /* shrink memory to actual size needed */+  pl = (plist *) vrna_realloc(pl, counter * sizeof(plist));++  gg += gi - 1; free(gg);+  free(my_index);+  free (tempprobs);+  return pl;+}++PUBLIC int+get_gquad_count(short *S,+                int i,+                int j){++  int *gg     = get_g_islands_sub(S, i, j);+  int p,q,counter = 0;++  FOR_EACH_GQUAD(p, q, i, j)+    process_gquad_enumeration(gg, p, q,+                              &gquad_count,+                              (void *)(&counter),+                              NULL,+                              NULL,+                              NULL);++  gg += i - 1;+  free(gg);+  return counter;+}++PUBLIC int+get_gquad_layer_count(short *S,+                      int i,+                      int j){++  int *gg     = get_g_islands_sub(S, i, j);+  int p,q,counter = 0;++  FOR_EACH_GQUAD(p, q, i, j)+    process_gquad_enumeration(gg, p, q,+                              &gquad_count_layers,+                              (void *)(&counter),+                              NULL,+                              NULL,+                              NULL);++  gg += i - 1;+  free(gg);+  return counter;+}++PUBLIC int parse_gquad(const char *struc, int *L, int l[3]) {+  int i, il, start, end, len;++  for (i=0; struc[i] && struc[i]!='+'; i++);+  if (struc[i] == '+') { /* start of gquad */+    for (il=0; il<=3; il++) {+      start=i; /* pos of first '+' */+      while (struc[++i] == '+'){+        if((il) && (i-start == *L))+          break;+      }+      end=i; len=end-start; +      if (il==0) *L=len;+      else if (len!=*L)+        vrna_message_error("unequal stack lengths in gquad");+      if (il==3) break;+      while (struc[++i] == '.'); /* linker */+      l[il] = i-end;+      if (struc[i] != '+')+        vrna_message_error("illegal character in gquad linker region");+    }+  }+  else return 0;+  /* printf("gquad at %d %d %d %d %d\n", end, *L, l[0], l[1], l[2]); */+  return end;+}++++/*+#########################################+# BEGIN OF PRIVATE FUNCTION DEFINITIONS #+#          (internal use only)          #+#########################################+*/++PRIVATE int gquad_ali_penalty(int i,+                              int L,+                              int l[3],+                              const short **S,+                              vrna_param_t *P){++  int s, cnt;+  int penalty     = 0;+  int gg_mismatch = 0;++  /* check for compatibility in the alignment */+  for(s = 0; S[s]; s++){+    unsigned int  ld  = 0; /* !=0 if layer destruction was detected */+    int           pen = 0;++    /* check bottom layer */+    if(S[s][i] != 3)                            ld |= 1U;+    if(S[s][i + L + l[0]] != 3)                 ld |= 2U;+    if(S[s][i + 2*L + l[0] + l[1]] != 3)        ld |= 4U;+    if(S[s][i + 3*L + l[0] + l[1] + l[2]] != 3) ld |= 8U;+     /* add 1x penalty for missing bottom layer */+    if(ld) pen += VRNA_GQUAD_MISMATCH_PENALTY;++    /* check top layer */+    ld = 0;+    if(S[s][i + L - 1] != 3)                        ld |= 1U;+    if(S[s][i + 2*L + l[0] - 1] != 3)               ld |= 2U;+    if(S[s][i + 3*L + l[0] + l[1] - 1] != 3)        ld |= 4U;+    if(S[s][i + 4*L + l[0] + l[1] + l[2] - 1] != 3) ld |= 8U;+     /* add 1x penalty for missing top layer */+    if(ld) pen += VRNA_GQUAD_MISMATCH_PENALTY;++    /* check inner layers */+    for(cnt=1;cnt<L-1;cnt++){+      if(S[s][i + cnt] != 3)                            ld |= 1U;+      if(S[s][i + L + l[0] + cnt] != 3)                 ld |= 2U;+      if(S[s][i + 2*L + l[0] + l[1] + cnt] != 3)        ld |= 4U;+      if(S[s][i + 3*L + l[0] + l[1] + l[2] + cnt] != 3) ld |= 8U;+      /* add 2x penalty for missing inner layer */+      if(ld) pen += 2*VRNA_GQUAD_MISMATCH_PENALTY;+    }++    /* if all layers are missing, we have a complete gg mismatch */+    if(pen >= (2*VRNA_GQUAD_MISMATCH_PENALTY * (L-1)))+      gg_mismatch++;++    /* add the penalty to the score */+    penalty += pen;+  }+  /* if gg_mismatch exceeds maximum allowed, this g-quadruplex is forbidden */+  if(gg_mismatch > VRNA_GQUAD_MISMATCH_NUM_ALI) return INF;+  else return penalty;+}+++PRIVATE void gquad_mfe( int i,+                        int L,+                        int *l,+                        void *data,+                        void *P,+                        void *NA,+                        void *NA2){++  int cc = ((vrna_param_t *)P)->gquad[L][l[0] + l[1] + l[2]];+  if(cc < *((int *)data))+    *((int *)data) = cc;+}++PRIVATE void gquad_mfe_pos( int i,+                            int L,+                            int *l,+                            void *data,+                            void *P,+                            void *Lmfe,+                            void *lmfe){++  int cc = ((vrna_param_t *)P)->gquad[L][l[0] + l[1] + l[2]];+  if(cc < *((int *)data)){+    *((int *)data)        = cc;+    *((int *)Lmfe)        = L;+    *((int *)lmfe)        = l[0];+    *(((int *)lmfe) + 1)  = l[1];+    *(((int *)lmfe) + 2)  = l[2];+  }+}++PRIVATE+void+gquad_pos_exhaustive( int i,+                      int L,+                      int *l,+                      void *data,+                      void *P,+                      void *Lex,+                      void *lex){++  int cnt;+  int cc = ((vrna_param_t *)P)->gquad[L][l[0] + l[1] + l[2]];+  if(cc <= *((int *)data)){+    /*  since Lex is an array of L values and lex an+        array of l triples we need to find out where+        the current gquad position is to be stored...+		the below implementation might be slow but we+		still use it for now+    */+    for(cnt = 0; ((int *)Lex)[cnt] != -1; cnt++);++    *((int *)Lex + cnt)           = L;+    *((int *)Lex + cnt + 1)       = -1;+    *(((int *)lex) + (3*cnt) + 0) = l[0];+    *(((int *)lex) + (3*cnt) + 1) = l[1];+    *(((int *)lex) + (3*cnt) + 2) = l[2];+  }+}++PRIVATE+void+gquad_count(int i,+            int L,+            int *l,+            void *data,+            void *NA,+            void *NA2,+            void *NA3){++  *((int *)data) += 1;+}++PRIVATE+void+gquad_count_layers( int i,+                    int L,+                    int *l,+                    void *data,+                    void *NA,+                    void *NA2,+                    void *NA3){++  *((int *)data) += L;+}+++PRIVATE void gquad_pf(int i,+                      int L,+                      int *l,+                      void *data,+                      void *pf,+                      void *NA,+                      void *NA2){++  *((FLT_OR_DBL *)data) += ((vrna_exp_param_t *)pf)->expgquad[L][l[0] + l[1] + l[2]];+}++PRIVATE void gquad_pf_pos(int i,+                          int L,+                          int *l,+                          void *data,+                          void *pf,+                          void *Lmax,+                          void *lmax){++  FLT_OR_DBL gq = ((vrna_exp_param_t *)pf)->expgquad[L][l[0] + l[1] + l[2]];+  if(gq > *((FLT_OR_DBL *)data)){+    *((FLT_OR_DBL *)data) = gq;+    *((int *)Lmax)        = L;+    *((int *)lmax)        = l[0];+    *(((int *)lmax) + 1)  = l[1];+    *(((int *)lmax) + 2)  = l[2];+  }+}++PRIVATE void gquad_mfe_ali( int i,+                            int L,+                            int *l,+                            void *data,+                            void *P,+                            void *S,+                            void *n_seq){++  int j, en[2], cc;+  en[0] = en[1] = INF;++  for(j=0;j<3;j++){+    if(l[j] > VRNA_GQUAD_MAX_LINKER_LENGTH) return;+    if(l[j] < VRNA_GQUAD_MIN_LINKER_LENGTH) return;+  }+  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return;+  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return;++  gquad_mfe_ali_en(i, L, l, (void *)(&(en[0])), P, S, n_seq);+  if(en[1] != INF){+    cc  = en[0] + en[1];+    if(cc < *((int *)data)) *((int *)data) = cc;+  }+}++PRIVATE void gquad_mfe_ali_en(int i,+                              int L,+                              int *l,+                              void *data,+                              void *P,+                              void *S,+                              void *n_seq){++  int en[2], cc, dd;+  en[0] = ((vrna_param_t *)P)->gquad[L][l[0] + l[1] + l[2]] * (*(int *)n_seq);+  en[1] = gquad_ali_penalty(i, L, l, (const short **)S, (vrna_param_t *)P);+  if(en[1] != INF){+    cc = en[0] + en[1];+    dd = ((int *)data)[0] + ((int *)data)[1];+    if(cc < dd){+      ((int *)data)[0] = en[0];+      ((int *)data)[1] = en[1];+    }+  }+}++PRIVATE void gquad_interact(int i,+                      int L,+                      int *l,+                      void *data,+                      void *pf,+                      void *index,+                      void *NA2){++  int x, *idx;+  FLT_OR_DBL gq, *pp;++  idx = (int *)index;+  pp  = (FLT_OR_DBL *)data;+  gq  = exp_E_gquad(L, l, (vrna_exp_param_t *)pf);++  for(x = 0; x < L; x++){+    pp[idx[i + x] - (i + x + 3*L + l[0] + l[1] + l[2])] += gq;+    pp[idx[i + x] - (i + x + L + l[0])] += gq;+    pp[idx[i + x + L + l[0]] - (i + x + 2*L + l[0] + l[1])] += gq;+    pp[idx[i + x + 2*L + l[0] + l[1]] - (i + x + 3*L + l[0] + l[1] + l[2])] += gq;+  }+  +}++PRIVATE INLINE int *get_g_islands(short *S){+  return get_g_islands_sub(S, 1, S[0]);+}++PRIVATE INLINE int *get_g_islands_sub(short *S, int i, int j){+  int x, *gg;++  gg = (int *)vrna_alloc(sizeof(int)*(j-i+2));+  gg -= i - 1;++  if(S[j]==3) gg[j] = 1;+  for(x = j - 1; x >= i; x--)+    if(S[x] == 3)+      gg[x] = gg[x+1]+1;++  return gg;+}++/**+ *  We could've also created a macro that loops over all G-quadruplexes+ *  delimited by i and j. However, for the fun of it we use this function+ *  that receives a pointer to a callback function which in turn does the+ *  actual computation for each quadruplex found.+ */+PRIVATE+void+process_gquad_enumeration(int *gg,+                          int i,+                          int j,+                          void (*f)(int, int, int *,+                                    void *, void *, void *, void *),+                          void *data,+                          void *P,+                          void *aux1,+                          void *aux2){++  int L, l[3], n, max_linker, maxl0, maxl1;++  n = j - i + 1;++  if((n >= VRNA_GQUAD_MIN_BOX_SIZE) && (n <= VRNA_GQUAD_MAX_BOX_SIZE))+    for(L = MIN2(gg[i], VRNA_GQUAD_MAX_STACK_SIZE);+        L >= VRNA_GQUAD_MIN_STACK_SIZE;+        L--)+      if(gg[j-L+1] >= L){+        max_linker = n-4*L;+        if(     (max_linker >= 3*VRNA_GQUAD_MIN_LINKER_LENGTH)+            &&  (max_linker <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH)){+          maxl0 = MIN2( VRNA_GQUAD_MAX_LINKER_LENGTH,+                        max_linker - 2*VRNA_GQUAD_MIN_LINKER_LENGTH+                      );+          for(l[0] = VRNA_GQUAD_MIN_LINKER_LENGTH;+              l[0] <= maxl0;+              l[0]++)+            if(gg[i+L+l[0]] >= L){+              maxl1 = MIN2( VRNA_GQUAD_MAX_LINKER_LENGTH,+                            max_linker - l[0] - VRNA_GQUAD_MIN_LINKER_LENGTH+                          );+              for(l[1] = VRNA_GQUAD_MIN_LINKER_LENGTH;+                  l[1] <= maxl1;+                  l[1]++)+                if(gg[i + 2*L + l[0] + l[1]] >= L){+                  l[2] = max_linker - l[0] - l[1];+                  f(i, L, &(l[0]), data, P, aux1, aux2);+                }+            }+        }+      }+}+
+ C/ViennaRNA/gquad.h view
@@ -0,0 +1,906 @@+#ifndef VIENNA_RNA_PACKAGE_GQUAD_H+#define VIENNA_RNA_PACKAGE_GQUAD_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++#ifndef INLINE+#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif+#endif++/**+ *  @file       gquad.h+ *  @ingroup    paired_modules+ *  @brief      G-quadruplexes+ */++/**+ *  @addtogroup gquads+ *  @brief Various functions related to G-quadruplex computations+ *  @{+ *  @ingroup gquads+ */+++int         E_gquad(int L,+                    int l[3],+                    vrna_param_t *P);++FLT_OR_DBL exp_E_gquad( int L,+                        int l[3],+                        vrna_exp_param_t *pf);++int         E_gquad_ali(int i,+                        int L,+                        int l[3],+                        const short **S,+                        int n_seq,+                        vrna_param_t *P);+++void        E_gquad_ali_en( int i,+                            int L,+                            int l[3],+                            const short **S,+                            int n_seq,+                            int en[2],+                            vrna_param_t *P);++/**+ *  @brief Get a triangular matrix prefilled with minimum free energy+ *  contributions of G-quadruplexes.+ *+ *  At each position ij in the matrix, the minimum free energy of any+ *  G-quadruplex delimited by i and j is stored. If no G-quadruplex formation+ *  is possible, the matrix element is set to INF.+ *  Access the elements in the matrix via matrix[indx[j]+i]. To get+ *  the integer array indx see get_jindx().+ *+ *  @see get_jindx(), encode_sequence()+ *+ *  @param S  The encoded sequence+ *  @param P  A pointer to the data structure containing the precomputed energy contributions+ *  @return   A pointer to the G-quadruplex contribution matrix+*/+int         *get_gquad_matrix(short *S, vrna_param_t *P);++int         *get_gquad_ali_matrix(short *S_cons,+                                  short **S,+                                  int n_seq,+                                  vrna_param_t *P);++FLT_OR_DBL  *get_gquad_pf_matrix( short *S,+                                  FLT_OR_DBL *scale,+                                  vrna_exp_param_t *pf);++int         **get_gquad_L_matrix( short *S,+                                  int start,+                                  int maxdist,+                                  int n,+                                  int **g,+                                  vrna_param_t *P);++void        vrna_gquad_mx_local_update( vrna_fold_compound_t *vc,+                                        int start);++void        get_gquad_pattern_mfe(short *S,+                                  int i,+                                  int j,+                                  vrna_param_t *P,+                                  int *L,+                                  int l[3]);++void+get_gquad_pattern_exhaustive( short *S,+                              int i,+                              int j,+                              vrna_param_t *P,+                              int *L,+                              int *l,+                              int threshold);++void        get_gquad_pattern_pf( short *S,+                                  int i,+                                  int j,+                                  vrna_exp_param_t *pf,+                                  int *L,+                                  int l[3]);++plist       *get_plist_gquad_from_pr( short *S,+                                      int gi,+                                      int gj,+                                      FLT_OR_DBL *G,+                                      FLT_OR_DBL *probs,+                                      FLT_OR_DBL *scale,+                                      vrna_exp_param_t *pf);+plist       *get_plist_gquad_from_pr_max(short *S,+                                      int gi,+                                      int gj,+                                      FLT_OR_DBL *G,+                                      FLT_OR_DBL *probs,+                                      FLT_OR_DBL *scale,+                                      int *L,+                                      int l[3],+                                      vrna_exp_param_t *pf);++plist       *get_plist_gquad_from_db( const char *structure,+                                      float pr);++int         get_gquad_count(short *S,+                            int i,+                            int j);++int         get_gquad_layer_count(short *S,+                            int i,+                            int j);+++/**+ *  given a dot-bracket structure (possibly) containing gquads encoded+ *  by '+' signs, find first gquad, return end position or 0 if none found+ *  Upon return L and l[] contain the number of stacked layers, as well as+ *  the lengths of the linker regions.  + *  To parse a string with many gquads, call parse_gquad repeatedly e.g.+ *  end1 = parse_gquad(struc, &L, l); ... ;+ *  end2 = parse_gquad(struc+end1, &L, l); end2+=end1; ... ;+ *  end3 = parse_gquad(struc+end2, &L, l); end3+=end2; ... ; + */+int         parse_gquad(const char *struc, int *L, int l[3]);++INLINE  PRIVATE int backtrack_GQuad_IntLoop(int c,+                                            int i,+                                            int j,+                                            int type,+                                            short *S,+                                            int *ggg,+                                            int *index,+                                            int *p,+                                            int *q,+                                            vrna_param_t *P);++INLINE  PRIVATE int backtrack_GQuad_IntLoop_L(int c,+                                              int i,+                                              int j,+                                              int type,+                                              short *S,+                                              int **ggg,+                                              int maxdist,+                                              int *p,+                                              int *q,+                                              vrna_param_t *P);++PRIVATE INLINE int+vrna_BT_gquad_mfe(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  vrna_bp_stack_t *bp_stack,+                  int *stack_count);++PRIVATE INLINE int+vrna_BT_gquad_int(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  int en,+                  vrna_bp_stack_t *bp_stack,+                  int *stack_count);++PRIVATE INLINE int+vrna_BT_gquad_mfe(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  vrna_bp_stack_t *bp_stack,+                  int *stack_count){++  /*+    here we do some fancy stuff to backtrace the stacksize and linker lengths+    of the g-quadruplex that should reside within position i,j+  */+  short         *S;+  int           l[3], L, a;+  vrna_param_t  *P;++  P = vc->params;+  S = vc->sequence_encoding2;+  L = -1;++  get_gquad_pattern_mfe(S, i, j, P, &L, l);++  if(L != -1){+    /* fill the G's of the quadruplex into base_pair2 */+    for(a=0;a<L;a++){+      bp_stack[++(*stack_count)].i = i+a;+      bp_stack[(*stack_count)].j   = i+a;+      bp_stack[++(*stack_count)].i = i+L+l[0]+a;+      bp_stack[(*stack_count)].j   = i+L+l[0]+a;+      bp_stack[++(*stack_count)].i = i+L+l[0]+L+l[1]+a;+      bp_stack[(*stack_count)].j   = i+L+l[0]+L+l[1]+a;+      bp_stack[++(*stack_count)].i = i+L+l[0]+L+l[1]+L+l[2]+a;+      bp_stack[(*stack_count)].j   = i+L+l[0]+L+l[1]+L+l[2]+a;+    }+    return 1;+  } else {+    return 0;+  }+}++PRIVATE INLINE int+vrna_BT_gquad_int(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  int en,+                  vrna_bp_stack_t *bp_stack,+                  int *stack_count){++  int           energy, dangles, *idx, ij, p, q, maxl, minl, c0, l1, *rtype, *ggg;+  unsigned char type;+  char          *ptype;+  short         si, sj, *S, *S1;++  vrna_param_t  *P;+  vrna_md_t     *md;++  idx         = vc->jindx;+  ij          = idx[j] + i;+  P           = vc->params;+  md          = &(P->model_details);+  ptype       = vc->ptype;+  rtype       = &(md->rtype[0]);+  type        = rtype[(unsigned char)ptype[ij]];+  S1          = vc->sequence_encoding;+  S           = vc->sequence_encoding2;+  dangles     = md->dangles;+  si          = S1[i + 1];+  sj          = S1[j - 1];+  ggg         = vc->matrices->ggg;+  energy      = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  p = i + 1;+  if(S1[p] == 3){+    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minl  = j - i + p - MAXLOOP - 2;+      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minl  = MAX2(c0, minl);+      c0    = j - 3;+      maxl  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxl  = MIN2(c0, maxl);+      for(q = minl; q < maxl; q++){+        if(S[q] != 3) continue;+        if(en == energy + ggg[idx[q] + p] + P->internal_loop[j - q - 1]){+          return vrna_BT_gquad_mfe(vc, p, q, bp_stack, stack_count);+        }+      }+    }+  }++  for(p = i + 2;+      p < j - VRNA_GQUAD_MIN_BOX_SIZE;+      p++){+    l1    = p - i - 1;+    if(l1>MAXLOOP) break;+    if(S1[p] != 3) continue;+    minl  = j - i + p - MAXLOOP - 2;+    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minl  = MAX2(c0, minl);+    c0    = j - 1;+    maxl  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxl  = MIN2(c0, maxl);+    for(q = minl; q < maxl; q++){+      if(S1[q] != 3) continue;+      if(en == energy + ggg[idx[q] + p] + P->internal_loop[l1 + j - q - 1]){+        return vrna_BT_gquad_mfe(vc, p, q, bp_stack, stack_count);+      }+    }+  }++  q = j - 1;+  if(S1[q] == 3)+    for(p = i + 4;+        p < j - VRNA_GQUAD_MIN_BOX_SIZE;+        p++){+      l1    = p - i - 1;+      if(l1>MAXLOOP) break;+      if(S1[p] != 3) continue;+      if(en == energy + ggg[idx[q] + p] + P->internal_loop[l1]){+        return vrna_BT_gquad_mfe(vc, p, q, bp_stack, stack_count);+      }+    }++  return 0;+}++/**+ *  backtrack an interior loop like enclosed g-quadruplex+ *  with closing pair (i,j)+ *+ *  @param c      The total contribution the loop should resemble+ *  @param i      position i of enclosing pair+ *  @param j      position j of enclosing pair+ *  @param type   base pair type of enclosing pair (must be reverse type)+ *  @param S      integer encoded sequence+ *  @param ggg    triangular matrix containing g-quadruplex contributions+ *  @param index  the index for accessing the triangular matrix+ *  @param p      here the 5' position of the gquad is stored+ *  @param q      here the 3' position of the gquad is stored+ *  @param P      the datastructure containing the precalculated contibutions+ *+ *  @return       1 on success, 0 if no gquad found+ */+INLINE  PRIVATE int backtrack_GQuad_IntLoop(int c,+                                            int i,+                                            int j,+                                            int type,+                                            short *S,+                                            int *ggg,+                                            int *index,+                                            int *p,+                                            int *q,+                                            vrna_param_t *P){++  int energy, dangles, k, l, maxl, minl, c0, l1;+  short si, sj;++  dangles = P->model_details.dangles;+  si      = S[i + 1];+  sj      = S[j - 1];+  energy  = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  k = i + 1;+  if(S[k] == 3){+    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minl  = j - i + k - MAXLOOP - 2;+      c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minl  = MAX2(c0, minl);+      c0    = j - 3;+      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxl  = MIN2(c0, maxl);+      for(l = minl; l < maxl; l++){+        if(S[l] != 3) continue;+        if(c == energy + ggg[index[l] + k] + P->internal_loop[j - l - 1]){+          *p = k; *q = l;+          return 1;+        }+      }+    }+  }++  for(k = i + 2;+      k < j - VRNA_GQUAD_MIN_BOX_SIZE;+      k++){+    l1    = k - i - 1;+    if(l1>MAXLOOP) break;+    if(S[k] != 3) continue;+    minl  = j - i + k - MAXLOOP - 2;+    c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minl  = MAX2(c0, minl);+    c0    = j - 1;+    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxl  = MIN2(c0, maxl);+    for(l = minl; l < maxl; l++){+      if(S[l] != 3) continue;+      if(c == energy + ggg[index[l] + k] + P->internal_loop[l1 + j - l - 1]){+        *p = k; *q = l;+        return 1;+      }+    }+  }++  l = j - 1;+  if(S[l] == 3)+    for(k = i + 4;+        k < j - VRNA_GQUAD_MIN_BOX_SIZE;+        k++){+      l1    = k - i - 1;+      if(l1>MAXLOOP) break;+      if(S[k] != 3) continue;+      if(c == energy + ggg[index[l] + k] + P->internal_loop[l1]){+        *p = k; *q = l;+        return 1;+      }+    }++  return 0;+}++/**+ *  backtrack an interior loop like enclosed g-quadruplex+ *  with closing pair (i,j) with underlying Lfold matrix+ *+ *  @param c      The total contribution the loop should resemble+ *  @param i      position i of enclosing pair+ *  @param j      position j of enclosing pair+ *  @param type   base pair type of enclosing pair (must be reverse type)+ *  @param S      integer encoded sequence+ *  @param ggg    triangular matrix containing g-quadruplex contributions+ *  @param p      here the 5' position of the gquad is stored+ *  @param q      here the 3' position of the gquad is stored+ *  @param P      the datastructure containing the precalculated contibutions+ *+ *  @return       1 on success, 0 if no gquad found+ */+INLINE  PRIVATE int backtrack_GQuad_IntLoop_L(int c,+                                              int i,+                                              int j,+                                              int type,+                                              short *S,+                                              int **ggg,+                                              int maxdist,+                                              int *p,+                                              int *q,+                                              vrna_param_t *P){++  int energy, dangles, k, l, maxl, minl, c0, l1;+  short si, sj;++  dangles = P->model_details.dangles;+  si      = S[i + 1];+  sj      = S[j - 1];+  energy  = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  k = i + 1;+  if(S[k] == 3){+    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minl  = j - i + k - MAXLOOP - 2;+      c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minl  = MAX2(c0, minl);+      c0    = j - 3;+      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxl  = MIN2(c0, maxl);+      for(l = minl; l < maxl; l++){+        if(S[l] != 3) continue;+        if(c == energy + ggg[k][l - k] + P->internal_loop[j - l - 1]){+          *p = k; *q = l;+          return 1;+        }+      }+    }+  }++  for(k = i + 2;+      k < j - VRNA_GQUAD_MIN_BOX_SIZE;+      k++){+    l1    = k - i - 1;+    if(l1>MAXLOOP) break;+    if(S[k] != 3) continue;+    minl  = j - i + k - MAXLOOP - 2;+    c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minl  = MAX2(c0, minl);+    c0    = j - 1;+    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxl  = MIN2(c0, maxl);+    for(l = minl; l < maxl; l++){+      if(S[l] != 3) continue;+      if(c == energy + ggg[k][l - k] + P->internal_loop[l1 + j - l - 1]){+        *p = k; *q = l;+        return 1;+      }+    }+  }++  l = j - 1;+  if(S[l] == 3)+    for(k = i + 4;+        k < j - VRNA_GQUAD_MIN_BOX_SIZE;+        k++){+      l1    = k - i - 1;+      if(l1>MAXLOOP) break;+      if(S[k] != 3) continue;+      if(c == energy + ggg[k][l - k] + P->internal_loop[l1]){+        *p = k; *q = l;+        return 1;+      }+    }++  return 0;+}++PRIVATE INLINE+int+E_GQuad_IntLoop(int i,+                int j,+                int type,+                short *S,+                int *ggg,+                int *index,+                vrna_param_t *P){++  int energy, ge, dangles, p, q, l1, minq, maxq, c0;+  short si, sj;++  dangles = P->model_details.dangles;+  si      = S[i + 1];+  sj      = S[j - 1];+  energy  = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  ge = INF;++  p = i + 1;+  if(S[p] == 3){+    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minq  = j - i + p - MAXLOOP - 2;+      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minq  = MAX2(c0, minq);+      c0    = j - 3;+      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxq  = MIN2(c0, maxq);+      for(q = minq; q < maxq; q++){+        if(S[q] != 3) continue;+        c0  = energy + ggg[index[q] + p] + P->internal_loop[j - q - 1];+        ge  = MIN2(ge, c0);+      }+    }+  }++  for(p = i + 2;+      p < j - VRNA_GQUAD_MIN_BOX_SIZE;+      p++){+    l1    = p - i - 1;+    if(l1>MAXLOOP) break;+    if(S[p] != 3) continue;+    minq  = j - i + p - MAXLOOP - 2;+    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minq  = MAX2(c0, minq);+    c0    = j - 1;+    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxq  = MIN2(c0, maxq);+    for(q = minq; q < maxq; q++){+      if(S[q] != 3) continue;+      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];+      ge   = MIN2(ge, c0);+    }+  }++  q = j - 1;+  if(S[q] == 3)+    for(p = i + 4;+        p < j - VRNA_GQUAD_MIN_BOX_SIZE;+        p++){+      l1    = p - i - 1;+      if(l1>MAXLOOP) break;+      if(S[p] != 3) continue;+      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1];+      ge  = MIN2(ge, c0);+    }++#if 0+  /* here comes the additional stuff for the odd dangle models */+  if(dangles % 1){+    en1 = energy + P->dangle5[type][si];+    en2 = energy + P->dangle5[type][sj];+    en3 = energy + P->mismatchI[type][si][sj];++    /* first case with 5' dangle (i.e. j-1) onto enclosing pair */+    p = i + 1;+    if(S[p] == 3){+      if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+        minq  = j - i + p - MAXLOOP - 2;+        c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+        minq  = MAX2(c0, minq);+        c0    = j - 4;+        maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+        maxq  = MIN2(c0, maxq);+        for(q = minq; q < maxq; q++){+          if(S[q] != 3) continue;+          c0  = en1 + ggg[index[q] + p] + P->internal_loop[j - q - 1];+          ge  = MIN2(ge, c0);+        }+      }+    }++    for(p = i + 2; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++){+      l1    = p - i - 1;+      if(l1>MAXLOOP) break;+      if(S[p] != 3) continue;+      minq  = j - i + p - MAXLOOP - 2;+      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minq  = MAX2(c0, minq);+      c0    = j - 2;+      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxq  = MIN2(c0, maxq);+      for(q = minq; q < maxq; q++){+        if(S[q] != 3) continue;+        c0  = en1 + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];+        ge   = MIN2(ge, c0);+      }+    }++    q = j - 2;+    if(S[q] == 3)+      for(p = i + 4; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++){+        l1    = p - i - 1;+        if(l1>MAXLOOP) break;+        if(S[p] != 3) continue;+        c0  = en1 + ggg[index[q] + p] + P->internal_loop[l1 + 1];+        ge  = MIN2(ge, c0);+      }++    /* second case with 3' dangle (i.e. i+1) onto enclosing pair */++  }+#endif+  return ge;+}++PRIVATE INLINE+int *+E_GQuad_IntLoop_exhaustive( int i,+                            int j,+                            int **p_p,+                            int **q_p,+                            int type,+                            short *S,+                            int *ggg,+                            int threshold,+                            int *index,+                            vrna_param_t *P){++  int energy, *ge, dangles, p, q, l1, minq, maxq, c0;+  short si, sj;+  int cnt = 0;++  dangles = P->model_details.dangles;+  si      = S[i + 1];+  sj      = S[j - 1];+  energy  = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  /* guess how many gquads are possible in interval [i+1,j-1] */+  *p_p  = (int *)vrna_alloc(sizeof(int) * 256);+  *q_p  = (int *)vrna_alloc(sizeof(int) * 256);+  ge    = (int *)vrna_alloc(sizeof(int) * 256);++  p = i + 1;+  if(S[p] == 3){+    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minq  = j - i + p - MAXLOOP - 2;+      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minq  = MAX2(c0, minq);+      c0    = j - 3;+      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxq  = MIN2(c0, maxq);+      for(q = minq; q < maxq; q++){+        if(S[q] != 3) continue;+        c0  = energy + ggg[index[q] + p] + P->internal_loop[j - q - 1];+        if(c0 <= threshold){+          ge[cnt]       = energy + P->internal_loop[j - q - 1];+          (*p_p)[cnt]   = p;+          (*q_p)[cnt++] = q;+        }+      }+    }+  }++  for(p = i + 2;+      p < j - VRNA_GQUAD_MIN_BOX_SIZE;+      p++){+    l1    = p - i - 1;+    if(l1>MAXLOOP) break;+    if(S[p] != 3) continue;+    minq  = j - i + p - MAXLOOP - 2;+    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minq  = MAX2(c0, minq);+    c0    = j - 1;+    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxq  = MIN2(c0, maxq);+    for(q = minq; q < maxq; q++){+      if(S[q] != 3) continue;+      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];+        if(c0 <= threshold){+          ge[cnt]       = energy + P->internal_loop[l1 + j - q - 1];+          (*p_p)[cnt]   = p;+          (*q_p)[cnt++] = q;+        }+    }+  }++  q = j - 1;+  if(S[q] == 3)+    for(p = i + 4;+        p < j - VRNA_GQUAD_MIN_BOX_SIZE;+        p++){+      l1    = p - i - 1;+      if(l1>MAXLOOP) break;+      if(S[p] != 3) continue;+      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1];+        if(c0 <= threshold){+          ge[cnt]       = energy + P->internal_loop[l1];+          (*p_p)[cnt]   = p;+          (*q_p)[cnt++] = q;+        }+    }+++  (*p_p)[cnt] = -1;++  return ge;+}++PRIVATE INLINE+int+E_GQuad_IntLoop_L(int i,+                  int j,+                  int type,+                  short *S,+                  int **ggg,+                  int maxdist,+                  vrna_param_t *P){++  int energy, ge, dangles, p, q, l1, minq, maxq, c0;+  short si, sj;++  dangles = P->model_details.dangles;+  si      = S[i + 1];+  sj      = S[j - 1];+  energy  = 0;++  if(dangles == 2)+    energy += P->mismatchI[type][si][sj];++  if(type > 2)+    energy += P->TerminalAU;++  ge = INF;++  p = i + 1;+  if(S[p] == 3){+    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minq  = j - i + p - MAXLOOP - 2;+      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minq  = MAX2(c0, minq);+      c0    = j - 3;+      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxq  = MIN2(c0, maxq);+      for(q = minq; q < maxq; q++){+        if(S[q] != 3) continue;+        c0  = energy + ggg[p][q-p] + P->internal_loop[j - q - 1];+        ge  = MIN2(ge, c0);+      }+    }+  }++  for(p = i + 2;+      p < j - VRNA_GQUAD_MIN_BOX_SIZE;+      p++){+    l1    = p - i - 1;+    if(l1>MAXLOOP) break;+    if(S[p] != 3) continue;+    minq  = j - i + p - MAXLOOP - 2;+    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minq  = MAX2(c0, minq);+    c0    = j - 1;+    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    maxq  = MIN2(c0, maxq);+    for(q = minq; q < maxq; q++){+      if(S[q] != 3) continue;+      c0  = energy + ggg[p][q - p] + P->internal_loop[l1 + j - q - 1];+      ge   = MIN2(ge, c0);+    }+  }++  q = j - 1;+  if(S[q] == 3)+    for(p = i + 4;+        p < j - VRNA_GQUAD_MIN_BOX_SIZE;+        p++){+      l1    = p - i - 1;+      if(l1>MAXLOOP) break;+      if(S[p] != 3) continue;+      c0  = energy + ggg[p][q - p] + P->internal_loop[l1];+      ge  = MIN2(ge, c0);+    }++  return ge;+}++PRIVATE INLINE+FLT_OR_DBL+exp_E_GQuad_IntLoop(int i,+                    int j,+                    int type,+                    short *S,+                    FLT_OR_DBL *G,+                    int *index,+                    vrna_exp_param_t *pf){++  int         k, l, minl, maxl, u, r;+  FLT_OR_DBL  q, qe;+  double      *expintern;+  short       si, sj;++  q         = 0;+  si        = S[i + 1];+  sj        = S[j - 1];+  qe        = (FLT_OR_DBL)pf->expmismatchI[type][si][sj];+  expintern = pf->expinternal;++  if(type > 2)+    qe *= (FLT_OR_DBL)pf->expTermAU;++  k = i + 1;+  if(S[k] == 3){+    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){+      minl  = j - i + k - MAXLOOP - 2;+      u     = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+      minl  = MAX2(u, minl);+      u     = j - 3;+      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+      maxl  = MIN2(u, maxl);+      for(l = minl; l < maxl; l++){+        if(S[l] != 3) continue;+        if(G[index[k]-l] == 0.) continue;+        q += qe * G[index[k]-l] * (FLT_OR_DBL)expintern[j - l - 1];+      }+    }+  }+++  for(k = i + 2;+      k <= j - VRNA_GQUAD_MIN_BOX_SIZE;+      k++){+    u = k - i - 1;+    if(u > MAXLOOP) break;+    if(S[k] != 3) continue;+    minl  = j - i + k - MAXLOOP - 2;+    r     = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;+    minl  = MAX2(r, minl);+    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;+    r     = j - 1;+    maxl  = MIN2(r, maxl);+    for(l = minl; l < maxl; l++){+      if(S[l] != 3) continue;+      if(G[index[k]-l] == 0.) continue;+      q += qe * G[index[k]-l] * (FLT_OR_DBL)expintern[u + j - l - 1];+    }+  }++  l = j - 1;+  if(S[l] == 3)+    for(k = i + 4; k < j - VRNA_GQUAD_MIN_BOX_SIZE; k++){+      u    = k - i - 1;+      if(u>MAXLOOP) break;+      if(S[k] != 3) continue;+      if(G[index[k]-l] == 0.) continue;+      q += qe * G[index[k]-l] * (FLT_OR_DBL)expintern[u];+    }++  return q;+}++/**+ * @}+ */+++#endif
+ C/ViennaRNA/grammar.h view
@@ -0,0 +1,31 @@+#ifndef VIENNA_RNA_PACKAGE_GRAMMAR_H+#define VIENNA_RNA_PACKAGE_GRAMMAR_H++/**+ *  @file     grammar.h+ *  @ingroup  grammar+ *  @brief    Implementations for the RNA folding grammar+ */++#include <ViennaRNA/data_structures.h>++typedef void (vrna_callback_gr_rule_aux)(vrna_fold_compound_t *vc, int i, int j, void *data);++typedef void (vrna_callback_gr_free_auxdata)(void *data);++typedef struct vrna_gr_aux_s  vrna_gr_aux_t;++struct vrna_gr_aux_s {++  vrna_callback_gr_rule_aux     *cb_aux_f;+  vrna_callback_gr_rule_aux     *cb_aux_c;+  vrna_callback_gr_rule_aux     *cb_aux_m;+  vrna_callback_gr_rule_aux     *cb_aux_m1;+  vrna_callback_gr_rule_aux     *cb_aux;++  void                          *auxdata;+  vrna_callback_gr_free_auxdata *free_auxdata;+};+++#endif
+ C/ViennaRNA/hairpin_loops.c view
@@ -0,0 +1,945 @@+#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/exterior_loops.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"+#include "ViennaRNA/hairpin_loops.h"++struct default_data {+  int                       n;+  int                       *idx;+  char                      *mx;+  int                       cp;+  int                       *hc_up;+  void                      *hc_dat;+  vrna_callback_hc_evaluate *hc_f;+};+++/*+ #################################+ # PRIVATE FUNCTION DECLARATIONS #+ #################################+ */++PRIVATE FLT_OR_DBL+exp_eval_hp_loop(vrna_fold_compound_t *vc,+                 int                  i,+                 int                  j);+++PRIVATE FLT_OR_DBL+exp_eval_ext_hp_loop(vrna_fold_compound_t *vc,+                     int                  i,+                     int                  j);+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data);+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data);+++PRIVATE int+eval_hp_loop_fake(vrna_fold_compound_t  *vc,+                  int                   i,+                  int                   j);+++PRIVATE FLT_OR_DBL+exp_eval_hp_loop_fake(vrna_fold_compound_t  *vc,+                      int                   i,+                      int                   j);++/*+ #################################+ # BEGIN OF FUNCTION DEFINITIONS #+ #################################+ */++/**+ *  @brief  Evaluate the free energy of a hairpin loop+ *          and consider possible hard constraints+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ */+PUBLIC int+vrna_E_hp_loop(vrna_fold_compound_t *vc,+               int                  i,+               int                  j)+{+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = vc->hc->matrix;+  hc_dat_local.hc_up  = vc->hc->up_hp;+  hc_dat_local.n      = vc->length;+  hc_dat_local.cp     = vc->cutpoint;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  if ((i > 0) && (j > 0)) {+    /* is this base pair allowed to close a hairpin (like) loop ? */+    if (evaluate(i, j, i, j, VRNA_DECOMP_PAIR_HP, &hc_dat_local)) {+      if (j > i)  /* linear case */+        return vrna_eval_hp_loop(vc, i, j);+      else        /* circular case */+        return vrna_eval_ext_hp_loop(vc, j, i);+    }+  }++  return INF;+}+++/**+ *  @brief High-Level function for hairpin loop energy evaluation (partition function variant)+ *+ *  @see E_hp_loop() for it's free energy counterpart+ */+PUBLIC FLT_OR_DBL+vrna_exp_E_hp_loop(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j)+{+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = vc->hc->matrix;+  hc_dat_local.hc_up  = vc->hc->up_hp;+  hc_dat_local.n      = vc->length;+  hc_dat_local.cp     = vc->cutpoint;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  if ((i > 0) && (j > 0)) {+    if (evaluate(i, j, i, j, VRNA_DECOMP_PAIR_HP, &hc_dat_local)) {+      if (j > i)  /* linear case */+        return exp_eval_hp_loop(vc, i, j);+      else        /* circular case */+        return exp_eval_ext_hp_loop(vc, j, i);+    }+  }++  return 0.;+}+++/**+ *  @brief  Evaluate the free energy of an exterior hairpin loop+ *          and consider possible hard constraints+ */+PUBLIC int+vrna_E_ext_hp_loop(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j)+{+  return vrna_E_hp_loop(vc, j, i);+}+++/**+ *  @brief Evaluate free energy of an exterior hairpin loop+ *+ *  @ingroup eval+ *+ */+PUBLIC int+vrna_eval_ext_hp_loop(vrna_fold_compound_t  *vc,+                      int                   i,+                      int                   j)+{+  char            **Ss, loopseq[10];+  unsigned short  **a2s;+  short           *S, **SS, **S5, **S3;+  int             u, e, s, type, *types, n_seq, length;+  vrna_param_t    *P;+  vrna_sc_t       *sc, **scs;+  vrna_md_t       *md;++  length  = vc->length;+  P       = vc->params;+  md      = &(P->model_details);+  e       = INF;++  switch (vc->type) {+    /* single sequences and cofolding hybrids */+    case  VRNA_FC_TYPE_SINGLE:+      S     = vc->sequence_encoding;+      sc    = vc->sc;+      u     = vc->length - j + i - 1;+      type  = md->pair[S[j]][S[i]];++      if (type == 0)+        type = 7;++      if (u < 7) {+        strcpy(loopseq, vc->sequence + j - 1);+        strncat(loopseq, vc->sequence, i);+      }++      e = E_Hairpin(u, type, S[j + 1], S[i - 1], loopseq, P);++      if (sc) {+        if (sc->energy_up)+          e += sc->energy_up[j + 1][vc->length - j]+               + sc->energy_up[1][i - 1];++        if (sc->f)+          e += sc->f(j, i, j, i, VRNA_DECOMP_PAIR_HP, sc->data);+      }+      break;++    /* sequence alignments */+    case  VRNA_FC_TYPE_COMPARATIVE:+      SS    = vc->S;+      S5    = vc->S5;                                 /*S5[s][i] holds next base 5' of i in sequence s*/+      S3    = vc->S3;                                 /*Sl[s][i] holds next base 3' of i in sequence s*/+      Ss    = vc->Ss;+      a2s   = vc->a2s;+      scs   = vc->scs;+      n_seq = vc->n_seq;+      e     = 0;+      types = (int *)vrna_alloc(sizeof(int) * n_seq);++      for (s = 0; s < n_seq; s++) {+        types[s] = md->pair[SS[s][j]][SS[s][i]];+        if (types[s] == 0) types[s] = 7;+      }++      for (s = 0; s < n_seq; s++) {+        char loopseq[10];+        u = a2s[s][length] - a2s[s][j] + a2s[s][i - 1];++        if (u < 9) {+          strcpy(loopseq, Ss[s] + a2s[s][j] - 1);+          strncat(loopseq, Ss[s], a2s[s][i]);+        }+        if (u < 3) e += 600;+        else e += E_Hairpin(u, types[s], S3[s][j], S5[s][i], loopseq, P);+      }+      if (scs) {+        for (s = 0; s < n_seq; s++) {+          if (scs[s]) {+            if (scs[s]->energy_up)+              e += ((i > 1) ? scs[s]->energy_up[1][a2s[s][i - 1]] : 0)+                   + ((j < length) ? scs[s]->energy_up[a2s[s][j + 1]][a2s[s][length] - a2s[s][j]] : 0);+            if (scs[s]->f)+              e += scs[s]->f(a2s[s][j], a2s[s][i], a2s[s][j], a2s[s][i], VRNA_DECOMP_PAIR_HP, scs[s]->data);+          }+        }+      }++      free(types);+      break;++    /* nothing */+    default:+      break;+  }++  return e;+}+++/**+ *  @brief Evaluate free energy of a hairpin loop+ *+ *  @ingroup eval+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @param  vc  The #vrna_fold_compound_t for the particular energy evaluation+ *  @param  i   5'-position of the base pair+ *  @param  j   3'-position of the base pair+ *  @returns    Free energy of the hairpin loop closed by @f$ (i,j) @f$ in deka-kal/mol+ */+PUBLIC int+vrna_eval_hp_loop(vrna_fold_compound_t  *vc,+                  int                   i,+                  int                   j)+{+  char            **Ss;+  unsigned short  **a2s;+  short           *S, **SS, **S5, **S3;+  unsigned int    *sn;+  int             u, e, s, ij, type, *types, *idx, n_seq, en;+  vrna_param_t    *P;+  vrna_sc_t       *sc, **scs;+  vrna_md_t       *md;+  vrna_ud_t       *domains_up;++  idx         = vc->jindx;+  P           = vc->params;+  md          = &(P->model_details);+  sn          = vc->strand_number;+  domains_up  = vc->domains_up;+  e           = INF;++  if (sn[j] != sn[i])+    return eval_hp_loop_fake(vc, i, j);++  /* regular hairpin loop */+  switch (vc->type) {+    /* single sequences and cofolding hybrids */+    case  VRNA_FC_TYPE_SINGLE:+      S     = vc->sequence_encoding;+      sc    = vc->sc;+      u     = j - i - 1;+      ij    = idx[j] + i;+      type  = md->pair[S[i]][S[j]];++      if (type == 0)+        type = 7;++      e = E_Hairpin(u, type, S[i + 1], S[j - 1], vc->sequence + i - 1, P);++      /* add soft constraints */+      if (sc) {+        if (sc->energy_up)+          e += sc->energy_up[i + 1][u];++        if (sc->energy_bp)+          e += sc->energy_bp[ij];+        if (sc->f)+          e += sc->f(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+      }++      /* consider possible ligand binding */+      if (domains_up && domains_up->energy_cb) {+        en = domains_up->energy_cb(vc,+                                   i + 1, j - 1,+                                   VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                   domains_up->data);+        if (en != INF)+          en += e;+        e = MIN2(e, en);+      }++      break;++    /* sequence alignments */+    case  VRNA_FC_TYPE_COMPARATIVE:+      SS    = vc->S;+      S5    = vc->S5;                                 /*S5[s][i] holds next base 5' of i in sequence s*/+      S3    = vc->S3;                                 /*Sl[s][i] holds next base 3' of i in sequence s*/+      Ss    = vc->Ss;+      a2s   = vc->a2s;+      scs   = vc->scs;+      n_seq = vc->n_seq;+      ij    = idx[j] + i;+      types = (int *)vrna_alloc(sizeof(int) * n_seq);++      for (s = 0; s < n_seq; s++) {+        types[s] = md->pair[SS[s][i]][SS[s][j]];+        if (types[s] == 0) types[s] = 7;+      }++      for (e = s = 0; s < n_seq; s++) {+        u = a2s[s][j - 1] - a2s[s][i];+        e += (u < 3) ? 600 : E_Hairpin(u, types[s], S3[s][i], S5[s][j], Ss[s] + (a2s[s][i - 1]), P);                          /* ??? really 600 ??? */+      }++      if (scs) {+        for (s = 0; s < n_seq; s++) {+          if (scs[s]) {+            u = a2s[s][j - 1] - a2s[s][i];++            if (scs[s]->energy_up)+              e += scs[s]->energy_up[a2s[s][i + 1]][u];++            if (scs[s]->energy_bp)+              e += scs[s]->energy_bp[ij];++            if (scs[s]->f)+              e += scs[s]->f(a2s[s][i], a2s[s][j], a2s[s][i], a2s[s][j], VRNA_DECOMP_PAIR_HP, scs[s]->data);+          }+        }+      }++      free(types);+      break;++    /* nothing */+    default:+      break;+  }++  return e;+}+++PRIVATE int+eval_hp_loop_fake(vrna_fold_compound_t  *vc,+                  int                   i,+                  int                   j)+{+  short         *S;+  unsigned int  *sn;+  int           u, e, ij, type, *idx, en;+  vrna_param_t  *P;+  vrna_sc_t     *sc;+  vrna_md_t     *md;+  vrna_ud_t     *domains_up;++  idx         = vc->jindx;+  P           = vc->params;+  md          = &(P->model_details);+  sn          = vc->strand_number;+  domains_up  = vc->domains_up;+  e           = INF;++  switch (vc->type) {+    /* single sequences and cofolding hybrids */+    case  VRNA_FC_TYPE_SINGLE:+      S     = vc->sequence_encoding;+      sc    = vc->sc;+      u     = j - i - 1;+      ij    = idx[j] + i;+      type  = md->pair[S[i]][S[j]];++      if (type == 0)+        type = 7;++      /* hairpin-like exterior loop (for cofolding) */+      short si, sj;++      si  = (sn[i + 1] == sn[i]) ? S[i + 1] : -1;+      sj  = (sn[j] == sn[j - 1]) ? S[j - 1] : -1;++      if (md->dangles)+        e = E_ExtLoop(md->rtype[type], sj, si, P);+      else+        e = E_ExtLoop(md->rtype[type], -1, -1, P);++      /* add soft constraints */+      if (sc) {+        if (sc->energy_up)+          e += sc->energy_up[i + 1][u];++        if (sc->energy_bp)+          e += sc->energy_bp[ij];+        if (sc->f)+          e += sc->f(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+      }++      /* consider possible ligand binding */+      if (domains_up && domains_up->energy_cb) {+        en = domains_up->energy_cb(vc,+                                   i + 1, j - 1,+                                   VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                   domains_up->data);+        if (en != INF)+          en += e;+        e = MIN2(e, en);+      }+      break;++    /* nothing */+    default:+      break;+  }++  return e;+}+++PRIVATE FLT_OR_DBL+exp_eval_hp_loop_fake(vrna_fold_compound_t  *vc,+                      int                   i,+                      int                   j)+{+  short             *S, s5, s3;+  unsigned int      *sn;+  int               u, cp, type, *iidx;+  FLT_OR_DBL        qq, temp, *q, *scale;+  vrna_exp_param_t  *pf_params;+  vrna_sc_t         *sc;+  vrna_md_t         *md;+  vrna_ud_t         *domains_up;++  cp          = vc->cutpoint;+  iidx        = vc->iindx;+  pf_params   = vc->exp_params;+  md          = &(pf_params->model_details);+  q           = vc->exp_matrices->q;+  scale       = vc->exp_matrices->scale;+  sn          = vc->strand_number;+  domains_up  = vc->domains_up;++  qq = 0;++  switch (vc->type) {+    /* single sequences and cofolding hybrids */+    case  VRNA_FC_TYPE_SINGLE:+      S     = vc->sequence_encoding;+      sc    = vc->sc;+      u     = j - i - 1;+      type  = md->pair[S[j]][S[i]];++      if (type == 0)+        type = 7;++      temp = q[iidx[i + 1] - (cp - 1)] * q[iidx[cp] - (j - 1)];+      if ((j == cp) && (i == cp - 1))+        temp = scale[2];+      else if (i == cp - 1)+        temp = q[iidx[cp] - (j - 1)] * scale[1];+      else if (j == cp)+        temp = q[iidx[i + 1] - (cp - 1)] * scale[1];+      if (j > cp)+        temp *= scale[1];+      if (i < cp - 1)+        temp *= scale[1];++      s5  = (sn[j] == sn[j - 1]) ? S[j - 1] : -1;+      s3  = (sn[i + 1] == sn[i]) ? S[i + 1] : -1;++      temp *= exp_E_ExtLoop(type, s5, s3, pf_params);++      qq += temp;++      /* add soft constraints */+      if (sc) {+        if (sc->exp_energy_up)+          qq *= sc->exp_energy_up[i + 1][u];++        if (sc->exp_energy_bp)+          qq *= sc->exp_energy_bp[iidx[i] - j];++        if (sc->exp_f)+          qq *= sc->exp_f(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+      }++      if (domains_up && domains_up->exp_energy_cb) {+        /* we always consider both, bound and unbound state */+        qq += qq * domains_up->exp_energy_cb(vc,+                                             i + 1, j - 1,+                                             VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                             domains_up->data);+      }+      break;++    /* nothing */+    default:+      break;+  }++  return qq;+}+++/*+ *************************************+ * Partition function variants below *+ *************************************+ */+PRIVATE FLT_OR_DBL+exp_eval_hp_loop(vrna_fold_compound_t *vc,+                 int                  i,+                 int                  j)+{+  char              **Ss;+  unsigned short    **a2s;+  short             *S, **SS, **S5, **S3;+  unsigned int      *sn;+  int               u, ij, type, n_seq, s, *types, *idx, *iidx;+  FLT_OR_DBL        q, qbt1, *scale;+  vrna_exp_param_t  *P;+  vrna_sc_t         *sc, **scs;+  vrna_md_t         *md;+  vrna_ud_t         *domains_up;++  idx         = vc->jindx;+  iidx        = vc->iindx;+  P           = vc->exp_params;+  md          = &(P->model_details);+  sn          = vc->strand_number;+  scale       = vc->exp_matrices->scale;+  types       = NULL;+  domains_up  = vc->domains_up;++  q   = 0.;+  ij  = idx[j] + i;++  if (sn[j] != sn[i])+    return exp_eval_hp_loop_fake(vc, i, j);++  switch (vc->type) {+    case VRNA_FC_TYPE_SINGLE:+      S     = vc->sequence_encoding;+      sc    = vc->sc;+      u     = j - i - 1;+      type  = vc->ptype[ij];++      if (type == 0)+        type = 7;++      if (sn[j] == sn[i]) {+        /* regular hairpin loop */+        q = exp_E_Hairpin(u, type, S[i + 1], S[j - 1], vc->sequence + i - 1, P);+      } else {+        /* hairpin-like exterior loop (for cofolding) */+        /* this is currently handle somewhere else */+      }++      /* add soft constraints */+      if (sc) {+        if (sc->exp_energy_up)+          q *= sc->exp_energy_up[i + 1][u];++        if (sc->exp_energy_bp)+          q *= sc->exp_energy_bp[iidx[i] - j];++        if (sc->exp_f)+          q *= sc->exp_f(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+      }++      q *= scale[u + 2];++      if (domains_up && domains_up->exp_energy_cb) {+        /* we always consider both, bound and unbound state */+        q += q * domains_up->exp_energy_cb(vc,+                                           i + 1, j - 1,+                                           VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                           domains_up->data);+      }+      break;++    case VRNA_FC_TYPE_COMPARATIVE:+      SS    = vc->S;+      S5    = vc->S5;                                 /*S5[s][i] holds next base 5' of i in sequence s*/+      S3    = vc->S3;                                 /*Sl[s][i] holds next base 3' of i in sequence s*/+      Ss    = vc->Ss;+      a2s   = vc->a2s;+      scs   = vc->scs;+      n_seq = vc->n_seq;+      qbt1  = 1.;+      types = (int *)vrna_alloc(sizeof(int) * n_seq);++      for (s = 0; s < n_seq; s++) {+        types[s] = md->pair[SS[s][i]][SS[s][j]];+        if (types[s] == 0) types[s] = 7;+      }++      for (s = 0; s < n_seq; s++) {+        u = a2s[s][j - 1] - a2s[s][i];+        if (a2s[s][i] < 1) continue;+        char loopseq[10];+        if (u < 9)+          strncpy(loopseq, Ss[s] + a2s[s][i] - 1, 10);+        qbt1 *= exp_E_Hairpin(u, types[s], S3[s][i], S5[s][j], loopseq, P);+      }++      /* add soft constraints */+      if (scs) {+        for (s = 0; s < n_seq; s++) {+          if (scs[s]) {+            u = a2s[s][j - 1] - a2s[s][i];++            if (scs[s]->exp_energy_bp)+              qbt1 *= scs[s]->exp_energy_bp[iidx[i] - j];++            if (scs[s]->exp_energy_up)+              qbt1 *= scs[s]->exp_energy_up[a2s[s][i + 1]][u];++            if (scs[s]->exp_f)+              qbt1 *= scs[s]->exp_f(a2s[s][i], a2s[s][j], a2s[s][i], a2s[s][j], VRNA_DECOMP_PAIR_HP, scs[s]->data);+          }+        }+      }++      q = qbt1 * scale[j - i + 1];+      break;++    default:+      break;+  }++  free(types);+  return q;+}+++PRIVATE FLT_OR_DBL+exp_eval_ext_hp_loop(vrna_fold_compound_t *vc,+                     int                  i,+                     int                  j)+{+  char              **Ss, *sequence;+  unsigned short    **a2s;+  short             *S, **SS, **S5, **S3;+  int               u, u1, ij, n, type, n_seq, s, *rtype, *types, *idx, noGUclosure;+  FLT_OR_DBL        q, qbt1, *scale;+  vrna_exp_param_t  *P;+  vrna_sc_t         *sc, **scs;+  vrna_md_t         *md;+  vrna_ud_t         *domains_up;++  n           = vc->length;+  idx         = vc->jindx;+  P           = vc->exp_params;+  md          = &(P->model_details);+  noGUclosure = md->noGUclosure;+  scale       = vc->exp_matrices->scale;+  types       = NULL;+  domains_up  = vc->domains_up;+  rtype       = &(md->rtype[0]);++  q   = 0.;+  u   = n - j + i - 1;+  ij  = idx[j] + i;++  switch (vc->type) {+    case VRNA_FC_TYPE_SINGLE:+      sequence  = vc->sequence;+      S         = vc->sequence_encoding;+      sc        = vc->sc;+      type      = rtype[vc->ptype[ij]];++      if (type == 0)+        type = 7;++      if (((type == 3) || (type == 4)) && noGUclosure)+        return q;++      /* get the loop sequence */+      char loopseq[10];+      if (u < 7) {+        strcpy(loopseq, sequence + j - 1);+        strncat(loopseq, sequence, i);+      }++      q = exp_E_Hairpin(u, type, S[j + 1], S[i - 1], loopseq, P);++      /* add soft constraints */+      if (sc) {+        if (sc->exp_energy_up)+          q *= ((i > 1) ? sc->exp_energy_up[1][i - 1] : 1.)+               * ((j < n) ? sc->exp_energy_up[j + 1][n - j] : 1.);++        if (sc->exp_f)+          q *= sc->exp_f(j, i, j, i, VRNA_DECOMP_PAIR_HP, sc->data);+      }++      q *= scale[u];++      if (domains_up && domains_up->exp_energy_cb) {+        /* we always consider both, bound and unbound state */+        q += q * domains_up->exp_energy_cb(vc,+                                           j + 1, i - 1,+                                           VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                                           domains_up->data);+      }+      break;++    case VRNA_FC_TYPE_COMPARATIVE:+      SS    = vc->S;+      S5    = vc->S5;                                 /*S5[s][i] holds next base 5' of i in sequence s*/+      S3    = vc->S3;                                 /*Sl[s][i] holds next base 3' of i in sequence s*/+      Ss    = vc->Ss;+      a2s   = vc->a2s;+      scs   = vc->scs;+      n_seq = vc->n_seq;+      qbt1  = 1.;+      types = (int *)vrna_alloc(sizeof(int) * n_seq);++      for (s = 0; s < n_seq; s++) {+        types[s] = md->pair[SS[s][j]][SS[s][i]];+        if (types[s] == 0) types[s] = 7;+      }++      for (s = 0; s < n_seq; s++) {+        u1 = a2s[s][i] - 1 + a2s[s][n] - a2s[s][j];+        char loopseq[10];+        if (u1 < 7) {+          strcpy(loopseq, Ss[s] + a2s[s][j] - 1);+          strncat(loopseq, Ss[s], a2s[s][i]);+        }+        qbt1 *= exp_E_Hairpin(u1, types[s], S3[s][j], S5[s][i], loopseq, P);+      }++      /* add soft constraints */+      if (scs) {+        for (s = 0; s < n_seq; s++) {+          if (scs[s]) {+            if (scs[s]->exp_energy_up)+              qbt1 *= ((i > 1) ? scs[s]->exp_energy_up[a2s[s][1]][a2s[s][i] - a2s[s][1]] : 1.)+                      * ((j < n) ? scs[s]->exp_energy_up[a2s[s][j] + 1][a2s[s][n] - a2s[s][j]] : 1.);++            if (scs[s]->exp_f)+              qbt1 *= scs[s]->exp_f(a2s[s][j], a2s[s][i], a2s[s][j], a2s[s][i], VRNA_DECOMP_PAIR_HP, scs[s]->data);+          }+        }+      }++      q = qbt1 * scale[u];++      free(types);+      break;++    default:+      break;+  }++  return q;+}+++/**+ *  @brief Backtrack a hairpin loop closed by @f$ (i,j) @f$+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ */+PUBLIC int+vrna_BT_hp_loop(vrna_fold_compound_t  *vc,+                int                   i,+                int                   j,+                int                   en,+                vrna_bp_stack_t       *bp_stack,+                int                   *stack_count)+{+  int       e, u;+  vrna_sc_t *sc;++  sc = NULL;++  u = j - i - 1;++  if (vc->hc->up_hp[i + 1] < u)+    return 0;++  e = vrna_E_hp_loop(vc, i, j);++  if (e == en) {+    switch (vc->type) {+      case  VRNA_FC_TYPE_SINGLE:+        sc = vc->sc;+        break;++      case  VRNA_FC_TYPE_COMPARATIVE:+        if (vc->scs)+          sc = vc->scs[0];+        break;++      default:+        break;+    }++    if (sc) {+      if (sc->bt) {+        vrna_basepair_t *ptr, *aux_bps;+        aux_bps = sc->bt(i, j, i, j, VRNA_DECOMP_PAIR_HP, sc->data);+        for (ptr = aux_bps; ptr && ptr->i != 0; ptr++) {+          bp_stack[++(*stack_count)].i  = ptr->i;+          bp_stack[(*stack_count)].j    = ptr->j;+        }+        free(aux_bps);+      }+    }++    return 1;+  }++  return 0;+}+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data)+{+  int                 ij, u, p, q;+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval = (char)0;++  if (j > i) {+    /* linear case */+    p = i;+    q = j;+    u = q - p - 1;+  } else {+    /* circular case */+    p = j;+    q = i;+    u = dat->n - q + p - 1;+  }++  ij = dat->idx[q] + p;+  if (dat->mx[ij] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP) {+    eval = (char)1;+    if (dat->hc_up[i + 1] < u)+      eval = (char)0;+  }++  return eval;+}+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data)+{+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval  = hc_default(i, j, k, l, d, data);+  eval  = (dat->hc_f(i, j, k, l, d, dat->hc_dat)) ? eval : (char)0;++  return eval;+}
+ C/ViennaRNA/hairpin_loops.h view
@@ -0,0 +1,303 @@+#ifndef VIENNA_RNA_PACKAGE_HAIRPIN_LOOPS_H+#define VIENNA_RNA_PACKAGE_HAIRPIN_LOOPS_H++#include <math.h>+#include <string.h>+#include <ViennaRNA/utils.h>+#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif++/**+ *+ *  @file     hairpin_loops.h+ *  @ingroup  loops+ *  @brief    Energy evaluation of hairpin loops for MFE and partition function calculations+ */++/**+ *+ *  @{+ *  @ingroup   loops+ */+++/**+ *  @brief Compute the Energy of a hairpin-loop+ *+ *  To evaluate the free energy of a hairpin-loop, several parameters have to be known.+ *  A general hairpin-loop has this structure:<BR>+ *  <PRE>+ *        a3 a4+ *      a2     a5+ *      a1     a6+ *        X - Y+ *        |   |+ *        5'  3'+ *  </PRE>+ *  where X-Y marks the closing pair [e.g. a <B>(G,C)</B> pair]. The length of this loop is 6 as there are+ *  six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is+ *  a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is &quot;a1.a2.a3.a4.a5.a6&quot; <BR>+ *  @note The parameter sequence should contain the sequence of the loop in capital letters of the nucleic acid+ *  alphabet if the loop size is below 7. This is useful for unusually stable tri-, tetra- and hexa-loops+ *  which are treated differently (based on experimental data) if they are tabulated.+ *  @see scale_parameters()+ *  @see vrna_param_t+ *  @warning Not (really) thread safe! A threadsafe implementation will replace this function in a future release!\n+ *  Energy evaluation may change due to updates in global variable "tetra_loop"+ * + *  @param  size  The size of the loop (number of unpaired nucleotides)+ *  @param  type  The pair type of the base pair closing the hairpin+ *  @param  si1   The 5'-mismatching nucleotide+ *  @param  sj1   The 3'-mismatching nucleotide+ *  @param  string  The sequence of the loop+ *  @param  P     The datastructure containing scaled energy parameters+ *  @return The Free energy of the Hairpin-loop in dcal/mol+ */+PRIVATE INLINE int+E_Hairpin(int size,+              int type,+              int si1,+              int sj1,+              const char *string,+              vrna_param_t *P);++/**+ *  @brief Compute Boltzmann weight @f$e^{-\Delta G/kT} @f$ of a hairpin loop+ *+ *  multiply by scale[u+2]+ *  @see get_scaled_pf_parameters()+ *  @see vrna_exp_param_t+ *  @see E_Hairpin()+ *  @warning Not (really) thread safe! A threadsafe implementation will replace this function in a future release!\n+ *  Energy evaluation may change due to updates in global variable "tetra_loop"+ * + *  @param  u       The size of the loop (number of unpaired nucleotides)+ *  @param  type    The pair type of the base pair closing the hairpin+ *  @param  si1     The 5'-mismatching nucleotide+ *  @param  sj1     The 3'-mismatching nucleotide+ *  @param  string  The sequence of the loop+ *  @param  P       The datastructure containing scaled Boltzmann weights of the energy parameters+ *  @return The Boltzmann weight of the Hairpin-loop+ */+PRIVATE INLINE FLT_OR_DBL+exp_E_Hairpin(  int u,+                int type,+                short si1,+                short sj1,+                const char *string,+                vrna_exp_param_t *P);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PRIVATE INLINE int+E_Hairpin(int size,+          int type,+          int si1,+          int sj1,+          const char *string,+          vrna_param_t *P){++  int energy;++  if(size <= 30)+    energy = P->hairpin[size];+  else+    energy = P->hairpin[30] + (int)(P->lxc*log((size)/30.));++  if(size < 3) return energy; /* should only be the case when folding alignments */++  if(P->model_details.special_hp){+    if(size == 4){ /* check for tetraloop bonus */+      char tl[7]={0}, *ts;+      strncpy(tl, string, 6);+      if ((ts=strstr(P->Tetraloops, tl)))+        return (P->Tetraloop_E[(ts - P->Tetraloops)/7]);+    }+    else if(size == 6){+      char tl[9]={0}, *ts;+      strncpy(tl, string, 8);+      if ((ts=strstr(P->Hexaloops, tl)))+        return (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);+    }+    else if(size == 3){+      char tl[6]={0,0,0,0,0,0}, *ts;+      strncpy(tl, string, 5);+      if ((ts=strstr(P->Triloops, tl))) {+        return (P->Triloop_E[(ts - P->Triloops)/6]);+      }+      return (energy + (type>2 ? P->TerminalAU : 0));+    }+  }+  energy += P->mismatchH[type][si1][sj1];++  return energy;+}++/**+ *  @brief  Evaluate the free energy of a hairpin loop+ *          and consider hard constraints if they apply+ *+ *  This function evaluates the free energy of a hairpin loop+ *+ *  In case the base pair is not allowed due to a constraint+ *  conflict, this function returns #INF.+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @param vc   The #vrna_fold_compound_t that stores all relevant model settings+ *  @param i    The 5' nucleotide of the base pair (3' to evaluate the pair as exterior hairpin loop)+ *  @param j    The 3' nucleotide of the base pair (5' to evaluate the pair as exterior hairpin loop)+ *  @returns    The free energy of the hairpin loop in 10cal/mol+ */+int+vrna_E_hp_loop( vrna_fold_compound_t *vc,+                int i,+                int j);++/**+ *  @brief  Evaluate the free energy of an exterior hairpin loop+ *          and consider possible hard constraints+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ */+int+vrna_E_ext_hp_loop( vrna_fold_compound_t *vc,+                    int i,+                    int j);++/**+ *  @brief Evaluate free energy of an exterior hairpin loop+ *+ *  @ingroup loops+ *+ */+int+vrna_eval_ext_hp_loop(vrna_fold_compound_t *vc,+                      int i,+                      int j);++/**+ *  @brief Evaluate free energy of a hairpin loop+ *+ *  @ingroup loops+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ *  @param  vc  The #vrna_fold_compound_t for the particular energy evaluation+ *  @param  i   5'-position of the base pair+ *  @param  j   3'-position of the base pair+ *  @returns    Free energy of the hairpin loop closed by @f$ (i,j) @f$ in deka-kal/mol+ */+int+vrna_eval_hp_loop(vrna_fold_compound_t *vc,+                  int i,+                  int j);++/*+*************************************+* Partition function variants below *+*************************************+*/++PRIVATE INLINE FLT_OR_DBL+exp_E_Hairpin(int u,+              int type,+              short si1,+              short sj1,+              const char *string,+              vrna_exp_param_t *P){++  double q, kT;+  kT = P->kT;   /* kT in cal/mol  */++  if(u <= 30)+    q = P->exphairpin[u];+  else+    q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);++  if(u < 3) return (FLT_OR_DBL)q; /* should only be the case when folding alignments */++  if(P->model_details.special_hp){+    if(u==4){+      char tl[7]={0,0,0,0,0,0,0}, *ts;+      strncpy(tl, string, 6);+      if ((ts=strstr(P->Tetraloops, tl))){+        if(type != 7)+          return (FLT_OR_DBL)(P->exptetra[(ts-P->Tetraloops)/7]);+        else+          q *= P->exptetra[(ts-P->Tetraloops)/7];+      }+    }+    else if(u==6){+      char tl[9]={0,0,0,0,0,0,0,0,0}, *ts;+      strncpy(tl, string, 8);+      if ((ts=strstr(P->Hexaloops, tl)))+        return  (FLT_OR_DBL)(P->exphex[(ts-P->Hexaloops)/9]);+    }+    else if(u==3){+      char tl[6]={0,0,0,0,0,0}, *ts;+      strncpy(tl, string, 5);+      if ((ts=strstr(P->Triloops, tl)))+        return (FLT_OR_DBL)(P->exptri[(ts-P->Triloops)/6]);+      if (type>2)+        return (FLT_OR_DBL)(q * P->expTermAU);+      else+        return (FLT_OR_DBL)q;+    }+  }+  q *= P->expmismatchH[type][si1][sj1];++  return (FLT_OR_DBL)q;+}+++/**+ *  @brief High-Level function for hairpin loop energy evaluation (partition function variant)+ *+ *  @see vrna_E_hp_loop() for it's free energy counterpart+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+*/+FLT_OR_DBL+vrna_exp_E_hp_loop( vrna_fold_compound_t *vc,+                    int i,+                    int j);++/**+ *  @brief Backtrack a hairpin loop closed by @f$ (i,j) @f$+ *+ *  @note This function is polymorphic! The provided #vrna_fold_compound_t may be of type+ *  #VRNA_FC_TYPE_SINGLE or #VRNA_FC_TYPE_COMPARATIVE+ *+ */+int+vrna_BT_hp_loop(vrna_fold_compound_t *vc,+                int i,+                int j,+                int en,+                vrna_bp_stack_t *bp_stack,+                int   *stack_count);++/**+ * @}+ */+++#endif
+ C/ViennaRNA/interior_loops.c view
@@ -0,0 +1,1807 @@+#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/exterior_loops.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"+#include "ViennaRNA/interior_loops.h"+++struct default_data {+  void                      *hc_dat;+  vrna_callback_hc_evaluate *hc_f;+};+++/*+ #################################+ # PRIVATE FUNCTION DECLARATIONS #+ #################################+ */++PRIVATE int+E_int_loop(vrna_fold_compound_t *vc,+           int                  i,+           int                  j);+++PRIVATE int+E_int_loop_comparative(vrna_fold_compound_t *vc,+                       int                  i,+                       int                  j);+++PRIVATE FLT_OR_DBL+exp_E_int_loop(vrna_fold_compound_t *vc,+               int                  i,+               int                  j);+++PRIVATE FLT_OR_DBL+exp_E_int_loop_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j);+++PRIVATE INLINE int+eval_interior_loop(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   int                  p,+                   int                  q);+++PRIVATE INLINE int+eval_int_loop(vrna_fold_compound_t  *vc,+              int                   i,+              int                   j,+              int                   k,+              int                   l);+++PRIVATE FLT_OR_DBL+exp_E_interior_loop(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    int                   k,+                    int                   l);+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data);+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data);+++/*+ #################################+ # BEGIN OF FUNCTION DEFINITIONS #+ #################################+ */+PUBLIC int+vrna_E_int_loop(vrna_fold_compound_t  *vc,+                int                   i,+                int                   j)+{+  int e = INF;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        e = E_int_loop(vc, i, j);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        e = E_int_loop_comparative(vc, i, j);+        break;+    }+  }++  return e;+}+++PUBLIC FLT_OR_DBL+vrna_exp_E_int_loop(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j)+{+  FLT_OR_DBL q = 0.;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        q = exp_E_int_loop(vc, i, j);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        q = exp_E_int_loop_comparative(vc, i, j);+        break;+    }+  }++  return q;+}+++PUBLIC int+vrna_eval_int_loop(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   int                  k,+                   int                  l)+{+  int e = INF;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        e = eval_int_loop(vc, i, j, k, l);+        break;+    }+  }++  return e;+}+++PRIVATE INLINE int+eval_int_loop(vrna_fold_compound_t  *vc,+              int                   i,+              int                   j,+              int                   k,+              int                   l)+{+  unsigned int  *sn;+  int           ij, kl, e, u1, u2, cp, *jindx, *hc_up, *rtype, type, type2;+  short         *S;+  vrna_sc_t     *sc;+  vrna_param_t  *P;+  vrna_md_t     *md;++  cp    = vc->cutpoint;+  jindx = vc->jindx;+  sc    = vc->sc;+  P     = vc->params;+  md    = &(P->model_details);+  sn    = vc->strand_number;+  rtype = &(md->rtype[0]);+  ij    = jindx[j] + i;+  kl    = jindx[l] + k;+  S     = vc->sequence_encoding;++  e = INF;++  u1  = k - i - 1;+  u2  = j - l - 1;++  if ((sn[k] != sn[i]) || (sn[j] != sn[l]))+    return e;++  type  = md->pair[S[i]][S[j]];+  type2 = md->pair[S[l]][S[k]];+  if (type == 0)+    type = 7;+  if (type2 == 0)+    type2 = 7;++  e = ubf_eval_int_loop(i, j, k, l,+                        i + 1, j - 1, k - 1, l + 1,+                        S[i + 1], S[j - 1], S[k - 1], S[l + 1],+                        type, type2, rtype,+                        ij, cp,+                        P, sc);++  return e;+}+++PRIVATE int+E_int_loop(vrna_fold_compound_t *vc,+           int                  i,+           int                  j)+{+  unsigned char             type, type_2;+  char                      *ptype, *ptype_pq, *hc_pq, *hc, eval_loop;+  short                     *S, S_i1, S_j1, *S_p1, *S_q1;+  unsigned int              *sn;+  int                       q, p, j_q, p_i, pq, *c_pq, max_q, max_p, tmp,+                            *rtype, noGUclosure, no_close, energy, cp, en,+                            *indx, *hc_up, ij, hc_decompose, e, *c, *ggg,+                            with_gquad, turn;+  vrna_sc_t                 *sc;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_mx_mfe_t             *matrices;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp            = vc->cutpoint;+  indx          = vc->jindx;+  hc            = vc->hc->matrix;+  hc_up         = vc->hc->up_int;+  P             = vc->params;+  matrices      = vc->matrices;+  ij            = indx[j] + i;+  hc_decompose  = hc[ij];+  e             = INF;+  sn            = vc->strand_number;+  c             = vc->matrices->c;+  ggg           = vc->matrices->ggg;+  md            = &(P->model_details);+  with_gquad    = md->gquad;+  turn          = md->min_loop_size;+  domains_up    = vc->domains_up;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  if (hc_decompose & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    /* prepare necessary variables */+    rtype       = &(md->rtype[0]);+    noGUclosure = md->noGUclosure;+    max_q       = i + turn + 2;+    max_q       = MAX2(max_q, j - MAXLOOP - 1);++    ptype     = vc->ptype;+    type      = (unsigned char)ptype[ij];+    no_close  = (((type == 3) || (type == 4)) && noGUclosure);+    S         = vc->sequence_encoding;++    S_i1  = S[i + 1];+    S_j1  = S[j - 1];+    sc    = vc->sc;++    if (type == 0)+      type = 7;++    if (domains_up && domains_up->energy_cb) {+      for (q = j - 1; q >= max_q; q--) {+        j_q = j - q - 1;++        if (hc_up[q + 1] < j_q) break;++        pq    = indx[q] + i + 1;+        p_i   = 0;+        max_p = i + 1;+        tmp   = i + 1 + MAXLOOP - j_q;+        max_p = MAX2(max_p, tmp);+        tmp   = q - turn;+        max_p = MIN2(max_p, tmp);+        tmp   = i + 1 + hc_up[i + 1];+        max_p = MIN2(max_p, tmp);+        c_pq  = c + pq;++        ptype_pq  = ptype + pq;+        S_p1      = S + i;+        S_q1      = S + q + 1;++        hc_pq = hc + pq;++        for (p = i + 1; p <= max_p; p++) {+          eval_loop = *hc_pq & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;+          /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+          if (eval_loop && evaluate(i, j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+            energy = *c_pq;+            if (energy != INF) {+              type_2 = rtype[(unsigned char)*ptype_pq];++              if (type_2 == 0)+                type_2 = 7;++              if (noGUclosure)+                if (no_close || (type_2 == 3) || (type_2 == 4))+                  if ((p > i + 1) || (q < j - 1)) continue;  /* continue unless stack */++              energy  += eval_interior_loop(vc, i, j, p, q);+              e       = MIN2(e, energy);+            }+          }+          hc_pq++;    /* get hc[pq + 1] */+          c_pq++;     /* get c[pq + 1] */+          p_i++;      /* increase unpaired region [i+1...p-1] */++          ptype_pq++; /* get ptype[pq + 1] */+          S_p1++;++          pq++;+        } /* end q-loop */+      }   /* end p-loop */+    } else {+      for (q = j - 1; q >= max_q; q--) {+        j_q = j - q - 1;++        if (hc_up[q + 1] < j_q) break;++        pq    = indx[q] + i + 1;+        p_i   = 0;+        max_p = i + 1;+        tmp   = i + 1 + MAXLOOP - j_q;+        max_p = MAX2(max_p, tmp);+        tmp   = q - turn;+        max_p = MIN2(max_p, tmp);+        tmp   = i + 1 + hc_up[i + 1];+        max_p = MIN2(max_p, tmp);+        hc_pq = hc + pq;+        c_pq  = c + pq;++        ptype_pq  = ptype + pq;+        S_p1      = S + i;+        S_q1      = S + q + 1;++        for (p = i + 1; p <= max_p; p++) {+          eval_loop = *hc_pq & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;+          /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+          if (eval_loop && evaluate(i, j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+            energy = *c_pq;+            if (energy != INF) {+              type_2 = rtype[(unsigned char)*ptype_pq];++              if (noGUclosure)+                if (no_close || (type_2 == 3) || (type_2 == 4))+                  if ((p > i + 1) || (q < j - 1)) continue;  /* continue unless stack */++              if (type_2 == 0)+                type_2 = 7;++              energy += ubf_eval_int_loop(i, j, p, q,+                                          i + 1, j - 1, p - 1, q + 1,+                                          S_i1, S_j1, *S_p1, *S_q1,+                                          type, type_2, rtype,+                                          ij, cp,+                                          P, sc);+              e = MIN2(e, energy);+            }+          }+          hc_pq++;    /* get hc[pq + 1] */+          c_pq++;     /* get c[pq + 1] */+          p_i++;      /* increase unpaired region [i+1...p-1] */++          ptype_pq++; /* get ptype[pq + 1] */+          S_p1++;++          pq++;+        } /* end q-loop */+      }   /* end p-loop */+    }++    if (with_gquad) {+      /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */+      if ((!no_close) && (sn[j] == sn[i])) {+        energy  = E_GQuad_IntLoop(i, j, type, S, ggg, indx, P);+        e       = MIN2(e, energy);+      }+    }+  }++  return e;+}+++PRIVATE INLINE int+ubf_eval_int_loop_comparative(int             col_i,+                              int             col_j,+                              int             col_p,+                              int             col_q,+                              unsigned char   type,+                              unsigned char   type_2,+                              int             *rtype,+                              int             ij,+                              int             cp,+                              vrna_param_t    *P,+                              short           *SS,+                              short           *S5,+                              short           *S3,+                              unsigned short  *a2s,+                              vrna_sc_t       *sc)+{+  short si, sj, sp, sq;+  int   energy, u1, u2;+  int   i, j, p, q, i1, j1, p1, q1;++  i   = a2s[col_i];+  j   = a2s[col_j];+  p   = a2s[col_p];+  q   = a2s[col_q];+  i1  = a2s[col_i + 1];+  j1  = a2s[col_j - 1];+  p1  = a2s[col_p - 1];+  q1  = a2s[col_q + 1];++  si  = S3[col_i];+  sj  = S5[col_j];+  sp  = S5[col_p];+  sq  = S3[col_q];++  u1  = p1 - i;+  u2  = j1 - q;++  energy = E_IntLoop(u1, u2, type, type_2, si, sj, sp, sq, P);++  /* add soft constraints */+  if (sc) {+    if (sc->energy_up)+      energy += sc->energy_up[i1][u1]+                + sc->energy_up[q1][u2];++    if (sc->energy_bp)+      energy += sc->energy_bp[ij];++    if (sc->energy_stack) {+      if (u1 + u2 == 0) {+        if (SS[col_i] && SS[col_j] && SS[col_p] && SS[col_q]) {+          /* no gap allowed */+          int a = sc->energy_stack[i]+                  + sc->energy_stack[p]+                  + sc->energy_stack[q]+                  + sc->energy_stack[j];+          energy += a;+        }+      }+    }+    if (sc->f)+      energy += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+  }++  return energy;+}+++PRIVATE int+E_int_loop_comparative(vrna_fold_compound_t *vc,+                       int                  i,+                       int                  j)+{+  unsigned char             type, type_2;+  char                      *hc_pq, *hc, eval_loop;+  unsigned short            **a2s;+  short                     **SS, **S5, **S3, *S_cons;+  int                       q, p, j_q, p_i, u, pq, *c_pq, min_q, max_q, max_p, tmp,+                            *rtype, *types, dangle_model, energy, c0, s, n_seq, cp,+                            *indx, *hc_up, ij, hc_decompose, e, *c, *ggg, with_gquad,+                            turn;+  vrna_sc_t                 *sc, **scs;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp            = vc->cutpoint;+  indx          = vc->jindx;+  hc            = vc->hc->matrix;+  hc_up         = vc->hc->up_int;+  P             = vc->params;+  ij            = indx[j] + i;+  hc_decompose  = hc[ij];+  e             = INF;+  c             = vc->matrices->c;+  ggg           = vc->matrices->ggg;+  md            = &(P->model_details);+  with_gquad    = md->gquad;+  turn          = md->min_loop_size;+  dangle_model  = md->dangles;+  types         = NULL;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  if (hc_decompose & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    SS      = vc->S;+    S5      = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+    S3      = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+    a2s     = vc->a2s;+    S_cons  = vc->S_cons;+    scs     = vc->scs;+    n_seq   = vc->n_seq;+    types   = (int *)vrna_alloc(sizeof(int) * n_seq);++    for (s = 0; s < n_seq; s++) {+      types[s] = md->pair[SS[s][i]][SS[s][j]];+      if (types[s] == 0)+        types[s] = 7;+    }++    /* prepare necessary variables */+    rtype = &(md->rtype[0]);+    max_q = i + turn + 2;+    max_q = MAX2(max_q, j - MAXLOOP - 1);++    for (q = j - 1; q >= max_q; q--) {+      j_q = j - q - 1;++      if (hc_up[q + 1] < j_q) break;++      pq    = indx[q] + i + 1;+      p_i   = 0;+      max_p = i + 1;+      tmp   = i + 1 + MAXLOOP - j_q;+      max_p = MAX2(max_p, tmp);+      tmp   = q - turn;+      max_p = MIN2(max_p, tmp);+      tmp   = i + 1 + hc_up[i + 1];+      max_p = MIN2(max_p, tmp);+      hc_pq = hc + pq;+      c_pq  = c + pq;++      for (p = i + 1; p <= max_p; p++) {+        eval_loop = *hc_pq & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;+        /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+        if (eval_loop && evaluate(i, j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+          energy = *c_pq;+          if (energy != INF) {+            for (s = 0; s < n_seq; s++) {+              type_2 = md->pair[SS[s][q]][SS[s][p]]; /* q,p not p,q! */+              if (type_2 == 0)+                type_2 = 7;++              sc = (scs && scs[s]) ? scs[s] : NULL;++              energy += ubf_eval_int_loop_comparative(i, j, p, q,+                                                      types[s], type_2, rtype,+                                                      ij, cp,+                                                      P,+                                                      SS[s],+                                                      S5[s],+                                                      S3[s],+                                                      a2s[s],+                                                      sc);+            }++            e = MIN2(e, energy);+          }+        }+        hc_pq++;    /* get hc[pq + 1] */+        c_pq++;     /* get c[pq + 1] */+        p_i++;      /* increase unpaired region [i+1...p-1] */++        pq++;+      } /* end q-loop */+    }   /* end p-loop */++    if (with_gquad) {+      /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */+      energy = 0;+      for (s = 0; s < n_seq; s++) {+        type = types[s];+        if (dangle_model == 2)+          energy += P->mismatchI[type][S3[s][i]][S5[s][j]];+        if (type > 2)+          energy += P->TerminalAU;+      }+      for (p = i + 2; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++) {+        u = p - i - 1;+        if (u > MAXLOOP) break;+        if (S_cons[p] != 3) continue;+        min_q = j - i + p - MAXLOOP - 2;+        c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+        min_q = MAX2(c0, min_q);+        c0    = j - 1;+        max_q = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+        max_q = MIN2(c0, max_q);+        for (q = min_q; q < max_q; q++) {+          if (S_cons[q] != 3) continue;+          c0  = energy + ggg[indx[q] + p] + n_seq * P->internal_loop[u + j - q - 1];+          e   = MIN2(e, c0);+        }+      }++      p = i + 1;+      if (S_cons[p] == 3) {+        if (p < j - VRNA_GQUAD_MIN_BOX_SIZE) {+          min_q = j - i + p - MAXLOOP - 2;+          c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+          min_q = MAX2(c0, min_q);+          c0    = j - 3;+          max_q = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+          max_q = MIN2(c0, max_q);+          for (q = min_q; q < max_q; q++) {+            if (S_cons[q] != 3) continue;+            c0  = energy + ggg[indx[q] + p] + n_seq * P->internal_loop[j - q - 1];+            e   = MIN2(e, c0);+          }+        }+      }+      q = j - 1;+      if (S_cons[q] == 3) {+        for (p = i + 4; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++) {+          u = p - i - 1;+          if (u > MAXLOOP) break;+          if (S_cons[p] != 3) continue;+          c0  = energy + ggg[indx[q] + p] + n_seq * P->internal_loop[u];+          e   = MIN2(e, c0);+        }+      }+    }+  }++  free(types);+  return e;+}+++PRIVATE INLINE int+eval_interior_loop(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   int                  p,+                   int                  q)+{+  int           energy, en, e, e5, e3, u1, u2, i1, j1, p1, q1, *idx;+  short         *S, si, sj, sp, sq;+  unsigned char type, type_2;+  unsigned int  *sn;+  int           *rtype, ij, cp, *bI;+  vrna_param_t  *P;+  vrna_sc_t     *sc;+  vrna_md_t     *md;+  vrna_ud_t     *domains_up;++  S           = vc->sequence_encoding;+  cp          = vc->cutpoint;+  P           = vc->params;+  sc          = vc->sc;+  domains_up  = vc->domains_up;+  md          = &(P->model_details);+  sn          = vc->strand_number;+  rtype       = &(md->rtype[0]);+  idx         = vc->jindx;+  type        = md->pair[S[i]][S[j]];+  type_2      = md->pair[S[q]][S[p]];++  i1  = i + 1;+  j1  = j - 1;+  p1  = p - 1;+  q1  = q + 1;+  u1  = p1 - i;+  u2  = j1 - q;++  si  = S[i1];+  sj  = S[j1];+  sp  = S[p1];+  sq  = S[q1];+  ij  = idx[j] + i;++  if (type == 0)+    type = 7;+  if (type_2 == 0)+    type_2 = 7;++  if ((sn[p] == sn[i]) && (sn[j] == sn[q])) {+    /* regular interior loop */+    energy = E_IntLoop(u1, u2, type, type_2, si, sj, sp, sq, P);+  } else {+    /* interior loop like cofold structure */+    short Si, Sj;+    Si      = (sn[i1] == sn[i]) ? si : -1;+    Sj      = (sn[j] == sn[j1]) ? sj : -1;+    energy  = E_IntLoop_Co(rtype[type], rtype[type_2],+                           i, j, p, q,+                           cp,+                           Si, Sj,+                           sp, sq,+                           P->model_details.dangles,+                           P);+  }++  /* add soft constraints */+  if (sc) {+    if (sc->energy_up)+      energy += sc->energy_up[i1][u1]+                + sc->energy_up[q1][u2];++    if (sc->energy_bp)+      energy += sc->energy_bp[ij];++    if (sc->energy_stack) {+      if (u1 + u2 == 0) {+        int a = sc->energy_stack[i]+                + sc->energy_stack[p]+                + sc->energy_stack[q]+                + sc->energy_stack[j];+        energy += a;+      }+    }+    if (sc->f)+      energy += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+  }++  e   = energy;+  e5  = e3 = 0;++  if (u1 > 0) {+    e5 = domains_up->energy_cb(vc,+                               i + 1, p - 1,+                               VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                               domains_up->data);+  }+  if (u2 > 0) {+    e3 = domains_up->energy_cb(vc,+                               q + 1, j - 1,+                               VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                               domains_up->data);+  }++  e = MIN2(e, energy + e5);+  e = MIN2(e, energy + e3);+  e = MIN2(e, energy + e5 + e3);+++  return e;+}+++PRIVATE FLT_OR_DBL+exp_E_int_loop(vrna_fold_compound_t *vc,+               int                  i,+               int                  j)+{+  unsigned char             type, type_2;+  char                      *ptype, *hc, eval_loop;+  short                     *S1, S_i1, S_j1;+  unsigned int              *sn;+  int                       k, l, u1, u2, kl, maxk, minl, *rtype, noGUclosure,+                            no_close, cp, *my_iindx, *jindx, *hc_up, ij,+                            with_gquad, turn;+  FLT_OR_DBL                qbt1, q_temp, *qb, *G, *scale;+  vrna_sc_t                 *sc;+  vrna_exp_param_t          *pf_params;+  vrna_md_t                 *md;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct  default_data      hc_dat_local;++  cp          = vc->cutpoint;+  ptype       = vc->ptype;+  S1          = vc->sequence_encoding;+  S_i1        = S1[i + 1];+  S_j1        = S1[j - 1];+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  hc          = vc->hc->matrix;+  hc_up       = vc->hc->up_int;+  sc          = vc->sc;+  sn          = vc->strand_number;+  pf_params   = vc->exp_params;+  ij          = jindx[j] + i;+  md          = &(pf_params->model_details);+  with_gquad  = md->gquad;+  turn        = md->min_loop_size;+  qb          = vc->exp_matrices->qb;+  G           = vc->exp_matrices->G;+  scale       = vc->exp_matrices->scale;+  domains_up  = vc->domains_up;+  qbt1        = 0.;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  if (hc[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    type        = (unsigned char)ptype[ij];+    rtype       = &(md->rtype[0]);+    noGUclosure = md->noGUclosure;+    no_close    = (((type == 3) || (type == 4)) && noGUclosure);+    maxk        = i + MAXLOOP + 1;+    maxk        = MIN2(maxk, j - turn - 2);+    maxk        = MIN2(maxk, i + 1 + hc_up[i + 1]);++    if (type == 0)+      type = 7;++    for (k = i + 1; k <= maxk; k++) {+      if (sn[k] != sn[i])+        break;+      u1 = k - i - 1;++      minl  = MAX2(k + turn + 1, j - 1 - MAXLOOP + u1);+      kl    = my_iindx[k] - j + 1;++      for (u2 = 0, l = j - 1; l >= minl; l--, kl++, u2++) {+        if (hc_up[l + 1] < u2) break;+        eval_loop = (hc[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC) ? (char)1 : (char)0;++        /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+        if (eval_loop && evaluate(i, j, k, l, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+          if (sn[j] != sn[l])+            break;+          type_2 = rtype[(unsigned char)ptype[jindx[l] + k]];++          if (type_2 == 0)+            type_2 = 7;++          q_temp = qb[kl]+                   * scale[u1 + u2 + 2]+                   * exp_E_IntLoop(u1, u2, type, type_2, S_i1, S_j1, S1[k - 1], S1[l + 1], pf_params);++          /* soft constraints */+          if (sc) {+            if (sc->exp_energy_up)+              q_temp *= sc->exp_energy_up[i + 1][u1]+                        * sc->exp_energy_up[l + 1][u2];++            if (sc->exp_f)+              q_temp *= sc->exp_f(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);++            if (sc->exp_energy_stack) {+              if ((i + 1 == k) && (j - 1 == l)) {+                q_temp *= sc->exp_energy_stack[i]+                          * sc->exp_energy_stack[k]+                          * sc->exp_energy_stack[l]+                          * sc->exp_energy_stack[j];+              }+            }+          }++          qbt1 += q_temp;++          /* unstructured domains */+          if (domains_up && domains_up->exp_energy_cb) {+            FLT_OR_DBL qq5, qq3;++            qq5 = qq3 = 0.;++            if (u1 > 0) {+              qq5 = domains_up->exp_energy_cb(vc,+                                              i + 1, k - 1,+                                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                              domains_up->data);+            }++            if (u2 > 0) {+              qq3 = domains_up->exp_energy_cb(vc,+                                              l + 1, j - 1,+                                              VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                              domains_up->data);+            }++            qbt1  += q_temp * qq5;        /* only motifs in 5' part */+            qbt1  += q_temp * qq3;        /* only motifs in 3' part */+            qbt1  += q_temp * qq5 * qq3;  /* motifs in both parts */+          }+        }+      }+    }++    if (with_gquad) {+      /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */+      if ((!no_close) && (sn[j] == sn[i]))+        qbt1 += exp_E_GQuad_IntLoop(i, j, type, S1, G, my_iindx, pf_params)+                * scale[2];+    }++    if (sc && sc->exp_energy_bp)+      qbt1 *= sc->exp_energy_bp[my_iindx[i] - j];+  }+  return qbt1;+}+++PUBLIC FLT_OR_DBL+vrna_exp_E_interior_loop(vrna_fold_compound_t *vc,+                         int                  i,+                         int                  j,+                         int                  k,+                         int                  l)+{+  if (vc)+    return exp_E_interior_loop(vc, i, j, k, l);++  return 0.;+}+++PRIVATE FLT_OR_DBL+exp_E_interior_loop(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    int                   k,+                    int                   l)+{+  unsigned char             type, type_2;+  char                      *ptype, *hc, eval_loop;+  short                     *S1, S_i1, S_j1;+  unsigned int              *sn;+  int                       u1, u2, kl, maxk, minl, *rtype, noGUclosure,+                            no_close, cp, *my_iindx, *jindx, *hc_up, ij,+                            with_gquad, turn;+  FLT_OR_DBL                qbt1, q_temp, *qb, *G, *scale;+  vrna_sc_t                 *sc;+  vrna_exp_param_t          *pf_params;+  vrna_md_t                 *md;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp          = vc->cutpoint;+  ptype       = vc->ptype;+  S1          = vc->sequence_encoding;+  S_i1        = S1[i + 1];+  S_j1        = S1[j - 1];+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  hc          = vc->hc->matrix;+  hc_up       = vc->hc->up_int;+  sc          = vc->sc;+  pf_params   = vc->exp_params;+  ij          = jindx[j] + i;+  kl          = my_iindx[k] - l;+  sn          = vc->strand_number;+  md          = &(pf_params->model_details);+  with_gquad  = md->gquad;+  turn        = md->min_loop_size;+  qb          = vc->exp_matrices->qb;+  G           = vc->exp_matrices->G;+  scale       = vc->exp_matrices->scale;+  domains_up  = vc->domains_up;+  qbt1        = 0.;+  u1          = k - i - 1;+  u2          = j - l - 1;++  if ((sn[k] != sn[i]) || (sn[j] != sn[l]))+    return qbt1;++  if (hc_up[l + 1] < u2)+    return qbt1;+  if (hc_up[i + 1] < u1)+    return qbt1;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  eval_loop = ((hc[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) && (hc[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC)) ? (char)1 : (char)0;++  /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+  if (eval_loop && evaluate(i, j, k, l, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+    type        = (unsigned char)ptype[ij];+    rtype       = &(md->rtype[0]);+    noGUclosure = md->noGUclosure;+    no_close    = (((type == 3) || (type == 4)) && noGUclosure);+    type        = (unsigned char)ptype[ij];+    type_2      = rtype[(unsigned char)ptype[jindx[l] + k]];++    if (type == 0)+      type = 7;++    if (type_2 == 0)+      type_2 = 7;++    q_temp = exp_E_IntLoop(u1, u2, type, type_2, S_i1, S_j1, S1[k - 1], S1[l + 1], pf_params)+             * scale[u1 + u2 + 2];++    /* soft constraints */+    if (sc) {+      if (sc->exp_energy_up)+        q_temp *= sc->exp_energy_up[i + 1][u1]+                  * sc->exp_energy_up[l + 1][u2];++      if (sc->exp_f)+        q_temp *= sc->exp_f(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);++      if (sc->exp_energy_stack) {+        if ((i + 1 == k) && (j - 1 == l)) {+          q_temp *= sc->exp_energy_stack[i]+                    * sc->exp_energy_stack[k]+                    * sc->exp_energy_stack[l]+                    * sc->exp_energy_stack[j];+        }+      }++      if (sc->exp_energy_bp)+        q_temp *= sc->exp_energy_bp[my_iindx[i] - j];+    }++    qbt1 += q_temp;++    /* unstructured domains */+    if (domains_up && domains_up->exp_energy_cb) {+      FLT_OR_DBL qq5, qq3;++      qq5 = qq3 = 0.;++      if (u1 > 0) {+        qq5 = domains_up->exp_energy_cb(vc,+                                        i + 1, k - 1,+                                        VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                        domains_up->data);+      }++      if (u2 > 0) {+        qq3 = domains_up->exp_energy_cb(vc,+                                        l + 1, j - 1,+                                        VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                                        domains_up->data);+      }++      qbt1  += q_temp * qq5;        /* only motifs in 5' part */+      qbt1  += q_temp * qq3;        /* only motigs in 3' part */+      qbt1  += q_temp * qq5 * qq3;  /* motifs in both parts */+    }+  }+  return qbt1;+}+++PRIVATE FLT_OR_DBL+exp_E_int_loop_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j)+{+  unsigned char             type_2;+  char                      *hc, eval_loop;+  unsigned short            **a2s;+  short                     **S, **S5, **S3;+  int                       n_seq, s, ij, jij, k, l, u1, u2, kl, maxk, minl, *types,+                            turn, with_gquad, *hc_up, *jindx, *my_iindx;+  FLT_OR_DBL                qbt1, *qb, *scale, qloop;+  vrna_sc_t                 **scs;+  vrna_exp_param_t          *pf_params;+  vrna_md_t                 *md;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  types       = NULL;+  my_iindx    = vc->iindx;+  jindx       = vc->jindx;+  hc          = vc->hc->matrix;+  hc_up       = vc->hc->up_int;+  pf_params   = vc->exp_params;+  md          = &(pf_params->model_details);+  with_gquad  = md->gquad;+  turn        = md->min_loop_size;+  qb          = vc->exp_matrices->qb;+  scale       = vc->exp_matrices->scale;+  qbt1        = 0.;+  jij         = jindx[j] + i;+  ij          = my_iindx[i] - j;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  if (hc[jij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    S     = vc->S;+    S5    = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+    S3    = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+    a2s   = vc->a2s;+    scs   = vc->scs;+    n_seq = vc->n_seq;+    types = (int *)vrna_alloc(sizeof(int) * n_seq);++    for (s = 0; s < n_seq; s++) {+      types[s] = md->pair[S[s][i]][S[s][j]];+      if (types[s] == 0)+        types[s] = 7;+    }++    /* prepare necessary variables */+    maxk  = i + MAXLOOP + 1;+    maxk  = MIN2(maxk, j - turn - 2);+    maxk  = MIN2(maxk, i + 1 + hc_up[i + 1]);++    for (k = i + 1; k <= maxk; k++) {+      u1 = k - i - 1;++      minl  = MAX2(k + turn + 1, j - 1 - MAXLOOP + u1);+      kl    = my_iindx[k] - j + 1;++      for (l = j - 1; l >= minl; l--, kl++, u2++) {+        if (hc_up[l + 1] < j - l - 1)+          break;++        eval_loop = (hc[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC) ? (char)1 : (char)0;++        /* discard this configuration if (p,q) is not allowed to be enclosed pair of an interior loop */+        if (eval_loop && evaluate(i, j, k, l, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+          qloop = 1.;++          for (s = 0; s < n_seq; s++) {+            u1      = a2s[s][k - 1] - a2s[s][i];+            u2      = a2s[s][j - 1] - a2s[s][l];+            type_2  = md->pair[S[s][l]][S[s][k]];++            if (type_2 == 0)+              type_2 = 7;++            qloop *= exp_E_IntLoop(u1, u2,+                                   types[s], type_2, S3[s][i],+                                   S5[s][j], S5[s][k], S3[s][l],+                                   pf_params+                                   );+          }++          if (scs) {+            for (s = 0; s < n_seq; s++) {+              if (scs[s]) {+                u1  = a2s[s][k - 1] - a2s[s][i];+                u2  = a2s[s][j - 1] - a2s[s][l];++                if (scs[s]->exp_energy_up)+                  qloop *= scs[s]->exp_energy_up[a2s[s][i] + 1][u1]+                           * scs[s]->exp_energy_up[a2s[s][l] + 1][u2];++                if (scs[s]->exp_energy_stack) {+                  if (u1 + u2 == 0) {+                    if (S[s][i] && S[s][j] && S[s][k] && S[s][l]) {+                      /* don't allow gaps in stack */+                      qloop *= scs[s]->exp_energy_stack[i]+                               * scs[s]->exp_energy_stack[k]+                               * scs[s]->exp_energy_stack[l]+                               * scs[s]->exp_energy_stack[j];+                    }+                  }+                }+              }+            }+          }++          qbt1 += qb[my_iindx[k] - l] * qloop * scale[k - i + j - l];+        }+      }+    }++    if (with_gquad) {+      /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */+      /* not implemented yet! */+    }++    if (scs) {+      for (s = 0; s < n_seq; s++)+        if (scs[s] && scs[s]->exp_energy_bp)+          qbt1 *= scs[s]->exp_energy_bp[ij];+    }+  }++  /* cleanup */+  free(types);++  return qbt1;+}+++PUBLIC int+vrna_E_ext_int_loop(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    int                   *ip,+                    int                   *iq)+{+  unsigned char             type, type_2;+  int                       ij, q, p, e, s, u1, u2, qmin, energy, *rtype, *types,+                            length, *indx, *hc_up, *c, turn, n_seq;+  char                      *ptype, *hc, eval_loop;+  unsigned short            **a2s;+  short                     *S, **SS, **S5, **S3;+  vrna_md_t                 *md;+  vrna_param_t              *P;+  vrna_sc_t                 *sc, **scs;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  length  = vc->length;+  indx    = vc->jindx;+  ptype   = vc->ptype;+  c       = vc->matrices->c;+  hc      = vc->hc->matrix;+  hc_up   = vc->hc->up_int;+  P       = vc->params;+  md      = &(P->model_details);+  turn    = md->min_loop_size;+  types   = NULL;+  ij      = indx[j] + i;+  rtype   = &(md->rtype[0]);+  e       = INF;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* CONSTRAINED INTERIOR LOOP start */+  if (hc[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    /* prepare necessary variables */+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        type = rtype[(unsigned char)ptype[ij]];++        if (type == 0)+          type = 7;++        S   = vc->sequence_encoding;+        sc  = vc->sc;+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        SS    = vc->S;+        S5    = vc->S5;                                 /*S5[s][i] holds next base 5' of i in sequence s*/+        S3    = vc->S3;                                 /*Sl[s][i] holds next base 3' of i in sequence s*/+        a2s   = vc->a2s;+        scs   = vc->scs;+        n_seq = vc->n_seq;+        types = (int *)vrna_alloc(sizeof(int) * n_seq);++        for (s = 0; s < n_seq; s++) {+          types[s] = md->pair[SS[s][j]][SS[s][i]];+          if (types[s] == 0)+            types[s] = 7;+        }+        break;++      default:+        return e;+        break;+    }++    for (p = j + 1; p < length; p++) {+      u1 = p - j - 1;+      if (u1 + i - 1 > MAXLOOP) break;+      if (hc_up[j + 1] < u1) break;++      qmin = u1 + i - 1 + length - MAXLOOP;+      if (qmin < p + turn + 1)+        qmin = p + turn + 1;+      for (q = length; q >= qmin; q--) {+        u2 = i - 1 + length - q;+        if (hc_up[q + 1] < u2)+          break;++        if (u1 + u2 > MAXLOOP)+          continue;++        eval_loop = hc[indx[q] + p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP;++        if (eval_loop && evaluate(i, j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+          switch (vc->type) {+            case VRNA_FC_TYPE_SINGLE:+              type_2 = rtype[(unsigned char)ptype[indx[q] + p]];++              if (type_2 == 0)+                type_2 = 7;++              energy = ubf_eval_ext_int_loop(i, j, p, q,+                                             i - 1, j + 1, p - 1, q + 1,+                                             S[j + 1], S[i - 1], S[p - 1], S[q + 1],+                                             type, type_2,+                                             length,+                                             P, sc);+              break;++            case VRNA_FC_TYPE_COMPARATIVE:+              for (energy = s = 0; s < n_seq; s++) {+                type_2 = md->pair[SS[s][q]][SS[s][p]];                             /* q,p not p,q! */+                if (type_2 == 0)+                  type_2 = 7;++                sc = (scs && scs[s]) ? scs[s] : NULL;++                energy += ubf_eval_ext_int_loop(a2s[s][i], a2s[s][j], a2s[s][p], a2s[s][q],+                                                a2s[s][i - 1], a2s[s][j + 1], a2s[s][p - 1], a2s[s][q + 1],+                                                S3[s][j], S5[s][i], S5[s][p], S3[s][q],+                                                types[s], type_2,+                                                a2s[s][length],+                                                P, sc);+              }+              break;+          }++          energy += c[indx[q] + p];++          if (energy < e) {+            e = energy;+            if ((ip != NULL) && (iq != NULL)) {+              *ip = p;+              *iq = q;+            }+          }+        }+      }+    }+  }++  free(types);++  return e;+}+++PUBLIC int+vrna_E_stack(vrna_fold_compound_t *vc,+             int                  i,+             int                  j)+{+  unsigned char             type, type_2;+  char                      *ptype, *hard_constraints, eval_loop;+  unsigned short            **a2s;+  short                     *S, **SS;+  unsigned int              *sn;+  int                       e, ij, pq, p, q, s, n_seq, cp, *rtype, *indx;+  vrna_sc_t                 *sc, **scs;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp                = vc->cutpoint;+  P                 = vc->params;+  md                = &(P->model_details);+  sn                = vc->strand_number;+  rtype             = &(md->rtype[0]);+  indx              = vc->jindx;+  hard_constraints  = vc->hc->matrix;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  e         = INF;+  p         = i + 1;+  q         = j - 1;+  ij        = indx[j] + i;+  pq        = indx[q] + p;+  eval_loop = (hard_constraints[pq] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC) && (hard_constraints[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP);++  if ((j - i - 1) < 2)+    return e;++  if (eval_loop && evaluate(i, j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        S       = vc->sequence_encoding;+        ptype   = vc->ptype;+        type    = (unsigned char)ptype[ij];+        type_2  = rtype[(unsigned char)ptype[pq]];+        sc      = vc->sc;++        if (type == 0)+          type = 7;+        if (type_2 == 0)+          type_2 = 7;++        if ((sn[p] == sn[i]) && (sn[j] == sn[q])) {+          /* regular stack */+          e = P->stack[type][type_2];+        } else {+          /* stack like cofold structure */+          short si, sj;+          si  = (sn[i + 1] == sn[i]) ? S[i + 1] : -1;+          sj  = (sn[j] == sn[j - 1]) ? S[j - 1] : -1;+          e   = E_IntLoop_Co(rtype[type], rtype[type_2],+                             i, j, p, q,+                             cp,+                             si, sj,+                             S[p - 1], S[q + 1],+                             md->dangles,+                             P);+        }++        /* add soft constraints */+        if (sc) {+          if (sc->energy_bp)+            e += sc->energy_bp[ij];++          if (sc->energy_stack) {+            e += sc->energy_stack[i]+                 + sc->energy_stack[p]+                 + sc->energy_stack[q]+                 + sc->energy_stack[j];+          }++          if (sc->f)+            e += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+        }+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        n_seq = vc->n_seq;+        SS    = vc->S;+        a2s   = vc->a2s;+        scs   = vc->scs;+        e     = 0;+        for (s = 0; s < n_seq; s++) {+          type    = md->pair[SS[s][i]][SS[s][j]];+          type_2  = md->pair[SS[s][q]][SS[s][p]];                            /* q,p not p,q! */+          if (type == 0)+            type = 7;+          if (type_2 == 0)+            type_2 = 7;+          e += P->stack[type][type_2];+        }++        if (scs) {+          for (s = 0; s < n_seq; s++) {+            if (scs[s]) {+              if (scs[s]->energy_bp)+                e += scs[s]->energy_bp[ij];++              if (scs[s]->energy_stack) {+                if (SS[s][i] && SS[s][j] && SS[s][p] && SS[s][q]) {+                  /* don't allow gaps in stack */+                  e += scs[s]->energy_stack[a2s[s][i]]+                       + scs[s]->energy_stack[a2s[s][p]]+                       + scs[s]->energy_stack[a2s[s][q]]+                       + scs[s]->energy_stack[a2s[s][j]];+                }+              }+              if (scs[s]->f)+                e += scs[s]->f(a2s[s][i], a2s[s][j], a2s[s][p], a2s[s][q], VRNA_DECOMP_PAIR_IL, scs[s]->data);+            }+          }+        }+        break;++      default:+        break;+    }+  }++  return e;+}+++PUBLIC int+vrna_BT_stack(vrna_fold_compound_t  *vc,+              int                   *i,+              int                   *j,+              int                   *en,+              vrna_bp_stack_t       *bp_stack,+              int                   *stack_count)+{+  unsigned char             type, type_2;+  char                      *ptype, eval_loop;+  unsigned int              *sn;+  int                       ij, p, q, *idx, *my_c, *rtype, cp;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp    = vc->cutpoint;+  idx   = vc->jindx;+  P     = vc->params;+  md    = &(P->model_details);+  hc    = vc->hc;+  sc    = vc->sc;+  sn    = vc->strand_number;+  my_c  = vc->matrices->c;+  ij    = idx[*j] + *i;+  ptype = vc->ptype;+  type  = (unsigned char)ptype[ij];+  rtype = &(md->rtype[0]);+  p     = *i + 1;+  q     = *j - 1;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  if (my_c[ij] == *en) {+    /*  always true, if (i.j) closes canonical structure,+     * thus (i+1.j-1) must be a pair+     */+    eval_loop = (hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP)+                && (hc->matrix[idx[q] + p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC);++    if (eval_loop && evaluate(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)) {+      type_2  = ptype[idx[q] + p];+      type_2  = rtype[type_2];++      if (type == 0)+        type = 7;+      if (type_2 == 0)+        type_2 = 7;++      if ((sn[p] == sn[*i]) && (sn[*j] == sn[q])) {+        /* regular stack */+        *en -= P->stack[type][type_2];+      } else {+        /* stack like cofold structure */+        short si, sj, *S;+        S   = vc->sequence_encoding;+        si  = (sn[p] == sn[*i]) ? S[p] : -1;+        sj  = (sn[*j] == sn[q]) ? S[q] : -1;+        *en -= E_IntLoop_Co(rtype[type], rtype[type_2],+                            *i, *j, p, q,+                            cp,+                            si, sj,+                            S[p - 1], S[q + 1],+                            md->dangles,+                            P);+      }++      if (sc) {+        if (sc->energy_bp)+          *en -= sc->energy_bp[ij];+        if (sc->energy_stack) {+          *en -= sc->energy_stack[*i]+                 + sc->energy_stack[p]+                 + sc->energy_stack[q]+                 + sc->energy_stack[*j];+        }+        if (sc->f)+          *en -= sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+      }+      bp_stack[++(*stack_count)].i  = p;+      bp_stack[(*stack_count)].j    = q;+      (*i)++;+      (*j)--;+      return 1;+    }+  }++  return 0;+}+++PUBLIC int+vrna_BT_int_loop(vrna_fold_compound_t *vc,+                 int                  *i,+                 int                  *j,+                 int                  en,+                 vrna_bp_stack_t      *bp_stack,+                 int                  *stack_count)+{+  unsigned char             type, type_2;+  char                      *ptype, eval_loop;+  short                     *S1;+  unsigned int              *sn;+  int                       cp, ij, p, q, minq, turn, *idx, noGUclosure, no_close,+                            energy, new, *my_c, *rtype;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp          = vc->cutpoint;+  idx         = vc->jindx;+  P           = vc->params;+  md          = &(P->model_details);+  hc          = vc->hc;+  sc          = vc->sc;+  sn          = vc->strand_number;+  my_c        = vc->matrices->c;+  turn        = md->min_loop_size;+  ij          = idx[*j] + *i;+  ptype       = vc->ptype;+  type        = (unsigned char)ptype[ij];+  rtype       = &(md->rtype[0]);+  S1          = vc->sequence_encoding;+  noGUclosure = md->noGUclosure;+  no_close    = (((type == 3) || (type == 4)) && noGUclosure);+  domains_up  = vc->domains_up;++  if (vc->hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = vc->hc->f;+    hc_dat_local.hc_dat = vc->hc->data;+  } else {+    evaluate = &hc_default;+  }++  if (hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP) {+    if (type == 0)+      type = 7;++    if (domains_up && domains_up->energy_cb) {+      for (p = *i + 1; p <= MIN2(*j - 2 - turn, *i + MAXLOOP + 1); p++) {+        minq = *j - *i + p - MAXLOOP - 2;+        if (minq < p + 1 + turn)+          minq = p + 1 + turn;++        if (hc->up_int[*i + 1] < (p - *i - 1))+          break;++        for (q = *j - 1; q >= minq; q--) {+          if (hc->up_int[q + 1] < (*j - q - 1))+            break;++          type_2    = (unsigned char)ptype[idx[q] + p];+          eval_loop = hc->matrix[idx[q] + p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;++          if (!(eval_loop && evaluate(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)))+            continue;++          type_2 = rtype[type_2];++          if (type_2 == 0)+            type_2 = 7;++          if (noGUclosure)+            if (no_close || (type_2 == 3) || (type_2 == 4))+              if ((p > *i + 1) || (q < *j - 1))+                continue;  /* continue unless stack */++          energy  = eval_interior_loop(vc, *i, *j, p, q);+          new     = energy + my_c[idx[q] + p];++          if (new == en) {+            bp_stack[++(*stack_count)].i  = p;+            bp_stack[(*stack_count)].j    = q;+            if (sc) {+              if (sc->bt) {+                vrna_basepair_t *ptr, *aux_bps;+                aux_bps = sc->bt(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+                for (ptr = aux_bps; ptr && ptr->i != 0; ptr++) {+                  bp_stack[++(*stack_count)].i  = ptr->i;+                  bp_stack[(*stack_count)].j    = ptr->j;+                }+                free(aux_bps);+              }+            }+            *i = p, *j = q;+            return 1; /* success */+          }+        }+      }+    } else {+      for (p = *i + 1; p <= MIN2(*j - 2 - turn, *i + MAXLOOP + 1); p++) {+        minq = *j - *i + p - MAXLOOP - 2;+        if (minq < p + 1 + turn)+          minq = p + 1 + turn;++        if (hc->up_int[*i + 1] < (p - *i - 1))+          break;++        for (q = *j - 1; q >= minq; q--) {+          if (hc->up_int[q + 1] < (*j - q - 1))+            break;++          type_2 = (unsigned char)ptype[idx[q] + p];++          eval_loop = hc->matrix[idx[q] + p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC;++          if (!(eval_loop && evaluate(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, &hc_dat_local)))+            continue;++          type_2 = rtype[type_2];++          if (type_2 == 0)+            type_2 = 7;++          if (noGUclosure)+            if (no_close || (type_2 == 3) || (type_2 == 4))+              if ((p > *i + 1) || (q < *j - 1))+                continue;  /* continue unless stack */++          energy = ubf_eval_int_loop(*i, *j, p, q,+                                     (*i) + 1, (*j) - 1, p - 1, q + 1,+                                     S1[*i + 1], S1[*j - 1], S1[p - 1], S1[q + 1],+                                     type, type_2,+                                     rtype,+                                     ij,+                                     -1,+                                     P,+                                     sc);+          new = energy + my_c[idx[q] + p];++          if (new == en) {+            bp_stack[++(*stack_count)].i  = p;+            bp_stack[(*stack_count)].j    = q;+            if (sc) {+              if (sc->bt) {+                vrna_basepair_t *ptr, *aux_bps;+                aux_bps = sc->bt(*i, *j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+                for (ptr = aux_bps; ptr && ptr->i != 0; ptr++) {+                  bp_stack[++(*stack_count)].i  = ptr->i;+                  bp_stack[(*stack_count)].j    = ptr->j;+                }+                free(aux_bps);+              }+            }+            *i = p, *j = q;+            return 1; /* success */+          }+        }+      }+    }+  }++  /* is it a g-quadruplex? */+  if (md->gquad) {+    /*+     * The case that is handled here actually resembles something like+     * an interior loop where the enclosing base pair is of regular+     * kind and the enclosed pair is not a canonical one but a g-quadruplex+     * that should then be decomposed further...+     */+    if (sn[*j] == sn[*i]) {+      if (vrna_BT_gquad_int(vc, *i, *j, en, bp_stack, stack_count)) {+        *i = *j = -1; /* tell the calling block to continue backtracking with next block */+        return 1;+      }+    }+  }++  return 0; /* unsuccessful */+}+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data)+{+  return (char)1;+}+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data)+{+  struct default_data *dat = (struct default_data *)data;++  return dat->hc_f(i, j, k, l, d, dat->hc_dat);+}
+ C/ViennaRNA/interior_loops.h view
@@ -0,0 +1,532 @@+#ifndef VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H+#define VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H++#include <ViennaRNA/utils.h>+#include "ViennaRNA/energy_par.h"+#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/constraints.h>++#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif++#ifdef ON_SAME_STRAND+#undef ON_SAME_STRAND+#endif++#define ON_SAME_STRAND(I,J,C)  (((I)>=(C))||((J)<(C)))++/**+ *  @file     interior_loops.h+ *  @ingroup  loops+ *  @brief    Energy evaluation of interior loops for MFE and partition function calculations+ */++/**+ *  @{+ *  @ingroup   loops+ */++/**+ *  <H2>Compute the Energy of an interior-loop</H2>+ *  This function computes the free energy @f$\Delta G@f$ of an interior-loop with the+ *  following structure: <BR>+ *  <PRE>+ *        3'  5'+ *        |   |+ *        U - V+ *    a_n       b_1+ *     .        .+ *     .        .+ *     .        .+ *    a_1       b_m+ *        X - Y+ *        |   |+ *        5'  3'+ *  </PRE>+ *  This general structure depicts an interior-loop that is closed by the base pair (X,Y).+ *  The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n+ *  that constitute the loop. In this example, the length of the interior-loop is @f$(n+m)@f$+ *  where n or m may be 0 resulting in a bulge-loop or base pair stack.+ *  The mismatching nucleotides for the closing pair (X,Y) are:<BR>+ *  5'-mismatch: a_1<BR>+ *  3'-mismatch: b_m<BR>+ *  and for the enclosed base pair (V,U):<BR>+ *  5'-mismatch: b_1<BR>+ *  3'-mismatch: a_n<BR>+ *  @note Base pairs are always denoted in 5'->3' direction. Thus the enclosed base pair+ *  must be 'turned arround' when evaluating the free energy of the interior-loop+ *  @see scale_parameters()+ *  @see vrna_param_t+ *  @note This function is threadsafe+ * + *  @param  n1      The size of the 'left'-loop (number of unpaired nucleotides)+ *  @param  n2      The size of the 'right'-loop (number of unpaired nucleotides)+ *  @param  type    The pair type of the base pair closing the interior loop+ *  @param  type_2  The pair type of the enclosed base pair+ *  @param  si1     The 5'-mismatching nucleotide of the closing pair+ *  @param  sj1     The 3'-mismatching nucleotide of the closing pair+ *  @param  sp1     The 3'-mismatching nucleotide of the enclosed pair+ *  @param  sq1     The 5'-mismatching nucleotide of the enclosed pair+ *  @param  P       The datastructure containing scaled energy parameters+ *  @return The Free energy of the Interior-loop in dcal/mol+ */+PRIVATE INLINE int E_IntLoop(int n1,+                              int n2,+                              int type,+                              int type_2,+                              int si1,+                              int sj1,+                              int sp1,+                              int sq1,+                              vrna_param_t *P);++/**+ *  <H2>Compute Boltzmann weight @f$e^{-\Delta G/kT} @f$ of interior loop</H2>+ *  multiply by scale[u1+u2+2] for scaling+ *  @see get_scaled_pf_parameters()+ *  @see vrna_exp_param_t+ *  @see E_IntLoop()+ *  @note This function is threadsafe+ * + *  @param  u1      The size of the 'left'-loop (number of unpaired nucleotides)+ *  @param  u2      The size of the 'right'-loop (number of unpaired nucleotides)+ *  @param  type    The pair type of the base pair closing the interior loop+ *  @param  type2   The pair type of the enclosed base pair+ *  @param  si1     The 5'-mismatching nucleotide of the closing pair+ *  @param  sj1     The 3'-mismatching nucleotide of the closing pair+ *  @param  sp1     The 3'-mismatching nucleotide of the enclosed pair+ *  @param  sq1     The 5'-mismatching nucleotide of the enclosed pair+ *  @param  P       The datastructure containing scaled Boltzmann weights of the energy parameters+ *  @return The Boltzmann weight of the Interior-loop+ */+PRIVATE INLINE FLT_OR_DBL exp_E_IntLoop(int u1,+                                        int u2,+                                        int type,+                                        int type2,+                                        short si1,+                                        short sj1,+                                        short sp1,+                                        short sq1,+                                        vrna_exp_param_t *P);+++PRIVATE INLINE int E_IntLoop_Co(int type,+                                int type_2,+                                int i,+                                int j,+                                int p,+                                int q,+                                int cutpoint,+                                short si1,+                                short sj1,+                                short sp1,+                                short sq1,+                                int dangles,+                                vrna_param_t *P);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++/*+ *  ugly but fast interior loop evaluation+ *+ *  Avoid including this function in your own code. It only serves+ *  as a fast inline block internally re-used throughout the RNAlib. It+ *  evalutes the free energy of interior loops in single sequences or sequence+ *  hybrids. Soft constraints are also applied if available.+ *+ *  NOTE: do not include into doxygen reference manual!+ */+PRIVATE INLINE int+ubf_eval_int_loop(  int i,+                    int j,+                    int p,+                    int q,+                    int i1,+                    int j1,+                    int p1,+                    int q1,+                    short si,+                    short sj,+                    short sp,+                    short sq,+                    unsigned char type,+                    unsigned char type_2,+                    int *rtype,+                    int ij,+                    int cp,+                    vrna_param_t *P,+                    vrna_sc_t *sc){++  int energy, u1, u2;++  u1 = p1 - i;+  u2 = j1 - q;++  if((cp < 0) || (ON_SAME_STRAND(i, p, cp) && ON_SAME_STRAND(q, j, cp))){ /* regular interior loop */+    energy = E_IntLoop(u1, u2, type, type_2, si, sj, sp, sq, P);+  } else { /* interior loop like cofold structure */+    short Si, Sj;+    Si  = ON_SAME_STRAND(i, i1, cp) ? si : -1;+    Sj  = ON_SAME_STRAND(j1, j, cp) ? sj : -1;+    energy = E_IntLoop_Co(rtype[type], rtype[type_2],+                            i, j, p, q,+                            cp,+                            Si, Sj,+                            sp, sq,+                            P->model_details.dangles,+                            P);+  }++  /* add soft constraints */+  if(sc){+    if(sc->energy_up)+      energy += sc->energy_up[i1][u1]+                + sc->energy_up[q1][u2];++    if(sc->energy_bp)+      energy += sc->energy_bp[ij];++    if(sc->energy_stack)+      if(u1 + u2 == 0){+        int a =   sc->energy_stack[i]+                  + sc->energy_stack[p]+                  + sc->energy_stack[q]+                  + sc->energy_stack[j];+        energy += a;+      }+    if(sc->f)+      energy += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+  }++  return energy;++}++/*+ *  ugly but fast exterior interior loop evaluation+ *+ *  Avoid including this function in your own code. It only serves+ *  as a fast inline block internally re-used throughout the RNAlib. It+ *  evalutes the free energy of interior loops in single sequences or sequence+ *  hybrids. Soft constraints are also applied if available.+ *+ *  NOTE: do not include into doxygen reference manual!+ */+PRIVATE INLINE int+ubf_eval_ext_int_loop(int i,+                      int j,+                      int p,+                      int q,+                      int i1,+                      int j1,+                      int p1,+                      int q1,+                      short si,+                      short sj,+                      short sp,+                      short sq,+                      unsigned char type,+                      unsigned char type_2,+                      int length,+                      vrna_param_t *P,+                      vrna_sc_t *sc){++  int energy, u1, u2, u3;+  +  u1 = i1;+  u2 = p1 - j;+  u3 = length - q;++  energy = E_IntLoop(u2, u1 + u3, type, type_2, si, sj, sp, sq, P);++  /* add soft constraints */+  if(sc){+    if(sc->energy_up){+      energy += sc->energy_up[j1][u2]+                + ((u3 > 0) ? sc->energy_up[q1][u3] : 0)+                + ((u1 > 0) ? sc->energy_up[1][u1] : 0);+    }+    if(sc->energy_stack)+      if(u1 + u2 + u3 == 0)+        energy +=   sc->energy_stack[i]+                  + sc->energy_stack[p]+                  + sc->energy_stack[q]+                  + sc->energy_stack[j];++    if(sc->f)+      energy += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+  }++  return energy;++}++PRIVATE INLINE int+E_IntLoop(int n1,+          int n2,+          int type,+          int type_2,+          int si1,+          int sj1,+          int sp1,+          int sq1,+          vrna_param_t *P){++  /* compute energy of degree 2 loop (stack bulge or interior) */+  int nl, ns, u, energy;+  energy = INF;++  if (n1>n2) { nl=n1; ns=n2;}+  else {nl=n2; ns=n1;}++  if (nl == 0)+    return P->stack[type][type_2];  /* stack */++  if (ns==0) {                      /* bulge */+    energy = (nl<=MAXLOOP)?P->bulge[nl]:+      (P->bulge[30]+(int)(P->lxc*log(nl/30.)));+    if (nl==1) energy += P->stack[type][type_2];+    else {+      if (type>2) energy += P->TerminalAU;+      if (type_2>2) energy += P->TerminalAU;+    }+    return energy;+  }+  else {                            /* interior loop */+    if (ns==1) {+      if (nl==1)                    /* 1x1 loop */+        return P->int11[type][type_2][si1][sj1];+      if (nl==2) {                  /* 2x1 loop */+        if (n1==1)+          energy = P->int21[type][type_2][si1][sq1][sj1];+        else+          energy = P->int21[type_2][type][sq1][si1][sp1];+        return energy;+      }+      else {  /* 1xn loop */+        energy = (nl+1<=MAXLOOP)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));+        energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);+        energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];+        return energy;+      }+    }+    else if (ns==2) {+      if(nl==2)      {              /* 2x2 loop */+        return P->int22[type][type_2][si1][sp1][sq1][sj1];}+      else if (nl==3){              /* 2x3 loop */+        energy = P->internal_loop[5]+P->ninio[2];+        energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];+        return energy;+      }++    }+    { /* generic interior loop (no else here!)*/+      u = nl + ns;+      energy = (u <= MAXLOOP) ? (P->internal_loop[u]) : (P->internal_loop[30]+(int)(P->lxc*log((u)/30.)));++      energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);++      energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];+    }+  }+  return energy;+}++PRIVATE INLINE FLT_OR_DBL+exp_E_IntLoop(int u1,+              int u2,+              int type,+              int type2,+              short si1,+              short sj1,+              short sp1,+              short sq1,+              vrna_exp_param_t *P){++  int ul, us, no_close = 0;+  double z = 0.;+  int noGUclosure = P->model_details.noGUclosure;++  if ((noGUclosure) && ((type2==3)||(type2==4)||(type==3)||(type==4)))+    no_close = 1;++  if (u1>u2) { ul=u1; us=u2;}+  else {ul=u2; us=u1;}++  if (ul==0) /* stack */+    z = P->expstack[type][type2];+  else if(!no_close){+    if (us==0) {                      /* bulge */+      z = P->expbulge[ul];+      if (ul==1) z *= P->expstack[type][type2];+      else {+        if (type>2) z *= P->expTermAU;+        if (type2>2) z *= P->expTermAU;+      }+      return (FLT_OR_DBL)z;+    }+    else if (us==1) {+      if (ul==1){                    /* 1x1 loop */+        return (FLT_OR_DBL)(P->expint11[type][type2][si1][sj1]);+      }+      if (ul==2) {                  /* 2x1 loop */+        if (u1==1)+          return (FLT_OR_DBL)(P->expint21[type][type2][si1][sq1][sj1]);+        else+          return (FLT_OR_DBL)(P->expint21[type2][type][sq1][si1][sp1]);+      }+      else {  /* 1xn loop */+        z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];+        return (FLT_OR_DBL)(z * P->expninio[2][ul-us]);+      }+    }+    else if (us==2) {+      if(ul==2) /* 2x2 loop */+        return (FLT_OR_DBL)(P->expint22[type][type2][si1][sp1][sq1][sj1]);+      else if(ul==3){              /* 2x3 loop */+        z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];+        return (FLT_OR_DBL)(z * P->expninio[2][1]);+      }+    }+    /* generic interior loop (no else here!)*/+    z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];+    return (FLT_OR_DBL)(z * P->expninio[2][ul-us]);++  }+  return (FLT_OR_DBL)z;+}++PRIVATE INLINE int+E_IntLoop_Co( int type,+              int type_2,+              int i,+              int j,+              int p,+              int q,+              int cutpoint,+              short si1,+              short sj1,+              short sp1,+              short sq1,+              int dangles,+              vrna_param_t *P){++  int energy, ci, cj, cp, cq, d3, d5, d5_2, d3_2, tmm, tmm_2;++  energy = 0;+  if(type > 2)   energy += P->TerminalAU;+  if(type_2 > 2) energy += P->TerminalAU;++  if(!dangles) return energy;++  ci = ON_SAME_STRAND(i, i + 1, cutpoint);+  cj = ON_SAME_STRAND(j - 1, j, cutpoint);+  cp = ON_SAME_STRAND(p - 1, p, cutpoint);+  cq = ON_SAME_STRAND(q, q + 1, cutpoint);++  d3    = ci  ? P->dangle3[type][si1]   : 0;+  d5    = cj  ? P->dangle5[type][sj1]   : 0;+  d5_2  = cp  ? P->dangle5[type_2][sp1] : 0;+  d3_2  = cq  ? P->dangle3[type_2][sq1] : 0;++  tmm   = (cj && ci) ? P->mismatchExt[type][sj1][si1]   : d5 + d3;+  tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;++  if(dangles == 2) return energy + tmm + tmm_2;++  /* now we may have non-double dangles only */+  if(i+2 < p){+    if(q+2 < j){ energy += tmm + tmm_2;}+    else if(q+2 == j){ energy += (cj && cq) ? MIN2(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}+    else energy += d3 + d5_2;+  }+  else if(i+2 == p){+    if(q+2 < j){ energy += (ci && cp) ? MIN2(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}+    else if(q+2 == j){+      energy += MIN2(tmm, MIN2(tmm_2, MIN2(d5 + d5_2, d3 + d3_2)));+    }+    else energy += MIN2(d3, d5_2);+  }+  else{+    if(q+2 < j){ energy += d5 + d3_2;}+    else if(q+2 == j){ energy += MIN2(d5, d3_2);}+  }+  return energy;+}++int+vrna_E_int_loop(vrna_fold_compound_t *vc,+                int i,+                int j);++int+vrna_eval_int_loop( vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    int k,+                    int l);++FLT_OR_DBL+vrna_exp_E_int_loop(vrna_fold_compound_t *vc,+                int i,+                int j);++FLT_OR_DBL+vrna_exp_E_interior_loop( vrna_fold_compound_t *vc,+                          int i,+                          int j,+                          int k,+                          int l);++int+vrna_E_ext_int_loop(vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    int *ip,+                    int *iq);++int+vrna_E_stack( vrna_fold_compound_t *vc,+              int i,+              int j);+++/**+ *  @brief Backtrack a stacked pair closed by @f$ (i,j) @f$+ *+ */+int+vrna_BT_stack(vrna_fold_compound_t *vc,+              int *i,+              int *j,+              int *en,+              vrna_bp_stack_t *bp_stack,+              int *stack_count);+/**+ *  @brief Backtrack an interior loop closed by @f$ (i,j) @f$+ *+ */+int+vrna_BT_int_loop( vrna_fold_compound_t *vc,+                  int *i,+                  int *j,+                  int en,+                  vrna_bp_stack_t *bp_stack,+                  int *stack_count);+++/**+ * @}+ */+++#endif
+ C/ViennaRNA/intl11.h view
@@ -0,0 +1,393 @@+PUBLIC int int11_37[NBPAIRS+1][NBPAIRS+1][5][5] =+{{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{    90,    90,    50,    50,    50}+  ,{    90,    90,    50,    50,    50}+  ,{    50,    50,    50,    50,    50}+  ,{    50,    50,    50,  -140,    50}+  ,{    50,    50,    50,    50,    40}+  }+ ,{{    90,    90,    50,    50,    60}+  ,{    90,    90,   -40,    50,    50}+  ,{    60,    30,    50,    50,    60}+  ,{    50,   -10,    50,  -220,    50}+  ,{    50,    50,     0,    50,   -10}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,    60,    50,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   -20,   120,  -140,   120}+  ,{   120,   120,   100,   120,   110}+  }+ ,{{   220,   220,   170,   120,   120}+  ,{   220,   220,   130,   120,   120}+  ,{   170,   120,   170,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   110}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,    80}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ ,{{   220,   220,   170,   120,   120}+  ,{   220,   220,   130,   120,   120}+  ,{   170,   120,   170,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{    90,    90,    60,    50,    50}+  ,{    90,    90,    30,   -10,    50}+  ,{    50,   -40,    50,    50,     0}+  ,{    50,    50,    50,  -220,    50}+  ,{    60,    50,    60,    50,   -10}+  }+ ,{{    80,    80,    50,    50,    50}+  ,{    80,    80,    50,    50,    50}+  ,{    50,    50,    50,    50,    50}+  ,{    50,    50,    50,  -230,    50}+  ,{    50,    50,    50,    50,   -60}+  }+ ,{{   190,   190,   120,   150,   150}+  ,{   190,   190,   120,   150,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   150,   120,   120,   120,   150}+  }+ ,{{   160,   160,   120,   120,   120}+  ,{   160,   160,   120,   100,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,    70}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,    80}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ ,{{   190,   190,   120,   150,   150}+  ,{   190,   190,   120,   150,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   150,   120,   120,   120,   150}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,    60,   120,   -20,   120}+  ,{   120,    50,   120,   120,   100}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   110}+  }+ ,{{   190,   190,   120,   120,   150}+  ,{   190,   190,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   150,   150,   120,  -140,   120}+  ,{   150,   120,   120,   120,   150}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   120}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   120}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   220,   220,   170,   120,   120}+  ,{   220,   220,   120,   120,   120}+  ,{   170,   130,   170,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   110}+  }+ ,{{   160,   160,   120,   120,   120}+  ,{   160,   160,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   100,   120,  -140,   120}+  ,{   120,   120,   120,   120,    70}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ ,{{   220,   220,   190,   190,   190}+  ,{   220,   220,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,    80}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,    80}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   120}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   120}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   150}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ ,{{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   150}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   170}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   220,   220,   170,   120,   120}+  ,{   220,   220,   120,   120,   120}+  ,{   170,   130,   170,   120,   120}+  ,{   120,   120,   120,  -140,   120}+  ,{   120,   120,   120,   120,   120}+  }+ ,{{   190,   190,   120,   120,   150}+  ,{   190,   190,   120,   120,   120}+  ,{   120,   120,   120,   120,   120}+  ,{   150,   150,   120,  -140,   120}+  ,{   150,   120,   120,   120,   150}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   220,   220,   190,   190,   190}+  ,{   220,   220,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   160}+  }+ ,{{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ ,{{   220,   220,   190,   190,   190}+  ,{   220,   220,   190,   190,   190}+  ,{   190,   190,   190,   190,   190}+  ,{   190,   190,   190,   -70,   190}+  ,{   190,   190,   190,   190,   190}+  }+ }};
+ C/ViennaRNA/intl11dH.h view
@@ -0,0 +1,393 @@+PUBLIC int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5] =+{{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1840, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  }+ ,{{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1840, -1050}+  ,{ -1050, -1050, -1050, -1050, -1390}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1840, -1050}+  ,{ -1050, -1050, -1050, -1050, -1390}+  }+ ,{{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1050, -1050}+  ,{ -1050, -1050, -1050, -1840, -1050}+  ,{ -1050, -1050, -1050, -1050, -1730}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550, -1230}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550, -1230}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550, -1230}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -730}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -730}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550, -1230}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -730}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -730}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ }+,{{{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  ,{   INF,   INF,   INF,   INF,   INF}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  }+ ,{{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550,  -550,  -550}+  ,{  -550,  -550,  -550, -1340,  -550}+  ,{  -550,  -550,  -550,  -550,  -890}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,  -390}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ ,{{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  ,{   -50,   -50,   -50,  -830,   -50}+  ,{   -50,   -50,   -50,   -50,   -50}+  }+ }};
+ C/ViennaRNA/intl21.h view
@@ -0,0 +1,1993 @@+PUBLIC int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5] =+{{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ }+,{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   230,   230,   230,   230,   230}+   ,{   230,   230,   230,   230,   230}+   ,{   230,   230,   230,   230,   230}+   ,{   230,   230,   230,   230,   230}+   ,{   230,   230,   230,   230,   230}+   }+  ,{{   230,   230,   230,   110,   230}+   ,{   230,   230,   230,   110,   230}+   ,{   230,   230,   230,   110,   230}+   ,{   110,   110,   110,   110,   110}+   ,{   230,   230,   230,   110,   230}+   }+  ,{{   230,   230,   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,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ }+,{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   190,   190,   190,   190,   190}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   190,   300,   190,   300}+   ,{   190,   190,   190,   190,   190}+   ,{   300,   190,   300,   190,   300}+   ,{   190,   190,   190,   190,   190}+   ,{   300,   190,   300,   190,   300}+   }+  ,{{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   220,   220,   220,   220,   220}+   }+  }+ ,{{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   190,   190,   190,   190,   190}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   ,{   300,   300,   300,   300,   300}+   }+  ,{{   300,   190,   300,   190,   300}+   ,{   300,   190,   300,   190,   300}+   ,{   300,   190,   300,   190,   300}+   ,{   190,   190,   190,   190,   190}+   ,{   300,   190,   300,   190,   300}+   }+  ,{{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   300,   300,   300,   300,   220}+   ,{   220,   220,   220,   220,   220}+   }+  }+ ,{{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   }+  ,{{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ ,{{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   }+  ,{{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ ,{{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   }+  ,{{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ ,{{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   }+  ,{{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ ,{{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   ,{   370,   370,   370,   370,   370}+   }+  ,{{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   370,   260,   370,   260,   370}+   ,{   260,   260,   260,   260,   260}+   ,{   370,   260,   370,   260,   370}+   }+  ,{{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   370,   370,   370,   370,   300}+   ,{   300,   300,   300,   300,   300}+   }+  }+ }};
+ C/ViennaRNA/intl21dH.h view
@@ -0,0 +1,1993 @@+PUBLIC int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5] =+{{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ }+,{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   }+  ,{{   350,   350,   350,  -230,   350}+   ,{   350,   350,   350,  -230,   350}+   ,{   350,   350,   350,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,   350,   350,  -230,   350}+   }+  ,{{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   }+  ,{{   350,  -230,   350,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,  -230,   350,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,  -230,   350,  -230,   350}+   }+  ,{{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{  -670,  -670,  -670,  -670,  -670}+   }+  }+ ,{{{   780,   640,   780,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   780,   350,   780,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   640,   640,   350,   350,   350}+   }+  ,{{   350,   350,   350,   250,   350}+   ,{   350,   260,   350,   250,   350}+   ,{   350,   350,  -250,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,   350,   350,  -230,   350}+   }+  ,{{   780,   640,   780,   350,   350}+   ,{   350,   160,   350,   350,   350}+   ,{   780,   350,   780,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   640,   640,   350,   350,   350}+   }+  ,{{   350,  -160,   350,  -230,   350}+   ,{   350,  -160,   350,  -410,   350}+   ,{   350,  -230,   350,  -230,   350}+   ,{  -230,  -310,  -230,  -230,  -230}+   ,{   350,  -230,   350,  -230,   350}+   }+  ,{{   580,   350,   580,   350,  -580}+   ,{   350,   350,   350,   350,  -670}+   ,{   580,   350,   580,   350,  -580}+   ,{   350,   350,   350,   350,  -670}+   ,{  -670,  -670,  -690,  -670,  -700}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   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280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   850,   850,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   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 INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   690,   690,   350,   350,   350}+   ,{   690,   690,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   }+  ,{{   690,   690,   350,   350,   350}+   ,{   690,   690,   350,   240,   350}+   ,{   350,   350,   350,   350,   350}+   ,{  -230,  -500,  -230,  -230,  -230}+   ,{   350,   350,   350,   350,   350}+   }+  ,{{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   350,   350,   350}+   ,{   350,   350,   130,   350,   350}+   }+  ,{{   350,  -230,   350,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,  -230,   350,  -230,   350}+   ,{  -230,  -230,  -230,  -230,  -230}+   ,{   350,  -230,   350,  -230,   350}+   }+  ,{{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{   350,   350,   350,   350,  -670}+   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350,  -670}+   ,{   350,   350,   350,   350,  -670}+   ,{  -670,  -670,  -670,  -670,  -670}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   690,   850,   240,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   280,  -500,   280,   280,   280}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   130,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  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280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   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1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{  1350,  1350,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ }+,{{{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  ,{{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   ,{   INF,   INF,   INF,   INF,   INF}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   ,{   850,   850,   850,   850,   850}+   }+  ,{{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   850,   280,   850,   280,   850}+   ,{   280,   280,   280,   280,   280}+   ,{   850,   280,   850,   280,   850}+   }+  ,{{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{   850,   850,   850,   850,  -160}+   ,{  -160,  -160,  -160,  -160,  -160}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ ,{{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   ,{  1350,  1350,  1350,  1350,  1350}+   }+  ,{{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{  1350,   780,  1350,   780,  1350}+   ,{   780,   780,   780,   780,   780}+   ,{  1350,   780,  1350,   780,  1350}+   }+  ,{{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{  1350,  1350,  1350,  1350,   340}+   ,{   340,   340,   340,   340,   340}+   }+  }+ }};
+ C/ViennaRNA/intl22.h view
@@ -0,0 +1,9993 @@+PUBLIC int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =+{{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,  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180,   130,   260,   260}+    ,{   320,   320,   280,   280,   280}+    }+   ,{{   350,   330,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   350,   320,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   290,   290,   200,   200,   200}+    }+   }+  ,{{{   350,   340,   310,   350,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   350,   320,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   350,   320,   290,   350,   290}+    }+   ,{{   340,   340,   310,   310,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   320,   320,   280,   280,   280}+    ,{   220,   220,   180,   180,   180}+    ,{   320,   320,   280,   280,   280}+    }+   ,{{   350,   330,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   350,   320,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   350,   320,   290,   350,   290}+    }+   ,{{   320,   320,   280,   280,   280}+    ,{   290,   290,   250,   250,   250}+    ,{   320,   320,   280,   280,   280}+    ,{   260,   170,   130,   260,   130}+    ,{   320,   320,   280,   280,   280}+    }+   ,{{   350,   330,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   350,   320,   290,   350,   290}+    ,{   330,   330,   290,   290,   290}+    ,{   290,   290,   200,   200,   200}+    }+   }+  ,{{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    }+   ,{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   280,   280,   280,   280,   280}+    ,{   240,   180,   240,   180,   240}+    ,{   280,   280,   280,   280,   280}+    }+   ,{{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    }+   ,{{   310,   280,   310,   280,   310}+    ,{   310,   250,   310,   250,   310}+    ,{   280,   280,   280,   280,   280}+    ,{   130,   130,   130,   130,   130}+    ,{   280,   280,   280,   280,   280}+    }+   ,{{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   200,   200,   200,   200,   200}+    }+   }+  ,{{{   310,   270,   310,   260,   310}+    ,{   310,   230,   310,   250,   310}+    ,{   290,   270,   290,   160,   290}+    ,{   290,   210,   290,   260,   290}+    ,{   290,   270,   290,   200,   290}+    }+   ,{{   310,   230,   310,   180,   310}+    ,{   310,   230,   310,   180,   310}+    ,{   280,   200,   280,   150,   280}+    ,{   180,   100,   180,   180,   180}+    ,{   280,   200,   280,   150,   280}+    }+   ,{{   290,   270,   290,   160,   290}+    ,{   290,   210,   290,   160,   290}+    ,{   290,   270,  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 290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    }+   ,{{   310,   280,   310,   280,   280}+    ,{   310,   250,   310,   250,   250}+    ,{   280,   280,   280,   280,   280}+    ,{   260,   130,   130,   130,   260}+    ,{   280,   280,   280,   280,   280}+    }+   ,{{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   290,   290,   290,   290,   290}+    ,{   200,   200,   200,   200,   200}+    }+   }+  }+ ,{{{{   370,   340,   310,   370,   370}+    ,{   370,   340,   310,   310,   370}+    ,{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    }+   ,{{   370,   340,   310,   310,   370}+    ,{   370,   340,   310,   310,   370}+    ,{   300,   300,   260,   260,   260}+    ,{   260,   240,   260,   200,   260}+    ,{   300,   300,   260,   260,   260}+    }+   ,{{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    }+   ,{{   300,   300,   270,   280,   280}+    ,{   270,   250,   270,   210,   270}+    ,{   300,   300,   260,   260,   260}+    ,{   280,   200,   150,   280,   280}+    ,{   300,   300,   260,   260,   260}+    }+   ,{{   340,   340,   310,   340,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   340,   310,   280,   340,   280}+    ,{   340,   340,   310,   310,   310}+    ,{   320,   320,   220,   220,   220}+    }+   }+  ,{{{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    }+   ,{{   340,   340,   310,   310,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   300,   300,   260,   260,   260}+    ,{   240,   240,   200,   200,   200}+    ,{   300,   300,   260,   260,   260}+    }+   ,{{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   370,   340,   310,   370,   310}+    }+   ,{{   300,   300,   260,   280,   260}+    ,{   250,   250,   210,   210,   210}+    ,{   300,   300,   260,   260,   260}+    ,{   280,   190,   150,   280,   150}+    ,{   300,   300,   260,   260,   260}+    }+   ,{{   340,   340,   310,   340,   310}+    ,{   340,   340,   310,   310,   310}+    ,{   340,   310,   280,   340,   280}+    ,{   340,   340,   310,   310,   310}+    ,{   320,   320,   220,   220,   220}+    }+   }+  ,{{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,  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 180,   310}+    ,{   310,   230,   310,   280,   310}+    ,{   310,   290,   310,   220,   310}+    }+   ,{{   310,   230,   310,   200,   310}+    ,{   310,   230,   310,   180,   310}+    ,{   260,   180,   260,   130,   260}+    ,{   200,   120,   200,   200,   200}+    ,{   260,   180,   260,   130,   260}+    }+   ,{{   310,   290,   310,   180,   310}+    ,{   310,   230,   310,   180,   310}+    ,{   310,   290,   310,   180,   310}+    ,{   310,   230,   310,   180,   310}+    ,{   310,   290,   310,   180,   310}+    }+   ,{{   280,   200,   260,   280,   260}+    ,{   210,   130,   210,   210,   210}+    ,{   260,   180,   260,   130,   260}+    ,{   280,   200,   150,   280,   150}+    ,{   260,   180,   260,   130,   260}+    }+   ,{{   310,   260,   310,   220,   310}+    ,{   310,   230,   310,   180,   310}+    ,{   280,   260,   280,   150,   280}+    ,{   310,   230,   310,   180,   310}+    ,{   220,   140,   220,   220,   220}+    }+   }+  ,{{{   370,   310,   310,   310,   370}+    ,{   370,   310,   310,   310,   370}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    }+   ,{{   370,   310,   310,   310,   370}+    ,{   370,   310,   310,   310,   370}+    ,{   260,   260,   260,   260,   260}+    ,{   260,   200,   260,   200,   200}+    ,{   260,   260,   260,   260,   260}+    }+   ,{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    }+   ,{{   280,   260,   270,   260,   280}+    ,{   270,   210,   270,   210,   210}+    ,{   260,   260,   260,   260,   260}+    ,{   280,   150,   150,   150,   280}+    ,{   260,   260,   260,   260,   260}+    }+   ,{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{   280,   280,   280,   280,   280}+    ,{   310,   310,   310,   310,   310}+    ,{   220,   220,   220,   220,   220}+    }+   }+  }+ ,{{{{   430,   430,   400,   400,   430}+    ,{   430,   410,   400,   370,   430}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   430,   430,   340,   400,   340}+    }+   ,{{   430,   410,   370,   370,   430}+    ,{   430,   410,   370,   370,   430}+    ,{   370,   370,   340,   340,   340}+    ,{   320,   290,   320,   260,   320}+    ,{   370,   370,   340,   340,   340}+    }+   ,{{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    }+   ,{{   400,   370,   400,   340,   400}+    ,{   400,   370,   400,   340,   400}+    ,{   370,   370,   340,   340,   340}+    ,{   340,   260,   210,   340,   340}+    ,{   370,   370,   340,   340,   340}+    }+   ,{{   430,   430,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   430,   430,   340,   340,   340}+    }+   }+  ,{{{   430,   430,   370,   400,   370}+    ,{   410,   410,   370,   370,   370}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   430,   430,   340,   400,   340}+    }+   ,{{   410,   410,   370,   370,   370}+    ,{   410,   410,   370,   370,   370}+    ,{   370,   370,   340,   340,   340}+    ,{   290,   290,   260,   260,   260}+    ,{   370,   370,   340,   340,   340}+    }+   ,{{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    }+   ,{{   370,   370,   340,   340,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   340,   240,   210,   340,   210}+    ,{   370,   370,   340,   340,   340}+    }+   ,{{   430,   430,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   400,   370,   340,   400,   340}+    ,{   370,   370,   340,   340,   340}+    ,{   430,   430,   340,   340,   340}+    }+   }+  ,{{{   400,   370,   400,   370,   400}+    ,{   400,   370,   400,   370,   400}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   370,   370,   370,   370,   370}+    ,{   370,   370,   370,   370,   370}+    ,{   340,   340,   340,   340,   340}+    ,{   320,   260,   320,   260,   320}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   400,   340,   400,   340,   400}+    ,{   400,   340,   400,   340,   400}+    ,{   340,   340,   340,   340,   340}+    ,{   210,   210,   210,   210,   210}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   }+  ,{{{   370,   320,   370,   340,   370}+    ,{   370,   290,   370,   340,   370}+    ,{   340,   320,   340,   210,   340}+    ,{   340,   260,   340,   340,   340}+    ,{   340,   320,   340,   340,   340}+    }+   ,{{   370,   290,   370,   260,   370}+    ,{   370,   290,   370,   240,   370}+    ,{   340,   260,   340,   210,   340}+    ,{   260,   180,   260,   260,   260}+    ,{   340,   260,   340,   210,   340}+    }+   ,{{   340,   320,   340,   210,   340}+    ,{   340,   260,   340,   210,   340}+    ,{   340,   320,   340,   210,   340}+    ,{   340,   260,   340,   210,   340}+    ,{   340,   320,   340,   210,   340}+    }+   ,{{   340,   260,   340,   340,   340}+    ,{   340,   260,   340,   340,   340}+    ,{   340,   260,   340,   210,   340}+    ,{   340,   260,   210,   340,   210}+    ,{   340,   260,   340,   210,   340}+    }+   ,{{   340,   320,   340,   340,   340}+    ,{   340,   260,   340,   210,   340}+    ,{   340,   320,   340,   210,   340}+    ,{   340,   260,   340,   210,   340}+    ,{   340,   260,   340,   340,   340}+    }+   }+  ,{{{   430,   370,   400,   370,   430}+    ,{   430,   370,   400,   370,   430}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   430,   370,   370,   370,   430}+    ,{   430,   370,   370,   370,   430}+    ,{   340,   340,   340,   340,   340}+    ,{   320,   260,   320,   260,   260}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   400,   340,   400,   340,   340}+    ,{   400,   340,   400,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   210,   210,   210,   340}+    ,{   340,   340,   340,   340,   340}+    }+   ,{{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    ,{   340,   340,   340,   340,   340}+    }+   }+  }+ }};
+ C/ViennaRNA/intl22dH.h view
@@ -0,0 +1,9993 @@+PUBLIC int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =+{{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  }+ ,{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  }+ ,{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  }+ ,{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+   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30}+    ,{  -430,  -980,  -620,  -430,  -620}+    }+   ,{{    80,  -230,  -110,    80,  -110}+    ,{    30,  -530,  -170,    30,  -170}+    ,{    80,  -230,  -110,    80,  -110}+    ,{    30,  -530,  -170,    30,  -170}+    ,{  -960, -1320,  -960, -2010,  -960}+    }+   }+  ,{{{   -30,  -430,   -30,  -430,  -860}+    ,{  -220,  -620,  -220,  -620,  -860}+    ,{  -170,  -570,  -170,  -570,  -900}+    ,{   -30,  -430,   -30,  -430,  -960}+    ,{  -280,  -680,  -280,  -680, -1010}+    }+   ,{{  -340,  -770,  -340,  -770,  -860}+    ,{  -370,  -770,  -370,  -770,  -860}+    ,{  -680, -1080,  -680, -1080, -1410}+    ,{  -340,  -980,  -340,  -980, -1320}+    ,{  -680, -1080,  -680, -1080, -1410}+    }+   ,{{  -220,  -620,  -220,  -620,  -960}+    ,{  -220,  -620,  -220,  -620,  -960}+    ,{  -230,  -630,  -230,  -630,  -960}+    ,{  -220,  -620,  -220,  -620,  -960}+    ,{  -280,  -680,  -280,  -680, -1010}+    }+   ,{{   -30,  -430,   -30,  -430, -1410}+    ,{  -630, -1270,  -630, -1270, -1600}+    ,{  -680, -1080,  -680, -1080, -1410}+    ,{   -30,  -430,   -30,  -430, -2010}+    ,{  -680, -1080,  -680, -1080, -1410}+    }+   ,{{  -170,  -570,  -170,  -570,  -900}+    ,{  -220,  -620,  -220,  -620,  -960}+    ,{  -170,  -570,  -170,  -570,  -900}+    ,{  -220,  -620,  -220,  -620,  -960}+    ,{ -1010, -1410, -1010, -1410, -1750}+    }+   }+  }+ ,{{{{   540,   180,    30,   540,   180}+    ,{    10,  -580,  -150,    10,   -90}+    ,{   540,  -350,  -600,   540,  -540}+    ,{   180,   180,    30,  -320,   180}+    ,{   -90,  -740,   -90,  -260,  -540}+    }+   ,{{   -90,  -350,  -150,  -100,   -90}+    ,{   -90,  -580,  -150,  -200,   -90}+    ,{  -100,  -350,  -600,  -100,  -540}+    ,{  -630, -1790,  -630, -1790, -1040}+    ,{  -400,  -740,  -600,  -400,  -540}+    }+   ,{{   540,  -660,  -510,   540,  -400}+    ,{    10,  -660,  -510,    10,  -400}+    ,{   540,  -940,  -820,   540,  -760}+    ,{  -320,  -660,  -510,  -320,  -460}+    ,{  -260,  -940,  -820,  -260,  -550}+    }+   ,{{   180,   180,    30,  -400,   180}+    ,{  -500, -1070,  -500, -1080,  -570}+    ,{  -400,  -740,  -600,  -400,  -540}+    ,{   180,   180,    30,  -430,   180}+    ,{  -400,  -740,  -600,  -400,  -540}+    }+   ,{{   -90,  -660,   -90,  -210,  -460}+    ,{  -320,  -660,  -510,  -320,  -460}+    ,{  -210, -1250, -1130,  -210, -1070}+    ,{  -320,  -660,  -510,  -320,  -460}+    ,{   -90,  -830,   -90,  -810,  -800}+    }+   }+  ,{{{   540,   180,   -90,   540,    30}+    ,{    10,  -580,  -220,    10,  -150}+    ,{   540,  -740,  -600,   540,  -600}+    ,{   180,   180,  -390, -1160,    30}+    ,{   -90,  -740,   -90,  -810,  -600}+    }+   ,{{  -100,  -580,  -220,  -100,  -150}+    ,{  -150,  -580,  -220,  -970,  -150}+    ,{  -100,  -740,  -600,  -100,  -600}+    ,{ -1340, -2010, -1650, -1980, -1340}+    ,{  -600,  -740,  -600, -1240,  -600}+    }+   ,{{   540,  -660,  -510,   540,  -510}+    ,{    10,  -660, -1150,    10,  -510}+    ,{   540,  -960,  -820,   540,  -820}+    ,{  -510,  -660,  -510, -1160,  -510}+    ,{  -820,  -960,  -820, -1220,  -820}+    }+   ,{{   180,   180,  -390, -1240,    30}+    ,{  -860, -1340,  -860, -2450,  -860}+    ,{  -600,  -740,  -600, -1240,  -600}+    ,{   180,   180,  -390, -1870,    30}+    ,{  -600,  -740,  -600, -1240,  -600}+    }+   ,{{   -90,  -660,   -90,  -810,  -510}+    ,{  -510,  -660,  -510, -1160,  -510}+    ,{ -1130, -1270, -1130, -1530, -1130}+    ,{  -510,  -660,  -510, -1160,  -510}+    ,{   -90, -1240,   -90,  -810,  -800}+    }+   }+  ,{{{   180,  -430,    20,  -430,   180}+    ,{   -90,  -600,  -500,  -600,   -90}+    ,{  -540, -1050,  -600, -1050,  -540}+    ,{   180,  -430,    20,  -430,   180}+    ,{  -540,  -830,  -600, -1050,  -540}+    }+   ,{{   -90,  -600,  -600,  -600,   -90}+    ,{   -90,  -600, -1070,  -600,   -90}+    ,{  -540, -1050,  -600, -1050,  -540}+    ,{  -630, -1790,  -630, -1790, -1040}+    ,{  -540, -1050,  -600, -1050,  -540}+    }+   ,{{  -460,  -970,  -520,  -970,  -460}+    ,{  -460,  -970,  -750,  -970,  -460}+    ,{  -760, -1270,  -820, -1270,  -760}+    ,{  -460,  -970,  -520,  -970,  -460}+    ,{  -550, -1270,  -820, -1270,  -550}+    }+   ,{{   180,  -430,    20,  -430,   180}+    ,{  -500, -1070,  -500, -1320,  -570}+    ,{  -540, -1050,  -600, -1050,  -540}+    ,{   180,  -430,    20,  -430,   180}+    ,{  -540, -1050,  -600, -1050,  -540}+    }+   ,{{  -460,  -830,  -520,  -970,  -460}+    ,{  -460,  -970,  -520,  -970,  -460}+    ,{ -1070, -1580, -1130, -1580, -1070}+    ,{  -460,  -970,  -520,  -970,  -460}+    ,{  -830,  -830, -1710, -1260, -1460}+    }+   }+  ,{{{    30,  -350,    30,  -200,    30}+    ,{  -150,  -870,  -150,  -200,  -150}+    ,{  -210,  -350,  -600,  -210,  -600}+    ,{    30,  -870,    30,  -320,    30}+    ,{  -260,  -940,  -600,  -260,  -600}+    }+   ,{{  -150,  -350,  -150,  -200,  -150}+    ,{  -150, -1600,  -150,  -200,  -150}+    ,{  -350,  -350,  -600,  -440,  -600}+    ,{ -1340, -3070, -1340, -2390, -1340}+    ,{  -400,  -960,  -600,  -400,  -600}+    }+   ,{{  -260,  -870,  -510,  -260,  -510}+    ,{  -320, -1110,  -510,  -320,  -510}+    ,{  -620,  -940,  -820,  -620,  -820}+    ,{  -320,  -870,  -510,  -320,  -510}+    ,{  -260,  -940,  -820,  -260,  -820}+    }+   ,{{    30,  -960,    30,  -400,    30}+    ,{  -860, -1880,  -860, -1080,  -860}+    ,{  -400,  -960,  -600,  -400,  -600}+    ,{    30, -1370,    30, -2280,    30}+    ,{  -400,  -960,  -600,  -400,  -600}+    }+   ,{{  -210,  -870,  -510,  -210,  -510}+    ,{  -320,  -870,  -510,  -320,  -510}+    ,{  -210, -1250, -1130,  -210, -1130}+    ,{  -320,  -870,  -510,  -320,  -510}+    ,{  -800, -1360,  -800, -1550,  -800}+    }+   }+  ,{{{  -200,  -430,  -200,  -430,  -230}+    ,{  -200,  -600,  -200,  -600,  -400}+    ,{  -650, -1050,  -650, -1050, -1390}+    ,{  -230,  -430,  -570,  -430,  -230}+    ,{  -650, -1050,  -650, -1050, -1390}+    }+   ,{{  -200,  -600,  -200,  -600, -1390}+    ,{  -200,  -600,  -200,  -600, -1490}+    ,{  -650, -1050,  -650, -1050, -1390}+    ,{ -1150, -1790, -1150, -1790, -1520}+    ,{  -650, -1050,  -650, -1050, -1390}+    }+   ,{{  -400,  -970,  -570,  -970,  -400}+    ,{  -400,  -970,  -570,  -970,  -400}+    ,{  -870, -1270,  -870, -1270, -1610}+    ,{  -570,  -970,  -570,  -970, -1300}+    ,{  -870, -1270,  -870, -1270, -1610}+    }+   ,{{  -230,  -430,  -650,  -430,  -230}+    ,{ -1300, -1320, -1750, -1320, -1300}+    ,{  -650, -1050,  -650, -1050, -1390}+    ,{  -230,  -430,  -880,  -430,  -230}+    ,{  -650, -1050,  -650, -1050, -1390}+    }+   ,{{  -570,  -970,  -570,  -970, -1300}+    ,{  -570,  -970,  -570,  -970, -1300}+    ,{ -1180, -1580, -1180, -1580, -1920}+    ,{  -570,  -970,  -570,  -970, -1300}+    ,{  -860, -1260,  -860, -1260, -2350}+    }+   }+  }+ ,{{{{   240,    40,   190,  -270,   240}+    ,{  -590, -1030,  -650,  -870,  -590}+    ,{  -870, -1180, -1060,  -870, -1010}+    ,{   240,    40,   190,  -270,   240}+    ,{  -870,  -970, -1060,  -870, -1010}+    }+   ,{{  -780, -1210,  -840,  -870,  -780}+    ,{ -1050, -1370, -1240, -1050, -1190}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{  -780, -1220,  -840, -1530,  -780}+    ,{  -870, -1210, -1060,  -870, -1010}+    }+   ,{{  -870, -1180, -1060,  -870, -1010}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{  -870, -1180, -1060,  -870, -1010}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{  -870, -1180, -1060,  -870, -1010}+    }+   ,{{   240,    40,   190,  -270,   240}+    ,{  -590, -1030,  -650, -1340,  -590}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{   240,    40,   190,  -270,   240}+    ,{  -870, -1210, -1060,  -870, -1010}+    }+   ,{{  -870,  -970, -1060,  -870, -1010}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{  -870, -1180, -1060,  -870, -1010}+    ,{  -870, -1210, -1060,  -870, -1010}+    ,{  -970,  -970, -1060, -1520, -1010}+    }+   }+  ,{{{   190,    40,   190, -1470,   190}+    ,{  -890, -1030,  -890, -1530,  -890}+    ,{ -1060, -1210, -1060, -1470, -1060}+    ,{   190,    40,   190, -1710,   190}+    ,{  -970,  -970, -1060, -1470, -1060}+    }+   ,{{ -1060, -1210, -1060, -1710, -1060}+    ,{ -1240, -1370, -1240, -1890, -1240}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{ -1080, -1220, -1080, -1720, -1080}+    ,{ -1060, -1210, -1060, -1710, -1060}+    }+   ,{{ -1060, -1210, -1060, -1470, -1060}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{ -1060, -1210, -1060, -1470, -1060}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{ -1060, -1210, -1060, -1470, -1060}+    }+   ,{{   190,    40,   190, -1530,   190}+    ,{  -890, -1030,  -890, -1530,  -890}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{   190,    40,   190, -1710,   190}+    ,{ -1060, -1210, -1060, -1710, -1060}+    }+   ,{{  -970,  -970, -1060, -1470, -1060}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{ -1060, -1210, -1060, -1470, -1060}+    ,{ -1060, -1210, -1060, -1710, -1060}+    ,{  -970,  -970, -1060, -1710, -1060}+    }+   }+  ,{{{   240,  -270,   180,  -270,   240}+    ,{  -590, -1340,  -650, -1340,  -590}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{   240,  -270,   180,  -270,   240}+    ,{ -1010, -1520, -1070, -1520, -1010}+    }+   ,{{  -780, -1520,  -840, -1520,  -780}+    ,{ -1190, -1700, -1250, -1700, -1190}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{  -780, -1530,  -840, -1530,  -780}+    ,{ -1010, -1520, -1070, -1520, -1010}+    }+   ,{{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    }+   ,{{   240,  -270,   180,  -270,   240}+    ,{  -590, -1340,  -650, -1340,  -590}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{   240,  -270,   180,  -270,   240}+    ,{ -1010, -1520, -1070, -1520, -1010}+    }+   ,{{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    ,{ -1010, -1520, -1070, -1520, -1010}+    }+   }+  ,{{{   190, -1180,   190,  -870,   190}+    ,{  -870, -1250,  -890,  -870,  -890}+    ,{  -870, -1180, -1060,  -870, -1060}+    ,{   190, -1420,   190,  -870,   190}+    ,{  -870, -1180, -1060,  -870, -1060}+    }+   ,{{  -870, -1420, -1060,  -870, -1060}+    ,{ -1050, -1600, -1240, -1050, -1240}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{ -1080, -1440, -1080, -2130, -1080}+    ,{  -870, -1420, -1060,  -870, -1060}+    }+   ,{{  -870, -1180, -1060,  -870, -1060}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{  -870, -1180, -1060,  -870, -1060}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{  -870, -1180, -1060,  -870, -1060}+    }+   ,{{   190, -1250,   190,  -870,   190}+    ,{  -890, -1250,  -890, -1940,  -890}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{   190, -1420,   190, -2120,   190}+    ,{  -870, -1420, -1060,  -870, -1060}+    }+   ,{{  -870, -1180, -1060,  -870, -1060}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{  -870, -1180, -1060,  -870, -1060}+    ,{  -870, -1420, -1060,  -870, -1060}+    ,{ -1060, -1420, -1060, -2120, -1060}+    }+   }+  ,{{{   130,  -270,   130,  -270, -1680}+    ,{  -700, -1340,  -700, -1340, -1680}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{   130,  -270,   130,  -270, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    }+   ,{{  -890, -1520,  -890, -1520, -1790}+    ,{ -1300, -1700, -1300, -1700, -1790}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{  -890, -1530,  -890, -1530, -1870}+    ,{ -1120, -1520, -1120, -1520, -1850}+    }+   ,{{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    }+   ,{{   130,  -270,   130,  -270, -1680}+    ,{  -700, -1340,  -700, -1340, -1680}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{   130,  -270,   130,  -270, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    }+   ,{{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    ,{ -1120, -1520, -1120, -1520, -1850}+    }+   }+  }+ ,{{{{   800,   600,   740,   290,   800}+    ,{   200,  -140,     0,   200,    50}+    ,{  -310,  -630,  -510,  -310,  -450}+    ,{   800,   600,   740,   290,   800}+    ,{  -310,  -410,  -510,  -310,  -450}+    }+   ,{{   200,  -140,     0,   200,    50}+    ,{   200,  -140,     0,   200,    50}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{  -550,  -990,  -610, -1300,  -550}+    ,{  -310,  -650,  -510,  -310,  -450}+    }+   ,{{  -310,  -630,  -510,  -310,  -450}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{  -310,  -630,  -510,  -310,  -450}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{  -310,  -630,  -510,  -310,  -450}+    }+   ,{{   800,   600,   740,   290,   800}+    ,{  -720, -1160,  -780, -1470,  -720}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{   800,   600,   740,   290,   800}+    ,{  -310,  -650,  -510,  -310,  -450}+    }+   ,{{  -310,  -410,  -510,  -310,  -450}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{  -310,  -630,  -510,  -310,  -450}+    ,{  -310,  -650,  -510,  -310,  -450}+    ,{  -410,  -410,  -510,  -960,  -450}+    }+   }+  ,{{{   740,   600,   740,  -640,   740}+    ,{     0,  -140,     0,  -640,     0}+    ,{  -510,  -650,  -510,  -910,  -510}+    ,{   740,   600,   740, -1150,   740}+    ,{  -410,  -410,  -510,  -910,  -510}+    }+   ,{{     0,  -140,     0,  -640,     0}+    ,{     0,  -140,     0,  -640,     0}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{  -850,  -990,  -850, -1490,  -850}+    ,{  -510,  -650,  -510, -1150,  -510}+    }+   ,{{  -510,  -650,  -510,  -910,  -510}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{  -510,  -650,  -510,  -910,  -510}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{  -510,  -650,  -510,  -910,  -510}+    }+   ,{{   740,   600,   740, -1150,   740}+    ,{ -1020, -1160, -1020, -1660, -1020}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{   740,   600,   740, -1150,   740}+    ,{  -510,  -650,  -510, -1150,  -510}+    }+   ,{{  -410,  -410,  -510,  -910,  -510}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{  -510,  -650,  -510,  -910,  -510}+    ,{  -510,  -650,  -510, -1150,  -510}+    ,{  -410,  -410,  -510, -1150,  -510}+    }+   }+  ,{{{   800,   290,   740,   290,   800}+    ,{    50,  -450,     0,  -450,    50}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{   800,   290,   740,   290,   800}+    ,{  -450,  -960,  -510,  -960,  -450}+    }+   ,{{    50,  -450,     0,  -450,    50}+    ,{    50,  -450,     0,  -450,    50}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -550, -1300,  -610, -1300,  -550}+    ,{  -450,  -960,  -510,  -960,  -450}+    }+   ,{{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    }+   ,{{   800,   290,   740,   290,   800}+    ,{  -720, -1470,  -780, -1470,  -720}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{   800,   290,   740,   290,   800}+    ,{  -450,  -960,  -510,  -960,  -450}+    }+   ,{{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    ,{  -450,  -960,  -510,  -960,  -450}+    }+   }+  ,{{{   740,  -360,   740,   200,   740}+    ,{   200,  -360,     0,   200,     0}+    ,{  -310,  -630,  -510,  -310,  -510}+    ,{   740,  -870,   740,  -310,   740}+    ,{  -310,  -630,  -510,  -310,  -510}+    }+   ,{{   200,  -360,     0,   200,     0}+    ,{   200,  -360,     0,   200,     0}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{  -850, -1210,  -850, -1900,  -850}+    ,{  -310,  -870,  -510,  -310,  -510}+    }+   ,{{  -310,  -630,  -510,  -310,  -510}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{  -310,  -630,  -510,  -310,  -510}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{  -310,  -630,  -510,  -310,  -510}+    }+   ,{{   740,  -870,   740,  -310,   740}+    ,{ -1020, -1380, -1020, -2070, -1020}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{   740,  -870,   740, -1560,   740}+    ,{  -310,  -870,  -510,  -310,  -510}+    }+   ,{{  -310,  -630,  -510,  -310,  -510}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{  -310,  -630,  -510,  -310,  -510}+    ,{  -310,  -870,  -510,  -310,  -510}+    ,{  -510,  -870,  -510, -1560,  -510}+    }+   }+  ,{{{   690,   290,   690,   290,  -550}+    ,{   -50,  -450,   -50,  -450,  -550}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{   690,   290,   690,   290, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    }+   ,{{   -50,  -450,   -50,  -450,  -550}+    ,{   -50,  -450,   -50,  -450,  -550}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -660, -1300,  -660, -1300, -1640}+    ,{  -560,  -960,  -560,  -960, -1300}+    }+   ,{{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    }+   ,{{   690,   290,   690,   290, -1300}+    ,{  -830, -1470,  -830, -1470, -1810}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{   690,   290,   690,   290, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    }+   ,{{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    ,{  -560,  -960,  -560,  -960, -1300}+    }+   }+  }+ ,{{{{  1170,   970,  1120,   780,  1170}+    ,{   780,   440,   580,   780,   640}+    ,{   480,   170,   280,   480,   340}+    ,{  1170,   970,  1120,   660,  1170}+    ,{   480,   170,   280,   480,   340}+    }+   ,{{   780,   440,   580,   780,   640}+    ,{   780,   440,   580,   780,   640}+    ,{   470,   130,   270,   470,   330}+    ,{  -510,  -950,  -570, -1260,  -510}+    ,{   470,   130,   270,   470,   330}+    }+   ,{{   490,   170,   290,   490,   340}+    ,{   490,   140,   290,   490,   340}+    ,{   480,   170,   280,   480,   340}+    ,{   490,   140,   290,   490,   340}+    ,{   480,   170,   280,   480,   340}+    }+   ,{{  1170,   970,  1120,   660,  1170}+    ,{  -330,  -770,  -390, -1080,  -330}+    ,{   470,   130,   270,   470,   330}+    ,{  1170,   970,  1120,   660,  1170}+    ,{   470,   130,   270,   470,   330}+    }+   ,{{   490,   170,   290,   490,   340}+    ,{   490,   140,   290,   490,   340}+    ,{   480,   170,   280,   480,   340}+    ,{   490,   140,   290,   490,   340}+    ,{  -600,  -600,  -690, -1150,  -640}+    }+   }+  ,{{{  1120,   970,  1120,   -60,  1120}+    ,{   580,   440,   580,   -60,   580}+    ,{   280,   140,   280,  -120,   280}+    ,{  1120,   970,  1120,  -350,  1120}+    ,{   280,   140,   280,  -120,   280}+    }+   ,{{   580,   440,   580,   -60,   580}+    ,{   580,   440,   580,   -60,   580}+    ,{   270,   130,   270,  -370,   270}+    ,{  -800,  -950,  -800, -1450,  -800}+    ,{   270,   130,   270,  -370,   270}+    }+   ,{{   290,   140,   290,  -120,   290}+    ,{   290,   140,   290,  -350,   290}+    ,{   280,   140,   280,  -120,   280}+    ,{   290,   140,   290,  -350,   290}+    ,{   280,   140,   280,  -120,   280}+    }+   ,{{  1120,   970,  1120,  -370,  1120}+    ,{  -620,  -770,  -620, -1270,  -620}+    ,{   270,   130,   270,  -370,   270}+    ,{  1120,   970,  1120,  -780,  1120}+    ,{   270,   130,   270,  -370,   270}+    }+   ,{{   290,   140,   290,  -120,   290}+    ,{   290,   140,   290,  -350,   290}+    ,{   280,   140,   280,  -120,   280}+    ,{   290,   140,   290,  -350,   290}+    ,{  -600,  -600,  -690, -1340,  -690}+    }+   }+  ,{{{  1170,   660,  1110,   660,  1170}+    ,{   640,   130,   580,   130,   640}+    ,{   340,  -170,   280,  -170,   340}+    ,{  1170,   660,  1110,   660,  1170}+    ,{   340,  -170,   280,  -170,   340}+    }+   ,{{   640,   130,   580,   130,   640}+    ,{   640,   130,   580,   130,   640}+    ,{   330,  -180,   270,  -180,   330}+    ,{  -510, -1260,  -570, -1260,  -510}+    ,{   330,  -180,   270,  -180,   330}+    }+   ,{{   340,  -160,   280,  -160,   340}+    ,{   340,  -160,   280,  -160,   340}+    ,{   340,  -170,   280,  -170,   340}+    ,{   340,  -160,   280,  -160,   340}+    ,{   340,  -170,   280,  -170,   340}+    }+   ,{{  1170,   660,  1110,   660,  1170}+    ,{  -330, -1080,  -390, -1080,  -330}+    ,{   330,  -180,   270,  -180,   330}+    ,{  1170,   660,  1110,   660,  1170}+    ,{   330,  -180,   270,  -180,   330}+    }+   ,{{   340,  -160,   280,  -160,   340}+    ,{   340,  -160,   280,  -160,   340}+    ,{   340,  -170,   280,  -170,   340}+    ,{   340,  -160,   280,  -160,   340}+    ,{  -640, -1150,  -700, -1150,  -640}+    }+   }+  ,{{{  1120,   220,  1120,   780,  1120}+    ,{   780,   220,   580,   780,   580}+    ,{   480,   170,   280,   480,   280}+    ,{  1120,   -70,  1120,   490,  1120}+    ,{   480,   170,   280,   480,   280}+    }+   ,{{   780,   220,   580,   780,   580}+    ,{   780,   220,   580,   780,   580}+    ,{   470,   -80,   270,   470,   270}+    ,{  -800, -1160,  -800, -1860,  -800}+    ,{   470,   -80,   270,   470,   270}+    }+   ,{{   490,   170,   290,   490,   290}+    ,{   490,   -70,   290,   490,   290}+    ,{   480,   170,   280,   480,   280}+    ,{   490,   -70,   290,   490,   290}+    ,{   480,   170,   280,   480,   280}+    }+   ,{{  1120,   -80,  1120,   470,  1120}+    ,{  -620,  -980,  -620, -1680,  -620}+    ,{   470,   -80,   270,   470,   270}+    ,{  1120,  -490,  1120, -1190,  1120}+    ,{   470,   -80,   270,   470,   270}+    }+   ,{{   490,   170,   290,   490,   290}+    ,{   490,   -70,   290,   490,   290}+    ,{   480,   170,   280,   480,   280}+    ,{   490,   -70,   290,   490,   290}+    ,{  -690, -1050,  -690, -1750,  -690}+    }+   }+  ,{{{  1060,   660,  1060,   660,    40}+    ,{   530,   130,   530,   130,    40}+    ,{   230,  -170,   230,  -170,  -500}+    ,{  1060,   660,  1060,   660,  -500}+    ,{   230,  -170,   230,  -170,  -500}+    }+   ,{{   530,   130,   530,   130,    40}+    ,{   530,   130,   530,   130,    40}+    ,{   220,  -180,   220,  -180,  -510}+    ,{  -620, -1260,  -620, -1260, -1590}+    ,{   220,  -180,   220,  -180,  -510}+    }+   ,{{   230,  -160,   230,  -160,  -500}+    ,{   230,  -160,   230,  -160,  -500}+    ,{   230,  -170,   230,  -170,  -500}+    ,{   230,  -160,   230,  -160,  -500}+    ,{   230,  -170,   230,  -170,  -500}+    }+   ,{{  1060,   660,  1060,   660,  -510}+    ,{  -440, -1080,  -440, -1080, -1410}+    ,{   220,  -180,   220,  -180,  -510}+    ,{  1060,   660,  1060,   660,  -920}+    ,{   220,  -180,   220,  -180,  -510}+    }+   ,{{   230,  -160,   230,  -160,  -500}+    ,{   230,  -160,   230,  -160,  -500}+    ,{   230,  -170,   230,  -170,  -500}+    ,{   230,  -160,   230,  -160,  -500}+    ,{  -750, -1150,  -750, -1150, -1480}+    }+   }+  }+ ,{{{{  1350,  1160,  1300,   850,  1350}+    ,{   850,   500,   650,   850,   700}+    ,{   720,   400,   520,   720,   570}+    ,{  1350,  1160,  1300,   850,  1350}+    ,{   590,   270,   390,   590,   440}+    }+   ,{{   850,   500,   650,   850,   700}+    ,{   850,   500,   650,   850,   700}+    ,{   570,   220,   370,   570,   420}+    ,{  -460,  -900,  -520, -1210,  -460}+    ,{   570,   220,   370,   570,   420}+    }+   ,{{   720,   400,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   720,   400,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   590,   270,   390,   590,   440}+    }+   ,{{  1350,  1160,  1300,   850,  1350}+    ,{  -760, -1200,  -820, -1510,  -760}+    ,{   570,   220,   370,   570,   420}+    ,{  1350,  1160,  1300,   850,  1350}+    ,{   570,   220,   370,   570,   420}+    }+   ,{{   720,   370,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   280,   -40,    80,   280,   130}+    ,{   720,   370,   520,   720,   570}+    ,{  -320,  -320,  -420,  -870,  -360}+    }+   }+  ,{{{  1300,  1160,  1300,   120,  1300}+    ,{   650,   500,   650,     0,   650}+    ,{   520,   370,   520,   120,   520}+    ,{  1300,  1160,  1300,  -120,  1300}+    ,{   390,   240,   390,   -10,   390}+    }+   ,{{   650,   500,   650,     0,   650}+    ,{   650,   500,   650,     0,   650}+    ,{   370,   220,   370,  -270,   370}+    ,{  -750,  -900,  -750, -1400,  -750}+    ,{   370,   220,   370,  -270,   370}+    }+   ,{{   520,   370,   520,   120,   520}+    ,{   520,   370,   520,  -120,   520}+    ,{   520,   370,   520,   120,   520}+    ,{   520,   370,   520,  -120,   520}+    ,{   390,   240,   390,   -10,   390}+    }+   ,{{  1300,  1160,  1300,  -270,  1300}+    ,{ -1050, -1200, -1050, -1700, -1050}+    ,{   370,   220,   370,  -270,   370}+    ,{  1300,  1160,  1300,  -590,  1300}+    ,{   370,   220,   370,  -270,   370}+    }+   ,{{   520,   370,   520,  -120,   520}+    ,{   520,   370,   520,  -120,   520}+    ,{    80,   -60,    80,  -320,    80}+    ,{   520,   370,   520,  -120,   520}+    ,{  -320,  -320,  -420, -1060,  -420}+    }+   }+  ,{{{  1350,   850,  1290,   850,  1350}+    ,{   700,   190,   640,   190,   700}+    ,{   570,    60,   510,    60,   570}+    ,{  1350,   850,  1290,   850,  1350}+    ,{   440,   -60,   380,   -60,   440}+    }+   ,{{   700,   190,   640,   190,   700}+    ,{   700,   190,   640,   190,   700}+    ,{   420,   -80,   360,   -80,   420}+    ,{  -460, -1210,  -520, -1210,  -460}+    ,{   420,   -80,   360,   -80,   420}+    }+   ,{{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   440,   -60,   380,   -60,   440}+    }+   ,{{  1350,   850,  1290,   850,  1350}+    ,{  -760, -1510,  -820, -1510,  -760}+    ,{   420,   -80,   360,   -80,   420}+    ,{  1350,   850,  1290,   850,  1350}+    ,{   420,   -80,   360,   -80,   420}+    }+   ,{{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   130,  -370,    70,  -370,   130}+    ,{   570,    60,   510,    60,   570}+    ,{  -360,  -870,  -420,  -870,  -360}+    }+   }+  ,{{{  1300,   400,  1300,   850,  1300}+    ,{   850,   290,   650,   850,   650}+    ,{   720,   400,   520,   720,   520}+    ,{  1300,   160,  1300,   720,  1300}+    ,{   590,   270,   390,   590,   390}+    }+   ,{{   850,   290,   650,   850,   650}+    ,{   850,   290,   650,   850,   650}+    ,{   570,    10,   370,   570,   370}+    ,{  -750, -1110,  -750, -1810,  -750}+    ,{   570,    10,   370,   570,   370}+    }+   ,{{   720,   400,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   720,   400,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   590,   270,   390,   590,   390}+    }+   ,{{  1300,    10,  1300,   570,  1300}+    ,{ -1050, -1410, -1050, -2110, -1050}+    ,{   570,    10,   370,   570,   370}+    ,{  1300,  -310,  1300, -1000,  1300}+    ,{   570,    10,   370,   570,   370}+    }+   ,{{   720,   160,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   280,   -40,    80,   280,    80}+    ,{   720,   160,   520,   720,   520}+    ,{  -420,  -780,  -420, -1470,  -420}+    }+   }+  ,{{{  1250,   850,  1250,   850,   100}+    ,{   590,   190,   590,   190,   100}+    ,{   460,    60,   460,    60,  -270}+    ,{  1250,   850,  1250,   850,  -270}+    ,{   330,   -60,   330,   -60,  -400}+    }+   ,{{   590,   190,   590,   190,   100}+    ,{   590,   190,   590,   190,   100}+    ,{   310,   -80,   310,   -80,  -420}+    ,{  -570, -1210,  -570, -1210, -1540}+    ,{   310,   -80,   310,   -80,  -420}+    }+   ,{{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   330,   -60,   330,   -60,  -400}+    }+   ,{{  1250,   850,  1250,   850,  -420}+    ,{  -870, -1510,  -870, -1510, -1840}+    ,{   310,   -80,   310,   -80,  -420}+    ,{  1250,   850,  1250,   850,  -740}+    ,{   310,   -80,   310,   -80,  -420}+    }+   ,{{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{    20,  -370,    20,  -370,  -710}+    ,{   460,    60,   460,    60,  -270}+    ,{  -470,  -870,  -470,  -870, -1210}+    }+   }+  }+ ,{{{{  1350,  1160,  1300,   850,  1350}+    ,{   850,   500,   650,   850,   700}+    ,{   720,   400,   520,   720,   570}+    ,{  1350,  1160,  1300,   850,  1350}+    ,{   590,   270,   390,   590,   440}+    }+   ,{{   850,   500,   650,   850,   700}+    ,{   850,   500,   650,   850,   700}+    ,{   570,   220,   370,   570,   420}+    ,{  -230,  -670,  -290,  -980,  -230}+    ,{   570,   220,   370,   570,   420}+    }+   ,{{   720,   400,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   720,   400,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   590,   270,   390,   590,   440}+    }+   ,{{  1350,  1160,  1300,   850,  1350}+    ,{  -330,  -770,  -390, -1080,  -330}+    ,{   570,   220,   370,   570,   420}+    ,{  1350,  1160,  1300,   850,  1350}+    ,{   570,   220,   370,   570,   420}+    }+   ,{{   720,   370,   520,   720,   570}+    ,{   720,   370,   520,   720,   570}+    ,{   480,   170,   280,   480,   340}+    ,{   720,   370,   520,   720,   570}+    ,{   -90,  -320,   -90,  -810,  -360}+    }+   }+  ,{{{  1300,  1160,  1300,   540,  1300}+    ,{   650,   500,   650,    10,   650}+    ,{   540,   370,   520,   540,   520}+    ,{  1300,  1160,  1300,  -120,  1300}+    ,{   390,   240,   390,   -10,   390}+    }+   ,{{   650,   500,   650,     0,   650}+    ,{   650,   500,   650,     0,   650}+    ,{   370,   220,   370,  -100,   370}+    ,{  -530,  -670,  -530, -1170,  -530}+    ,{   370,   220,   370,  -270,   370}+    }+   ,{{   540,   370,   520,   540,   520}+    ,{   520,   370,   520,    10,   520}+    ,{   540,   370,   520,   540,   520}+    ,{   520,   370,   520,  -120,   520}+    ,{   390,   240,   390,   -10,   390}+    }+   ,{{  1300,  1160,  1300,  -270,  1300}+    ,{  -620,  -770,  -620, -1270,  -620}+    ,{   370,   220,   370,  -270,   370}+    ,{  1300,  1160,  1300,  -590,  1300}+    ,{   370,   220,   370,  -270,   370}+    }+   ,{{   520,   370,   520,  -120,   520}+    ,{   520,   370,   520,  -120,   520}+    ,{   280,   140,   280,  -120,   280}+    ,{   520,   370,   520,  -120,   520}+    ,{   -90,  -320,   -90,  -810,  -420}+    }+   }+  ,{{{  1350,   850,  1290,   850,  1350}+    ,{   700,   190,   640,   190,   700}+    ,{   570,    60,   510,    60,   570}+    ,{  1350,   850,  1290,   850,  1350}+    ,{   440,   -60,   380,   -60,   440}+    }+   ,{{   700,   190,   640,   190,   700}+    ,{   700,   190,   640,   190,   700}+    ,{   420,   -80,   360,   -80,   420}+    ,{  -230,  -980,  -290,  -980,  -230}+    ,{   420,   -80,   360,   -80,   420}+    }+   ,{{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   440,   -60,   380,   -60,   440}+    }+   ,{{  1350,   850,  1290,   850,  1350}+    ,{  -330, -1070,  -390, -1080,  -330}+    ,{   420,   -80,   360,   -80,   420}+    ,{  1350,   850,  1290,   850,  1350}+    ,{   420,   -80,   360,   -80,   420}+    }+   ,{{   570,    60,   510,    60,   570}+    ,{   570,    60,   510,    60,   570}+    ,{   340,  -170,   280,  -170,   340}+    ,{   570,    60,   510,    60,   570}+    ,{  -360,  -830,  -420,  -870,  -360}+    }+   }+  ,{{{  1300,   400,  1300,   850,  1300}+    ,{   850,   290,   650,   850,   650}+    ,{   720,   400,   520,   720,   520}+    ,{  1300,   160,  1300,   720,  1300}+    ,{   590,   270,   390,   590,   390}+    }+   ,{{   850,   290,   650,   850,   650}+    ,{   850,   290,   650,   850,   650}+    ,{   570,    10,   370,   570,   370}+    ,{  -530,  -890,  -530, -1580,  -530}+    ,{   570,    10,   370,   570,   370}+    }+   ,{{   720,   400,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   720,   400,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   590,   270,   390,   590,   390}+    }+   ,{{  1300,    10,  1300,   570,  1300}+    ,{  -620,  -980,  -620, -1080,  -620}+    ,{   570,    10,   370,   570,   370}+    ,{  1300,  -310,  1300, -1000,  1300}+    ,{   570,    10,   370,   570,   370}+    }+   ,{{   720,   170,   520,   720,   520}+    ,{   720,   160,   520,   720,   520}+    ,{   480,   170,   280,   480,   280}+    ,{   720,   160,   520,   720,   520}+    ,{  -420,  -780,  -420, -1470,  -420}+    }+   }+  ,{{{  1250,   850,  1250,   850,   100}+    ,{   590,   190,   590,   190,   100}+    ,{   460,    60,   460,    60,  -270}+    ,{  1250,   850,  1250,   850,  -230}+    ,{   330,   -60,   330,   -60,  -400}+    }+   ,{{   590,   190,   590,   190,   100}+    ,{   590,   190,   590,   190,   100}+    ,{   310,   -80,   310,   -80,  -420}+    ,{  -340,  -980,  -340,  -980, -1320}+    ,{   310,   -80,   310,   -80,  -420}+    }+   ,{{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   330,   -60,   330,   -60,  -400}+    }+   ,{{  1250,   850,  1250,   850,  -230}+    ,{  -440, -1080,  -440, -1080, -1300}+    ,{   310,   -80,   310,   -80,  -420}+    ,{  1250,   850,  1250,   850,  -230}+    ,{   310,   -80,   310,   -80,  -420}+    }+   ,{{   460,    60,   460,    60,  -270}+    ,{   460,    60,   460,    60,  -270}+    ,{   230,  -170,   230,  -170,  -500}+    ,{   460,    60,   460,    60,  -270}+    ,{  -470,  -870,  -470,  -870, -1210}+    }+   }+  }+ }+,{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF, 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INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   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INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+ 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 ,{  -600,  -600,  -820,  -600, -1130}+    ,{  -600,  -600,  -820,  -600, -1130}+    ,{  -600,  -600,  -820,  -600, -1130}+    ,{  -650,  -650,  -870,  -650, -1180}+    }+   ,{{   540,  -100,   540,  -400,  -210}+    ,{   540,  -100,   540, -1240, -1530}+    ,{ -1050, -1050, -1270, -1050, -1580}+    ,{  -210,  -440,  -620,  -400,  -210}+    ,{ -1050, -1050, -1270, -1050, -1580}+    }+   ,{{  -540,  -540,  -760,  -540, -1070}+    ,{  -600,  -600,  -820,  -600, -1130}+    ,{  -540,  -540,  -760,  -540, -1070}+    ,{  -600,  -600,  -820,  -600, -1130}+    ,{ -1390, -1390, -1610, -1390, -1920}+    }+   }+  ,{{{   180,  -630,  -320,   180,  -320}+    ,{   180, -1340,  -510,   180,  -510}+    ,{   180,  -630,  -460,   180,  -460}+    ,{    30, -1340,  -320,    30,  -320}+    ,{  -230, -1150,  -570,  -230,  -570}+    }+   ,{{   180, -1790,  -660,   180,  -660}+    ,{   180, -2010,  -660,   180,  -660}+    ,{  -430, -1790,  -970,  -430,  -970}+    ,{  -870, -3070,  -870, -1370,  -870}+    ,{  -430, -1790,  -970,  -430,  -970}+    }+   ,{{    30,  -630,  -510,    30,  -510}+    ,{  -390, -1650,  -510,  -390,  -510}+    ,{    20,  -630,  -520,    20,  -520}+    ,{    30, -1340,  -510,    30,  -510}+    ,{  -570, -1150,  -570,  -880,  -570}+    }+   ,{{  -320, -1790,  -320,  -430,  -320}+    ,{ -1160, -1980, -1160, -1870, -1160}+    ,{  -430, -1790,  -970,  -430,  -970}+    ,{  -320, -2390,  -320, -2280,  -320}+    ,{  -430, -1790,  -970,  -430,  -970}+    }+   ,{{   180, -1040,  -460,   180,  -460}+    ,{    30, -1340,  -510,    30,  -510}+    ,{   180, -1040,  -460,   180,  -460}+    ,{    30, -1340,  -510,    30,  -510}+    ,{  -230, -1520, -1300,  -230, -1300}+    }+   }+  ,{{{   -90,  -400,  -260,  -400,   -90}+    ,{   -90,  -600,  -820,  -600,   -90}+    ,{  -540,  -540,  -550,  -540,  -830}+    ,{  -260,  -400,  -260,  -400,  -800}+    ,{  -650,  -650,  -870,  -650,  -860}+    }+   ,{{  -740,  -740,  -940,  -740,  -830}+    ,{  -740,  -740,  -960,  -740, -1240}+    ,{  -830, -1050, -1270, -1050,  -830}+    ,{  -940,  -960,  -940,  -960, -1360}+    ,{ -1050, -1050, -1270, -1050, -1260}+    }+   ,{{   -90,  -600,  -820,  -600,   -90}+    ,{   -90,  -600,  -820,  -600,   -90}+    ,{  -600,  -600,  -820,  -600, -1710}+    ,{  -600,  -600,  -820,  -600,  -800}+    ,{  -650,  -650,  -870,  -650,  -860}+    }+   ,{{  -260,  -400,  -260,  -400,  -810}+    ,{  -810, -1240, -1220, -1240,  -810}+    ,{ -1050, -1050, -1270, -1050, -1260}+    ,{  -260,  -400,  -260,  -400, -1550}+    ,{ -1050, -1050, -1270, -1050, -1260}+    }+   ,{{  -540,  -540,  -550,  -540,  -800}+    ,{  -600,  -600,  -820,  -600,  -800}+    ,{  -540,  -540,  -550,  -540, -1460}+    ,{  -600,  -600,  -820,  -600,  -800}+    ,{ -1390, -1390, -1610, -1390, -2350}+    }+   }+  }+ ,{{{{    50,    50,  -320,    50,  -320}+    ,{    50,  -130,  -490,    50,  -490}+    ,{  -400,  -580,  -940,  -400,  -940}+    ,{    50,    50,  -320,  -320,  -320}+    ,{  -400,  -540,  -940,  -400,  -940}+    }+   ,{{    50,  -130,  -490,    50,  -490}+    ,{    50,  -130,  -490,    50,  -490}+    ,{  -400,  -580,  -940,  -400,  -940}+    ,{ -1320, -1320, -1680, -1770, -1680}+    ,{  -400,  -580,  -940,  -400,  -940}+    }+   ,{{  -320,  -490,  -860,  -320,  -860}+    ,{  -320,  -490,  -860,  -320,  -860}+    ,{  -620,  -800, -1160,  -620, -1160}+    ,{  -320,  -490,  -860,  -320,  -860}+    ,{  -620,  -800, -1160,  -620, -1160}+    }+   ,{{    50,    50,  -320,  -400,  -320}+    ,{  -840,  -840, -1210, -1290, -1210}+    ,{  -400,  -580,  -940,  -400,  -940}+    ,{    50,    50,  -320,  -400,  -320}+    ,{  -400,  -580,  -940,  -400,  -940}+    }+   ,{{  -320,  -490,  -860,  -320,  -860}+    ,{  -320,  -490,  -860,  -320,  -860}+    ,{  -930, -1110, -1470,  -930, -1470}+    ,{  -320,  -490,  -860,  -320,  -860}+    ,{  -540,  -540, -1150, -1230, -1150}+    }+   }+  ,{{{    50,    50,  -320,  -840,  -320}+    ,{  -130,  -130,  -490,  -840,  -490}+    ,{  -580,  -580,  -940, -1270,  -940}+    ,{    50,    50,  -320, -1210,  -320}+    ,{  -540,  -540,  -940, -1270,  -940}+    }+   ,{{  -130,  -130,  -490,  -840,  -490}+    ,{  -130,  -130,  -490,  -840,  -490}+    ,{  -580,  -580,  -940, -1290,  -940}+    ,{ -1320, -1320, -1680, -2030, -1680}+    ,{  -580,  -580,  -940, -1290,  -940}+    }+   ,{{  -490,  -490,  -860, -1210,  -860}+    ,{  -490,  -490,  -860, -1210,  -860}+    ,{  -800,  -800, -1160, -1270, -1160}+    ,{  -490,  -490,  -860, -1210,  -860}+    ,{  -800,  -800, -1160, -1270, -1160}+    }+   ,{{    50,    50,  -320, -1290,  -320}+    ,{  -840,  -840, -1210, -1560, -1210}+    ,{  -580,  -580,  -940, -1290,  -940}+    ,{    50,    50,  -320, -1920,  -320}+    ,{  -580,  -580,  -940, -1290,  -940}+    }+   ,{{  -490,  -490,  -860, -1210,  -860}+    ,{  -490,  -490,  -860, -1210,  -860}+    ,{ -1110, -1110, -1470, -1580, -1470}+    ,{  -490,  -490,  -860, -1210,  -860}+    ,{  -540,  -540, -1150, -1500, -1150}+    }+   }+  ,{{{  -400,  -400,  -620,  -400,  -930}+    ,{  -580,  -580,  -800,  -580, -1110}+    ,{ -1030, -1030, -1250, -1030, -1560}+    ,{  -400,  -400,  -620,  -400,  -930}+    ,{ -1030, -1030, -1250, -1030, -1560}+    }+   ,{{  -580,  -580,  -800,  -580, -1110}+    ,{  -580,  -580,  -800,  -580, -1110}+    ,{ -1030, -1030, -1250, -1030, -1560}+    ,{ -1750, -1770, -1750, -1770, -2060}+    ,{ -1030, -1030, -1250, -1030, -1560}+    }+   ,{{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{ -1250, -1250, -1470, -1250, -1780}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{ -1250, -1250, -1470, -1250, -1780}+    }+   ,{{  -400,  -400,  -620,  -400,  -930}+    ,{ -1270, -1290, -1270, -1290, -1580}+    ,{ -1030, -1030, -1250, -1030, -1560}+    ,{  -400,  -400,  -620,  -400,  -930}+    ,{ -1030, -1030, -1250, -1030, -1560}+    }+   ,{{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{ -1560, -1560, -1780, -1560, -2090}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{ -1230, -1230, -1450, -1230, -1760}+    }+   }+  ,{{{    50, -1320,  -320,    50,  -320}+    ,{    50, -1320,  -490,    50,  -490}+    ,{  -400, -1750,  -940,  -400,  -940}+    ,{  -320, -1680,  -320,  -320,  -320}+    ,{  -400, -1750,  -940,  -400,  -940}+    }+   ,{{    50, -1320,  -490,    50,  -490}+    ,{    50, -1320,  -490,    50,  -490}+    ,{  -400, -1770,  -940,  -400,  -940}+    ,{ -1680, -2510, -1680, -2390, -1680}+    ,{  -400, -1770,  -940,  -400,  -940}+    }+   ,{{  -320, -1680,  -860,  -320,  -860}+    ,{  -320, -1680,  -860,  -320,  -860}+    ,{  -620, -1750, -1160,  -620, -1160}+    ,{  -320, -1680,  -860,  -320,  -860}+    ,{  -620, -1750, -1160,  -620, -1160}+    }+   ,{{  -320, -1770,  -320,  -400,  -320}+    ,{ -1210, -2030, -1210, -1920, -1210}+    ,{  -400, -1770,  -940,  -400,  -940}+    ,{  -320, -2390,  -320, -2280,  -320}+    ,{  -400, -1770,  -940,  -400,  -940}+    }+   ,{{  -320, -1680,  -860,  -320,  -860}+    ,{  -320, -1680,  -860,  -320,  -860}+    ,{  -930, -2060, -1470,  -930, -1470}+    ,{  -320, -1680,  -860,  -320,  -860}+    ,{ -1150, -1970, -1150, -1860, -1150}+    }+   }+  ,{{{  -400,  -400,  -620,  -400,  -540}+    ,{  -540,  -580,  -800,  -580,  -540}+    ,{ -1030, -1030, -1250, -1030, -1230}+    ,{  -400,  -400,  -620,  -400, -1150}+    ,{ -1030, -1030, -1250, -1030, -1230}+    }+   ,{{  -540,  -580,  -800,  -580,  -540}+    ,{  -540,  -580,  -800,  -580,  -540}+    ,{ -1030, -1030, -1250, -1030, -1230}+    ,{ -1750, -1770, -1750, -1770, -1970}+    ,{ -1030, -1030, -1250, -1030, -1230}+    }+   ,{{  -940,  -940, -1160,  -940, -1150}+    ,{  -940,  -940, -1160,  -940, -1150}+    ,{ -1250, -1250, -1470, -1250, -1450}+    ,{  -940,  -940, -1160,  -940, -1150}+    ,{ -1250, -1250, -1470, -1250, -1450}+    }+   ,{{  -400,  -400,  -620,  -400, -1230}+    ,{ -1270, -1290, -1270, -1290, -1500}+    ,{ -1030, -1030, -1250, -1030, -1230}+    ,{  -400,  -400,  -620,  -400, -1860}+    ,{ -1030, -1030, -1250, -1030, -1230}+    }+   ,{{  -940,  -940, -1160,  -940, -1150}+    ,{  -940,  -940, -1160,  -940, -1150}+    ,{ -1560, -1560, -1780, -1560, -1760}+    ,{  -940,  -940, -1160,  -940, -1150}+    ,{ -1230, -1230, -1450, -1230, -1440}+    }+   }+  }+ ,{{{{   210,   210,  -160,  -240,  -160}+    ,{  -870,  -870, -1230,  -870, -1230}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{   210,   210,  -160,  -240,  -160}+    ,{  -800,  -800, -1410,  -870, -1410}+    }+   ,{{  -870, -1040, -1410,  -870, -1410}+    ,{ -1050, -1220, -1590, -1050, -1590}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{ -1060, -1060, -1420, -1510, -1420}+    ,{  -870, -1040, -1410,  -870, -1410}+    }+   ,{{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    }+   ,{{   210,   210,  -160,  -240,  -160}+    ,{  -870,  -870, -1230, -1320, -1230}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{   210,   210,  -160,  -240,  -160}+    ,{  -870, -1040, -1410,  -870, -1410}+    }+   ,{{  -800,  -800, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -870, -1040, -1410,  -870, -1410}+    ,{  -800,  -800, -1410, -1490, -1410}+    }+   }+  ,{{{   210,   210,  -160, -1520,  -160}+    ,{  -870,  -870, -1230, -1580, -1230}+    ,{ -1040, -1040, -1410, -1520, -1410}+    ,{   210,   210,  -160, -1760,  -160}+    ,{  -800,  -800, -1410, -1520, -1410}+    }+   ,{{ -1040, -1040, -1410, -1760, -1410}+    ,{ -1220, -1220, -1590, -1940, -1590}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{ -1060, -1060, -1420, -1770, -1420}+    ,{ -1040, -1040, -1410, -1760, -1410}+    }+   ,{{ -1040, -1040, -1410, -1520, -1410}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{ -1040, -1040, -1410, -1520, -1410}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{ -1040, -1040, -1410, -1520, -1410}+    }+   ,{{   210,   210,  -160, -1580,  -160}+    ,{  -870,  -870, -1230, -1580, -1230}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{   210,   210,  -160, -1760,  -160}+    ,{ -1040, -1040, -1410, -1760, -1410}+    }+   ,{{  -800,  -800, -1410, -1520, -1410}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{ -1040, -1040, -1410, -1520, -1410}+    ,{ -1040, -1040, -1410, -1760, -1410}+    ,{  -800,  -800, -1410, -1760, -1410}+    }+   }+  ,{{{  -240,  -240,  -460,  -240,  -770}+    ,{ -1300, -1320, -1300, -1320, -1610}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{  -240,  -240,  -460,  -240,  -770}+    ,{ -1490, -1490, -1710, -1490, -2020}+    }+   ,{{ -1490, -1490, -1490, -1490, -1800}+    ,{ -1670, -1670, -1890, -1670, -2200}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1510, -1490, -1510, -1800}+    ,{ -1490, -1490, -1710, -1490, -2020}+    }+   ,{{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    }+   ,{{  -240,  -240,  -460,  -240,  -770}+    ,{ -1300, -1320, -1300, -1320, -1610}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{  -240,  -240,  -460,  -240,  -770}+    ,{ -1490, -1490, -1710, -1490, -2020}+    }+   ,{{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    ,{ -1490, -1490, -1710, -1490, -2020}+    }+   }+  ,{{{  -160, -1990,  -160,  -870,  -160}+    ,{  -870, -2060, -1230,  -870, -1230}+    ,{  -870, -1990, -1410,  -870, -1410}+    ,{  -160, -2230,  -160,  -870,  -160}+    ,{  -870, -1990, -1410,  -870, -1410}+    }+   ,{{  -870, -2230, -1410,  -870, -1410}+    ,{ -1050, -2410, -1590, -1050, -1590}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{ -1420, -2250, -1420, -2130, -1420}+    ,{  -870, -2230, -1410,  -870, -1410}+    }+   ,{{  -870, -1990, -1410,  -870, -1410}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{  -870, -1990, -1410,  -870, -1410}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{  -870, -1990, -1410,  -870, -1410}+    }+   ,{{  -160, -2060,  -160,  -870,  -160}+    ,{ -1230, -2060, -1230, -1940, -1230}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{  -160, -2230,  -160, -2120,  -160}+    ,{  -870, -2230, -1410,  -870, -1410}+    }+   ,{{  -870, -1990, -1410,  -870, -1410}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{  -870, -1990, -1410,  -870, -1410}+    ,{  -870, -2230, -1410,  -870, -1410}+    ,{ -1410, -2230, -1410, -2120, -1410}+    }+   }+  ,{{{  -240,  -240,  -460,  -240, -1520}+    ,{ -1300, -1320, -1300, -1320, -1520}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{  -240,  -240,  -460,  -240, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    }+   ,{{ -1490, -1490, -1490, -1490, -1640}+    ,{ -1640, -1670, -1890, -1670, -1640}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1510, -1490, -1510, -1710}+    ,{ -1490, -1490, -1710, -1490, -1700}+    }+   ,{{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    }+   ,{{  -240,  -240,  -460,  -240, -1520}+    ,{ -1300, -1320, -1300, -1320, -1520}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{  -240,  -240,  -460,  -240, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    }+   ,{{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    ,{ -1490, -1490, -1710, -1490, -1700}+    }+   }+  }+ ,{{{{   760,   760,   400,   310,   400}+    ,{   200,  -430,  -340,   200,  -340}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{   760,   760,   400,   310,   400}+    ,{  -250,  -250,  -850,  -310,  -850}+    }+   ,{{   200,  -430,  -340,   200,  -340}+    ,{   200,  -430,  -340,   200,  -340}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -830,  -830, -1190, -1280, -1190}+    ,{  -310,  -490,  -850,  -310,  -850}+    }+   ,{{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    }+   ,{{   760,   760,   400,   310,   400}+    ,{ -1000, -1000, -1360, -1450, -1360}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{   760,   760,   400,   310,   400}+    ,{  -310,  -490,  -850,  -310,  -850}+    }+   ,{{  -250,  -250,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -310,  -490,  -850,  -310,  -850}+    ,{  -250,  -250,  -850,  -940,  -850}+    }+   }+  ,{{{   760,   760,   400,  -690,   400}+    ,{  -340,  -490,  -340,  -690,  -340}+    ,{  -490,  -490,  -850,  -960,  -850}+    ,{   760,   760,   400, -1200,   400}+    ,{  -250,  -250,  -850,  -960,  -850}+    }+   ,{{  -340,  -490,  -340,  -690,  -340}+    ,{  -340, -2040,  -340,  -690,  -340}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{  -830,  -830, -1190, -1540, -1190}+    ,{  -490,  -490,  -850, -1200,  -850}+    }+   ,{{  -490,  -490,  -850,  -960,  -850}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{  -490,  -490,  -850,  -960,  -850}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{  -490,  -490,  -850,  -960,  -850}+    }+   ,{{   760,   760,   400, -1200,   400}+    ,{ -1000, -1000, -1360, -1710, -1360}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{   760,   760,   400, -1200,   400}+    ,{  -490,  -490,  -850, -1200,  -850}+    }+   ,{{  -250,  -250,  -850,  -960,  -850}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{  -490,  -490,  -850,  -960,  -850}+    ,{  -490,  -490,  -850, -1200,  -850}+    ,{  -250,  -250,  -850, -1200,  -850}+    }+   }+  ,{{{   310,   310,    90,   310,  -220}+    ,{  -430,  -430,  -650,  -430,  -960}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{   310,   310,    90,   310,  -220}+    ,{  -940,  -940, -1160,  -940, -1470}+    }+   ,{{  -430,  -430,  -650,  -430,  -960}+    ,{  -430,  -430,  -650,  -430,  -960}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{ -1260, -1280, -1260, -1280, -1570}+    ,{  -940,  -940, -1160,  -940, -1470}+    }+   ,{{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    }+   ,{{   310,   310,    90,   310,  -220}+    ,{ -1430, -1450, -1430, -1450, -1740}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{   310,   310,    90,   310,  -220}+    ,{  -940,  -940, -1160,  -940, -1470}+    }+   ,{{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    ,{  -940,  -940, -1160,  -940, -1470}+    }+   }+  ,{{{   400, -1170,   400,   200,   400}+    ,{   200, -1170,  -340,   200,  -340}+    ,{  -310, -1440,  -850,  -310,  -850}+    ,{   400, -1680,   400,  -310,   400}+    ,{  -310, -1440,  -850,  -310,  -850}+    }+   ,{{   200, -1170,  -340,   200,  -340}+    ,{   200, -1170,  -340,   200,  -340}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{ -1190, -2020, -1190, -1900, -1190}+    ,{  -310, -1680,  -850,  -310,  -850}+    }+   ,{{  -310, -1440,  -850,  -310,  -850}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{  -310, -1440,  -850,  -310,  -850}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{  -310, -1440,  -850,  -310,  -850}+    }+   ,{{   400, -1680,   400,  -310,   400}+    ,{ -1360, -2190, -1360, -2070, -1360}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{   400, -1680,   400, -1560,   400}+    ,{  -310, -1680,  -850,  -310,  -850}+    }+   ,{{  -310, -1440,  -850,  -310,  -850}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{  -310, -1440,  -850,  -310,  -850}+    ,{  -310, -1680,  -850,  -310,  -850}+    ,{  -850, -1680,  -850, -1560,  -850}+    }+   }+  ,{{{   310,   310,    90,   310,  -390}+    ,{  -390,  -430,  -650,  -430,  -390}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{   310,   310,    90,   310, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    }+   ,{{  -390,  -430,  -650,  -430,  -390}+    ,{  -390,  -430,  -650,  -430,  -390}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{ -1260, -1280, -1260, -1280, -1480}+    ,{  -940,  -940, -1160,  -940, -1140}+    }+   ,{{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    }+   ,{{   310,   310,    90,   310, -1140}+    ,{ -1430, -1450, -1430, -1450, -1650}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{   310,   310,    90,   310, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    }+   ,{{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    ,{  -940,  -940, -1160,  -940, -1140}+    }+   }+  }+ ,{{{{  1140,  1140,   770,   780,   770}+    ,{   780,   600,   240,   780,   240}+    ,{   480,   300,   -60,   480,   -60}+    ,{  1140,  1140,   770,   690,   770}+    ,{   480,   300,   -60,   480,   -60}+    }+   ,{{   780,   600,   240,   780,   240}+    ,{   780,   600,   240,   780,   240}+    ,{   470,   290,   -70,   470,   -70}+    ,{  -780,  -780, -1150, -1230, -1150}+    ,{   470,   290,   -70,   470,   -70}+    }+   ,{{   490,   310,   -50,   490,   -50}+    ,{   490,   310,   -50,   490,   -50}+    ,{   480,   300,   -60,   480,   -60}+    ,{   490,   310,   -50,   490,   -50}+    ,{   480,   300,   -60,   480,   -60}+    }+   ,{{  1140,  1140,   770,   690,   770}+    ,{  -600,  -600,  -970, -1050,  -970}+    ,{   470,   290,   -70,   470,   -70}+    ,{  1140,  1140,   770,   690,   770}+    ,{   470,   290,   -70,   470,   -70}+    }+   ,{{   490,   310,   -50,   490,   -50}+    ,{   490,   310,   -50,   490,   -50}+    ,{   480,   300,   -60,   480,   -60}+    ,{   490,   310,   -50,   490,   -50}+    ,{  -430,  -430, -1040, -1120, -1040}+    }+   }+  ,{{{  1140,  1140,   770,  -110,   770}+    ,{   600,   600,   240,  -110,   240}+    ,{   300,   300,   -60,  -170,   -60}+    ,{  1140,  1140,   770,  -400,   770}+    ,{   300,   300,   -60,  -170,   -60}+    }+   ,{{   600,   600,   240,  -110,   240}+    ,{   600,   600,   240,  -110,   240}+    ,{   290,   290,   -70,  -420,   -70}+    ,{  -780,  -780, -1150, -1500, -1150}+    ,{   290,   290,   -70,  -420,   -70}+    }+   ,{{   310,   310,   -50,  -170,   -50}+    ,{   310,   310,   -50,  -400,   -50}+    ,{   300,   300,   -60,  -170,   -60}+    ,{   310,   310,   -50,  -400,   -50}+    ,{   300,   300,   -60,  -170,   -60}+    }+   ,{{  1140,  1140,   770,  -420,   770}+    ,{  -600,  -600,  -970, -1320,  -970}+    ,{   290,   290,   -70,  -420,   -70}+    ,{  1140,  1140,   770,  -830,   770}+    ,{   290,   290,   -70,  -420,   -70}+    }+   ,{{   310,   310,   -50,  -170,   -50}+    ,{   310,   310,   -50,  -400,   -50}+    ,{   300,   300,   -60,  -170,   -60}+    ,{   310,   310,   -50,  -400,   -50}+    ,{  -430,  -430, -1040, -1390, -1040}+    }+   }+  ,{{{   690,   690,   470,   690,   160}+    ,{   150,   150,   -60,   150,  -370}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{   690,   690,   470,   690,   160}+    ,{  -140,  -140,  -360,  -140,  -670}+    }+   ,{{   150,   150,   -60,   150,  -370}+    ,{   150,   150,   -60,   150,  -370}+    ,{  -150,  -150,  -370,  -150,  -680}+    ,{ -1210, -1230, -1210, -1230, -1520}+    ,{  -150,  -150,  -370,  -150,  -680}+    }+   ,{{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    }+   ,{{   690,   690,   470,   690,   160}+    ,{ -1030, -1050, -1030, -1050, -1340}+    ,{  -150,  -150,  -370,  -150,  -680}+    ,{   690,   690,   470,   690,   160}+    ,{  -150,  -150,  -370,  -150,  -680}+    }+   ,{{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{ -1120, -1120, -1340, -1120, -1650}+    }+   }+  ,{{{   780,  -580,   770,   780,   770}+    ,{   780,  -580,   240,   780,   240}+    ,{   480,  -640,   -60,   480,   -60}+    ,{   770,  -880,   770,   490,   770}+    ,{   480,  -640,   -60,   480,   -60}+    }+   ,{{   780,  -580,   240,   780,   240}+    ,{   780,  -580,   240,   780,   240}+    ,{   470,  -890,   -70,   470,   -70}+    ,{ -1150, -1970, -1150, -1860, -1150}+    ,{   470,  -890,   -70,   470,   -70}+    }+   ,{{   490,  -640,   -50,   490,   -50}+    ,{   490,  -880,   -50,   490,   -50}+    ,{   480,  -640,   -60,   480,   -60}+    ,{   490,  -880,   -50,   490,   -50}+    ,{   480,  -640,   -60,   480,   -60}+    }+   ,{{   770,  -890,   770,   470,   770}+    ,{  -970, -1790,  -970, -1680,  -970}+    ,{   470,  -890,   -70,   470,   -70}+    ,{   770, -1300,   770, -1190,   770}+    ,{   470,  -890,   -70,   470,   -70}+    }+   ,{{   490,  -640,   -50,   490,   -50}+    ,{   490,  -880,   -50,   490,   -50}+    ,{   480,  -640,   -60,   480,   -60}+    ,{   490,  -880,   -50,   490,   -50}+    ,{ -1040, -1860, -1040, -1750, -1040}+    }+   }+  ,{{{   690,   690,   470,   690,   190}+    ,{   190,   150,   -60,   150,   190}+    ,{  -140,  -140,  -360,  -140,  -350}+    ,{   690,   690,   470,   690,  -340}+    ,{  -140,  -140,  -360,  -140,  -350}+    }+   ,{{   190,   150,   -60,   150,   190}+    ,{   190,   150,   -60,   150,   190}+    ,{  -150,  -150,  -370,  -150,  -360}+    ,{ -1210, -1230, -1210, -1230, -1440}+    ,{  -150,  -150,  -370,  -150,  -360}+    }+   ,{{  -140,  -140,  -360,  -140,  -340}+    ,{  -140,  -140,  -360,  -140,  -340}+    ,{  -140,  -140,  -360,  -140,  -350}+    ,{  -140,  -140,  -360,  -140,  -340}+    ,{  -140,  -140,  -360,  -140,  -350}+    }+   ,{{   690,   690,   470,   690,  -360}+    ,{ -1030, -1050, -1030, -1050, -1260}+    ,{  -150,  -150,  -370,  -150,  -360}+    ,{   690,   690,   470,   690,  -770}+    ,{  -150,  -150,  -370,  -150,  -360}+    }+   ,{{  -140,  -140,  -360,  -140,  -340}+    ,{  -140,  -140,  -360,  -140,  -340}+    ,{  -140,  -140,  -360,  -140,  -350}+    ,{  -140,  -140,  -360,  -140,  -340}+    ,{ -1120, -1120, -1340, -1120, -1330}+    }+   }+  }+ ,{{{{  1320,  1320,   960,   870,   960}+    ,{   850,   670,   300,   850,   300}+    ,{   720,   540,   170,   720,   170}+    ,{  1320,  1320,   960,   870,   960}+    ,{   590,   410,    40,   590,    40}+    }+   ,{{   850,   670,   300,   850,   300}+    ,{   850,   670,   300,   850,   300}+    ,{   570,   390,    20,   570,    20}+    ,{  -730,  -730, -1100, -1180, -1100}+    ,{   570,   390,    20,   570,    20}+    }+   ,{{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   590,   410,    40,   590,    40}+    }+   ,{{  1320,  1320,   960,   870,   960}+    ,{ -1030, -1030, -1400, -1480, -1400}+    ,{   570,   390,    20,   570,    20}+    ,{  1320,  1320,   960,   870,   960}+    ,{   570,   390,    20,   570,    20}+    }+   ,{{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   280,   100,  -260,   280,  -260}+    ,{   720,   540,   170,   720,   170}+    ,{  -160,  -160,  -760,  -850,  -760}+    }+   }+  ,{{{  1320,  1320,   960,    70,   960}+    ,{   670,   670,   300,   -40,   300}+    ,{   540,   540,   170,    70,   170}+    ,{  1320,  1320,   960,  -170,   960}+    ,{   410,   410,    40,   -60,    40}+    }+   ,{{   670,   670,   300,   -40,   300}+    ,{   670,   670,   300,   -40,   300}+    ,{   390,   390,    20,  -320,    20}+    ,{  -730,  -730, -1100, -1450, -1100}+    ,{   390,   390,    20,  -320,    20}+    }+   ,{{   540,   540,   170,    70,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   540,   540,   170,    70,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   410,   410,    40,   -60,    40}+    }+   ,{{  1320,  1320,   960,  -320,   960}+    ,{ -1030, -1030, -1400, -1750, -1400}+    ,{   390,   390,    20,  -320,    20}+    ,{  1320,  1320,   960,  -640,   960}+    ,{   390,   390,    20,  -320,    20}+    }+   ,{{   540,   540,   170,  -170,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   100,   100,  -260,  -370,  -260}+    ,{   540,   540,   170,  -170,   170}+    ,{  -160,  -160,  -760, -1110,  -760}+    }+   }+  ,{{{   870,   870,   650,   870,   340}+    ,{   220,   220,     0,   220,  -310}+    ,{    90,    90,  -130,    90,  -440}+    ,{   870,   870,   650,   870,   340}+    ,{   -40,   -40,  -260,   -40,  -570}+    }+   ,{{   220,   220,     0,   220,  -310}+    ,{   220,   220,     0,   220,  -310}+    ,{   -60,   -60,  -280,   -60,  -590}+    ,{ -1160, -1180, -1160, -1180, -1470}+    ,{   -60,   -60,  -280,   -60,  -590}+    }+   ,{{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{   -40,   -40,  -260,   -40,  -570}+    }+   ,{{   870,   870,   650,   870,   340}+    ,{ -1460, -1480, -1460, -1480, -1770}+    ,{   -60,   -60,  -280,   -60,  -590}+    ,{   870,   870,   650,   870,   340}+    ,{   -60,   -60,  -280,   -60,  -590}+    }+   ,{{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{  -350,  -350,  -570,  -350,  -880}+    ,{    90,    90,  -130,    90,  -440}+    ,{  -850,  -850, -1070,  -850, -1380}+    }+   }+  ,{{{   960,  -410,   960,   850,   960}+    ,{   850,  -520,   300,   850,   300}+    ,{   720,  -410,   170,   720,   170}+    ,{   960,  -650,   960,   720,   960}+    ,{   590,  -540,    40,   590,    40}+    }+   ,{{   850,  -520,   300,   850,   300}+    ,{   850,  -520,   300,   850,   300}+    ,{   570,  -800,    20,   570,    20}+    ,{ -1100, -1920, -1100, -1810, -1100}+    ,{   570,  -800,    20,   570,    20}+    }+   ,{{   720,  -410,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   720,  -410,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   590,  -540,    40,   590,    40}+    }+   ,{{   960,  -800,   960,   570,   960}+    ,{ -1400, -2220, -1400, -2110, -1400}+    ,{   570,  -800,    20,   570,    20}+    ,{   960, -1120,   960, -1000,   960}+    ,{   570,  -800,    20,   570,    20}+    }+   ,{{   720,  -650,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   280,  -850,  -260,   280,  -260}+    ,{   720,  -650,   170,   720,   170}+    ,{  -760, -1590,  -760, -1470,  -760}+    }+   }+  ,{{{   870,   870,   650,   870,   250}+    ,{   250,   220,     0,   220,   250}+    ,{    90,    90,  -130,    90,  -110}+    ,{   870,   870,   650,   870,  -110}+    ,{   -40,   -40,  -260,   -40,  -240}+    }+   ,{{   250,   220,     0,   220,   250}+    ,{   250,   220,     0,   220,   250}+    ,{   -60,   -60,  -280,   -60,  -260}+    ,{ -1160, -1180, -1160, -1180, -1390}+    ,{   -60,   -60,  -280,   -60,  -260}+    }+   ,{{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{   -40,   -40,  -260,   -40,  -240}+    }+   ,{{   870,   870,   650,   870,  -260}+    ,{ -1460, -1480, -1460, -1480, -1690}+    ,{   -60,   -60,  -280,   -60,  -260}+    ,{   870,   870,   650,   870,  -580}+    ,{   -60,   -60,  -280,   -60,  -260}+    }+   ,{{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{  -350,  -350,  -570,  -350,  -550}+    ,{    90,    90,  -130,    90,  -110}+    ,{  -850,  -850, -1070,  -850, -1050}+    }+   }+  }+ ,{{{{  1320,  1320,   960,   870,   960}+    ,{   850,   670,   540,   850,   300}+    ,{   720,   540,   170,   720,   170}+    ,{  1320,  1320,   960,   870,   960}+    ,{   590,   410,    40,   590,    40}+    }+   ,{{   850,   670,   300,   850,   300}+    ,{   850,   670,   300,   850,   300}+    ,{   570,   390,    20,   570,    20}+    ,{  -350,  -350,  -870,  -960,  -870}+    ,{   570,   390,    20,   570,    20}+    }+   ,{{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   590,   410,    40,   590,    40}+    }+   ,{{  1320,  1320,   960,   870,   960}+    ,{   540,  -100,   540, -1050,  -810}+    ,{   570,   390,    20,   570,    20}+    ,{  1320,  1320,   960,   870,   960}+    ,{   570,   390,    20,   570,    20}+    }+   ,{{   720,   540,   170,   720,   170}+    ,{   720,   540,   170,   720,   170}+    ,{   480,   300,   -60,   480,   -60}+    ,{   720,   540,   170,   720,   170}+    ,{  -160,  -160,  -400,  -230,  -760}+    }+   }+  ,{{{  1320,  1320,   960,    70,   960}+    ,{   670,   670,   300,   -40,   300}+    ,{   540,   540,   170,    70,   170}+    ,{  1320,  1320,   960,  -170,   960}+    ,{   410,   410,    40,   -60,    40}+    }+   ,{{   670,   670,   300,   -40,   300}+    ,{   670,   670,   300,   -40,   300}+    ,{   390,   390,    20,  -320,    20}+    ,{  -730,  -730, -1100, -1450,  -870}+    ,{   390,   390,    20,  -320,    20}+    }+   ,{{   540,   540,   170,    70,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   540,   540,   170,    70,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   410,   410,    40,   -60,    40}+    }+   ,{{  1320,  1320,   960,  -320,   960}+    ,{    10,  -600,    10, -1320,  -970}+    ,{   390,   390,    20,  -320,    20}+    ,{  1320,  1320,   960,  -640,   960}+    ,{   390,   390,    20,  -320,    20}+    }+   ,{{   540,   540,   170,  -170,   170}+    ,{   540,   540,   170,  -170,   170}+    ,{   300,   300,   -60,  -170,   -60}+    ,{   540,   540,   170,  -170,   170}+    ,{  -160,  -160,  -400, -1110,  -760}+    }+   }+  ,{{{   870,   870,   650,   870,   340}+    ,{   540,   220,   540,   220,  -310}+    ,{    90,    90,  -130,    90,  -440}+    ,{   870,   870,   650,   870,   340}+    ,{   -40,   -40,  -260,   -40,  -570}+    }+   ,{{   220,   220,     0,   220,  -310}+    ,{   220,   220,     0,   220,  -310}+    ,{   -60,   -60,  -280,   -60,  -590}+    ,{  -350,  -350,  -940,  -960, -1250}+    ,{   -60,   -60,  -280,   -60,  -590}+    }+   ,{{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{   -40,   -40,  -260,   -40,  -570}+    }+   ,{{   870,   870,   650,   870,   340}+    ,{   540,  -100,   540, -1050, -1340}+    ,{   -60,   -60,  -280,   -60,  -590}+    ,{   870,   870,   650,   870,   340}+    ,{   -60,   -60,  -280,   -60,  -590}+    }+   ,{{    90,    90,  -130,    90,  -440}+    ,{    90,    90,  -130,    90,  -440}+    ,{  -140,  -140,  -360,  -140,  -670}+    ,{    90,    90,  -130,    90,  -440}+    ,{  -850,  -850, -1070,  -850, -1380}+    }+   }+  ,{{{   960,  -410,   960,   850,   960}+    ,{   850,  -520,   300,   850,   300}+    ,{   720,  -410,   170,   720,   170}+    ,{   960,  -650,   960,   720,   960}+    ,{   590,  -540,    40,   590,    40}+    }+   ,{{   850,  -520,   300,   850,   300}+    ,{   850,  -520,   300,   850,   300}+    ,{   570,  -800,    20,   570,    20}+    ,{  -870, -1920,  -870, -1370,  -870}+    ,{   570,  -800,    20,   570,    20}+    }+   ,{{   720,  -410,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   720,  -410,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   590,  -540,    40,   590,    40}+    }+   ,{{   960,  -800,   960,   570,   960}+    ,{  -970, -1790,  -970, -1680,  -970}+    ,{   570,  -800,    20,   570,    20}+    ,{   960, -1120,   960, -1000,   960}+    ,{   570,  -800,    20,   570,    20}+    }+   ,{{   720,  -640,   170,   720,   170}+    ,{   720,  -650,   170,   720,   170}+    ,{   480,  -640,   -60,   480,   -60}+    ,{   720,  -650,   170,   720,   170}+    ,{  -230, -1520,  -760,  -230,  -760}+    }+   }+  ,{{{   870,   870,   650,   870,   250}+    ,{   250,   220,     0,   220,   250}+    ,{    90,    90,  -130,    90,  -110}+    ,{   870,   870,   650,   870,  -110}+    ,{   -40,   -40,  -260,   -40,  -240}+    }+   ,{{   250,   220,     0,   220,   250}+    ,{   250,   220,     0,   220,   250}+    ,{   -60,   -60,  -280,   -60,  -260}+    ,{  -940,  -960,  -940,  -960, -1360}+    ,{   -60,   -60,  -280,   -60,  -260}+    }+   ,{{    90,    90,  -130,    90,   -90}+    ,{    90,    90,  -130,    90,   -90}+    ,{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{   -40,   -40,  -260,   -40,  -240}+    }+   ,{{   870,   870,   650,   870,  -260}+    ,{  -810, -1050, -1030, -1050,  -810}+    ,{   -60,   -60,  -280,   -60,  -260}+    ,{   870,   870,   650,   870,  -580}+    ,{   -60,   -60,  -280,   -60,  -260}+    }+   ,{{    90,    90,  -130,    90,  -110}+    ,{    90,    90,  -130,    90,  -110}+    ,{  -140,  -140,  -360,  -140,  -350}+    ,{    90,    90,  -130,    90,  -110}+    ,{  -850,  -850, -1070,  -850, -1050}+    }+   }+  }+ }+,{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF, 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INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  }+ ,{{{{   240,  -780,  -870,   240,  -870}+    ,{   190, -1060, -1060,   190,  -970}+    ,{   240,  -780, -1010,   240, -1010}+    ,{   190,  -870,  -870,   190,  -870}+    ,{   130,  -890, -1120,   130, -1120}+    }+   ,{{    40, -1210, -1180,    40,  -970}+    ,{    40, -1210, -1210,    40,  -970}+    ,{  -270, -1520, -1520,  -270, -1520}+    ,{ -1180, -1420, -1180, -1250, -1180}+    ,{  -270, -1520, -1520,  -270, -1520}+    }+   ,{{   190,  -840, -1060,   190, -1060}+    ,{   190, -1060, -1060,   190, -1060}+    ,{   180,  -840, -1070,   180, -1070}+    ,{   190, -1060, -1060,   190, -1060}+    ,{   130,  -890, -1120,   130, -1120}+    }+   ,{{  -270,  -870,  -870,  -270,  -870}+    ,{ -1470, -1710, -1470, -1530, -1470}+    ,{  -270, -1520, -1520,  -270, -1520}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{  -270, -1520, -1520,  -270, -1520}+    }+   ,{{   240,  -780, -1010,   240, -1010}+    ,{   190, -1060, -1060,   190, -1060}+    ,{   240,  -780, -1010,   240, -1010}+    ,{   190, -1060, -1060,   190, -1060}+    ,{ -1680, -1790, -1850, -1680, -1850}+    }+   }+  ,{{{  -590, -1050,  -870,  -590,  -870}+    ,{  -890, -1240, -1060,  -890, -1060}+    ,{  -590, -1190, -1010,  -590, -1010}+    ,{  -870, -1050,  -870,  -890,  -870}+    ,{  -700, -1300, -1120,  -700, -1120}+    }+   ,{{ -1030, -1370, -1210, -1030, -1210}+    ,{ -1030, -1370, -1210, -1030, -1210}+    ,{ -1340, -1700, -1520, -1340, -1520}+    ,{ -1250, -1600, -1420, -1250, -1420}+    ,{ -1340, -1700, -1520, -1340, -1520}+    }+   ,{{  -650, -1240, -1060,  -650, -1060}+    ,{  -890, -1240, -1060,  -890, -1060}+    ,{  -650, -1250, -1070,  -650, -1070}+    ,{  -890, -1240, -1060,  -890, -1060}+    ,{  -700, -1300, -1120,  -700, -1120}+    }+   ,{{  -870, -1050,  -870, -1340,  -870}+    ,{ -1530, -1890, -1710, -1530, -1710}+    ,{ -1340, -1700, -1520, -1340, -1520}+    ,{  -870, -1050,  -870, -1940,  -870}+    ,{ -1340, -1700, -1520, -1340, -1520}+    }+   ,{{  -590, -1190, -1010,  -590, -1010}+    ,{  -890, -1240, -1060,  -890, -1060}+    ,{  -590, -1190, -1010,  -590, -1010}+    ,{  -890, -1240, -1060,  -890, -1060}+    ,{ -1680, -1790, -1850, -1680, -1850}+    }+   }+  ,{{{  -870,  -870,  -870,  -870,  -870}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1010, -1010, -1010, -1010, -1010}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{ -1120, -1120, -1120, -1120, -1120}+    }+   ,{{ -1180, -1210, -1180, -1210, -1180}+    ,{ -1210, -1210, -1210, -1210, -1210}+    ,{ -1520, -1520, -1520, -1520, -1520}+    ,{ -1180, -1420, -1180, -1420, -1180}+    ,{ -1520, -1520, -1520, -1520, -1520}+    }+   ,{{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1070, -1070, -1070, -1070, -1070}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1120, -1120, -1120, -1120, -1120}+    }+   ,{{  -870,  -870,  -870,  -870,  -870}+    ,{ -1470, -1710, -1470, -1710, -1470}+    ,{ -1520, -1520, -1520, -1520, -1520}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{ -1520, -1520, -1520, -1520, -1520}+    }+   ,{{ -1010, -1010, -1010, -1010, -1010}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1010, -1010, -1010, -1010, -1010}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1850, -1850, -1850, -1850, -1850}+    }+   }+  ,{{{   240,  -780,  -870,   240,  -870}+    ,{   190, -1080, -1060,   190, -1060}+    ,{   240,  -780, -1010,   240, -1010}+    ,{   190, -1080,  -870,   190,  -870}+    ,{   130,  -890, -1120,   130, -1120}+    }+   ,{{    40, -1220, -1210,    40, -1210}+    ,{    40, -1220, -1210,    40, -1210}+    ,{  -270, -1530, -1520,  -270, -1520}+    ,{ -1420, -1440, -1420, -1420, -1420}+    ,{  -270, -1530, -1520,  -270, -1520}+    }+   ,{{   190,  -840, -1060,   190, -1060}+    ,{   190, -1080, -1060,   190, -1060}+    ,{   180,  -840, -1070,   180, -1070}+    ,{   190, -1080, -1060,   190, -1060}+    ,{   130,  -890, -1120,   130, -1120}+    }+   ,{{  -270, -1530,  -870,  -270,  -870}+    ,{ -1710, -1720, -1710, -1710, -1710}+    ,{  -270, -1530, -1520,  -270, -1520}+    ,{  -870, -2130,  -870, -2120,  -870}+    ,{  -270, -1530, -1520,  -270, -1520}+    }+   ,{{   240,  -780, -1010,   240, -1010}+    ,{   190, -1080, -1060,   190, -1060}+    ,{   240,  -780, -1010,   240, -1010}+    ,{   190, -1080, -1060,   190, -1060}+    ,{ -1850, -1870, -1850, -1850, -1850}+    }+   }+  ,{{{  -870,  -870,  -870,  -870,  -970}+    ,{  -970, -1060, -1060, -1060,  -970}+    ,{ -1010, -1010, -1010, -1010, -1010}+    ,{  -870,  -870,  -870,  -870, -1060}+    ,{ -1120, -1120, -1120, -1120, -1120}+    }+   ,{{  -970, -1210, -1180, -1210,  -970}+    ,{  -970, -1210, -1210, -1210,  -970}+    ,{ -1520, -1520, -1520, -1520, -1520}+    ,{ -1180, -1420, -1180, -1420, -1420}+    ,{ -1520, -1520, -1520, -1520, -1520}+    }+   ,{{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1070, -1070, -1070, -1070, -1070}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1120, -1120, -1120, -1120, -1120}+    }+   ,{{  -870,  -870,  -870,  -870, -1520}+    ,{ -1470, -1710, -1470, -1710, -1710}+    ,{ -1520, -1520, -1520, -1520, -1520}+    ,{  -870,  -870,  -870,  -870, -2120}+    ,{ -1520, -1520, -1520, -1520, -1520}+    }+   ,{{ -1010, -1010, -1010, -1010, -1010}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1010, -1010, -1010, -1010, -1010}+    ,{ -1060, -1060, -1060, -1060, -1060}+    ,{ -1850, -1850, -1850, -1850, -1850}+    }+   }+  }+ ,{{{{   210,  -870,  -870,   210,  -800}+    ,{   210, -1040, -1040,   210,  -800}+    ,{  -240, -1490, -1490,  -240, -1490}+    ,{  -160,  -870,  -870,  -160,  -870}+    ,{  -240, -1490, -1490,  -240, -1490}+    }+   ,{{   210, -1040, -1040,   210,  -800}+    ,{   210, -1040, -1040,   210,  -800}+    ,{  -240, -1490, -1490,  -240, -1490}+    ,{ -1990, -2230, -1990, -2060, -1990}+    ,{  -240, -1490, -1490,  -240, -1490}+    }+   ,{{  -160, -1410, -1410,  -160, -1410}+    ,{  -160, -1410, -1410,  -160, -1410}+    ,{  -460, -1490, -1710,  -460, -1710}+    ,{  -160, -1410, -1410,  -160, -1410}+    ,{  -460, -1490, -1710,  -460, -1710}+    }+   ,{{  -240,  -870,  -870,  -240,  -870}+    ,{ -1520, -1760, -1520, -1580, -1520}+    ,{  -240, -1490, -1490,  -240, -1490}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{  -240, -1490, -1490,  -240, -1490}+    }+   ,{{  -160, -1410, -1410,  -160, -1410}+    ,{  -160, -1410, -1410,  -160, -1410}+    ,{  -770, -1800, -2020,  -770, -2020}+    ,{  -160, -1410, -1410,  -160, -1410}+    ,{ -1520, -1640, -1700, -1520, -1700}+    }+   }+  ,{{{  -870, -1050,  -870,  -870,  -870}+    ,{  -870, -1220, -1040,  -870, -1040}+    ,{ -1300, -1670, -1490, -1300, -1490}+    ,{  -870, -1050,  -870, -1230,  -870}+    ,{ -1300, -1640, -1490, -1300, -1490}+    }+   ,{{  -870, -1220, -1040,  -870, -1040}+    ,{  -870, -1220, -1040,  -870, -1040}+    ,{ -1320, -1670, -1490, -1320, -1490}+    ,{ -2060, -2410, -2230, -2060, -2230}+    ,{ -1320, -1670, -1490, -1320, -1490}+    }+   ,{{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1300, -1890, -1710, -1300, -1710}+    ,{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1300, -1890, -1710, -1300, -1710}+    }+   ,{{  -870, -1050,  -870, -1320,  -870}+    ,{ -1580, -1940, -1760, -1580, -1760}+    ,{ -1320, -1670, -1490, -1320, -1490}+    ,{  -870, -1050,  -870, -1940,  -870}+    ,{ -1320, -1670, -1490, -1320, -1490}+    }+   ,{{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1610, -2200, -2020, -1610, -2020}+    ,{ -1230, -1590, -1410, -1230, -1410}+    ,{ -1520, -1640, -1700, -1520, -1700}+    }+   }+  ,{{{  -870,  -870,  -870,  -870,  -870}+    ,{ -1040, -1040, -1040, -1040, -1040}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{ -1040, -1040, -1040, -1040, -1040}+    ,{ -1040, -1040, -1040, -1040, -1040}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{ -1990, -2230, -1990, -2230, -1990}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1710, -1710, -1710, -1710, -1710}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1710, -1710, -1710, -1710, -1710}+    }+   ,{{  -870,  -870,  -870,  -870,  -870}+    ,{ -1520, -1760, -1520, -1760, -1520}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{  -870,  -870,  -870,  -870,  -870}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -2020, -2020, -2020, -2020, -2020}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1700, -1700, -1700, -1700, -1700}+    }+   }+  ,{{{   210, -1060,  -870,   210,  -870}+    ,{   210, -1060, -1040,   210, -1040}+    ,{  -240, -1490, -1490,  -240, -1490}+    ,{  -160, -1420,  -870,  -160,  -870}+    ,{  -240, -1490, -1490,  -240, -1490}+    }+   ,{{   210, -1060, -1040,   210, -1040}+    ,{   210, -1060, -1040,   210, -1040}+    ,{  -240, -1510, -1490,  -240, -1490}+    ,{ -2230, -2250, -2230, -2230, -2230}+    ,{  -240, -1510, -1490,  -240, -1490}+    }+   ,{{  -160, -1420, -1410,  -160, -1410}+    ,{  -160, -1420, -1410,  -160, -1410}+    ,{  -460, -1490, -1710,  -460, -1710}+    ,{  -160, -1420, -1410,  -160, -1410}+    ,{  -460, -1490, -1710,  -460, -1710}+    }+   ,{{  -240, -1510,  -870,  -240,  -870}+    ,{ -1760, -1770, -1760, -1760, -1760}+    ,{  -240, -1510, -1490,  -240, -1490}+    ,{  -870, -2130,  -870, -2120,  -870}+    ,{  -240, -1510, -1490,  -240, -1490}+    }+   ,{{  -160, -1420, -1410,  -160, -1410}+    ,{  -160, -1420, -1410,  -160, -1410}+    ,{  -770, -1800, -2020,  -770, -2020}+    ,{  -160, -1420, -1410,  -160, -1410}+    ,{ -1700, -1710, -1700, -1700, -1700}+    }+   }+  ,{{{  -800,  -870,  -870,  -870,  -800}+    ,{  -800, -1040, -1040, -1040,  -800}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{  -870,  -870,  -870,  -870, -1410}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{  -800, -1040, -1040, -1040,  -800}+    ,{  -800, -1040, -1040, -1040,  -800}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{ -1990, -2230, -1990, -2230, -2230}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1710, -1710, -1710, -1710, -1710}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1710, -1710, -1710, -1710, -1710}+    }+   ,{{  -870,  -870,  -870,  -870, -1490}+    ,{ -1520, -1760, -1520, -1760, -1760}+    ,{ -1490, -1490, -1490, -1490, -1490}+    ,{  -870,  -870,  -870,  -870, -2120}+    ,{ -1490, -1490, -1490, -1490, -1490}+    }+   ,{{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -2020, -2020, -2020, -2020, -2020}+    ,{ -1410, -1410, -1410, -1410, -1410}+    ,{ -1700, -1700, -1700, -1700, -1700}+    }+   }+  }+ ,{{{{  -710,  -710,  -710,  -710,  -710}+    ,{  -710, -1780, -1540,  -710, -1540}+    ,{  -710, -1730, -1960,  -710, -1960}+    ,{  -710,  -710,  -710,  -710,  -710}+    ,{  -710, -1730, -1960,  -710, -1960}+    }+   ,{{  -710, -1960, -1730,  -710, -1730}+    ,{  -890, -2140, -2140,  -890, -1900}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{ -1730, -1970, -1730, -1800, -1730}+    ,{  -710, -1960, -1960,  -710, -1960}+    }+   ,{{  -710, -1730, -1960,  -710, -1960}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{  -710, -1730, -1960,  -710, -1960}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{  -710, -1730, -1960,  -710, -1960}+    }+   ,{{  -710,  -710,  -710,  -710,  -710}+    ,{ -1540, -1780, -1540, -1610, -1540}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{  -710,  -710,  -710,  -710,  -710}+    ,{  -710, -1960, -1960,  -710, -1960}+    }+   ,{{  -710, -1730, -1960,  -710, -1960}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{  -710, -1730, -1960,  -710, -1960}+    ,{  -710, -1960, -1960,  -710, -1960}+    ,{ -1780, -1900, -1960, -1780, -1960}+    }+   }+  ,{{{  -710,  -890,  -710, -1540,  -710}+    ,{ -1610, -1960, -1780, -1610, -1780}+    ,{ -1540, -2140, -1960, -1540, -1960}+    ,{  -710,  -890,  -710, -1780,  -710}+    ,{ -1540, -1900, -1960, -1540, -1960}+    }+   ,{{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1960, -2320, -2140, -1960, -2140}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1800, -2150, -1970, -1800, -1970}+    ,{ -1780, -2140, -1960, -1780, -1960}+    }+   ,{{ -1540, -2140, -1960, -1540, -1960}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1540, -2140, -1960, -1540, -1960}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1540, -2140, -1960, -1540, -1960}+    }+   ,{{  -710,  -890,  -710, -1610,  -710}+    ,{ -1610, -1960, -1780, -1610, -1780}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{  -710,  -890,  -710, -1780,  -710}+    ,{ -1780, -2140, -1960, -1780, -1960}+    }+   ,{{ -1540, -1900, -1960, -1540, -1960}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1540, -2140, -1960, -1540, -1960}+    ,{ -1780, -2140, -1960, -1780, -1960}+    ,{ -1780, -1900, -1960, -1780, -1960}+    }+   }+  ,{{{  -710,  -710,  -710,  -710,  -710}+    ,{ -1540, -1780, -1540, -1780, -1540}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{  -710,  -710,  -710,  -710,  -710}+    ,{ 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 -710,  -710,  -710,  -710, -1780}+    ,{ -1540, -1780, -1540, -1780, -1780}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{  -710,  -710,  -710,  -710, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    }+   ,{{ -1730, -1960, -1730, -1960, -1900}+    ,{ -1900, -2140, -2140, -2140, -1900}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1730, -1970, -1730, -1970, -1970}+    ,{ -1960, -1960, -1960, -1960, -1960}+    }+   ,{{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    }+   ,{{  -710,  -710,  -710,  -710, -1780}+    ,{ -1540, -1780, -1540, -1780, -1780}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{  -710,  -710,  -710,  -710, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    }+   ,{{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    ,{ -1960, -1960, -1960, -1960, -1960}+    }+   }+  }+ ,{{{{   360,   -70,  -150,   360,  -150}+    ,{   360,   -70,  -890,   360,  -650}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{  -150, -1180, -1400,  -150, -1400}+    }+   ,{{   360,   -70,  -890,   360,  -650}+    ,{   360,   -70,  -890,   360,  -650}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{ -1500, -1600, -1500, -1570, -1500}+    ,{  -150, -1400, -1400,  -150, -1400}+    }+   ,{{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    }+   ,{{  -150,  -150,  -150,  -150,  -150}+    ,{ -1670, -1910, -1670, -1740, -1670}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{  -150, -1400, -1400,  -150, -1400}+    }+   ,{{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1400, -1400,  -150, -1400}+    ,{ -1230, -1340, -1400, -1230, -1400}+    }+   }+  ,{{{   -30,   -70,  -150,   -30,  -150}+    ,{   -30,   -70,  -890,   -30,  -890}+    ,{  -990, -1580, -1400,  -990, -1400}+    ,{  -150,  -330,  -150, -1230,  -150}+    ,{  -990, -1340, -1400,  -990, -1400}+    }+   ,{{   -30,   -70,  -890,   -30,  -890}+    ,{   -30,   -70,  -890,   -30,  -890}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{ -1570, -1600, -1740, -1570, -1740}+    ,{ -1230, -1580, -1400, -1230, -1400}+    }+   ,{{  -990, -1580, -1400,  -990, -1400}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{  -990, -1580, -1400,  -990, -1400}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{  -990, -1580, -1400,  -990, -1400}+    }+   ,{{  -150,  -330,  -150, -1230,  -150}+    ,{ -1740, -2090, -1910, -1740, -1910}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{  -150,  -330,  -150, -1230,  -150}+    ,{ -1230, -1580, -1400, -1230, -1400}+    }+   ,{{  -990, -1340, -1400,  -990, -1400}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{  -990, -1580, -1400,  -990, -1400}+    ,{ -1230, -1580, -1400, -1230, -1400}+    ,{ -1230, -1340, -1400, -1230, -1400}+    }+   }+  ,{{{  -150,  -150,  -150,  -150,  -150}+    ,{  -890,  -890,  -890,  -890,  -890}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -890,  -890,  -890,  -890,  -890}+    ,{  -890,  -890,  -890,  -890,  -890}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1500, -1740, -1500, -1740, -1500}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -150,  -150,  -150,  -150,  -150}+    ,{ -1670, -1910, -1670, -1910, -1670}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   }+  ,{{{   360,  -910,  -150,   360,  -150}+    ,{   360,  -910,  -890,   360,  -890}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1420,  -150,  -150,  -150}+    ,{  -150, -1180, -1400,  -150, -1400}+    }+   ,{{   360,  -910,  -890,   360,  -890}+    ,{   360,  -910,  -890,   360,  -890}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{ -1740, -3040, -1740, -1740, -1740}+    ,{  -150, -1420, -1400,  -150, -1400}+    }+   ,{{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    }+   ,{{  -150, -1420,  -150,  -150,  -150}+    ,{ -1910, -1930, -1910, -1910, -1910}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{  -150, -1420,  -150, -1400,  -150}+    ,{  -150, -1420, -1400,  -150, -1400}+    }+   ,{{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{  -150, -1180, -1400,  -150, -1400}+    ,{  -150, -1420, -1400,  -150, -1400}+    ,{ -1400, -1420, -1400, -1400, -1400}+    }+   }+  ,{{{  -150,  -150,  -150,  -150,  -650}+    ,{  -650,  -890,  -890,  -890,  -650}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -650,  -890,  -890,  -890,  -650}+    ,{  -650,  -890,  -890,  -890,  -650}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1500, -1740, -1500, -1740, -1740}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -150,  -150,  -150,  -150, -1400}+    ,{ -1670, -1910, -1670, -1910, -1910}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   }+  }+ ,{{{{   940,   220,   220,   940,   220}+    ,{   940,  -310,  -310,   940,   -70}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,   220,   220,   650,   220}+    ,{   640,  -380,  -610,   640,  -610}+    }+   ,{{   940,  -310,  -310,   940,   -70}+    ,{   940,  -310,  -310,   940,   -70}+    ,{   630,  -620,  -620,   630,  -620}+    ,{ -1460, -1700, -1460, -1520, -1460}+    ,{   630,  -620,  -620,   630,  -620}+    }+   ,{{   650,  -380,  -600,   650,  -600}+    ,{   650,  -600,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,  -600,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    }+   ,{{   630,   220,   220,   630,   220}+    ,{ -1280, -1520, -1280, -1340, -1280}+    ,{   630,  -620,  -620,   630,  -620}+    ,{   220,   220,   220,   220,   220}+    ,{   630,  -620,  -620,   630,  -620}+    }+   ,{{   650,  -380,  -600,   650,  -600}+    ,{   650,  -600,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,  -600,  -600,   650,  -600}+    ,{ -1410, -1530, -1590, -1410, -1590}+    }+   }+  ,{{{   220,    40,   220,  -130,   220}+    ,{  -130,  -490,  -310,  -130,  -310}+    ,{  -190,  -790,  -610,  -190,  -610}+    ,{   220,    40,   220,  -430,   220}+    ,{  -190,  -790,  -610,  -190,  -610}+    }+   ,{{  -130,  -490,  -310,  -130,  -310}+    ,{  -130,  -490,  -310,  -130,  -310}+    ,{  -440,  -800,  -620,  -440,  -620}+    ,{ -1520, -1880, -1700, -1520, -1700}+    ,{  -440,  -800,  -620,  -440,  -620}+    }+   ,{{  -190,  -780,  -600,  -190,  -600}+    ,{  -430,  -780,  -600,  -430,  -600}+    ,{  -190,  -790,  -610,  -190,  -610}+    ,{  -430,  -780,  -600,  -430,  -600}+    ,{  -190,  -790,  -610,  -190,  -610}+    }+   ,{{   220,    40,   220,  -440,   220}+    ,{ -1340, -1700, -1520, -1340, -1520}+    ,{  -440,  -800,  -620,  -440,  -620}+    ,{   220,    40,   220,  -850,   220}+    ,{  -440,  -800,  -620,  -440,  -620}+    }+   ,{{  -190,  -780,  -600,  -190,  -600}+    ,{  -430,  -780,  -600,  -430,  -600}+    ,{  -190,  -790,  -610,  -190,  -610}+    ,{  -430,  -780,  -600,  -430,  -600}+    ,{ -1410, -1530, -1590, -1410, -1590}+    }+   }+  ,{{{   220,   220,   220,   220,   220}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{   220,   220,   220,   220,   220}+    ,{  -610,  -610,  -610,  -610,  -610}+    }+   ,{{  -310,  -310,  -310,  -310,  -310}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -620,  -620,  -620,  -620,  -620}+    ,{ -1460, -1700, -1460, -1700, -1460}+    ,{  -620,  -620,  -620,  -620,  -620}+    }+   ,{{  -600,  -600,  -600,  -600,  -600}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    }+   ,{{   220,   220,   220,   220,   220}+    ,{ -1280, -1520, -1280, -1520, -1280}+    ,{  -620,  -620,  -620,  -620,  -620}+    ,{   220,   220,   220,   220,   220}+    ,{  -620,  -620,  -620,  -620,  -620}+    }+   ,{{  -600,  -600,  -600,  -600,  -600}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{ -1590, -1590, -1590, -1590, -1590}+    }+   }+  ,{{{   940,  -320,   220,   940,   220}+    ,{   940,  -320,  -310,   940,  -310}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,  -620,   220,   650,   220}+    ,{   640,  -380,  -610,   640,  -610}+    }+   ,{{   940,  -320,  -310,   940,  -310}+    ,{   940,  -320,  -310,   940,  -310}+    ,{   630,  -630,  -620,   630,  -620}+    ,{ -1700, -1710, -1700, -1700, -1700}+    ,{   630,  -630,  -620,   630,  -620}+    }+   ,{{   650,  -380,  -600,   650,  -600}+    ,{   650,  -620,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,  -620,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    }+   ,{{   630,  -630,   220,   630,   220}+    ,{ -1520, -1530, -1520, -1520, -1520}+    ,{   630,  -630,  -620,   630,  -620}+    ,{   220, -1040,   220, -1030,   220}+    ,{   630,  -630,  -620,   630,  -620}+    }+   ,{{   650,  -380,  -600,   650,  -600}+    ,{   650,  -620,  -600,   650,  -600}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   650,  -620,  -600,   650,  -600}+    ,{ -1590, -1600, -1590, -1590, -1590}+    }+   }+  ,{{{   220,   220,   220,   220,   -70}+    ,{   -70,  -310,  -310,  -310,   -70}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{   220,   220,   220,   220,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    }+   ,{{   -70,  -310,  -310,  -310,   -70}+    ,{   -70,  -310,  -310,  -310,   -70}+    ,{  -620,  -620,  -620,  -620,  -620}+    ,{ -1460, -1700, -1460, -1700, -1700}+    ,{  -620,  -620,  -620,  -620,  -620}+    }+   ,{{  -600,  -600,  -600,  -600,  -600}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    }+   ,{{   220,   220,   220,   220,  -620}+    ,{ -1280, -1520, -1280, -1520, -1520}+    ,{  -620,  -620,  -620,  -620,  -620}+    ,{   220,   220,   220,   220, -1030}+    ,{  -620,  -620,  -620,  -620,  -620}+    }+   ,{{  -600,  -600,  -600,  -600,  -600}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{  -600,  -600,  -600,  -600,  -600}+    ,{ -1590, -1590, -1590, -1590, -1590}+    }+   }+  }+ ,{{{{  1010,   410,   410,  1010,   410}+    ,{  1010,  -240,  -240,  1010,     0}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,   410,   410,   880,   410}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{  1010,  -240,  -240,  1010,     0}+    ,{  1010,  -240,  -240,  1010,     0}+    ,{   730,  -520,  -520,   730,  -520}+    ,{ -1410, -1650, -1410, -1470, -1410}+    ,{   730,  -520,  -520,   730,  -520}+    }+   ,{{   880,  -150,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{   730,   410,   410,   730,   410}+    ,{ -1710, -1950, -1710, -1770, -1710}+    ,{   730,  -520,  -520,   730,  -520}+    ,{   410,   410,   410,   410,   410}+    ,{   730,  -520,  -520,   730,  -520}+    }+   ,{{   880,  -370,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   440,  -590,  -810,   440,  -810}+    ,{   880,  -370,  -370,   880,  -370}+    ,{ -1140, -1250, -1310, -1140, -1310}+    }+   }+  ,{{{   410,   230,   410,    40,   410}+    ,{   -70,  -420,  -240,   -70,  -240}+    ,{    40,  -550,  -370,    40,  -370}+    ,{   410,   230,   410,  -200,   410}+    ,{   -90,  -680,  -500,   -90,  -500}+    }+   ,{{   -70,  -420,  -240,   -70,  -240}+    ,{   -70,  -420,  -240,   -70,  -240}+    ,{  -350,  -700,  -520,  -350,  -520}+    ,{ -1470, -1830, -1650, -1470, -1650}+    ,{  -350,  -700,  -520,  -350,  -520}+    }+   ,{{    40,  -550,  -370,    40,  -370}+    ,{  -200,  -550,  -370,  -200,  -370}+    ,{    40,  -550,  -370,    40,  -370}+    ,{  -200,  -550,  -370,  -200,  -370}+    ,{   -90,  -680,  -500,   -90,  -500}+    }+   ,{{   410,   230,   410,  -350,   410}+    ,{ -1770, -2130, -1950, -1770, -1950}+    ,{  -350,  -700,  -520,  -350,  -520}+    ,{   410,   230,   410,  -670,   410}+    ,{  -350,  -700,  -520,  -350,  -520}+    }+   ,{{  -200,  -550,  -370,  -200,  -370}+    ,{  -200,  -550,  -370,  -200,  -370}+    ,{  -400,  -990,  -810,  -400,  -810}+    ,{  -200,  -550,  -370,  -200,  -370}+    ,{ -1140, -1250, -1310, -1140, -1310}+    }+   }+  ,{{{   410,   410,   410,   410,   410}+    ,{  -240,  -240,  -240,  -240,  -240}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{   410,   410,   410,   410,   410}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{  -240,  -240,  -240,  -240,  -240}+    ,{  -240,  -240,  -240,  -240,  -240}+    ,{  -520,  -520,  -520,  -520,  -520}+    ,{ -1410, -1650, -1410, -1650, -1410}+    ,{  -520,  -520,  -520,  -520,  -520}+    }+   ,{{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{   410,   410,   410,   410,   410}+    ,{ -1710, -1950, -1710, -1950, -1710}+    ,{  -520,  -520,  -520,  -520,  -520}+    ,{   410,   410,   410,   410,   410}+    ,{  -520,  -520,  -520,  -520,  -520}+    }+   ,{{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -810,  -810,  -810,  -810,  -810}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{ -1310, -1310, -1310, -1310, -1310}+    }+   }+  ,{{{  1010,  -150,   410,  1010,   410}+    ,{  1010,  -260,  -240,  1010,  -240}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,   410,   880,   410}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{  1010,  -260,  -240,  1010,  -240}+    ,{  1010,  -260,  -240,  1010,  -240}+    ,{   730,  -540,  -520,   730,  -520}+    ,{ -1650, -1660, -1650, -1650, -1650}+    ,{   730,  -540,  -520,   730,  -520}+    }+   ,{{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{   730,  -540,   410,   730,   410}+    ,{ -1950, -1960, -1950, -1950, -1950}+    ,{   730,  -540,  -520,   730,  -520}+    ,{   410,  -860,   410,  -840,   410}+    ,{   730,  -540,  -520,   730,  -520}+    }+   ,{{   880,  -390,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   440,  -590,  -810,   440,  -810}+    ,{   880,  -390,  -370,   880,  -370}+    ,{ -1310, -1330, -1310, -1310, -1310}+    }+   }+  ,{{{   410,   410,   410,   410,     0}+    ,{     0,  -240,  -240,  -240,     0}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{   410,   410,   410,   410,  -370}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{     0,  -240,  -240,  -240,     0}+    ,{     0,  -240,  -240,  -240,     0}+    ,{  -520,  -520,  -520,  -520,  -520}+    ,{ -1410, -1650, -1410, -1650, -1650}+    ,{  -520,  -520,  -520,  -520,  -520}+    }+   ,{{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{   410,   410,   410,   410,  -520}+    ,{ -1710, -1950, -1710, -1950, -1950}+    ,{  -520,  -520,  -520,  -520,  -520}+    ,{   410,   410,   410,   410,  -840}+    ,{  -520,  -520,  -520,  -520,  -520}+    }+   ,{{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -810,  -810,  -810,  -810,  -810}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{ -1310, -1310, -1310, -1310, -1310}+    }+   }+  }+ ,{{{{  1010,   410,   410,  1010,   410}+    ,{  1010,   -70,  -240,  1010,     0}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,   410,   410,   880,   410}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{  1010,   -70,  -240,  1010,     0}+    ,{  1010,   -70,  -240,  1010,     0}+    ,{   730,  -520,  -520,   730,  -520}+    ,{ -1180, -1420, -1180, -1250, -1180}+    ,{   730,  -520,  -520,   730,  -520}+    }+   ,{{   880,  -150,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{   730,   410,   410,   730,   410}+    ,{ -1280, -1520, -1280, -1340, -1280}+    ,{   730,  -520,  -520,   730,  -520}+    ,{   410,   410,   410,   410,   410}+    ,{   730,  -520,  -520,   730,  -520}+    }+   ,{{   880,  -370,  -370,   880,  -370}+    ,{   880,  -370,  -370,   880,  -370}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   880,  -370,  -370,   880,  -370}+    ,{ -1140, -1250, -1310, -1140, -1310}+    }+   }+  ,{{{   410,   230,   410,    40,   410}+    ,{   -30,   -70,  -240,   -30,  -240}+    ,{    40,  -550,  -370,    40,  -370}+    ,{   410,   230,   410,  -200,   410}+    ,{   -90,  -680,  -500,   -90,  -500}+    }+   ,{{   -30,   -70,  -240,   -30,  -240}+    ,{   -30,   -70,  -240,   -30,  -240}+    ,{  -350,  -700,  -520,  -350,  -520}+    ,{ -1250, -1600, -1420, -1250, -1420}+    ,{  -350,  -700,  -520,  -350,  -520}+    }+   ,{{    40,  -550,  -370,    40,  -370}+    ,{  -200,  -550,  -370,  -200,  -370}+    ,{    40,  -550,  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-370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{   410,   410,   410,   410,   410}+    ,{ -1280, -1520, -1280, -1520, -1280}+    ,{  -520,  -520,  -520,  -520,  -520}+    ,{   410,   410,   410,   410,   410}+    ,{  -520,  -520,  -520,  -520,  -520}+    }+   ,{{  -370,  -370,  -370,  -370,  -370}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{  -610,  -610,  -610,  -610,  -610}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{ -1310, -1310, -1310, -1310, -1310}+    }+   }+  ,{{{  1010,  -150,   410,  1010,   410}+    ,{  1010,  -260,  -240,  1010,  -240}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,   410,   880,   410}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{  1010,  -260,  -240,  1010,  -240}+    ,{  1010,  -260,  -240,  1010,  -240}+    ,{   730,  -540,  -520,   730,  -520}+    ,{ -1420, -1440, -1420, -1420, -1420}+    ,{   730,  -540,  -520,   730,  -520}+    }+   ,{{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   880,  -150,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   750,  -280,  -500,   750,  -500}+    }+   ,{{   730,  -540,   410,   730,   410}+    ,{ -1520, -1530, -1520, -1520, -1520}+    ,{   730,  -540,  -520,   730,  -520}+    ,{   410,  -860,   410,  -840,   410}+    ,{   730,  -540,  -520,   730,  -520}+    }+   ,{{   880,  -380,  -370,   880,  -370}+    ,{   880,  -390,  -370,   880,  -370}+    ,{   640,  -380,  -610,   640,  -610}+    ,{   880,  -390,  -370,   880,  -370}+    ,{ -1310, -1330, -1310, -1310, -1310}+    }+   }+  ,{{{   410,   410,   410,   410,     0}+    ,{     0,  -240,  -240,  -240,     0}+    ,{  -370,  -370,  -370,  -370,  -370}+    ,{   410,   410,   410,   410,  -370}+    ,{  -500,  -500,  -500,  -500,  -500}+    }+   ,{{     0,  -240,  -240,  -240,     0}+    ,{     0,  -240,  -240, 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-1470,  -310}+    ,{  -640,  -640, -1150, -1660, -1150}+    ,{  -450,  -450,  -960, -1470,  -960}+    ,{   200,   200,  -310, -2070,  -310}+    ,{  -450,  -450,  -960, -1470,  -960}+    }+   ,{{    50,    50,  -450,  -720,  -450}+    ,{     0,     0,  -510, -1020,  -510}+    ,{    50,    50,  -450,  -720,  -450}+    ,{     0,     0,  -510, -1020,  -510}+    ,{  -550,  -550, -1300, -1810, -1300}+    }+   }+  ,{{{  -310,  -310,  -310,  -310,  -310}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -450,  -450,  -450,  -450,  -450}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -560,  -560,  -560,  -560,  -560}+    }+   ,{{  -630,  -650,  -630,  -650,  -630}+    ,{  -650,  -650,  -650,  -650,  -650}+    ,{  -960,  -960,  -960,  -960,  -960}+    ,{  -630,  -870,  -630,  -870,  -630}+    ,{  -960,  -960,  -960,  -960,  -960}+    }+   ,{{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -560,  -560,  -560,  -560,  -560}+    }+   ,{{  -310,  -310,  -310,  -310,  -310}+    ,{  -910, -1150,  -910, -1150,  -910}+    ,{  -960,  -960,  -960,  -960,  -960}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -960,  -960,  -960,  -960,  -960}+    }+   ,{{  -450,  -450,  -450,  -450,  -450}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -450,  -450,  -450,  -450,  -450}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{ -1300, -1300, -1300, -1300, -1300}+    }+   }+  ,{{{   800,  -550,  -310,   800,  -310}+    ,{   740,  -850,  -510,   740,  -510}+    ,{   800,  -550,  -450,   800,  -450}+    ,{   740,  -850,  -310,   740,  -310}+    ,{   690,  -660,  -560,   690,  -560}+    }+   ,{{   600,  -990,  -650,   600,  -650}+    ,{   600,  -990,  -650,   600,  -650}+    ,{   290, -1300,  -960,   290,  -960}+    ,{  -870, -1210,  -870,  -870,  -870}+    ,{   290, -1300,  -960,   290,  -960}+    }+   ,{{   740,  -610,  -510,   740,  -510}+    ,{   740,  -850,  -510,   740,  -510}+    ,{   740,  -610,  -510,   740,  -510}+    ,{   740,  -850,  -510,   740,  -510}+    ,{   690,  -660,  -560,   690,  -560}+    }+   ,{{   290, -1300,  -310,   290,  -310}+    ,{ -1150, -1490, -1150, -1150, -1150}+    ,{   290, -1300,  -960,   290,  -960}+    ,{  -310, -1900,  -310, -1560,  -310}+    ,{   290, -1300,  -960,   290,  -960}+    }+   ,{{   800,  -550,  -450,   800,  -450}+    ,{   740,  -850,  -510,   740,  -510}+    ,{   800,  -550,  -450,   800,  -450}+    ,{   740,  -850,  -510,   740,  -510}+    ,{ -1300, -1640, -1300, -1300, -1300}+    }+   }+  ,{{{  -310,  -310,  -310,  -310,  -410}+    ,{  -410,  -510,  -510,  -510,  -410}+    ,{  -450,  -450,  -450,  -450,  -450}+    ,{  -310,  -310,  -310,  -310,  -510}+    ,{  -560,  -560,  -560,  -560,  -560}+    }+   ,{{  -410,  -650,  -630,  -650,  -410}+    ,{  -410,  -650,  -650,  -650,  -410}+    ,{  -960,  -960,  -960,  -960,  -960}+    ,{  -630,  -870,  -630,  -870,  -870}+    ,{  -960,  -960,  -960,  -960,  -960}+    }+   ,{{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -560,  -560,  -560,  -560,  -560}+    }+   ,{{  -310,  -310,  -310,  -310,  -960}+    ,{  -910, -1150,  -910, -1150, -1150}+    ,{  -960,  -960,  -960,  -960,  -960}+    ,{  -310,  -310,  -310,  -310, -1560}+    ,{  -960,  -960,  -960,  -960,  -960}+    }+   ,{{  -450,  -450,  -450,  -450,  -450}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{  -450,  -450,  -450,  -450,  -450}+    ,{  -510,  -510,  -510,  -510,  -510}+    ,{ -1300, -1300, -1300, -1300, -1300}+    }+   }+  }+ ,{{{{   760,   200,  -310,   760,  -250}+    ,{   760,  -340,  -490,   760,  -250}+    ,{   310,  -430,  -940,   310,  -940}+    ,{   400,   200,  -310,   400,  -310}+    ,{   310,  -390,  -940,   310,  -940}+    }+   ,{{   760,  -430,  -490,   760,  -250}+    ,{   760,  -490,  -490,   760,  -250}+    ,{   310,  -430,  -940,   310,  -940}+    ,{ -1170, -1170, -1440, -1680, -1440}+    ,{   310,  -430,  -940,   310,  -940}+    }+   ,{{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{    90,  -650, -1160,    90, -1160}+    ,{   400,  -340,  -850,   400,  -850}+    ,{    90,  -650, -1160,    90, -1160}+    }+   ,{{   310,   200,  -310,   310,  -310}+    ,{  -690,  -690,  -960, -1200,  -960}+    ,{   310,  -430,  -940,   310,  -940}+    ,{   200,   200,  -310,  -310,  -310}+    ,{   310,  -430,  -940,   310,  -940}+    }+   ,{{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{  -220,  -960, -1470,  -220, -1470}+    ,{   400,  -340,  -850,   400,  -850}+    ,{  -390,  -390, -1140, -1140, -1140}+    }+   }+  ,{{{   200,   200,  -310, -1000,  -310}+    ,{  -340,  -340,  -490, -1000,  -490}+    ,{  -430,  -430,  -940, -1430,  -940}+    ,{   200,   200,  -310, -1360,  -310}+    ,{  -390,  -390,  -940, -1430,  -940}+    }+   ,{{  -430,  -430,  -490, -1000,  -490}+    ,{  -490, -2040,  -490, -1000,  -490}+    ,{  -430,  -430,  -940, -1450,  -940}+    ,{ -1170, -1170, -1680, -2190, -1680}+    ,{  -430,  -430,  -940, -1450,  -940}+    }+   ,{{  -340,  -340,  -850, -1360,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -650,  -650, -1160, -1430, -1160}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -650,  -650, -1160, -1430, -1160}+    }+   ,{{   200,   200,  -310, -1450,  -310}+    ,{  -690,  -690, -1200, -1710, -1200}+    ,{  -430,  -430,  -940, -1450,  -940}+    ,{   200,   200,  -310, -2070,  -310}+    ,{  -430,  -430,  -940, -1450,  -940}+    }+   ,{{  -340,  -340,  -850, -1360,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -960,  -960, -1470, -1740, -1470}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -390,  -390, -1140, -1650, -1140}+    }+   }+  ,{{{  -310,  -310,  -310,  -310,  -310}+    ,{  -490,  -490,  -490,  -490,  -490}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -490,  -490,  -490,  -490,  -490}+    ,{  -490,  -490,  -490,  -490,  -490}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{ -1440, -1680, -1440, -1680, -1440}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1160, -1160, -1160, -1160, -1160}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1160, -1160, -1160, -1160, -1160}+    }+   ,{{  -310,  -310,  -310,  -310,  -310}+    ,{  -960, -1200,  -960, -1200,  -960}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{  -310,  -310,  -310,  -310,  -310}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1470, -1470, -1470, -1470, -1470}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1140, -1140, -1140, -1140, -1140}+    }+   }+  ,{{{   760,  -830,  -310,   760,  -310}+    ,{   760,  -830,  -490,   760,  -490}+    ,{   310, -1260,  -940,   310,  -940}+    ,{   400, -1190,  -310,   400,  -310}+    ,{   310, -1260,  -940,   310,  -940}+    }+   ,{{   760,  -830,  -490,   760,  -490}+    ,{   760,  -830,  -490,   760,  -490}+    ,{   310, -1280,  -940,   310,  -940}+    ,{ -1680, -2020, -1680, -1680, -1680}+    ,{   310, -1280,  -940,   310,  -940}+    }+   ,{{   400, -1190,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{    90, -1260, -1160,    90, -1160}+    ,{   400, -1190,  -850,   400,  -850}+    ,{    90, -1260, -1160,    90, -1160}+    }+   ,{{   310, -1280,  -310,   310,  -310}+    ,{ -1200, -1540, -1200, -1200, -1200}+    ,{   310, -1280,  -940,   310,  -940}+    ,{  -310, -1900,  -310, -1560,  -310}+    ,{   310, -1280,  -940,   310,  -940}+    }+   ,{{   400, -1190,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{  -220, -1570, -1470,  -220, -1470}+    ,{   400, -1190,  -850,   400,  -850}+    ,{ -1140, -1480, -1140, -1140, -1140}+    }+   }+  ,{{{  -250,  -310,  -310,  -310,  -250}+    ,{  -250,  -490,  -490,  -490,  -250}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{  -310,  -310,  -310,  -310,  -850}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -250,  -490,  -490,  -490,  -250}+    ,{  -250,  -490,  -490,  -490,  -250}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{ -1440, -1680, -1440, -1680, -1680}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1160, -1160, -1160, -1160, -1160}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1160, -1160, -1160, -1160, -1160}+    }+   ,{{  -310,  -310,  -310,  -310,  -940}+    ,{  -960, -1200,  -960, -1200, -1200}+    ,{  -940,  -940,  -940,  -940,  -940}+    ,{  -310,  -310,  -310,  -310, -1560}+    ,{  -940,  -940,  -940,  -940,  -940}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1470, -1470, -1470, -1470, -1470}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{ -1140, -1140, -1140, -1140, -1140}+    }+   }+  }+ ,{{{{   360,   360,  -150,  -150,  -150}+    ,{   -30,   -30,  -990,  -150,  -990}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{   360,   360,  -150,  -150,  -150}+    ,{  -150,  -650, -1400,  -150, -1400}+    }+   ,{{   -70,   -70, -1180,  -150, -1180}+    ,{   -70,   -70, -1580,  -330, -1340}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -910,  -910, -1180, -1420, -1180}+    ,{  -150,  -890, -1400,  -150, -1400}+    }+   ,{{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    }+   ,{{   360,   360,  -150,  -150,  -150}+    ,{   -30,   -30,  -990, -1230,  -990}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{   360,   360,  -150,  -150,  -150}+    ,{  -150,  -890, -1400,  -150, -1400}+    }+   ,{{  -150,  -650, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -150,  -890, -1400,  -150, -1400}+    ,{  -650,  -650, -1400, -1400, -1400}+    }+   }+  ,{{{   360,   360,  -150, -1670,  -150}+    ,{   -30,   -30, -1230, -1740, -1230}+    ,{  -890,  -890, -1400, -1670, -1400}+    ,{   360,   360,  -150, -1910,  -150}+    ,{  -650,  -650, -1400, -1670, -1400}+    }+   ,{{   -70,   -70, -1400, -1910, -1400}+    ,{   -70,   -70, -1580, -2090, -1580}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{  -910,  -910, -1420, -1930, -1420}+    ,{  -890,  -890, -1400, -1910, -1400}+    }+   ,{{  -890,  -890, -1400, -1670, -1400}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{  -890,  -890, -1400, -1670, -1400}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{  -890,  -890, -1400, -1670, -1400}+    }+   ,{{   360,   360,  -150, -1740,  -150}+    ,{   -30,   -30, -1230, -1740, -1230}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{   360,   360,  -150, -1910,  -150}+    ,{  -890,  -890, -1400, -1910, -1400}+    }+   ,{{  -650,  -650, -1400, -1670, -1400}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{  -890,  -890, -1400, -1670, -1400}+    ,{  -890,  -890, -1400, -1910, -1400}+    ,{  -650,  -650, -1400, -1910, -1400}+    }+   }+  ,{{{  -150,  -150,  -150,  -150,  -150}+    ,{  -990, -1230,  -990, -1230,  -990}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1180, -1400, -1180, -1400, -1180}+    ,{ -1580, -1580, -1580, -1580, -1580}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1180, -1420, -1180, -1420, -1180}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -150,  -150,  -150,  -150,  -150}+    ,{  -990, -1230,  -990, -1230,  -990}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150,  -150}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   }+  ,{{{  -150, -1500,  -150,  -150,  -150}+    ,{  -150, -1570, -1230,  -150, -1230}+    ,{  -150, -1500, -1400,  -150, -1400}+    ,{  -150, -1740,  -150,  -150,  -150}+    ,{  -150, -1500, -1400,  -150, -1400}+    }+   ,{{  -150, -1600, -1400,  -150, -1400}+    ,{  -330, -1600, -1580,  -330, -1580}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{ -1420, -3040, -1420, -1420, -1420}+    ,{  -150, -1740, -1400,  -150, -1400}+    }+   ,{{  -150, -1500, -1400,  -150, -1400}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{  -150, -1500, -1400,  -150, -1400}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{  -150, -1500, -1400,  -150, -1400}+    }+   ,{{  -150, -1570,  -150,  -150,  -150}+    ,{ -1230, -1570, -1230, -1230, -1230}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{  -150, -1740,  -150, -1400,  -150}+    ,{  -150, -1740, -1400,  -150, -1400}+    }+   ,{{  -150, -1500, -1400,  -150, -1400}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{  -150, -1500, -1400,  -150, -1400}+    ,{  -150, -1740, -1400,  -150, -1400}+    ,{ -1400, -1740, -1400, -1400, -1400}+    }+   }+  ,{{{  -150,  -150,  -150,  -150, -1230}+    ,{  -990, -1230,  -990, -1230, -1230}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1180, -1400, -1180, -1400, -1340}+    ,{ -1340, -1580, -1580, -1580, -1340}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1180, -1420, -1180, -1420, -1420}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{  -150,  -150,  -150,  -150, -1230}+    ,{  -990, -1230,  -990, -1230, -1230}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{  -150,  -150,  -150,  -150, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   ,{{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    ,{ -1400, -1400, -1400, -1400, -1400}+    }+   }+  }+ ,{{{{   910,   910,   400,   910,   400}+    ,{   910,   170,  -340,   910,  -100}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   910,   910,   400,   400,   400}+    ,{   400,  -100,  -850,   400,  -850}+    }+   ,{{   910,   170,  -340,   910,  -100}+    ,{   910,   170,  -340,   910,  -100}+    ,{   400,  -340,  -850,   400,  -850}+    ,{  -680,  -680,  -950, -1190,  -950}+    ,{   400,  -340,  -850,   400,  -850}+    }+   ,{{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    }+   ,{{   910,   910,   400,   400,   400}+    ,{  -850,  -850, -1120, -1360, -1120}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   910,   910,   400,   400,   400}+    ,{   400,  -340,  -850,   400,  -850}+    }+   ,{{   400,  -100,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{   400,  -340,  -850,   400,  -850}+    ,{  -100,  -100,  -850,  -850,  -850}+    }+   }+  ,{{{   910,   910,   400,  -850,   400}+    ,{   170,   170,  -340,  -850,  -340}+    ,{  -340,  -340,  -850, -1120,  -850}+    ,{   910,   910,   400, -1360,   400}+    ,{  -100,  -100,  -850, -1120,  -850}+    }+   ,{{   170,   170,  -340,  -850,  -340}+    ,{   170,   170,  -340,  -850,  -340}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -680,  -680, -1190, -1700, -1190}+    ,{  -340,  -340,  -850, -1360,  -850}+    }+   ,{{  -340,  -340,  -850, -1120,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -340,  -340,  -850, -1120,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -340,  -340,  -850, -1120,  -850}+    }+   ,{{   910,   910,   400, -1360,   400}+    ,{  -850,  -850, -1360, -1870, -1360}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{   910,   910,   400, -1360,   400}+    ,{  -340,  -340,  -850, -1360,  -850}+    }+   ,{{  -100,  -100,  -850, -1120,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -340,  -340,  -850, -1120,  -850}+    ,{  -340,  -340,  -850, -1360,  -850}+    ,{  -100,  -100,  -850, -1360,  -850}+    }+   }+  ,{{{   400,   400,   400,   400,   400}+    ,{  -340,  -340,  -340,  -340,  -340}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{   400,   400,   400,   400,   400}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -340,  -340,  -340,  -340,  -340}+    ,{  -340,  -340,  -340,  -340,  -340}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -950, -1190,  -950, -1190,  -950}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{   400,   400,   400,   400,   400}+    ,{ -1120, -1360, -1120, -1360, -1120}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{   400,   400,   400,   400,   400}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   }+  ,{{{   910,  -680,   400,   910,   400}+    ,{   910,  -680,  -340,   910,  -340}+    ,{   400,  -950,  -850,   400,  -850}+    ,{   400, -1190,   400,   400,   400}+    ,{   400,  -950,  -850,   400,  -850}+    }+   ,{{   910,  -680,  -340,   910,  -340}+    ,{   910,  -680,  -340,   910,  -340}+    ,{   400, -1190,  -850,   400,  -850}+    ,{ -1190, -1530, -1190, -1190, -1190}+    ,{   400, -1190,  -850,   400,  -850}+    }+   ,{{   400,  -950,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{   400,  -950,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{   400,  -950,  -850,   400,  -850}+    }+   ,{{   400, -1190,   400,   400,   400}+    ,{ -1360, -1700, -1360, -1360, -1360}+    ,{   400, -1190,  -850,   400,  -850}+    ,{   400, -1190,   400,  -850,   400}+    ,{   400, -1190,  -850,   400,  -850}+    }+   ,{{   400,  -950,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{   400,  -950,  -850,   400,  -850}+    ,{   400, -1190,  -850,   400,  -850}+    ,{  -850, -1190,  -850,  -850,  -850}+    }+   }+  ,{{{   400,   400,   400,   400,  -100}+    ,{  -100,  -340,  -340,  -340,  -100}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{   400,   400,   400,   400,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -100,  -340,  -340,  -340,  -100}+    ,{  -100,  -340,  -340,  -340,  -100}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -950, -1190,  -950, -1190, -1190}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{   400,   400,   400,   400,  -850}+    ,{ -1120, -1360, -1120, -1360, -1360}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{   400,   400,   400,   400,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   ,{{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    ,{  -850,  -850,  -850,  -850,  -850}+    }+   }+  }+ ,{{{{  1490,  1280,   780,  1490,   780}+    ,{  1490,   750,   240,  1490,   480}+    ,{  1200,   450,   -50,  1200,   -50}+    ,{  1280,  1280,   780,  1200,   780}+    ,{  1200,   450,   -50,  1200,   -50}+    }+   ,{{  1490,   750,   240,  1490,   480}+    ,{  1490,   750,   240,  1490,   480}+    ,{  1190,   440,   -60,  1190,   -60}+    ,{  -630,  -630,  -900, -1140,  -900}+    ,{  1190,   440,   -60,  1190,   -60}+    }+   ,{{  1200,   460,   -50,  1200,   -50}+    ,{  1200,   460,   -50,  1200,   -50}+    ,{  1200,   450,   -50,  1200,   -50}+    ,{  1200,   460,   -50,  1200,   -50}+    ,{  1200,   450,   -50,  1200,   -50}+    }+   ,{{  1280,  1280,   780,  1190,   780}+    ,{  -450,  -450,  -720,  -960,  -720}+    ,{  1190,   440,   -60,  1190,   -60}+    ,{  1280,  1280,   780,   780,   780}+    ,{  1190,   440,   -60,  1190,   -60}+    }+   ,{{  1200,   460,   -50,  1200,   -50}+    ,{  1200,   460,   -50,  1200,   -50}+    ,{  1200,   450,   -50,  1200,   -50}+    ,{  1200,   460,   -50,  1200,   -50}+    ,{  -280,  -280, -1030, -1030, -1030}+    }+   }+  ,{{{  1280,  1280,   780,  -260,   780}+    ,{   750,   750,   240,  -260,   240}+    ,{   450,   450,   -50,  -320,   -50}+    ,{  1280,  1280,   780,  -560,   780}+    ,{   450,   450,   -50,  -320,   -50}+    }+   ,{{   750,   750,   240,  -260,   240}+    ,{   750,   750,   240,  -260,   240}+    ,{   440,   440,   -60,  -570,   -60}+    ,{  -630,  -630, -1140, -1650, -1140}+    ,{   440,   440,   -60,  -570,   -60}+    }+   ,{{   460,   460,   -50,  -320,   -50}+    ,{   460,   460,   -50,  -560,   -50}+    ,{   450,   450,   -50,  -320,   -50}+    ,{   460,   460,   -50,  -560,   -50}+    ,{   450,   450,   -50,  -320,   -50}+    }+   ,{{  1280,  1280,   780,  -570,   780}+    ,{  -450,  -450,  -960, -1470,  -960}+    ,{   440,   440,   -60,  -570,   -60}+    ,{  1280,  1280,   780,  -980,   780}+    ,{   440,   440,   -60,  -570,   -60}+    }+   ,{{   460,   460,   -50,  -320,   -50}+    ,{   460,   460,   -50,  -560,   -50}+    ,{   450,   450,   -50,  -320,   -50}+    ,{   460,   460,   -50,  -560,   -50}+    ,{  -280,  -280, -1030, -1540, -1030}+    }+   }+  ,{{{   780,   780,   780,   780,   780}+    ,{   240,   240,   240,   240,   240}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   780,   780,   780,   780,   780}+    ,{   -50,   -50,   -50,   -50,   -50}+    }+   ,{{   240,   240,   240,   240,   240}+    ,{   240,   240,   240,   240,   240}+    ,{   -60,   -60,   -60,   -60,   -60}+    ,{  -900, -1140,  -900, -1140,  -900}+    ,{   -60,   -60,   -60,   -60,   -60}+    }+   ,{{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    }+   ,{{   780,   780,   780,   780,   780}+    ,{  -720,  -960,  -720,  -960,  -720}+    ,{   -60,   -60,   -60,   -60,   -60}+    ,{   780,   780,   780,   780,   780}+    ,{   -60,   -60,   -60,   -60,   -60}+    }+   ,{{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{ -1030, -1030, -1030, -1030, -1030}+    }+   }+  ,{{{  1490,   -90,   780,  1490,   780}+    ,{  1490,   -90,   240,  1490,   240}+    ,{  1200,  -150,   -50,  1200,   -50}+    ,{  1200,  -390,   780,  1200,   780}+    ,{  1200,  -150,   -50,  1200,   -50}+    }+   ,{{  1490,   -90,   240,  1490,   240}+    ,{  1490,   -90,   240,  1490,   240}+    ,{  1190,  -400,   -60,  1190,   -60}+    ,{ -1140, -1480, -1140, -1140, -1140}+    ,{  1190,  -400,   -60,  1190,   -60}+    }+   ,{{  1200,  -150,   -50,  1200,   -50}+    ,{  1200,  -390,   -50,  1200,   -50}+    ,{  1200,  -150,   -50,  1200,   -50}+    ,{  1200,  -390,   -50,  1200,   -50}+    ,{  1200,  -150,   -50,  1200,   -50}+    }+   ,{{  1190,  -400,   780,  1190,   780}+    ,{  -960, -1300,  -960,  -960,  -960}+    ,{  1190,  -400,   -60,  1190,   -60}+    ,{   780,  -810,   780,  -470,   780}+    ,{  1190,  -400,   -60,  1190,   -60}+    }+   ,{{  1200,  -150,   -50,  1200,   -50}+    ,{  1200,  -390,   -50,  1200,   -50}+    ,{  1200,  -150,   -50,  1200,   -50}+    ,{  1200,  -390,   -50,  1200,   -50}+    ,{ -1030, -1370, -1030, -1030, -1030}+    }+   }+  ,{{{   780,   780,   780,   780,   480}+    ,{   480,   240,   240,   240,   480}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   780,   780,   780,   780,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    }+   ,{{   480,   240,   240,   240,   480}+    ,{   480,   240,   240,   240,   480}+    ,{   -60,   -60,   -60,   -60,   -60}+    ,{  -900, -1140,  -900, -1140, -1140}+    ,{   -60,   -60,   -60,   -60,   -60}+    }+   ,{{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    }+   ,{{   780,   780,   780,   780,   -60}+    ,{  -720,  -960,  -720,  -960,  -960}+    ,{   -60,   -60,   -60,   -60,   -60}+    ,{   780,   780,   780,   780,  -470}+    ,{   -60,   -60,   -60,   -60,   -60}+    }+   ,{{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{ -1030, -1030, -1030, -1030, -1030}+    }+   }+  }+ ,{{{{  1560,  1470,   960,  1560,   960}+    ,{  1560,   820,   310,  1560,   550}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1470,  1470,   960,  1430,   960}+    ,{  1300,   560,    50,  1300,    50}+    }+   ,{{  1560,   820,   310,  1560,   550}+    ,{  1560,   820,   310,  1560,   550}+    ,{  1280,   540,    30,  1280,    30}+    ,{  -580,  -580,  -850, -1090,  -850}+    ,{  1280,   540,    30,  1280,    30}+    }+   ,{{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1300,   560,    50,  1300,    50}+    }+   ,{{  1470,  1470,   960,  1280,   960}+    ,{  -880,  -880, -1150, -1390, -1150}+    ,{  1280,   540,    30,  1280,    30}+    ,{  1470,  1470,   960,   960,   960}+    ,{  1280,   540,    30,  1280,    30}+    }+   ,{{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{   990,   250,  -260,   990,  -260}+    ,{  1430,   690,   180,  1430,   180}+    ,{   -10,   -10,  -760,  -760,  -760}+    }+   }+  ,{{{  1470,  1470,   960,   -90,   960}+    ,{   820,   820,   310,  -200,   310}+    ,{   690,   690,   180,   -90,   180}+    ,{  1470,  1470,   960,  -330,   960}+    ,{   560,   560,    50,  -220,    50}+    }+   ,{{   820,   820,   310,  -200,   310}+    ,{   820,   820,   310,  -200,   310}+    ,{   540,   540,    30,  -480,    30}+    ,{  -580,  -580, -1090, -1600, -1090}+    ,{   540,   540,    30,  -480,    30}+    }+   ,{{   690,   690,   180,   -90,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   690,   690,   180,   -90,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   560,   560,    50,  -220,    50}+    }+   ,{{  1470,  1470,   960,  -480,   960}+    ,{  -880,  -880, -1390, -1900, -1390}+    ,{   540,   540,    30,  -480,    30}+    ,{  1470,  1470,   960,  -800,   960}+    ,{   540,   540,    30,  -480,    30}+    }+   ,{{   690,   690,   180,  -330,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   250,   250,  -260,  -530,  -260}+    ,{   690,   690,   180,  -330,   180}+    ,{   -10,   -10,  -760, -1270,  -760}+    }+   }+  ,{{{   960,   960,   960,   960,   960}+    ,{   310,   310,   310,   310,   310}+    ,{   180,   180,   180,   180,   180}+    ,{   960,   960,   960,   960,   960}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{    30,    30,    30,    30,    30}+    ,{  -850, -1090,  -850, -1090,  -850}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   960,   960,   960,   960,   960}+    ,{ -1150, -1390, -1150, -1390, -1150}+    ,{    30,    30,    30,    30,    30}+    ,{   960,   960,   960,   960,   960}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{  -260,  -260,  -260,  -260,  -260}+    ,{   180,   180,   180,   180,   180}+    ,{  -760,  -760,  -760,  -760,  -760}+    }+   }+  ,{{{  1560,    80,   960,  1560,   960}+    ,{  1560,   -30,   310,  1560,   310}+    ,{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   960,  1430,   960}+    ,{  1300,   -50,    50,  1300,    50}+    }+   ,{{  1560,   -30,   310,  1560,   310}+    ,{  1560,   -30,   310,  1560,   310}+    ,{  1280,  -310,    30,  1280,    30}+    ,{ -1090, -1430, -1090, -1090, -1090}+    ,{  1280,  -310,    30,  1280,    30}+    }+   ,{{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  1300,   -50,    50,  1300,    50}+    }+   ,{{  1280,  -310,   960,  1280,   960}+    ,{ -1390, -1730, -1390, -1390, -1390}+    ,{  1280,  -310,    30,  1280,    30}+    ,{   960,  -630,   960,  -290,   960}+    ,{  1280,  -310,    30,  1280,    30}+    }+   ,{{  1430,  -160,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{   990,  -360,  -260,   990,  -260}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  -760, -1100,  -760,  -760,  -760}+    }+   }+  ,{{{   960,   960,   960,   960,   550}+    ,{   550,   310,   310,   310,   550}+    ,{   180,   180,   180,   180,   180}+    ,{   960,   960,   960,   960,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   550,   310,   310,   310,   550}+    ,{   550,   310,   310,   310,   550}+    ,{    30,    30,    30,    30,    30}+    ,{  -850, -1090,  -850, -1090, -1090}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   960,   960,   960,   960,    30}+    ,{ -1150, -1390, -1150, -1390, -1390}+    ,{    30,    30,    30,    30,    30}+    ,{   960,   960,   960,   960,  -290}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{  -260,  -260,  -260,  -260,  -260}+    ,{   180,   180,   180,   180,   180}+    ,{  -760,  -760,  -760,  -760,  -760}+    }+   }+  }+ ,{{{{  1560,  1470,   960,  1560,   960}+    ,{  1560,   820,   310,  1560,   550}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1470,  1470,   960,  1430,   960}+    ,{  1300,   560,    50,  1300,    50}+    }+   ,{{  1560,   820,   310,  1560,   550}+    ,{  1560,   820,   310,  1560,   550}+    ,{  1280,   540,    30,  1280,    30}+    ,{  -360,  -360,  -630,  -870,  -630}+    ,{  1280,   540,    30,  1280,    30}+    }+   ,{{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1300,   560,    50,  1300,    50}+    }+   ,{{  1470,  1470,   960,  1280,   960}+    ,{   -30,   -30,  -720,  -960,  -720}+    ,{  1280,   540,    30,  1280,    30}+    ,{  1470,  1470,   960,   960,   960}+    ,{  1280,   540,    30,  1280,    30}+    }+   ,{{  1430,   690,   180,  1430,   180}+    ,{  1430,   690,   180,  1430,   180}+    ,{  1200,   450,   -50,  1200,   -50}+    ,{  1430,   690,   180,  1430,   180}+    ,{   -10,   -10,  -760,  -760,  -760}+    }+   }+  ,{{{  1470,  1470,   960,   -90,   960}+    ,{   820,   820,   310,  -200,   310}+    ,{   690,   690,   180,   -90,   180}+    ,{  1470,  1470,   960,  -330,   960}+    ,{   560,   560,    50,  -220,    50}+    }+   ,{{   820,   820,   310,  -200,   310}+    ,{   820,   820,   310,  -200,   310}+    ,{   540,   540,    30,  -480,    30}+    ,{  -360,  -360,  -870, -1380,  -870}+    ,{   540,   540,    30,  -480,    30}+    }+   ,{{   690,   690,   180,   -90,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   690,   690,   180,   -90,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   560,   560,    50,  -220,    50}+    }+   ,{{  1470,  1470,   960,  -480,   960}+    ,{   -30,   -30,  -960, -1470,  -960}+    ,{   540,   540,    30,  -480,    30}+    ,{  1470,  1470,   960,  -800,   960}+    ,{   540,   540,    30,  -480,    30}+    }+   ,{{   690,   690,   180,  -320,   180}+    ,{   690,   690,   180,  -330,   180}+    ,{   450,   450,   -50,  -320,   -50}+    ,{   690,   690,   180,  -330,   180}+    ,{   -10,   -10,  -760, -1270,  -760}+    }+   }+  ,{{{   960,   960,   960,   960,   960}+    ,{   310,   310,   310,   310,   310}+    ,{   180,   180,   180,   180,   180}+    ,{   960,   960,   960,   960,   960}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   310,   310,   310,   310,   310}+    ,{   310,   310,   310,   310,   310}+    ,{    30,    30,    30,    30,    30}+    ,{  -630,  -870,  -630,  -870,  -630}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   960,   960,   960,   960,   960}+    ,{  -720,  -960,  -720,  -960,  -720}+    ,{    30,    30,    30,    30,    30}+    ,{   960,   960,   960,   960,   960}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   180,   180,   180,   180,   180}+    ,{  -760,  -760,  -760,  -760,  -760}+    }+   }+  ,{{{  1560,    80,   960,  1560,   960}+    ,{  1560,   -30,   310,  1560,   310}+    ,{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   960,  1430,   960}+    ,{  1300,   -50,    50,  1300,    50}+    }+   ,{{  1560,   -30,   310,  1560,   310}+    ,{  1560,   -30,   310,  1560,   310}+    ,{  1280,  -310,    30,  1280,    30}+    ,{  -870, -1210,  -870,  -870,  -870}+    ,{  1280,  -310,    30,  1280,    30}+    }+   ,{{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  1430,    80,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  1300,   -50,    50,  1300,    50}+    }+   ,{{  1280,  -310,   960,  1280,   960}+    ,{  -960, -1300,  -960,  -960,  -960}+    ,{  1280,  -310,    30,  1280,    30}+    ,{   960,  -630,   960,  -290,   960}+    ,{  1280,  -310,    30,  1280,    30}+    }+   ,{{  1430,  -150,   180,  1430,   180}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  1200,  -150,   -50,  1200,   -50}+    ,{  1430,  -160,   180,  1430,   180}+    ,{  -760, -1100,  -760,  -760,  -760}+    }+   }+  ,{{{   960,   960,   960,   960,   550}+    ,{   550,   310,   310,   310,   550}+    ,{   180,   180,   180,   180,   180}+    ,{   960,   960,   960,   960,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   550,   310,   310,   310,   550}+    ,{   550,   310,   310,   310,   550}+    ,{    30,    30,    30,    30,    30}+    ,{  -630,  -870,  -630,  -870,  -870}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{    50,    50,    50,    50,    50}+    }+   ,{{   960,   960,   960,   960,    30}+    ,{  -720,  -960,  -720,  -960,  -960}+    ,{    30,    30,    30,    30,    30}+    ,{   960,   960,   960,   960,  -290}+    ,{    30,    30,    30,    30,    30}+    }+   ,{{   180,   180,   180,   180,   180}+    ,{   180,   180,   180,   180,   180}+    ,{   -50,   -50,   -50,   -50,   -50}+    ,{   180,   180,   180,   180,   180}+    ,{  -760,  -760,  -760,  -760,  -760}+    }+   }+  }+ }+,{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF, 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INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,  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130,  -160,   660,  -160}+    ,{   220,   220,   170,   -80,   170}+    ,{   660,   130,  -160,   660,  -160}+    }+   ,{{  1120,   580,   290,  1120,   290}+    ,{  1120,   580,   290,  1120,   290}+    ,{  1110,   580,   280,  1110,   280}+    ,{  1120,   580,   290,  1120,   290}+    ,{  1060,   530,   230,  1060,   230}+    }+   ,{{   780,   780,   490,   660,   490}+    ,{   -60,   -60,  -120,  -370,  -120}+    ,{   660,   130,  -160,   660,  -160}+    ,{   780,   780,   490,   470,   490}+    ,{   660,   130,  -160,   660,  -160}+    }+   ,{{  1170,   640,   340,  1170,   340}+    ,{  1120,   580,   290,  1120,   290}+    ,{  1170,   640,   340,  1170,   340}+    ,{  1120,   580,   290,  1120,   290}+    ,{    40,    40,  -500,  -510,  -500}+    }+   }+  ,{{{   780,   780,   490,  -330,   490}+    ,{   580,   580,   290,  -620,   290}+    ,{   640,   640,   340,  -330,   340}+    ,{   780,   780,   490,  -620,   490}+    ,{   530,   530,   230,  -440,   230}+    }+   ,{{   440,   440,   140,  -770,   140}+    ,{   440,   440,   140,  -770,   140}+    ,{   130,   130,  -160, -1080,  -160}+    ,{   220,   220,   -70,  -980,   -70}+    ,{   130,   130,  -160, -1080,  -160}+    }+   ,{{   580,   580,   290,  -390,   290}+    ,{   580,   580,   290,  -620,   290}+    ,{   580,   580,   280,  -390,   280}+    ,{   580,   580,   290,  -620,   290}+    ,{   530,   530,   230,  -440,   230}+    }+   ,{{   780,   780,   490, -1080,   490}+    ,{   -60,   -60,  -350, -1270,  -350}+    ,{   130,   130,  -160, -1080,  -160}+    ,{   780,   780,   490, -1680,   490}+    ,{   130,   130,  -160, -1080,  -160}+    }+   ,{{   640,   640,   340,  -330,   340}+    ,{   580,   580,   290,  -620,   290}+    ,{   640,   640,   340,  -330,   340}+    ,{   580,   580,   290,  -620,   290}+    ,{    40,    40,  -500, -1410,  -500}+    }+   }+  ,{{{   480,   470,   480,   470,   480}+    ,{   280,   270,   280,   270,   280}+    ,{   340,   330,   340,   330,   340}+    ,{   480,   470,   480,   470,   480}+    ,{   230,   220,   230,   220,   230}+    }+   ,{{   170,   130,   170,   130,   170}+    ,{   140,   130,   140,   130,   140}+    ,{  -170,  -180,  -170,  -180,  -170}+    ,{   170,   -80,   170,   -80,   170}+    ,{  -170,  -180,  -170,  -180,  -170}+    }+   ,{{   280,   270,   280,   270,   280}+    ,{   280,   270,   280,   270,   280}+    ,{   280,   270,   280,   270,   280}+    ,{   280,   270,   280,   270,   280}+    ,{   230,   220,   230,   220,   230}+    }+   ,{{   480,   470,   480,   470,   480}+    ,{  -120,  -370,  -120,  -370,  -120}+    ,{  -170,  -180,  -170,  -180,  -170}+    ,{   480,   470,   480,   470,   480}+    ,{  -170,  -180,  -170,  -180,  -170}+    }+   ,{{   340,   330,   340,   330,   340}+    ,{   280,   270,   280,   270,   280}+    ,{   340,   330,   340,   330,   340}+    ,{   280,   270,   280,   270,   280}+    ,{  -500,  -510,  -500,  -510,  -500}+    }+   }+  ,{{{  1170,  -510,   490,  1170,   490}+    ,{  1120,  -800,   290,  1120,   290}+    ,{  1170,  -510,   340,  1170,   340}+    ,{  1120,  -800,   490,  1120,   490}+    ,{  1060,  -620,   230,  1060,   230}+    }+   ,{{   970,  -950,   140,   970,   140}+    ,{   970,  -950,   140,   970,   140}+    ,{   660, -1260,  -160,   660,  -160}+    ,{   -70, -1160,   -70,  -490,   -70}+    ,{   660, -1260,  -160,   660,  -160}+    }+   ,{{  1120,  -570,   290,  1120,   290}+    ,{  1120,  -800,   290,  1120,   290}+    ,{  1110,  -570,   280,  1110,   280}+    ,{  1120,  -800,   290,  1120,   290}+    ,{  1060,  -620,   230,  1060,   230}+    }+   ,{{   660, -1260,   490,   660,   490}+    ,{  -350, -1450,  -350,  -780,  -350}+    ,{   660, -1260,  -160,   660,  -160}+    ,{   490, -1860,   490, -1190,   490}+    ,{   660, -1260,  -160,   660,  -160}+    }+   ,{{  1170,  -510,   340,  1170,   340}+    ,{  1120,  -800,   290,  1120,   290}+    ,{  1170,  -510,   340,  1170,   340}+    ,{  1120,  -800,   290,  1120,   290}+    ,{  -500, -1590,  -500,  -920,  -500}+    }+   }+  ,{{{   480,   470,   480,   470,  -600}+    ,{   280,   270,   280,   270,  -600}+    ,{   340,   330,   340,   330,  -640}+    ,{   480,   470,   480,   470,  -690}+    ,{   230,   220,   230,   220,  -750}+    }+   ,{{   170,   130,   170,   130,  -600}+    ,{   140,   130,   140,   130,  -600}+    ,{  -170,  -180,  -170,  -180, -1150}+    ,{   170,   -80,   170,   -80, -1050}+    ,{  -170,  -180,  -170,  -180, -1150}+    }+   ,{{   280,   270,   280,   270,  -690}+    ,{   280,   270,   280,   270,  -690}+    ,{   280,   270,   280,   270,  -700}+    ,{   280,   270,   280,   270,  -690}+    ,{   230,   220,   230,   220,  -750}+    }+   ,{{   480,   470,   480,   470, -1150}+    ,{  -120,  -370,  -120,  -370, -1340}+    ,{  -170,  -180,  -170,  -180, -1150}+    ,{   480,   470,   480,   470, -1750}+    ,{  -170,  -180,  -170,  -180, -1150}+    }+   ,{{   340,   330,   340,   330,  -640}+    ,{   280,   270,   280,   270,  -690}+    ,{   340,   330,   340,   330,  -640}+    ,{   280,   270,   280,   270,  -690}+    ,{  -500,  -510,  -500,  -510, -1480}+    }+   }+  }+ ,{{{{  1140,   780,   490,  1140,   490}+    ,{  1140,   600,   310,  1140,   310}+    ,{   690,   150,  -140,   690,  -140}+    ,{   780,   780,   490,   770,   490}+    ,{   690,   190,  -140,   690,  -140}+    }+   ,{{  1140,   600,   310,  1140,   310}+    ,{  1140,   600,   310,  1140,   310}+    ,{   690,   150,  -140,   690,  -140}+    ,{  -580,  -580,  -640,  -890,  -640}+    ,{   690,   150,  -140,   690,  -140}+    }+   ,{{   770,   240,   -50,   770,   -50}+    ,{   770,   240,   -50,   770,   -50}+    ,{   470,   -60,  -360,   470,  -360}+    ,{   770,   240,   -50,   770,   -50}+    ,{   470,   -60,  -360,   470,  -360}+    }+   ,{{   780,   780,   490,   690,   490}+    ,{  -110,  -110,  -170,  -420,  -170}+    ,{   690,   150,  -140,   690,  -140}+    ,{   780,   780,   490,   470,   490}+    ,{   690,   150,  -140,   690,  -140}+    }+   ,{{   770,   240,   -50,   770,   -50}+    ,{   770,   240,   -50,   770,   -50}+    ,{   160,  -370,  -670,   160,  -670}+    ,{   770,   240,   -50,   770,   -50}+    ,{   190,   190,  -340,  -360,  -340}+    }+   }+  ,{{{   780,   780,   490,  -600,   490}+    ,{   600,   600,   310,  -600,   310}+    ,{   150,   150,  -140, -1030,  -140}+    ,{   780,   780,   490,  -970,   490}+    ,{   190,   190,  -140, -1030,  -140}+    }+   ,{{   600,   600,   310,  -600,   310}+    ,{   600,   600,   310,  -600,   310}+    ,{   150,   150,  -140, -1050,  -140}+    ,{  -580,  -580,  -880, -1790,  -880}+    ,{   150,   150,  -140, -1050,  -140}+    }+   ,{{   240,   240,   -50,  -970,   -50}+    ,{   240,   240,   -50,  -970,   -50}+    ,{   -60,   -60,  -360, -1030,  -360}+    ,{   240,   240,   -50,  -970,   -50}+    ,{   -60,   -60,  -360, -1030,  -360}+    }+   ,{{   780,   780,   490, -1050,   490}+    ,{  -110,  -110,  -400, -1320,  -400}+    ,{   150,   150,  -140, -1050,  -140}+    ,{   780,   780,   490, -1680,   490}+    ,{   150,   150,  -140, -1050,  -140}+    }+   ,{{   240,   240,   -50,  -970,   -50}+    ,{   240,   240,   -50,  -970,   -50}+    ,{  -370,  -370,  -670, -1340,  -670}+    ,{   240,   240,   -50,  -970,   -50}+    ,{   190,   190,  -340, -1260,  -340}+    }+   }+  ,{{{   480,   470,   480,   470,   480}+    ,{   300,   290,   300,   290,   300}+    ,{  -140,  -150,  -140,  -150,  -140}+    ,{   480,   470,   480,   470,   480}+    ,{  -140,  -150,  -140,  -150,  -140}+    }+   ,{{   300,   290,   300,   290,   300}+    ,{   300,   290,   300,   290,   300}+    ,{  -140,  -150,  -140,  -150,  -140}+    ,{  -640,  -890,  -640,  -890,  -640}+    ,{  -140,  -150,  -140,  -150,  -140}+    }+   ,{{   -60,   -70,   -60,   -70,   -60}+    ,{   -60,   -70,   -60,   -70,   -60}+    ,{  -360,  -370,  -360,  -370,  -360}+    ,{   -60,   -70,   -60,   -70,   -60}+    ,{  -360,  -370,  -360,  -370,  -360}+    }+   ,{{   480,   470,   480,   470,   480}+    ,{  -170,  -420,  -170,  -420,  -170}+    ,{  -140,  -150,  -140,  -150,  -140}+    ,{   480,   470,   480,   470,   480}+    ,{  -140,  -150,  -140,  -150,  -140}+    }+   ,{{   -60,   -70,   -60,   -70,   -60}+    ,{   -60,   -70,   -60,   -70,   -60}+    ,{  -670,  -680,  -670,  -680,  -670}+    ,{   -60,   -70,   -60,   -70,   -60}+    ,{  -350,  -360,  -350,  -360,  -350}+    }+   }+  ,{{{  1140,  -780,   490,  1140,   490}+    ,{  1140,  -780,   310,  1140,   310}+    ,{   690, -1210,  -140,   690,  -140}+    ,{   770, -1150,   490,   770,   490}+    ,{   690, -1210,  -140,   690,  -140}+    }+   ,{{  1140,  -780,   310,  1140,   310}+    ,{  1140,  -780,   310,  1140,   310}+    ,{   690, -1230,  -140,   690,  -140}+    ,{  -880, -1970,  -880, -1300,  -880}+    ,{   690, -1230,  -140,   690,  -140}+    }+   ,{{   770, -1150,   -50,   770,   -50}+    ,{   770, -1150,   -50,   770,   -50}+    ,{   470, -1210,  -360,   470,  -360}+    ,{   770, -1150,   -50,   770,   -50}+    ,{   470, -1210,  -360,   470,  -360}+    }+   ,{{   690, -1230,   490,   690,   490}+    ,{  -400, -1500,  -400,  -830,  -400}+    ,{   690, -1230,  -140,   690,  -140}+    ,{   490, -1860,   490, -1190,   490}+    ,{   690, -1230,  -140,   690,  -140}+    }+   ,{{   770, -1150,   -50,   770,   -50}+    ,{   770, -1150,   -50,   770,   -50}+    ,{   160, -1520,  -670,   160,  -670}+    ,{   770, -1150,   -50,   770,   -50}+    ,{  -340, -1440,  -340,  -770,  -340}+    }+   }+  ,{{{   480,   470,   480,   470,  -430}+    ,{   300,   290,   300,   290,  -430}+    ,{  -140,  -150,  -140,  -150, -1120}+    ,{   480,   470,   480,   470, -1040}+    ,{  -140,  -150,  -140,  -150, -1120}+    }+   ,{{   300,   290,   300,   290,  -430}+    ,{   300,   290,   300,   290,  -430}+    ,{  -140,  -150,  -140,  -150, -1120}+    ,{  -640,  -890,  -640,  -890, -1860}+    ,{  -140,  -150,  -140,  -150, -1120}+    }+   ,{{   -60,   -70,   -60,   -70, -1040}+    ,{   -60,   -70,   -60,   -70, -1040}+    ,{  -360,  -370,  -360,  -370, -1340}+    ,{   -60,   -70,   -60,   -70, -1040}+    ,{  -360,  -370,  -360,  -370, -1340}+    }+   ,{{   480,   470,   480,   470, -1120}+    ,{  -170,  -420,  -170,  -420, -1390}+    ,{  -140,  -150,  -140,  -150, -1120}+    ,{   480,   470,   480,   470, -1750}+    ,{  -140,  -150,  -140,  -150, -1120}+    }+   ,{{   -60,   -70,   -60,   -70, -1040}+    ,{   -60,   -70,   -60,   -70, -1040}+    ,{  -670,  -680,  -670,  -680, -1650}+    ,{   -60,   -70,   -60,   -70, -1040}+    ,{  -350,  -360,  -350,  -360, -1330}+    }+   }+  }+ ,{{{{   940,   940,   650,   630,   650}+    ,{   220,  -130,  -190,   220,  -190}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   940,   940,   650,   630,   650}+    ,{   220,   -70,  -600,   220,  -600}+    }+   ,{{   220,  -310,  -380,   220,  -380}+    ,{    40,  -490,  -780,    40,  -780}+    ,{   220,  -310,  -600,   220,  -600}+    ,{  -320,  -320,  -380,  -630,  -380}+    ,{   220,  -310,  -600,   220,  -600}+    }+   ,{{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    }+   ,{{   940,   940,   650,   630,   650}+    ,{  -130,  -130,  -190,  -440,  -190}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   940,   940,   650,   630,   650}+    ,{   220,  -310,  -600,   220,  -600}+    }+   ,{{   220,   -70,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   220,  -310,  -600,   220,  -600}+    ,{   -70,   -70,  -600,  -620,  -600}+    }+   }+  ,{{{   940,   940,   650, -1280,   650}+    ,{  -130,  -130,  -430, -1340,  -430}+    ,{  -310,  -310,  -600, -1280,  -600}+    ,{   940,   940,   650, -1520,   650}+    ,{   -70,   -70,  -600, -1280,  -600}+    }+   ,{{  -310,  -310,  -600, -1520,  -600}+    ,{  -490,  -490,  -780, -1700,  -780}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{  -320,  -320,  -620, -1530,  -620}+    ,{  -310,  -310,  -600, -1520,  -600}+    }+   ,{{  -310,  -310,  -600, -1280,  -600}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{  -310,  -310,  -600, -1280,  -600}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{  -310,  -310,  -600, -1280,  -600}+    }+   ,{{   940,   940,   650, -1340,   650}+    ,{  -130,  -130,  -430, -1340,  -430}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{   940,   940,   650, -1520,   650}+    ,{  -310,  -310,  -600, -1520,  -600}+    }+   ,{{   -70,   -70,  -600, -1280,  -600}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{  -310,  -310,  -600, -1280,  -600}+    ,{  -310,  -310,  -600, -1520,  -600}+    ,{   -70,   -70,  -600, -1520,  -600}+    }+   }+  ,{{{   640,   630,   640,   630,   640}+    ,{  -190,  -440,  -190,  -440,  -190}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{   640,   630,   640,   630,   640}+    ,{  -610,  -620,  -610,  -620,  -610}+    }+   ,{{  -380,  -620,  -380,  -620,  -380}+    ,{  -790,  -800,  -790,  -800,  -790}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -380,  -630,  -380,  -630,  -380}+    ,{  -610,  -620,  -610,  -620,  -610}+    }+   ,{{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    }+   ,{{   640,   630,   640,   630,   640}+    ,{  -190,  -440,  -190,  -440,  -190}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{   640,   630,   640,   630,   640}+    ,{  -610,  -620,  -610,  -620,  -610}+    }+   ,{{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    ,{  -610,  -620,  -610,  -620,  -610}+    }+   }+  ,{{{   650, -1460,   650,   220,   650}+    ,{   220, -1520,  -430,   220,  -430}+    ,{   220, -1460,  -600,   220,  -600}+    ,{   650, -1700,   650,   220,   650}+    ,{   220, -1460,  -600,   220,  -600}+    }+   ,{{   220, -1700,  -600,   220,  -600}+    ,{    40, -1880,  -780,    40,  -780}+    ,{   220, -1700,  -600,   220,  -600}+    ,{  -620, -1710,  -620, -1040,  -620}+    ,{   220, -1700,  -600,   220,  -600}+    }+   ,{{   220, -1460,  -600,   220,  -600}+    ,{   220, -1700,  -600,   220,  -600}+    ,{   220, -1460,  -600,   220,  -600}+    ,{   220, -1700,  -600,   220,  -600}+    ,{   220, -1460,  -600,   220,  -600}+    }+   ,{{   650, -1520,   650,   220,   650}+    ,{  -430, -1520,  -430,  -850,  -430}+    ,{   220, -1700,  -600,   220,  -600}+    ,{   650, -1700,   650, -1030,   650}+    ,{   220, -1700,  -600,   220,  -600}+    }+   ,{{   220, -1460,  -600,   220,  -600}+    ,{   220, -1700,  -600,   220,  -600}+    ,{   220, -1460,  -600,   220,  -600}+    ,{   220, -1700,  -600,   220,  -600}+    ,{  -600, -1700,  -600, -1030,  -600}+    }+   }+  ,{{{   640,   630,   640,   630, -1410}+    ,{  -190,  -440,  -190,  -440, -1410}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{   640,   630,   640,   630, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    }+   ,{{  -380,  -620,  -380,  -620, -1530}+    ,{  -790,  -800,  -790,  -800, -1530}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -380,  -630,  -380,  -630, -1600}+    ,{  -610,  -620,  -610,  -620, -1590}+    }+   ,{{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    }+   ,{{   640,   630,   640,   630, -1410}+    ,{  -190,  -440,  -190,  -440, -1410}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{   640,   630,   640,   630, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    }+   ,{{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    ,{  -610,  -620,  -610,  -620, -1590}+    }+   }+  }+ ,{{{{  1490,  1490,  1200,  1280,  1200}+    ,{  1280,   750,   460,  1280,   460}+    ,{   780,   240,   -50,   780,   -50}+    ,{  1490,  1490,  1200,  1190,  1200}+    ,{   780,   480,   -50,   780,   -50}+    }+   ,{{  1280,   750,   460,  1280,   460}+    ,{  1280,   750,   460,  1280,   460}+    ,{   780,   240,   -50,   780,   -50}+    ,{   -90,   -90,  -150,  -400,  -150}+    ,{   780,   240,   -50,   780,   -50}+    }+   ,{{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    }+   ,{{  1490,  1490,  1200,  1190,  1200}+    ,{  -260,  -260,  -320,  -570,  -320}+    ,{   780,   240,   -50,   780,   -50}+    ,{  1490,  1490,  1200,  1190,  1200}+    ,{   780,   240,   -50,   780,   -50}+    }+   ,{{   780,   480,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   780,   240,   -50,   780,   -50}+    ,{   480,   480,   -50,   -60,   -50}+    }+   }+  ,{{{  1490,  1490,  1200,  -450,  1200}+    ,{   750,   750,   460,  -450,   460}+    ,{   240,   240,   -50,  -720,   -50}+    ,{  1490,  1490,  1200,  -960,  1200}+    ,{   480,   480,   -50,  -720,   -50}+    }+   ,{{   750,   750,   460,  -450,   460}+    ,{   750,   750,   460,  -450,   460}+    ,{   240,   240,   -50,  -960,   -50}+    ,{   -90,   -90,  -390, -1300,  -390}+    ,{   240,   240,   -50,  -960,   -50}+    }+   ,{{   240,   240,   -50,  -720,   -50}+    ,{   240,   240,   -50,  -960,   -50}+    ,{   240,   240,   -50,  -720,   -50}+    ,{   240,   240,   -50,  -960,   -50}+    ,{   240,   240,   -50,  -720,   -50}+    }+   ,{{  1490,  1490,  1200,  -960,  1200}+    ,{  -260,  -260,  -560, -1470,  -560}+    ,{   240,   240,   -50,  -960,   -50}+    ,{  1490,  1490,  1200,  -960,  1200}+    ,{   240,   240,   -50,  -960,   -50}+    }+   ,{{   480,   480,   -50,  -720,   -50}+    ,{   240,   240,   -50,  -960,   -50}+    ,{   240,   240,   -50,  -720,   -50}+    ,{   240,   240,   -50,  -960,   -50}+    ,{   480,   480,   -50,  -960,   -50}+    }+   }+  ,{{{  1200,  1190,  1200,  1190,  1200}+    ,{   450,   440,   450,   440,   450}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{  1200,  1190,  1200,  1190,  1200}+    ,{   -50,   -60,   -50,   -60,   -50}+    }+   ,{{   450,   440,   450,   440,   450}+    ,{   450,   440,   450,   440,   450}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{  -150,  -400,  -150,  -400,  -150}+    ,{   -50,   -60,   -50,   -60,   -50}+    }+   ,{{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    }+   ,{{  1200,  1190,  1200,  1190,  1200}+    ,{  -320,  -570,  -320,  -570,  -320}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{  1200,  1190,  1200,  1190,  1200}+    ,{   -50,   -60,   -50,   -60,   -50}+    }+   ,{{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    ,{   -50,   -60,   -50,   -60,   -50}+    }+   }+  ,{{{  1280,  -630,  1200,  1280,  1200}+    ,{  1280,  -630,   460,  1280,   460}+    ,{   780,  -900,   -50,   780,   -50}+    ,{  1200, -1140,  1200,   780,  1200}+    ,{   780,  -900,   -50,   780,   -50}+    }+   ,{{  1280,  -630,   460,  1280,   460}+    ,{  1280,  -630,   460,  1280,   460}+    ,{   780, -1140,   -50,   780,   -50}+    ,{  -390, -1480,  -390,  -810,  -390}+    ,{   780, -1140,   -50,   780,   -50}+    }+   ,{{   780,  -900,   -50,   780,   -50}+    ,{   780, -1140,   -50,   780,   -50}+    ,{   780,  -900,   -50,   780,   -50}+    ,{   780, -1140,   -50,   780,   -50}+    ,{   780,  -900,   -50,   780,   -50}+    }+   ,{{  1200, -1140,  1200,   780,  1200}+    ,{  -560, -1650,  -560,  -980,  -560}+    ,{   780, -1140,   -50,   780,   -50}+    ,{  1200, -1140,  1200,  -470,  1200}+    ,{   780, -1140,   -50,   780,   -50}+    }+   ,{{   780,  -900,   -50,   780,   -50}+    ,{   780, -1140,   -50,   780,   -50}+    ,{   780,  -900,   -50,   780,   -50}+    ,{   780, -1140,   -50,   780,   -50}+    ,{   -50, -1140,   -50,  -470,   -50}+    }+   }+  ,{{{  1200,  1190,  1200,  1190,  -280}+    ,{   450,   440,   450,   440,  -280}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{  1200,  1190,  1200,  1190, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    }+   ,{{   450,   440,   450,   440,  -280}+    ,{   450,   440,   450,   440,  -280}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{  -150,  -400,  -150,  -400, -1370}+    ,{   -50,   -60,   -50,   -60, -1030}+    }+   ,{{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    }+   ,{{  1200,  1190,  1200,  1190, -1030}+    ,{  -320,  -570,  -320,  -570, -1540}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{  1200,  1190,  1200,  1190, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    }+   ,{{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    ,{   -50,   -60,   -50,   -60, -1030}+    }+   }+  }+ ,{{{{  1870,  1870,  1570,  1870,  1570}+    ,{  1870,  1340,  1040,  1870,  1040}+    ,{  1570,  1040,   740,  1570,   740}+    ,{  1870,  1870,  1570,  1570,  1570}+    ,{  1570,  1040,   740,  1570,   740}+    }+   ,{{  1870,  1340,  1040,  1870,  1040}+    ,{  1870,  1340,  1040,  1870,  1040}+    ,{  1560,  1030,   730,  1560,   730}+    ,{   -50,   -50,  -110,  -360,  -110}+    ,{  1560,  1030,   730,  1560,   730}+    }+   ,{{  1570,  1040,   750,  1570,   750}+    ,{  1570,  1040,   750,  1570,   750}+    ,{  1570,  1040,   740,  1570,   740}+    ,{  1570,  1040,   750,  1570,   750}+    ,{  1570,  1040,   740,  1570,   740}+    }+   ,{{  1870,  1870,  1570,  1560,  1570}+    ,{   130,   130,    70,  -180,    70}+    ,{  1560,  1030,   730,  1560,   730}+    ,{  1870,  1870,  1570,  1560,  1570}+    ,{  1560,  1030,   730,  1560,   730}+    }+   ,{{  1570,  1040,   750,  1570,   750}+    ,{  1570,  1040,   750,  1570,   750}+    ,{  1570,  1040,   740,  1570,   740}+    ,{  1570,  1040,   750,  1570,   750}+    ,{   300,   300,  -230,  -250,  -230}+    }+   }+  ,{{{  1870,  1870,  1570,   130,  1570}+    ,{  1340,  1340,  1040,   130,  1040}+    ,{  1040,  1040,   740,    70,   740}+    ,{  1870,  1870,  1570,  -160,  1570}+    ,{  1040,  1040,   740,    70,   740}+    }+   ,{{  1340,  1340,  1040,   130,  1040}+    ,{  1340,  1340,  1040,   130,  1040}+    ,{  1030,  1030,   730,  -180,   730}+    ,{   -50,   -50,  -340, -1260,  -340}+    ,{  1030,  1030,   730,  -180,   730}+    }+   ,{{  1040,  1040,   750,    70,   750}+    ,{  1040,  1040,   750,  -160,   750}+    ,{  1040,  1040,   740,    70,   740}+    ,{  1040,  1040,   750,  -160,   750}+    ,{  1040,  1040,   740,    70,   740}+    }+   ,{{  1870,  1870,  1570,  -180,  1570}+    ,{   130,   130,  -160, -1080,  -160}+    ,{  1030,  1030,   730,  -180,   730}+    ,{  1870,  1870,  1570,  -590,  1570}+    ,{  1030,  1030,   730,  -180,   730}+    }+   ,{{  1040,  1040,   750,    70,   750}+    ,{  1040,  1040,   750,  -160,   750}+    ,{  1040,  1040,   740,    70,   740}+    ,{  1040,  1040,   750,  -160,   750}+    ,{   300,   300,  -230, -1150,  -230}+    }+   }+  ,{{{  1570,  1560,  1570,  1560,  1570}+    ,{  1040,  1030,  1040,  1030,  1040}+    ,{   740,   730,   740,   730,   740}+    ,{  1570,  1560,  1570,  1560,  1570}+    ,{   740,   730,   740,   730,   740}+    }+   ,{{  1040,  1030,  1040,  1030,  1040}+    ,{  1040,  1030,  1040,  1030,  1040}+    ,{   730,   720,   730,   720,   730}+    ,{  -110,  -360,  -110,  -360,  -110}+    ,{   730,   720,   730,   720,   730}+    }+   ,{{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    }+   ,{{  1570,  1560,  1570,  1560,  1570}+    ,{    70,  -180,    70,  -180,    70}+    ,{   730,   720,   730,   720,   730}+    ,{  1570,  1560,  1570,  1560,  1570}+    ,{   730,   720,   730,   720,   730}+    }+   ,{{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{   740,   730,   740,   730,   740}+    ,{  -240,  -250,  -240,  -250,  -240}+    }+   }+  ,{{{  1870,   -50,  1570,  1870,  1570}+    ,{  1870,   -50,  1040,  1870,  1040}+    ,{  1570,  -110,   740,  1570,   740}+    ,{  1570,  -340,  1570,  1570,  1570}+    ,{  1570,  -110,   740,  1570,   740}+    }+   ,{{  1870,   -50,  1040,  1870,  1040}+    ,{  1870,   -50,  1040,  1870,  1040}+    ,{  1560,  -360,   730,  1560,   730}+    ,{  -340, -1440,  -340,  -770,  -340}+    ,{  1560,  -360,   730,  1560,   730}+    }+   ,{{  1570,  -110,   750,  1570,   750}+    ,{  1570,  -340,   750,  1570,   750}+    ,{  1570,  -110,   740,  1570,   740}+    ,{  1570,  -340,   750,  1570,   750}+    ,{  1570,  -110,   740,  1570,   740}+    }+   ,{{  1570,  -360,  1570,  1560,  1570}+    ,{  -160, -1260,  -160,  -590,  -160}+    ,{  1560,  -360,   730,  1560,   730}+    ,{  1570,  -770,  1570,  -100,  1570}+    ,{  1560,  -360,   730,  1560,   730}+    }+   ,{{  1570,  -110,   750,  1570,   750}+    ,{  1570,  -340,   750,  1570,   750}+    ,{  1570,  -110,   740,  1570,   740}+    ,{  1570,  -340,   750,  1570,   750}+    ,{  -230, -1330,  -230,  -660,  -230}+    }+   }+  ,{{{  1570,  1560,  1570,  1560,   300}+    ,{  1040,  1030,  1040,  1030,   300}+    ,{   740,   730,   740,   730,  -240}+    ,{  1570,  1560,  1570,  1560,  -230}+    ,{   740,   730,   740,   730,  -240}+    }+   ,{{  1040,  1030,  1040,  1030,   300}+    ,{  1040,  1030,  1040,  1030,   300}+    ,{   730,   720,   730,   720,  -250}+    ,{  -110,  -360,  -110,  -360, -1330}+    ,{   730,   720,   730,   720,  -250}+    }+   ,{{   740,   730,   740,   730,  -230}+    ,{   740,   730,   740,   730,  -230}+    ,{   740,   730,   740,   730,  -240}+    ,{   740,   730,   740,   730,  -230}+    ,{   740,   730,   740,   730,  -240}+    }+   ,{{  1570,  1560,  1570,  1560,  -250}+    ,{    70,  -180,    70,  -180, -1150}+    ,{   730,   720,   730,   720,  -250}+    ,{  1570,  1560,  1570,  1560,  -660}+    ,{   730,   720,   730,   720,  -250}+    }+   ,{{   740,   730,   740,   730,  -230}+    ,{   740,   730,   740,   730,  -230}+    ,{   740,   730,   740,   730,  -240}+    ,{   740,   730,   740,   730,  -230}+    ,{  -240,  -250,  -240,  -250, -1220}+    }+   }+  }+ ,{{{{  2050,  2050,  1760,  1930,  1760}+    ,{  1930,  1400,  1110,  1930,  1110}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  2050,  2050,  1760,  1800,  1760}+    ,{  1670,  1140,   850,  1670,   850}+    }+   ,{{  1930,  1400,  1110,  1930,  1110}+    ,{  1930,  1400,  1110,  1930,  1110}+    ,{  1650,  1120,   830,  1650,   830}+    ,{     0,     0,   -60,  -310,   -60}+    ,{  1650,  1120,   830,  1650,   830}+    }+   ,{{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1670,  1140,   850,  1670,   850}+    }+   ,{{  2050,  2050,  1760,  1740,  1760}+    ,{  -300,  -300,  -360,  -610,  -360}+    ,{  1650,  1120,   830,  1650,   830}+    ,{  2050,  2050,  1760,  1740,  1760}+    ,{  1650,  1120,   830,  1650,   830}+    }+   ,{{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1360,   830,   540,  1360,   540}+    ,{  1800,  1270,   980,  1800,   980}+    ,{   570,   570,    40,    20,    40}+    }+   }+  ,{{{  2050,  2050,  1760,   300,  1760}+    ,{  1400,  1400,  1110,   190,  1110}+   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,{{{  1750,  1740,  1750,  1740,  1750}+    ,{  1100,  1090,  1100,  1090,  1100}+    ,{   970,   960,   970,   960,   970}+    ,{  1750,  1740,  1750,  1740,  1750}+    ,{   840,   830,   840,   830,   840}+    }+   ,{{  1100,  1090,  1100,  1090,  1100}+    ,{  1100,  1090,  1100,  1090,  1100}+    ,{   820,   810,   820,   810,   820}+    ,{   -60,  -310,   -60,  -310,   -60}+    ,{   820,   810,   820,   810,   820}+    }+   ,{{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   840,   830,   840,   830,   840}+    }+   ,{{  1750,  1740,  1750,  1740,  1750}+    ,{  -360,  -610,  -360,  -610,  -360}+    ,{   820,   810,   820,   810,   820}+    ,{  1750,  1740,  1750,  1740,  1750}+    ,{   820,   810,   820,   810,   820}+    }+   ,{{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   530,   520,   530,   520,   530}+    ,{   970,   960,   970,   960,   970}+    ,{    30,    20,    30,    20,    30}+    }+   }+  ,{{{  1930,   130,  1760,  1930,  1760}+    ,{  1930,    10,  1110,  1930,  1110}+    ,{  1800,   130,   980,  1800,   980}+    ,{  1800,  -110,  1760,  1800,  1760}+    ,{  1670,     0,   850,  1670,   850}+    }+   ,{{  1930,    10,  1110,  1930,  1110}+    ,{  1930,    10,  1110,  1930,  1110}+    ,{  1650,  -260,   830,  1650,   830}+    ,{  -290, -1390,  -290,  -720,  -290}+    ,{  1650,  -260,   830,  1650,   830}+    }+   ,{{  1800,   130,   980,  1800,   980}+    ,{  1800,  -110,   980,  1800,   980}+    ,{  1800,   130,   980,  1800,   980}+    ,{  1800,  -110,   980,  1800,   980}+    ,{  1670,     0,   850,  1670,   850}+    }+   ,{{  1760,  -260,  1760,  1650,  1760}+    ,{  -590, -1690,  -590, -1020,  -590}+    ,{  1650,  -260,   830,  1650,   830}+    ,{  1760,  -580,  1760,    80,  1760}+    ,{  1650,  -260,   830,  1650,   830}+    }+   ,{{  1800,  -110,   980,  1800,   980}+    ,{  1800,  -110,   980,  1800,   980}+    ,{  1360,  -310,   540,  1360,   540}+    ,{  1800,  -110,   980,  1800,   980}+    ,{    40, -1050,    40,  -380,    40}+    }+   }+  ,{{{  1750,  1740,  1750,  1740,   360}+    ,{  1100,  1090,  1100,  1090,   360}+    ,{   970,   960,   970,   960,     0}+    ,{  1750,  1740,  1750,  1740,     0}+    ,{   840,   830,   840,   830,  -130}+    }+   ,{{  1100,  1090,  1100,  1090,   360}+    ,{  1100,  1090,  1100,  1090,   360}+    ,{   820,   810,   820,   810,  -150}+    ,{   -60,  -310,   -60,  -310, -1280}+    ,{   820,   810,   820,   810,  -150}+    }+   ,{{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   840,   830,   840,   830,  -130}+    }+   ,{{  1750,  1740,  1750,  1740,  -150}+    ,{  -360,  -610,  -360,  -610, -1580}+    ,{   820,   810,   820,   810,  -150}+    ,{  1750,  1740,  1750,  1740,  -470}+    ,{   820,   810,   820,   810,  -150}+    }+   ,{{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   530,   520,   530,   520,  -440}+    ,{   970,   960,   970,   960,     0}+    ,{    30,    20,    30,    20,  -940}+    }+   }+  }+ ,{{{{  2050,  2050,  1760,  1930,  1760}+    ,{  1930,  1400,  1110,  1930,  1110}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  2050,  2050,  1760,  1800,  1760}+    ,{  1670,  1140,   850,  1670,   850}+    }+   ,{{  1930,  1400,  1110,  1930,  1110}+    ,{  1930,  1400,  1110,  1930,  1110}+    ,{  1650,  1120,   830,  1650,   830}+    ,{   220,   220,   170,   -80,   170}+    ,{  1650,  1120,   830,  1650,   830}+    }+   ,{{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1670,  1140,   850,  1670,   850}+    }+   ,{{  2050,  2050,  1760,  1740,  1760}+    ,{   130,   130,    70,  -180,    70}+    ,{  1650,  1120,   830,  1650,   830}+    ,{  2050,  2050,  1760,  1740,  1760}+    ,{  1650,  1120,   830,  1650,   830}+    }+   ,{{  1800,  1270,   980,  1800,   980}+    ,{  1800,  1270,   980,  1800,   980}+    ,{  1570,  1040,   740,  1570,   740}+    ,{  1800,  1270,   980,  1800,   980}+    ,{   570,   570,    40,    20,    40}+    }+   }+  ,{{{  2050,  2050,  1760,   300,  1760}+    ,{  1400,  1400,  1110,   190,  1110}+    ,{  1270,  1270,   980,   300,   980}+    ,{  2050,  2050,  1760,    60,  1760}+    ,{  1140,  1140,   850,   180,   850}+    }+   ,{{  1400,  1400,  1110,   190,  1110}+    ,{  1400,  1400,  1110,   190,  1110}+    ,{  1120,  1120,   830,   -80,   830}+    ,{   220,   220,   -70,  -980,   -70}+    ,{  1120,  1120,   830,   -80,   830}+    }+   ,{{  1270,  1270,   980,   300,   980}+    ,{  1270,  1270,   980,    60,   980}+    ,{  1270,  1270,   980,   300,   980}+    ,{  1270,  1270,   980,    60,   980}+    ,{  1140,  1140,   850,   180,   850}+    }+   ,{{  2050,  2050,  1760,   -80,  1760}+    ,{   130,   130,  -160, -1080,  -160}+    ,{  1120,  1120,   830,   -80,   830}+    ,{  2050,  2050,  1760,  -400,  1760}+    ,{  1120,  1120,   830,   -80,   830}+    }+   ,{{  1270,  1270,   980,    70,   980}+    ,{  1270,  1270,   980,    60,   980}+    ,{  1040,  1040,   740,    70,   740}+    ,{  1270,  1270,   980,    60,   980}+    ,{   570,   570,    40,  -870,    40}+    }+   }+  ,{{{  1750,  1740,  1750,  1740,  1750}+    ,{  1100,  1090,  1100,  1090,  1100}+    ,{   970,   960,   970,   960,   970}+    ,{  1750,  1740,  1750,  1740,  1750}+    ,{   840,   830,   840,   830,   840}+    }+   ,{{  1100,  1090,  1100,  1090,  1100}+    ,{  1100,  1090,  1100,  1090,  1100}+    ,{   820,   810,   820,   810,   820}+    ,{   170,   -80,   170,   -80,   170}+    ,{   820,   810,   820,   810,   820}+    }+   ,{{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   970,   960,   970,   960,   970}+    ,{   970, 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810,   820,   810,  -150}+    }+   ,{{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   840,   830,   840,   830,  -130}+    }+   ,{{  1750,  1740,  1750,  1740,  -150}+    ,{    70,  -180,    70,  -180, -1150}+    ,{   820,   810,   820,   810,  -150}+    ,{  1750,  1740,  1750,  1740,  -470}+    ,{   820,   810,   820,   810,  -150}+    }+   ,{{   970,   960,   970,   960,     0}+    ,{   970,   960,   970,   960,     0}+    ,{   740,   730,   740,   730,  -240}+    ,{   970,   960,   970,   960,     0}+    ,{    30,    20,    30,    20,  -940}+    }+   }+  }+ }+,{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   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INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   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700,   570,  1350,   570}+    ,{  1300,   650,   520,  1300,   520}+    ,{  1350,   700,   570,  1350,   570}+    ,{  1300,   650,   520,  1300,   520}+    ,{   100,   100,  -270,  -420,  -270}+    }+   }+  ,{{{   850,   850,   720,  -760,   720}+    ,{   650,   650,   520, -1050,   520}+    ,{   700,   700,   570,  -760,   570}+    ,{   850,   850,   720, -1050,   720}+    ,{   590,   590,   460,  -870,   460}+    }+   ,{{   500,   500,   370, -1200,   370}+    ,{   500,   500,   370, -1200,   370}+    ,{   190,   190,    60, -1510,    60}+    ,{   290,   290,   160, -1410,   160}+    ,{   190,   190,    60, -1510,    60}+    }+   ,{{   650,   650,   520,  -820,   520}+    ,{   650,   650,   520, -1050,   520}+    ,{   640,   640,   510,  -820,   510}+    ,{   650,   650,   520, -1050,   520}+    ,{   590,   590,   460,  -870,   460}+    }+   ,{{   850,   850,   720, -1510,   720}+    ,{     0,     0,  -120, -1700,  -120}+    ,{   190,   190,    60, -1510,    60}+    ,{   850,   850,  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  360,  -420}+    ,{   390,   370,   390,   370,  -420}+    ,{   330,   310,   330,   310,  -470}+    }+   ,{{   590,   570,   590,   570,  -870}+    ,{   -10,  -270,   -10,  -270, -1060}+    ,{   -60,   -80,   -60,   -80,  -870}+    ,{   590,   570,   590,   570, -1470}+    ,{   -60,   -80,   -60,   -80,  -870}+    }+   ,{{   440,   420,   440,   420,  -360}+    ,{   390,   370,   390,   370,  -420}+    ,{   440,   420,   440,   420,  -360}+    ,{   390,   370,   390,   370,  -420}+    ,{  -400,  -420,  -400,  -420, -1210}+    }+   }+  }+ ,{{{{  1320,   850,   720,  1320,   720}+    ,{  1320,   670,   540,  1320,   540}+    ,{   870,   220,    90,   870,    90}+    ,{   960,   850,   720,   960,   720}+    ,{   870,   250,    90,   870,    90}+    }+   ,{{  1320,   670,   540,  1320,   540}+    ,{  1320,   670,   540,  1320,   540}+    ,{   870,   220,    90,   870,    90}+    ,{  -410,  -520,  -410,  -800,  -650}+    ,{   870,   220,    90,   870,    90}+    }+   ,{{   960,   300,   170,   960,   170}+    ,{   960,   300,   170,   960,   170}+    ,{   650,     0,  -130,   650,  -130}+    ,{   960,   300,   170,   960,   170}+    ,{   650,     0,  -130,   650,  -130}+    }+   ,{{   870,   850,   720,   870,   720}+    ,{    70,   -40,    70,  -320,  -170}+    ,{   870,   220,    90,   870,    90}+    ,{   850,   850,   720,   570,   720}+    ,{   870,   220,    90,   870,    90}+    }+   ,{{   960,   300,   170,   960,   170}+    ,{   960,   300,   170,   960,   170}+    ,{   340,  -310,  -440,   340,  -440}+    ,{   960,   300,   170,   960,   170}+    ,{   250,   250,  -110,  -260,  -110}+    }+   }+  ,{{{   850,   850,   720, -1030,   720}+    ,{   670,   670,   540, -1030,   540}+    ,{   220,   220,    90, -1460,    90}+    ,{   850,   850,   720, -1400,   720}+    ,{   250,   250,    90, -1460,    90}+    }+   ,{{   670,   670,   540, -1030,   540}+    ,{   670,   670,   540, -1030,   540}+    ,{   220,   220,    90, -1480,    90}+    ,{  -520,  -520,  -650, -2220,  -650}+    ,{   220,   220,    90, -1480,    90}+    }+   ,{{   300,   300,   170, -1400,   170}+    ,{   300,   300,   170, -1400,   170}+    ,{     0,     0,  -130, -1460,  -130}+    ,{   300,   300,   170, -1400,   170}+    ,{     0,     0,  -130, -1460,  -130}+    }+   ,{{   850,   850,   720, -1480,   720}+    ,{   -40,   -40,  -170, -1750,  -170}+    ,{   220,   220,    90, -1480,    90}+    ,{   850,   850,   720, -2110,   720}+    ,{   220,   220,    90, -1480,    90}+    }+   ,{{   300,   300,   170, -1400,   170}+    ,{   300,   300,   170, -1400,   170}+    ,{  -310,  -310,  -440, -1770,  -440}+    ,{   300,   300,   170, -1400,   170}+    ,{   250,   250,  -110, -1690,  -110}+    }+   }+  ,{{{   720,   570,   720,   570,   280}+    ,{   540,   390,   540,   390,   100}+    ,{    90,   -60,    90,   -60,  -350}+    ,{   720,   570,   720,   570,   280}+    ,{    90,   -60,    90,   -60,  -350}+    }+   ,{{   540,   390,   540,   390,   100}+    ,{   540,   390,   540,   390,   100}+    ,{    90,   -60,    90,   -60,  -350}+    ,{  -410,  -800,  -410,  -800,  -850}+    ,{    90,   -60,    90,   -60,  -350}+    }+   ,{{   170,    20,   170,    20,  -260}+    ,{   170,    20,   170,    20,  -260}+    ,{  -130,  -280,  -130,  -280,  -570}+    ,{   170,    20,   170,    20,  -260}+    ,{  -130,  -280,  -130,  -280,  -570}+    }+   ,{{   720,   570,   720,   570,   280}+    ,{    70,  -320,    70,  -320,  -370}+    ,{    90,   -60,    90,   -60,  -350}+    ,{   720,   570,   720,   570,   280}+    ,{    90,   -60,    90,   -60,  -350}+    }+   ,{{   170,    20,   170,    20,  -260}+    ,{   170,    20,   170,    20,  -260}+    ,{  -440,  -590,  -440,  -590,  -880}+    ,{   170,    20,   170,    20,  -260}+    ,{  -110,  -260,  -110,  -260,  -550}+    }+   }+  ,{{{  1320,  -730,   720,  1320,   720}+    ,{  1320,  -730,   540,  1320,   540}+    ,{   870, -1160,    90,   870,    90}+    ,{   960, -1100,   720,   960,   720}+    ,{   870, -1160,    90,   870,    90}+    }+   ,{{  1320,  -730,   540,  1320,   540}+    ,{  1320,  -730,   540,  1320,   540}+    ,{   870, -1180,    90,   870,    90}+    ,{  -650, -1920,  -650, -1120,  -650}+    ,{   870, -1180,    90,   870,    90}+    }+   ,{{   960, -1100,   170,   960,   170}+    ,{   960, -1100,   170,   960,   170}+    ,{   650, -1160,  -130,   650,  -130}+    ,{   960, -1100,   170,   960,   170}+    ,{   650, -1160,  -130,   650,  -130}+    }+   ,{{   870, -1180,   720,   870,   720}+    ,{  -170, -1450,  -170,  -640,  -170}+    ,{   870, -1180,    90,   870,    90}+    ,{   720, -1810,   720, -1000,   720}+    ,{   870, -1180,    90,   870,    90}+    }+   ,{{   960, -1100,   170,   960,   170}+    ,{   960, -1100,   170,   960,   170}+    ,{   340, -1470,  -440,   340,  -440}+    ,{   960, -1100,   170,   960,   170}+    ,{  -110, -1390,  -110,  -580,  -110}+    }+   }+  ,{{{   590,   570,   590,   570,  -160}+    ,{   410,   390,   410,   390,  -160}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{   590,   570,   590,   570,  -760}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{   410,   390,   410,   390,  -160}+    ,{   410,   390,   410,   390,  -160}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{  -540,  -800,  -540,  -800, -1590}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{    40,    20,    40,    20,  -760}+    ,{    40,    20,    40,    20,  -760}+    ,{  -260,  -280,  -260,  -280, -1070}+    ,{    40,    20,    40,    20,  -760}+    ,{  -260,  -280,  -260,  -280, -1070}+    }+   ,{{   590,   570,   590,   570,  -850}+    ,{   -60,  -320,   -60,  -320, -1110}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{   590,   570,   590,   570, -1470}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{    40,    20,    40,    20,  -760}+    ,{    40,    20,    40,    20,  -760}+    ,{  -570,  -590,  -570,  -590, -1380}+    ,{    40,    20,    40,    20,  -760}+    ,{  -240,  -260,  -240,  -260, -1050}+    }+   }+  }+ ,{{{{  1010,  1010,   880,   730,   880}+    ,{   410,   -70,    40,   410,  -200}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  1010,  1010,   880,   730,   880}+    ,{   410,     0,  -370,   410,  -370}+    }+   ,{{   410,  -240,  -150,   410,  -370}+    ,{   230,  -420,  -550,   230,  -550}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  -150,  -260,  -150,  -540,  -390}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{  1010,  1010,   880,   730,   880}+    ,{    40,   -70,    40,  -350,  -200}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  1010,  1010,   880,   730,   880}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{   410,     0,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{     0,     0,  -370,  -520,  -370}+    }+   }+  ,{{{  1010,  1010,   880, -1710,   880}+    ,{   -70,   -70,  -200, -1770,  -200}+    ,{  -240,  -240,  -370, -1710,  -370}+    ,{  1010,  1010,   880, -1950,   880}+    ,{     0,     0,  -370, -1710,  -370}+    }+   ,{{  -240,  -240,  -370, -1950,  -370}+    ,{  -420,  -420,  -550, -2130,  -550}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{  -260,  -260,  -390, -1960,  -390}+    ,{  -240,  -240,  -370, -1950,  -370}+    }+   ,{{  -240,  -240,  -370, -1710,  -370}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{  -240,  -240,  -370, -1710,  -370}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{  -240,  -240,  -370, -1710,  -370}+    }+   ,{{  1010,  1010,   880, -1770,   880}+    ,{   -70,   -70,  -200, -1770,  -200}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{  1010,  1010,   880, -1950,   880}+    ,{  -240,  -240,  -370, -1950,  -370}+    }+   ,{{     0,     0,  -370, -1710,  -370}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{  -240,  -240,  -370, -1710,  -370}+    ,{  -240,  -240,  -370, -1950,  -370}+    ,{     0,     0,  -370, -1950,  -370}+    }+   }+  ,{{{   880,   730,   880,   730,   440}+    ,{    40,  -350,    40,  -350,  -400}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{   880,   730,   880,   730,   440}+    ,{  -370,  -520,  -370,  -520,  -810}+    }+   ,{{  -150,  -520,  -150,  -520,  -590}+    ,{  -550,  -700,  -550,  -700,  -990}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -150,  -540,  -150,  -540,  -590}+    ,{  -370,  -520,  -370,  -520,  -810}+    }+   ,{{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    }+   ,{{   880,   730,   880,   730,   440}+    ,{    40,  -350,    40,  -350,  -400}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{   880,   730,   880,   730,   440}+    ,{  -370,  -520,  -370,  -520,  -810}+    }+   ,{{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    ,{  -370,  -520,  -370,  -520,  -810}+    }+   }+  ,{{{   880, -1410,   880,   410,   880}+    ,{   410, -1470,  -200,   410,  -200}+    ,{   410, -1410,  -370,   410,  -370}+    ,{   880, -1650,   880,   410,   880}+    ,{   410, -1410,  -370,   410,  -370}+    }+   ,{{   410, -1650,  -370,   410,  -370}+    ,{   230, -1830,  -550,   230,  -550}+    ,{   410, -1650,  -370,   410,  -370}+    ,{  -390, -1660,  -390,  -860,  -390}+    ,{   410, -1650,  -370,   410,  -370}+    }+   ,{{   410, -1410,  -370,   410,  -370}+    ,{   410, -1650,  -370,   410,  -370}+    ,{   410, -1410,  -370,   410,  -370}+    ,{   410, -1650,  -370,   410,  -370}+    ,{   410, -1410,  -370,   410,  -370}+    }+   ,{{   880, -1470,   880,   410,   880}+    ,{  -200, -1470,  -200,  -670,  -200}+    ,{   410, -1650,  -370,   410,  -370}+    ,{   880, -1650,   880,  -840,   880}+    ,{   410, -1650,  -370,   410,  -370}+    }+   ,{{   410, -1410,  -370,   410,  -370}+    ,{   410, -1650,  -370,   410,  -370}+    ,{   410, -1410,  -370,   410,  -370}+    ,{   410, -1650,  -370,   410,  -370}+    ,{  -370, -1650,  -370,  -840,  -370}+    }+   }+  ,{{{   750,   730,   750,   730, -1140}+    ,{   -90,  -350,   -90,  -350, -1140}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{   750,   730,   750,   730, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -280,  -520,  -280,  -520, -1250}+    ,{  -680,  -700,  -680,  -700, -1250}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -280,  -540,  -280,  -540, -1330}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{   750,   730,   750,   730, -1140}+    ,{   -90,  -350,   -90,  -350, -1140}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{   750,   730,   750,   730, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   }+  }+ ,{{{{  1560,  1560,  1430,  1470,  1430}+    ,{  1470,   820,   690,  1470,   690}+    ,{   960,   310,   180,   960,   180}+    ,{  1560,  1560,  1430,  1280,  1430}+    ,{   960,   550,   180,   960,   180}+    }+   ,{{  1470,   820,   690,  1470,   690}+    ,{  1470,   820,   690,  1470,   690}+    ,{   960,   310,   180,   960,   180}+    ,{    80,   -30,    80,  -310,  -160}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{  1560,  1560,  1430,  1280,  1430}+    ,{   -90,  -200,   -90,  -480,  -330}+    ,{   960,   310,   180,   960,   180}+    ,{  1560,  1560,  1430,  1280,  1430}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{   960,   550,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   550,   550,   180,    30,   180}+    }+   }+  ,{{{  1560,  1560,  1430,  -880,  1430}+    ,{   820,   820,   690,  -880,   690}+    ,{   310,   310,   180, -1150,   180}+    ,{  1560,  1560,  1430, -1390,  1430}+    ,{   550,   550,   180, -1150,   180}+    }+   ,{{   820,   820,   690,  -880,   690}+    ,{   820,   820,   690,  -880,   690}+    ,{   310,   310,   180, -1390,   180}+    ,{   -30,   -30,  -160, -1730,  -160}+    ,{   310,   310,   180, -1390,   180}+    }+   ,{{   310,   310,   180, -1150,   180}+    ,{   310,   310,   180, -1390,   180}+    ,{   310,   310,   180, -1150,   180}+    ,{   310,   310,   180, -1390,   180}+    ,{   310,   310,   180, -1150,   180}+    }+   ,{{  1560,  1560,  1430, -1390,  1430}+    ,{  -200,  -200,  -330, -1900,  -330}+    ,{   310,   310,   180, -1390,   180}+    ,{  1560,  1560,  1430, -1390,  1430}+    ,{   310,   310,   180, -1390,   180}+    }+   ,{{   550,   550,   180, -1150,   180}+    ,{   310,   310,   180, -1390,   180}+    ,{   310,   310,   180, -1150,   180}+    ,{   310,   310,   180, -1390,   180}+    ,{   550,   550,   180, -1390,   180}+    }+   }+  ,{{{  1430,  1280,  1430,  1280,   990}+    ,{   690,   540,   690,   540,   250}+    ,{   180,    30,   180,    30,  -260}+    ,{  1430,  1280,  1430,  1280,   990}+    ,{   180,    30,   180,    30,  -260}+    }+   ,{{   690,   540,   690,   540,   250}+    ,{   690,   540,   690,   540,   250}+    ,{   180,    30,   180,    30,  -260}+    ,{    80,  -310,    80,  -310,  -360}+    ,{   180,    30,   180,    30,  -260}+    }+   ,{{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    }+   ,{{  1430,  1280,  1430,  1280,   990}+    ,{   -90,  -480,   -90,  -480,  -530}+    ,{   180,    30,   180,    30,  -260}+    ,{  1430,  1280,  1430,  1280,   990}+    ,{   180,    30,   180,    30,  -260}+    }+   ,{{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    ,{   180,    30,   180,    30,  -260}+    }+   }+  ,{{{  1470,  -580,  1430,  1470,  1430}+    ,{  1470,  -580,   690,  1470,   690}+    ,{   960,  -850,   180,   960,   180}+    ,{  1430, -1090,  1430,   960,  1430}+    ,{   960,  -850,   180,   960,   180}+    }+   ,{{  1470,  -580,   690,  1470,   690}+    ,{  1470,  -580,   690,  1470,   690}+    ,{   960, -1090,   180,   960,   180}+    ,{  -160, -1430,  -160,  -630,  -160}+    ,{   960, -1090,   180,   960,   180}+    }+   ,{{   960,  -850,   180,   960,   180}+    ,{   960, -1090,   180,   960,   180}+    ,{   960,  -850,   180,   960,   180}+    ,{   960, -1090,   180,   960,   180}+    ,{   960,  -850,   180,   960,   180}+    }+   ,{{  1430, -1090,  1430,   960,  1430}+    ,{  -330, -1600,  -330,  -800,  -330}+    ,{   960, -1090,   180,   960,   180}+    ,{  1430, -1090,  1430,  -290,  1430}+    ,{   960, -1090,   180,   960,   180}+    }+   ,{{   960,  -850,   180,   960,   180}+    ,{   960, -1090,   180,   960,   180}+    ,{   960,  -850,   180,   960,   180}+    ,{   960, -1090,   180,   960,   180}+    ,{   180, -1090,   180,  -290,   180}+    }+   }+  ,{{{  1300,  1280,  1300,  1280,   -10}+    ,{   560,   540,   560,   540,   -10}+    ,{    50,    30,    50,    30,  -760}+    ,{  1300,  1280,  1300,  1280,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{   560,   540,   560,   540,   -10}+    ,{   560,   540,   560,   540,   -10}+    ,{    50,    30,    50,    30,  -760}+    ,{   -50,  -310,   -50,  -310, -1100}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{  1300,  1280,  1300,  1280,  -760}+    ,{  -220,  -480,  -220,  -480, -1270}+    ,{    50,    30,    50,    30,  -760}+    ,{  1300,  1280,  1300,  1280,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   }+  }+ ,{{{{  2050,  1930,  1800,  2050,  1800}+    ,{  2050,  1400,  1270,  2050,  1270}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1930,  1930,  1800,  1760,  1800}+    ,{  1750,  1100,   970,  1750,   970}+    }+   ,{{  2050,  1400,  1270,  2050,  1270}+    ,{  2050,  1400,  1270,  2050,  1270}+    ,{  1740,  1090,   960,  1740,   960}+    ,{   130,    10,   130,  -260,  -110}+    ,{  1740,  1090,   960,  1740,   960}+    }+   ,{{  1760,  1110,   980,  1760,   980}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    }+   ,{{  1930,  1930,  1800,  1740,  1800}+    ,{   300,   190,   300,   -80,    60}+    ,{  1740,  1090,   960,  1740,   960}+    ,{  1930,  1930,  1800,  1650,  1800}+    ,{  1740,  1090,   960,  1740,   960}+    }+   ,{{  1760,  1110,   980,  1760,   980}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1760,  1110,   980,  1760,   980}+    ,{   360,   360,     0,  -150,     0}+    }+   }+  ,{{{  1930,  1930,  1800,  -300,  1800}+    ,{  1400,  1400,  1270,  -300,  1270}+    ,{  1100,  1100,   970,  -360,   970}+    ,{  1930,  1930,  1800,  -590,  1800}+    ,{  1100,  1100,   970,  -360,   970}+    }+   ,{{  1400,  1400,  1270,  -300,  1270}+    ,{  1400,  1400,  1270,  -300,  1270}+    ,{  1090,  1090,   960,  -610,   960}+    ,{    10,    10,  -110, -1690,  -110}+    ,{  1090,  1090,   960,  -610,   960}+    }+   ,{{  1110,  1110,   980,  -360,   980}+    ,{  1110,  1110,   980,  -590,   980}+    ,{  1100,  1100,   970,  -360,   970}+    ,{  1110,  1110,   980,  -590,   980}+    ,{  1100,  1100,   970,  -360,   970}+    }+   ,{{  1930,  1930,  1800,  -610,  1800}+    ,{   190,   190,    60, -1510,    60}+    ,{  1090,  1090,   960,  -610,   960}+    ,{  1930,  1930,  1800, -1020,  1800}+    ,{  1090,  1090,   960,  -610,   960}+    }+   ,{{  1110,  1110,   980,  -360,   980}+    ,{  1110,  1110,   980,  -590,   980}+    ,{  1100,  1100,   970,  -360,   970}+    ,{  1110,  1110,   980,  -590,   980}+    ,{   360,   360,     0, -1580,     0}+    }+   }+  ,{{{  1800,  1650,  1800,  1650,  1360}+    ,{  1270,  1120,  1270,  1120,   830}+    ,{   970,   820,   970,   820,   530}+    ,{  1800,  1650,  1800,  1650,  1360}+    ,{   970,   820,   970,   820,   530}+    }+   ,{{  1270,  1120,  1270,  1120,   830}+    ,{  1270,  1120,  1270,  1120,   830}+    ,{   960,   810,   960,   810,   520}+    ,{   130,  -260,   130,  -260,  -310}+    ,{   960,   810,   960,   810,   520}+    }+   ,{{   980,   830,   980,   830,   540}+    ,{   980,   830,   980,   830,   540}+    ,{   970,   820,   970,   820,   530}+    ,{   980,   830,   980,   830,   540}+    ,{   970,   820,   970,   820,   530}+    }+   ,{{  1800,  1650,  1800,  1650,  1360}+    ,{   300,   -80,   300,   -80,  -130}+    ,{   960,   810,   960,   810,   520}+    ,{  1800,  1650,  1800,  1650,  1360}+    ,{   960,   810,   960,   810,   520}+    }+   ,{{   980,   830,   980,   830,   540}+    ,{   980,   830,   980,   830,   540}+    ,{   970,   820,   970,   820,   530}+    ,{   980,   830,   980,   830,   540}+    ,{     0,  -150,     0,  -150,  -440}+    }+   }+  ,{{{  2050,     0,  1800,  2050,  1800}+    ,{  2050,     0,  1270,  2050,  1270}+    ,{  1750,   -60,   970,  1750,   970}+    ,{  1800,  -290,  1800,  1760,  1800}+    ,{  1750,   -60,   970,  1750,   970}+    }+   ,{{  2050,     0,  1270,  2050,  1270}+    ,{  2050,     0,  1270,  2050,  1270}+    ,{  1740,  -310,   960,  1740,   960}+    ,{  -110, -1390,  -110,  -580,  -110}+    ,{  1740,  -310,   960,  1740,   960}+    }+   ,{{  1760,   -60,   980,  1760,   980}+    ,{  1760,  -290,   980,  1760,   980}+    ,{  1750,   -60,   970,  1750,   970}+    ,{  1760,  -290,   980,  1760,   980}+    ,{  1750,   -60,   970,  1750,   970}+    }+   ,{{  1800,  -310,  1800,  1740,  1800}+    ,{    60, -1210,    60,  -400,    60}+    ,{  1740,  -310,   960,  1740,   960}+    ,{  1800,  -720,  1800,    80,  1800}+    ,{  1740,  -310,   960,  1740,   960}+    }+   ,{{  1760,   -60,   980,  1760,   980}+    ,{  1760,  -290,   980,  1760,   980}+    ,{  1750,   -60,   970,  1750,   970}+    ,{  1760,  -290,   980,  1760,   980}+    ,{     0, -1280,     0,  -470,     0}+    }+   }+  ,{{{  1670,  1650,  1670,  1650,   570}+    ,{  1140,  1120,  1140,  1120,   570}+    ,{   840,   820,   840,   820,    30}+    ,{  1670,  1650,  1670,  1650,    40}+    ,{   840,   820,   840,   820,    30}+    }+   ,{{  1140,  1120,  1140,  1120,   570}+    ,{  1140,  1120,  1140,  1120,   570}+    ,{   830,   810,   830,   810,    20}+    ,{     0,  -260,     0,  -260, -1050}+    ,{   830,   810,   830,   810,    20}+    }+   ,{{   850,   830,   850,   830,    40}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    }+   ,{{  1670,  1650,  1670,  1650,    20}+    ,{   180,   -80,   180,   -80,  -870}+    ,{   830,   810,   830,   810,    20}+    ,{  1670,  1650,  1670,  1650,  -380}+    ,{   830,   810,   830,   810,    20}+    }+   ,{{   850,   830,   850,   830,    40}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    ,{   850,   830,   850,   830,    40}+    ,{  -130,  -150,  -130,  -150,  -940}+    }+   }+  }+ ,{{{{  2120,  2120,  1990,  2120,  1990}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  2120,  2120,  1990,  1990,  1990}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  1470,  1340,  2120,  1340}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{   180,    60,   180,  -210,   -60}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  2120,  1990,  1840,  1990}+    ,{  -120,  -230,  -120,  -510,  -360}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{  2120,  2120,  1990,  1840,  1990}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1550,   900,   770,  1550,   770}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{   640,   640,   270,   120,   270}+    }+   }+  ,{{{  2120,  2120,  1990,  -120,  1990}+    ,{  1470,  1470,  1340,  -230,  1340}+    ,{  1340,  1340,  1210,  -120,  1210}+    ,{  2120,  2120,  1990,  -360,  1990}+    ,{  1210,  1210,  1080,  -250,  1080}+    }+   ,{{  1470,  1470,  1340,  -230,  1340}+    ,{  1470,  1470,  1340,  -230,  1340}+    ,{  1190,  1190,  1060,  -510,  1060}+    ,{    60,    60,   -60, -1640,   -60}+    ,{  1190,  1190,  1060,  -510,  1060}+    }+   ,{{  1340,  1340,  1210,  -120,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{  1340,  1340,  1210,  -120,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{  1210,  1210,  1080,  -250,  1080}+    }+   ,{{  2120,  2120,  1990,  -510,  1990}+    ,{  -230,  -230,  -360, -1940,  -360}+    ,{  1190,  1190,  1060,  -510,  1060}+    ,{  2120,  2120,  1990,  -830,  1990}+    ,{  1190,  1190,  1060,  -510,  1060}+    }+   ,{{  1340,  1340,  1210,  -360,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{   900,   900,   770,  -560,   770}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{   640,   640,   270, -1300,   270}+    }+   }+  ,{{{  1990,  1840,  1990,  1840,  1550}+    ,{  1340,  1190,  1340,  1190,   900}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1990,  1840,  1990,  1840,  1550}+    ,{  1080,   930,  1080,   930,   640}+    }+   ,{{  1340,  1190,  1340,  1190,   900}+    ,{  1340,  1190,  1340,  1190,   900}+    ,{  1060,   910,  1060,   910,   620}+    ,{   180,  -210,   180,  -210,  -260}+    ,{  1060,   910,  1060,   910,   620}+    }+   ,{{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1080,   930,  1080,   930,   640}+    }+   ,{{  1990,  1840,  1990,  1840,  1550}+    ,{  -120,  -510,  -120,  -510,  -560}+    ,{  1060,   910,  1060,   910,   620}+    ,{  1990,  1840,  1990,  1840,  1550}+    ,{  1060,   910,  1060,   910,   620}+    }+   ,{{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{   770,   620,   770,   620,   330}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{   270,   120,   270,   120,  -170}+    }+   }+  ,{{{  2120,   180,  1990,  2120,  1990}+    ,{  2120,    60,  1340,  2120,  1340}+    ,{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1990,  1990,  1990}+    ,{  1860,    50,  1080,  1860,  1080}+    }+   ,{{  2120,    60,  1340,  2120,  1340}+    ,{  2120,    60,  1340,  2120,  1340}+    ,{  1840,  -210,  1060,  1840,  1060}+    ,{   -60, -1340,   -60,  -530,   -60}+    ,{  1840,  -210,  1060,  1840,  1060}+    }+   ,{{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1860,    50,  1080,  1860,  1080}+    }+   ,{{  1990,  -210,  1990,  1840,  1990}+    ,{  -360, -1640,  -360,  -830,  -360}+    ,{  1840,  -210,  1060,  1840,  1060}+    ,{  1990,  -530,  1990,   270,  1990}+    ,{  1840,  -210,  1060,  1840,  1060}+    }+   ,{{  1990,   -60,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1550,  -260,   770,  1550,   770}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{   270, -1000,   270,  -200,   270}+    }+   }+  ,{{{  1860,  1840,  1860,  1840,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1860,  1840,  1860,  1840,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1210,  1190,  1210,  1190,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{   930,   910,   930,   910,   120}+    ,{    50,  -210,    50,  -210, -1000}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1860,  1840,  1860,  1840,   120}+    ,{  -250,  -510,  -250,  -510, -1300}+    ,{   930,   910,   930,   910,   120}+    ,{  1860,  1840,  1860,  1840,  -200}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   640,   620,   640,   620,  -170}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   140,   120,   140,   120,  -670}+    }+   }+  }+ ,{{{{  2120,  2120,  1990,  2120,  1990}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  2120,  2120,  1990,  1990,  1990}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  1470,  1340,  2120,  1340}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{   400,   290,   400,    10,   160}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  2120,  1990,  1840,  1990}+    ,{   300,   190,   300,   -80,    60}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{  2120,  2120,  1990,  1840,  1990}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{   640,   640,   270,   120,   270}+    }+   }+  ,{{{  2120,  2120,  1990,  -120,  1990}+    ,{  1470,  1470,  1340,  -230,  1340}+    ,{  1340,  1340,  1210,  -120,  1210}+    ,{  2120,  2120,  1990,  -360,  1990}+    ,{  1210,  1210,  1080,  -250,  1080}+    }+   ,{{  1470,  1470,  1340,  -230,  1340}+    ,{  1470,  1470,  1340,  -230,  1340}+    ,{  1190,  1190,  1060,  -510,  1060}+    ,{   290,   290,   160, -1410,   160}+    ,{  1190,  1190,  1060,  -510,  1060}+    }+   ,{{  1340,  1340,  1210,  -120,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{  1340,  1340,  1210,  -120,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{  1210,  1210,  1080,  -250,  1080}+    }+   ,{{  2120,  2120,  1990,  -510,  1990}+    ,{   190,   190,    60, -1510,    60}+    ,{  1190,  1190,  1060,  -510,  1060}+    ,{  2120,  2120,  1990,  -830,  1990}+    ,{  1190,  1190,  1060,  -510,  1060}+    }+   ,{{  1340,  1340,  1210,  -360,  1210}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{  1100,  1100,   970,  -360,   970}+    ,{  1340,  1340,  1210,  -360,  1210}+    ,{   640,   640,   270, -1300,   270}+    }+   }+  ,{{{  1990,  1840,  1990,  1840,  1550}+    ,{  1340,  1190,  1340,  1190,   900}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1990,  1840,  1990,  1840,  1550}+    ,{  1080,   930,  1080,   930,   640}+    }+   ,{{  1340,  1190,  1340,  1190,   900}+    ,{  1340,  1190,  1340,  1190,   900}+    ,{  1060,   910,  1060,   910,   620}+    ,{   400,    10,   400,    10,   -40}+    ,{  1060,   910,  1060,   910,   620}+    }+   ,{{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{  1080,   930,  1080,   930,   640}+    }+   ,{{  1990,  1840,  1990,  1840,  1550}+    ,{   300,   -80,   300,   -80,  -130}+    ,{  1060,   910,  1060,   910,   620}+    ,{  1990,  1840,  1990,  1840,  1550}+    ,{  1060,   910,  1060,   910,   620}+    }+   ,{{  1210,  1060,  1210,  1060,   770}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{   970,   820,   970,   820,   530}+    ,{  1210,  1060,  1210,  1060,   770}+    ,{   270,   120,   270,   120,  -170}+    }+   }+  ,{{{  2120,   180,  1990,  2120,  1990}+    ,{  2120,    60,  1340,  2120,  1340}+    ,{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1990,  1990,  1990}+    ,{  1860,    50,  1080,  1860,  1080}+    }+   ,{{  2120,    60,  1340,  2120,  1340}+    ,{  2120,    60,  1340,  2120,  1340}+    ,{  1840,  -210,  1060,  1840,  1060}+    ,{   160, -1110,   160,  -310,   160}+    ,{  1840,  -210,  1060,  1840,  1060}+    }+   ,{{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1990,   180,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1860,    50,  1080,  1860,  1080}+    }+   ,{{  1990,  -210,  1990,  1840,  1990}+    ,{    60, -1210,    60,  -400,    60}+    ,{  1840,  -210,  1060,  1840,  1060}+    ,{  1990,  -530,  1990,   270,  1990}+    ,{  1840,  -210,  1060,  1840,  1060}+    }+   ,{{  1990,   -60,  1210,  1990,  1210}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{  1750,   -60,   970,  1750,   970}+    ,{  1990,   -60,  1210,  1990,  1210}+    ,{   270, -1000,   270,  -200,   270}+    }+   }+  ,{{{  1860,  1840,  1860,  1840,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1860,  1840,  1860,  1840,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1210,  1190,  1210,  1190,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{   930,   910,   930,   910,   120}+    ,{   270,    10,   270,    10,  -780}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1860,  1840,  1860,  1840,   120}+    ,{   180,   -80,   180,   -80,  -870}+    ,{   930,   910,   930,   910,   120}+    ,{  1860,  1840,  1860,  1840,  -200}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   840,   820,   840,   820,    30}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   140,   120,   140,   120,  -670}+    }+   }+  }+ }+,{{{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+   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INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  ,{{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   ,{{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    ,{   INF,   INF,   INF,   INF,   INF}+    }+   }+  }+ ,{{{{  1350,   850,   720,  1350,   720}+    ,{  1300,   650,   540,  1300,   520}+    ,{  1350,   700,   570,  1350,   570}+    ,{  1300,   850,   720,  1300,   720}+    ,{  1250,   590,   460,  1250,   460}+    }+   ,{{  1160,   500,   400,  1160,   370}+    ,{  1160,   500,   370,  1160,   370}+    ,{   850,   190,    60,   850,    60}+    ,{   400,   290,   400,    10,   170}+    ,{   850,   190,    60,   850,    60}+    }+   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290,   290,   160,  -980,   160}+    ,{   190,   190,    60, -1080,    60}+    }+   ,{{   650,   650,   520,  -390,   520}+    ,{   650,   650,   520,  -620,   520}+    ,{   640,   640,   510,  -390,   510}+    ,{   650,   650,   520,  -620,   520}+    ,{   590,   590,   460,  -440,   460}+    }+   ,{{   850,   850,   720, -1080,   720}+    ,{    10,     0,    10, -1270,  -120}+    ,{   190,   190,    60, -1080,    60}+    ,{   850,   850,   720, -1080,   720}+    ,{   190,   190,    60, -1080,    60}+    }+   ,{{   700,   700,   570,  -330,   570}+    ,{   650,   650,   520,  -620,   520}+    ,{   700,   700,   570,  -330,   570}+    ,{   650,   650,   520,  -620,   520}+    ,{   100,   100,  -270, -1300,  -270}+    }+   }+  ,{{{   720,   570,   720,   570,   480}+    ,{   540,   370,   540,   370,   280}+    ,{   570,   420,   570,   420,   340}+    ,{   720,   570,   720,   570,   480}+    ,{   460,   310,   460,   310,   230}+    }+   ,{{   400,   220,   400,   220,   170}+    ,{   370,   220,   370,   220,   140}+    ,{    60,   -80,    60,   -80,  -170}+    ,{   400,    10,   400,    10,   170}+    ,{    60,   -80,    60,   -80,  -170}+    }+   ,{{   520,   370,   520,   370,   280}+    ,{   520,   370,   520,   370,   280}+    ,{   510,   360,   510,   360,   280}+    ,{   520,   370,   520,   370,   280}+    ,{   460,   310,   460,   310,   230}+    }+   ,{{   720,   570,   720,   570,   480}+    ,{   540,  -100,   540,  -270,  -120}+    ,{    60,   -80,    60,   -80,  -170}+    ,{   720,   570,   720,   570,   480}+    ,{    60,   -80,    60,   -80,  -170}+    }+   ,{{   570,   420,   570,   420,   340}+    ,{   520,   370,   520,   370,   280}+    ,{   570,   420,   570,   420,   340}+    ,{   520,   370,   520,   370,   280}+    ,{  -270,  -420,  -270,  -420,  -500}+    }+   }+  ,{{{  1350,  -230,   720,  1350,   720}+    ,{  1300,  -530,   520,  1300,   520}+    ,{  1350,  -230,   570,  1350,   570}+    ,{  1300,  -530,   720,  1300,   720}+    ,{  1250,  -340,   460,  1250,   460}+    }+   ,{{  1160,  -670,   370,  1160,   370}+    ,{  1160,  -670,   370,  1160,   370}+    ,{   850,  -980,    60,   850,    60}+    ,{   160,  -890,   160,  -310,   160}+    ,{   850,  -980,    60,   850,    60}+    }+   ,{{  1300,  -290,   520,  1300,   520}+    ,{  1300,  -530,   520,  1300,   520}+    ,{  1290,  -290,   510,  1290,   510}+    ,{  1300,  -530,   520,  1300,   520}+    ,{  1250,  -340,   460,  1250,   460}+    }+   ,{{   850,  -980,   720,   850,   720}+    ,{  -120, -1170,  -120,  -590,  -120}+    ,{   850,  -980,    60,   850,    60}+    ,{   720, -1580,   720, -1000,   720}+    ,{   850,  -980,    60,   850,    60}+    }+   ,{{  1350,  -230,   570,  1350,   570}+    ,{  1300,  -530,   520,  1300,   520}+    ,{  1350,  -230,   570,  1350,   570}+    ,{  1300,  -530,   520,  1300,   520}+    ,{  -230, -1320,  -270,  -230,  -270}+    }+   }+  ,{{{   590,   570,   590,   570,   -90}+    ,{   390,   370,   390,   370,   -90}+    ,{   440,  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1320,   850,   720,  1320,   720}+    ,{  1320,   670,   540,  1320,   540}+    ,{   870,   220,    90,   870,    90}+    ,{   960,   850,   720,   960,   720}+    ,{   870,   250,    90,   870,    90}+    }+   ,{{  1320,   670,   540,  1320,   540}+    ,{  1320,   670,   540,  1320,   540}+    ,{   870,   220,    90,   870,    90}+    ,{  -410,  -520,  -410,  -800,  -640}+    ,{   870,   220,    90,   870,    90}+    }+   ,{{   960,   300,   170,   960,   170}+    ,{   960,   300,   170,   960,   170}+    ,{   650,     0,  -130,   650,  -130}+    ,{   960,   300,   170,   960,   170}+    ,{   650,     0,  -130,   650,  -130}+    }+   ,{{   870,   850,   720,   870,   720}+    ,{    70,   -40,    70,  -320,  -170}+    ,{   870,   220,    90,   870,    90}+    ,{   850,   850,   720,   570,   720}+    ,{   870,   220,    90,   870,    90}+    }+   ,{{   960,   300,   170,   960,   170}+    ,{   960,   300,   170,   960,   170}+    ,{   340,  -310,  -440,   340,  -440}+    ,{   960,   300,   170,   960,   170}+    ,{   250,   250,   -90,  -260,  -110}+    }+   }+  ,{{{   850,   850,   720,   540,   720}+    ,{   670,   670,   540,    10,   540}+    ,{   540,   220,    90,   540,    90}+    ,{   850,   850,   720,  -970,   720}+    ,{   250,   250,    90,  -810,    90}+    }+   ,{{   670,   670,   540,  -100,   540}+    ,{   670,   670,   540,  -600,   540}+    ,{   220,   220,    90,  -100,    90}+    ,{  -520,  -520,  -650, -1790,  -650}+    ,{   220,   220,    90, -1050,    90}+    }+   ,{{   540,   300,   170,   540,   170}+    ,{   300,   300,   170,    10,   170}+    ,{   540,     0,  -130,   540,  -130}+    ,{   300,   300,   170,  -970,   170}+    ,{     0,     0,  -130, -1030,  -130}+    }+   ,{{   850,   850,   720, -1050,   720}+    ,{   -40,   -40,  -170, -1320,  -170}+    ,{   220,   220,    90, -1050,    90}+    ,{   850,   850,   720, -1680,   720}+    ,{   220,   220,    90, -1050,    90}+    }+   ,{{   300,   300,   170,  -810,   170}+    ,{   300,   300,   170,  -970,   170}+    ,{  -310,  -310,  -440, -1340,  -440}+    ,{   300,   300,   170,  -970,   170}+    ,{   250,   250,   -90,  -810,  -110}+    }+   }+  ,{{{   720,   570,   720,   570,   480}+    ,{   540,   390,   540,   390,   300}+    ,{    90,   -60,    90,   -60,  -140}+    ,{   720,   570,   720,   570,   480}+    ,{    90,   -60,    90,   -60,  -140}+    }+   ,{{   540,   390,   540,   390,   300}+    ,{   540,   390,   540,   390,   300}+    ,{    90,   -60,    90,   -60,  -140}+    ,{  -410,  -800,  -410,  -800,  -640}+    ,{    90,   -60,    90,   -60,  -140}+    }+   ,{{   170,    20,   170,    20,   -60}+    ,{   170,    20,   170,    20,   -60}+    ,{  -130,  -280,  -130,  -280,  -360}+    ,{   170,    20,   170,    20,   -60}+    ,{  -130,  -280,  -130,  -280,  -360}+    }+   ,{{   720,   570,   720,   570,   480}+    ,{    70,  -320,    70,  -320,  -170}+    ,{    90,   -60,    90,   -60,  -140}+    ,{   720,   570,   720,   570,   480}+    ,{    90,   -60,    90,   -60,  -140}+    }+   ,{{   170,    20,   170,    20,   -60}+    ,{   170,    20,   170,    20,   -60}+    ,{  -440,  -590,  -440,  -590,  -670}+    ,{   170,    20,   170,    20,   -60}+    ,{  -110,  -260,  -110,  -260,  -350}+    }+   }+  ,{{{  1320,  -350,   720,  1320,   720}+    ,{  1320,  -730,   540,  1320,   540}+    ,{   870,  -350,    90,   870,    90}+    ,{   960,  -870,   720,   960,   720}+    ,{   870,  -940,    90,   870,    90}+    }+   ,{{  1320,  -350,   540,  1320,   540}+    ,{  1320,  -730,   540,  1320,   540}+    ,{   870,  -350,    90,   870,    90}+    ,{  -650, -1920,  -650, -1120,  -650}+    ,{   870,  -960,    90,   870,    90}+    }+   ,{{   960,  -870,   170,   960,   170}+    ,{   960, -1100,   170,   960,   170}+    ,{   650,  -940,  -130,   650,  -130}+    ,{   960,  -870,   170,   960,   170}+    ,{   650,  -940,  -130,   650,  -130}+    }+   ,{{   870,  -960,   720,   870,   720}+    ,{  -170, -1450,  -170,  -640,  -170}+    ,{   870,  -960,    90,   870,    90}+    ,{   720, -1370,   720, -1000,   720}+    ,{   870,  -960,    90,   870,    90}+    }+   ,{{   960,  -870,   170,   960,   170}+    ,{   960,  -870,   170,   960,   170}+    ,{   340, -1250,  -440,   340,  -440}+    ,{   960,  -870,   170,   960,   170}+    ,{  -110, -1360,  -110,  -580,  -110}+    }+   }+  ,{{{   590,   570,   590,   570,  -160}+    ,{   410,   390,   410,   390,  -160}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{   590,   570,   590,   570,  -230}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{   410,   390,   410,   390,  -160}+    ,{   410,   390,   410,   390,  -160}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{  -540,  -800,  -540,  -800, -1520}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{    40,    20,    40,    20,  -400}+    ,{    40,    20,    40,    20,  -400}+    ,{  -260,  -280,  -260,  -280, -1070}+    ,{    40,    20,    40,    20,  -760}+    ,{  -260,  -280,  -260,  -280, -1070}+    }+   ,{{   590,   570,   590,   570,  -230}+    ,{   -60,  -320,   -60,  -320, -1110}+    ,{   -40,   -60,   -40,   -60,  -850}+    ,{   590,   570,   590,   570,  -230}+    ,{   -40,   -60,   -40,   -60,  -850}+    }+   ,{{    40,    20,    40,    20,  -760}+    ,{    40,    20,    40,    20,  -760}+    ,{  -570,  -590,  -570,  -590, -1380}+    ,{    40,    20,    40,    20,  -760}+    ,{  -240,  -260,  -240,  -260, -1050}+    }+   }+  }+ ,{{{{  1010,  1010,   880,   730,   880}+    ,{   410,   -30,    40,   410,  -190}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  1010,  1010,   880,   730,   880}+    ,{   410,     0,  -370,   410,  -370}+    }+   ,{{   410,   -70,  -150,   410,  -370}+    ,{   230,   -70,  -550,   230,  -550}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  -150,  -260,  -150,  -540,  -380}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{  1010,  1010,   880,   730,   880}+    ,{    40,   -30,    40,  -350,  -190}+    ,{   410,  -240,  -370,   410,  -370}+    ,{  1010,  1010,   880,   730,   880}+    ,{   410,  -240,  -370,   410,  -370}+    }+   ,{{   410,     0,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{   410,  -240,  -370,   410,  -370}+    ,{     0,     0,  -370,  -520,  -370}+    }+   }+  ,{{{  1010,  1010,   880, -1280,   880}+    ,{   -30,   -30,  -200, -1340,  -200}+    ,{  -240,  -240,  -370, -1280,  -370}+    ,{  1010,  1010,   880, -1520,   880}+    ,{     0,     0,  -370, -1280,  -370}+    }+   ,{{   -70,   -70,  -370, -1520,  -370}+    ,{   -70,   -70,  -550, -1700,  -550}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{  -260,  -260,  -390, -1530,  -390}+    ,{  -240,  -240,  -370, -1520,  -370}+    }+   ,{{  -240,  -240,  -370, -1280,  -370}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{  -240,  -240,  -370, -1280,  -370}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{  -240,  -240,  -370, -1280,  -370}+    }+   ,{{  1010,  1010,   880, -1340,   880}+    ,{   -30,   -30,  -200, -1340,  -200}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{  1010,  1010,   880, -1520,   880}+    ,{  -240,  -240,  -370, -1520,  -370}+    }+   ,{{     0,     0,  -370, -1280,  -370}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{  -240,  -240,  -370, -1280,  -370}+    ,{  -240,  -240,  -370, -1520,  -370}+    ,{     0,     0,  -370, -1520,  -370}+    }+   }+  ,{{{   880,   730,   880,   730,   640}+    ,{    40,  -350,    40,  -350,  -190}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{   880,   730,   880,   730,   640}+    ,{  -370,  -520,  -370,  -520,  -610}+    }+   ,{{  -150,  -520,  -150,  -520,  -380}+    ,{  -550,  -700,  -550,  -700,  -790}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -150,  -540,  -150,  -540,  -380}+    ,{  -370,  -520,  -370,  -520,  -610}+    }+   ,{{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    }+   ,{{   880,   730,   880,   730,   640}+    ,{    40,  -350,    40,  -350,  -190}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{   880,   730,   880,   730,   640}+    ,{  -370,  -520,  -370,  -520,  -610}+    }+   ,{{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    ,{  -370,  -520,  -370,  -520,  -610}+    }+   }+  ,{{{   880, -1180,   880,   410,   880}+    ,{   410, -1250,  -200,   410,  -200}+    ,{   410, -1180,  -370,   410,  -370}+    ,{   880, -1420,   880,   410,   880}+    ,{   410, -1180,  -370,   410,  -370}+    }+   ,{{   410, -1420,  -370,   410,  -370}+    ,{   230, -1600,  -550,   230,  -550}+    ,{   410, -1420,  -370,   410,  -370}+    ,{  -390, -1440,  -390,  -860,  -390}+    ,{   410, -1420,  -370,   410,  -370}+    }+   ,{{   410, -1180,  -370,   410,  -370}+    ,{   410, -1420,  -370,   410,  -370}+    ,{   410, -1180,  -370,   410,  -370}+    ,{   410, -1420,  -370,   410,  -370}+    ,{   410, -1180,  -370,   410,  -370}+    }+   ,{{   880, -1250,   880,   410,   880}+    ,{  -200, -1250,  -200,  -670,  -200}+    ,{   410, -1420,  -370,   410,  -370}+    ,{   880, -1420,   880,  -840,   880}+    ,{   410, -1420,  -370,   410,  -370}+    }+   ,{{   410, -1180,  -370,   410,  -370}+    ,{   410, -1420,  -370,   410,  -370}+    ,{   410, -1180,  -370,   410,  -370}+    ,{   410, -1420,  -370,   410,  -370}+    ,{  -370, -1420,  -370,  -840,  -370}+    }+   }+  ,{{{   750,   730,   750,   730, -1140}+    ,{   -90,  -350,   -90,  -350, -1140}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{   750,   730,   750,   730, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -280,  -520,  -280,  -520, -1250}+    ,{  -680,  -700,  -680,  -700, -1250}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -280,  -540,  -280,  -540, -1330}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{   750,   730,   750,   730, -1140}+    ,{   -90,  -350,   -90,  -350, -1140}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{   750,   730,   750,   730, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   ,{{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    ,{  -500,  -520,  -500,  -520, -1310}+    }+   }+  }+ ,{{{{  1560,  1560,  1430,  1470,  1430}+    ,{  1470,   820,   690,  1470,   690}+    ,{   960,   310,   180,   960,   180}+    ,{  1560,  1560,  1430,  1280,  1430}+    ,{   960,   550,   180,   960,   180}+    }+   ,{{  1470,   820,   690,  1470,   690}+    ,{  1470,   820,   690,  1470,   690}+    ,{   960,   310,   180,   960,   180}+    ,{    80,   -30,    80,  -310,  -150}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{  1560,  1560,  1430,  1280,  1430}+    ,{   -90,  -200,   -90,  -480,  -320}+    ,{   960,   310,   180,   960,   180}+    ,{  1560,  1560,  1430,  1280,  1430}+    ,{   960,   310,   180,   960,   180}+    }+   ,{{   960,   550,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   960,   310,   180,   960,   180}+    ,{   550,   550,   180,    30,   180}+    }+   }+  ,{{{  1560,  1560,  1430,   -30,  1430}+    ,{   820,   820,   690,   -30,   690}+    ,{   310,   310,   180,  -720,   180}+    ,{  1560,  1560,  1430,  -960,  1430}+    ,{   550,   550,   180,  -720,   180}+    }+   ,{{   820,   820,   690,   -30,   690}+    ,{   820,   820,   690,   -30,   690}+    ,{   310,   310,   180,  -960,   180}+    ,{   -30,   -30,  -160, -1300,  -160}+    ,{   310,   310,   180,  -960,   180}+    }+   ,{{   310,   310,   180,  -720,   180}+    ,{   310,   310,   180,  -960,   180}+    ,{   310,   310,   180,  -720,   180}+    ,{   310,   310,   180,  -960,   180}+    ,{   310,   310,   180,  -720,   180}+    }+   ,{{  1560,  1560,  1430,  -960,  1430}+    ,{  -200,  -200,  -330, -1470,  -330}+    ,{   310,   310,   180,  -960,   180}+    ,{  1560,  1560,  1430,  -960,  1430}+    ,{   310,   310,   180,  -960,   180}+    }+   ,{{   550,   550,   180,  -720,   180}+    ,{   310,   310,   180,  -960,   180}+    ,{   310,   310,   180,  -720,   180}+    ,{   310,   310,   180,  -960,   180}+    ,{   550,   550,   180,  -960,   180}+    }+   }+  ,{{{  1430,  1280,  1430,  1280,  1200}+    ,{   690,   540,   690,   540,   450}+    ,{   180,    30,   180,    30,   -50}+    ,{  1430,  1280,  1430,  1280,  1200}+    ,{   180,    30,   180,    30,   -50}+    }+   ,{{   690,   540,   690,   540,   450}+    ,{   690,   540,   690,   540,   450}+    ,{   180,    30,   180,    30,   -50}+    ,{    80,  -310,    80,  -310,  -150}+    ,{   180,    30,   180,    30,   -50}+    }+   ,{{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    }+   ,{{  1430,  1280,  1430,  1280,  1200}+    ,{   -90,  -480,   -90,  -480,  -320}+    ,{   180,    30,   180,    30,   -50}+    ,{  1430,  1280,  1430,  1280,  1200}+    ,{   180,    30,   180,    30,   -50}+    }+   ,{{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    ,{   180,    30,   180,    30,   -50}+    }+   }+  ,{{{  1470,  -360,  1430,  1470,  1430}+    ,{  1470,  -360,   690,  1470,   690}+    ,{   960,  -630,   180,   960,   180}+    ,{  1430,  -870,  1430,   960,  1430}+    ,{   960,  -630,   180,   960,   180}+    }+   ,{{  1470,  -360,   690,  1470,   690}+    ,{  1470,  -360,   690,  1470,   690}+    ,{   960,  -870,   180,   960,   180}+    ,{  -160, -1210,  -160,  -630,  -160}+    ,{   960,  -870,   180,   960,   180}+    }+   ,{{   960,  -630,   180,   960,   180}+    ,{   960,  -870,   180,   960,   180}+    ,{   960,  -630,   180,   960,   180}+    ,{   960,  -870,   180,   960,   180}+    ,{   960,  -630,   180,   960,   180}+    }+   ,{{  1430,  -870,  1430,   960,  1430}+    ,{  -330, -1380,  -330,  -800,  -330}+    ,{   960,  -870,   180,   960,   180}+    ,{  1430,  -870,  1430,  -290,  1430}+    ,{   960,  -870,   180,   960,   180}+    }+   ,{{   960,  -630,   180,   960,   180}+    ,{   960,  -870,   180,   960,   180}+    ,{   960,  -630,   180,   960,   180}+    ,{   960,  -870,   180,   960,   180}+    ,{   180,  -870,   180,  -290,   180}+    }+   }+  ,{{{  1300,  1280,  1300,  1280,   -10}+    ,{   560,   540,   560,   540,   -10}+    ,{    50,    30,    50,    30,  -760}+    ,{  1300,  1280,  1300,  1280,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{   560,   540,   560,   540,   -10}+    ,{   560,   540,   560,   540,   -10}+    ,{    50,    30,    50,    30,  -760}+    ,{   -50,  -310,   -50,  -310, -1100}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{  1300,  1280,  1300,  1280,  -760}+    ,{  -220,  -480,  -220,  -480, -1270}+    ,{    50,    30,    50,    30,  -760}+    ,{  1300,  1280,  1300,  1280,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   ,{{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    ,{    50,    30,    50,    30,  -760}+    }+   }+  }+ ,{{{{  2050,  1930,  1800,  2050,  1800}+    ,{  2050,  1400,  1270,  2050,  1270}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1930,  1930,  1800,  1760,  1800}+    ,{  1750,  1100,   970,  1750,   970}+    }+   ,{{  2050,  1400,  1270,  2050,  1270}+    ,{  2050,  1400,  1270,  2050,  1270}+    ,{  1740,  1090,   960,  1740,   960}+    ,{   130,    10,   130,  -260,  -110}+    ,{  1740,  1090,   960,  1740,   960}+    }+   ,{{  1760,  1110,   980,  1760,   980}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    }+   ,{{  1930,  1930,  1800,  1740,  1800}+    ,{   300,   190,   300,   -80,    70}+    ,{  1740,  1090,   960,  1740,   960}+    ,{  1930,  1930,  1800,  1650,  1800}+    ,{  1740,  1090,   960,  1740,   960}+    }+   ,{{  1760,  1110,   980,  1760,   980}+    ,{  1760,  1110,   980,  1760,   980}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1760,  1110,   980,  1760,   980}+    ,{   360,   360,     0,  -150,     0}+    }+   }+  ,{{{  1930,  1930,  1800,   130,  1800}+    ,{  1400,  1400,  1270,   130,  1270}+    ,{  1100,  1100,   970,    70,   970}+    ,{  1930,  1930,  1800,  -160,  1800}+    ,{  1100,  1100,   970,    70,   970}+    }+   ,{{  1400,  1400,  1270,   130,  1270}+    ,{  1400,  1400,  1270,   130,  1270}+    ,{  1090,  1090,   960,  -180,   960}+    ,{    10,    10,  -110, -1260,  -110}+    ,{  1090,  1090,   960,  -180,   960}+    }+   ,{{  1110,  1110,   980,    70,   980}+    ,{  1110,  1110,   980,  -160,   980}+    ,{  1100,  1100,   970,    70,   970}+    ,{  1110,  1110,   980,  -160,   980}+    ,{  1100,  1100,   970,    70,   970}+    }+   ,{{  1930,  1930,  1800,  -180,  1800}+    ,{   190,   190,    60, -1080,    60}+    ,{  1090,  1090,   960,  -180,   960}+    ,{  1930,  1930,  1800,  -590,  1800}+    ,{  1090,  1090,   960,  -180,   960}+    }+   ,{{  1110,  1110,   980,    70,   980}+    ,{  1110,  1110,   980,  -160,   980}+    ,{  1100,  1100,   970,    70,   970}+    ,{  1110,  1110,   980,  -160,   980}+    ,{   360,   360,     0, -1150,     0}+    }+   }+  ,{{{  1800,  1650,  1800,  1650,  1570}+    ,{  1270,  1120,  1270,  1120,  1040}+    ,{   970,   820,   970,   820,   740}+    ,{  1800,  1650,  1800,  1650,  1570}+    ,{   970,   820,   970,   820,   740}+    }+   ,{{  1270,  1120,  1270,  1120,  1040}+    ,{  1270,  1120,  1270,  1120,  1040}+    ,{   960,   810,   960,   810,   730}+    ,{   130,  -260,   130,  -260,  -110}+    ,{   960,   810,   960,   810,   730}+    }+   ,{{   980,   830,   980,   830,   740}+    ,{   980,   830,   980,   830,   740}+    ,{   970,   820,   970,   820,   740}+    ,{   980,   830,   980,   830,   740}+    ,{   970,   820,   970,   820,   740}+    }+   ,{{  1800,  1650,  1800,  1650,  1570}+    ,{   300,   -80,   300,   -80,    70}+    ,{   960,   810,   960,   810,   730}+    ,{  1800,  1650,  1800,  1650,  1570}+    ,{   960,   810,   960,   810,   730}+    }+   ,{{   980,   830,   980,   830,   740}+    ,{   980,   830,   980,   830,   740}+    ,{   970,   820,   970,   820,   740}+    ,{   980,   830,   980,   830,   740}+    ,{     0,  -150,     0,  -150,  -240}+    }+   }+  ,{{{  2050,   220,  1800,  2050,  1800}+    ,{  2050,   220,  1270,  2050,  1270}+    ,{  1750,   170,   970,  1750,   970}+    ,{  1800,   -70,  1800,  1760,  1800}+    ,{  1750,   170,   970,  1750,   970}+    }+   ,{{  2050,   220,  1270,  2050,  1270}+    ,{  2050,   220,  1270,  2050,  1270}+    ,{  1740,   -80,   960,  1740,   960}+    ,{  -110, -1160,  -110,  -580,  -110}+    ,{  1740,   -80,   960,  1740,   960}+    }+   ,{{  1760,   170,   980,  1760,   980}+    ,{  1760,   -70,   980,  1760,   980}+    ,{  1750,   170,   970,  1750,   970}+    ,{  1760,   -70,   980,  1760,   980}+    ,{  1750,   170,   970,  1750,   970}+    }+   ,{{  1800,   -80,  1800,  1740,  1800}+    ,{    60,  -980,    60,  -400,    60}+    ,{  1740,   -80,   960,  1740,   960}+    ,{  1800,  -490,  1800,    80,  1800}+    ,{  1740,   -80,   960,  1740,   960}+    }+   ,{{  1760,   170,   980,  1760,   980}+    ,{  1760,   -70,   980,  1760,   980}+    ,{  1750,   170,   970,  1750,   970}+    ,{  1760,   -70,   980,  1760,   980}+    ,{     0, -1050,     0,  -470,     0}+    }+   }+  ,{{{  1670,  1650,  1670,  1650,   570}+    ,{  1140,  1120,  1140,  1120,   570}+    ,{   840,   820,   840,   820,    30}+    ,{  1670,  1650,  1670,  1650,    40}+    ,{   840,   820,   840,   820,    30}+    }+   ,{{  1140,  1120,  1140,  1120,   570}+    ,{  1140,  1120,  1140,  1120,   570}+    ,{   830,   810,   830,   810,    20}+    ,{     0,  -260,     0,  -260, -1050}+    ,{   830,   810,   830,   810,    20}+    }+   ,{{   850,   830,   850,   830,    40}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    }+   ,{{  1670,  1650,  1670,  1650,    20}+    ,{   180,   -80,   180,   -80,  -870}+    ,{   830,   810,   830,   810,    20}+    ,{  1670,  1650,  1670,  1650,  -380}+    ,{   830,   810,   830,   810,    20}+    }+   ,{{   850,   830,   850,   830,    40}+    ,{   850,   830,   850,   830,    40}+    ,{   840,   820,   840,   820,    30}+    ,{   850,   830,   850,   830,    40}+    ,{  -130,  -150,  -130,  -150,  -940}+    }+   }+  }+ ,{{{{  2120,  2120,  1990,  2120,  1990}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  2120,  2120,  1990,  1990,  1990}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  1470,  1340,  2120,  1340}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{   180,    60,   180,  -210,   -60}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  2120,  1990,  1840,  1990}+    ,{  -120,  -230,  -120,  -510,  -360}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{  2120,  2120,  1990,  1840,  1990}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1550,   900,   770,  1550,   770}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{   640,   640,   270,   120,   270}+    }+   }+  ,{{{  2120,  2120,  1990,   300,  1990}+    ,{  1470,  1470,  1340,   190,  1340}+    ,{  1340,  1340,  1210,   300,  1210}+    ,{  2120,  2120,  1990,    60,  1990}+    ,{  1210,  1210,  1080,   180,  1080}+    }+   ,{{  1470,  1470,  1340,   190,  1340}+    ,{  1470,  1470,  1340,   190,  1340}+    ,{  1190,  1190,  1060,   -80,  1060}+    ,{    60,    60,   -60, -1210,   -60}+    ,{  1190,  1190,  1060,   -80,  1060}+    }+   ,{{  1340,  1340,  1210,   300,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{  1340,  1340,  1210,   300,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{  1210,  1210,  1080,   180,  1080}+    }+   ,{{  2120,  2120,  1990,   -80,  1990}+    ,{  -230,  -230,  -360, -1510,  -360}+    ,{  1190,  1190,  1060,   -80,  1060}+    ,{  2120,  2120,  1990,  -400,  1990}+    ,{  1190,  1190,  1060,   -80,  1060}+    }+   ,{{  1340,  1340,  1210,    60,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{   900,   900,   770,  -130,   770}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{   640,   640,   270,  -870,   270}+    }+   }+  ,{{{  1990,  1840,  1990,  1840,  1750}+    ,{  1340,  1190,  1340,  1190,  1100}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1990,  1840,  1990,  1840,  1750}+    ,{  1080,   930,  1080,   930,   840}+    }+   ,{{  1340,  1190,  1340,  1190,  1100}+    ,{  1340,  1190,  1340,  1190,  1100}+    ,{  1060,   910,  1060,   910,   820}+    ,{   180,  -210,   180,  -210,   -60}+    ,{  1060,   910,  1060,   910,   820}+    }+   ,{{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1080,   930,  1080,   930,   840}+    }+   ,{{  1990,  1840,  1990,  1840,  1750}+    ,{  -120,  -510,  -120,  -510,  -360}+    ,{  1060,   910,  1060,   910,   820}+    ,{  1990,  1840,  1990,  1840,  1750}+    ,{  1060,   910,  1060,   910,   820}+    }+   ,{{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{   770,   620,   770,   620,   530}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{   270,   120,   270,   120,    30}+    }+   }+  ,{{{  2120,   400,  1990,  2120,  1990}+    ,{  2120,   290,  1340,  2120,  1340}+    ,{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1990,  1990,  1990}+    ,{  1860,   270,  1080,  1860,  1080}+    }+   ,{{  2120,   290,  1340,  2120,  1340}+    ,{  2120,   290,  1340,  2120,  1340}+    ,{  1840,    10,  1060,  1840,  1060}+    ,{   -60, -1110,   -60,  -530,   -60}+    ,{  1840,    10,  1060,  1840,  1060}+    }+   ,{{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1860,   270,  1080,  1860,  1080}+    }+   ,{{  1990,    10,  1990,  1840,  1990}+    ,{  -360, -1410,  -360,  -830,  -360}+    ,{  1840,    10,  1060,  1840,  1060}+    ,{  1990,  -310,  1990,   270,  1990}+    ,{  1840,    10,  1060,  1840,  1060}+    }+   ,{{  1990,   160,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1550,   -40,   770,  1550,   770}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{   270,  -780,   270,  -200,   270}+    }+   }+  ,{{{  1860,  1840,  1860,  1840,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1860,  1840,  1860,  1840,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1210,  1190,  1210,  1190,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{   930,   910,   930,   910,   120}+    ,{    50,  -210,    50,  -210, -1000}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1860,  1840,  1860,  1840,   120}+    ,{  -250,  -510,  -250,  -510, -1300}+    ,{   930,   910,   930,   910,   120}+    ,{  1860,  1840,  1860,  1840,  -200}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   640,   620,   640,   620,  -170}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   140,   120,   140,   120,  -670}+    }+   }+  }+ ,{{{{  2120,  2120,  1990,  2120,  1990}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  2120,  2120,  1990,  1990,  1990}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  1470,  1340,  2120,  1340}+    ,{  2120,  1470,  1340,  2120,  1340}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{   400,   290,   400,    10,   170}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1860,  1210,  1080,  1860,  1080}+    }+   ,{{  2120,  2120,  1990,  1840,  1990}+    ,{   540,   190,   540,   -80,    70}+    ,{  1840,  1190,  1060,  1840,  1060}+    ,{  2120,  2120,  1990,  1840,  1990}+    ,{  1840,  1190,  1060,  1840,  1060}+    }+   ,{{  1990,  1340,  1210,  1990,  1210}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{  1750,  1100,   970,  1750,   970}+    ,{  1990,  1340,  1210,  1990,  1210}+    ,{   640,   640,   270,   120,   270}+    }+   }+  ,{{{  2120,  2120,  1990,   540,  1990}+    ,{  1470,  1470,  1340,   190,  1340}+    ,{  1340,  1340,  1210,   540,  1210}+    ,{  2120,  2120,  1990,    60,  1990}+    ,{  1210,  1210,  1080,   180,  1080}+    }+   ,{{  1470,  1470,  1340,   190,  1340}+    ,{  1470,  1470,  1340,   190,  1340}+    ,{  1190,  1190,  1060,   -80,  1060}+    ,{   290,   290,   160,  -980,   160}+    ,{  1190,  1190,  1060,   -80,  1060}+    }+   ,{{  1340,  1340,  1210,   540,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{  1340,  1340,  1210,   540,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{  1210,  1210,  1080,   180,  1080}+    }+   ,{{  2120,  2120,  1990,   -80,  1990}+    ,{   190,   190,    60, -1080,    60}+    ,{  1190,  1190,  1060,   -80,  1060}+    ,{  2120,  2120,  1990,  -400,  1990}+    ,{  1190,  1190,  1060,   -80,  1060}+    }+   ,{{  1340,  1340,  1210,    70,  1210}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{  1100,  1100,   970,    70,   970}+    ,{  1340,  1340,  1210,    60,  1210}+    ,{   640,   640,   270,  -810,   270}+    }+   }+  ,{{{  1990,  1840,  1990,  1840,  1750}+    ,{  1340,  1190,  1340,  1190,  1100}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1990,  1840,  1990,  1840,  1750}+    ,{  1080,   930,  1080,   930,   840}+    }+   ,{{  1340,  1190,  1340,  1190,  1100}+    ,{  1340,  1190,  1340,  1190,  1100}+    ,{  1060,   910,  1060,   910,   820}+    ,{   400,    10,   400,    10,   170}+    ,{  1060,   910,  1060,   910,   820}+    }+   ,{{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{  1080,   930,  1080,   930,   840}+    }+   ,{{  1990,  1840,  1990,  1840,  1750}+    ,{   540,   -80,   540,   -80,    70}+    ,{  1060,   910,  1060,   910,   820}+    ,{  1990,  1840,  1990,  1840,  1750}+    ,{  1060,   910,  1060,   910,   820}+    }+   ,{{  1210,  1060,  1210,  1060,   970}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{   970,   820,   970,   820,   740}+    ,{  1210,  1060,  1210,  1060,   970}+    ,{   270,   120,   270,   120,    30}+    }+   }+  ,{{{  2120,   400,  1990,  2120,  1990}+    ,{  2120,   290,  1340,  2120,  1340}+    ,{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1990,  1990,  1990}+    ,{  1860,   270,  1080,  1860,  1080}+    }+   ,{{  2120,   290,  1340,  2120,  1340}+    ,{  2120,   290,  1340,  2120,  1340}+    ,{  1840,    10,  1060,  1840,  1060}+    ,{   160,  -890,   160,  -310,   160}+    ,{  1840,    10,  1060,  1840,  1060}+    }+   ,{{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1990,   400,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1860,   270,  1080,  1860,  1080}+    }+   ,{{  1990,    10,  1990,  1840,  1990}+    ,{    60,  -980,    60,  -400,    60}+    ,{  1840,    10,  1060,  1840,  1060}+    ,{  1990,  -310,  1990,   270,  1990}+    ,{  1840,    10,  1060,  1840,  1060}+    }+   ,{{  1990,   170,  1210,  1990,  1210}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{  1750,   170,   970,  1750,   970}+    ,{  1990,   160,  1210,  1990,  1210}+    ,{   270,  -780,   270,  -200,   270}+    }+   }+  ,{{{  1860,  1840,  1860,  1840,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1860,  1840,  1860,  1840,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1210,  1190,  1210,  1190,   640}+    ,{  1210,  1190,  1210,  1190,   640}+    ,{   930,   910,   930,   910,   120}+    ,{   270,    10,   270,    10,  -780}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   950,   930,   950,   930,   140}+    }+   ,{{  1860,  1840,  1860,  1840,   120}+    ,{   180,   -80,   180,   -80,  -810}+    ,{   930,   910,   930,   910,   120}+    ,{  1860,  1840,  1860,  1840,  -200}+    ,{   930,   910,   930,   910,   120}+    }+   ,{{  1080,  1060,  1080,  1060,   270}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   840,   820,   840,   820,    30}+    ,{  1080,  1060,  1080,  1060,   270}+    ,{   140,   120,   140,   120,  -670}+    }+   }+  }+ }};
+ C/ViennaRNA/inverse.c view
@@ -0,0 +1,528 @@+/*+		      search for sequences that+		  fold into a given target structure++			    c Ivo Hofacker+			  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#define TDIST 0     /* use tree distance */+#define PF    1     /* include support for partiton function */++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include <math.h>+#include <float.h>+#if PF+#include "ViennaRNA/part_func.h"+#endif+#include "ViennaRNA/fold.h"+#if TDIST+#include "ViennaRNA/dist_vars.h"+#include "ViennaRNA/treedist.h"+#include "ViennaRNA/RNAstruct.h"+#endif+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"++PRIVATE double  adaptive_walk(char *start, const char *target);+PRIVATE void   shuffle(int *list, int len);+PRIVATE void   make_start(char* start, const char *structure);+PRIVATE void   make_ptable(const char *structure, int *table);+PRIVATE void   make_pairset(void);+PRIVATE double  mfe_cost(const char *, char*, const char *);+PRIVATE double  pf_cost(const char *, char *, const char *);+PRIVATE char  *aux_struct(const char* structure );++/* for backward compatibility, make sure symbolset can hold 20 characters */+PRIVATE char   default_alpha[21] = "AUGC";+PUBLIC  char   *symbolset = default_alpha;+PUBLIC  int    give_up = 0;+PUBLIC  float  final_cost = 0; /* when to stop inverse_pf_fold */+PUBLIC  int    inv_verbose=0;  /* print out substructure on which inverse_fold() fails */++PRIVATE char   pairset[2*MAXALPHA+1];+PRIVATE int    base, npairs;+PRIVATE int    nc2;++/*-------------------------------------------------------------------------*/+PRIVATE int fold_type;+#if TDIST+PRIVATE Tree *T0;+#endif+PRIVATE double cost2;++PRIVATE double adaptive_walk(char *start, const char *target)+{+#ifdef DUMMY+   printf("%s\n%s %c\n", start, target, backtrack_type );+   return 0.;+#endif+   int i,j,p,tt,w1,w2, n_pos, len, flag;+   long  walk_len;+   char *string, *string2, *cstring, *structure, *struct2;+   int *mut_pos_list, mut_sym_list[MAXALPHA+1], mut_pair_list[2*MAXALPHA+1];+   int *w1_list, *w2_list, mut_position, symbol, bp;+   int *target_table, *test_table;+   char cont;+   double cost, current_cost, ccost2;+   double (*cost_function)(const char *, char *, const char *);++   len = strlen(start);+   if (strlen(target)!=len) {+      vrna_message_error("%s\n%s\nadaptive_walk: start and target have unequal length", start, target);+   }+   string    = (char *) vrna_alloc(sizeof(char)*(len+1));+   cstring   = (char *) vrna_alloc(sizeof(char)*(len+1));+   string2   = (char *) vrna_alloc(sizeof(char)*(len+1));+   structure = (char *) vrna_alloc(sizeof(char)*(len+1));+   struct2   = (char *) vrna_alloc(sizeof(char)*(len+1));+   mut_pos_list = (int *) vrna_alloc(sizeof(int)*len);+   w1_list = (int *) vrna_alloc(sizeof(int)*len);+   w2_list = (int *) vrna_alloc(sizeof(int)*len);+   target_table = (int *) vrna_alloc(sizeof(int)*len);+   test_table = (int *) vrna_alloc(sizeof(int)*len);++   make_ptable(target, target_table);++   for (i=0; i<base; i++) mut_sym_list[i] = i;+   for (i=0; i<npairs; i++) mut_pair_list[i] = i;++   for (i=0; i<len; i++)+      string[i] = (islower(start[i]))?toupper(start[i]):start[i];+   walk_len = 0;++   if (fold_type==0) cost_function = mfe_cost;+   else cost_function = pf_cost;++   cost = cost_function(string, structure, target);++   if (fold_type==0) ccost2=cost2;+   else { ccost2 = -1.; cost2=0; }++   strcpy(cstring, string);+   current_cost = cost;++   if (cost>0) do {+      cont=0;++      if (fold_type==0) { /* min free energy fold */+	 make_ptable(structure, test_table);+	 for (j=w1=w2=flag=0; j<len; j++)+	    if ((tt=target_table[j])!=test_table[j]) {+	       if ((tt<j)&&(isupper(start[j]))) w1_list[w1++] = j;   /* incorrectly paired */+	       if ((flag==0)&&(j>0))+		  if ((target_table[j-1]<j-1)&&isupper(start[j-1]))+			w2_list[w2++] = j-1;                  /* adjacent to incorrect position */+	       if (w2>1) if (w2_list[w2-2]==w2_list[w2-1]) w2--;++	       flag = 1;+	    } else {+	       if (flag==1) if ((tt<j)&&isupper(start[j]))+		  w2_list[w2++] = j;                          /* adjacent to incorrect position */+	       flag = 0;+	    }+	 shuffle(w1_list, w1);+	 shuffle(w2_list, w2);+	 for (j=n_pos=0; j<w1; j++) mut_pos_list[n_pos++] = w1_list[j];+	 for (j=0; j<w2; j++) mut_pos_list[n_pos++] = w2_list[j];+      } else { /* partition_function */+	 for (j=n_pos=0; j<len; j++) if (isupper(start[j]))+	    if (target_table[j]<=j) mut_pos_list[n_pos++] = j;+	 shuffle(mut_pos_list, n_pos);+      }++      string2[0]='\0';+      for (mut_position=0; mut_position<n_pos; mut_position++){++	 strcpy(string, cstring);+	 shuffle(mut_sym_list,  base);+	 shuffle(mut_pair_list, npairs);++	 i = mut_pos_list[mut_position];++	 if (target_table[i]<0) /* unpaired base */+	    for (symbol=0;symbol<base;symbol++) {++	       if(cstring[i]==+		  symbolset[mut_sym_list[symbol]]) continue;++	       string[i] = symbolset[mut_sym_list[symbol]];++	       cost = cost_function(string, structure, target);++	       if ( cost + DBL_EPSILON < current_cost  ) break;+	       if (( cost == current_cost)&&(cost2<ccost2)){+		  strcpy(string2, string);+		  strcpy(struct2, structure);+		  ccost2 = cost2;+	       }+	    }+	 else  /* paired base */+	    for  (bp=0; bp<npairs; bp++) {+	       j = target_table[i];+	       p = mut_pair_list[bp]*2;+	       if ((cstring[i] == pairset[p]) &&+		   (cstring[j] == pairset[p+1]))+		  continue;+	       string[i] = pairset[p];+	       string[j] = pairset[p+1];++	       cost = cost_function(string, structure, target);++	       if ( cost < current_cost ) break;+	       if (( cost == current_cost)&&(cost2<ccost2)){+		  strcpy(string2, string);+		  strcpy(struct2, structure);+		  ccost2 = cost2;+	       }+	    }++	 if ( cost < current_cost ) {+	    strcpy(cstring, string);+	    current_cost = cost;+	    ccost2 = cost2;+	    walk_len++;+	    if (cost>0) cont=1;+	    break;+	 }+      }+      if ((current_cost>0)&&(cont==0)&&(string2[0])) {+	 /* no mutation that decreased cost was found,+	    but the the sequence in string2 decreases cost2 while keeping+	    cost constant */+	 strcpy(cstring, string2);+	 strcpy(structure, struct2);+	 nc2++; cont=1;+      }+   } while (cont);++   for (i=0; i<len; i++) if (isupper(start[i])) start[i]=cstring[i];++#if TDIST+   if (fold_type==0) { free_tree(T0); T0=NULL; }+#endif+   free(test_table);+   free(target_table);+   free(mut_pos_list);+   free(w2_list);+   free(w1_list);+   free(struct2);+   free(structure);+   free(string2);+   free(cstring);+   free(string);++   return current_cost;+}++/*-------------------------------------------------------------------------*/++/* shuffle produces a ronaom list by doing len exchanges */+PRIVATE void shuffle(int *list, int len)+{+   int i, rn;++   for (i=0;i<len;i++) {+     int temp;+     rn = i + (int) (vrna_urn()*(len-i));   /* [i..len-1] */+     /* swap element i and rn */+     temp = list[i];+     list[i] = list[rn];+     list[rn] = temp;+   }+}++/*-------------------------------------------------------------------------*/++PRIVATE void make_ptable(const char *structure, int *table)+{+   int i,j,hx;+   int *stack;++   hx=0;+   stack = (int *) vrna_alloc(sizeof(int)*(strlen(structure)+1));++   for (i=0; i<strlen(structure); i++) {+      switch (structure[i]) {+       case '.':+	 table[i]= -1;+	 break;+       case '(':+	 stack[hx++]=i;+	 break;+       case ')':+	 j = stack[--hx];+	 if (hx<0) {+	    vrna_message_error("%s\nunbalanced brackets in make_ptable", structure);+	 }+	 table[i]=j;+	 table[j]=i;+	 break;+      }+   }+   if (hx!=0) {+      vrna_message_error("%s\nunbalanced brackets in make_ptable", structure);+   }+   free(stack);+}++/*-------------------------------------------------------------------------*/++#define WALK(i,j) \+    strncpy(wstruct, structure+i, j-i+1); \+    wstruct[j-i+1]='\0'; \+    strncpy(wstring, string+i, j-i+1); \+    wstring[j-i+1]='\0'; \+    dist=adaptive_walk(wstring, wstruct); \+    strncpy(string+i, wstring, j-i+1); \+    if ((dist>0)&&(give_up)) goto adios++PUBLIC float inverse_fold(char *start, char *structure)+{+   int i, j, jj, len, o;+   int *pt;+   char *string, *wstring, *wstruct, *aux;+   double dist=0;++   nc2 = j = o = fold_type = 0;++   len = strlen(structure);+   if (strlen(start)!=len) {+      vrna_message_error("%s\n%s\ninverse_fold: start and structure have unequal length", start, structure);+   }+   string = (char *) vrna_alloc(len+1);+   wstring = (char *) vrna_alloc(len+1);+   wstruct = (char *) vrna_alloc(len+1);+   pt = (int *) vrna_alloc(sizeof(int)*(len+2));+   pt[len] = len+1;++   aux = aux_struct(structure);+   strcpy(string, start);+   make_pairset();+   make_start(string, structure);++   make_ptable(structure, pt);++   while (j<len) {+      while ((j<len)&&(structure[j]!=')')) {+	 if (aux[j]=='[') o++;+	 if (aux[j]==']') o--;+	 j++;+      }+      i=j;+      while ((i>0) && structure[--i]!='(');+      if (structure[i]=='.') { /* no pair found -> open chain */+	WALK(0,len-1);+      }++      if (aux[i]!='[') { i--; j++;}+      while (pt[j]==i) {+	 backtrack_type='C';+	 if (aux[i]!='[') {+	    while (aux[--i]!='[');+	    while (aux[++j]!=']');+	    /* WALK(i,j); */+	 }+	 WALK(i,j);+	 o--;+	 jj = j; i--;+	 while (aux[++j]=='.');+	 while ((i>=0)&&(aux[i]=='.')) i--;+	 if (pt[j]!=i) {+	    backtrack_type = (o==0)? 'F' : 'M';+	    if (j-jj>8) { WALK((i+1),(jj)); }+	    WALK((i+1), (j-1));+	    while ((i>=0) &&(aux[i]==']')) {+	       i=pt[i]-1;+	       while ((i>=0)&&(aux[i]=='.')) i--;+	       WALK((i+1), (j-1));+	    }+	 }+      }+   }+ adios:+   backtrack_type='F';+   if ((dist>0)&&(inv_verbose)) printf("%s\n%s\n", wstring, wstruct);+   /*if ((dist==0)||(give_up==0))*/ strcpy(start, string);+   free(wstring); free(wstruct);+   free(string); free(aux);+   free(pt);+/*   if (dist>0) printf("%3d \n", nc2); */+   return dist;+}++/*-------------------------------------------------------------------------*/++PUBLIC float inverse_pf_fold(char *start, char *target)+{+   double dist;+   int dang;++   dang=dangles;+   if (dangles!=0) dangles=2;++   update_fold_params();    /* make sure there is a valid pair matrix */+   make_pairset();+   make_start(start, target);+   fold_type=1;+   do_backtrack = 0;+   dist = adaptive_walk(start, target);+   dangles=dang;+   return (dist+final_cost);+}++/*-------------------------------------------------------------------------*/++PRIVATE void make_start(char* start, const char *structure)+{+   int i,j,k,l,r,length;+   int *table, *S, sym[MAXALPHA], ss;++   length=strlen(start);+   table = (int *) vrna_alloc(sizeof(int)*length);+   S = (int *) vrna_alloc(sizeof(int)*length);++   make_ptable(structure, table);+   for (i=0; i<strlen(start); i++) S[i] = encode_char(toupper(start[i]));+   for (i=0; i<strlen(symbolset); i++) sym[i] = i;++   for (k=0; k<length; k++) {+      if (table[k]<k) continue;+      if (((vrna_urn()<0.5) && isupper(start[k])) ||+	  islower(start[table[k]])) {+	i = table[k]; j = k;+      } else {+	i = k; j = table[k];+      }++      if (!pair[S[i]][S[j]]) {   /* make a valid pair by mutating j */+	shuffle(sym, (int) base);+	for (l=0; l<base; l++) {+	  ss = encode_char(symbolset[sym[l]]);+	  if (pair[S[i]][ss]) break;+	}+	if (l==base) { /* nothing pairs start[i] */+	  r = 2*vrna_int_urn(0, npairs-1);+	  start[i] = pairset[r];+	  start[j] = pairset[r+1];+	} else start[j] = symbolset[sym[l]];+      }+   }+   free(table);+   free(S);+}++/*---------------------------------------------------------------------------*/++PRIVATE void make_pairset(void)+{+   int i,j;+   int sym[MAXALPHA];++   make_pair_matrix();+   base = strlen(symbolset);++   for (i=0; i< base; i++) sym[i] = encode_char(symbolset[i]);++   for (i=npairs=0; i< base; i++)+      for (j=0; j<base; j++)+	 if (pair[sym[i]][sym[j]]) {+	    pairset[npairs++] = symbolset[i];+	    pairset[npairs++] = symbolset[j];+	 }+   npairs /= 2;+   if (npairs==0) vrna_message_error("No pairs in this alphabet!");+}+/*---------------------------------------------------------------------------*/++PRIVATE double mfe_cost(const char *string, char *structure, const char *target)+{+#if TDIST+   Tree *T1;+   char *xstruc;+#endif+   double energy, distance;++   if (strlen(string)!=strlen(target)) {+      vrna_message_error("%s\n%s\nunequal length in mfe_cost", string, target);+   }+   energy = fold(string, structure);+#if TDIST+   if (T0 == NULL) {+      xstruc = expand_Full(target);+      T0=make_tree(xstruc);+      free(xstruc);+   }++   xstruc = expand_Full(structure);+   T1=make_tree(xstruc);+   distance = tree_edit_distance(T0,T1);+   free(xstruc);+   free_tree(T1);+#else+   distance = (double) vrna_bp_distance(target, structure);+#endif+   cost2 = energy_of_structure(string, target, 0) - energy;+   return (double) distance;+}+/*---------------------------------------------------------------------------*/++PRIVATE double pf_cost(const char *string, char *structure, const char *target)+{+#if PF+   double  f, e;++   f = pf_fold(string, structure);+   e = energy_of_structure(string, target, 0);+   return (double) (e-f-final_cost);+#else+   vrna_message_error("this version not linked with pf_fold");+   return 0;+#endif+}++/*---------------------------------------------------------------------------*/++PRIVATE char *aux_struct(const char* structure )+{+   int       *match_paren;+   int          i, o, p;+   char        *string;++   string = (char *) vrna_alloc(sizeof(char)*(strlen(structure)+1));+   match_paren = (int *) vrna_alloc(sizeof(int)*(strlen(structure)/2+1));+   strcpy(string, structure);++   i = o = 0;+   while (string[i]) {+      switch (string[i]) {+       case '.': break;+       case '(':+	 match_paren[++o]=i;+	 break;+       case ')':+	 p=i;+	 while ((string[p+1]==')')&&(match_paren[o-1]==match_paren[o]-1)) {+	    p++; o--;+	 }+	 string[p]=']';+	 i=p;+	 string[match_paren[o]]='[';+	 o--;+	 break;+       default:+	 vrna_message_error("Junk in structure at aux_structure\n");+      }+      i++;+   }+   free(match_paren);+   return(string);+}
+ C/ViennaRNA/inverse.h view
@@ -0,0 +1,68 @@+#ifndef VIENNA_RNA_PACKAGE_INVERSE_H+#define VIENNA_RNA_PACKAGE_INVERSE_H++/**+ *  @file     inverse.h+ *  @ingroup  inverse_fold+ *  @brief    Inverse folding routines+ */++/**+ *  @addtogroup inverse_fold+ *  @brief RNA sequence design+ *  + *  @{+ *  @ingroup  inverse_fold+ */++/**+ *  \brief This global variable points to the allowed bases, initially "AUGC".+ *  It can be used to design sequences from reduced alphabets.+ */+extern char *symbolset;+/** when to stop inverse_pf_fold() */+extern  float final_cost;+/** default 0: try to minimize structure distance even if no exact solution can be found */+extern  int   give_up;+/** print out substructure on which inverse_fold() fails */+extern  int   inv_verbose;++/**+ *  \brief Find sequences with predefined structure+ * + *  This function searches for a sequence with minimum free energy structure+ *  provided in the parameter 'target', starting with sequence 'start'.+ *  It returns 0 if the search was successful, otherwise a structure distance+ *  in terms of the energy difference between the search result and the actual+ *  target 'target' is returned. The found sequence is returned in 'start'.+ *  If #give_up is set to 1, the function will return as soon as it is+ *  clear that the search will be unsuccessful, this speeds up the algorithm+ *  if you are only interested in exact solutions.+ * + *  \param  start   The start sequence+ *  \param  target  The target secondary structure in dot-bracket notation+ *  \return         The distance to the target in case a search was unsuccessful, 0 otherwise+ */+float inverse_fold( char *start,+                    const char *target);++/**+ *  \brief Find sequence that maximizes probability of a predefined structure+ * + *  This function searches for a sequence with maximum probability to fold into+ *  the provided structure 'target' using the partition function algorithm.+ *  It returns \f$-kT \cdot \log(p)\f$ where \f$p\f$ is the frequency of 'target' in+ *  the ensemble of possible structures. This is usually much slower than+ *  inverse_fold().+ * + *  \param  start   The start sequence+ *  \param  target  The target secondary structure in dot-bracket notation+ *  \return         The distance to the target in case a search was unsuccessful, 0 otherwise+ */+float inverse_pf_fold(char *start,+                      const char *target);++/**+ *  @}+ */+#endif
+ C/ViennaRNA/ligand.c view
@@ -0,0 +1,699 @@+/*+ * Reference implementation for including ligand binding to hairpins, or+ * interior loops, with known sequence and/or structure motif, and+ * binding free energy utilizing generic soft constraint feature+ *+ * (c) 2015 Ronny Lorenz - ViennaRNA Package+ */++#include <stdlib.h>+#include <stdio.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/model.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/eval.h"+#include "ViennaRNA/ligand.h"+++/*+#################################+# PRIVATE DATA STRUCTURES       #+#################################+*/++typedef struct{+  int i;+  int j;+  int k;+  int l;+} quadruple_position;++typedef struct{+  char  *seq_motif_5;+  char  *seq_motif_3;+  char  *struct_motif_5;+  char  *struct_motif_3;+  int   energy;+  int   energy_alt;+  int   pair_count;+  vrna_basepair_t *pairs;++  quadruple_position *positions;+} ligand_data;++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++static void+split_sequence( const char *string,+                      char **seq1,+                      char **seq2,+                      int cp);++static void+correctMotifContribution( const char *seq,+                          const char *struct_motif,+                          const char *struct_motif_alt,+                          int *contribution,+                          int *contribution_alt,+                          vrna_md_t *md);++static void+delete_ligand_data(void *data);++static int+AptamerContrib(int i, int j, int k, int l, char d, void *data);++static int+AptamerContribHairpin(int i, int j, int k, int l, char d, void *data);++static FLT_OR_DBL+expAptamerContrib(int i, int j, int k, int l, char d, void *data);++static FLT_OR_DBL+expAptamerContribHairpin(int i, int j, int k, int l, char d, void *data);++static vrna_basepair_t *+backtrack_int_motif(int i, int j, int k, int l, char d, void *data);++static vrna_basepair_t *+backtrack_hp_motif(int i, int j, int k, int l, char d, void *data);++static quadruple_position *+scanForMotif( const char *seq,+              const char *motif1,+              const char *motif2);++static vrna_basepair_t *+scanForPairs( const char  *motif5,+              const char  *motif3,+              int         *pair_count);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC int+vrna_sc_detect_hi_motif(vrna_fold_compound_t *vc,+                        const char *structure,+                        int *i,+                        int *j,+                        int *k,+                        int *l){++  int p, q, n;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(vc && vc->sc && vc->sc->data){+    n = vc->length;+    ldata = (ligand_data *)vc->sc->data;++    for(p = *i; p < n; p++){+      for(pos = ldata->positions; pos->i; pos++){+        if(pos->i == p){+          /* check whether we find the motif in the provided structure */+          int i_m, j_m, k_m, l_m;+          i_m = pos->i;+          j_m = pos->j;+          k_m = pos->k;+          l_m = pos->l;+          for(q = 0; q < strlen(ldata->struct_motif_5); q++){+            if(ldata->struct_motif_5[q] != structure[i_m+q-1])+              break;+          }+          if(q == strlen(ldata->struct_motif_5)){ /* 5' motif detected */+            if(k_m > 0){+              for(q = 0; q < strlen(ldata->struct_motif_3); q++){+                if(ldata->struct_motif_3[q] != structure[l_m+q-1])+                  break;+              }+              if(q == strlen(ldata->struct_motif_3)){ /* 3' motif detected */+                *i = i_m;+                *j = j_m;+                *k = k_m;+                *l = l_m;+                return 1;+              }+            } else {+                *i = i_m;+                *j = j_m;+                *k = k_m;+                *l = l_m;+                return 1;+            }+          }+        }+      }+    }+      +  }+  return 0;+}++PUBLIC int+vrna_sc_get_hi_motif( vrna_fold_compound_t *vc,+                      int *i,+                      int *j,+                      int *k,+                      int *l){++  int p, n;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(vc && vc->sc && vc->sc->data){+    n = vc->length;+    ldata = (ligand_data *)vc->sc->data;++    for(p = *i; p < n; p++){+      for(pos = ldata->positions; pos->i; pos++){+        if(pos->i == p){+          *i = pos->i;+          *j = pos->j;+          *k = pos->k;+          *l = pos->l;+          return 1;+        }+      }+    }+  }+  return 0;+}++PUBLIC int+vrna_sc_add_hi_motif( vrna_fold_compound_t *vc,+                      const char *seq,+                      const char *structure,+                      FLT_OR_DBL energy,+                      unsigned int options){++    int                   i, cp, cp2;+    char                  *sequence, *motif, *motif_alt;+    vrna_md_t             *md_p;+    ligand_data           *ldata;++    sequence              = NULL;+    motif                 = NULL;+    motif_alt             = NULL;+    ldata                 = NULL;+    md_p                  = NULL;++    sequence  = vrna_cut_point_remove(seq, &cp);                /* ligand sequence motif  */+    motif     = vrna_cut_point_remove(structure, &cp2);         /* ligand structure motif */++    /* check for obvious inconsistencies in input sequence/structure motif */+    if(cp != cp2){+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: Cutpoint in sequence and structure motif differ!");+      goto hi_motif_error;+    } else if(strlen(seq) != strlen(structure)){+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: length of sequence and structure motif differ!");+      goto hi_motif_error;+    }++    /* create auxiliary soft constraints data structure */+    ldata                 = vrna_alloc(sizeof(ligand_data));+    ldata->seq_motif_5    = NULL;+    ldata->seq_motif_3    = NULL;+    ldata->struct_motif_5 = NULL;+    ldata->struct_motif_3 = NULL;+    ldata->positions      = NULL;+    ldata->energy         = (int)(energy * 100.);++    split_sequence(sequence, &(ldata->seq_motif_5), &(ldata->seq_motif_3), cp);+    split_sequence(motif, &(ldata->struct_motif_5), &(ldata->struct_motif_3), cp);++    motif_alt = vrna_alloc(sizeof(char) * (strlen(motif) + 1)); /* alternative structure motif */+    memset(motif_alt, '.', strlen(motif) - 1);++    if(cp > 0){+      if((motif[0] != '(') || (motif[strlen(motif) - 1] != ')') || (motif[cp-2] != '(') || (motif[cp-1] != ')')){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: No closing and/or enclosed pair in interior loop motif!");+        goto hi_motif_error;+      }+      /* construct corresponding alternative interior loop motif (....(&)...) */+      motif_alt[0] = '(';+      motif_alt[cp-2] = '(';+      motif_alt[cp-1] = ')';+      motif_alt[strlen(motif) - 1] = ')';+      motif_alt[strlen(motif)] = '\0';++      vrna_sc_add_bt(vc, &backtrack_int_motif);+      vrna_sc_add_f(vc, &AptamerContrib);+      vrna_sc_add_exp_f(vc, &expAptamerContrib);++    } else {+      if((motif[0] != '(') || (motif[strlen(motif) - 1] != ')')){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: No closing pair in hairpin motif!");+        goto hi_motif_error;+      }++      /* construct corresponding alternative hairpin motif (....) */+      motif_alt[0] = '(';+      motif_alt[strlen(motif) - 1] = ')';+      motif_alt[strlen(motif)] = '\0';++      vrna_sc_add_bt(vc, &backtrack_hp_motif);+      vrna_sc_add_f(vc, &AptamerContribHairpin);+      vrna_sc_add_exp_f(vc, &expAptamerContribHairpin);+    }++    /* correct motif contributions */+    if(vc->params)+      md_p = &(vc->params->model_details);+    else+      md_p = &(vc->exp_params->model_details);++    correctMotifContribution(seq, motif, motif_alt, &(ldata->energy), &(ldata->energy_alt), md_p);++    /* scan for sequence motif positions */+    ldata->positions = scanForMotif(vc->sequence, ldata->seq_motif_5, ldata->seq_motif_3);++    /* scan for additional base pairs in the structure motif */+    int pair_count = 0;+    vrna_basepair_t *pairs = scanForPairs(ldata->struct_motif_5, ldata->struct_motif_3, &pair_count);+    if((pair_count > 0) && (pairs == NULL)){ /* error while parsing structure motif */+      vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: Error while parsing additional pairs in structure motif");+      goto hi_motif_error;+    }++    ldata->pairs      = pairs;+    ldata->pair_count = pair_count;++    /* add generalized soft-constraint data structure and corresponding 'delete' function */+    vrna_sc_add_data(vc, (void *)ldata, &delete_ligand_data);++    free(sequence);+    free(motif);+    free(motif_alt);++    return 1; /* success */++/* exit with error */+hi_motif_error:++    free(sequence);+    free(motif);+    free(motif_alt);+    delete_ligand_data(ldata);++    return 0;+}++static void+split_sequence( const char *string,+                      char **seq1,+                      char **seq2,+                      int cp){++  int l = (int)strlen(string);+  *seq1 = NULL;+  *seq2 = NULL;++  if(cp > 0){+    if(cp < l){+      *seq1 = vrna_alloc(sizeof(char) * cp);+      strncpy(*seq1, string, cp - 1);+      (*seq1)[cp - 1] = '\0';+      *seq2 = vrna_alloc(sizeof(char) * (l - cp + 2));+      strncpy(*seq2, string + cp - 1, (l - cp + 1));+      (*seq2)[l - cp + 1] = '\0';+    }+  } else {+    *seq1 = vrna_alloc(sizeof(char) * (l+1));+    strncpy(*seq1, string, l);+    (*seq1)[l] = '\0';+  }+}++static void+correctMotifContribution( const char *seq,+                          const char *struct_motif,+                          const char *struct_motif_alt,+                          int *contribution,+                          int *contribution_alt,+                          vrna_md_t *md){++  float                 alt, corr, energy;+  vrna_fold_compound_t  *tmp_vc;++  tmp_vc  = vrna_fold_compound(seq, md, VRNA_OPTION_EVAL_ONLY);+  alt     = vrna_eval_structure(tmp_vc, struct_motif_alt);+  corr    = vrna_eval_structure(tmp_vc, struct_motif);+  energy  = corr - alt;++  *contribution     += (int)(energy * 100.);+  *contribution_alt  = (int)(alt    * 100.);++  vrna_fold_compound_free(tmp_vc);+}++static void+delete_ligand_data(void *data){++  ligand_data *ldata = (ligand_data *)data;++  free(ldata->seq_motif_5);+  free(ldata->seq_motif_3);+  free(ldata->struct_motif_5);+  free(ldata->struct_motif_3);+  free(ldata->positions);+  free(ldata->pairs);++  free(data);+}++static int+AptamerContrib(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    for(pos = ((ligand_data *)data)->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        return ldata->energy;+      }+    }+  }++  return 0;+}++static int+AptamerContribHairpin(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    for(pos = ((ligand_data *)data)->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        return ldata->energy;+      }+    }+  }++  return 0;+}++static FLT_OR_DBL+expAptamerContrib(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;+  FLT_OR_DBL          exp_e;+  double              kT;++  exp_e = 1.;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    kT    = (37. + K0) * GASCONST;++    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        exp_e =   (FLT_OR_DBL)exp((double) (-ldata->energy) * 10./kT);+        exp_e +=  (FLT_OR_DBL)exp((double) (-ldata->energy_alt) * 10./kT); /* add alternative, i.e. unbound ligand */+        break;+      }+    }+  }++  return exp_e;+}++static FLT_OR_DBL+expAptamerContribHairpin(int i, int j, int k, int l, char d, void *data){++  quadruple_position  *pos;+  ligand_data         *ldata;+  FLT_OR_DBL          exp_e;+  double              kT;++  exp_e = 1.;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    kT    = (37. + K0) * GASCONST;++    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        exp_e =   (FLT_OR_DBL)exp((double) (-ldata->energy) * 10./kT);+        exp_e +=  (FLT_OR_DBL)exp((double) (-ldata->energy_alt) * 10./kT); /* add alternative, i.e. unbound ligand */+        break;+      }+    }+  }++  return exp_e;+}++static vrna_basepair_t *+backtrack_int_motif(int i, int j, int k, int l, char d, void *data){++  int                 bp_size = 15;+  vrna_basepair_t     *pairs = NULL;+  quadruple_position  *pos;+  ligand_data         *ldata;++  if(d == VRNA_DECOMP_PAIR_IL){+    ldata = (ligand_data *)data;+    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j) && (pos->k == k) && (pos->l == l)){+        /* found motif in our list, lets create pairs */+        char  *ptr;+#if 0+        int   actual_size = 0;+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * bp_size);++        for(ptr=ldata->struct_motif_5; *ptr != '\0'; ptr++, i++){+          if(*ptr == '.'){+            pairs[actual_size].i = pairs[actual_size].j = i;+            actual_size++;+            if(actual_size == bp_size){+              bp_size *= 2;+              pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * bp_size);+            }+          }+        }+        for(ptr=ldata->struct_motif_3; *ptr != '\0'; ptr++, l++){+          if(*ptr == '.'){+            pairs[actual_size].i = pairs[actual_size].j = l;+            actual_size++;+            if(actual_size == bp_size){+              bp_size *= 2;+              pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * bp_size);+            }+          }+        }+        pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * (actual_size + 1));+        pairs[actual_size].i = pairs[actual_size].j = -1;+#else+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * (ldata->pair_count + 1));+        vrna_basepair_t *pptr;+        int             count;+        for(count = 0,pptr = ldata->pairs; pptr && (pptr->i != 0); pptr++, count++){+          pairs[count].i = (pptr->i < 0) ? j + pptr->i : i + pptr->i - 1;+          pairs[count].j = (pptr->j < 0) ? j + pptr->j : i + pptr->j - 1;+        }+        pairs[count].i = pairs[count].j = 0;+#endif++        return pairs;+      }+    }+  }++  return pairs;+}++static vrna_basepair_t *+backtrack_hp_motif(int i, int j, int k, int l, char d, void *data){++  int                 count;+  vrna_basepair_t     *pairs = NULL;+  quadruple_position  *pos;+  ligand_data         *ldata;+  vrna_basepair_t     *pptr;++  if(d == VRNA_DECOMP_PAIR_HP){+    ldata = (ligand_data *)data;+    for(pos = ldata->positions; pos->i; pos++){+      if((pos->i == i) && (pos->j == j)){+        /* found motif in our list, lets create pairs */+        pairs = vrna_alloc(sizeof(vrna_basepair_t) * (ldata->pair_count + 1));+        for(count = 0,pptr = ldata->pairs; pptr && (pptr->i != 0); pptr++, count++){+          pairs[count].i = i + pptr->i - 1;+          pairs[count].j = i + pptr->j - 1;+        }+        pairs[count].i = pairs[count].j = 0;+        return pairs;+      }+    }+  }++  return pairs;+}++static quadruple_position *+scanForMotif( const char *seq,+              const char *motif1,+              const char *motif2){++  int   i, j, k, l, l1, l2, n, cnt, cnt2;+  char  *ptr;+  quadruple_position *pos;+  +  n     = (int) strlen(seq);+  l1    = (int) strlen(motif1);+  l2    = (motif2) ? (int) strlen(motif2) : 0;+  cnt   = 0;+  cnt2  = 5; /* initial guess how many matching motifs we might encounter */++  pos = (quadruple_position *)vrna_alloc(sizeof(quadruple_position) * cnt2);++  for(i = 0; i <= n - l1 - l2; i++){+    if(seq[i] == motif1[0]){+      for(j = i+1; j < i + l1; j++){+        if(seq[j] == motif1[j-i]){+          continue;+        }+        else goto next_i;+      }+      /* found 5' motif */+      if(motif2){+        for(k = j + 1; k <= n - l2; k++){+          if(seq[k] == motif2[0]){+            for(l = k + 1; l < k + l2; l++){+              if(seq[l] == motif2[l-k]){+                continue;+              }+              else goto next_k;+            }+            /* we found a quadruple, so store it */+            pos[cnt].i   = i + 1;+            pos[cnt].j   = l;+            pos[cnt].k   = j;+            pos[cnt++].l = k + 1;++            /* allocate more memory if necessary */+            if(cnt == cnt2){+              cnt2 *= 2;+              pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * cnt2);+            }+          }+/* early exit from l loop */+next_k: continue;+        }+      } else { /* hairpin loop motif */+        /* store it */+        pos[cnt].i   = i + 1;+        pos[cnt].j   = j;+        pos[cnt].k   = 0;+        pos[cnt++].l = 0;++        /* allocate more memory if necessary */+        if(cnt == cnt2){+          cnt2 *= 2;+          pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * cnt2);+        }+      }+    }+/* early exit from j loop */+next_i: continue;+  }++  /* reallocate to actual size */+  pos = (quadruple_position *)vrna_realloc(pos, sizeof(quadruple_position) * (cnt + 1));++  /* set end marker */+  pos[cnt].i = pos[cnt].j = pos[cnt].k = pos[cnt].l = 0;++  return pos;+}++static vrna_basepair_t *+scanForPairs( const char  *motif5,+              const char  *motif3,+              int         *pair_count){++  int             i, l5, l3, stack_size, stack_count, *stack;+  vrna_basepair_t *pairs;++  l5          = (motif5) ? strlen(motif5) : 0;+  l3          = (motif3) ? strlen(motif3) : 0;+  stack_count = 0;+  stack_size  = l5 + l3 + 1;+  *pair_count = 0;+  stack       = vrna_alloc(sizeof(int)              * stack_size);+  pairs       = vrna_alloc(sizeof(vrna_basepair_t)  * stack_size);++  /* go through 5' side of structure motif */+  for(i = 2; i < l5; i++){+    if(motif5[i - 1] == '('){+      stack[stack_count++] = i;+    } else if(motif5[i - 1] == ')'){+      pairs[*pair_count].i = stack[--stack_count];+      pairs[*pair_count].j = i;+      /* printf("5' p[%d, %d]\n", pairs[*pair_count].i, pairs[*pair_count].j); */+      (*pair_count)++;+      if(stack_count < 0){+        vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: 5' structure motif contains unbalanced brackets");+        free(stack);+        free(pairs);+        return NULL;+      }+    }+  }++  if(motif3){+    for(i = 2; i < l3; i++){ /* go through 3' side of motif */+      if(motif3[i-1] == '('){+        stack[stack_count++] = -(l3 - i);+      } else if(motif3[i-1] == ')'){+        pairs[*pair_count].i = stack[--stack_count];+        pairs[*pair_count].j = -(l3 - i);+        /* printf("3' p[%d, %d]\n", pairs[*pair_count].i, pairs[*pair_count].j); */+        (*pair_count)++;+        if(stack_count < 0){+          vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: 3' structure motif contains unbalanced brackets");+          free(stack);+          free(pairs);+          return NULL;+        }+      }+    }+  }++  if(stack_count != 0){+    vrna_message_warning("vrna_sc_add_ligand_binding@ligand.c: structure motif contains unbalanced brackets");+    (*pair_count)++;+    free(stack);+    free(pairs);+    return NULL;+  }++  if(*pair_count > 0){+    pairs = vrna_realloc(pairs, sizeof(vrna_basepair_t) * (*pair_count + 1));+    pairs[*pair_count].i = pairs[*pair_count].j = 0;+  } else {+    free(pairs);+    pairs = NULL;+  }++  free(stack);++  return pairs;+}+
+ C/ViennaRNA/ligand.h view
@@ -0,0 +1,63 @@+#ifndef VIENNA_RNA_PACKAGE_LIGAND_H+#define VIENNA_RNA_PACKAGE_LIGAND_H++/**+ *  @file     ligand.h+ *  @ingroup  ligands+ *  @brief    Functions for incorporation of ligands binding to haipirn and interior loop motifs+ */++/**+ *  @addtogroup ligands+ *+ *  @brief  This module covers functions that enable the incorporation of ligand binding+ *  free energies to specific hairpin/interior loop motifs by means of generic soft constraints.+ */+#include <ViennaRNA/data_structures.h>+++/**+ *  @brief  Add soft constraints for hairpin or interior loop binding motif+ *+ *  @ingroup  ligands+ *+ *  Here is an example that adds a theophylline binding motif. Free energy+ *  contribution is derived from @f$k_d = 0.32 \mu mol / l @f$, taken from+ *  Jenison et al. 1994+ *  @code{.c}+vrna_sc_add_hi_motif( vc,+                      "GAUACCAG&CCCUUGGCAGC",+                      "(...((((&)...)))...)",+                      -9.22, VRNA_OPTION_DEFAULT); @endcode+ *+ *  @param  vc        The #vrna_fold_compound_t the motif is applied to+ *  @param  seq       The sequence motif (may be interspaced by '&' character+ *  @param  structure The structure motif (may be interspaced by '&' character+ *  @param  energy    The free energy of the motif (e.g. binding free energy)+ *  @param  options   Options+ *  @return           non-zero value if application of the motif using soft constraints was successful+ *  + */+int+vrna_sc_add_hi_motif( vrna_fold_compound_t *vc,+                      const char *seq,+                      const char *structure,+                      FLT_OR_DBL energy,+                      unsigned int options);++int+vrna_sc_detect_hi_motif(vrna_fold_compound_t *vc,+                        const char *structure,+                        int *i,+                        int *j,+                        int *k,+                        int *l);++int+vrna_sc_get_hi_motif( vrna_fold_compound_t *vc,+                      int *i,+                      int *j,+                      int *k,+                      int *l);++#endif
+ C/ViennaRNA/list.c view
@@ -0,0 +1,412 @@+/*+  $Log: list.c,v $+  Revision 1.5  2003/07/14 13:36:58  ivo+  use vrna_alloc() instead of malloc++  Revision 1.4  2000/10/10 08:53:52  ivo+  include dmalloc.h header if DMALLOC defined++  Revision 1.4  2000/10/10 08:04:34  ivo+  include dmalloc header id DMALLOC defined++  Revision 1.3  1998/03/30 14:24:51  ivo+  use RNA package utils.h++  Revision 1.2  1997/10/09  19:01:50  steve+  *** empty log message ***++  Revision 1.1  1997/08/04 21:05:32  walter+  Initial revision++*/+/*+   (C) 1991 Kendall Bennett.+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/list.h"++#define PUBLIC+PUBLIC void *+lst_newnode (int size)+/****************************************************************************+*+* Function:	lst_newnode+* Parameters:	size - Amount of memory to allocate for node+* Returns:      Pointer to the allocated node's user space.+*+* Description:	Allocates the memory required for a node, adding a small+*		header at the start of the node. We return a reference to+*		the user space of the node, as if it had been allocated via+*		malloc().+*+****************************************************************************/+{+  LST_BUCKET *node;++  node = (LST_BUCKET *) vrna_alloc(size + sizeof (LST_BUCKET));++  return LST_USERSPACE (node);	/* Return pointer to user space */+}++PUBLIC void+lst_freenode (void *node)+/****************************************************************************+*+* Function:	lst_freenode+* Parameters:	node - Node to free.+*+* Description:  Frees a node previously allocated with lst_newnode().+*+****************************************************************************/+{+  free (LST_HEADER (node));+}++PUBLIC LIST *+lst_init (void)+/****************************************************************************+*+* Function:	lst_init+* Returns:      Pointer to a newly created list.+*+* Description:	Initialises a list and returns a pointer to it.+*+****************************************************************************/+{+  LIST *l;++  if ((l = (LIST *) vrna_alloc(sizeof (LIST))) != NULL)+    {+      l->count = 0;+      l->head = &(l->hz[0]);+      l->z = &(l->hz[1]);+      l->head->next = l->z->next = l->z;+    }++  return l;+}++PUBLIC void+lst_kill (LIST * l, void (*freeNode) (void *node))+/****************************************************************************+*+* Function:	lst_kill+* Parameters:	l - List to kill+*		freeNode - Pointer to user routine to free a node+*+* Description:	Kills the list l, by deleting all of the elements contained+*		within the list one by one and then deleting the list+*		itself. Note that we call the user supplied routine+*		(*freeNode)() to free each list node. This allows the user+*		program to perform any extra processing needed to kill each+*		node (if each node contains pointers to other items on the+*		heap for example). If no extra processing is required, just+*		pass the address of lst_freenode(), ie:+*+*		lst_kill(myList,lst_freenode);+*+****************************************************************************/+{+  LST_BUCKET *n, *p;++  n = l->head->next;+  while (n != l->z)+    {				/* Free all nodes in list  */+      p = n;+      n = n->next;+      (*freeNode) (LST_USERSPACE (p));+    }+  free (l);			/* Free the list itself    */+}++PUBLIC void+lst_insertafter (LIST * l, void *node, void *after)+/****************************************************************************+*+* Function:	lst_insertafter+* Parameters:	l - List to insert node into+*		node - Pointer to user space of node to insert+*		after - Pointer to user space of node to insert node after+*+* Description:	Inserts a new node into the list after the node 'after'. To+*		insert a new node at the beginning of the list, user the+*		macro LST_HEAD in place of 'after'. ie:+*+*		lst_insertafter(mylist,node,LST_HEAD(mylist));+*+****************************************************************************/+{+  LST_BUCKET *n = LST_HEADER (node), *a = LST_HEADER (after);++  n->next = a->next;+  a->next = n;+  l->count++;+}++PUBLIC void *+lst_deletenext (LIST * l, void *node)+/****************************************************************************+*+* Function:	lst_deletenext+* Parameters:	l - List to delete node from.+*		node - Node to delete the next node from+* Returns:	Pointer to the deleted node's userspace.+*+* Description:	Removes the node AFTER 'node' from the list l.+*+****************************************************************************/+{+  LST_BUCKET *n = LST_HEADER (node);++  node = LST_USERSPACE (n->next);+  n->next = n->next->next;+  l->count--;+  return node;+}++PUBLIC void *+lst_first (LIST * l)+/****************************************************************************+*+* Function:	lst_first+* Parameters:	l - List to obtain first node from+* Returns:	Pointer to first node in list, NULL if list is empty.+*+* Description:	Returns a pointer to the user space of the first node in+*		the list. If the list is empty, we return NULL.+*+****************************************************************************/+{+  LST_BUCKET *n;++  n = l->head->next;+  return (n == l->z ? NULL : LST_USERSPACE (n));+}++PUBLIC void *+lst_next (void *prev)+/****************************************************************************+*+* Function:	lst_next+* Parameters:	prev - Previous node in list to obtain next node from+* Returns:	Pointer to the next node in the list, NULL at end of list.+*+* Description:	Returns a pointer to the user space of the next node in the+*		list given a pointer to the user space of the previous node.+*		If we have reached the end of the list, we return NULL. The+*		end of the list is detected when the next pointer of a node+*		points back to itself, as does the dummy last node's next+*		pointer. This enables us to detect the end of the list+*		without needed access to the list data structure itself.+*+*		NOTE:	We do no checking to ensure that 'prev' is NOT a+*			NULL pointer.+*+****************************************************************************/+{+  LST_BUCKET *n = LST_HEADER (prev);++  n = n->next;+  return (n == n->next ? NULL : LST_USERSPACE (n));+}++/* Static globals required by merge()   */++static LST_BUCKET *z;+static int (*cmp) (void *, void *);++static LST_BUCKET *+merge (LST_BUCKET * a, LST_BUCKET * b, LST_BUCKET ** end)+/****************************************************************************+*+* Function:	merge+* Parameters:	a,b - Sublist's to merge+* Returns:	Pointer to the merged sublists.+*+* Description:	Merges two sorted lists of nodes together into a single+*		sorted list.+*+****************************************************************************/+{+  LST_BUCKET *c;++  /* Go through the lists, merging them together in sorted order  */++  c = z;+  while (a != z && b != z)+    {+      if ((*cmp) (LST_USERSPACE (a), LST_USERSPACE (b)) <= 0)+	{+	  c->next = a;+	  c = a;+	  a = a->next;+	}+      else+	{+	  c->next = b;+	  c = b;+	  b = b->next;+	}+    };++  /* If one of the lists is not exhausted, then re-attach it to the end+   * of the newly merged list+   */++  if (a != z)+    c->next = a;+  if (b != z)+    c->next = b;++  /* Set *end to point to the end of the newly merged list        */++  while (c->next != z)+    c = c->next;+  *end = c;++  /* Determine the start of the merged lists, and reset z to point to+   * itself+   */++  c = z->next;+  z->next = z;+  return c;+}++PUBLIC void+lst_mergesort (LIST * l, int (*cmp_func) (void *, void *))+/****************************************************************************+*+* Function:	lst_mergesort+* Parameters:	l - List to merge sort+*		cmp_func - Function to compare two user spaces+*+* Description:	Mergesort's all the nodes in the list. 'cmp' must point to+*		a comparison function that can compare the user spaces of+*		two different nodes. 'cmp' should work the same as+*		strcmp(), in terms of the values it returns.+*+****************************************************************************/+{+  int i, N;+  LST_BUCKET *a, *b;		/* Pointers to sublists to merge                */+  LST_BUCKET *c;		/* Pointer to end of sorted sublists            */+  LST_BUCKET *head;		/* Pointer to dummy head node for list          */+  LST_BUCKET *todo;		/* Pointer to sublists yet to be sorted         */+  LST_BUCKET *t;		/* Temporary                                                            */++  /* Set up globals required by merge() and pointer to head       */++  z = l->z;+  cmp = cmp_func;+  head = l->head;++  for (N = 1, a = z; a != head->next; N = N + N)+    {+      todo = head->next;+      c = head;+      while (todo != z)+	{++	  /* Build first sublist to be merged, and splice from main list+	   */++	  a = t = todo;+	  for (i = 1; i < N; i++)+	    t = t->next;+	  b = t->next;+	  t->next = z;+	  t = b;++	  /* Build second sublist to be merged and splice from main list+	   */++	  for (i = 1; i < N; i++)+	    t = t->next;+	  todo = t->next;+	  t->next = z;++	  /* Merge the two sublists created, and set 'c' to point to the+	   * end of the newly merged sublists.+	   */++	  c->next = merge (a, b, &t);+	  c = t;+	}+    }+}++#ifdef LIST_TEST++/*---------------------------------------------------------------*/+/*---------------------------------------------------------------*/++/* Simple program to test the list routines */++typedef struct+{+  char name[40];+  int age;+}+REC;++/*---------------------------------------------------------------*/++int+my_cmp (REC * r1, REC * r2)+{+  return strcmp (r1->name, r2->name);+}++/*---------------------------------------------------------------*/++void+main (void)+{+  LIST *list;+  int done = 0;+  REC *rec;+  char line[80];++  list = lst_init ();++  printf ("Type a list of names and ages. Empty line quits\n\n");++  while (!done)+    {+      rec = lst_newnode (sizeof (REC));+      gets (line);+      if ((done = (line[0] == '\0')) != 1)+	{+	  strcpy (rec->name, line);+	  gets (line);+	  rec->age = atoi (line);+	  lst_insertafter (list, rec, LST_HEAD (list));+	}+    };++  printf ("\nThe list you typed in was:\n\n");++  for (rec = lst_first (list); rec; rec = lst_next (rec))+    printf ("Name: %s, Age: %d\n", rec->name, rec->age);++  printf ("\nSorting the list...\n\n");++  lst_mergesort (list, my_cmp);++  for (rec = lst_first (list); rec; rec = lst_next (rec))+    printf ("Name: %s, Age: %d\n", rec->name, rec->age);++  lst_kill (list, lst_freenode);+}++/*---------------------------------------------------------------*/++#endif
+ C/ViennaRNA/list.h view
@@ -0,0 +1,65 @@+/*+  $Log: list.h,v $+  Revision 1.2  2000/10/10 08:50:01  ivo+  some annotation for lclint++  Revision 1.1  1997/08/04 21:05:32  walter+  Initial revision++*/++#ifndef	__LIST_H+#define	__LIST_H++/*---------------------- Macros and type definitions ----------------------*/++typedef struct LST_BUCKET {+  struct LST_BUCKET *next;+}+LST_BUCKET;++typedef struct {+  int count;			/* Number of elements currently in list */+  LST_BUCKET *head;		/* Pointer to head element of list      */+  LST_BUCKET *z;		/* Pointer to last node of list         */+  LST_BUCKET hz[2];		/* Space for head and z nodes           */+}+LIST;++/* Return a pointer to the user space given the address of the header of+ * a node.+ */++#define	LST_USERSPACE(h)	((void*)((LST_BUCKET*)(h) + 1))++/* Return a pointer to the header of a node, given the address of the+ * user space.+ */++#define	LST_HEADER(n)		((LST_BUCKET*)(n) - 1)++/* Return a pointer to the user space of the list's head node. This user+ * space does not actually exist, but it is useful to be able to address+ * it to enable insertion at the start of the list.+ */++#define	LST_HEAD(l)		LST_USERSPACE((l)->head)++/* Determine if a list is empty+ */++#define	LST_EMPTY(l)		((l)->count == 0)++/*-------------------------- Function Prototypes --------------------------*/++/*@only@*//*@out@*/ void *lst_newnode (int size);+void lst_freenode (/*@only@*/ void *node);+/*@only@*//*@out@*/  LIST *lst_init (void);+void lst_kill (LIST * l, void (*freeNode) ());+void lst_insertafter (LIST * l, /*@keep@*/ void *node, void *after);+void *lst_deletenext (/*@only@*/ LIST * l, void *node);+/*@dependent@*/ void *lst_first (LIST * l);+/*@dependent@*/ void *lst_next (void *prev);+void lst_mergesort (LIST * l, int (*cmp_func) ());++#endif
+ C/ViennaRNA/loop_energies.h view
@@ -0,0 +1,41 @@+#ifndef VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H+#define VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H++/**+ *  @file     loop_energies.h+ *  @ingroup  loops+ *  @brief    Energy evaluation for MFE and partition function calculations+ */++/**+ *  @{+ *  @ingroup   loops+ * + *  <P>+ *  This file contains functions for the calculation of the free energy @f$\Delta G@f$+ *  of a hairpin- [ E_Hairpin() ] or interior-loop [ E_IntLoop()] .<BR>+ *  The unit of the free energy returned is @f$10^{-2} * \mathrm{kcal}/\mathrm{mol}@f$+ *  </P>+ *  <P>+ *  In case of computing the partition function, this file also supplies functions+ *  which return the Boltzmann weights @f$e^{-\Delta G/kT} @f$ for a hairpin- [ exp_E_Hairpin() ]+ *  or interior-loop [ exp_E_IntLoop() ].+ *  </P>+ */+++/* below we include the loop type specific energy evaluation functions */++#include <ViennaRNA/exterior_loops.h>++#include <ViennaRNA/hairpin_loops.h>++#include <ViennaRNA/interior_loops.h>++#include <ViennaRNA/multibranch_loops.h>++/**+ * @}+ */++#endif
+ C/ViennaRNA/mfe.c view
@@ -0,0 +1,1259 @@+/** \file **/++/*+                  minimum free energy+                  RNA secondary structure prediction++                  c Ivo Hofacker, Chrisoph Flamm+                  original implementation by+                  Walter Fontana+                  g-quadruplex support and threadsafety+                  by Ronny Lorenz++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/data_structures.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/mfe.h"++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#define MAXSECTORS        500     /* dimension for a backtrack array */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE int           fill_arrays(vrna_fold_compound_t *vc);+PRIVATE void          fill_arrays_circ(vrna_fold_compound_t *vc, sect bt_stack[], int *bt);+PRIVATE void          backtrack(vrna_fold_compound_t *vc, vrna_bp_stack_t *bp_stack, sect bt_stack[], int s);++PRIVATE int           fill_arrays_comparative(vrna_fold_compound_t *vc);+PRIVATE void          fill_arrays_comparative_circ(vrna_fold_compound_t *vc, sect bt_stack[], int *bt);+PRIVATE void          backtrack_comparative(vrna_fold_compound_t *vc, vrna_bp_stack_t *bp_stack, sect bt_stack[], int s);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_mfe( vrna_fold_compound_t *vc,+          char *structure){++  char    *ss;+  int     length, energy, s;+  float   mfe;+  sect    bt_stack[MAXSECTORS]; /* stack of partial structures for backtracking */+  vrna_bp_stack_t   *bp;++  s       = 0;+  mfe     = (float)(INF/100.);++  if(vc){+    length  = (int) vc->length;++    if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_MFE)){+      vrna_message_warning("vrna_mfe@mfe.c: Failed to prepare vrna_fold_compound");+      return mfe;+    }++    /* call user-defined recursion status callback function */+    if(vc->stat_cb)+      vc->stat_cb(VRNA_STATUS_MFE_PRE, vc->auxdata);++    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     energy = fill_arrays(vc);+                                    if(vc->params->model_details.circ){+                                      fill_arrays_circ(vc, bt_stack, &s);+                                      energy = vc->matrices->Fc;+                                    }+                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  energy = fill_arrays_comparative(vc);+                                    if(vc->params->model_details.circ){+                                      fill_arrays_comparative_circ(vc, bt_stack, &s);+                                      energy = vc->matrices->Fc;+                                    }+                                    break;++      default:                      vrna_message_warning("unrecognized fold compound type");+                                    return mfe;+                                    break;+    }+++    /* call user-defined recursion status callback function */+    if(vc->stat_cb)+      vc->stat_cb(VRNA_STATUS_MFE_POST, vc->auxdata);++    if(structure && vc->params->model_details.backtrack){+      bp = (vrna_bp_stack_t *)vrna_alloc(sizeof(vrna_bp_stack_t) * (4*(1+length/2))); /* add a guess of how many G's may be involved in a G quadruplex */++      switch(vc->type){+        case VRNA_FC_TYPE_COMPARATIVE:  backtrack_comparative(vc, bp, bt_stack, s);+                                      break;++        case VRNA_FC_TYPE_SINGLE:     /* fall through */++        default:                      backtrack(vc, bp, bt_stack, s);+                                      break;+      }++      ss = vrna_db_from_bp_stack(bp, length);+      strncpy(structure, ss, length + 1);+      free(ss);+      free(bp);+    }++    if (vc->params->model_details.backtrack_type=='C')+      mfe = (float) vc->matrices->c[vc->jindx[length]+1]/100.;+    else if (vc->params->model_details.backtrack_type=='M')+      mfe = (float) vc->matrices->fML[vc->jindx[length]+1]/100.;+    else+      mfe = (float) energy/100.;++    if(vc->type == VRNA_FC_TYPE_COMPARATIVE)+      mfe /= (float)vc->n_seq;+  }++  return mfe;+}++/**+*** fill "c", "fML" and "f5" arrays and return  optimal energy+**/+PRIVATE int+fill_arrays(vrna_fold_compound_t *vc){++  unsigned char     type;+  char              *ptype, *hard_constraints;+  int               i, j, ij, length, energy, new_c, stackEnergy, no_close, turn,+                    noGUclosure, noLP, uniq_ML, dangle_model, *indx, *my_f5,+                    *my_c, *my_fML, *my_fM1, hc_decompose, *cc, *cc1, *Fmi, *DMLi,+                    *DMLi1, *DMLi2;+  vrna_param_t      *P;+  vrna_mx_mfe_t     *matrices;+  vrna_hc_t         *hc;+  vrna_ud_t         *domains_up;++  length            = (int)vc->length;+  ptype             = vc->ptype;+  indx              = vc->jindx;+  P                 = vc->params;+  noGUclosure       = P->model_details.noGUclosure;+  noLP              = P->model_details.noLP;+  uniq_ML           = P->model_details.uniq_ML;+  dangle_model      = P->model_details.dangles;+  turn              = P->model_details.min_loop_size;+  hc                = vc->hc;+  hard_constraints  = hc->matrix;+  matrices          = vc->matrices;+  my_f5             = matrices->f5;+  my_c              = matrices->c;+  my_fML            = matrices->fML;+  my_fM1            = matrices->fM1;+  domains_up        = vc->domains_up;++  /* allocate memory for all helper arrays */+  cc    = (int *) vrna_alloc(sizeof(int)*(length + 2)); /* auxilary arrays for canonical structures     */+  cc1   = (int *) vrna_alloc(sizeof(int)*(length + 2)); /* auxilary arrays for canonical structures     */+  Fmi   = (int *) vrna_alloc(sizeof(int)*(length + 1)); /* holds row i of fML (avoids jumps in memory)  */+  DMLi  = (int *) vrna_alloc(sizeof(int)*(length + 1)); /* DMLi[j] holds  MIN(fML[i,k]+fML[k+1,j])      */+  DMLi1 = (int *) vrna_alloc(sizeof(int)*(length + 1)); /*                MIN(fML[i+1,k]+fML[k+1,j])    */+  DMLi2 = (int *) vrna_alloc(sizeof(int)*(length + 1)); /*                MIN(fML[i+2,k]+fML[k+1,j])    */++  if((turn < 0) || (turn > length))+    turn = length; /* does this make any sense? */++  /* pre-processing ligand binding production rule(s) */+  if(domains_up && domains_up->prod_cb)+    domains_up->prod_cb(vc, domains_up->data);++  /* prefill helper arrays */+  for(j = 0; j <= length; j++){+    Fmi[j] = DMLi[j] = DMLi1[j] = DMLi2[j] = INF;+  }+++  /* prefill matrices with init contributions */+  for(j = 1; j <= length; j++)+    for(i = (j > turn ? (j - turn) : 1); i <= j; i++){+      my_c[indx[j] + i] = my_fML[indx[j] + i] = INF;+      if(uniq_ML)+        my_fM1[indx[j] + i] = INF;+    }++  /* start recursion */++  if (length <= turn){+    /* clean up memory */+    free(cc);+    free(cc1);+    free(Fmi);+    free(DMLi);+    free(DMLi1);+    free(DMLi2);+    /* return free energy of unfolded chain */+    return 0;+  }++  for (i = length-turn-1; i >= 1; i--) { /* i,j in [1..length] */++    for (j = i+turn+1; j <= length; j++) {+      ij            = indx[j]+i;+      type          = (unsigned char)ptype[ij];+      hc_decompose  = hard_constraints[ij];+      energy        = INF;++      no_close = (((type==3)||(type==4))&&noGUclosure);++      if (hc_decompose) {   /* we evaluate this pair */+        new_c = INF;++        if(!no_close){+          /* check for hairpin loop */+          energy = vrna_E_hp_loop(vc, i, j);+          new_c = MIN2(new_c, energy);++          /* check for multibranch loops */+          energy  = vrna_E_mb_loop_fast(vc, i, j, DMLi1, DMLi2);+          new_c   = MIN2(new_c, energy);+        }++        if(dangle_model == 3){ /* coaxial stacking */+          energy  = E_mb_loop_stack(i, j, vc);+          new_c   = MIN2(new_c, energy);+        }++        /* check for interior loops */+        energy = vrna_E_int_loop(vc, i, j);+        new_c = MIN2(new_c, energy);++        /* remember stack energy for --noLP option */+        if(noLP){+          stackEnergy = vrna_E_stack(vc, i, j);+          new_c       = MIN2(new_c, cc1[j-1]+stackEnergy);+          cc[j]       = new_c;+          my_c[ij]    = cc1[j-1]+stackEnergy;+        } else {+          my_c[ij]    = new_c;+        }+      } /* end >> if (pair) << */++      else my_c[ij] = INF;++      /* done with c[i,j], now compute fML[i,j] and fM1[i,j] */++      my_fML[ij] = vrna_E_ml_stems_fast(vc, i, j, Fmi, DMLi);++      if(uniq_ML){  /* compute fM1 for unique decomposition */+        my_fM1[ij] = E_ml_rightmost_stem(i, j, vc);+      }++    } /* end of j-loop */++    {+      int *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+    }+  } /* end of i-loop */++  /* calculate energies of 5' fragments */+  E_ext_loop_5(vc);++  /* clean up memory */+  free(cc);+  free(cc1);+  free(Fmi);+  free(DMLi);+  free(DMLi1);+  free(DMLi2);++  return my_f5[length];+}++#include "circfold.inc"+++/**+*** the actual forward recursion to fill the energy arrays+**/+PRIVATE int+fill_arrays_comparative(vrna_fold_compound_t *vc){++  char              *hard_constraints;+  unsigned short    **a2s;+  short             **S, **S5, **S3;+  int               i, j, turn, energy, stackEnergy, new_c, s, *type, tt, *cc,+                    *cc1, *Fmi, *DMLi, *DMLi1, *DMLi2, n_seq, length, *indx,+                    *c, *f5, *fML, *ggg, *pscore, dangle_model;+  vrna_param_t      *P;+  vrna_md_t         *md;+  vrna_hc_t         *hc;+  vrna_sc_t         **sc;++  n_seq             = vc->n_seq;+  length            = vc->length;+  S                 = vc->S;+  S5                = vc->S5;             /* S5[s][i] holds next base 5' of i in sequence s */+  S3                = vc->S3;             /* Sl[s][i] holds next base 3' of i in sequence s */+  a2s               = vc->a2s;+  P                 = vc->params;+  md                = &(P->model_details);+  indx              = vc->jindx;          /* index for moving in the triangle matrices c[] and fMl[] */+  c                 = vc->matrices->c;    /* energy array, given that i-j pair */+  f5                = vc->matrices->f5;   /* energy of 5' end */+  fML               = vc->matrices->fML;  /* multi-loop auxiliary energy array */+  ggg               = vc->matrices->ggg;+  pscore            = vc->pscore;         /* precomputed array of pair types */+  dangle_model      = md->dangles;+  turn              = md->min_loop_size;+  hc                = vc->hc;+  sc                = vc->scs;+  hard_constraints  = hc->matrix;++  /* allocate some memory for helper arrays */+  type  = (int *) vrna_alloc(n_seq*sizeof(int));+  cc    = (int *) vrna_alloc(sizeof(int)*(length+2)); /* linear array for calculating canonical structures */+  cc1   = (int *) vrna_alloc(sizeof(int)*(length+2)); /*   "     "        */+  Fmi   = (int *) vrna_alloc(sizeof(int)*(length+1)); /* holds row i of fML (avoids jumps in memory) */+  DMLi  = (int *) vrna_alloc(sizeof(int)*(length+1)); /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */+  DMLi1 = (int *) vrna_alloc(sizeof(int)*(length+1)); /*             MIN(fML[i+1,k]+fML[k+1,j])  */+  DMLi2 = (int *) vrna_alloc(sizeof(int)*(length+1)); /*             MIN(fML[i+2,k]+fML[k+1,j])  */+++  if((turn < 0) || (turn > length))+    turn = length;++  /* init energies */+  for (j=1; j<=length; j++){+    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;+    for (i=(j>turn?(j-turn):1); i<j; i++) {+      c[indx[j]+i] = fML[indx[j]+i] = INF;+    }+  }++  /* begin recursions */+  for (i = length-turn-1; i >= 1; i--) { /* i,j in [1..length] */+    for (j = i+turn+1; j <= length; j++) {+      int ij, psc;+      ij = indx[j]+i;++      for (s=0; s<n_seq; s++) {+        type[s] = md->pair[S[s][i]][S[s][j]];+        if (type[s]==0) type[s]=7;+      }++      psc = pscore[indx[j]+i];+      if (hard_constraints[ij]) {   /* a pair to consider */+        new_c = INF;++        /* hairpin ----------------------------------------------*/+        energy  = vrna_E_hp_loop(vc, i, j);+        new_c   = MIN2(new_c, energy);++        /* check for multibranch loops */+        energy  = vrna_E_mb_loop_fast(vc, i, j, DMLi1, DMLi2);+        new_c   = MIN2(new_c, energy);++        /* check for interior loops */+        energy  = vrna_E_int_loop(vc, i, j);+        new_c   = MIN2(new_c, energy);++        /* remember stack energy for --noLP option */+        if(md->noLP){+          stackEnergy = vrna_E_stack(vc, i, j);+          new_c       = MIN2(new_c, cc1[j-1]+stackEnergy);+          cc[j]       = new_c - psc; /* add covariance bonnus/penalty */+          c[ij]       = cc1[j-1] + stackEnergy - psc;+        } else {+          c[ij]       = new_c - psc; /* add covariance bonnus/penalty */+        }+      } /* end >> if (pair) << */++      else c[ij] = INF;++      /* done with c[i,j], now compute fML[i,j] */+      fML[ij] = vrna_E_ml_stems_fast(vc, i, j, Fmi, DMLi);++    } /* END for j */++    {+      int *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+    }+  } /* END for i */+  /* calculate energies of 5' and 3' fragments */++  f5[0] = 0;+  for(j = 1; j <= turn + 1; j++){+    if(hc->up_ext[j]){+      energy = f5[j-1];+      if((energy < INF) && sc)+        for(s=0;s < n_seq; s++){+          if(sc[s]){+            if(sc[s]->energy_up)+              energy += sc[s]->energy_up[a2s[s][j]][1];+          }+        }+    } else {+      energy = INF;+    }+    f5[j] = energy;+  }++  switch(dangle_model){+    case 0:   for(j = turn + 2; j <= length; j++){+                f5[j] = INF;++                if(hc->up_ext[j]){+                  energy = f5[j-1];+                  if((energy < INF) && sc)+                    for(s=0; s < n_seq; s++){+                      if(sc[s]){+                        if(sc[s]->energy_up)+                          energy += sc[s]->energy_up[a2s[s][j]][1];+                      }+                    }+                  f5[j] = MIN2(f5[j], energy);+                }++                if (hard_constraints[indx[j]+1] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                  if(c[indx[j]+1] < INF){+                    energy = c[indx[j]+1];+                    for(s = 0; s < n_seq; s++){+                      tt = md->pair[S[s][1]][S[s][j]];+                      if(tt==0) tt=7;+                      energy += E_ExtLoop(tt, -1, -1, P);+                    }+                    f5[j] = MIN2(f5[j], energy);+                  }++                  if(md->gquad){+                    if(ggg[indx[j]+1] < INF)+                      f5[j] = MIN2(f5[j], ggg[indx[j]+1]);+                  }+                }++                for(i = j - turn - 1; i > 1; i--){+                  if(hard_constraints[indx[j]+i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                    if(c[indx[j]+i]<INF){+                      energy = f5[i-1] + c[indx[j]+i];+                      for(s = 0; s < n_seq; s++){+                        tt = md->pair[S[s][i]][S[s][j]];+                        if(tt==0) tt=7;+                        energy += E_ExtLoop(tt, -1, -1, P);+                      }+                      f5[j] = MIN2(f5[j], energy);+                    }++                    if(md->gquad){+                      if(ggg[indx[j]+i] < INF)+                        f5[j] = MIN2(f5[j], f5[i-1] + ggg[indx[j]+i]);+                    }+                  }+                }+              }+              break;++    default:  for(j = turn + 2; j <= length; j++){+                f5[j] = INF;++                if(hc->up_ext[j]){+                  energy = f5[j-1];+                  if((energy < INF) && sc)+                    for(s=0; s < n_seq; s++){+                      if(sc[s]){+                        if(sc[s]->energy_up)+                          energy += sc[s]->energy_up[a2s[s][j]][1];+                      }+                    }+                  f5[j] = MIN2(f5[j], energy);+                }++                if(hard_constraints[indx[j]+1] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                  if (c[indx[j]+1]<INF) {+                    energy = c[indx[j]+1];+                    for(s = 0; s < n_seq; s++){+                      tt = md->pair[S[s][1]][S[s][j]];+                      if(tt==0) tt=7;+                      energy += E_ExtLoop(tt, -1, (j<length) ? S3[s][j] : -1, P);+                    }+                    f5[j] = MIN2(f5[j], energy);+                  }++                  if(md->gquad){+                    if(ggg[indx[j]+1] < INF)+                      f5[j] = MIN2(f5[j], ggg[indx[j]+1]);+                  }+                }++                for(i = j - turn - 1; i > 1; i--){+                  if(hard_constraints[indx[j]+i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                    if (c[indx[j]+i]<INF) {+                      energy = f5[i-1] + c[indx[j]+i];+                      for(s = 0; s < n_seq; s++){+                        tt = md->pair[S[s][i]][S[s][j]];+                        if(tt==0) tt=7;+                        energy += E_ExtLoop(tt, S5[s][i], (j < length) ? S3[s][j] : -1, P);+                      }+                      f5[j] = MIN2(f5[j], energy);+                    }++                    if(md->gquad){+                      if(ggg[indx[j]+i] < INF)+                        f5[j] = MIN2(f5[j], f5[i-1] + ggg[indx[j]+i]);+                    }+                  }+                }+              }+              break;+  }+  free(type);+  free(cc);+  free(cc1);+  free(Fmi);+  free(DMLi);+  free(DMLi1);+  free(DMLi2);+  return(f5[length]);+}++#include "ViennaRNA/alicircfold.inc"++PUBLIC void+vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,+                              vrna_bp_stack_t *bp_stack,+                              sect bt_stack[],+                              int s){++  if(vc){+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:       backtrack(vc, bp_stack, bt_stack, s);+                                      break;++      case VRNA_FC_TYPE_COMPARATIVE:  backtrack_comparative(vc, bp_stack, bt_stack, s);+                                      break;+    }+  }+}++/**+*** trace back through the "c", "f5" and "fML" arrays to get the+*** base pairing list. No search for equivalent structures is done.+*** This is fast, since only few structure elements are recalculated.+***+*** normally s=0.+*** If s>0 then s items have been already pushed onto the bt_stack+**/+PRIVATE void+backtrack(vrna_fold_compound_t *vc,+          vrna_bp_stack_t *bp_stack,+          sect bt_stack[],+          int s){++  unsigned char   type;+  char            *string, *ptype, backtrack_type;+  int             i, j, ij, k, length, no_close, b, *my_c, *indx, noLP, noGUclosure;+  vrna_param_t    *P;++  b               = 0;+  length          = vc->length;+  my_c            = vc->matrices->c;+  indx            = vc->jindx;+  P               = vc->params;+  noLP            = P->model_details.noLP;+  noGUclosure     = P->model_details.noGUclosure;+  string          = vc->sequence;+  ptype           = vc->ptype;+  backtrack_type  = P->model_details.backtrack_type;++  if (s==0) {+    bt_stack[++s].i = 1;+    bt_stack[s].j = length;+    bt_stack[s].ml = (backtrack_type=='M') ? 1 : ((backtrack_type=='C')? 2: 0);+  }+  while (s>0) {+    int ml, cij;+    int canonical = 1;     /* (i,j) closes a canonical structure */++    /* pop one element from stack */+    i  = bt_stack[s].i;+    j  = bt_stack[s].j;+    ml = bt_stack[s--].ml;++    switch(ml){+      /* backtrack in f5 */+      case 0:   {+                  int p, q;+                  if(vrna_BT_ext_loop_f5(vc, &j, &p, &q, bp_stack, &b)){+                    if(j > 0){+                      bt_stack[++s].i = 1;+                      bt_stack[s].j   = j;+                      bt_stack[s].ml  = 0;+                    }+                    if(p > 0){+                      i = p;+                      j = q;+                      goto repeat1;+                    }++                    continue;+                  } else {+                    vrna_message_error("backtracking failed in f5 for sequence:\n%s\n", string);+                  }+                }+                break;++      /* trace back in fML array */+      case 1:   {+                  int p, q, comp1, comp2;+                  if(vrna_BT_mb_loop_split(vc, &i, &j, &p, &q, &comp1, &comp2, bp_stack, &b)){+                    if(i > 0){+                      bt_stack[++s].i = i;+                      bt_stack[s].j   = j;+                      bt_stack[s].ml  = comp1;+                    }+                    if(p > 0){+                      bt_stack[++s].i = p;+                      bt_stack[s].j   = q;+                      bt_stack[s].ml  = comp2;+                    }++                    continue;+                  } else {+                    vrna_message_error("backtracking failed in fML for sequence:\n%s\n", string);+                  }+                }+                break;++      /* backtrack in c */+      case 2:   bp_stack[++b].i = i;+                bp_stack[b].j   = j;+                goto repeat1;++      default:  vrna_message_error("Backtracking failed due to unrecognized DP matrix!");+                break;+    }++  repeat1:++    /*----- begin of "repeat:" -----*/+    ij = indx[j]+i;++    if (canonical)+      cij = my_c[ij];++    type = (unsigned char)ptype[ij];++    if (noLP)+      if(vrna_BT_stack(vc, &i, &j, &cij, bp_stack, &b)){+        canonical = 0;+        goto repeat1;+      }++    canonical = 1;++    no_close = (((type==3)||(type==4))&&noGUclosure);++    if (no_close) {+      if (cij == FORBIDDEN) continue;+    } else {+      if(vrna_BT_hp_loop(vc, i, j, cij, bp_stack, &b))+        continue;+    }++    if(vrna_BT_int_loop(vc, &i, &j, cij, bp_stack, &b)){+      if(i < 0)+        continue;+      else+        goto repeat1;+    }++    /* (i.j) must close a multi-loop */+    int comp1, comp2;++    if(vrna_BT_mb_loop(vc, &i, &j, &k, cij, &comp1, &comp2)){+      bt_stack[++s].i = i;+      bt_stack[s].j   = k;+      bt_stack[s].ml  = comp1;+      bt_stack[++s].i = k + 1;+      bt_stack[s].j   = j;+      bt_stack[s].ml  = comp2;+    } else {+      vrna_message_error("backtracking failed in repeat for sequence:\n%s\n", string);+    }++    /* end of repeat: --------------------------------------------------*/++  } /* end of infinite while loop */++  bp_stack[0].i = b;    /* save the total number of base pairs */+}+++/**+*** backtrack in the energy matrices to obtain a structure with MFE+**/+PRIVATE void+backtrack_comparative(vrna_fold_compound_t *vc,+                      vrna_bp_stack_t *bp_stack,+                      sect bt_stack[],+                      int s) {++  /*------------------------------------------------------------------+    trace back through the "c", "f5" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This inverts the folding procedure, hence it's very fast.+    ------------------------------------------------------------------*/+   /* normally s=0.+     If s>0 then s items have been already pushed onto the sector stack */++  unsigned short  **a2s;+  short           **S, **S5, **S3, *S_cons;+  int             i, j, k, p, q, turn, energy, en, c0, l1, minq, maxq,+                  type_2, tt, mm, b, cov_en, *type, n_seq, length, *indx,+                  *c, *f5, *fML, *pscore, *ggg, *rtype, dangle_model, with_gquad;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_hc_t       *hc;+  vrna_sc_t       **sc;++  n_seq         = vc->n_seq;+  length        = vc->length;+  S             = vc->S;+  S5            = vc->S5;     /*S5[s][i] holds next base 5' of i in sequence s*/+  S3            = vc->S3;     /*Sl[s][i] holds next base 3' of i in sequence s*/+  a2s           = vc->a2s;+  P             = vc->params;+  md            = &(P->model_details);+  indx          = vc->jindx;     /* index for moving in the triangle matrices c[] and fMl[]*/+  c             = vc->matrices->c;     /* energy array, given that i-j pair */+  f5            = vc->matrices->f5;     /* energy of 5' end */+  fML           = vc->matrices->fML;     /* multi-loop auxiliary energy array */+  pscore        = vc->pscore;     /* precomputed array of pair types */+  ggg           = vc->matrices->ggg;+  S_cons        = vc->S_cons;+  rtype         = &(md->rtype[0]);+  dangle_model  = md->dangles;+  with_gquad    = md->gquad;+  hc            = vc->hc;+  sc            = vc->scs;+  turn          = md->min_loop_size;+  b             = 0;+  cov_en        = 0;++  type  = (int *) vrna_alloc(n_seq*sizeof(int));++  if((turn < 0) || (turn > length))+    turn = length;++  if (s==0) {+    bt_stack[++s].i = 1;+    bt_stack[s].j = length;+    bt_stack[s].ml = (md->backtrack_type=='M') ? 1 : ((md->backtrack_type=='C')?2:0);+  }+  while (s>0) {+    int ss, ml, fij, fi, cij, traced, i1, j1, jj=0, gq=0;+    int canonical = 1;     /* (i,j) closes a canonical structure */+    i  = bt_stack[s].i;+    j  = bt_stack[s].j;+    ml = bt_stack[s--].ml;   /* ml is a flag indicating if backtracking is to+                              occur in the fML- (1) or in the f-array (0) */+    if (ml==2) {+      bp_stack[++b].i = i;+      bp_stack[b].j   = j;+      cov_en += pscore[indx[j]+i];+      goto repeat1_comparative;+    }++    if (j < i+turn+1) continue; /* no more pairs in this interval */++    if(ml != 0){+      fij = fML[indx[j]+i];+      fi  = (hc->up_ml[j]) ? fML[indx[j-1]+i] + n_seq*P->MLbase : INF;+    } else {+      fij = f5[j];+      fi  = (hc->up_ext[j]) ? f5[j-1] : INF;+    }++    if(sc)+      for(ss = 0; ss < n_seq; ss++)+        if(sc[ss]){+          if(sc[ss]->energy_up)+            fi += sc[ss]->energy_up[a2s[ss][j]][1];+        }++    if (fij == fi) {  /* 3' end is unpaired */+      bt_stack[++s].i = i;+      bt_stack[s].j   = j-1;+      bt_stack[s].ml  = ml;+      continue;+    }++    if (ml == 0) { /* backtrack in f5 */+      switch(dangle_model){+        case 0:   /* j or j-1 is paired. Find pairing partner */+                  for (i=j-turn-1,traced=0; i>=1; i--) {+                    int en;+                    jj = i-1;++                    if (hc->matrix[indx[j] + i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                      en = c[indx[j]+i] + f5[i-1];+                      for(ss = 0; ss < n_seq; ss++){+                        type[ss] = md->pair[S[ss][i]][S[ss][j]];+                        if (type[ss]==0) type[ss] = 7;+                        en += E_ExtLoop(type[ss], -1, -1, P);+                      }+                      if (fij == en) traced=j;+                    }++                    if(with_gquad){+                      if(fij == f5[i-1] + ggg[indx[j]+i]){+                        /* found the decomposition */+                        traced = j; jj = i - 1; gq = 1;+                        break;+                      }+                    }++                    if (traced) break;+                  }+                  break;+        default:  /* j or j-1 is paired. Find pairing partner */+                  for (i=j-turn-1,traced=0; i>=1; i--) {+                    int en;+                    jj = i-1;+                    if (hc->matrix[indx[j] + i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+                      en = c[indx[j]+i] + f5[i-1];+                      for(ss = 0; ss < n_seq; ss++){+                        type[ss] = md->pair[S[ss][i]][S[ss][j]];+                        if (type[ss]==0) type[ss] = 7;+                        en += E_ExtLoop(type[ss], (i>1) ? S5[ss][i]: -1, (j < length) ? S3[ss][j] : -1, P);+                      }+                      if (fij == en) traced=j;+                    }++                    if(with_gquad){+                      if(fij == f5[i-1] + ggg[indx[j]+i]){+                        /* found the decomposition */+                        traced = j; jj = i - 1; gq = 1;+                        break;+                      }+                    }++                    if (traced) break;+                  }+                  break;+      }++      if (!traced) vrna_message_error("backtrack failed in f5");+      /* push back the remaining f5 portion */+      bt_stack[++s].i = 1;+      bt_stack[s].j   = jj;+      bt_stack[s].ml  = ml;++      /* trace back the base pair found */+      j=traced;++      if(with_gquad && gq){+        /* goto backtrace of gquadruplex */+        goto repeat_gquad_comparative;+      }++      bp_stack[++b].i = i;+      bp_stack[b].j   = j;+      cov_en += pscore[indx[j]+i];+      goto repeat1_comparative;+    }+    else { /* trace back in fML array */+      if(hc->up_ml[i]){+        en = fML[indx[j]+i+1] + n_seq * P->MLbase;++        if(sc)+          for(ss = 0; ss < n_seq; ss++)+            if(sc[ss]){+              if(sc[ss]->energy_up)+                en += sc[ss]->energy_up[a2s[ss][i]][1];+            }++        if(en == fij) { /* 5' end is unpaired */+          bt_stack[++s].i = i+1;+          bt_stack[s].j   = j;+          bt_stack[s].ml  = ml;+          continue;+        }+      }++      if(md->gquad){+        if(fij == ggg[indx[j]+i] + n_seq * E_MLstem(0, -1, -1, P)){+          /* go to backtracing of quadruplex */+          goto repeat_gquad_comparative;+        }+      }++      if(hc->matrix[indx[j] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+        cij = c[indx[j]+i];+        if(dangle_model){+          for(ss = 0; ss < n_seq; ss++){+            tt = md->pair[S[ss][i]][S[ss][j]];+            if(tt==0) tt=7;+            cij += E_MLstem(tt, S5[ss][i], S3[ss][j], P);+          }+        }+        else{+          for(ss = 0; ss < n_seq; ss++){+            tt = md->pair[S[ss][i]][S[ss][j]];+            if(tt==0) tt=7;+            cij += E_MLstem(tt, -1, -1, P);+          }+        }++        if (fij==cij){+          /* found a pair */+          bp_stack[++b].i = i;+          bp_stack[b].j   = j;+          cov_en += pscore[indx[j]+i];+          goto repeat1_comparative;+        }+      }++      for (k = i+1+turn; k <= j-2-turn; k++)+        if (fij == (fML[indx[k]+i]+fML[indx[j]+k+1]))+          break;++      bt_stack[++s].i = i;+      bt_stack[s].j   = k;+      bt_stack[s].ml  = ml;+      bt_stack[++s].i = k+1;+      bt_stack[s].j   = j;+      bt_stack[s].ml  = ml;++      if (k>j-2-turn) vrna_message_error("backtrack failed in fML");+      continue;+    }++  repeat1_comparative:++    /*----- begin of "repeat:" -----*/+    if (canonical)  cij = c[indx[j]+i];++    for (ss=0; ss<n_seq; ss++) {+      type[ss] = md->pair[S[ss][i]][S[ss][j]];+      if (type[ss]==0) type[ss] = 7;+    }++    if (md->noLP)+      if (cij == c[indx[j]+i]) {+        /* (i.j) closes canonical structures, thus+           (i+1.j-1) must be a pair                */+        for (ss=0; ss<n_seq; ss++) {+          type_2 = md->pair[S[ss][j-1]][S[ss][i+1]];  /* j,i not i,j */+          if (type_2==0) type_2 = 7;+          cij -= P->stack[type[ss]][type_2];+          if(sc){+            if(sc[ss]->energy_bp)+              cij -= sc[s]->energy_bp[indx[j] + i];+          }+        }+        cij += pscore[indx[j]+i];+        bp_stack[++b].i = i+1;+        bp_stack[b].j   = j-1;+        cov_en += pscore[indx[j-1]+i+1];+        i++; j--;+        canonical=0;+        goto repeat1_comparative;+      }+    canonical = 1;+    cij += pscore[indx[j]+i];++    /* does (i,j) close a hairpin loop ? */+    if(vrna_BT_hp_loop(vc, i, j, cij, bp_stack, &b))+      continue;++    for (p = i+1; p <= MIN2(j-2-turn,i+MAXLOOP+1); p++) {+      minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+turn) minq = p+1+turn;+      if(hc->up_int[i+1] < (p - i - 1)) break;++      for (q = j-1; q >= minq; q--) {++        if(hc->up_int[q+1] < (j - q - 1)) break;++        if (c[indx[q]+p]>=INF) continue;++        for (ss=energy=0; ss<n_seq; ss++) {+          int u1 = a2s[ss][p-1] - a2s[ss][i];+          int u2 = a2s[ss][j-1] - a2s[ss][q];+          type_2 = md->pair[S[ss][q]][S[ss][p]];  /* q,p not p,q */+          if (type_2==0) type_2 = 7;+          energy += E_IntLoop(u1, u2, type[ss], type_2, S3[ss][i], S5[ss][j], S5[ss][p], S3[ss][q], P);++        }++        if(sc)+          for(ss = 0; ss < n_seq; ss++)+            if(sc[ss]){+              int u1 = a2s[ss][p-1] - a2s[ss][i];+              int u2 = a2s[ss][j-1] - a2s[ss][q];+/*+              int u1 = p - i - 1;+              int u2 = j - q - 1;+*/+              if(u1 + u2 == 0)+                if(sc[ss]->energy_stack){+                  if(S[ss][i] && S[ss][j] && S[ss][p] && S[ss][q]){ /* don't allow gaps in stack */+                    energy +=   sc[ss]->energy_stack[a2s[ss][i]]+                              + sc[ss]->energy_stack[a2s[ss][p]]+                              + sc[ss]->energy_stack[a2s[ss][q]]+                              + sc[ss]->energy_stack[a2s[ss][j]];+                  }+                }+              if(sc[ss]->energy_bp)+                energy += sc[ss]->energy_bp[indx[j] + i];++              if(sc[ss]->energy_up)+                energy +=   sc[ss]->energy_up[a2s[ss][i] + 1][u1]+                          + sc[ss]->energy_up[a2s[ss][q] + 1][u2];+            }++        traced = (cij == energy+c[indx[q]+p]);+        if (traced) {+          bp_stack[++b].i = p;+          bp_stack[b].j   = q;+          cov_en += pscore[indx[q]+p];+          i = p, j = q;+          goto repeat1_comparative;+        }+      }+    }++    /* end of repeat: --------------------------------------------------*/++    /* (i.j) must close a multi-loop */++    i1 = i+1;+    j1 = j-1;++    if(with_gquad){+      /*+        The case that is handled here actually resembles something like+        an interior loop where the enclosing base pair is of regular+        kind and the enclosed pair is not a canonical one but a g-quadruplex+        that should then be decomposed further...+      */+      mm = 0;+      for(ss=0;ss<n_seq;ss++){+        tt = type[ss];+        if(tt == 0) tt = 7;+        if(dangle_model == 2)+          mm += P->mismatchI[tt][S3[ss][i]][S5[ss][j]];+        if(tt > 2)+          mm += P->TerminalAU;+      }++      for(p = i + 2;+        p < j - VRNA_GQUAD_MIN_BOX_SIZE;+        p++){+        if(S_cons[p] != 3) continue;+        l1    = p - i - 1;+        if(l1>MAXLOOP) break;+        minq  = j - i + p - MAXLOOP - 2;+        c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+        minq  = MAX2(c0, minq);+        c0    = j - 1;+        maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+        maxq  = MIN2(c0, maxq);+        for(q = minq; q < maxq; q++){+          if(S_cons[q] != 3) continue;+          c0  = mm + ggg[indx[q] + p] + n_seq * P->internal_loop[l1 + j - q - 1];+          if(cij == c0){+            i=p;j=q;+            goto repeat_gquad_comparative;+          }+        }+      }+      p = i1;+      if(S_cons[p] == 3){+        if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){+          minq  = j - i + p - MAXLOOP - 2;+          c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;+          minq  = MAX2(c0, minq);+          c0    = j - 3;+          maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;+          maxq  = MIN2(c0, maxq);+          for(q = minq; q < maxq; q++){+            if(S_cons[q] != 3) continue;+            if(cij == mm + ggg[indx[q] + p] + n_seq * P->internal_loop[j - q - 1]){+              i = p; j=q;+              goto repeat_gquad_comparative;+            }+          }+        }+      }+      q = j1;+      if(S_cons[q] == 3)+        for(p = i1 + 3; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++){+          l1    = p - i - 1;+          if(l1>MAXLOOP) break;+          if(S_cons[p] != 3) continue;+          if(cij == mm + ggg[indx[q] + p] + n_seq * P->internal_loop[l1]){+            i = p; j = q;+            goto repeat_gquad_comparative;+          }+        }+    }++    if(hc->matrix[indx[j] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+      mm = n_seq*P->MLclosing;+      switch(dangle_model){+        case 0:   for(ss = 0; ss < n_seq; ss++){+                    tt = rtype[type[ss]];+                    mm += E_MLstem(tt, -1, -1, P);+                  }+                  break;+        default:  for(ss = 0; ss < n_seq; ss++){+                    tt = rtype[type[ss]];+                    mm += E_MLstem(tt, S5[ss][j], S3[ss][i], P);+                  }+                  break;+      }++      if(sc)+        for(ss = 0; ss < n_seq; ss++)+          if(sc[ss]){+            if(sc[ss]->energy_bp)+              mm += sc[ss]->energy_bp[indx[j] + i];+          }++      bt_stack[s+1].ml  = bt_stack[s+2].ml = 1;++      for (k = i1+turn+1; k < j1-turn-1; k++){+        if(cij == fML[indx[k]+i1] + fML[indx[j1]+k+1] + mm) break;+      }++      if (k<=j-3-turn) { /* found the decomposition */+        bt_stack[++s].i = i1;+        bt_stack[s].j   = k;+        bt_stack[++s].i = k+1;+        bt_stack[s].j   = j1;+      } else {+          vrna_message_error("backtracking failed in repeat");+      }+    } else+      vrna_message_error("backtracking failed in repeat");++    continue; /* this is a workarround to not accidentally proceed in the following block */++  repeat_gquad_comparative:+    /*+      now we do some fancy stuff to backtrace the stacksize and linker lengths+      of the g-quadruplex that should reside within position i,j+    */+    {+      int cnt1, l[3], L, size;+      size = j-i+1;++      for(L=0; L < VRNA_GQUAD_MIN_STACK_SIZE;L++){+        if(S_cons[i+L] != 3) break;+        if(S_cons[j-L] != 3) break;+      }++      if(L == VRNA_GQUAD_MIN_STACK_SIZE){+        /* continue only if minimum stack size starting from i is possible */+        for(; L<=VRNA_GQUAD_MAX_STACK_SIZE;L++){+          if(S_cons[i+L-1] != 3) break; /* break if no more consecutive G's 5' */+          if(S_cons[j-L+1] != 3) break; /* break if no more consecutive G'1 3' */+          for(    l[0] = VRNA_GQUAD_MIN_LINKER_LENGTH;+                  (l[0] <= VRNA_GQUAD_MAX_LINKER_LENGTH)+              &&  (size - 4*L - 2*VRNA_GQUAD_MIN_LINKER_LENGTH - l[0] >= 0);+              l[0]++){+            /* check whether we find the second stretch of consecutive G's */+            for(cnt1 = 0; (cnt1 < L) && (S_cons[i+L+l[0]+cnt1] == 3); cnt1++);+            if(cnt1 < L) continue;+            for(    l[1] = VRNA_GQUAD_MIN_LINKER_LENGTH;+                    (l[1] <= VRNA_GQUAD_MAX_LINKER_LENGTH)+                &&  (size - 4*L - VRNA_GQUAD_MIN_LINKER_LENGTH - l[0] - l[1] >= 0);+                l[1]++){+              /* check whether we find the third stretch of consectutive G's */+              for(cnt1 = 0; (cnt1 < L) && (S_cons[i+2*L+l[0]+l[1]+cnt1] == 3); cnt1++);+              if(cnt1 < L) continue;++              /*+                the length of the third linker now depends on position j as well+                as the other linker lengths... so we do not have to loop too much+              */+              l[2] = size - 4*L - l[0] - l[1];+              if(l[2] < VRNA_GQUAD_MIN_LINKER_LENGTH) break;+              if(l[2] > VRNA_GQUAD_MAX_LINKER_LENGTH) continue;+              /* check for contribution */+              if(ggg[indx[j]+i] == E_gquad_ali(i, L, l, (const short **)S, n_seq, P)){+                int a;+                /* fill the G's of the quadruplex into base pair stack */+                for(a=0;a<L;a++){+                  bp_stack[++b].i = i+a;+                  bp_stack[b].j   = i+a;+                  bp_stack[++b].i = i+L+l[0]+a;+                  bp_stack[b].j   = i+L+l[0]+a;+                  bp_stack[++b].i = i+L+l[0]+L+l[1]+a;+                  bp_stack[b].j   = i+L+l[0]+L+l[1]+a;+                  bp_stack[++b].i = i+L+l[0]+L+l[1]+L+l[2]+a;+                  bp_stack[b].j   = i+L+l[0]+L+l[1]+L+l[2]+a;+                }+                goto repeat_gquad_comparative_exit;+              }+            }+          }+        }+      }+      vrna_message_error("backtracking failed in repeat_gquad_comparative");+    }+  repeat_gquad_comparative_exit:+    __asm("nop");++  }++  bp_stack[0].i = b;    /* save the total number of base pairs */+  free(type);+}+
+ C/ViennaRNA/mfe.h view
@@ -0,0 +1,119 @@+#ifndef VIENNA_RNA_PACKAGE_MFE_H+#define VIENNA_RNA_PACKAGE_MFE_H++#include <stdio.h>+#include <ViennaRNA/data_structures.h>++/**+ *  @brief Compute minimum free energy and an appropriate secondary+ *  structure of an RNA sequence, or RNA sequence alignment+ *+ *  Depending on the type of the provided #vrna_fold_compound_t, this function+ *  predicts the MFE for a single sequence, or a corresponding averaged MFE for+ *  a sequence alignment. If backtracking is activated, it also constructs the+ *  corresponding secondary structure, or consensus structure.+ *  Therefore, the second parameter, @a structure, has to point to an allocated+ *  block of memory with a size of at least @f$\mathrm{strlen}(\mathrm{sequence})+1@f$ to+ *  store the backtracked MFE structure. (For consensus structures, this is the length of+ *  the alignment + 1. If @p NULL is passed, no backtracking will be performed.+ *+ *  @ingroup mfe_fold+ *+ *  @note This function is polymorphic. It accepts #vrna_fold_compound_t of type+ *        #VRNA_FC_TYPE_SINGLE, and #VRNA_FC_TYPE_COMPARATIVE.+ *+ *  @see #vrna_fold_compound_t, vrna_fold_compound(), vrna_fold(), vrna_circfold(),+ *        vrna_fold_compound_comparative(), vrna_alifold(), vrna_circalifold()+ *+ *  @param vc             fold compound+ *  @param structure      A pointer to the character array where the+ *                        secondary structure in dot-bracket notation will be written to (Maybe NULL)+ *+ *  @return the minimum free energy (MFE) in kcal/mol+ */+float+vrna_mfe(vrna_fold_compound_t *vc,+          char *structure);++/**+ *  @brief Compute the minimum free energy of two interacting RNA molecules+ *+ *  The code is analog to the vrna_mfe() function.+ *+ *  @ingroup mfe_cofold+ *+ *  @param    vc  fold compound+ *  @param    structure Will hold the barcket dot structure of the dimer molecule+ *  @return   minimum free energy of the structure+ */+float vrna_mfe_dimer( vrna_fold_compound_t *vc,+                      char *structure);++/**+ *  @brief Local MFE prediction using a sliding window approach.+ *+ *  Computes minimum free energy structures using a sliding window+ *  approach, where base pairs may not span outside the window.+ *  In contrast to vrna_mfe(), where a maximum base pair span+ *  may be set using the #vrna_md_t.max_bp_span attribute and one+ *  globally optimal structure is predicted, this function uses a+ *  sliding window to retrieve all locally optimal structures within+ *  each window.+ *  The size of the sliding window is set in the #vrna_md_t.window_size+ *  attribute, prior to the retrieval of the #vrna_fold_compound_t+ *  using vrna_fold_compound() with option #VRNA_OPTION_WINDOW+ *+ *  The predicted structures are written on-the-fly, either to+ *  stdout, if a NULL pointer is passed as file parameter, or to+ *  the corresponding filehandle.+ *+ *  @ingroup local_mfe_fold+ * + *  @see  vrna_fold_compound(), vrna_mfe_window_zscore(), vrna_mfe(),+ *        vrna_Lfold(), vrna_Lfoldz(),+ *        #VRNA_OPTION_WINDOW, #vrna_md_t.max_bp_span, #vrna_md_t.window_size+ *+ *  @param  vc        The #vrna_fold_compound_t with preallocated memory for the DP matrices+ *  @param  file      The output file handle where predictions are written to (maybe NULL)+ */+float vrna_mfe_window( vrna_fold_compound_t *vc, FILE *file);++#ifdef USE_SVM+/**+ *  @brief Local MFE prediction using a sliding window approach (with z-score cut-off)+ *+ *  Computes minimum free energy structures using a sliding window+ *  approach, where base pairs may not span outside the window.+ *  This function is the z-score version of vrna_mfe_window(), i.e.+ *  only predictions above a certain z-score cut-off value are+ *  printed.+ *  As for vrna_mfe_window(), the size of the sliding window is set in+ *  the #vrna_md_t.window_size attribute, prior to the retrieval of+ *  the #vrna_fold_compound_t using vrna_fold_compound() with option+ *  #VRNA_OPTION_WINDOW.+ *+ *  The predicted structures are written on-the-fly, either to+ *  stdout, if a NULL pointer is passed as file parameter, or to+ *  the corresponding filehandle.+ *+ *  @ingroup local_mfe_fold+ * + *  @see  vrna_fold_compound(), vrna_mfe_window_zscore(), vrna_mfe(),+ *        vrna_Lfold(), vrna_Lfoldz(),+ *        #VRNA_OPTION_WINDOW, #vrna_md_t.max_bp_span, #vrna_md_t.window_size+ *+ *  @param  vc        The #vrna_fold_compound_t with preallocated memory for the DP matrices+ *  @param  min_z     The minimal z-score for a predicted structure to appear in the output+ *  @param  file      The output file handle where predictions are written to (maybe NULL)+ */+float vrna_mfe_window_zscore(vrna_fold_compound_t *vc, double min_z, FILE *file);+#endif++void+vrna_backtrack_from_intervals(vrna_fold_compound_t *vc,+                              vrna_bp_stack_t *bp_stack,+                              sect bt_stack[],+                              int s);+++#endif
+ C/ViennaRNA/mm.c view
@@ -0,0 +1,103 @@+/*+      Implementation of Nussinov Maximum Matching+      Ronny Lorenz+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"++/* the encoded string MUST have the length of the sequence at position 0!!! */+PUBLIC unsigned int maximumMatching(const char *string){+  unsigned int i, j, l, length, max = 0;+  unsigned int *mm;            /* holds maximum matching on subsequence [i,j] */+  short *encodedString = encode_sequence(string, 0);+  int *iindx = vrna_idx_row_wise((unsigned) encodedString[0]);+  make_pair_matrix();+  length = (unsigned int)encodedString[0];+  mm = (unsigned int *) vrna_alloc(sizeof(unsigned int)*((length*(length+1))/2+2));+  for(j = 1; j<=length; j++)+    for(i=(j>TURN?(j-TURN):1); i<j; i++)+      mm[iindx[i]-j] = 0;+  for(i=length-TURN-1;i>0; i--)+    for(j=i+TURN+1; j<= length; j++){+      max = mm[iindx[i]-j+1];+      for(l=j-TURN-1; l>=i; l--)+        if(pair[encodedString[l]][encodedString[j]])+          max = MAX2(max, ((l>i) ? mm[iindx[i]-l+1] : 0) + 1 + mm[iindx[l+1]-j+1]);+       mm[iindx[i]-j] = max;+    }+  max = mm[iindx[1]-length];+  free(mm);+  free(iindx);+  free(encodedString);+  return max;+}++/* the encoded string MUST have the length of the sequence at position 0!!! */+PUBLIC unsigned int *maximumMatchingConstraint(const char *string, short *ptable){+  unsigned int i, j, l, length, max = 0;+  unsigned int *mm;            /* holds maximum matching on subsequence [i,j] */+  short *encodedString = encode_sequence(string, 0);+  int *iindx = vrna_idx_row_wise((unsigned) encodedString[0]);+  make_pair_matrix();+  length = (unsigned int)encodedString[0];+  mm = (unsigned int *) vrna_alloc(sizeof(unsigned int)*((length*(length+1))/2+2));+  for(j = 1; j<=length; j++)+    for(i=(j>TURN?(j-TURN):1); i<j; i++)+      mm[iindx[i]-j] = 0;+  for(i=length-TURN-1;i>0; i--)+    for(j=i+TURN+1; j<= length; j++){+      max = mm[iindx[i]-j+1];+      for(l=j-TURN-1; l>=i; l--){+        if(pair[encodedString[l]][encodedString[j]]){+          if(ptable[l] != j)+            max = MAX2(max, ((l>i) ? mm[iindx[i]-l+1] : 0) + 1 + mm[iindx[l+1]-j+1]);+        }+      }+      mm[iindx[i]-j] = max;+    }+  free(iindx);+  free(encodedString);+  return mm;+}++/* the encoded string MUST have the length of the sequence at position 0!!! */+PUBLIC unsigned int *maximumMatching2Constraint(const char *string, short *ptable, short *ptable2){+  unsigned int i, j, l, length, max = 0;+  unsigned int *mm;            /* holds maximum matching on subsequence [i,j] */+  short *encodedString = encode_sequence(string, 0);+  int *iindx = vrna_idx_row_wise((unsigned) encodedString[0]);+  make_pair_matrix();+  length = (unsigned int)encodedString[0];+  mm = (unsigned int *) vrna_alloc(sizeof(unsigned int)*((length*(length+1))/2+2));+  for(j = 1; j<=length; j++)+    for(i=(j>TURN?(j-TURN):1); i<j; i++)+      mm[iindx[i]-j] = 0;+  for(i=length-TURN-1;i>0; i--)+    for(j=i+TURN+1; j<= length; j++){+      max = mm[iindx[i]-j+1];+      for(l=j-TURN-1; l>=i; l--){+        if(pair[encodedString[l]][encodedString[j]]){+          if(ptable[l] != j && ptable2[l] != j)+            max = MAX2(max, ((l>i) ? mm[iindx[i]-l+1] : 0) + 1 + mm[iindx[l+1]-j+1]);+        }+      }+      mm[iindx[i]-j] = max;+    }+  free(iindx);+  free(encodedString);+  return mm;+}+
+ C/ViennaRNA/mm.h view
@@ -0,0 +1,23 @@+#ifndef VIENNA_RNA_PACKAGE_MM_H+#define VIENNA_RNA_PACKAGE_MM_H++/**+ *+ *  @file mm.h+ *  @ingroup subopt_and_representatives+ *  @brief Several Maximum Matching implementations+ *+ *  This file contains the declarations for several maximum matching implementations+ */+++unsigned int  maximumMatching(const char *string);++unsigned int *maximumMatchingConstraint(const char *string,+                                        short *ptable);++unsigned int *maximumMatching2Constraint( const char *string,+                                          short *ptable,+                                          short *ptable2);++#endif
+ C/ViennaRNA/model.c view
@@ -0,0 +1,908 @@+/*+                  Model Details structure creation/modification/destruction++                  This file contains everything which is necessary to+                  obtain, modify, and destroy the model_details datastructure+                  used in the folding recurrences throughout the ViennaRNA+                  Package++                  c Ronny Lorenx++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <limits.h>++#include "ViennaRNA/energy_const.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/model.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++/*  below are the evil global variables that will vanish+    as soon as we drop backward compatibility in ViennaRNA+    Package v3+*/++double  temperature     = VRNA_MODEL_DEFAULT_TEMPERATURE;+double  pf_scale        = VRNA_MODEL_DEFAULT_PF_SCALE;+int     dangles         = VRNA_MODEL_DEFAULT_DANGLES;+int     tetra_loop      = VRNA_MODEL_DEFAULT_SPECIAL_HP;+int     noLonelyPairs   = VRNA_MODEL_DEFAULT_NO_LP;+int     noGU            = VRNA_MODEL_DEFAULT_NO_GU;+int     no_closingGU    = VRNA_MODEL_DEFAULT_NO_GU_CLOSURE;+int     circ            = VRNA_MODEL_DEFAULT_CIRC;+int     gquad           = VRNA_MODEL_DEFAULT_GQUAD;+int     canonicalBPonly = VRNA_MODEL_DEFAULT_CANONICAL_BP;+int     uniq_ML         = VRNA_MODEL_DEFAULT_UNIQ_ML;+int     energy_set      = VRNA_MODEL_DEFAULT_ENERGY_SET;+int     do_backtrack    = VRNA_MODEL_DEFAULT_COMPUTE_BPP;+char    backtrack_type  = VRNA_MODEL_DEFAULT_BACKTRACK_TYPE;+char    *nonstandards   = NULL;+int     max_bp_span     = VRNA_MODEL_DEFAULT_MAX_BP_SPAN;+int     oldAliEn        = VRNA_MODEL_DEFAULT_ALI_OLD_EN;+int     ribo            = VRNA_MODEL_DEFAULT_ALI_RIBO;+double  cv_fact         = VRNA_MODEL_DEFAULT_ALI_CV_FACT;+double  nc_fact         = VRNA_MODEL_DEFAULT_ALI_NC_FACT;+int     logML           = VRNA_MODEL_DEFAULT_LOG_ML;++/* below are some more deprecated global symbols we need to get rid off */++int         james_rule = 1;       /* interior loops of size 2 get energy 0.8Kcal and+                                    no mismatches (no longer used) */+char        *RibosumFile = NULL;  /* TODO: compile ribosums into program+                                    Warning: this variable will vanish */+int         csv = 0;              /*generate comma seperated output*/+vrna_bp_stack_t       *base_pair = NULL;+FLT_OR_DBL  *pr = NULL;           /* base pairing prob. matrix */+int         *iindx = NULL;        /* pr[i,j] -> pr[iindx[i]-j] */+int         fold_constrained = 0; /* fold with constraints */++#endif++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};+PRIVATE int BP_pair[NBASES][NBASES]=+/* _  A  C  G  U  X  K  I */+{{ 0, 0, 0, 0, 0, 0, 0, 0},+ { 0, 0, 0, 0, 5, 0, 0, 5},+ { 0, 0, 0, 1, 0, 0, 0, 0},+ { 0, 0, 2, 0, 3, 0, 0, 0},+ { 0, 6, 0, 4, 0, 0, 0, 6},+ { 0, 0, 0, 0, 0, 0, 2, 0},+ { 0, 0, 0, 0, 0, 1, 0, 0},+ { 0, 6, 0, 0, 5, 0, 0, 0}};++PRIVATE vrna_md_t defaults = {+  VRNA_MODEL_DEFAULT_TEMPERATURE,+  1.,+  VRNA_MODEL_DEFAULT_DANGLES,+  VRNA_MODEL_DEFAULT_SPECIAL_HP,+  VRNA_MODEL_DEFAULT_NO_LP,+  VRNA_MODEL_DEFAULT_NO_GU,+  VRNA_MODEL_DEFAULT_NO_GU_CLOSURE,+  VRNA_MODEL_DEFAULT_LOG_ML,+  VRNA_MODEL_DEFAULT_CIRC,+  VRNA_MODEL_DEFAULT_GQUAD,+  VRNA_MODEL_DEFAULT_CANONICAL_BP,+  VRNA_MODEL_DEFAULT_UNIQ_ML,+  VRNA_MODEL_DEFAULT_ENERGY_SET,+  VRNA_MODEL_DEFAULT_BACKTRACK,+  VRNA_MODEL_DEFAULT_BACKTRACK_TYPE,+  VRNA_MODEL_DEFAULT_COMPUTE_BPP,+  {0},+  VRNA_MODEL_DEFAULT_MAX_BP_SPAN,+  TURN,+  VRNA_MODEL_DEFAULT_WINDOW_SIZE,+  VRNA_MODEL_DEFAULT_ALI_OLD_EN,+  VRNA_MODEL_DEFAULT_ALI_RIBO,+  VRNA_MODEL_DEFAULT_ALI_CV_FACT,+  VRNA_MODEL_DEFAULT_ALI_NC_FACT,+  1.07,+  {0, 2, 1, 4, 3, 6, 5, 7},+  {0, 1, 2, 3, 4, 3, 2, 0},+  {+    { 0, 0, 0, 0, 0, 0, 0, 0},+    { 0, 0, 0, 0, 5, 0, 0, 5},+    { 0, 0, 0, 1, 0, 0, 0, 0},+    { 0, 0, 2, 0, 3, 0, 0, 0},+    { 0, 6, 0, 4, 0, 0, 0, 6},+    { 0, 0, 0, 0, 0, 0, 2, 0},+    { 0, 0, 0, 0, 0, 1, 0, 0},+    { 0, 6, 0, 0, 5, 0, 0, 0}+  }+};++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++/* Fill the base pair type encodings according to the model details */+PRIVATE void fill_pair_matrices(vrna_md_t *md);+PRIVATE void copy_nonstandards(vrna_md_t *md, const char *ns);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC vrna_md_t *+vrna_md_copy( vrna_md_t       *md_to,+              const vrna_md_t *md_from){++  int i;+  vrna_md_t *md;++  md = NULL;++  /* only process if md_from is non-NULL */+  if(md_from){+    if(!md_to){+      /* create container to be filled */+      md = (vrna_md_t *)vrna_alloc(sizeof(vrna_md_t));+    } else {+      /* or directly write to target */+      md = md_to;+    }++    /* check if not the same object */+    if(md_to != md_from){+      /* copy simple members */+      memcpy(md, md_from, sizeof(vrna_md_t));+      /* copy arrays */+      memcpy(md->rtype, &(md_from->rtype[0]), 8 * sizeof(int));+      memcpy(md->alias, &(md_from->alias[0]), (MAXALPHA + 1) * sizeof(short));+      memcpy(md->nonstandards, &(md_from->nonstandards[0]), 64 * sizeof(char));+      /* copy matrices */+      for(i = 0; i <= MAXALPHA; i++){+        memcpy(md->pair[i], (md_from->pair[i]), (MAXALPHA + 1) * sizeof(int));+      }+    }+  }++  return md;+}++PUBLIC void+vrna_md_set_default(vrna_md_t *md){++  if(md) /* copy defaults */+    vrna_md_copy(md, &defaults);+}++PUBLIC char *+vrna_md_option_string(vrna_md_t  *md){+  static char options[255];+  *options = '\0';++  if(md){+    if(md->dangles != VRNA_MODEL_DEFAULT_DANGLES)+      sprintf(options + strlen(options), "-d%d ", md->dangles);+    if(!md->special_hp)+      strcat(options, "-4 ");+    if(md->noLP)+      strcat(options, "--noLP ");+    if(md->noGU)+      strcat(options, "--noGU ");+    if(md->noGUclosure)+      strcat(options, "--noClosingGU ");+    if(md->temperature != VRNA_MODEL_DEFAULT_TEMPERATURE)+      sprintf(options + strlen(options), "-T %f ", md->temperature);+  }++  return options;+}++PRIVATE void+copy_nonstandards(vrna_md_t *md, const char *ns){++  unsigned int n = strlen(ns);+  if(n < 64){+    memcpy(md->nonstandards, ns, strlen(ns)*sizeof(char));+    md->nonstandards[n] = '\0';+  }+}++PUBLIC void+vrna_md_set_nonstandards(vrna_md_t *md, const char *ns_bases){++  const char    *c;+  unsigned int  n;+  int           i, sym;++  if(md){+    if(ns_bases){+      n = strlen(ns_bases);+      if(n < 33){ /* parse the ns_bases list */+        c = ns_bases;+        i = sym = 0;+        if(*c == '-'){+          sym=1;+          c++;+        }++        while(*c != '\0'){+          if(*c != ','){+            md->nonstandards[i++] = *c++;+            md->nonstandards[i++] = *c;+            if((sym) && (*c != *(c-1))){+              md->nonstandards[i++] = *c;+              md->nonstandards[i++] = *(c-1);+            }+          }+          c++;+        }+        md->nonstandards[i] = '\0';++#ifdef  VRNA_BACKWARD_COMPAT+        free(nonstandards);+        nonstandards = vrna_alloc(33);+        memcpy(nonstandards, &(md->nonstandards[0]), 33*sizeof(char));+#endif+      } else {+        vrna_message_warning("vrna_md_set_nonstandards: list too long, dropping nonstandards!");+      }+    } else { /* remove nonstandards */+      md->nonstandards[0] = '\0';+#ifdef  VRNA_BACKWARD_COMPAT+      free(nonstandards);+      nonstandards = NULL;+#endif+    }++    /* update pair/rtype/alias arrays accordingly */+    vrna_md_update(md);+  }+}++PUBLIC void+vrna_md_defaults_reset(vrna_md_t *md_p){++  int i = 0;++  /* first, reset to factory defaults */+  defaults.dangles           = VRNA_MODEL_DEFAULT_DANGLES;+  defaults.special_hp        = VRNA_MODEL_DEFAULT_SPECIAL_HP;+  defaults.noLP              = VRNA_MODEL_DEFAULT_NO_LP;+  defaults.noGU              = VRNA_MODEL_DEFAULT_NO_GU;+  defaults.noGUclosure       = VRNA_MODEL_DEFAULT_NO_GU_CLOSURE;+  defaults.logML             = VRNA_MODEL_DEFAULT_LOG_ML;+  defaults.gquad             = VRNA_MODEL_DEFAULT_GQUAD;+  defaults.canonicalBPonly   = VRNA_MODEL_DEFAULT_CANONICAL_BP;+  defaults.circ              = VRNA_MODEL_DEFAULT_CIRC;+  defaults.uniq_ML           = VRNA_MODEL_DEFAULT_UNIQ_ML;+  defaults.compute_bpp       = VRNA_MODEL_DEFAULT_COMPUTE_BPP;+  defaults.backtrack         = VRNA_MODEL_DEFAULT_BACKTRACK;+  defaults.backtrack_type    = VRNA_MODEL_DEFAULT_BACKTRACK_TYPE;+  defaults.energy_set        = VRNA_MODEL_DEFAULT_ENERGY_SET;+  defaults.max_bp_span       = VRNA_MODEL_DEFAULT_MAX_BP_SPAN;+  defaults.min_loop_size     = TURN;+  defaults.window_size       = VRNA_MODEL_DEFAULT_WINDOW_SIZE;+  defaults.oldAliEn          = VRNA_MODEL_DEFAULT_ALI_OLD_EN;+  defaults.ribo              = VRNA_MODEL_DEFAULT_ALI_RIBO;+  defaults.cv_fact           = VRNA_MODEL_DEFAULT_ALI_CV_FACT;+  defaults.nc_fact           = VRNA_MODEL_DEFAULT_ALI_NC_FACT;+  defaults.temperature       = VRNA_MODEL_DEFAULT_TEMPERATURE;+  defaults.betaScale         = VRNA_MODEL_DEFAULT_BETA_SCALE;+  defaults.sfact             = 1.07;+  defaults.nonstandards[0]   = '\0';++  if(md_p){ /* now try to apply user settings */+    /*+        Note that we use wrapper functions here instead of+        faster direct memory copy because we want to ensure+        that model settings always comply to the constraints+        we set in the wrappers+    */+    vrna_md_defaults_dangles(md_p->dangles);+    vrna_md_defaults_special_hp(md_p->special_hp);+    vrna_md_defaults_noLP(md_p->noLP);+    vrna_md_defaults_noGU(md_p->noGU);+    vrna_md_defaults_noGUclosure(md_p->noGUclosure);+    vrna_md_defaults_logML(md_p->logML);+    vrna_md_defaults_gquad(md_p->gquad);+    defaults.canonicalBPonly = md_p->canonicalBPonly;+    vrna_md_defaults_circ(md_p->circ);+    vrna_md_defaults_uniq_ML(md_p->uniq_ML);+    vrna_md_defaults_compute_bpp(md_p->compute_bpp);+    vrna_md_defaults_backtrack(md_p->backtrack);+    vrna_md_defaults_backtrack_type(md_p->backtrack_type);+    vrna_md_defaults_energy_set(md_p->energy_set);+    vrna_md_defaults_max_bp_span(md_p->max_bp_span);+    vrna_md_defaults_min_loop_size(md_p->min_loop_size);+    vrna_md_defaults_window_size(md_p->window_size);+    vrna_md_defaults_oldAliEn(md_p->oldAliEn);+    vrna_md_defaults_ribo(md_p->ribo);+    vrna_md_defaults_cv_fact(md_p->cv_fact);+    vrna_md_defaults_nc_fact(md_p->nc_fact);+    vrna_md_defaults_temperature(md_p->temperature);+    vrna_md_defaults_betaScale(md_p->betaScale);+    vrna_md_defaults_sfact(md_p->sfact);+    copy_nonstandards(&defaults, &(md_p->nonstandards[0]));+  }++  /* update pair/rtype/alias arrays accordingly */+  vrna_md_update(&defaults);++#ifdef  VRNA_BACKWARD_COMPAT+  temperature     = defaults.temperature;+  pf_scale        = VRNA_MODEL_DEFAULT_PF_SCALE;+  dangles         = defaults.dangles;+  tetra_loop      = defaults.special_hp;+  noLonelyPairs   = defaults.noLP;+  noGU            = defaults.noGU;+  no_closingGU    = defaults.noGUclosure;+  circ            = defaults.circ;+  gquad           = defaults.gquad;+  canonicalBPonly = defaults.canonicalBPonly;+  uniq_ML         = defaults.uniq_ML;+  energy_set      = defaults.energy_set;+  do_backtrack    = defaults.compute_bpp;+  backtrack_type  = defaults.backtrack_type;+  nonstandards    = defaults.nonstandards;+  max_bp_span     = defaults.max_bp_span;+  oldAliEn        = defaults.oldAliEn;+  ribo            = defaults.ribo;+  cv_fact         = defaults.cv_fact;+  nc_fact         = defaults.nc_fact;+  logML           = defaults.logML;+#endif+}++/* below are the setter functions for global default settings */++PUBLIC void+vrna_md_defaults_temperature(double T){++  if(T >= -K0){+    defaults.temperature = T;+#ifdef VRNA_BACKWARD_COMPAT+    temperature = T;+#endif+  } else+    vrna_message_warning("vrna_md_defaults_temperature@model.c: Temperature out of range, T must be above absolute zero. Not changing anything!");+}++PUBLIC double+vrna_md_defaults_temperature_get(void){++  return defaults.temperature;+}++PUBLIC void+vrna_md_defaults_betaScale(double b){++  defaults.betaScale = b;+}++PUBLIC double+vrna_md_defaults_betaScale_get(void){++  return defaults.betaScale;+}++PUBLIC void+vrna_md_defaults_dangles(int d){+  if((d >= 0) && (d <= 3)){+    defaults.dangles = d;+#ifdef VRNA_BACKWARD_COMPAT+    dangles = d;+#endif+  } else+    vrna_message_warning("vrna_md_defaults_dangles@model.c: Dangles out of range, must be (0 <= d <= 3). Not changing anything!");+}++PUBLIC int+vrna_md_defaults_dangles_get(void){++  return defaults.dangles;+}++PUBLIC void+vrna_md_defaults_special_hp(int flag){++  defaults.special_hp = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  tetra_loop = defaults.special_hp;+#endif+}++PUBLIC int+vrna_md_defaults_special_hp_get(void){++  return defaults.special_hp;+}++PUBLIC void+vrna_md_defaults_noLP(int flag){++  defaults.noLP = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  noLonelyPairs = defaults.noLP;+#endif+}++PUBLIC int+vrna_md_defaults_noLP_get(void){++  return defaults.noLP;+}++PUBLIC void+vrna_md_defaults_noGU(int flag){++  defaults.noGU = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  noGU = defaults.noGU;+#endif+  /* update pair/rtype/alias arrays accordingly */+  vrna_md_update(&defaults);+}++PUBLIC int+vrna_md_defaults_noGU_get(void){++  return defaults.noGU;+}++PUBLIC void+vrna_md_defaults_noGUclosure(int flag){++  defaults.noGUclosure = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  no_closingGU = defaults.noGUclosure;+#endif+}++PUBLIC int+vrna_md_defaults_noGUclosure_get(void){++  return defaults.noGUclosure;+}++PUBLIC void+vrna_md_defaults_logML(int flag){++  defaults.logML = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  logML = defaults.logML;+#endif+}++PUBLIC int+vrna_md_defaults_logML_get(void){++  return defaults.logML;+}++PUBLIC void+vrna_md_defaults_circ(int flag){++  defaults.circ = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  circ = defaults.circ;+#endif+}++PUBLIC int+vrna_md_defaults_circ_get(void){++  return defaults.circ;+}++PUBLIC void+vrna_md_defaults_gquad(int flag){++  defaults.gquad = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  gquad = defaults.gquad;+#endif+}++PUBLIC int+vrna_md_defaults_gquad_get(void){++  return defaults.gquad;+}++PUBLIC void+vrna_md_defaults_uniq_ML(int flag){++  defaults.uniq_ML = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  uniq_ML = defaults.uniq_ML;+#endif+}++PUBLIC int+vrna_md_defaults_uniq_ML_get(void){++  return defaults.uniq_ML;+}++PUBLIC void+vrna_md_defaults_energy_set(int e){++  if((e >= 0) && (e <= 3)){+    defaults.energy_set = e;+#ifdef VRNA_BACKWARD_COMPAT+    energy_set = e;+#endif+    /* update pair/rtype/alias arrays accordingly */+    vrna_md_update(&defaults);+  } else+    vrna_message_warning("vrna_md_defaults_energy_set@model.c: Energy Set out of range, must be (0 <= e <= 3). Not changing anything!");+}++PUBLIC int+vrna_md_defaults_energy_set_get(void){++  return defaults.energy_set;+}++PUBLIC void+vrna_md_defaults_backtrack(int flag){++  defaults.backtrack = flag ? 1 : 0;+}++PUBLIC int+vrna_md_defaults_backtrack_get(void){++  return defaults.backtrack;+}++PUBLIC void+vrna_md_defaults_backtrack_type(char t){++  switch(t){+    case 'M': /* fall through */+    case 'C': /* fall through */+    case 'F': defaults.backtrack_type = t;+#ifdef VRNA_BACKWARD_COMPAT+              backtrack_type = t;+#endif+              break;+    default:  vrna_message_warning("vrna_md_defaults_backtrack_type@model.c: Backtrack type must be any of 'F', 'C', or 'M'. Not changing anything!");+  }+}++PUBLIC char+vrna_md_defaults_backtrack_type_get(void){++  return defaults.backtrack_type;+}++PUBLIC void+vrna_md_defaults_compute_bpp(int flag){++  if((flag >= 0) && (flag <= 2)){+    defaults.compute_bpp = flag;+#ifdef VRNA_BACKWARD_COMPAT+    do_backtrack = flag;+#endif+  } else+    defaults.compute_bpp = 1;+}++PUBLIC int+vrna_md_defaults_compute_bpp_get(void){++  return defaults.compute_bpp;+}++PUBLIC void+vrna_md_defaults_max_bp_span(int span){++  defaults.max_bp_span = (span <= 0) ? -1 : span;+#ifdef VRNA_BACKWARD_COMPAT+  max_bp_span = defaults.max_bp_span;+#endif+}++PUBLIC int+vrna_md_defaults_max_bp_span_get(void){++  return defaults.max_bp_span;+}++PUBLIC void+vrna_md_defaults_min_loop_size(int size){++  defaults.min_loop_size = (size < 0) ? 0 : size;+}++PUBLIC int+vrna_md_defaults_min_loop_size_get(void){++  return defaults.min_loop_size;+}++PUBLIC void+vrna_md_defaults_window_size(int size){++  defaults.window_size = (size <= 0) ? -1 : size;+}++PUBLIC int+vrna_md_defaults_window_size_get(void){++  return defaults.window_size;+}++PUBLIC void+vrna_md_defaults_oldAliEn(int flag){++  defaults.oldAliEn = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  oldAliEn = defaults.oldAliEn;+#endif+}++PUBLIC int+vrna_md_defaults_oldAliEn_get(void){++  return defaults.oldAliEn;+}++PUBLIC void+vrna_md_defaults_ribo(int flag){++  defaults.ribo = flag ? 1 : 0;+#ifdef VRNA_BACKWARD_COMPAT+  ribo = defaults.ribo;+#endif+}++PUBLIC int+vrna_md_defaults_ribo_get(void){++  return defaults.ribo;+}++PUBLIC void+vrna_md_defaults_cv_fact(double factor){++  defaults.cv_fact = factor;+#ifdef VRNA_BACKWARD_COMPAT+  cv_fact = factor;+#endif+}++PUBLIC double+vrna_md_defaults_cv_fact_get(void){++  return defaults.cv_fact;+}++PUBLIC void+vrna_md_defaults_nc_fact(double factor){++  defaults.nc_fact = factor;+#ifdef VRNA_BACKWARD_COMPAT+  nc_fact = factor;+#endif+}++PUBLIC double+vrna_md_defaults_nc_fact_get(void){++  return defaults.nc_fact;+}++PUBLIC void+vrna_md_defaults_sfact(double factor){++  defaults.sfact = factor;+}++PUBLIC double+vrna_md_defaults_sfact_get(void){++  return defaults.sfact;+}+++PUBLIC void+vrna_md_update(vrna_md_t *md){++  if(md)+    fill_pair_matrices(md);+}+++/*+    This function updates the pair/alias/rtype arrays according to model settings.+    It should be called whenever there is a change in the following model settings:+    - energy_set+    - noGU+    - nonstandards+*/+PRIVATE void+fill_pair_matrices(vrna_md_t *md){++  int i,j;++  /* nullify everything */+  for(i = 0;i <= MAXALPHA; i++)+    memset(md->pair[i], 0, (MAXALPHA + 1) * sizeof(int));++  memset(md->alias, 0, (MAXALPHA + 1) * sizeof(short));++  /* start setting actual base pair type encodings */+  switch(md->energy_set){+    case  0:    for(i = 0; i < 5; i++)+                  md->alias[i] = (short) i;++                md->alias[5] = 3; /* X <-> G */+                md->alias[6] = 2; /* K <-> C */+                md->alias[7] = 0; /* I <-> default base '@' */++                for(i = 0; i < NBASES; i++)+                    for(j = 0; j < NBASES; j++)+                      md->pair[i][j] = BP_pair[i][j];++                if(md->noGU)+                  md->pair[3][4] = md->pair[4][3] = 0;++                if(md->nonstandards[0] != '\0') {  /* allow nonstandard bp's (encoded by type=7) */+                   for(i = 0; i < (int)strlen(md->nonstandards); i += 2)+                      md->pair[vrna_nucleotide_encode(md->nonstandards[i], md)]+                        [vrna_nucleotide_encode(md->nonstandards[i+1], md)] = 7;+                }++                break;++    case 1:     for(i = 1; i < MAXALPHA;){+                  md->alias[i++] = 3;  /* A <-> G */+                  md->alias[i++] = 2;  /* B <-> C */+                }+                for(i = 1; i < MAXALPHA; i++){+                  md->pair[i][i+1] = 2;    /* AB <-> GC */+                  i++;+                  md->pair[i][i-1] = 1;    /* BA <-> CG */+                }++                break;++    case 2:     for(i = 1; i < MAXALPHA;){+                  md->alias[i++] = 1;  /* A <-> A*/+                  md->alias[i++] = 4;  /* B <-> U */+                }+                for(i = 1; i < MAXALPHA; i++){+                  md->pair[i][i+1] = 5;    /* AB <-> AU */+                  i++;+                  md->pair[i][i-1] = 6;    /* BA <-> UA */+                }++                break;++    case 3:     for(i = 1; i < MAXALPHA - 2; ){+                  md->alias[i++] = 3;  /* A <-> G */+                  md->alias[i++] = 2;  /* B <-> C */+                  md->alias[i++] = 1;  /* C <-> A */+                  md->alias[i++] = 4;  /* D <-> U */+                }+                for(i = 1; i < MAXALPHA - 2; i++){+                  md->pair[i][i+1] = 2;    /* AB <-> GC */+                  i++;+                  md->pair[i][i-1] = 1;    /* BA <-> CG */+                  i++;+                  md->pair[i][i+1] = 5;    /* CD <-> AU */+                  i++;+                  md->pair[i][i-1] = 6;    /* DC <-> UA */+                }++                break;++    default:    vrna_message_error("Which energy_set are YOU using??");+                break;+  }++  /* set the reverse base pair types */+  for(i = 0; i <= MAXALPHA; i++){+    for(j = 0; j <= MAXALPHA; j++){+      md->rtype[md->pair[i][j]] = md->pair[j][i];+    }+  }++  /* handle special cases separately */+  md->rtype[0] = 0;+  md->rtype[7] = 7;++  /* was used for energy_set == 0+  for(i = 0; i < NBASES; i++)+      for(j = 0; j < NBASES; j++)+       md->rtype[md->pair[i][j]] = md->pair[j][i];+  */+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC void+set_model_details(vrna_md_t *md){++  if(md){+    /* make sure there are no uninitialized data fields */+    memset(md, 0, sizeof(vrna_md_t));++    md->dangles           = dangles;+    md->special_hp        = tetra_loop;+    md->noLP              = noLonelyPairs;+    md->noGU              = noGU;+    md->noGUclosure       = no_closingGU;+    md->logML             = logML;+    md->gquad             = gquad;+    md->canonicalBPonly   = canonicalBPonly;+    md->circ              = circ;+    md->uniq_ML           = uniq_ML;+    md->compute_bpp       = do_backtrack;+    md->backtrack         = VRNA_MODEL_DEFAULT_BACKTRACK;+    md->backtrack_type    = backtrack_type;+    md->energy_set        = energy_set;+    md->max_bp_span       = max_bp_span;+    md->min_loop_size     = TURN;+    md->window_size       = VRNA_MODEL_DEFAULT_WINDOW_SIZE;+    md->oldAliEn          = oldAliEn;+    md->ribo              = ribo;+    md->cv_fact           = cv_fact;+    md->nc_fact           = nc_fact;+    md->temperature       = temperature;+    md->betaScale         = VRNA_MODEL_DEFAULT_BETA_SCALE;+    md->sfact             = 1.07;++    if (nonstandards)+      copy_nonstandards(md, nonstandards);++    /* set default values for the pair/rtype[pair] stuff */+    vrna_md_update(md);++  }+}+++PUBLIC char *+option_string(void){++  vrna_md_t md;+  set_model_details(&md);++  return vrna_md_option_string(&md);+}+++#endif++
+ C/ViennaRNA/model.h view
@@ -0,0 +1,879 @@+#ifndef VIENNA_RNA_PACKAGE_MODEL_H+#define VIENNA_RNA_PACKAGE_MODEL_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif+++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     model.h+ *  @ingroup  model_details+ *  @brief    The model details data structure and its corresponding modifiers+ */++/**+ *  @{+ *  @ingroup   model_details+ */++#ifndef NBASES+#define NBASES 8+#endif++/** @brief Typename for the model details data structure #vrna_md_s */+typedef struct vrna_md_s  vrna_md_t;++/**+ *  @brief+ *  @htmlonly Default temperature for structure prediction and free energy evaluation in &#176C @endhtmlonly+ *  @latexonly Default temperature for structure prediction and free energy evaluation in $^\circ C$ @endlatexonly+ *  @see  #vrna_md_t.temperature, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_TEMPERATURE    37.0++/**+ *  @brief  Default scaling factor for partition function computations+ *  @see  #vrna_exp_param_t.pf_scale, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_PF_SCALE       -1++/**+ *  @brief  Default scaling factor for absolute thermodynamic temperature in Boltzmann factors+ *  @see    #vrna_exp_param_t.alpha, #vrna_md_t.betaScale, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_BETA_SCALE     1.++/** @brief  Default dangling end model+ *  @see  #vrna_md_t.dangles, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_DANGLES        2++/**+ *  @brief  Default model behavior for lookup of special tri-, tetra-, and hexa-loops+ *  @see    #vrna_md_t.special_hp, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_SPECIAL_HP     1++/**+ *  @brief  Default model behavior for so-called 'lonely pairs'+ *  @see    #vrna_md_t.noLP, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_NO_LP          0++/**+ *  @brief  Default model behavior for G-U base pairs+ *  @see    #vrna_md_t.noGU, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_NO_GU          0++/**+ *  @brief  Default model behavior for G-U base pairs closing a loop+ *  @see    #vrna_md_t.noGUclosure, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_NO_GU_CLOSURE  0++/**+ *  @brief  Default model behavior to treat a molecule as a circular RNA (DNA)+ *  @see    #vrna_md_t.circ, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_CIRC           0++/**+ *  @brief  Default model behavior regarding the treatment of G-Quadruplexes+ *  @see    #vrna_md_t.gquad, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_GQUAD          0++#define VRNA_MODEL_DEFAULT_CANONICAL_BP   0++/**+ *  @brief  Default behavior of the model regarding unique multi-branch loop decomposition+ *  @see    #vrna_md_t.uniq_ML, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_UNIQ_ML        0++/**+ *  @brief  Default model behavior on which energy set to use+ *  @see    #vrna_md_t.energy_set, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_ENERGY_SET     0++/**+ *  @brief  Default model behavior with regards to backtracking of structures+ *  @see    #vrna_md_t.backtrack, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_BACKTRACK      1++/**+ *  @brief  Default model behavior on what type of backtracking to perform+ *  @see    #vrna_md_t.backtrack_type, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_BACKTRACK_TYPE 'F'++/**+ *  @brief  Default model behavior with regards to computing base pair probabilities+ *  @see    #vrna_md_t.compute_bpp, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_COMPUTE_BPP    1++/**+ *  @brief  Default model behavior for the allowed maximum base pair span+ *  @see    #vrna_md_t.max_bp_span, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_MAX_BP_SPAN    -1++/**+ *  @brief  Default model behavior for the sliding window approach+ *  @see    #vrna_md_t.window_size, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_WINDOW_SIZE    -1++/**+ *  @brief  Default model behavior on how to evaluate the energy contribution of multi-branch loops+ *  @see    #vrna_md_t.logML, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_LOG_ML         0++/**+ *  @brief  Default model behavior for consensus structure energy evaluation+ *  @see    #vrna_md_t.oldAliEn, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_ALI_OLD_EN     0++/**+ *  @brief  Default model behavior for consensus structure co-variance contribution assessment+ *  @see    #vrna_md_t.ribo, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_ALI_RIBO       0++/**+ *  @brief  Default model behavior for weighting the co-variance score in consensus structure prediction+ *  @see    #vrna_md_t.cv_fact, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_ALI_CV_FACT    1.++/** @brief  Default model behavior for weighting the nucleotide conservation? in consensus structure prediction+ *  @see    #vrna_md_t.nc_fact, vrna_md_defaults_reset(), vrna_md_set_default()+ */+#define VRNA_MODEL_DEFAULT_ALI_NC_FACT    1.+++#ifdef  VRNA_BACKWARD_COMPAT++#ifndef MAXALPHA+/**+ *  @brief Maximal length of alphabet+ */+#define MAXALPHA              20+#endif++#endif++/**+ *  @brief The data structure that contains the complete model details used throughout the calculations+ *+ *  For convenience reasons, we provide the type name #vrna_md_t to address this data structure+ *  without the use of the struct keyword+ *+ *  @see  vrna_md_set_default(), set_model_details(), vrna_md_update(), #vrna_md_t+ *+ */+struct vrna_md_s {+  double  temperature;                  /**<  @brief  The temperature used to scale the thermodynamic parameters */+  double  betaScale;                    /**<  @brief  A scaling factor for the thermodynamic temperature of the Boltzmann factors */+  int     dangles;                      /**<  @brief  Specifies the dangle model used in any energy evaluation (0,1,2 or 3)++                                              If set to 0 no stabilizing energies are assigned to bases adjacent to+                                              helices in free ends and multiloops (so called dangling ends). Normally+                                              (dangles = 1) dangling end energies are assigned only to unpaired+                                              bases and a base cannot participate simultaneously in two dangling ends. In+                                              the partition function algorithm vrna_pf() these checks are neglected.+                                              To provide comparability between free energy minimization and partition function+                                              algorithms, the default setting is 2.+                                              This treatment of dangling ends gives more favorable energies to helices+                                              directly adjacent to one another, which can be beneficial since such+                                              helices often do engage in stabilizing interactions through co-axial+                                              stacking.\n+                                              If set to 3 co-axial stacking is explicitly included for+                                              adjacent helices in multiloops. The option affects only mfe folding+                                              and energy evaluation (vrna_mfe() and vrna_eval_structure()), as+                                              well as suboptimal folding (vrna_subopt()) via re-evaluation of energies.+                                              Co-axial stacking with one intervening mismatch is not considered so far.+                                              @note   Some function do not implement all dangle model but only a subset of+                                                      (0,1,2,3). In particular, partition function algorithms can only handle+                                                      0 and 2. Read the documentation of the particular recurrences or+                                                      energy evaluation function for information about the provided dangle+                                                      model.+                                        */+  int     special_hp;                   /**<  @brief  Include special hairpin contributions for tri, tetra and hexaloops */+  int     noLP;                         /**<  @brief  Only consider canonical structures, i.e. no 'lonely' base pairs */+  int     noGU;                         /**<  @brief  Do not allow GU pairs */+  int     noGUclosure;                  /**<  @brief  Do not allow loops to be closed by GU pair */+  int     logML;                        /**<  @brief  Use logarithmic scaling for multiloops */+  int     circ;                         /**<  @brief  Assume RNA to be circular instead of linear */+  int     gquad;                        /**<  @brief  Include G-quadruplexes in structure prediction */+  int     canonicalBPonly;              /**<  @brief  remove non-canonical bp's from constraint structures  */+  int     uniq_ML;                      /**<  @brief  Flag to ensure unique multi-branch loop decomposition during folding */+  int     energy_set;                   /**<  @brief  Specifies the energy set that defines set of compatible base pairs */+  int     backtrack;                    /**<  @brief  Specifies whether or not secondary structures should be backtraced */+  char    backtrack_type;               /**<  @brief  Specifies in which matrix to backtrack */+  int     compute_bpp;                  /**<  @brief  Specifies whether or not backward recursions for base pair probability (bpp) computation will be performed */+  char    nonstandards[64];             /**<  @brief  contains allowed non standard bases */+  int     max_bp_span;                  /**<  @brief  maximum allowed base pair span */++  int     min_loop_size;                /**<  @brief  Minimum size of hairpin loops+                                              @note The default value for this field is #TURN, however, it may+                                              be 0 in cofolding context.+                                        */+  int     window_size;                  /**<  @brief  Size of the sliding window for locally optimal structure prediction */+  int     oldAliEn;                     /**<  @brief  Use old alifold energy model */+  int     ribo;                         /**<  @brief  Use ribosum scoring table in alifold energy model */+  double  cv_fact;                      /**<  @brief  Co-variance scaling factor for consensus structure prediction */+  double  nc_fact;                      /**<  @brief  Scaling factor to weight co-variance contributions of non-canonical pairs */+  double  sfact;                        /**<  @brief  Scaling factor for partition function scaling */+  int     rtype[8];                     /**<  @brief  Reverse base pair type array */+  short   alias[MAXALPHA+1];            /**<  @brief  alias of an integer nucleotide representation */+  int     pair[MAXALPHA+1][MAXALPHA+1]; /**<  @brief  Integer representation of a base pair */+};+++/**+ * @brief Apply default model details to a provided #vrna_md_t data structure+ *+ *  Use this function to initialize a #vrna_md_t data structure with+ *  its default values+ *+ *  @param md A pointer to the data structure that is about to be initialized+ */+void+vrna_md_set_default(vrna_md_t *md);++/**+ *  @brief Update the model details data structure+ *+ *  This function should be called after changing the vrna_md_t.energy_set attribute+ *  since it re-initializes base pairing related arrays within the #vrna_md_t data+ *  structure. In particular, #vrna_md_t.pair, #vrna_md_t.alias, and #vrna_md_t.rtype+ *  are set to the values that correspond to the specified #vrna_md_t.energy_set+ *  option+ *+ *  @see  #vrna_md_t, #vrna_md_t.energy_set, #vrna_md_t.pair, #vrna_md_t.rtype,+ *        #vrna_md_t.alias, vrna_md_set_default()+ */+void+vrna_md_update(vrna_md_t *md);++/**+ *  @brief Copy/Clone a #vrna_md_t model+ *+ *  Use this function to clone a given model either inplace (target container @p md_to+ *  given) or create a copy by cloning the source model and returning it (@p md_to == NULL).+ *+ *  @param md_to    The model to be overwritten (if non-NULL and @p md_to != @p md_from)+ *  @param md_from  The model to copy (if non-NULL)+ *  @return         A pointer to the copy model (or NULL if @p md_from == NULL)+ */+vrna_md_t *+vrna_md_copy( vrna_md_t       *md_to,+              const vrna_md_t *md_from);++/**+ *  @brief  Get a corresponding commandline parameter string of the options in a #vrna_md_t+ *+ *  @note This function is not threadsafe!+ */+char *+vrna_md_option_string(vrna_md_t  *md);++void+vrna_md_set_nonstandards(vrna_md_t *md, const char *ns_bases);++/**+ *  @brief  Reset the global default model details to a specific set of parameters, or their initial values+ *+ *  This function resets the global default model details to their initial values,+ *  i.e. as specified by the ViennaRNA Package release, upon passing NULL as argument.+ *  Alternatively it resets them according to a set of provided parameters.+ *+ *  @note The global default parameters affect all function calls of RNAlib where+ *        model details are not explicitly provided. Hence, any change of them+ *        is not considered threadsafe+ *  @warning  This function first resets the global default settings to factory+ *            defaults, and only then applies user provided settings (if any).+ *            User settings that do not meet specifications are skipped.+ *  @see  vrna_md_set_default(), #vrna_md_t+ *+ *  @param md_p A set of model details to use as global default (if NULL is passed, factory defaults are restored)+ */+void+vrna_md_defaults_reset(vrna_md_t *md_p);++/**+ *  @brief  Set default temperature for energy evaluation of loops+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_TEMPERATURE+ *  @param T  Temperature in centigrade+ */+void+vrna_md_defaults_temperature(double T);++/**+ *  @brief  Get default temperature for energy evaluation of loops+ *  @see vrna_md_defaults_temperature(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_TEMPERATURE+ *  @return  The global default settings for temperature in centigrade+ */+double+vrna_md_defaults_temperature_get(void);++/**+ *  @brief  Set default scaling factor of thermodynamic temperature in Boltzmann factors+ *+ *  Bolzmann factors are then computed as @f$ exp(-E / (b \cdot kT))@f$.+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BETA_SCALE+ *  @param b  The scaling factor, default is 1.0+ */+void+vrna_md_defaults_betaScale(double b);++/**+ *  @brief  Get default scaling factor of thermodynamic temperature in Boltzmann factors+ *+ *  @see vrna_md_defaults_betaScale(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BETA_SCALE+ *  @return  The global default thermodynamic temperature scaling factor+ */+double+vrna_md_defaults_betaScale_get(void);++/**+ *  @brief  Set default dangle model for structure prediction+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_DANGLES+ *  @param d  The dangle model+ */+void+vrna_md_defaults_dangles(int d);++/**+ *  @brief  Get default dangle model for structure prediction+ *  @see vrna_md_defaults_dangles(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_DANGLES+ *  @return The global default settings for the dangle model+ */+int+vrna_md_defaults_dangles_get(void);++/**+ *  @brief  Set default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_SPECIAL_HP+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_special_hp(int flag);++/**+ *  @brief  Get default behavior for lookup of tabulated free energies for special hairpin loops, such as Tri-, Tetra-, or Hexa-loops.+ *  @see vrna_md_defaults_special_hp(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_SPECIAL_HP+ *  @return  The global default settings for the treatment of special hairpin loops+ */+int+vrna_md_defaults_special_hp_get(void);++/**+ *  @brief  Set default behavior for prediction of canonical secondary structures+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_LP+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_noLP(int flag);++/**+ *  @brief  Get default behavior for prediction of canonical secondary structures+ *  @see vrna_md_defaults_noLP(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_LP+ *  @return  The global default settings for predicting canonical secondary structures+ */+int+vrna_md_defaults_noLP_get(void);++/**+ *  @brief  Set default behavior for treatment of G-U wobble pairs+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_noGU(int flag);++/**+ *  @brief  Get default behavior for treatment of G-U wobble pairs+ *  @see vrna_md_defaults_noGU(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU+ *  @return The global default settings for treatment of G-U wobble pairs+ */+int+vrna_md_defaults_noGU_get(void);++/**+ *  @brief  Set default behavior for G-U pairs as closing pair for loops+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU_CLOSURE+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_noGUclosure(int flag);++/**+ *  @brief  Get default behavior for G-U pairs as closing pair for loops+ *  @see vrna_md_defaults_noGUclosure(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_NO_GU_CLOSURE+ *  @return The global default settings for treatment of G-U pairs closing a loop+ */+int+vrna_md_defaults_noGUclosure_get(void);++/**+ *  @brief  Set default behavior recomputing free energies of multi-branch loops using a logarithmic model+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_LOG_ML+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_logML(int flag);++/**+ *  @brief  Get default behavior recomputing free energies of multi-branch loops using a logarithmic model+ *  @see vrna_md_defaults_logML(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_LOG_ML+ *  @return The global default settings for logarithmic model in multi-branch loop free energy evaluation+ */+int+vrna_md_defaults_logML_get(void);++/**+ *  @brief  Set default behavior whether input sequences are circularized+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_CIRC+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_circ(int flag);++/**+ *  @brief  Get default behavior whether input sequences are circularized+ *  @see vrna_md_defaults_circ(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_CIRC+ *  @return The global default settings for treating input sequences as circular+ */+int+vrna_md_defaults_circ_get(void);++/**+ *  @brief  Set default behavior for treatment of G-Quadruplexes+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_GQUAD+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_gquad(int flag);++/**+ *  @brief  Get default behavior for treatment of G-Quadruplexes+ *  @see vrna_md_defaults_gquad(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_GQUAD+ *  @return The global default settings for treatment of G-Quadruplexes+ */+int+vrna_md_defaults_gquad_get(void);++/**+ *  @brief  Set default behavior for creating additional matrix for unique multi-branch loop prediction+ *  @note   Activating this option usually results in higher memory consumption!+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_UNIQ_ML+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_uniq_ML(int flag);++/**+ *  @brief  Get default behavior for creating additional matrix for unique multi-branch loop prediction+ *  @see vrna_md_defaults_uniq_ML(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_UNIQ_ML+ *  @return The global default settings for creating additional matrices for unique multi-branch loop prediction+ */+int+vrna_md_defaults_uniq_ML_get(void);++/**+ *  @brief  Set default energy set+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ENERGY_SET+ *  @param  e   Energy set (0, 1, 2, 3)+ */+void+vrna_md_defaults_energy_set(int e);++/**+ *  @brief  Get default energy set+ *  @see vrna_md_defaults_energy_set(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ENERGY_SET+ *  @return The global default settings for the energy set+ */+int+vrna_md_defaults_energy_set_get(void);++/**+ *  @brief  Set default behavior for whether to backtrack secondary structures+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_backtrack(int flag);++/**+ *  @brief  Get default behavior for whether to backtrack secondary structures+ *  @see vrna_md_defaults_backtrack(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK+ *  @return The global default settings for backtracking structures+ */+int+vrna_md_defaults_backtrack_get(void);++/**+ *  @brief  Set default backtrack type, i.e. which DP matrix is used+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK_TYPE+ *  @param  t   The type ('F', 'C', or 'M')+ */+void+vrna_md_defaults_backtrack_type(char t);++/**+ *  @brief  Get default backtrack type, i.e. which DP matrix is used+ *  @see vrna_md_defaults_backtrack_type(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_BACKTRACK_TYPE+ *  @return The global default settings that specify which DP matrix is used for backtracking+ */+char+vrna_md_defaults_backtrack_type_get(void);++/**+ *  @brief  Set the default behavior for whether to compute base pair probabilities after partition function computation+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_COMPUTE_BPP+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_compute_bpp(int flag);++/**+ *  @brief  Get the default behavior for whether to compute base pair probabilities after partition function computation+ *  @see vrna_md_defaults_compute_bpp(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_COMPUTE_BPP+ *  @return The global default settings that specify whether base pair probabilities are computed together with partition function+ */+int+vrna_md_defaults_compute_bpp_get(void);++/**+ *  @brief  Set default maximal base pair span+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_MAX_BP_SPAN+ *  @param  span  Maximal base pair span+ */+void+vrna_md_defaults_max_bp_span(int span);++/**+ *  @brief  Get default maximal base pair span+ *  @see vrna_md_defaults_max_bp_span(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_MAX_BP_SPAN+ *  @return The global default settings for maximum base pair span+ */+int+vrna_md_defaults_max_bp_span_get(void);++/**+ *  @brief  Set default minimal loop size+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #TURN+ *  @param  size  Minimal size, i.e. number of unpaired nucleotides for a hairpin loop+ */+void+vrna_md_defaults_min_loop_size(int size);++/**+ *  @brief  Get default minimal loop size+ *  @see vrna_md_defaults_min_loop_size(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #TURN+ *  @return The global default settings for minimal size of hairpin loops+ */+int+vrna_md_defaults_min_loop_size_get(void);++/**+ *  @brief  Set default window size for sliding window structure prediction approaches+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_WINDOW_SIZE+ *  @param  size  The size of the sliding window+ */+void+vrna_md_defaults_window_size(int size);++/**+ *  @brief  Get default window size for sliding window structure prediction approaches+ *  @see vrna_md_defaults_window_size(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_WINDOW_SIZE+ *  @return The global default settings for the size of the sliding window+ */+int+vrna_md_defaults_window_size_get(void);++/**+ *  @brief  Set default behavior for whether to use old energy model for comparative structure prediction+ *  @note   This option is outdated. Activating the old energy model usually results in worse consensus+ *          structure predictions.+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_OLD_EN+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_oldAliEn(int flag);++/**+ *  @brief  Get default behavior for whether to use old energy model for comparative structure prediction+ *  @see vrna_md_defaults_oldAliEn(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_OLD_EN+ *  @return The global default settings for using old energy model for comparative structure prediction+ */+int+vrna_md_defaults_oldAliEn_get(void);++/**+ *  @brief  Set default behavior for whether to use Ribosum Scoring in comparative structure prediction+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_RIBO+ *  @param  flag  On/Off switch (0 = OFF, else = ON)+ */+void+vrna_md_defaults_ribo(int flag);++/**+ *  @brief  Get default behavior for whether to use Ribosum Scoring in comparative structure prediction+ *  @see vrna_md_defaults_ribo(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_RIBO+ *  @return The global default settings for using Ribosum scoring in comparative structure prediction+ */+int+vrna_md_defaults_ribo_get(void);++/**+ *  @brief  Set the default co-variance scaling factor used in comparative structure prediction+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_CV_FACT+ *  @param  factor  The co-variance factor+ */+void+vrna_md_defaults_cv_fact(double factor);++/**+ *  @brief  Get the default co-variance scaling factor used in comparative structure prediction+ *  @see vrna_md_defaults_cv_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_CV_FACT+ *  @return The global default settings for the co-variance factor+ */+double+vrna_md_defaults_cv_fact_get(void);++/**+ *  @brief+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_NC_FACT+ *  @param factor+ */+void+vrna_md_defaults_nc_fact(double factor);++/**+ *  @brief+ *  @see vrna_md_defaults_nc_fact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t, #VRNA_MODEL_DEFAULT_ALI_NC_FACT+ *  @return+ */+double+vrna_md_defaults_nc_fact_get(void);++/**+ *  @brief  Set the default scaling factor used to avoid under-/overflows in partition function computation+ *  @see vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t+ *  @param  factor  The scaling factor  (default: 1.07)+ */+void+vrna_md_defaults_sfact(double factor);++/**+ *  @brief  Get the default scaling factor used to avoid under-/overflows in partition function computation+ *  @see vrna_md_defaults_sfact(), vrna_md_defaults_reset(), vrna_md_set_default(), #vrna_md_t+ *  @return The global default settings of the scaling factor+ */+double+vrna_md_defaults_sfact_get(void);++#ifdef  VRNA_BACKWARD_COMPAT++#define model_detailsT        vrna_md_t               /* restore compatibility of struct rename */++/* BEGIN deprecated global variables: */++/**+ *  @brief Rescale energy parameters to a temperature in degC.+ * + *  Default is 37C. You have to call the update_..._params() functions after+ *  changing this parameter.+ *  @deprecated   Use vrna_md_defaults_temperature(), and vrna_md_defaults_temperature_get()+ *                to change, and read the global default temperature settings+ *  @see vrna_md_defaults_temperature(), vrna_md_defaults_temperature_get(), vrna_md_defaults_reset()+ */+extern double temperature;++/**+ *  @brief A scaling factor used by pf_fold() to avoid overflows.+ * + *  Should be set to approximately @f$exp{((-F/kT)/length)}@f$, where @f$F@f$ is an estimate+ *  for the ensemble free energy, for example the minimum free energy. You must+ *  call update_pf_params() after changing this parameter.\n+ *  If pf_scale is -1 (the default) , an estimate will be provided+ *  automatically when computing partition functions, e.g. pf_fold()+ *  The automatic estimate is usually insufficient for sequences more+ *  than a few hundred bases long.+ */+extern double pf_scale;++/**+ *  @brief Switch the energy model for dangling end contributions (0, 1, 2, 3)+ * + *  If set to 0 no stabilizing energies are assigned to bases adjacent to+ *  helices in free ends and multiloops (so called dangling ends). Normally+ *  (dangles = 1) dangling end energies are assigned only to unpaired+ *  bases and a base cannot participate simultaneously in two dangling ends. In+ *  the partition function algorithm pf_fold() these checks are neglected.+ *  If #dangles is set to 2, all folding routines will follow this convention.+ *  This treatment of dangling ends gives more favorable energies to helices+ *  directly adjacent to one another, which can be beneficial since such+ *  helices often do engage in stabilizing interactions through co-axial+ *  stacking.\n+ *  If dangles = 3 co-axial stacking is explicitly included for+ *  adjacent helices in multiloops. The option affects only mfe folding+ *  and energy evaluation (fold() and energy_of_structure()), as+ *  well as suboptimal folding (subopt()) via re-evaluation of energies.+ *  Co-axial stacking with one intervening mismatch is not considered so far.+ * + *  Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2+ */+extern int  dangles;++/**+ *  @brief Include special stabilizing energies for some tri-, tetra- and hexa-loops;+ * + *  default is 1.+ */+extern int  tetra_loop;++/**+ *  @brief Global switch to avoid/allow helices of length 1+ * + *  Disallow all pairs which can only occur as lonely pairs (i.e. as helix+ *  of length 1). This avoids lonely base pairs in the predicted structures in+ *  most cases.+ */+extern int    noLonelyPairs;++/**+ *  @brief Global switch to forbid/allow GU base pairs at all+ */+extern int  noGU;++/**+ *  @brief GU allowed only inside stacks if set to 1+ */+extern int  no_closingGU;++/**+ *  @brief backward compatibility variable.. this does not effect anything+ */+extern int  circ;++/**+ *  @brief Allow G-quadruplex formation+ */+extern int gquad;++/**+ *  Do not use this variable, it will eventually be removed in one of the next versions+ */+extern int canonicalBPonly;++/**+ *  @brief do ML decomposition uniquely (for subopt)+ */+extern  int uniq_ML;++/**+ *  @brief 0 = BP; 1=any with GC; 2=any with AU-parameter+ * + *  If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A+ *  pairs B, C pairs D, etc. using either GC (1) or AU parameters (2);+ *  default is 0, you probably don't want to change it.+ */+extern int  energy_set;++/**+ *  @brief do backtracking, i.e. compute secondary structures or base pair probabilities+ * + *  If 0, do not calculate pair probabilities in pf_fold(); this is about+ *  twice as fast. Default is 1.+ */+extern int    do_backtrack;++/**+ *  @brief A backtrack array marker for inverse_fold()+ * + *  If set to 'C': force (1,N) to be paired,+ *  'M' fold as if the sequence were inside a multiloop. Otherwise ('F') the+ *  usual mfe structure is computed.+ */+extern char backtrack_type;++/**+ *  @brief contains allowed non standard base pairs+ * + *  Lists additional base pairs that will be allowed to form in addition to+ *  GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking+ *  energy of 0.+ */+extern char *nonstandards;++/**+ *  @brief Maximum allowed base pair span+ *+ *  A value of -1 indicates no restriction for distant base pairs.+ */+extern int max_bp_span;++/**+ *  @brief use old alifold energies (with gaps)+ */+extern int oldAliEn;++/**+ *  @brief use ribosum matrices+ */+extern int ribo;            ++extern double cv_fact;++extern double nc_fact;++/** @brief if nonzero use logarithmic ML energy in energy_of_struct  */+extern  int logML;++/* END deprecated global variables: */++/**+ * @brief Set default model details+ *+ *  Use this function if you wish to initialize a #vrna_md_t data structure with+ *  its default values, i.e. the global model settings as provided by the deprecated+ *  global variables.+ *+ *  @deprecated This function will vanish as soon as backward compatibility of+ *              RNAlib is dropped (expected in version 3).+ *              Use vrna_md_set_default() instead!+ *+ *  @param md A pointer to the data structure that is about to be initialized+ */+void+set_model_details(vrna_md_t *md);++char *+option_string(void);++#endif+/**+ * @}+ */++#endif
+ C/ViennaRNA/model_avg.inc view
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4:1 \n";
+ C/ViennaRNA/move_set.c view
@@ -0,0 +1,1138 @@++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <limits.h>+#include <time.h>++#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/utils.h"++#include "ViennaRNA/move_set.h"+++/* maximum degeneracy value - if degeneracy is greater than this, program segfaults */+#define MAX_DEGEN 100+#define MINGAP 3+++#define bool int+#define true 1+#define false 0++/*+#################################+# PRIVATE DATA STRUCTURES       #+#################################+*/++/* internal struct with moves, sequence, degeneracy and options*/+typedef struct _Encoded {+  /* sequence*/+  short *s0;+  short *s1;++  const char  *seq;++  /* moves*/+  int   bp_left;+  int   bp_right;+  int   bp_left2;   /* if noLP is enabled (and for shift moves)*/+  int   bp_right2;++  /* options*/+  int noLP;+  int verbose_lvl;+  int first;+  int shift;++  /* degeneracy*/+  int begin_unpr;+  int begin_pr;+  int end_unpr;+  int end_pr;+  short *processed[MAX_DEGEN];+  short *unprocessed[MAX_DEGEN];+  int current_en;++  /* moves in random (needs to be freed afterwards)*/+  int *moves_from;+  int *moves_to;+  int num_moves;++  /* function for flooding */+  int (*funct) (struct_en*, struct_en*);+++} Encoded;++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE int cnt_move = 0;++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE int     compare(short *lhs, short *rhs);+PRIVATE int     find_min(short *arr[MAX_DEGEN], int begin, int end);+PRIVATE int     equals(const short *first, const short *second);+PRIVATE int     count_move(void);+PRIVATE int     lone_base(short *pt, int i);+PRIVATE void    free_degen(Encoded *Enc);+PRIVATE inline void do_move(short *pt, int bp_left, int bp_right);+PRIVATE int     update_deepest(Encoded *Enc, struct_en *str, struct_en *min);+PRIVATE int     deletions(Encoded *Enc, struct_en *str, struct_en *minim);+PRIVATE inline  bool compat(char a, char b);+PRIVATE inline  bool try_insert(const short *pt, const char *seq, int i, int j);+PRIVATE inline  bool try_insert_seq(const char *seq, int i, int j);+PRIVATE int     insertions(Encoded *Enc, struct_en *str, struct_en *minim);+PRIVATE int     shifts(Encoded *Enc, struct_en *str, struct_en *minim);+PRIVATE int     move_set(Encoded *Enc, struct_en *str);+PRIVATE void    construct_moves(Encoded *Enc, short *structure);+PRIVATE int     move_rset(Encoded *Enc, struct_en *str);+PRIVATE int     find_lone_pair(short* str);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PRIVATE int+compare(short *lhs, short *rhs){++  /* printf("%d ", (int)lhs[0]); */++  int i=1;+  char l=0,r=0;+  while (i<=lhs[0]) {+    l = (lhs[i]==0?'.':(lhs[i]<lhs[lhs[i]]?')':'('));+    r = (rhs[i]==0?'.':(rhs[i]<rhs[rhs[i]]?')':'('));+    if (l != r) break;+    i++;+  }++  return (i<=lhs[0] && l>r);+}++PRIVATE int+find_min(short *arr[MAX_DEGEN], int begin, int end){++  short *min = arr[begin];+  short min_num = begin;+  int i;++  for (i=begin+1; i<end; i++) {+    if (compare(arr[i], min)) {+      min = arr[i];+      min_num = i;+    }+  }+  return min_num;+}++PRIVATE int+equals(const short *first, const short *second){++  int i=1;+  while (i<=first[0] && first[i]==second[i]) {+    i++;+  }+  if (i>first[0]) return 1;+  else return 0;+}++PUBLIC void+copy_arr(short *dest, short *src){+  if (!src || !dest) {+    vrna_message_warning("Empty pointer in copying");+    return;+  }+  memcpy(dest, src, sizeof(short)*(src[0]+1));+}++PUBLIC short *+allocopy(short *src){+  short *res = (short*) vrna_alloc(sizeof(short)*(src[0]+1));+  copy_arr(res, src);+  return res;+}++PRIVATE int+count_move(void){++  return cnt_move;+}++++/* frees all things allocated by degeneracy...*/+PRIVATE void+free_degen(Encoded *Enc){++  int i;+  for (i=Enc->begin_unpr; i<Enc->end_unpr; i++) {+    if (Enc->unprocessed[i]) {+      free(Enc->unprocessed[i]);+      Enc->unprocessed[i]=NULL;+    }+  }+  for (i=Enc->begin_pr; i<Enc->end_pr; i++) {+    if (Enc->processed[i]) {+      free(Enc->processed[i]);+      Enc->processed[i]=NULL;+    }+  }+  Enc->begin_pr=0;+  Enc->begin_unpr=0;+  Enc->end_pr=0;+  Enc->end_unpr=0;+}++PRIVATE inline void+do_move(short *pt, int bp_left, int bp_right){++  /* delete*/+  if (bp_left<0) {+    pt[-bp_left]=0;+    pt[-bp_right]=0;+  } else { /* insert*/+    pt[bp_left]=bp_right;+    pt[bp_right]=bp_left;+  }+}++/* done with all structures along the way to deepest*/+PRIVATE int+update_deepest(Encoded *Enc, struct_en *str, struct_en *min){++  /* apply move + get its energy*/+  int tmp_en;+  tmp_en = str->energy + energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left, Enc->bp_right);+  do_move(str->structure, Enc->bp_left, Enc->bp_right);+  if (Enc->bp_left2 != 0) {+    tmp_en += energy_of_move_pt(str->structure, Enc->s0, Enc->s1, Enc->bp_left2, Enc->bp_right2);+    do_move(str->structure, Enc->bp_left2, Enc->bp_right2);+  }+  int last_en = str->energy;+  str->energy = tmp_en;+++  /* use f_point if we have it */+  if (Enc->funct) {+    int end = Enc->funct(str, min);++    /*  undo moves */+    if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);+    do_move(str->structure, -Enc->bp_left, -Enc->bp_right);+    str->energy = last_en;+    Enc->bp_left=0;+    Enc->bp_right=0;+    Enc->bp_left2=0;+    Enc->bp_right2=0;++    return (end?1:0);+  }++  if (Enc->verbose_lvl>1) { fprintf(stderr, "  "); print_str(stderr, str->structure); fprintf(stderr, " %d\n", tmp_en); }++  /* better deepest*/+  if (tmp_en < min->energy) {+    min->energy = tmp_en;+    copy_arr(min->structure, str->structure);++    /* delete degeneracy*/+    free_degen(Enc);++    /* undo moves*/+    if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);+    do_move(str->structure, -Enc->bp_left, -Enc->bp_right);+    str->energy = last_en;+    Enc->bp_left=0;+    Enc->bp_right=0;+    Enc->bp_left2=0;+    Enc->bp_right2=0;+    return 1;+  }++  /* degeneracy*/+  if ((str->energy == min->energy) && (Enc->current_en == min->energy)) {+    int found = 0;+    int i;+    for (i=Enc->begin_pr; i<Enc->end_pr; i++) {+      if (equals(Enc->processed[i], str->structure)) {+        found = 1;+        break;+      }+    }+    for (i=Enc->begin_unpr; !found && i<Enc->end_unpr; i++) {+      if (equals(Enc->unprocessed[i], str->structure)) {+        found = 1;+        break;+      }+    }++    if (!found) {+      /* print_stren(stderr, str); // fprintf(stderr, " %6.2f\n", str->energy); */+      Enc->unprocessed[Enc->end_unpr]=allocopy(str->structure);+      Enc->end_unpr++;+    }+  }++  /* undo moves*/+  if (Enc->bp_left2!=0) do_move(str->structure, -Enc->bp_left2, -Enc->bp_right2);+  do_move(str->structure, -Enc->bp_left, -Enc->bp_right);+  str->energy = last_en;+  Enc->bp_left=0;+  Enc->bp_right=0;+  Enc->bp_left2=0;+  Enc->bp_right2=0;+  return 0;+}+++/* deletions move set*/+PRIVATE int+deletions(Encoded *Enc, struct_en *str, struct_en *minim){++  int cnt = 0;+  short *pt = str->structure;+  int len = pt[0];+  int i;++  for (i=1; i<=len; i++) {+    if (pt[i]>pt[pt[i]]) {  /* '('*/+      Enc->bp_left=-i;+      Enc->bp_right=-pt[i];++      /*if nolp enabled, make (maybe) 2nd delete*/+      if (Enc->noLP) {+        int lone = -1;+        if (lone_base(pt, i-1)) lone=i-1;+        else if (lone_base(pt, i+1)) lone=i+1;+        else if (lone_base(pt, pt[i]-1)) lone=pt[i]-1;+        else if (lone_base(pt, pt[i]+1)) lone=pt[i]+1;++        /* check*/+        if (lone != -1 && (pt[lone]==0 || pt[pt[lone]]==0)) {+          vrna_message_warning("pt[%d(or %d)]!=\'.\'", lone, pt[lone]);+        }++        if (lone != -1) {+          Enc->bp_left2=-lone-1;+          Enc->bp_right2=-pt[lone]-1;+        }+        if (!lone_base(pt, pt[lone]-1) && !lone_base(pt, pt[lone]+1)) {+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }+      } else {  /* nolp not enabled*/+        cnt += update_deepest(Enc, str, minim);+        /* in case useFirst is on and structure is found, end*/+        if (Enc->first && cnt > 0) return cnt;+      }+    }+  }+  return cnt;+}++  /* compatible base pair?*/+PRIVATE inline bool+compat(char a, char b){++  if (a=='A' && b=='U') return true;+  if (a=='C' && b=='G') return true;+  if (a=='G' && b=='U') return true;+  if (a=='U' && b=='A') return true;+  if (a=='G' && b=='C') return true;+  if (a=='U' && b=='G') return true;+  /* and with T's*/+  if (a=='A' && b=='T') return true;+  if (a=='T' && b=='A') return true;+  if (a=='G' && b=='T') return true;+  if (a=='T' && b=='G') return true;+  return false;+}++/* try insert base pair (i,j)*/+PRIVATE inline bool+try_insert(const short *pt, const char *seq, int i, int j){++  if (i<=0 || j<=0 || i>pt[0] || j>pt[0]) return false;+  return (j-i>MINGAP && pt[j]==0 && pt[i]==0 && compat(seq[i-1], seq[j-1]));+}++/*  try insert base pair (i,j) */+PRIVATE inline bool+try_insert_seq(const char *seq, int i, int j){+  if (i<=0 || j<=0) return false;+  return (j-i>MINGAP && compat(seq[i-1], seq[j-1]));+}++/* insertions move set*/+PRIVATE int+insertions(Encoded *Enc, struct_en *str, struct_en *minim){++  int cnt = 0;+  short *pt = str->structure;+  int len = pt[0];+  int i,j;++  for (i=1; i<=len; i++) {+    if (pt[i]==0) {+      for (j=i+1; j<=len; j++) {+        /* end if found closing bracket*/+        if (pt[j]!=0 && pt[j]<j) break;  /*')'*/+        if (pt[j]!=0 && pt[j]>j) {       /*'('*/+          j = pt[j];+          continue;+        }+        /* if conditions are met, do insert*/+        if (try_insert(pt, Enc->seq, i, j)) {+          Enc->bp_left=i;+          Enc->bp_right=j;++          if (Enc->noLP) {+            /* if lone bases occur, try inserting one another base*/+            if (lone_base(pt, i) || lone_base(pt, j)) {+              /* inside*/+              if (try_insert(pt, Enc->seq, i+1, j-1)) {+                Enc->bp_left2=i+1;+                Enc->bp_right2=j-1;+                cnt += update_deepest(Enc, str, minim);+                /* in case useFirst is on and structure is found, end*/+                if (Enc->first && cnt > 0) return cnt;+              } else  /*outside*/+              if (try_insert(pt, Enc->seq, i-1, j+1)) {+                Enc->bp_left2=i-1;+                Enc->bp_right2=j+1;+                cnt += update_deepest(Enc, str, minim);+                /* in case useFirst is on and structure is found, end*/+                if (Enc->first && cnt > 0) return cnt;+              }+            } else {+              cnt += update_deepest(Enc, str, minim);+              /* in case useFirst is on and structure is found, end*/+              if (Enc->first && cnt > 0) return cnt;+            }+          } else {+            cnt += update_deepest(Enc, str, minim);+            /* in case useFirst is on and structure is found, end*/+            if (Enc->first && cnt > 0) return cnt;+          }+        }+      }+    }+  }+  return cnt;+}++/*shift move set*/+PRIVATE int+shifts(Encoded *Enc, struct_en *str, struct_en *minim){++  int cnt = 0;+  int brack_num = 0;+  short *pt = str->structure;+  int len = pt[0];+  int i, k;++  for (i=1; i<=len; i++) {+    if (pt[i]!=0 && pt[i]>i) {  /*'('*/+      int j=pt[i];++      /* outer switch left*/+      if (Enc->verbose_lvl>1)+        vrna_message_info(stderr, "%2d bracket %2d position, outer switch left", brack_num+1, i);+      for (k=i-1; k>0; k--) {+        if (pt[k]!=0 && pt[k]>k/*'('*/) break;+        if (pt[k]!=0 && pt[k]<k/*')'*/) {+          k = pt[k];+          continue;+        }+        /* checks*/+        if (pt[k]!=0) {+          vrna_message_warning("\'%c\'should be \'.\' at pos %d!", pt[k], k);+        }++        /* switch (i,j) to (k,j)*/+        if (j-k>MINGAP && compat(Enc->seq[k-1], Enc->seq[j-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=k;+          Enc->bp_right2=j;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }++        /* switch (i,j) to (k,i)*/+        if (i-k>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=k;+          Enc->bp_right2=i;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;++        }+      }++      /* outer switch right*/+      if (Enc->verbose_lvl>1)+        vrna_message_info(stderr, "%2d bracket %2d position, outer switch right", brack_num+1, i);+      for (k=j+1; k<=len; k++) {+        if (pt[k]!=0 && pt[k]<k/*')'*/) break;+        if (pt[k]!=0 && pt[k]>k/*'('*/) {+          k = pt[k];+          continue;+        }++        /* check*/+        if (pt[k]!=0) {+          vrna_message_warning("\'%c\'should be \'.\' at pos %d!", pt[k], k);+        }+        /* switch (i,j) to (i,k)*/+        if (k-i>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=i;+          Enc->bp_right2=k;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }+        /* switch (i,j) to (j,k)*/+        if (k-j>MINGAP && compat(Enc->seq[j-1], Enc->seq[k-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=j;+          Enc->bp_right2=k;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }+      }++      if (Enc->verbose_lvl>1)+        vrna_message_info(stderr, "%2d bracket %2d position, inner switch", brack_num+1, i);+      /* inner switch*/+      for (k=i+1; k<j; k++) {+        /* jump to end of the sub-bracketing*/+        if (pt[k]!=0 && pt[k]>k/*'('*/) {+            k=pt[k];+            continue;+        }++        /* left switch (i,j) to (k,j)*/+        if (j-k>MINGAP && compat(Enc->seq[k-1], Enc->seq[j-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=k;+          Enc->bp_right2=j;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }++        /* right switch (i,j) to (i,k)*/+        if (k-i>MINGAP && compat(Enc->seq[i-1], Enc->seq[k-1])) {+          Enc->bp_left=-i;+          Enc->bp_right=-j;+          Enc->bp_left2=i;+          Enc->bp_right2=k;+          cnt += update_deepest(Enc, str, minim);+          /* in case useFirst is on and structure is found, end*/+          if (Enc->first && cnt > 0) return cnt;+        }+      } /* end inner switch for*/+      brack_num++;+    } /* end if (pt[i]=='(')*/+  } /* end for in switches*/+  return cnt;+}++/* move to deepest (or first) neighbour*/+PRIVATE int+move_set(Encoded *Enc, struct_en *str){++  /* count how many times called*/+  cnt_move++;++  /* count better neighbours*/+  int cnt = 0;++  /* deepest descent*/+  struct_en min;+  min.structure = allocopy(str->structure);+  min.energy = str->energy;+  Enc->current_en = str->energy;++  if (Enc->verbose_lvl>0) { fprintf(stderr, "  start of MS:\n  "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }++  /* if using first dont do all of them*/+  bool end = false;+  /* insertions*/+  if (!end) cnt += insertions(Enc, str, &min);+  if (Enc->first && cnt>0) end = true;+  if (Enc->verbose_lvl>1) fprintf(stderr, "\n");++  /* deletions*/+  if (!end) cnt += deletions(Enc, str, &min);+  if (Enc->first && cnt>0) end = true;++  /* shifts (only if enabled + noLP disabled)*/+  if (!end && Enc->shift && !Enc->noLP) {+    cnt += shifts(Enc, str, &min);+    if (Enc->first && cnt>0) end = true;+  }++  /* if degeneracy occurs, solve it!*/+  if (!end && (Enc->end_unpr - Enc->begin_unpr)>0) {+    Enc->processed[Enc->end_pr] = str->structure;+    Enc->end_pr++;+    str->structure = Enc->unprocessed[Enc->begin_unpr];+    Enc->unprocessed[Enc->begin_unpr]=NULL;+    Enc->begin_unpr++;+    cnt += move_set(Enc, str);+  } else {+    /* write output to str*/+    copy_arr(str->structure, min.structure);+    str->energy = min.energy;+  }+  /* release minimal*/+  free(min.structure);++  /* resolve degeneracy in local minima*/+  if ((Enc->end_pr - Enc->begin_pr)>0) {+    Enc->processed[Enc->end_pr]=str->structure;+    Enc->end_pr++;++    int min = find_min(Enc->processed, Enc->begin_pr, Enc->end_pr);+    short *tmp = Enc->processed[min];+    Enc->processed[min] = Enc->processed[Enc->begin_pr];+    Enc->processed[Enc->begin_pr] = tmp;+    str->structure = Enc->processed[Enc->begin_pr];+    Enc->begin_pr++;+    free_degen(Enc);+  }++  if (Enc->verbose_lvl>1 && !(Enc->first)) { fprintf(stderr, "\n  end of MS:\n  "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }++  return cnt;+}++PRIVATE void+construct_moves(Encoded *Enc, short *structure){++  /* generate all possible moves (less than n^2)*/+  Enc->num_moves = 0;+  int i;+  for (i=1; i<=structure[0]; i++) {+    if (structure[i]!=0) {+      if (structure[i]<i) continue;+      Enc->moves_from[Enc->num_moves]=-i;+      Enc->moves_to[Enc->num_moves]=-structure[i];+      Enc->num_moves++;+      /* fprintf(stderr, "add  d(%d, %d)\n", i, str.structure[i]); */+    } else {+      int j;+      for (j=i+1; j<=structure[0]; j++) {+        /* fprintf(stderr, "check (%d, %d)\n", i, j); */+        if (structure[j]==0) {+          if (try_insert_seq(Enc->seq,i,j)) {+            Enc->moves_from[Enc->num_moves]=i;+            Enc->moves_to[Enc->num_moves]=j;+            Enc->num_moves++;+            /* fprintf(stderr, "add  i(%d, %d)\n", i, j); */+            continue;+          }+        } else if (structure[j]>j) { /*  '(' */+          j = structure[j];+        } else break;+      }+    }+  }++  /* permute them */+  for (i=0; i<Enc->num_moves-1; i++) {+    int rnd = rand();+    rnd = rnd % (Enc->num_moves-i) + i;+    int swp;+    swp = Enc->moves_from[i];+    Enc->moves_from[i]=Enc->moves_from[rnd];+    Enc->moves_from[rnd]=swp;+    swp = Enc->moves_to[i];+    Enc->moves_to[i]=Enc->moves_to[rnd];+    Enc->moves_to[rnd]=swp;+  }+}++PRIVATE int+move_rset(Encoded *Enc, struct_en *str){++  /* count how many times called*/+  cnt_move++;++  /* count better neighbours*/+  int cnt = 0;++  /* deepest descent*/+  struct_en min;+  min.structure = allocopy(str->structure);+  min.energy = str->energy;+  Enc->current_en = str->energy;++  if (Enc->verbose_lvl>0) { fprintf(stderr, "  start of MR:\n  "); print_str(stderr, str->structure); fprintf(stderr, " %d\n\n", str->energy); }++  /*  construct and permute possible moves */+  construct_moves(Enc, str->structure);++  /* find first lower one*/+  int i;+  for (i=0; i<Enc->num_moves; i++) {+    Enc->bp_left = Enc->moves_from[i];+    Enc->bp_right = Enc->moves_to[i];+    cnt = update_deepest(Enc, str, &min);+    if (cnt) break;+  }++  /* if degeneracy occurs, solve it!*/+  if (!cnt && (Enc->end_unpr - Enc->begin_unpr)>0) {+    Enc->processed[Enc->end_pr] = str->structure;+    Enc->end_pr++;+    str->structure = Enc->unprocessed[Enc->begin_unpr];+    Enc->unprocessed[Enc->begin_unpr]=NULL;+    Enc->begin_unpr++;+    cnt += move_rset(Enc, str);+  } else {+    /* write output to str*/+    copy_arr(str->structure, min.structure);+    str->energy = min.energy;+  }+  /* release minimal*/+  free(min.structure);++  /* resolve degeneracy in local minima*/+  if ((Enc->end_pr - Enc->begin_pr)>0) {+    Enc->processed[Enc->end_pr]=str->structure;+    Enc->end_pr++;++    int min = find_min(Enc->processed, Enc->begin_pr, Enc->end_pr);+    short *tmp = Enc->processed[min];+    Enc->processed[min] = Enc->processed[Enc->begin_pr];+    Enc->processed[Enc->begin_pr] = tmp;+    str->structure = Enc->processed[Enc->begin_pr];+    Enc->begin_pr++;+    free_degen(Enc);+  }++  return cnt;+}++/*check if base is lone*/+PRIVATE int+lone_base(short *pt, int i){++  if (i<=0 || i>pt[0]) return 0;+  /* is not a base pair*/+  if (pt[i]==0) return 0;++  /* base is lone:*/+  if (i-1>0) {+    /* is base pair and is the same bracket*/+    if (pt[i-1]!=0 && ((pt[i-1]<pt[pt[i-1]]) == (pt[i]<pt[pt[i]]))) return 0;+  }++  if (i+1<=pt[0]) {+    if (pt[i+1]!=0 && ((pt[i-1]<pt[pt[i-1]]) == (pt[i]<pt[pt[i]]))) return 0;+  }++  return 1;+}++/* if the structure has lone pairs*/+PRIVATE int+find_lone_pair(short* str){++  int i;+  for(i=1; i<str[0]; i++) {+    if (str[i]==0) continue; /* '.'*/++    if (str[i]>str[str[i]]) {  /* '('*/+      if (i+1==str[0] || str[i+1]==0 || str[i+1]<str[str[i+1]]) {+        return i;+      } else while (i+1!=str[0] && str[i+1]!=0 && str[i+1]>str[str[i+1]]) i++;+    }++    if (str[i]<str[str[i]]) {  /* ')'*/+      if (i+1==str[0] || str[i+1]==0 || str[i+1]>str[str[i+1]]) {+        return i;+      } else while (i+1!=str[0] && str[i+1]!=0 && str[i+1]<str[str[i+1]]) i++;+    }+  }++  return -1;+}++PUBLIC int+move_standard(char *seq,+              char *struc,+              enum MOVE_TYPE type,+              int verbosity_level,+              int shifts,+              int noLP){++  make_pair_matrix();++  short int *s0 = encode_sequence(seq, 0);+  short int *s1 = encode_sequence(seq, 1);+  short int *str = vrna_ptable(struc);++  int energy = 0;+  switch (type){+  case GRADIENT: energy = move_gradient(seq, str, s0, s1, verbosity_level, shifts, noLP); break;+  case FIRST: energy = move_first(seq, str, s0, s1, verbosity_level, shifts, noLP); break;+  case ADAPTIVE: energy = move_adaptive(seq, str, s0, s1, verbosity_level); break;+  }++  int i=1;+  for (; i<=str[0]; i++) {+    if (str[i]==0) struc[i-1]='.';+    else if (str[i]>str[str[i]]) struc[i-1]='(';+      else struc[i-1]=')';+  }++  free(s0);+  free(s1);+  free(str);++  return energy;+}++PUBLIC int+move_gradient(char *string,+              short *ptable,+              short *s,+              short *s1,+              int verbosity_level,+              int shifts,+              int noLP){++  cnt_move = 0;++  Encoded enc;+  enc.seq = string;+  enc.s0 = s;+  enc.s1 = s1;++  /* moves*/+  enc.bp_left=0;+  enc.bp_right=0;+  enc.bp_left2=0;+  enc.bp_right2=0;++  /* options*/+  enc.noLP=noLP;+  enc.verbose_lvl=verbosity_level;+  enc.first=0;+  enc.shift=shifts;++  /* degeneracy*/+  enc.begin_unpr=0;+  enc.begin_pr=0;+  enc.end_unpr=0;+  enc.end_pr=0;+  enc.current_en=0;++  /*  function */+  enc.funct=NULL;++  int i;+  for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;++  struct_en str;+  str.structure = allocopy(ptable);+  str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);++  while (move_set(&enc, &str)!=0) {+    free_degen(&enc);+  }+  free_degen(&enc);++  copy_arr(ptable, str.structure);+  free(str.structure);++  return str.energy;+}++PUBLIC int+move_first( char *string,+            short *ptable,+            short *s,+            short *s1,+            int verbosity_level,+            int shifts,+            int noLP){++  cnt_move = 0;++  Encoded enc;+  enc.seq = string;+  enc.s0 = s;+  enc.s1 = s1;++  /* moves*/+  enc.bp_left=0;+  enc.bp_right=0;+  enc.bp_left2=0;+  enc.bp_right2=0;++  /* options*/+  enc.noLP=noLP;+  enc.verbose_lvl=verbosity_level;+  enc.first=1;+  enc.shift=shifts;++  /* degeneracy*/+  enc.begin_unpr=0;+  enc.begin_pr=0;+  enc.end_unpr=0;+  enc.end_pr=0;+  enc.current_en=0;++  /*  function */+  enc.funct=NULL;++  int i;+  for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;++  struct_en str;+  str.structure = allocopy(ptable);+  str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);++  while (move_set(&enc, &str)!=0) {+    free_degen(&enc);+  }+  free_degen(&enc);++  copy_arr(ptable, str.structure);+  free(str.structure);++  return str.energy;+}++PUBLIC int+move_adaptive(char *string,+              short *ptable,+              short *s,+              short *s1,+              int verbosity_level){++  srand(time(NULL));++  cnt_move = 0;++  Encoded enc;+  enc.seq = string;+  enc.s0 = s;+  enc.s1 = s1;++  /* moves*/+  enc.bp_left=0;+  enc.bp_right=0;+  enc.bp_left2=0;+  enc.bp_right2=0;++  /* options*/+  enc.noLP=0;+  enc.verbose_lvl=verbosity_level;+  enc.first=1;+  enc.shift=0;++  /* degeneracy*/+  enc.begin_unpr=0;+  enc.begin_pr=0;+  enc.end_unpr=0;+  enc.end_pr=0;+  enc.current_en=0;++  /*  function */+  enc.funct=NULL;++  /*  allocate memory for moves */+  enc.moves_from = (int*) vrna_alloc(ptable[0]*ptable[0]*sizeof(int));+  enc.moves_to = (int*) vrna_alloc(ptable[0]*ptable[0]*sizeof(int));++  int i;+  for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;++  struct_en str;+  str.structure = allocopy(ptable);+  str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);++  while (move_rset(&enc, &str)!=0) {+    free_degen(&enc);+  }+  free_degen(&enc);++  copy_arr(ptable, str.structure);+  free(str.structure);+  free(enc.moves_from);+  free(enc.moves_to);++  return str.energy;+}++PUBLIC int+browse_neighs(char *seq,+              char *struc,+              int verbosity_level,+              int shifts,+              int noLP,+              int (*funct) (struct_en*, struct_en*)){++  make_pair_matrix();++  short int *s0 = encode_sequence(seq, 0);+  short int *s1 = encode_sequence(seq, 1);+  short int *str = vrna_ptable(struc);++  int res = browse_neighs_pt(seq, str, s0, s1, verbosity_level, shifts, noLP, funct);++  free(s0);+  free(s1);+  free(str);++  return res;+}++PUBLIC int+browse_neighs_pt( char *string,+                  short *ptable,+                  short *s,+                  short *s1,+                  int verbosity_level,+                  int shifts,+                  int noLP,+                  int (*funct) (struct_en*, struct_en*)){++  cnt_move = 0;++  Encoded enc;+  enc.seq = string;+  enc.s0 = s;+  enc.s1 = s1;++  /* moves*/+  enc.bp_left=0;+  enc.bp_right=0;+  enc.bp_left2=0;+  enc.bp_right2=0;++  /* options*/+  enc.noLP=noLP;+  enc.verbose_lvl=verbosity_level;+  enc.first=1;+  enc.shift=shifts;++  /* degeneracy*/+  enc.begin_unpr=0;+  enc.begin_pr=0;+  enc.end_unpr=0;+  enc.end_pr=0;+  enc.current_en=0;++  /*  function */+  enc.funct=funct;++  int i;+  for (i=0; i<MAX_DEGEN; i++) enc.processed[i]=enc.unprocessed[i]=NULL;++  struct_en str;+  str.structure = allocopy(ptable);+  str.energy = energy_of_structure_pt(enc.seq, str.structure, enc.s0, enc.s1, 0);++  move_set(&enc, &str);+  free_degen(&enc);++  copy_arr(ptable, str.structure);+  free(str.structure);++  return str.energy;+}++/* printf*/+PUBLIC void+print_stren(FILE *out, struct_en *str) {+  print_str(out, str->structure);+  fprintf(out, " %6.2f\n", str->energy/100.0);+}++PUBLIC void+print_str(FILE *out, short *str) {+  int i;+  for (i=1; i<=str[0]; i++) {+    if (str[i]==0) fprintf(out, ".");+    else if (str[i]<i) fprintf(out, ")");+    else fprintf(out, "(");+  }+}+++#ifdef TEST_MOVESET+/*  sample usage: */+int main() {+  char seq[20] = "ACCCCCCTCTGTAGGGGGA";+  char str[20] = ".((.(.........).)).";++  /*  move to the local minimum and display it */+  int energy = move_standard(seq, str, GRADIENT, 0, 0, 0);+  fprintf(stdout, "%s %6.2f\n\n", str, energy/100.0);++  /* now create an array of every structure in neighbourhood of str structure */+  struct_en *list = NULL;+  int list_length = 0;++  int get_list(struct_en *new_one, struct_en *old_one)+  {+    /*  enlarge the list */+    list_length++;+    list = (struct_en*) realloc(list, list_length*sizeof(struct_en));++    /*  copy the structure */+    list[list_length-1].energy = new_one->energy;+    list[list_length-1].structure = allocopy(new_one->structure);++    /*  we want to continue -> return 0 */+    return 0;+  }+  browse_neighs(seq, str, 0, 0, 0, get_list);++  /*  print them and free the memory: */+  int i;+  for (i=0; i<list_length; i++) {+    print_stren(stdout, &list[i]);+    free(list[i].structure);+  }+  free(list);++  return 0;+}++#endif
+ C/ViennaRNA/move_set.h view
@@ -0,0 +1,91 @@+#ifndef __MOVE_SET_H+#define __MOVE_SET_H++/**+ *  @brief  Data structure for energy_of_move()+ */+typedef struct _struct_en{+  int energy;        /* energy in 10kcal/mol*/+  short *structure;  /* structure in energy_of_move format*/+} struct_en;++/* prints structure*/+void print_stren(FILE *out, struct_en *str);+void print_str(FILE *out, short *str);++/* copying functions*/+void copy_arr(short *dest, short *src); /*just copy*/+short *allocopy(short *src);            /*copy and make space*/++enum MOVE_TYPE {GRADIENT, FIRST, ADAPTIVE};++/* walking methods (verbose_lvl 0-2, shifts = use shift moves? noLP = no lone pairs? (not compatible with shifts))+    input:    seq - sequence+              ptable - structure encoded with make_pair_table() from pair_mat.h+              s, s1 - sequence encoded with encode_sequence from pair_mat.h+    methods:  deepest - lowest energy structure is used+              first - first found lower energy structure is used+              rand - random lower energy structure is used+    returns local minima structure in ptable and its energy in 10kcal/mol as output */++int move_gradient( char *seq,+                  short *ptable,+                  short *s,+                  short *s1,+                  int verbosity_level,+                  int shifts,+                  int noLP);+int move_first( char *seq,+                short *ptable,+                short *s,+                short *s1,+                int verbosity_level,+                int shifts,+                int noLP);+int move_adaptive(  char *seq,+                short *ptable,+                short *s,+                short *s1,+                int verbosity_level);++/* standardized method that encapsulates above "_pt" methods+  input:  seq - sequence+          struc - structure in dot-bracket notation+          type - type of move selection according to MOVE_TYPE enum+  return: energy of LM+          structure of LM in struc in bracket-dot notation+*/+int move_standard(char *seq,+                  char *struc,+                  enum MOVE_TYPE type,+                  int verbosity_level,+                  int shifts,+                  int noLP);+++/* browse_neighbours and perform funct function on each of them (used mainly for user specified flooding)+    input:    seq - sequence+              ptable - structure encoded with make_pair_table() from pair_mat.h+              s, s1 - sequence encoded with encode_sequence from pair_mat.h+              funct - function (structure from neighbourhood, structure from input) toperform on every structure in neigbourhood (if the function returns non-zero, the iteration through neighbourhood stops.)+    returns energy of the structure funct sets as second argument*/+int browse_neighs_pt( char *seq,+                   short *ptable,+                   short *s,+                   short *s1,+                   int verbosity_level,+                   int shifts,+                   int noLP,+                   int (*funct) (struct_en*, struct_en*));++int browse_neighs( char *seq,+                   char *struc,+                   int verbosity_level,+                   int shifts,+                   int noLP,+                   int (*funct) (struct_en*, struct_en*));++#endif+++
+ C/ViennaRNA/multibranch_loops.c view
@@ -0,0 +1,3072 @@+#ifdef HAVE_CONFIG_H+#include "config.h"+#endif+++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/exterior_loops.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structured_domains.h"+#include "ViennaRNA/unstructured_domains.h"+#include "ViennaRNA/multibranch_loops.h"++struct default_data {+  int                       *idx;+  char                      *mx;+  int                       cp;+  int                       *hc_up;+  void                      *hc_dat;+  vrna_callback_hc_evaluate *hc_f;+};+++/*+ #################################+ # PRIVATE FUNCTION DECLARATIONS #+ #################################+ */++PRIVATE int+E_mb_loop_fast(vrna_fold_compound_t *vc,+               int                  i,+               int                  j,+               int                  *dmli1,+               int                  *dmli2);+++PRIVATE int+E_mb_loop_fast_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j,+                           int                  *dmli1,+                           int                  *dmli2);+++PRIVATE FLT_OR_DBL+exp_E_mb_loop_fast(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   FLT_OR_DBL           *qqm1);+++PRIVATE FLT_OR_DBL+exp_E_mb_loop_fast_comparative(vrna_fold_compound_t *vc,+                               int                  i,+                               int                  j,+                               FLT_OR_DBL           *qqm1);+++PRIVATE int+E_ml_stems_fast(vrna_fold_compound_t  *vc,+                int                   i,+                int                   j,+                int                   *fmi,+                int                   *dmli);+++PRIVATE int+E_ml_stems_fast_comparative(vrna_fold_compound_t  *vc,+                            int                   i,+                            int                   j,+                            int                   *fmi,+                            int                   *dmli);+++PRIVATE int+extend_fm_3p(int                  i,+             int                  j,+             int                  *fm,+             vrna_fold_compound_t *vc);+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data);+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data);+++PRIVATE FLT_OR_DBL+exp_E_ml_fast(vrna_fold_compound_t  *vc,+              int                   i,+              int                   j,+              vrna_mx_pf_aux_ml_t   *aux_mx);+++PRIVATE FLT_OR_DBL+exp_E_ml_fast_comparative(vrna_fold_compound_t  *vc,+                          int                   i,+                          int                   j,+                          vrna_mx_pf_aux_ml_t   *aux_mx);+++/*+ #################################+ # BEGIN OF FUNCTION DEFINITIONS #+ #################################+ */+PUBLIC int+vrna_E_mb_loop_fast(vrna_fold_compound_t  *vc,+                    int                   i,+                    int                   j,+                    int                   *dmli1,+                    int                   *dmli2)+{+  int e = INF;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        e = E_mb_loop_fast(vc, i, j, dmli1, dmli2);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        e = E_mb_loop_fast_comparative(vc, i, j, dmli1, dmli2);+        break;+    }+  }++  return e;+}+++PUBLIC int+vrna_E_ml_stems_fast(vrna_fold_compound_t *vc,+                     int                  i,+                     int                  j,+                     int                  *fmi,+                     int                  *dmli)+{+  int e = INF;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        e = E_ml_stems_fast(vc, i, j, fmi, dmli);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        e = E_ml_stems_fast_comparative(vc, i, j, fmi, dmli);+        break;+    }+  }++  return e;+}+++PUBLIC FLT_OR_DBL+vrna_exp_E_mb_loop_fast(vrna_fold_compound_t  *vc,+                        int                   i,+                        int                   j,+                        FLT_OR_DBL            *qqm1)+{+  FLT_OR_DBL q = 0.;++  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        q = exp_E_mb_loop_fast(vc, i, j, qqm1);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        q = exp_E_mb_loop_fast_comparative(vc, i, j, qqm1);+        break;+    }+  }++  return q;+}+++PRIVATE int+E_mb_loop_fast_comparative(vrna_fold_compound_t *vc,+                           int                  i,+                           int                  j,+                           int                  *dmli1,+                           int                  *dmli2)+{+  short                     **S, **S5, **S3;+  int                       *indx, e, decomp, s, n_seq, dangle_model, *type;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 **scs;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  n_seq         = vc->n_seq;+  indx          = vc->jindx;+  P             = vc->params;+  md            = &(P->model_details);+  hc            = vc->hc;+  scs           = vc->scs;+  dangle_model  = md->dangles;+  e             = INF;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }+++  /* multi-loop decomposition ------------------------*/+  if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+    decomp = dmli1[j - 1];++    type  = (int *)vrna_alloc(n_seq * sizeof(int));+    S     = vc->S;+    S5    = vc->S5;     /* S5[s][i] holds next base 5' of i in sequence s */+    S3    = vc->S3;     /* Sl[s][i] holds next base 3' of i in sequence s */++    for (s = 0; s < n_seq; s++) {+      type[s] = md->pair[S[s][j]][S[s][i]];+      if (type[s] == 0)+        type[s] = 7;+    }++    if (dangle_model)+      for (s = 0; s < n_seq; s++)+        decomp += E_MLstem(type[s], S5[s][j], S3[s][i], P);+    else+      for (s = 0; s < n_seq; s++)+        decomp += E_MLstem(type[s], -1, -1, P);+    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->energy_bp)+            decomp += scs[s]->energy_bp[indx[j] + i];+      }+    }++    free(type);++    e = decomp + n_seq * P->MLclosing;+  }++  return e;+}+++PRIVATE int+E_mb_loop_fast(vrna_fold_compound_t *vc,+               int                  i,+               int                  j,+               int                  *dmli1,+               int                  *dmli2)+{+  unsigned char             type, tt;+  char                      *ptype;+  short                     S_i1, S_j1, *S;+  unsigned int              *sn;+  int                       decomp, en, e, cp, *indx, *fc, ij, dangle_model, *rtype;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_param_t              *P;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp            = vc->cutpoint;+  ptype         = vc->ptype;+  S             = vc->sequence_encoding;+  indx          = vc->jindx;+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  fc            = vc->matrices->fc;+  P             = vc->params;+  ij            = indx[j] + i;+  dangle_model  = P->model_details.dangles;+  rtype         = &(P->model_details.rtype[0]);+  type          = (unsigned char)ptype[ij];+  /* init values */+  e       = INF;+  decomp  = INF;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  if (cp < 0) {+    S_i1  = S[i + 1];+    S_j1  = S[j - 1];+  } else {+    S_i1  = (sn[i] == sn[i + 1]) ? S[i + 1] : -1;+    S_j1  = (sn[j - 1] == sn[j]) ? S[j - 1] : -1;+  }++  if ((S_i1 >= 0) && (S_j1 >= 0)) {+    /* regular multi branch loop */+    /* new closing pair (i,j) with mb part [i+1,j-1] */+    if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+      decomp  = dmli1[j - 1];+      tt      = rtype[type];++      if (tt == 0)+        tt = 7;++      if (decomp != INF) {+        switch (dangle_model) {+          /* no dangles */+          case 0:+            decomp += E_MLstem(tt, -1, -1, P);+            if (sc) {+              if (sc->energy_bp)+                decomp += sc->energy_bp[ij];++              if (sc->f)+                decomp += sc->f(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, sc->data);+            }+            break;++          /* double dangles */+          case 2:+            decomp += E_MLstem(tt, S_j1, S_i1, P);+            if (sc) {+              if (sc->energy_bp)+                decomp += sc->energy_bp[ij];++              if (sc->f)+                decomp += sc->f(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, sc->data);+            }+            break;++          /* normal dangles, aka dangles = 1 || 3 */+          default:+            decomp += E_MLstem(tt, -1, -1, P);+            if (sc) {+              if (sc->energy_bp)+                decomp += sc->energy_bp[ij];++              if (sc->f)+                decomp += sc->f(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, sc->data);+            }+            break;+        }+      }+    }++    if (dangle_model % 2) {+      /* dangles == 1 || dangles == 3 */+      /* new closing pair (i,j) with mb part [i+2,j-1] */+      if (evaluate(i, j, i + 2, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if (dmli2[j - 1] != INF) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en = dmli2[j - 1] + E_MLstem(tt, -1, S_i1, P) + P->MLbase;+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[i + 1][1];++            if (sc->energy_bp)+              en += sc->energy_bp[ij];++            if (sc->f)+              en += sc->f(i, j, i + 2, j - 1, VRNA_DECOMP_PAIR_ML, sc->data);+          }+          decomp = MIN2(decomp, en);+        }+      }++      /* new closing pair (i,j) with mb part [i+2.j-2] */+      if (evaluate(i, j, i + 2, j - 2, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if (dmli2[j - 2] != INF) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en = dmli2[j - 2] + E_MLstem(tt, S_j1, S_i1, P) + 2 * P->MLbase;+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[i + 1][1]+                    + sc->energy_up[j - 1][1];++            if (sc->energy_bp)+              en += sc->energy_bp[ij];++            if (sc->f)+              en += sc->f(i, j, i + 2, j - 2, VRNA_DECOMP_PAIR_ML, sc->data);+          }+          decomp = MIN2(decomp, en);+        }+      }++      /* new closing pair (i,j) with mb part [i+1, j-2] */+      if (evaluate(i, j, i + 1, j - 2, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if (dmli1[j - 2] != INF) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en = dmli1[j - 2] + E_MLstem(tt, S_j1, -1, P) + P->MLbase;+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[j - 1][1];++            if (sc->energy_bp)+              en += sc->energy_bp[ij];++            if (sc->f)+              en += sc->f(i, j, i + 1, j - 2, VRNA_DECOMP_PAIR_ML, sc->data);+          }+          decomp = MIN2(decomp, en);+        }+      }+    } /* end if dangles % 2 */++    if (decomp != INF)+      e = decomp + P->MLclosing;+  } /* end regular multibranch loop */++  if (sn[i] != sn[j]) {+    /* multibrach like cofold structure with cut somewhere between i and j */+    if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+      if ((fc[i + 1] != INF) && (fc[j - 1] != INF)) {+        decomp  = fc[i + 1] + fc[j - 1];+        tt      = rtype[type];++        if (tt == 0)+          tt = 7;++        switch (dangle_model) {+          case 0:+            decomp += E_ExtLoop(tt, -1, -1, P);+            break;++          case 2:+            decomp += E_ExtLoop(tt, S_j1, S_i1, P);+            break;++          default:+            decomp += E_ExtLoop(tt, -1, -1, P);+            break;+        }+      }+    }++    if (dangle_model % 2) {+      /* dangles == 1 || dangles == 3 */+      if (evaluate(i, j, i + 2, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if ((fc[i + 2] != INF) && (fc[j - 1] != INF)) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en      = fc[i + 2] + fc[j - 1] + E_ExtLoop(tt, -1, S_i1, P);+          decomp  = MIN2(decomp, en);+        }+      }++      if (evaluate(i, j, i + 1, j - 2, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if ((fc[i + 1] != INF) && (fc[j - 2] != INF)) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en      = fc[i + 1] + fc[j - 2] + E_ExtLoop(tt, S_j1, -1, P);+          decomp  = MIN2(decomp, en);+        }+      }++      if (evaluate(i, j, i + 2, j - 2, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+        if ((fc[i + 2] != INF) && (fc[j - 2] != INF)) {+          tt = rtype[type];++          if (tt == 0)+            tt = 7;++          en      = fc[i + 2] + fc[j - 2] + E_ExtLoop(tt, S_j1, S_i1, P);+          decomp  = MIN2(decomp, en);+        }+      }+    }++    e = MIN2(e, decomp);+  }+  return e;+}+++PUBLIC int+E_mb_loop_stack(int                   i,+                int                   j,+                vrna_fold_compound_t  *vc)+{+  unsigned char             type, type_2;+  char                      *ptype;+  int                       e, decomp, en, i1k, k1j1, ij, k, *indx, *c, *fML, turn, *rtype;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  indx  = vc->jindx;+  hc    = vc->hc;+  c     = vc->matrices->c;+  fML   = vc->matrices->fML;+  P     = vc->params;+  md    = &(P->model_details);+  turn  = md->min_loop_size;+  ptype = vc->ptype;+  rtype = &(md->rtype[0]);+  sc    = vc->sc;+  e     = INF;+  ij    = indx[j] + i;+  type  = ptype[ij];++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+    if (type == 0)+      type = 7;++    decomp  = INF;+    k1j1    = indx[j - 1] + i + 2 + turn + 1;+    for (k = i + 2 + turn; k < j - 2 - turn; k++, k1j1++) {+      i1k = indx[k] + i + 1;++      if (evaluate(i, j, i + 1, k, VRNA_DECOMP_ML_COAXIAL, &hc_dat_local)) {+        type_2 = rtype[(unsigned char)ptype[i1k]];++        if (type_2 == 0)+          type_2 = 7;++        en = c[i1k] + P->stack[type][type_2] + fML[k1j1];+        if (sc)+          if (sc->f)+            en += sc->f(i, j, i + 1, k, VRNA_DECOMP_ML_COAXIAL, sc->data);+        decomp = MIN2(decomp, en);+      }++      if (evaluate(i, j, k + 1, j - 1, VRNA_DECOMP_ML_COAXIAL, &hc_dat_local)) {+        type_2 = rtype[(unsigned char)ptype[k1j1]];++        if (type_2 == 0)+          type_2 = 7;++        en = c[k1j1] + P->stack[type][type_2] + fML[i1k];+        if (sc)+          if (sc->f)+            en += sc->f(i, j, k + 1, j - 1, VRNA_DECOMP_ML_COAXIAL, sc->data);+        decomp = MIN2(decomp, en);+      }+    }+    /* no TermAU penalty if coax stack */+    decomp += 2 * P->MLintern[1] + P->MLclosing;+    if (sc) {+      if (sc->energy_bp)+        decomp += sc->energy_bp[ij];+      if (sc->f)+        decomp += sc->f(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, sc->data);+    }+    e = decomp;+  }+  return e;+}+++PUBLIC int+E_ml_rightmost_stem(int                   i,+                    int                   j,+                    vrna_fold_compound_t  *vc)+{+  if ((vc) && (vc->matrices) && (vc->matrices->fM1))+    return extend_fm_3p(i, j, vc->matrices->fM1, vc);++  return INF;+}+++/*+ * compose a multibranch loop part fm[i:j]+ * by either c[i,j]/ggg[i,j] or fm[i:j-1]+ *+ * This function can be used for fM and fM1+ */+PRIVATE int+extend_fm_3p(int                  i,+             int                  j,+             int                  *fm,+             vrna_fold_compound_t *vc)+{+  short                     *S;+  unsigned int              *sn;+  int                       en, length, *indx, *c, *ggg, ij, type,+                            dangle_model, with_gquad, e, u, k, cnt, with_ud;+  vrna_param_t              *P;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  P             = vc->params;+  length        = vc->length;+  S             = vc->sequence_encoding;+  indx          = vc->jindx;+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  c             = vc->matrices->c;+  ggg           = vc->matrices->ggg;+  ij            = indx[j] + i;+  type          = vc->ptype[ij];+  dangle_model  = P->model_details.dangles;+  with_gquad    = P->model_details.gquad;+  domains_up    = vc->domains_up;+  with_ud       = (domains_up && domains_up->energy_cb) ? 1 : 0;+  e             = INF;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  if (sn[i - 1] == sn[i]) {+    if (sn[j] == sn[j + 1]) {+      if (evaluate(i, j, i, j, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        if (type == 0)+          type = 7;++        e = c[ij];+        if (e != INF) {+          switch (dangle_model) {+            case 2:+              e += E_MLstem(type, (i == 1) ? S[length] : S[i - 1], S[j + 1], P);+              break;++            default:+              e += E_MLstem(type, -1, -1, P);+              break;+          }+          if (sc)+            if (sc->f)+              e += sc->f(i, j, i, j, VRNA_DECOMP_ML_STEM, sc->data);+        }+      }++      if (with_gquad) {+        if (sn[i] == sn[j]) {+          en  = ggg[ij] + E_MLstem(0, -1, -1, P);+          e   = MIN2(e, en);+        }+      }+    }++    if (sn[j - 1] == sn[j]) {+      if (evaluate(i, j, i, j - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        if (fm[indx[j - 1] + i] != INF) {+          en = fm[indx[j - 1] + i] + P->MLbase;+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[j][1];+            if (sc->f)+              en += sc->f(i, j, i, j - 1, VRNA_DECOMP_ML_ML, sc->data);+          }+          e = MIN2(e, en);+        }+      }+    }++    if (with_ud) {+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u = domains_up->uniq_motif_size[cnt];+        k = j - u + 1;+        if ((k > i) && (sn[j - u] == sn[j])) {+          if (evaluate(i, j, i, k - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+            if (fm[indx[k - 1] + i] != INF) {+              en = domains_up->energy_cb(vc,+                                         k, j,+                                         VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                         domains_up->data);+              if (en != INF) {+                en += fm[indx[k - 1] + i]+                      + u * P->MLbase;++                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[k][u];+                  if (sc->f)+                    en += sc->f(i, j, i, k - 1, VRNA_DECOMP_ML_ML, sc->data);+                }+                e = MIN2(e, en);+              }+            }+          }+        }+      }+    }+  }+  return e;+}+++PRIVATE int+E_ml_stems_fast(vrna_fold_compound_t  *vc,+                int                   i,+                int                   j,+                int                   *fmi,+                int                   *dmli)+{+  char                      *ptype;+  short                     *S;+  unsigned int              *sn;+  int                       k, en, decomp, mm5, mm3, type_2, k1j, stop, length, *indx,+                            *c, *fm, ij, dangle_model, turn, type, *rtype, circular, cp, e, u,+                            cnt, with_ud;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_param_t              *P;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  length        = (int)vc->length;+  ptype         = vc->ptype;+  S             = vc->sequence_encoding;+  indx          = vc->jindx;+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  c             = vc->matrices->c;+  fm            = vc->matrices->fML;+  P             = vc->params;+  ij            = indx[j] + i;+  dangle_model  = P->model_details.dangles;+  turn          = P->model_details.min_loop_size;+  type          = ptype[ij];+  rtype         = &(P->model_details.rtype[0]);+  circular      = P->model_details.circ;+  cp            = vc->cutpoint;+  domains_up    = vc->domains_up;+  with_ud       = (domains_up && domains_up->energy_cb) ? 1 : 0;+  e             = INF;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  /*+   *  extension with one unpaired nucleotide at the right (3' site)+   *  or full branch of (i,j)+   */+  e = extend_fm_3p(i, j, fm, vc);++  /*+   *  extension with one unpaired nucleotide at 5' site+   *  and all other variants which are needed for odd+   *  dangle models+   */+  if (sn[i - 1] == sn[i]) {+    if (sn[i] == sn[i + 1]) {+      if (evaluate(i, j, i + 1, j, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        if (fm[ij + 1] != INF) {+          en = fm[ij + 1] + P->MLbase;+          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[i][1];+            if (sc->f)+              en += sc->f(i, j, i + 1, j, VRNA_DECOMP_ML_ML, sc->data);+          }+          e = MIN2(e, en);+        }+      }+    }++    /* extension with bound ligand on 5'site */+    if (with_ud) {+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u = domains_up->uniq_motif_size[cnt];+        k = i + u - 1;+        if ((k < j) && (sn[i] == sn[k + 1])) {+          if (evaluate(i, j, k + 1, j, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+            if (fm[ij + u] != INF) {+              en = domains_up->energy_cb(vc,+                                         i, k,+                                         VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                         domains_up->data);+              if (en != INF) {+                en += fm[ij + u]+                      + u * P->MLbase;++                if (sc) {+                  if (sc->energy_up)+                    en += sc->energy_up[i][u];+                  if (sc->f)+                    en += sc->f(i, j, k + 1, j, VRNA_DECOMP_ML_ML, sc->data);+                }+                e = MIN2(e, en);+              }+            }+          }+        }+      }+    }++    if (dangle_model % 2) {+      /* dangle_model = 1 || 3 */++      mm5 = ((i > 1) || circular) ? S[i] : -1;+      mm3 = ((j < length) || circular) ? S[j] : -1;++      if (sn[i] == sn[i + 1]) {+        if (evaluate(i, j, i + 1, j, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+          if (c[ij + 1] != INF) {+            type = ptype[ij + 1];++            if (type == 0)+              type = 7;++            en = c[ij + 1] + E_MLstem(type, mm5, -1, P) + P->MLbase;+            if (sc) {+              if (sc->energy_up)+                en += sc->energy_up[i][1];+              if (sc->f)+                en += sc->f(i, j, i + 1, j, VRNA_DECOMP_ML_STEM, sc->data);+            }+            e = MIN2(e, en);+          }+        }+      }++      if (sn[j - 1] == sn[j]) {+        if (evaluate(i, j, i, j - 1, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+          if (c[indx[j - 1] + i] != INF) {+            type = ptype[indx[j - 1] + i];++            if (type == 0)+              type = 7;++            en = c[indx[j - 1] + i] + E_MLstem(type, -1, mm3, P) + P->MLbase;+            if (sc) {+              if (sc->energy_up)+                en += sc->energy_up[j][1];+              if (sc->f)+                en += sc->f(i, j, i, j - 1, VRNA_DECOMP_ML_STEM, sc->data);+            }+            e = MIN2(e, en);+          }+        }+      }++      if ((sn[j - 1] == sn[j]) && (sn[i] == sn[i + 1])) {+        if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+          if (c[indx[j - 1] + i + 1] != INF) {+            type = ptype[indx[j - 1] + i + 1];++            if (type == 0)+              type = 7;++            en = c[indx[j - 1] + i + 1] + E_MLstem(type, mm5, mm3, P) + 2 * P->MLbase;+            if (sc) {+              if (sc->energy_up)+                en += sc->energy_up[j][1] + sc->energy_up[i][1];+              if (sc->f)+                en += sc->f(i, j, i + 1, j - 1, VRNA_DECOMP_ML_STEM, sc->data);+            }+            e = MIN2(e, en);+          }+        }+      }+    } /* end special cases for dangles == 1 || dangles == 3 */+  }++  /* modular decomposition -------------------------------*/+  k1j   = indx[j] + i + turn + 2;+  stop  = (cp > 0) ? (cp - 1) : (j - 2 - turn);++  /* duplicated code is faster than conditions in loop */+  if (hc->f) {+    if (sc && sc->f) {+      for (decomp = INF, k = i + 1 + turn; k <= stop; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF) && hc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+          en      = fmi[k] + fm[k1j];+          en      += sc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+          decomp  = MIN2(decomp, en);+        }+      }+      k++; k1j++;+      for (; k <= j - 2 - turn; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF) && hc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+          en      = fmi[k] + fm[k1j];+          en      += sc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+          decomp  = MIN2(decomp, en);+        }+      }+    } else {+      for (decomp = INF, k = i + 1 + turn; k <= stop; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF) && hc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+          en      = fmi[k] + fm[k1j];+          decomp  = MIN2(decomp, en);+        }+      }+      k++; k1j++;+      for (; k <= j - 2 - turn; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF) && hc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+          en      = fmi[k] + fm[k1j];+          decomp  = MIN2(decomp, en);+        }+      }+    }+  } else {+    if (sc && sc->f) {+      for (decomp = INF, k = i + 1 + turn; k <= stop; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF)) {+          en      = fmi[k] + fm[k1j];+          en      += sc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+          decomp  = MIN2(decomp, en);+        }+      }+      k++; k1j++;+      for (; k <= j - 2 - turn; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF)) {+          en      = fmi[k] + fm[k1j];+          en      += sc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+          decomp  = MIN2(decomp, en);+        }+      }+    } else {+      for (decomp = INF, k = i + 1 + turn; k <= stop; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF)) {+          en      = fmi[k] + fm[k1j];+          decomp  = MIN2(decomp, en);+        }+      }+      k++; k1j++;+      for (; k <= j - 2 - turn; k++, k1j++) {+        if ((fmi[k] != INF) && (fm[k1j] != INF)) {+          en      = fmi[k] + fm[k1j];+          decomp  = MIN2(decomp, en);+        }+      }+    }+  }++  dmli[j] = decomp;               /* store for use in fast ML decompositon */+  e       = MIN2(e, decomp);++  /* coaxial stacking */+  if (dangle_model == 3) {+    /* additional ML decomposition as two coaxially stacked helices */+    int ik;+    k1j = indx[j] + i + turn + 2;+    for (decomp = INF, k = i + 1 + turn; k <= stop; k++, k1j++) {+      ik = indx[k] + i;+      if (evaluate(i, k, k + 1, j, VRNA_DECOMP_ML_COAXIAL_ENC, &hc_dat_local)) {+        type    = rtype[(unsigned char)ptype[ik]];+        type_2  = rtype[(unsigned char)ptype[k1j]];++        if (type == 0)+          type = 7;+        if (type_2 == 0)+          type_2 = 7;++        en = c[ik] + c[k1j] + P->stack[type][type_2];+        if (sc)+          if (sc->f)+            en += sc->f(i, k, k + 1, j, VRNA_DECOMP_ML_COAXIAL_ENC, sc->data);+        decomp = MIN2(decomp, en);+      }+    }+    k++; k1j++;+    for (; k <= j - 2 - turn; k++, k1j++) {+      ik = indx[k] + i;+      if (evaluate(i, k, k + 1, j, VRNA_DECOMP_ML_COAXIAL_ENC, &hc_dat_local)) {+        type    = rtype[(unsigned char)ptype[ik]];+        type_2  = rtype[(unsigned char)ptype[k1j]];++        if (type == 0)+          type = 7;+        if (type_2 == 0)+          type_2 = 7;++        en = c[ik] + c[k1j] + P->stack[type][type_2];+        if (sc)+          if (sc->f)+            en += sc->f(i, k, k + 1, j, VRNA_DECOMP_ML_COAXIAL, sc->data);+        decomp = MIN2(decomp, en);+      }+    }++    decomp += 2 * P->MLintern[1];        /* no TermAU penalty if coax stack */+#if 0+    /*+     * This is needed for Y shaped ML loops with coax stacking of+     * interior pairts, but backtracking will fail if activated+     */+    DMLi[j] = MIN2(DMLi[j], decomp);+    DMLi[j] = MIN2(DMLi[j], DMLi[j - 1] + P->MLbase);+    DMLi[j] = MIN2(DMLi[j], DMLi1[j] + P->MLbase);+    new_fML = MIN2(new_fML, DMLi[j]);+#endif+    e = MIN2(e, decomp);+  }++  fmi[j] = e;++  return e;+}+++PRIVATE int+E_ml_stems_fast_comparative(vrna_fold_compound_t  *vc,+                            int                   i,+                            int                   j,+                            int                   *fmi,+                            int                   *dmli)+{+  char            *hard_constraints;+  short           **S, **S5, **S3;+  unsigned short  **a2s;+  int             e, energy, *c, *fML, *ggg, ij, *indx, s, n_seq, k,+                  dangle_model, decomp, turn, *type;+  vrna_param_t    *P;+  vrna_md_t       *md;+  vrna_mx_mfe_t   *matrices;+  vrna_hc_t       *hc;+  vrna_sc_t       **scs;++  n_seq             = vc->n_seq;+  matrices          = vc->matrices;+  P                 = vc->params;+  md                = &(P->model_details);+  c                 = matrices->c;+  fML               = matrices->fML;+  ggg               = matrices->ggg;+  indx              = vc->jindx;+  hc                = vc->hc;+  scs               = vc->scs;+  hard_constraints  = hc->matrix;+  dangle_model      = md->dangles;+  turn              = md->min_loop_size;+  a2s               = vc->a2s;+  ij                = indx[j] + i;+  e                 = INF;++  if (hc->up_ml[i]) {+    energy = fML[ij + 1] + n_seq * P->MLbase;+    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->energy_up)+            energy += scs[s]->energy_up[a2s[s][i]][1];+      }+    }+    e = MIN2(e, energy);+  }++  if (hc->up_ml[j]) {+    energy = fML[indx[j - 1] + i] + n_seq * P->MLbase;+    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->energy_up)+            energy += scs[s]->energy_up[a2s[s][j]][1];+      }+    }+    e = MIN2(e, energy);+  }++  if (hard_constraints[ij] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC) {+    energy = c[ij];++    type  = (int *)vrna_alloc(n_seq * sizeof(int));+    S     = vc->S;+    S5    = vc->S5;     /* S5[s][i] holds next base 5' of i in sequence s */+    S3    = vc->S3;     /* Sl[s][i] holds next base 3' of i in sequence s */++    for (s = 0; s < n_seq; s++) {+      type[s] = md->pair[S[s][i]][S[s][j]];+      if (type[s] == 0)+        type[s] = 7;+    }++    if (dangle_model)+      for (s = 0; s < n_seq; s++)+        energy += E_MLstem(type[s], S5[s][i], S3[s][j], P);+    else+      for (s = 0; s < n_seq; s++)+        energy += E_MLstem(type[s], -1, -1, P);+    e = MIN2(e, energy);++    if (md->gquad) {+      decomp  = ggg[indx[j] + i] + n_seq * E_MLstem(0, -1, -1, P);+      e       = MIN2(e, decomp);+    }++    free(type);+  }+++  /* modular decomposition -------------------------------*/+  for (decomp = INF, k = i + 1 + turn; k <= j - 2 - turn; k++)+    decomp = MIN2(decomp, fmi[k] + fML[indx[j] + k + 1]);++  dmli[j] = decomp; /* store for later use in ML decompositon */++  e = MIN2(e, decomp);++  fmi[j] = e; /* store for later use in ML decompositon */++  return e;+}+++PRIVATE FLT_OR_DBL+exp_E_mb_loop_fast(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   FLT_OR_DBL           *qqm1)+{+  unsigned char             type, tt;+  char                      *ptype;+  short                     *S1;+  unsigned int              *sn;+  int                       ij, k, kl, *my_iindx, *jindx, *rtype;+  FLT_OR_DBL                qbt1, temp, qqqmmm, *qm, *scale, expMLclosing;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_exp_param_t          *pf_params;+  vrna_md_t                 *md;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  sc            = vc->sc;+  ptype         = vc->ptype;+  S1            = vc->sequence_encoding;+  qm            = vc->exp_matrices->qm;+  scale         = vc->exp_matrices->scale;+  pf_params     = vc->exp_params;+  md            = &(pf_params->model_details);+  ij            = jindx[j] + i;+  sn            = vc->strand_number;+  hc            = vc->hc;+  expMLclosing  = pf_params->expMLclosing;+  qbt1          = 0.;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* multiple stem loop contribution */+  if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local) && (sn[i] == sn[i + 1]) && (sn[j - 1] == sn[j])) {+    type  = (unsigned char)ptype[ij];+    rtype = &(md->rtype[0]);+    tt    = rtype[type];++    if (tt == 0)+      tt = 7;++    qqqmmm = expMLclosing+             * exp_E_MLstem(tt, S1[j - 1], S1[i + 1], pf_params)+             * scale[2];++    temp  = 0.0;+    kl    = my_iindx[i + 1] - (i + 1);++    if (sc) {+      if (sc->exp_energy_bp)+        qqqmmm *= sc->exp_energy_bp[my_iindx[i] - j];++      if (sc->exp_f) {+        qqqmmm *= sc->exp_f(i, j, i, j, VRNA_DECOMP_PAIR_ML, sc->data);++        for (k = i + 2; k <= j - 1; k++, kl--) {+          if (sn[k - 1] == sn[k]) {+            temp += qm[kl]+                    * qqm1[k]+                    * sc->exp_f(i + 1, j - 1, k - 1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+          }+        }+      } else {+        for (k = i + 2; k <= j - 1; k++, kl--) {+          if (sn[k - 1] == sn[k])+            temp += qm[kl]+                    * qqm1[k];+        }+      }+    } else {+      for (k = i + 2; k <= j - 1; k++, kl--) {+        if (sn[k - 1] == sn[k])+          temp += qm[kl]+                  * qqm1[k];+      }+    }++    qbt1 += temp * qqqmmm;+  }++  return qbt1;+}+++PRIVATE FLT_OR_DBL+exp_E_mb_loop_fast_comparative(vrna_fold_compound_t *vc,+                               int                  i,+                               int                  j,+                               FLT_OR_DBL           *qqm1)+{+  short                     **S, **S5, **S3;+  int                       k, kl, *my_iindx, *types, n_seq, s;+  FLT_OR_DBL                qbt1, temp, qqqmmm, *qm, *scale, expMLclosing;+  vrna_hc_t                 *hc;+  vrna_sc_t                 **scs;+  vrna_exp_param_t          *pf_params;+  vrna_md_t                 *md;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  my_iindx      = vc->iindx;+  qm            = vc->exp_matrices->qm;+  scale         = vc->exp_matrices->scale;+  pf_params     = vc->exp_params;+  md            = &(pf_params->model_details);+  hc            = vc->hc;+  expMLclosing  = pf_params->expMLclosing;+  qbt1          = 0.;+  types         = NULL;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  /* multiple stem loop contribution */+  if (evaluate(i, j, i + 1, j - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+    S     = vc->S;+    S5    = vc->S5;       /* S5[s][i] holds next base 5' of i in sequence s */+    S3    = vc->S3;       /* Sl[s][i] holds next base 3' of i in sequence s */+    scs   = vc->scs;+    n_seq = vc->n_seq;+    types = (int *)vrna_alloc(sizeof(int) * n_seq);++    qqqmmm = 1.;++    for (s = 0; s < n_seq; s++) {+      types[s] = md->pair[S[s][j]][S[s][i]];+      if (types[s] == 0)+        types[s] = 7;+    }++    for (s = 0; s < n_seq; s++)+      qqqmmm *= exp_E_MLstem(types[s], S5[s][j], S3[s][i], pf_params)+                * expMLclosing;++    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->exp_energy_bp)+            qqqmmm *= scs[s]->exp_energy_bp[my_iindx[i] - j];+      }+    }++    /* multi-loop loop contribution */+    temp  = 0.;+    kl    = my_iindx[i + 1] - (i + 1);++    for (k = i + 2; k <= j - 1; k++, kl--)+      temp += qm[kl] * qqm1[k];++    temp *= scale[2];++    qbt1 = temp * qqqmmm;+  }++  /* cleanup */+  free(types);++  return qbt1;+}+++/*+ #################################+ # Backtracking functions below  #+ #################################+ */+PUBLIC int+vrna_BT_mb_loop_fake(vrna_fold_compound_t *vc,+                     int                  *u,+                     int                  *i,+                     int                  *j,+                     vrna_bp_stack_t      *bp_stack,+                     int                  *stack_count)+{+  unsigned char type;+  char          *ptype;+  short         mm5, mm3, *S1;+  unsigned int  *sn;+  int           length, ii, jj, k, en, cp, fij, fi, *my_c, *my_fc, *my_ggg,+                *idx, with_gquad, dangle_model, turn;+  vrna_param_t  *P;+  vrna_md_t     *md;+  vrna_hc_t     *hc;+  vrna_sc_t     *sc;++  cp            = vc->cutpoint;+  length        = vc->length;+  P             = vc->params;+  md            = &(P->model_details);+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype;+  idx           = vc->jindx;+  my_c          = vc->matrices->c;+  my_fc         = vc->matrices->fc;+  my_ggg        = vc->matrices->ggg;+  turn          = md->min_loop_size;+  with_gquad    = md->gquad;+  dangle_model  = md->dangles;++  ii  = *i;+  jj  = *j;++  if (ii < cp) {+    /* 'lower' part (fc[i<cut,j=cut-1]) */++    /* nibble off unpaired 5' bases */+    do {+      fij = my_fc[ii];+      fi  = (hc->up_ext[ii]) ? my_fc[ii + 1] : INF;++      if (sc)+        if (sc->energy_up)+          fi += sc->energy_up[ii][1];++      if (++ii == jj)+        break;+    } while (fij == fi);+    ii--;++    if (jj < ii + turn + 2) {+      /* no more pairs */+      *u = *i = *j = -1;+      return 1;+    }++    mm5 = (ii > 1 && (sn[ii - 1] == sn[ii])) ? S1[ii - 1] : -1;++    /* i or i+1 is paired. Find pairing partner */+    switch (dangle_model) {+      case 0:+        for (k = ii + turn + 1; k <= jj; k++) {+          if (hc->matrix[idx[k] + ii] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            type = (unsigned char)ptype[idx[k] + ii];++            if (type == 0)+              type = 7;++            if (fij == my_fc[k + 1] + my_c[idx[k] + ii] + E_ExtLoop(type, -1, -1, P)) {+              bp_stack[++(*stack_count)].i  = ii;+              bp_stack[(*stack_count)].j    = k;+              *u                            = k + 1;+              *i                            = ii;+              *j                            = k;+              return 1;+            }+          }++          if (with_gquad) {+            if (fij == my_fc[k + 1] + my_ggg[idx[k] + ii]) {+              *u  = k + 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, ii, k, bp_stack, stack_count);+              return 1;+            }+          }+        }+        break;++      case 2:+        for (k = ii + turn + 1; k <= jj; k++) {+          if (hc->matrix[idx[k] + ii] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            mm3   = (sn[k] == sn[k + 1]) ? S1[k + 1] : -1;+            type  = (unsigned char)ptype[idx[k] + ii];++            if (type == 0)+              type = 7;++            if (fij == my_fc[k + 1] + my_c[idx[k] + ii] + E_ExtLoop(type, mm5, mm3, P)) {+              bp_stack[++(*stack_count)].i  = ii;+              bp_stack[(*stack_count)].j    = k;+              *u                            = k + 1;+              *i                            = ii;+              *j                            = k;+              return 1;+            }+          }++          if (with_gquad) {+            if (fij == my_fc[k + 1] + my_ggg[idx[k] + ii]) {+              *u  = k + 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, ii, k, bp_stack, stack_count);+              return 1;+            }+          }+        }+        break;++      default:+        for (k = ii + turn + 1; k <= jj; k++) {+          if (hc->matrix[idx[k] + ii] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            type = (unsigned char)ptype[idx[k] + ii];++            if (type == 0)+              type = 7;++            if (fij == my_fc[k + 1] + my_c[idx[k] + ii] + E_ExtLoop(type, -1, -1, P)) {+              bp_stack[++(*stack_count)].i  = ii;+              bp_stack[(*stack_count)].j    = k;+              *u                            = k + 1;+              *i                            = ii;+              *j                            = k;+              return 1;+            }+            if (hc->up_ext[k + 1]) {+              mm3 = (sn[k] == sn[k + 1]) ? S1[k + 1] : -1;+              en  = my_c[idx[k] + ii];+              if (sc)+                if (sc->energy_up)+                  en += sc->energy_up[k + 1][1];++              if (fij == my_fc[k + 2] + en + E_ExtLoop(type, -1, mm3, P)) {+                bp_stack[++(*stack_count)].i  = ii;+                bp_stack[(*stack_count)].j    = k;+                *u                            = k + 2;+                *i                            = ii;+                *j                            = k;+                return 1;+              }+            }+          }++          if (with_gquad) {+            if (fij == my_fc[k + 1] + my_ggg[idx[k] + ii]) {+              *u  = k + 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, ii, k, bp_stack, stack_count);+              return 1;+            }+          }++          if (hc->matrix[idx[k] + ii + 1] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            if (hc->up_ext[ii]) {+              mm5   = (sn[ii] == sn[ii + 1]) ? S1[ii] : -1;+              mm3   = (sn[k] == sn[k + 1]) ? S1[k + 1] : -1;+              type  = ptype[idx[k] + ii + 1];++              if (type == 0)+                type = 7;++              en = my_c[idx[k] + ii + 1];+              if (sc)+                if (sc->energy_up)+                  en += sc->energy_up[ii][1];++              if (fij == en + my_fc[k + 1] + E_ExtLoop(type, mm5, -1, P)) {+                bp_stack[++(*stack_count)].i  = ii + 1;+                bp_stack[(*stack_count)].j    = k;+                *u                            = k + 1;+                *i                            = ii + 1;+                *j                            = k;+                return 1;+              }++              if (k < jj) {+                if (hc->up_ext[k + 1]) {+                  if (sc)+                    if (sc->energy_up)+                      en += sc->energy_up[k + 1][1];++                  if (fij == en + my_fc[k + 2] + E_ExtLoop(type, mm5, mm3, P)) {+                    bp_stack[++(*stack_count)].i  = ii + 1;+                    bp_stack[(*stack_count)].j    = k;+                    *u                            = k + 2;+                    *i                            = ii + 1;+                    *j                            = k;+                    return 1;+                  }+                }+              }+            }+          }+        }+        break;+    }+  } else {+    /* 'upper' part (fc[i=cut,j>cut]) */++    /* nibble off unpaired 3' bases */+    do {+      fij = my_fc[jj];+      fi  = (hc->up_ext[jj]) ? my_fc[jj - 1] : INF;++      if (sc)+        if (sc->energy_up)+          fi += sc->energy_up[jj][1];++      if (--jj == ii)+        break;+    } while (fij == fi);+    jj++;++    if (jj < ii + turn + 2) {+      /* no more pairs */+      *u = *i = *j = -1;+      return 1;+    }++    /* j or j-1 is paired. Find pairing partner */+    mm3 = ((jj < length) && (sn[jj] == sn[jj + 1])) ? S1[jj + 1] : -1;+    switch (dangle_model) {+      case 0:+        for (k = jj - turn - 1; k >= ii; k--) {+          if (with_gquad) {+            if (fij == my_fc[k - 1] + my_ggg[idx[jj] + k]) {+              *u  = k - 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, k, jj, bp_stack, stack_count);+              return 1;+            }+          }++          if (hc->matrix[idx[jj] + k] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            type = (unsigned char)ptype[idx[jj] + k];++            if (type == 0)+              type = 7;++            en = my_c[idx[jj] + k];+            if (sn[k] != sn[jj])+              en += P->DuplexInit;++            if (fij == my_fc[k - 1] + en + E_ExtLoop(type, -1, -1, P)) {+              bp_stack[++(*stack_count)].i  = k;+              bp_stack[(*stack_count)].j    = jj;+              *u                            = k - 1;+              *i                            = k;+              *j                            = jj;+              return 1;+            }+          }+        }+        break;++      case 2:+        for (k = jj - turn - 1; k >= ii; k--) {+          if (with_gquad) {+            if (fij == my_fc[k - 1] + my_ggg[idx[jj] + k]) {+              *u  = k - 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, k, jj, bp_stack, stack_count);+              return 1;+            }+          }++          if (hc->matrix[idx[jj] + k] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            mm5   = ((k > 1) && (sn[k - 1] == sn[k])) ? S1[k - 1] : -1;+            type  = (unsigned char)ptype[idx[jj] + k];++            if (type == 0)+              type = 7;++            en = my_c[idx[jj] + k];+            if (sn[k] != sn[jj])+              en += P->DuplexInit;++            if (fij == my_fc[k - 1] + en + E_ExtLoop(type, mm5, mm3, P)) {+              bp_stack[++(*stack_count)].i  = k;+              bp_stack[(*stack_count)].j    = jj;+              *u                            = k - 1;+              *i                            = k;+              *j                            = jj;+              return 1;+            }+          }+        }+        break;++      default:+        for (k = jj - turn - 1; k >= ii; k--) {+          if (with_gquad) {+            if (fij == my_fc[k - 1] + my_ggg[idx[jj] + k]) {+              *u  = k - 1;+              *i  = *j = -1;+              vrna_BT_gquad_mfe(vc, k, jj, bp_stack, stack_count);+              return 1;+            }+          }++          if (hc->matrix[idx[jj] + k] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            type = (unsigned char)ptype[idx[jj] + k];++            if (type == 0)+              type = 7;++            en = my_c[idx[jj] + k];+            if (sn[k] != sn[jj])+              en += P->DuplexInit;++            if (fij == my_fc[k - 1] + en + E_ExtLoop(type, -1, -1, P)) {+              bp_stack[++(*stack_count)].i  = k;+              bp_stack[(*stack_count)].j    = jj;+              *u                            = k - 1;+              *i                            = k;+              *j                            = jj;+              return 1;+            }+            if (hc->up_ext[k - 1]) {+              if ((k > 1) && (sn[k - 1] == sn[k])) {+                mm5 = S1[k - 1];+                if (sc)+                  if (sc->energy_up)+                    en += sc->energy_up[k - 1][1];++                if (fij == my_fc[k - 2] + en + E_ExtLoop(type, mm5, -1, P)) {+                  bp_stack[++(*stack_count)].i  = k;+                  bp_stack[(*stack_count)].j    = jj;+                  *u                            = k - 2;+                  *i                            = k;+                  *j                            = jj;+                  return 1;+                }+              }+            }+          }++          if (hc->matrix[idx[jj - 1] + k] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) {+            type = (unsigned char)ptype[idx[jj - 1] + k];++            if (type == 0)+              type = 7;++            if (hc->up_ext[jj]) {+              if (sn[jj - 1] == sn[jj]) {+                mm3 = S1[jj];+                en  = my_c[idx[jj - 1] + k];+                if (sn[k] != sn[jj - 1])+                  en += P->DuplexInit;         /* ??? */+                if (sc)+                  if (sc->energy_up)+                    en += sc->energy_up[jj][1];++                if (fij == en + my_fc[k - 1] + E_ExtLoop(type, -1, mm3, P)) {+                  bp_stack[++(*stack_count)].i  = k;+                  bp_stack[(*stack_count)].j    = jj - 1;+                  *u                            = k - 1;+                  *i                            = k;+                  *j                            = jj - 1;+                  return 1;+                }++                if (k > ii) {+                  if (hc->up_ext[k - 1]) {+                    mm5 = (sn[k - 1] == sn[k]) ? S1[k - 1] : -1;+                    if (sc)+                      if (sc->energy_up)+                        en += sc->energy_up[k - 1][1];++                    if (fij == my_fc[k - 2] + en + E_ExtLoop(type, mm5, mm3, P)) {+                      bp_stack[++(*stack_count)].i  = k;+                      bp_stack[(*stack_count)].j    = jj - 1;+                      *u                            = k - 2;+                      *i                            = k;+                      *j                            = jj - 1;+                      return 1;+                    }+                  }+                }+              }+            }+          }+        }+        break;+    }+  }++  return 0;+}+++PUBLIC int+vrna_BT_mb_loop_split(vrna_fold_compound_t  *vc,+                      int                   *i,+                      int                   *j,+                      int                   *k,+                      int                   *l,+                      int                   *component1,+                      int                   *component2,+                      vrna_bp_stack_t       *bp_stack,+                      int                   *stack_count)+{+  unsigned char             type, type_2;+  char                      *ptype;+  short                     *S1;+  int                       ij, ii, jj, fij, fi, u, en, *my_c, *my_fML, *my_ggg,+                            turn, *idx, with_gquad, dangle_model, *rtype, kk, cnt,+                            with_ud;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_ud_t                 *domains_up;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  P           = vc->params;+  md          = &(P->model_details);+  hc          = vc->hc;+  sc          = vc->sc;+  idx         = vc->jindx;+  ptype       = vc->ptype;+  rtype       = &(md->rtype[0]);+  S1          = vc->sequence_encoding;+  domains_up  = vc->domains_up;++  my_c          = vc->matrices->c;+  my_fML        = vc->matrices->fML;+  my_ggg        = vc->matrices->ggg;+  turn          = md->min_loop_size;+  with_gquad    = md->gquad;+  with_ud       = (domains_up && domains_up->energy_cb) ? 1 : 0;+  dangle_model  = md->dangles;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  ii  = *i;+  jj  = *j;++  if (with_ud) {+    /* nibble off unpaired stretches at 3' site */+    do {+      fij = my_fML[idx[jj] + ii];+      fi  = INF;++      /* process regular unpaired nucleotides (unbound by ligand) first */+      if (evaluate(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        fi = my_fML[idx[jj - 1] + ii] + P->MLbase;++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[jj][1];+          if (sc->f)+            fi += sc->f(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_ML, sc->data);+        }++        if (jj == ii)+          return 0; /* no more pairs */++        if (fij == fi) {+          jj--;+          continue;+        }+      }++      /* next try to nibble off ligand */+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u   = domains_up->uniq_motif_size[cnt];+        kk  = jj - u + 1;+        if ((kk >= ii) && evaluate(ii, jj, ii, jj - u, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+          en = domains_up->energy_cb(vc,+                                     kk, jj,+                                     VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                     domains_up->data);++          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[kk][u];+            if (sc->f)+              en += sc->f(ii, jj, ii, jj - u, VRNA_DECOMP_ML_ML, sc->data);+          }++          fi  = my_fML[idx[kk - 1] + ii] + u * P->MLbase;+          fi  += en;++          if (fij == fi) {+            /* skip remaining motifs after first hit */+            jj = kk - 1;+            break;+          }+        }+      }++      if (jj < ii)+        return 0; /* no more pairs */+    } while (fij == fi);++    /* nibble off unpaired stretches at 5' site */+    do {+      fij = my_fML[idx[jj] + ii];+      fi  = INF;++      /* again, process regular unpaired nucleotides (unbound by ligand) first */+      if (evaluate(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        fi = my_fML[idx[jj] + ii + 1] + P->MLbase;++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[ii][1];+          if (sc->f)+            fi += sc->f(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_ML, sc->data);+        }++        if (ii + 1 == jj)+          return 0; /* no more pairs */++        if (fij == fi) {+          ii++;+          continue;+        }+      }++      /* next try to nibble off ligand again */+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u   = domains_up->uniq_motif_size[cnt];+        kk  = ii + u - 1;+        if ((kk <= jj) && evaluate(ii, jj, ii + u, jj, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+          en = domains_up->energy_cb(vc,+                                     ii, kk,+                                     VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                     domains_up->data);++          if (sc) {+            if (sc->energy_up)+              en += sc->energy_up[ii][u];+            if (sc->f)+              en += sc->f(ii, jj, ii + u, jj, VRNA_DECOMP_ML_ML, sc->data);+          }++          fi  = my_fML[idx[jj] + kk + 1] + u * P->MLbase;+          fi  += en;++          if (fij == fi) {+            /* skip remaining motifs after first hit */+            ii = kk + 1;+            break;+          }+        }+      }++      if (ii > jj)+        return 0; /* no more pairs */+    } while (fij == fi);+  } else {+    /* nibble off unpaired 3' bases */+    do {+      fij = my_fML[idx[jj] + ii];+      fi  = INF;++      if (evaluate(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        fi = my_fML[idx[jj - 1] + ii] + P->MLbase;++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[jj][1];+          if (sc->f)+            fi += sc->f(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_ML, sc->data);+        }+      }+      if (--jj == 0)+        break;+    } while (fij == fi);+    jj++;++    /* nibble off unpaired 5' bases */+    do {+      fij = my_fML[idx[jj] + ii];+      fi  = INF;++      if (evaluate(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+        fi = my_fML[idx[jj] + ii + 1] + P->MLbase;++        if (sc) {+          if (sc->energy_up)+            fi += sc->energy_up[ii][1];+          if (sc->f)+            fi += sc->f(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_ML, sc->data);+        }+      }+      if (++ii == jj)+        break;+    } while (fij == fi);+    ii--;++    if (jj < ii + turn + 1) /* no more pairs */+      return 0;+  }++  ij = idx[jj] + ii;++  *component1 = *component2 = 1; /* split into two multi loop parts by default */++  /* 1. test for single component */++  if (with_gquad) {+    if (fij == my_ggg[ij] + E_MLstem(0, -1, -1, P)) {+      *i  = *j = -1;+      *k  = *l = -1;+      vrna_BT_gquad_mfe(vc, ii, jj, bp_stack, stack_count);+      return 1;+    }+  }++  type  = (unsigned char)ptype[ij];+  en    = my_c[ij];++  if (sc)+    if (sc->f)+      en += sc->f(ii, jj, ii, jj, VRNA_DECOMP_ML_STEM, sc->data);++  switch (dangle_model) {+    case 0:+      if (evaluate(ii, jj, ii, jj, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        if (type == 0)+          type = 7;++        if (fij == en + E_MLstem(type, -1, -1, P)) {+          *i          = *j = -1;+          *k          = ii;+          *l          = jj;+          *component2 = 2;          /* 2nd part is structure enclosed by base pair */+          return 1;+        }+      }+      break;++    case 2:+      if (evaluate(ii, jj, ii, jj, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        if (type == 0)+          type = 7;++        if (fij == en + E_MLstem(type, S1[ii - 1], S1[jj + 1], P)) {+          *i          = *j = -1;+          *k          = ii;+          *l          = jj;+          *component2 = 2;+          return 1;+        }+      }+      break;++    default:+      if (evaluate(ii, jj, ii, jj, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        if (type == 0)+          type = 7;++        if (fij == en + E_MLstem(type, -1, -1, P)) {+          *i          = *j = -1;+          *k          = ii;+          *l          = jj;+          *component2 = 2;+          return 1;+        }+      }++      if (evaluate(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        int tmp_en = fij;+        if (sc) {+          if (sc->energy_up)+            tmp_en -= sc->energy_up[ii][1];+          if (sc->f)+            tmp_en -= sc->f(ii, jj, ii + 1, jj, VRNA_DECOMP_ML_STEM, sc->data);+        }+        type = (unsigned char)ptype[ij + 1];++        if (type == 0)+          type = 7;++        if (tmp_en == my_c[ij + 1] + E_MLstem(type, S1[ii], -1, P) + P->MLbase) {+          *i          = *j = -1;+          *k          = ii + 1;+          *l          = jj;+          *component2 = 2;+          return 1;+        }+      }++      if (evaluate(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        int tmp_en = fij;+        if (sc) {+          if (sc->energy_up)+            tmp_en -= sc->energy_up[jj][1];+          if (sc->f)+            tmp_en -= sc->f(ii, jj, ii, jj - 1, VRNA_DECOMP_ML_STEM, sc->data);+        }+        type = (unsigned char)ptype[idx[jj - 1] + ii];++        if (type == 0)+          type = 7;++        if (tmp_en == my_c[idx[jj - 1] + ii] + E_MLstem(type, -1, S1[jj], P) + P->MLbase) {+          *i          = *j = -1;+          *k          = ii;+          *l          = jj - 1;+          *component2 = 2;+          return 1;+        }+      }++      if (evaluate(ii, jj, ii + 1, jj - 1, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+        int tmp_en = fij;+        if (sc) {+          if (sc->energy_up)+            tmp_en -= sc->energy_up[ii][1] + sc->energy_up[jj][1];+          if (sc->f)+            tmp_en -= sc->f(ii, jj, ii + 1, jj - 1, VRNA_DECOMP_ML_STEM, sc->data);+        }+        type = (unsigned char)ptype[idx[jj - 1] + ii + 1];++        if (type == 0)+          type = 7;++        if (tmp_en == my_c[idx[jj - 1] + ii + 1] + E_MLstem(type, S1[ii], S1[jj], P) + 2 * P->MLbase) {+          *i          = *j = -1;+          *k          = ii + 1;+          *l          = jj - 1;+          *component2 = 2;+          return 1;+        }+      }++      break;+  }++  /* 2. Test for possible split point */+  for (u = ii + 1 + turn; u <= jj - 2 - turn; u++) {+    en = my_fML[idx[u] + ii] + my_fML[idx[jj] + u + 1];+    if (sc)+      if (sc->f)+        en += sc->f(ii, jj, u, u + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+    if (fij == en) {+      *i  = ii;+      *j  = u;+      *k  = u + 1;+      *l  = jj;+      return 1;+    }+  }++  /* 3. last chance! Maybe coax stack */+  if (dangle_model == 3) {+    int ik, k1j, tmp_en;+    for (k1j = idx[jj] + ii + turn + 2, u = ii + 1 + turn; u <= jj - 2 - turn; u++, k1j++) {+      ik = idx[u] + ii;+      if (evaluate(ii, u, u + 1, jj, VRNA_DECOMP_ML_COAXIAL_ENC, &hc_dat_local)) {+        type    = rtype[(unsigned char)ptype[ik]];+        type_2  = rtype[(unsigned char)ptype[k1j]];++        if (type == 0)+          type = 7;+        if (type_2 == 0)+          type_2 = 7;++        tmp_en = my_c[ik] + my_c[k1j] + P->stack[type][type_2] + 2 * P->MLintern[1];+        if (sc)+          if (sc->f)+            tmp_en += sc->f(ii, u, u + 1, jj, VRNA_DECOMP_ML_COAXIAL, sc->data);+        if (fij == tmp_en) {+          *i          = ii;+          *j          = u;+          *k          = u + 1;+          *l          = jj;+          *component1 = *component2 = 2;+          return 1;+        }+      }+    }+  }++  return 0;+}+++PUBLIC int+vrna_BT_mb_loop(vrna_fold_compound_t  *vc,+                int                   *i,+                int                   *j,+                int                   *k,+                int                   en,+                int                   *component1,+                int                   *component2)+{+  unsigned char             type, type_2, tt;+  char                      *ptype;+  short                     s5, s3, *S1;+  unsigned int              *sn;+  int                       ij, p, q, r, e, tmp_en, cp, *idx, turn, dangle_model,+                            *my_c, *my_fML, *my_fc, *rtype;+  vrna_param_t              *P;+  vrna_md_t                 *md;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  cp            = vc->cutpoint;+  idx           = vc->jindx;+  ij            = idx[*j] + *i;+  S1            = vc->sequence_encoding;+  P             = vc->params;+  md            = &(P->model_details);+  sn            = vc->strand_number;+  hc            = vc->hc;+  sc            = vc->sc;+  my_c          = vc->matrices->c;+  my_fML        = vc->matrices->fML;+  my_fc         = vc->matrices->fc;+  turn          = md->min_loop_size;+  ptype         = vc->ptype;+  rtype         = &(md->rtype[0]);+  type          = (unsigned char)ptype[ij];+  tt            = type;+  type          = rtype[type];+  dangle_model  = md->dangles;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  p = *i + 1;+  q = *j - 1;++  r = q - turn - 1;++  if (evaluate(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+    if (type == 0)+      type = 7;+    if (tt == 0)+      tt = 7;++    /* is it a fake multi-loop? */+    /* NOTE: do we really want to evaluate it hard-constraint-wise as a multibranch loop? */+    if (sn[*i] != sn[*j]) {+      int ii, jj;+      ii  = jj = 0;+      e   = my_fc[p] + my_fc[q];+      if (sc)+        if (sc->energy_bp)+          e += sc->energy_bp[ij];+      s5  = (sn[q] == sn[*j]) ? S1[q] : -1;+      s3  = (sn[*i] == sn[p]) ? S1[p] : -1;++      switch (dangle_model) {+        case 0:+          if (en == e + E_ExtLoop(type, -1, -1, P))+            ii = p, jj = q;+          break;++        case 2:+          if (en == e + E_ExtLoop(type, s5, s3, P))+            ii = p, jj = q;+          break;++        default:+          if (en == e + E_ExtLoop(type, -1, -1, P)) {+            ii = p, jj = q;+            break;+          }+          if (hc->up_ext[p]) {+            e = my_fc[p + 1] + my_fc[q];+            if (sc) {+              if (sc->energy_up)+                e += sc->energy_up[p][1];+              if (sc->energy_bp)+                e += sc->energy_bp[ij];+            }+            if (en == e + E_ExtLoop(type, -1, s3, P)) {+              ii = p + 1; jj = q;+              break;+            }+          }+          if (hc->up_ext[q]) {+            e = my_fc[p] + my_fc[q - 1];+            if (sc) {+              if (sc->energy_up)+                e += sc->energy_up[q][1];+              if (sc->energy_bp)+                e += sc->energy_bp[ij];+            }+            if (en == e + E_ExtLoop(type, s5, -1, P)) {+              ii = p; jj = q - 1;+              break;+            }+          }+          if ((hc->up_ext[q]) && (hc->up_ext[p])) {+            e = my_fc[p + 1] + my_fc[q - 1];+            if (sc) {+              if (sc->energy_up)+                e += sc->energy_up[p][1] + sc->energy_up[q][1];+              if (sc->energy_bp)+                e += sc->energy_bp[ij];+            }+            if (en == e + E_ExtLoop(type, s5, s3, P)) {+              ii = p + 1; jj = q - 1;+              break;+            }+          }+          break;+      }++      if (ii) {+        /* found a decomposition */+        *component1 = 3;+        *i          = ii;+        *k          = cp - 1;+        *j          = jj;+        *component2 = 4;+        return 1;+      }+    }++    /* true multi loop? */+    *component1 = *component2 = 1;  /* both components are MB loop parts by default */++    s5  = (sn[q] == sn[*j]) ? S1[q] : -1;+    s3  = (sn[*i] == sn[p]) ? S1[p] : -1;++    switch (dangle_model) {+      case 0:+        e = en - E_MLstem(type, -1, -1, P) - P->MLclosing;+        if (sc) {+          if (sc->energy_bp)+            e -= sc->energy_bp[ij];+          if (sc->f)+            e -= sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, sc->data);+        }+        for (r = *i + 2 + turn; r < *j - 2 - turn; ++r) {+          if (evaluate(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+            tmp_en = my_fML[idx[r] + p] + my_fML[idx[q] + r + 1];+            if (sc)+              if (sc->f)+                tmp_en += sc->f(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+            if (e == tmp_en)+              break;+          }+        }+        break;++      case 2:+        e = en - E_MLstem(type, s5, s3, P) - P->MLclosing;+        if (sc) {+          if (sc->energy_bp)+            e -= sc->energy_bp[ij];+          if (sc->f)+            e -= sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, sc->data);+        }+        for (r = p + turn + 1; r < q - turn - 1; ++r) {+          if (evaluate(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+            tmp_en = my_fML[idx[r] + p] + my_fML[idx[q] + r + 1];+            if (sc)+              if (sc->f)+                tmp_en += sc->f(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+            if (e == tmp_en)+              break;+          }+        }+        break;++      default:+        e = en - P->MLclosing;+        if (sc)+          if (sc->energy_bp)+            e -= sc->energy_bp[ij];+        for (r = p + turn + 1; r < q - turn - 1; ++r) {+          if (evaluate(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+            tmp_en = my_fML[idx[r] + p] + my_fML[idx[q] + r + 1] + E_MLstem(type, -1, -1, P);+            if (sc) {+              if (sc->f) {+                tmp_en  += sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, sc->data);+                tmp_en  += sc->f(p, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+              }+            }+            if (e == tmp_en)+              break;+          }++          if (evaluate(*i, *j, p + 1, q, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+            if (evaluate(p + 1, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+              tmp_en = e;+              if (sc) {+                if (sc->energy_up)+                  tmp_en -= sc->energy_up[p][1];+                if (sc->f) {+                  tmp_en  -= sc->f(*i, *j, p + 1, q, VRNA_DECOMP_PAIR_ML, sc->data);+                  tmp_en  -= sc->f(p + 1, q, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+                }+              }+              if (tmp_en == my_fML[idx[r] + p + 1] + my_fML[idx[q] + r + 1] + E_MLstem(type, -1, s3, P) + P->MLbase) {+                p += 1;+                break;+              }+            }+          }++          if (evaluate(*i, *j, p, q - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+            if (evaluate(p, q - 1, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+              tmp_en = e;+              if (sc) {+                if (sc->energy_up)+                  tmp_en -= sc->energy_up[q][1];+                if (sc->f) {+                  tmp_en  -= sc->f(*i, *j, p, q - 1, VRNA_DECOMP_PAIR_ML, sc->data);+                  tmp_en  -= sc->f(p, q - 1, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+                }+              }+              if (tmp_en == my_fML[idx[r] + p] + my_fML[idx[q - 1] + r + 1] + E_MLstem(type, s5, -1, P) + P->MLbase) {+                q -= 1;+                break;+              }+            }+          }++          if (evaluate(*i, *j, p + 1, q - 1, VRNA_DECOMP_PAIR_ML, &hc_dat_local)) {+            if (evaluate(p + 1, q - 1, r, r + 1, VRNA_DECOMP_ML_ML_ML, &hc_dat_local)) {+              tmp_en = e;+              if (sc) {+                if (sc->energy_up)+                  tmp_en -= sc->energy_up[p][1] + sc->energy_up[q][1];+                if (sc->f) {+                  tmp_en  -= sc->f(*i, *j, p + 1, q - 1, VRNA_DECOMP_PAIR_ML, sc->data);+                  tmp_en  -= sc->f(p + 1, q - 1, r, r + 1, VRNA_DECOMP_ML_ML_ML, sc->data);+                }+              }+              if (tmp_en == my_fML[idx[r] + p + 1] + my_fML[idx[q - 1] + r + 1] + E_MLstem(type, s5, s3, P) + 2 * P->MLbase) {+                p += 1;+                q -= 1;+                break;+              }+            }+          }++          /* coaxial stacking of (i.j) with (i+1.r) or (r.j-1) */+          /* use MLintern[1] since coax stacked pairs don't get TerminalAU */+          if (dangle_model == 3) {+            tmp_en = e;+            if (evaluate(*i, *j, p, r, VRNA_DECOMP_ML_COAXIAL, &hc_dat_local)) {+              type_2 = rtype[(unsigned char)ptype[idx[r] + p]];++              if (type_2 == 0)+                type_2 = 7;++              tmp_en = my_c[idx[r] + p] + P->stack[tt][type_2] + my_fML[idx[q] + r + 1];+              if (sc) {+                if (sc->f) {+                  tmp_en  += sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, sc->data);+                  tmp_en  += sc->f(*i, *j, p, r, VRNA_DECOMP_ML_COAXIAL, sc->data);+                }+              }+              if (e == tmp_en + 2 * P->MLintern[1]) {+                *component1 = 2;+                break;+              }+            }++            if (evaluate(*i, *j, r + 1, q, VRNA_DECOMP_ML_COAXIAL, &hc_dat_local)) {+              type_2 = rtype[(unsigned char)ptype[idx[q] + r + 1]];++              if (type_2 == 0)+                type_2 = 7;++              tmp_en = my_c[idx[q] + r + 1] + P->stack[tt][type_2] + my_fML[idx[r] + p];+              if (sc) {+                if (sc->f) {+                  tmp_en  += sc->f(*i, *j, p, q, VRNA_DECOMP_PAIR_ML, sc->data);+                  tmp_en  += sc->f(*i, *j, r + 1, q, VRNA_DECOMP_ML_COAXIAL, sc->data);+                }+              }+              if (e == tmp_en + 2 * P->MLintern[1]) {+                *component2 = 2;+                break;+              }+            }+          }+        }+        break;+    }+  }++  if (r <= *j - turn - 3) {+    *i  = p;+    *k  = r;+    *j  = q;+    return 1;+  } else {+#if 0+    /* Y shaped ML loops fon't work yet */+    if (dangle_model == 3) {+      d5  = P->dangle5[tt][S1[j - 1]];+      d3  = P->dangle3[tt][S1[i + 1]];+      /* (i,j) must close a Y shaped ML loop with coax stacking */+      if (cij == fML[indx[j - 2] + i + 2] + mm + d3 + d5 + P->MLbase + P->MLbase) {+        i1  = i + 2;+        j1  = j - 2;+      } else if (cij == fML[indx[j - 2] + i + 1] + mm + d5 + P->MLbase) {+        j1 = j - 2;+      } else if (cij == fML[indx[j - 1] + i + 2] + mm + d3 + P->MLbase) {+        i1 = i + 2;+      } else /* last chance */+      if (cij != fML[indx[j - 1] + i + 1] + mm + P->MLbase) {+        fprintf(stderr, "backtracking failed in repeat");+      }+      /* if we arrive here we can express cij via fML[i1,j1]+dangles */+      bt_stack[++s].i = i1;+      bt_stack[s].j   = j1;+    }+#endif+  }++  return 0;+}+++PUBLIC vrna_mx_pf_aux_ml_t *+vrna_exp_E_ml_fast_init(vrna_fold_compound_t *vc)+{+  vrna_mx_pf_aux_ml_t *aux_mx = NULL;++  if (vc) {+    int         i, j, d, n, u, turn, ij, *iidx;+    FLT_OR_DBL  *qm;++    n     = (int)vc->length;+    iidx  = vc->iindx;+    turn  = vc->exp_params->model_details.min_loop_size;+    qm    = vc->exp_matrices->qm;++    /* allocate memory for helper arrays */+    aux_mx            = (vrna_mx_pf_aux_ml_t *)vrna_alloc(sizeof(vrna_mx_pf_aux_ml_t));+    aux_mx->qqm       = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+    aux_mx->qqm1      = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+    aux_mx->qqmu_size = 0;+    aux_mx->qqmu      = NULL;++    if (vc->type == VRNA_FC_TYPE_SINGLE) {+      vrna_ud_t *domains_up = vc->domains_up;+      int       with_ud     = (domains_up && domains_up->exp_energy_cb);+      int       ud_max_size = 0;++      /* pre-processing ligand binding production rule(s) and auxiliary memory */+      if (with_ud) {+        for (u = 0; u < domains_up->uniq_motif_count; u++)+          if (ud_max_size < domains_up->uniq_motif_size[u])+            ud_max_size = domains_up->uniq_motif_size[u];++        aux_mx->qqmu_size = ud_max_size;+        aux_mx->qqmu      = (FLT_OR_DBL **)vrna_alloc(sizeof(FLT_OR_DBL *) * (ud_max_size + 1));+        for (u = 0; u <= ud_max_size; u++)+          aux_mx->qqmu[u] = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n + 2));+      }+    }++    for (d = 0; d <= turn; d++)+      for (i = 1; i <= n - d; i++) {+        j   = i + d;+        ij  = iidx[i] - j;++        if (j > n)+          continue;++        qm[ij] = 0.;+      }+  }++  return aux_mx;+}+++PUBLIC void+vrna_exp_E_ml_fast_rotate(vrna_fold_compound_t  *vc,+                          vrna_mx_pf_aux_ml_t   *aux_mx)+{+  if (vc && aux_mx) {+    int         u;+    FLT_OR_DBL  *tmp;++    tmp           = aux_mx->qqm1;+    aux_mx->qqm1  = aux_mx->qqm;+    aux_mx->qqm   = tmp;++    /* rotate auxiliary arrays for unstructured domains */+    if (aux_mx->qqmu) {+      tmp = aux_mx->qqmu[aux_mx->qqmu_size];+      for (u = aux_mx->qqmu_size; u > 0; u--)+        aux_mx->qqmu[u] = aux_mx->qqmu[u - 1];+      aux_mx->qqmu[0] = tmp;+    }+  }+}+++PUBLIC void+vrna_exp_E_ml_fast_free(vrna_fold_compound_t  *vc,+                        vrna_mx_pf_aux_ml_t   *aux_mx)+{+  if (vc && aux_mx) {+    int u;++    free(aux_mx->qqm);+    free(aux_mx->qqm1);++    if (aux_mx->qqmu) {+      for (u = 0; u <= aux_mx->qqmu_size; u++)+        free(aux_mx->qqmu[u]);++      free(aux_mx->qqmu);+    }++    free(aux_mx);+  }+}+++PUBLIC FLT_OR_DBL+vrna_exp_E_ml_fast(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   vrna_mx_pf_aux_ml_t  *aux_mx)+{+  if (vc) {+    switch (vc->type) {+      case VRNA_FC_TYPE_SINGLE:+        return exp_E_ml_fast(vc, i, j, aux_mx);+        break;++      case VRNA_FC_TYPE_COMPARATIVE:+        return exp_E_ml_fast_comparative(vc, i, j, aux_mx);+        break;++      default:+        vrna_message_warning("vrna_exp_E_ml_fast@multibranch_loops.c: Unknown fold_compound type");+        return 0.;+        break;+    }+  } else {+    return 0.;+  }+}+++PRIVATE FLT_OR_DBL+exp_E_ml_fast(vrna_fold_compound_t  *vc,+              int                   i,+              int                   j,+              vrna_mx_pf_aux_ml_t   *aux_mx)+{+  short                     *S1;+  unsigned char             type;+  int                       n, *iidx, k, ij, kl, maxk, ii, with_ud, u, circular, with_gquad, *hc_up_ml;+  FLT_OR_DBL                qbt1, temp, *qm, *qb, *qqm, *qqm1, **qqmu, q_temp, q_temp2, *G, *expMLbase,+                            expMLstem;+  vrna_md_t                 *md;+  vrna_exp_param_t          *pf_params;+  vrna_ud_t                 *domains_up;+  vrna_hc_t                 *hc;+  vrna_sc_t                 *sc;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  n                   = (int)vc->length;+  iidx                = vc->iindx;+  ij                  = iidx[i] - j;+  qqm                 = aux_mx->qqm;+  qqm1                = aux_mx->qqm1;+  qqmu                = aux_mx->qqmu;+  qm                  = vc->exp_matrices->qm;+  qb                  = vc->exp_matrices->qb;+  G                   = vc->exp_matrices->G;+  expMLbase           = vc->exp_matrices->expMLbase;+  pf_params           = vc->exp_params;+  md                  = &(pf_params->model_details);+  hc                  = vc->hc;+  sc                  = vc->sc;+  domains_up          = vc->domains_up;+  circular            = md->circ;+  with_gquad          = md->gquad;+  with_ud             = (domains_up && domains_up->exp_energy_cb);+  hc_up_ml            = hc->up_ml;+  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  qbt1    = 0;+  q_temp  = 0.;++  qqm[i] = 0.;++  if (with_ud)+    qqmu[0][i] = 0.;++  if (with_gquad)+    expMLstem = exp_E_MLstem(0, -1, -1, pf_params);++  if (evaluate(i, j, i, j - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+    q_temp = qqm1[i] * expMLbase[1];++    if (sc) {+      if (sc->exp_energy_up)+        q_temp *= sc->exp_energy_up[j][1];++      if (sc->exp_f)+        q_temp *= sc->exp_f(i, j, i, j - 1, VRNA_DECOMP_ML_ML, sc->data);+    }++    if (with_ud) {+      int cnt;+      for (cnt = 0; cnt < domains_up->uniq_motif_count; cnt++) {+        u = domains_up->uniq_motif_size[cnt];+        if (j - u >= i) {+          if (evaluate(i, j, i, j - u, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+            q_temp2 = qqmu[u][i]+                      * domains_up->exp_energy_cb(vc,+                                                  j - u + 1, j,+                                                  VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MOTIF,+                                                  domains_up->data)+                      * expMLbase[u];++            if (sc) {+              if (sc->exp_energy_up)+                q_temp2 *= sc->exp_energy_up[j - u + 1][u];+              if (sc->exp_f)+                q_temp2 *= sc->exp_f(i, j, i, j - 1, VRNA_DECOMP_ML_ML, sc->data);+            }+            q_temp += q_temp2;+          }+        }+      }+      qqmu[0][i] += q_temp;+    }++    qqm[i] += q_temp;+  }++  if (evaluate(i, j, i, j, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+    S1    = vc->sequence_encoding;+    type  = md->pair[S1[i]][S1[j]];+    if (type == 0)+      type = 7;++    qbt1 = qb[ij] * exp_E_MLstem(type, ((i > 1) || circular) ? S1[i - 1] : -1, ((j < n) || circular) ? S1[j + 1] : -1, pf_params);+    if (sc)+      if (sc->exp_f)+        qbt1 *= sc->exp_f(i, j, i, j, VRNA_DECOMP_ML_STEM, sc->data);++    qqm[i] += qbt1;++    if (with_ud)+      qqmu[0][i] += qbt1;+  }++  if (with_gquad) {+    /*include gquads into qqm*/+    qqm[i] += G[ij] * expMLstem;++    if (with_ud)+      qqmu[0][i] += G[ij] * expMLstem;+  }++  /*+   *  construction of qm matrix containing multiple loop+   *  partition function contributions from segment i,j+   */+  temp  = 0.0;+  kl    = iidx[i] - j + 1; /* ii-k=[i,k-1] */+  if (sc && sc->exp_f) {+    for (k = j; k > i; k--, kl++) {+      q_temp  = qm[kl] * qqm[k];+      q_temp  *= sc->exp_f(i, j, k - 1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+      temp    += q_temp;+    }+  } else {+    for (k = j; k > i; k--, kl++)+      temp += qm[kl] * qqm[k];+  }++  maxk  = MIN2(i + hc_up_ml[i], j);+  ii    = maxk - i; /* length of unpaired stretch */+  if (with_ud) {+    if (sc) {+      for (k = maxk; k > i; k--, ii--) {+        q_temp = expMLbase[ii]+                 * qqm[k];++        if (sc->exp_energy_up)+          q_temp *= sc->exp_energy_up[i][ii];++        if (sc->exp_f)+          q_temp *= sc->exp_f(i, j, k, j, VRNA_DECOMP_ML_ML, sc->data);++        temp  += q_temp;+        temp  += q_temp+                 * domains_up->exp_energy_cb(vc,+                                             i, k - 1,+                                             VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                             domains_up->data);+      }+    } else {+      for (k = maxk; k > i; k--, ii--) {+        q_temp = expMLbase[ii]+                 * qqm[k];++        temp  += q_temp;+        temp  += q_temp+                 * domains_up->exp_energy_cb(vc,+                                             i, k - 1,+                                             VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP,+                                             domains_up->data);+      }+    }+  } else {+    if (sc) {+      for (k = maxk; k > i; k--, ii--) {+        q_temp = expMLbase[ii] * qqm[k];+        if (sc->exp_energy_up)+          q_temp *= sc->exp_energy_up[i][ii];++        if (sc->exp_f)+          q_temp *= sc->exp_f(i, j, k, j, VRNA_DECOMP_ML_ML, sc->data);++        temp += q_temp;+      }+    } else {+      for (k = maxk; k > i; k--, ii--)+        temp += expMLbase[ii] * qqm[k];+    }+  }++  return temp + qqm[i];+}+++PRIVATE FLT_OR_DBL+exp_E_ml_fast_comparative(vrna_fold_compound_t  *vc,+                          int                   i,+                          int                   j,+                          vrna_mx_pf_aux_ml_t   *aux_mx)+{+  unsigned char             type;+  unsigned short            **a2s;+  short                     **S, **S5, **S3;+  int                       n, s, n_seq, *iidx, k, ij, kl, maxk, ii, circular, *hc_up_ml;+  FLT_OR_DBL                qbt1, temp, *qm, *qb, *qqm, *qqm1, q_temp, *expMLbase;+  vrna_md_t                 *md;+  vrna_exp_param_t          *pf_params;+  vrna_hc_t                 *hc;+  vrna_sc_t                 **scs;+  vrna_callback_hc_evaluate *evaluate;+  struct default_data       hc_dat_local;++  n         = (int)vc->length;+  n_seq     = vc->n_seq;+  iidx      = vc->iindx;+  ij        = iidx[i] - j;+  S         = vc->S;+  S5        = vc->S5;               /* S5[s][i] holds next base 5' of i in sequence s */+  S3        = vc->S3;               /* Sl[s][i] holds next base 3' of i in sequence s */+  a2s       = vc->a2s;+  qqm       = aux_mx->qqm;+  qqm1      = aux_mx->qqm1;+  qm        = vc->exp_matrices->qm;+  qb        = vc->exp_matrices->qb;+  expMLbase = vc->exp_matrices->expMLbase;+  pf_params = vc->exp_params;+  md        = &(pf_params->model_details);+  hc        = vc->hc;+  scs       = vc->scs;+  circular  = md->circ;+  hc_up_ml  = hc->up_ml;++  hc_dat_local.idx    = vc->jindx;+  hc_dat_local.mx     = hc->matrix;+  hc_dat_local.hc_up  = hc->up_ml;+  hc_dat_local.cp     = vc->cutpoint;++  if (hc->f) {+    evaluate            = &hc_default_user;+    hc_dat_local.hc_f   = hc->f;+    hc_dat_local.hc_dat = hc->data;+  } else {+    evaluate = &hc_default;+  }++  qbt1    = 0;+  q_temp  = 0.;++  qqm[i] = 0.;+++  if (evaluate(i, j, i, j - 1, VRNA_DECOMP_ML_ML, &hc_dat_local)) {+    q_temp = qqm1[i] * expMLbase[1];++    if (scs) {+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->exp_energy_up)+            q_temp *= scs[s]->exp_energy_up[a2s[s][j]][1];+      }+    }++    qqm[i] += q_temp;+  }++  if (evaluate(i, j, i, j, VRNA_DECOMP_ML_STEM, &hc_dat_local)) {+    q_temp = qb[ij];++    for (s = 0; s < n_seq; s++) {+      type = md->pair[S[s][i]][S[s][j]];+      if (type == 0)+        type = 7;++      q_temp *= exp_E_MLstem(type, ((i > 1) || circular) ? S5[s][i] : -1, ((j < n) || circular) ? S3[s][j] : -1, pf_params);+    }++    qqm[i] += q_temp;+  }+++  /*+   *  construction of qm matrix containing multiple loop+   *  partition function contributions from segment i,j+   */+  temp  = 0.0;+  kl    = iidx[i] - j + 1; /* ii-k=[i,k-1] */+  for (k = j; k > i; k--, kl++)+    temp += qm[kl] * qqm[k];++  maxk  = MIN2(i + hc_up_ml[i], j);+  ii    = maxk - i; /* length of unpaired stretch */++  if (scs) {+    for (k = maxk; k > i; k--, ii--) {+      q_temp = expMLbase[ii] * qqm[k];+      for (s = 0; s < n_seq; s++) {+        if (scs[s])+          if (scs[s]->exp_energy_up)+            q_temp *= scs[s]->exp_energy_up[a2s[s][i]][a2s[s][k] - a2s[s][i]];+      }+      temp += q_temp;+    }+  } else {+    for (k = maxk; k > i; k--, ii--)+      temp += expMLbase[ii] * qqm[k];+  }++  return temp + qqm[i];+}+++PRIVATE char+hc_default(int  i,+           int  j,+           int  k,+           int  l,+           char d,+           void *data)+{+  int                 ij, kl, di, dj, u;+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval  = (char)0;+  di    = k - i;+  dj    = j - l;++  switch (d) {+    case VRNA_DECOMP_ML_ML_ML:+      u     = l - k - 1;+      eval  = (char)1;+      if ((u != 0) && (dat->hc_up[k + 1] < u))+        eval = (char)0;+      break;++    case VRNA_DECOMP_ML_ML:+      eval = (char)1;+      if ((di != 0) && (dat->hc_up[i] < di))+        eval = (char)0;+      if ((dj != 0) && (dat->hc_up[l + 1] < dj))+        eval = (char)0;+      break;++    case VRNA_DECOMP_ML_STEM:+      kl = dat->idx[l] + k;+      if (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC) {+        eval = (char)1;+        if ((di != 0) && (dat->hc_up[i] < di))+          eval = (char)0;+        if ((dj != 0) && (dat->hc_up[l + 1] < dj))+          eval = (char)0;+      }+      break;++    case VRNA_DECOMP_PAIR_ML:+      ij = dat->idx[j] + i;+      if (dat->mx[ij] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP) {+        eval = (char)1;+        di--; dj--;+        if ((di != 0) && (dat->hc_up[i + 1] < di))+          eval = (char)0;+        if ((dj != 0) && (dat->hc_up[l + 1] < dj))+          eval = (char)0;+      }+      break;++    case VRNA_DECOMP_ML_COAXIAL:+      kl = dat->idx[l] + k;+      if (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC)+        eval = (char)1;+      break;++    case VRNA_DECOMP_ML_COAXIAL_ENC:+      ij  = dat->idx[j] + i;+      kl  = dat->idx[l] + k;+      if ((dat->mx[ij] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC) && (dat->mx[kl] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC))+        eval = (char)1;+      break;++    default:+      nrerror("wtf");+  }++  return eval;+}+++PRIVATE char+hc_default_user(int   i,+                int   j,+                int   k,+                int   l,+                char  d,+                void  *data)+{+  char                eval;+  struct default_data *dat = (struct default_data *)data;++  eval  = hc_default(i, j, k, l, d, data);+  eval  = (dat->hc_f(i, j, k, l, d, dat->hc_dat)) ? eval : (char)0;++  return eval;+}
+ C/ViennaRNA/multibranch_loops.h view
@@ -0,0 +1,252 @@+#ifndef VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H+#define VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H++#include <ViennaRNA/utils.h>+#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++#ifdef __GNUC__+# define INLINE inline+#else+# define INLINE+#endif++/**+ *  @file     multibranch_loops.h+ *  @ingroup  loops+ *  @brief    Energy evaluation of multibranch loops for MFE and partition function calculations+ */++/**+ *  @{+ *  @ingroup  loops+ *+ */++/**+ *  @brief  Auxiliary helper arrays for fast exterior loop computations+ *+ *  @see vrna_exp_E_ml_fast_init(), vrna_exp_E_ml_fast_rotate(),+ *  vrna_exp_E_ml_fast_free(), vrna_exp_E_ml_fast()+ */+typedef struct {+  FLT_OR_DBL  *qqm;+  FLT_OR_DBL  *qqm1;++  int         qqmu_size;+  FLT_OR_DBL  **qqmu;+} vrna_mx_pf_aux_ml_t;+++/**+ *  @def E_MLstem(A,B,C,D)+ *  <H2>Compute the Energy contribution of a Multiloop stem</H2>+ *  This definition is a wrapper for the E_Stem() funtion.+ *  It is substituted by an E_Stem() funtion call with argument+ *  extLoop=0, so the energy contribution returned reflects a+ *  stem introduced in a multiloop.<BR>+ *  As for the parameters B (si1) and C (sj1) of the substituted+ *  E_Stem() function, you can inhibit to take 5'-, 3'-dangles+ *  or mismatch contributions to be taken into account by passing+ *  -1 to these parameters.+ * + *  @see    E_Stem()+ *  @param  A The pair type of the stem-closing pair+ *  @param  B The 5'-mismatching nucleotide+ *  @param  C The 3'-mismatching nucleotide+ *  @param  D The datastructure containing scaled energy parameters+ *  @return   The energy contribution of the introduced multiloop stem+ */+PRIVATE INLINE int E_MLstem( int type,+                              int si1,+                              int sj1,+                              vrna_param_t *P);++/**+ *  @def exp_E_MLstem(A,B,C,D)+ *  This is the partition function variant of @ref E_MLstem()+ *  @see E_MLstem()+ *  @return The Boltzmann weighted energy contribution of the introduced multiloop stem+ */+PRIVATE INLINE FLT_OR_DBL exp_E_MLstem(int type,+                                    int si1,+                                    int sj1,+                                    vrna_exp_param_t *P);++++/**+ *  @brief Evaluate energy of a multi branch helices stacking onto closing pair (i,j)+ *+ *  Computes total free energy for coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1)+ */+int E_mb_loop_stack(int i, int j, vrna_fold_compound_t *vc);++/**+ *  @brief  Backtrack the decomposition of a multi branch loop closed by @f$ (i,j) @f$+ *+ *  @param    vc          The #vrna_fold_compound_t filled with all relevant data for backtracking+ *  @param    i           5' position of base pair closing the loop (will be set to 5' position+ *                        of leftmost decomposed block upon successful backtracking)+ *  @param    j           3' position of base pair closing the loop (will be set to 3' position+ *                        of rightmost decomposed block upon successful backtracking)+ *  @param    k           Split position that delimits leftmost from rightmost block, [i,k] and+ *                        [k+1, j], respectively. (Will be set upon successful backtracking)+ *  @param    en          The energy contribution of the substructure enclosed by @f$ (i,j) @f$+ *  @param    component1  Type of leftmost block (1 = ML, 2 = C)+ *  @param    component2  Type of rightmost block (1 = ML, 2 = C)+ *  @returns              1, if backtracking succeeded, 0 otherwise.+ */+int+vrna_BT_mb_loop(vrna_fold_compound_t *vc,+                int *i,+                int *j,+                int *k,+                int en,+                int *component1,+                int *component2);++int+vrna_E_mb_loop_fast(vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    int *dmli1,+                    int *dmli2);++int+E_mb_loop_stack(int i,+                int j,+                vrna_fold_compound_t *vc);++int+E_ml_rightmost_stem(int i,+                    int j,+                    vrna_fold_compound_t *vc);++int+vrna_E_ml_stems_fast( vrna_fold_compound_t *vc,+                      int i,+                      int j,+                      int *fmi,+                      int *dmli);+++FLT_OR_DBL+vrna_exp_E_mb_loop_fast( vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    FLT_OR_DBL *qqm1);+++vrna_mx_pf_aux_ml_t *+vrna_exp_E_ml_fast_init(vrna_fold_compound_t *vc);+++void+vrna_exp_E_ml_fast_rotate(vrna_fold_compound_t  *vc,+                          vrna_mx_pf_aux_ml_t   *aux_mx);+++void+vrna_exp_E_ml_fast_free(vrna_fold_compound_t  *vc,+                          vrna_mx_pf_aux_ml_t *aux_mx);+++FLT_OR_DBL+vrna_exp_E_ml_fast(vrna_fold_compound_t *vc,+                   int                  i,+                   int                  j,+                   vrna_mx_pf_aux_ml_t  *aux_mx);++/*+#################################+# Backtracking functions below  #+#################################+*/++int+vrna_BT_mb_loop_fake( vrna_fold_compound_t *vc,+                      int *u,+                      int *i,+                      int *j,+                      vrna_bp_stack_t *bp_stack,+                      int *stack_count);++int+vrna_BT_mb_loop_split(vrna_fold_compound_t *vc,+                      int *i,+                      int *j,+                      int *k,+                      int *l,+                      int *component1,+                      int *component2,+                      vrna_bp_stack_t *bp_stack,+                      int *stack_count);++int+vrna_BT_mb_loop(vrna_fold_compound_t *vc,+                int *i,+                int *j,+                int *k,+                int en,+                int *component1,+                int *component2);++/*+########################################+# BEGIN OF INLINE FUNCTION DEFINITIONS #+########################################+*/+++PRIVATE INLINE int E_MLstem(int type, int si1, int sj1, vrna_param_t *P){+  int energy = 0;+  if(si1 >= 0 && sj1 >= 0){+    energy += P->mismatchM[type][si1][sj1];+  }+  else if (si1 >= 0){+    energy += P->dangle5[type][si1];+  }+  else if (sj1 >= 0){+    energy += P->dangle3[type][sj1];+  }++  if(type > 2)+    energy += P->TerminalAU;++  energy += P->MLintern[type];++  return energy;+}++++PRIVATE INLINE FLT_OR_DBL+exp_E_MLstem( int type,+              int si1,+              int sj1,+              vrna_exp_param_t *P){++  double energy = 1.0;+  if(si1 >= 0 && sj1 >= 0){+    energy = P->expmismatchM[type][si1][sj1];+  }+  else if(si1 >= 0){+    energy = P->expdangle5[type][si1];+  }+  else if(sj1 >= 0){+    energy = P->expdangle3[type][sj1];+  }++  if(type > 2)+    energy *= P->expTermAU;++  energy *= P->expMLintern[type];+  return (FLT_OR_DBL)energy;+}++/**+ * @}+ */++#endif
+ C/ViennaRNA/naview.c view
@@ -0,0 +1,1171 @@+/*+*   NAVIEW -- A program to make a modified radial drawing of an RNA+*   secondary structure.+*+*   Copyright (c) 1988 Robert E. Bruccoleri+*   Copying of this software, in whole or in part, is permitted+*   provided that the copies are not made for commercial purposes,+*   appropriate credit for the use of the software is given, this+*   copyright notice appears, and notice is given that the copying+*   is by permission of Robert E. Bruccoleri. Any other copying+*   requires specific permission.+*+*   See R. Bruccoleri and G. Heinrich, Computer Applications in the+*   Biosciences, 4, 167-173 (1988) for a full description.+*+*   In November 1997, Michael Zuker made a number of changes to bring+*   naview up to modern standards. All functions defined in naview are+*   now declared before main() with arguments and argument types.+*   When functions are defined, their argument types are declared+*   with the function and these definitions are removed after the '{'.+*   The 'void' declaration was used as necessary for functions.+*+*   The troublesome na_scanf function was deleted and replaced by+*   scanf. Finally, there is now no default for the minimum separation+*   of bases. A floating point number must be entered. However, as+*   before an entry < 0 will be moved up to 0 and an entry > 0.5+*   will be reduced to 0.5.+*+*   Adapted for use as a subroutine in the Vienna RNA Package+*   by Ivo Hofacker, May 1998:+*   deleted output routines, replaced main() by naview_xy_coordinates(),+*   which fills the X and Y arrays used by PS_rna_plot() etc.+*   added ansi prototypes and fixed memory leaks.+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/naview.h"++typedef int LOGICAL;+#define logical LOGICAL++#define true 1+#define false 0+#define FATAL_ERROR 1+#define SUCCESS 0++#define type_alloc(type) (type *) vrna_alloc(sizeof(type))++#define struct_alloc(structure_name) type_alloc(struct structure_name)++#define add_double_list(head,tail,newp) {\+	(newp)->next = (newp)->prev = NULL; \+        if ((head) == NULL) (head) = (tail) = (newp); \+	else { \+	     (tail)->next = (newp); \+	     (newp)->prev = (tail); \+	     (tail) = (newp); \+	     } \+	}++static double pi = 3.141592653589793;+static double anum = 9999.0;++++/*+*   Function data type definitions+*/++#define minf2(x1, x2) ((x1)<(x2))?(x1):(x2)+#define maxf2(x1, x2) ((x1)>(x2))?(x1):(x2)++static struct base {+  int mate;+  double x,y;+  logical extracted;+  struct region *region;+} *bases;++struct region {+  int start1,end1,start2,end2;+};++struct loop {+  int nconnection;+  struct connection **connections;+  int number;+  int depth;+  logical mark;+  double x,y,radius;+};++struct connection {+  struct loop *loop;+  struct region *region;+  int start,end;       /* Start and end form the 1st base pair of the region. */+  double xrad,yrad,angle;+  logical extruded;	  /* True if segment between this connection and+			     the next must be extruded out of the circle */+  logical broken;	  /* True if the extruded segment must be drawn long. */+};++static int nbase, nregion, loop_count;++static struct loop *root, *loops;++static struct region *regions;++static struct loop *construct_loop(int ibase);++struct radloop {+  double radius;+  int loopnumber;+  struct radloop *next, *prev;+};++static struct radloop *rlphead;++static double lencut;++static logical debug = false;++static void read_in_bases(short *pair_table);+static void find_regions(void);+static void dump_loops(void);+static void find_central_loop(void);+static void determine_depths(void);+static void traverse_loop(struct loop *lp,struct connection *anchor_connection);+static void determine_radius(struct loop *lp,double lencut);+static void generate_region(struct connection *cp);+static void construct_extruded_segment(struct connection *cp,struct connection *cpnext);+static void find_center_for_arc(int n,double b,double *hp,double *thetap);+static int depth(struct loop *lp);++static logical connected_connection(struct connection *cp, struct connection *cpnext);+static int    find_ic_middle(int icstart, int icend, struct connection *anchor_connection, struct connection *acp, struct loop *lp);++++int naview_xy_coordinates(short *pair_table, float *X, float *Y) {+  int i;++  nbase = pair_table[0]; /* length */+  bases = (struct base *) vrna_alloc(sizeof(struct base)*(nbase+1));+  regions = (struct region *) vrna_alloc(sizeof(struct region)*(nbase+1));+  read_in_bases(pair_table);+  lencut = 0.5;+  rlphead = NULL;+  find_regions();+  loop_count = 0;+  loops = (struct loop *) vrna_alloc(sizeof(struct loop)*(nbase+1));+  construct_loop(0);+  find_central_loop();+  if (debug) dump_loops();++  traverse_loop(root,NULL);+  for (i=0; i<nbase; i++) {+    X[i] = 100 + 15*bases[i+1].x;+    Y[i] = 100 + 15*bases[i+1].y;+  }+  free(bases);+  free(regions);+  free(loops);+  return nbase;+}+++static void read_in_bases(short *pair_table)+{+  int i,npairs;++  /* Set up an origin.  */+  bases[0].mate = 0;+  bases[0].extracted = false;+  bases[0].x = anum;+  bases[0].y = anum;++  for (npairs=0,i=1; i<=nbase; i++) {+    bases[i].extracted = false;+    bases[i].x = anum;+    bases[i].y = anum;+    bases[i].mate = pair_table[i];+    if ((int) pair_table[i]>i) npairs++;+  }+  if (npairs==0) { /* must have at least 1 pair to avoid segfault */+    bases[1].mate=nbase;+    bases[nbase].mate=1;+  }+}+++static void find_regions(void)+/*+*   Identifies the regions in the structure.+*/++{+  int i,mate,nb1;+  logical *mark;++  nb1 = nbase + 1;+  mark = (int *) vrna_alloc(sizeof(int)*nb1);+  for (i = 0; i < nb1; i++) mark[i] = false;+  nregion = 0;+  for (i=0; i<=nbase; i++) {+    if ( (mate = bases[i].mate) && !mark[i]) {+      regions[nregion].start1 = i;+      regions[nregion].end2 = mate;+      mark[i] = true;+      mark[mate] = true;+      bases[i].region = bases[mate].region = &regions[nregion];+      for (i++,mate--;+	   i<mate && bases[i].mate == mate;+	   i++,mate--) {+	mark[i] = mark[mate] = true;+	bases[i].region = bases[mate].region = &regions[nregion];+      }+      regions[nregion].end1 = --i;+      regions[nregion].start2 = mate+1;+      if (debug) {+	if (nregion == 0) printf("\nRegions are:\n");+	printf("Region %d is %d-%d and %d-%d with gap of %d.\n",+	       nregion+1,regions[nregion].start1,regions[nregion].end1,+	       regions[nregion].start2,regions[nregion].end2,+	       regions[nregion].start2-regions[nregion].end1+1);+      }+      nregion++;+    }+  }+  free(mark);+}+++static struct loop *construct_loop(int ibase)+/*+*   Starting at residue ibase, recursively constructs the loop containing+*   said base and all deeper bases.+*/++{+  int i,mate;+  struct loop *retloop,*lp;+  struct connection *cp;+  struct region *rp;+  struct radloop *rlp;++  retloop = &loops[loop_count++];+  retloop->nconnection = 0;+  retloop->connections = (struct connection **) vrna_alloc(sizeof(struct connection *));+  retloop->depth = 0;+  retloop->number = loop_count;+  retloop->radius = 0.0;+  for (rlp = rlphead;  rlp;  rlp = rlp->next)+    if (rlp->loopnumber == loop_count) retloop->radius = rlp->radius;+  i = ibase;+  do {+    if ((mate = bases[i].mate) != 0) {+      rp = bases[i].region;+      if (!bases[rp->start1].extracted) {+	if (i == rp->start1) {+	  bases[rp->start1].extracted = true;+	  bases[rp->end1].extracted = true;+	  bases[rp->start2].extracted = true;+	  bases[rp->end2].extracted = true;+	  lp = construct_loop(rp->end1 < nbase ? rp->end1+1 : 0);+	}+	else if (i == rp->start2){+	  bases[rp->start2].extracted = true;+	  bases[rp->end2].extracted = true;+	  bases[rp->start1].extracted = true;+	  bases[rp->end1].extracted = true;+	  lp = construct_loop(rp->end2 < nbase ? rp->end2+1 : 0);+	}+	else {+	  vrna_message_error("naview: Error detected in construct_loop. i = %d not found in region table.",i);+	  exit(FATAL_ERROR);+	}+	retloop->connections = (struct connection **)+	  realloc(retloop->connections,+		  (++retloop->nconnection+1) *+		  sizeof(struct connection *));+	retloop->connections[retloop->nconnection-1] = cp =+	  struct_alloc(connection);+	retloop->connections[retloop->nconnection] = NULL;+	cp->loop = lp;+	cp->region = rp;+	if (i == rp->start1) {+	  cp->start = rp->start1;+	  cp->end = rp->end2;+	}+	else {+	  cp->start = rp->start2;+	  cp->end = rp->end1;+	}+	cp->extruded = false;+	cp->broken = false;+	lp->connections = (struct connection **)+	  realloc(lp->connections,+		  (++lp->nconnection+1) *+		  sizeof(struct connection *));+	lp->connections[lp->nconnection-1] = cp =+	  struct_alloc(connection);+	lp->connections[lp->nconnection] = NULL;+	cp->loop = retloop;+	cp->region = rp;+	if (i == rp->start1) {+	  cp->start = rp->start2;+	  cp->end = rp->end1;+	}+	else {+	  cp->start = rp->start1;+	  cp->end = rp->end2;+	}+	cp->extruded = false;+	cp->broken = false;+      }+      i = mate;+    }+    if (++i > nbase) i = 0;+  }+  while (i != ibase);+  return retloop;+}+++static void dump_loops(void)+/*+*   Displays all the loops.+*/++{+  int il,ilp,irp;+  struct loop *lp;+  struct connection *cp,**cpp;++  printf("\nRoot loop is #%ld\n",(root-loops)+1);+  for (il=0; il < loop_count; il++) {+    lp = &loops[il];+    printf("Loop %d has %d connections:\n",il+1,lp->nconnection);+    for (cpp = lp->connections; (cp = *cpp); cpp++) {+      ilp = (cp->loop - loops) + 1;+      irp = (cp->region - regions) + 1;+      printf("  Loop %d Region %d (%d-%d)\n",+	     ilp,irp,cp->start,cp->end);+    }+  }+}+++static void find_central_loop(void)+/*+*   Find node of greatest branching that is deepest.+*/++{+  struct loop *lp;+  int maxconn,maxdepth,i;++  determine_depths();+  maxconn = 0;+  maxdepth = -1;++  for (i=0; i<loop_count; i++) {+    lp = &loops[i];+    if (lp->nconnection > maxconn) {+      maxdepth = lp->depth;+      maxconn = lp->nconnection;+      root = lp;+    }+    else if (lp->depth > maxdepth && lp->nconnection == maxconn) {+      maxdepth = lp->depth;+      root = lp;+    }+  }+}+++static void determine_depths(void)+/*+*   Determine the depth of all loops.+*/++{+  struct loop *lp;+  int i,j;++  for (i=0; i<loop_count; i++) {+    lp = &loops[i];+    for (j=0; j<loop_count; j++) loops[j].mark = false;+    lp->depth = depth(lp);+  }+}++++static int depth(struct loop *lp)+/*+*   Determines the depth of loop, lp. Depth is defined as the minimum+*   distance to a leaf loop where a leaf loop is one that has only one+*   or no connections.+*/++{+  struct connection *cp,**cpp;+  int count,ret,d;++  if (lp->nconnection <= 1) return 0;+  if (lp->mark) return -1;+  lp->mark = true;+  count = 0;+  ret = 0;+  for (cpp=lp->connections; (cp = *cpp); cpp++) {+    d = depth(cp->loop);+    if (d >= 0) {+      if (++count == 1) ret = d;+      else if (ret > d) ret = d;+    }+  }+  lp->mark = false;+  return ret+1;+}+++static void traverse_loop(struct loop *lp, struct connection *anchor_connection)+/*+*   This is the workhorse of the display program. The algorithm is+*   recursive based on processing individual loops. Each base pairing+*   region is displayed using the direction given by the circle diagram,+*   and the connections between the regions is drawn by equally spaced+*   points. The radius of the loop is set to minimize the square error+*   for lengths between sequential bases in the loops. The "correct"+*   length for base links is 1. If the least squares fitting of the+*   radius results in loops being less than 1/2 unit apart, then that+*   segment is extruded.+*+*   The variable, anchor_connection, gives the connection to the loop+*   processed in an previous level of recursion.+*/++{+  double xs,ys,xe,ye,xn,yn,angleinc,r;+  double radius,xc,yc,xo,yo,astart,aend,a;+  struct connection *cp,*cpnext,**cpp,*acp,*cpprev;+  int i,j,n,ic;+  double da,maxang;+  int count,icstart,icend,icmiddle,icroot;+  logical done,done_all_connections,rooted;+  int sign;+  double midx,midy,nrx,nry,mx,my,vx,vy,dotmv,nmidx,nmidy;+  int icstart1,icup,icdown,icnext,direction;+  double dan,dx,dy,rr;+  double cpx,cpy,cpnextx,cpnexty,cnx,cny,rcn,rc,lnx,lny,rl,ac,acn,sx,sy,dcp;+  int imaxloop;++  angleinc = 2 * pi / (nbase+1);+  acp = NULL;+  icroot = -1;+  for (cpp=lp->connections, ic = 0; (cp = *cpp); cpp++, ic++) {+    /*	xs = cos(angleinc*cp->start);+	ys = sin(angleinc*cp->start);+	xe = cos(angleinc*cp->end);+	ye = sin(angleinc*cp->end); */+    xs = -sin(angleinc*cp->start);+    ys = cos(angleinc*cp->start);+    xe = -sin(angleinc*cp->end);+    ye = cos(angleinc*cp->end);+    xn = ye-ys;+    yn = xs-xe;+    r = sqrt(xn*xn + yn*yn);+    cp->xrad = xn/r;+    cp->yrad = yn/r;+    cp->angle = atan2(yn,xn);+    if (cp->angle < 0.0) cp->angle += 2*pi;+    if (anchor_connection != NULL &&+	anchor_connection->region == cp->region) {+      acp = cp;+      icroot = ic;+    }+  }++ set_radius:+  determine_radius(lp,lencut);+  radius = lp->radius;+  if (anchor_connection == NULL) xc = yc = 0.0;+  else {+    xo = (bases[acp->start].x+bases[acp->end].x) / 2.0;+    yo = (bases[acp->start].y+bases[acp->end].y) / 2.0;+    xc = xo - radius * acp->xrad;+    yc = yo - radius * acp->yrad;+  }++  /*+   *   The construction of the connectors will proceed in blocks of+   *   connected connectors, where a connected connector pairs means+   *   two connectors that are forced out of the drawn circle because they+   *   are too close together in angle.+   */++  /*+   *   First, find the start of a block of connected connectors+   */++  if (icroot == -1)+    icstart = 0;+  else icstart = icroot;+  cp = lp->connections[icstart];+  count = 0;+  if (debug) printf("Now processing loop %d\n",lp->number);+  done = false;+  do {+    j = icstart - 1;+    if (j < 0) j = lp->nconnection - 1;+    cpprev = lp->connections[j];+    if (!connected_connection(cpprev,cp)) {+      done = true;+    }+    else {+      icstart = j;+      cp = cpprev;+    }+    if (++count > lp->nconnection) {+      /*+       *  Here everything is connected. Break on maximum angular separation+       *  between connections.+       */+      maxang = -1.0;+      for (ic = 0;  ic < lp->nconnection;  ic++) {+	j = ic + 1;+	if (j >= lp->nconnection) j = 0;+	cp = lp->connections[ic];+	cpnext = lp->connections[j];+	ac = cpnext->angle - cp->angle;+	if (ac < 0.0) ac += 2*pi;+	if (ac > maxang) {+	  maxang = ac;+	  imaxloop = ic;+	}+      }+      icend = imaxloop;+      icstart = imaxloop + 1;+      if (icstart >= lp->nconnection) icstart = 0;+      cp = lp->connections[icend];+      cp->broken = true;+      done = true;+    }+  } while    (!done);+  done_all_connections = false;+  icstart1 = icstart;+  if (debug) printf("Icstart1 = %d\n",icstart1);+  while (!done_all_connections) {+    count = 0;+    done = false;+    icend = icstart;+    rooted = false;+    while (!done) {+      cp = lp->connections[icend];+      if (icend == icroot) rooted = true;+      j = icend + 1;+      if (j >= lp->nconnection) {+	j = 0;+      }+      cpnext = lp->connections[j];+      if (connected_connection(cp,cpnext)) {+	if (++count >= lp->nconnection) break;+	icend = j;+      }+      else {+	done = true;+      }+    }+    icmiddle = find_ic_middle(icstart,icend,anchor_connection,acp,lp);+    ic = icup = icdown = icmiddle;+    if (debug)+      printf("IC start = %d  middle = %d  end = %d\n",+	     icstart,icmiddle,icend);+    done = false;+    direction = 0;+    while (!done) {+      if (direction < 0) {+	ic = icup;+      }+      else if (direction == 0) {+	ic = icmiddle;+      }+      else {+	ic = icdown;+      }+      if (ic >= 0) {+	cp = lp->connections[ic];+	if (anchor_connection == NULL || acp != cp) {+	  if (direction == 0) {+	    astart = cp->angle - asin(1.0/2.0/radius);+	    aend = cp->angle + asin(1.0/2.0/radius);+	    bases[cp->start].x = xc + radius*cos(astart);+	    bases[cp->start].y = yc + radius*sin(astart);+	    bases[cp->end].x = xc + radius*cos(aend);+	    bases[cp->end].y = yc + radius*sin(aend);+	  }+	  else if (direction < 0) {+	    j = ic + 1;+	    if (j >= lp->nconnection) j = 0;+	    cp = lp->connections[ic];+	    cpnext = lp->connections[j];+	    cpx = cp->xrad;+	    cpy = cp->yrad;+	    ac = (cp->angle + cpnext->angle) / 2.0;+	    if (cp->angle > cpnext->angle) ac -= pi;+	    cnx = cos(ac);+	    cny = sin(ac);+	    lnx = cny;+	    lny = -cnx;+	    da = cpnext->angle - cp->angle;+	    if (da < 0.0) da += 2*pi;+	    if (cp->extruded) {+	      if (da <= pi/2) rl = 2.0;+	      else rl = 1.5;+	    }+	    else {+	      rl = 1.0;+	    }+	    bases[cp->end].x = bases[cpnext->start].x + rl*lnx;+	    bases[cp->end].y = bases[cpnext->start].y + rl*lny;+	    bases[cp->start].x = bases[cp->end].x + cpy;+	    bases[cp->start].y = bases[cp->end].y - cpx;+	  }+	  else {+	    j = ic - 1;+	    if (j < 0) j = lp->nconnection - 1;+	    cp = lp->connections[j];+	    cpnext = lp->connections[ic];+	    cpnextx = cpnext->xrad;+	    cpnexty = cpnext->yrad;+	    ac = (cp->angle + cpnext->angle) / 2.0;+	    if (cp->angle > cpnext->angle) ac -= pi;+	    cnx = cos(ac);+	    cny = sin(ac);+	    lnx = -cny;+	    lny = cnx;+	    da = cpnext->angle - cp->angle;+	    if (da < 0.0) da += 2*pi;+	    if (cp->extruded) {+	      if (da <= pi/2) rl = 2.0;+	      else rl = 1.5;+	    }+	    else {+	      rl = 1.0;+	    }+	    bases[cpnext->start].x = bases[cp->end].x + rl*lnx;+	    bases[cpnext->start].y = bases[cp->end].y + rl*lny;+	    bases[cpnext->end].x = bases[cpnext->start].x - cpnexty;+	    bases[cpnext->end].y = bases[cpnext->start].y + cpnextx;+	  }+	}+      }+      if (direction < 0) {+	if (icdown == icend) {+	  icdown = -1;+	}+	else if (icdown >= 0) {+	  if (++icdown >= lp->nconnection) {+	    icdown = 0;+	  }+	}+	direction = 1;+      }+      else {+	if (icup == icstart) icup = -1;+	else if (icup >= 0) {+	  if (--icup < 0) {+	    icup = lp->nconnection - 1;+	  }+	}+	direction = -1;+      }+      done = icup == -1 && icdown == -1;+    }+    icnext = icend + 1;+    if (icnext >= lp->nconnection) icnext = 0;+    if (icend != icstart && (! (icstart == icstart1 && icnext == icstart1))) {+      /*+       *	    Move the bases just constructed (or the radius) so+       *	    that the bisector of the end points is radius distance+       *	    away from the loop center.+       */+      cp = lp->connections[icstart];+      cpnext = lp->connections[icend];+      dx = bases[cpnext->end].x - bases[cp->start].x;+      dy = bases[cpnext->end].y - bases[cp->start].y;+      midx = bases[cp->start].x + dx/2.0;+      midy = bases[cp->start].y + dy/2.0;+      rr = sqrt(dx*dx + dy*dy);+      mx = dx / rr;+      my = dy / rr;+      vx = xc - midx;+      vy = yc - midy;+      rr = sqrt(dx*dx + dy*dy);+      vx /= rr;+      vy /= rr;+      dotmv = vx*mx + vy*my;+      nrx = dotmv*mx - vx;+      nry = dotmv*my - vy;+      rr = sqrt(nrx*nrx + nry*nry);+      nrx /= rr;+      nry /= rr;+      /*+       *	    Determine which side of the bisector the center should be.+       */+      dx = bases[cp->start].x - xc;+      dy = bases[cp->start].y - yc;+      ac = atan2(dy,dx);+      if (ac < 0.0) ac += 2*pi;+      dx = bases[cpnext->end].x - xc;+      dy = bases[cpnext->end].y - yc;+      acn = atan2(dy,dx);+      if (acn < 0.0) acn += 2*pi;+      if (acn < ac) acn += 2*pi;+      if (acn - ac > pi) sign = -1;+      else sign = 1;+      nmidx = xc + sign*radius*nrx;+      nmidy = yc + sign*radius*nry;+      if (rooted) {+	xc -= nmidx - midx;+	yc -= nmidy - midy;+      }+      else {+	for (ic=icstart; ; ++ic >= lp->nconnection ? (ic = 0) : 0) {+	  cp = lp->connections[ic];+	  i = cp->start;+	  bases[i].x += nmidx - midx;+	  bases[i].y += nmidy - midy;+	  i = cp->end;+	  bases[i].x += nmidx - midx;+	  bases[i].y += nmidy - midy;+	  if (ic == icend) break;+	}+      }+    }+    icstart = icnext;+    done_all_connections = icstart == icstart1;+  }+  for (ic=0; ic < lp->nconnection; ic++) {+    cp = lp->connections[ic];+    j = ic + 1;+    if (j >= lp->nconnection) j = 0;+    cpnext = lp->connections[j];+    dx = bases[cp->end].x - xc;+    dy = bases[cp->end].y - yc;+    rc = sqrt(dx*dx + dy*dy);+    ac = atan2(dy,dx);+    if (ac < 0.0) ac += 2*pi;+    dx = bases[cpnext->start].x - xc;+    dy = bases[cpnext->start].y - yc;+    rcn = sqrt(dx*dx + dy*dy);+    acn = atan2(dy,dx);+    if (acn < 0.0) acn += 2*pi;+    if (acn < ac) acn += 2*pi;+    dan = acn - ac;+    dcp = cpnext->angle - cp->angle;+    if (dcp <= 0.0) dcp += 2*pi;+    if (fabs(dan-dcp) > pi) {+      if (cp->extruded) {+        vrna_message_warning("...from traverse_loop. Loop %d has crossed regions",+                                    lp->number);+      }+      else if ((cpnext->start - cp->end) != 1) {+	cp->extruded = true;+	goto set_radius;	    /* Forever shamed */+      }+    }+    if (cp->extruded) {+      construct_extruded_segment(cp,cpnext);+    }+    else {+      n = cpnext->start - cp->end;+      if (n < 0) n += nbase + 1;+      angleinc = dan / n;+      for (j = 1;  j < n;  j++) {+	i = cp->end + j;+	if (i > nbase) i -= nbase + 1;+	a = ac + j*angleinc;+	rr = rc + (rcn-rc)*(a-ac)/dan;+	bases[i].x = xc + rr*cos(a);+	bases[i].y = yc + rr*sin(a);+      }+    }+  }+  for (ic=0; ic < lp->nconnection; ic++) {+    if (icroot != ic) {+      cp = lp->connections[ic];+      generate_region(cp);+      traverse_loop(cp->loop,cp);+    }+  }+  n = 0;+  sx = 0.0;+  sy = 0.0;+  for (ic = 0;  ic < lp->nconnection;  ic++) {+    j = ic + 1;+    if (j >= lp->nconnection) j = 0;+    cp = lp->connections[ic];+    cpnext = lp->connections[j];+    n += 2;+    sx += bases[cp->start].x + bases[cp->end].x;+    sy += bases[cp->start].y + bases[cp->end].y;+    if (!cp->extruded) {+      for (j = cp->end + 1;  j != cpnext->start;  j++) {+	if (j > nbase) j -= nbase + 1;+	n++;+	sx += bases[j].x;+	sy += bases[j].y;+      }+    }+  }+  lp->x = sx / n;+  lp->y = sy / n;++  /* free connections (ih) */+  for (ic = 0;  ic < lp->nconnection;  ic++)+    free(lp->connections[ic]);+  free(lp->connections);+}++++static void determine_radius(struct loop *lp,double lencut)+/*+*   For the loop pointed to by lp, determine the radius of+*   the loop that will ensure that each base around the loop will+*   have a separation of at least lencut around the circle.+*   If a segment joining two connectors will not support this separation,+*   then the flag, extruded, will be set in the first of these+*   two indicators. The radius is set in lp.+*+*   The radius is selected by a least squares procedure where the sum of the+*   squares of the deviations of length from the ideal value of 1 is used+*   as the error function.+*/++{+  double mindit,ci,dt,sumn,sumd,radius,dit;+  int i,j,end,start,imindit;+  struct connection *cp,*cpnext;+  static double rt2_2 = 0.7071068;++  do {+    mindit = 1.0e10;+    for (sumd=0.0, sumn=0.0, i=0;+	 i < lp->nconnection;+	 i++) {+      cp = lp->connections[i];+      j = i + 1;+      if (j >= lp->nconnection) j = 0;+      cpnext = lp->connections[j];+      end =  cp->end;+      start = cpnext->start;+      if (start < end) start += nbase + 1;+      dt = cpnext->angle - cp->angle;+      if (dt <= 0.0) dt += 2*pi;+      if (!cp->extruded)+	ci = start - end;+      else {+	if (dt <= pi/2) ci = 2.0;+	else ci = 1.5;+      }+      sumn += dt * (1.0/ci + 1.0);+      sumd += dt * dt / ci;+      dit = dt/ci;+      if (dit < mindit && !cp->extruded && ci > 1.0) {+	mindit = dit;+	imindit = i;+      }+    }+    radius = sumn/sumd;+    if (radius < rt2_2) radius = rt2_2;+    if (mindit*radius < lencut) {+      lp->connections[imindit]->extruded = true;+    }+  } while (mindit*radius < lencut);+  if (lp->radius > 0.0)+    radius = lp->radius;+  else lp->radius = radius;+}+++static logical    connected_connection(struct connection *cp, struct connection *cpnext)+/*+*   Determines if the connections cp and cpnext are connected+*/++{++  if (cp->extruded) {+    return true;+  }+  else if (cp->end+1 == cpnext->start) {+    return true;+  }+  else {+    return false;+  }+}+++static int    find_ic_middle(int icstart, int icend, struct connection *anchor_connection, struct connection *acp, struct loop *lp)+/*+*   Finds the middle of a set of connected connectors. This is normally+*   the middle connection in the sequence except if one of the connections+*   is the anchor, in which case that connection will be used.+*/++{+  int count,ret,ic,i;+  logical done;++  count = 0;+  ret = -1;+  ic = icstart;+  done = false;+  while (!done) {+    if (count++ > lp->nconnection * 2) {+      printf("Infinite loop detected in find_ic_middle\n");+      exit(FATAL_ERROR);+    }+    if (anchor_connection != NULL && lp->connections[ic] == acp) {+      ret = ic;+    }+    done = ic == icend;+    if (++ic >= lp->nconnection) {+      ic = 0;+    }+  }+  if (ret == -1) {+    for (i=1, ic=icstart; i<(count+1)/2; i++) {+      if (++ic >= lp->nconnection) ic = 0;+    }+    ret = ic;+  }+  return ret;+}+++static void generate_region(struct connection *cp)+/*+*   Generates the coordinates for the base pairing region of a connection+*   given the position of the starting base pair.+*/++{+  int l,start,end,i,mate;+  struct region *rp;++  rp = cp->region;+  l = 0;+  if (cp->start == rp->start1) {+    start = rp->start1;+    end = rp->end1;+  }+  else {+    start = rp->start2;+    end = rp->end2;+  }+  if (bases[cp->start].x > anum - 100.0 ||+      bases[cp->end].x > anum - 100.0) {+    printf("Bad region passed to generate_region. Coordinates not defined.\n");+    exit(FATAL_ERROR);+  }+  for (i=start+1; i<=end; i++) {+    l++;+    bases[i].x = bases[cp->start].x + l*cp->xrad;+    bases[i].y = bases[cp->start].y + l*cp->yrad;+    mate = bases[i].mate;+    bases[mate].x = bases[cp->end].x + l*cp->xrad;+    bases[mate].y = bases[cp->end].y + l*cp->yrad;+  }+}+++static void construct_circle_segment(int start, int end)+/*+*   Draws the segment of residue between the bases numbered start+*   through end, where start and end are presumed to be part of a base+*   pairing region. They are drawn as a circle which has a chord given+*   by the ends of two base pairing regions defined by the connections.+*/++{+  double dx,dy,rr,h,angleinc,midx,midy,xn,yn,nrx,nry,mx,my,a;+  int l,j,i;++  dx = bases[end].x - bases[start].x;+  dy = bases[end].y - bases[start].y;+  rr = sqrt(dx*dx + dy*dy);+  l = end - start;+  if (l < 0) l += nbase + 1;+  if (rr >= l) {+    dx /= rr;+    dy /= rr;+    for (j = 1;  j < l;  j++) {+      i = start + j;+      if (i > nbase) i -= nbase + 1;+      bases[i].x = bases[start].x + dx*(double)j/(double)l;+      bases[i].y = bases[start].y + dy*(double)j/(double)l;+    }+  }+  else {+    find_center_for_arc(l-1,rr,&h,&angleinc);+    dx /= rr;+    dy /= rr;+    midx = bases[start].x + dx*rr/2.0;+    midy = bases[start].y + dy*rr/2.0;+    xn = dy;+    yn = -dx;+    nrx = midx + h*xn;+    nry = midy + h*yn;+    mx = bases[start].x - nrx;+    my = bases[start].y - nry;+    rr = sqrt(mx*mx + my*my);+    a = atan2(my,mx);+    for (j = 1;  j < l;  j++) {+      i = start + j;+      if (i > nbase) i -= nbase + 1;+      bases[i].x = nrx + rr*cos(a+j*angleinc);+      bases[i].y = nry + rr*sin(a+j*angleinc);+    }+  }+}+++static void construct_extruded_segment(struct connection *cp, struct connection *cpnext)+/*+*   Constructs the segment between cp and cpnext as a circle if possible.+*   However, if the segment is too large, the lines are drawn between+*   the two connecting regions, and bases are placed there until the+*   connecting circle will fit.+*/++{+  double astart,aend1,aend2,aave,dx,dy,a1,a2,ac,rr,da,dac;+  int start,end,n,nstart,nend;+  logical collision;++  astart = cp->angle;+  aend2 = aend1 = cpnext->angle;+  if (aend2 < astart) aend2 += 2*pi;+  aave = (astart + aend2) / 2.0;+  start = cp->end;+  end = cpnext->start;+  n = end - start;+  if (n < 0) n += nbase + 1;+  da = cpnext->angle - cp->angle;+  if (da < 0.0) {+    da += 2*pi;+  }+  if (n == 2) construct_circle_segment(start,end);+  else {+    dx = bases[end].x - bases[start].x;+    dy = bases[end].y - bases[start].y;+    rr = sqrt(dx*dx + dy*dy);+    dx /= rr;+    dy /= rr;+    if (rr >= 1.5 && da <= pi/2) {+      nstart = start + 1;+      if (nstart > nbase) nstart -= nbase + 1;+      nend = end - 1;+      if (nend < 0) nend += nbase + 1;+      bases[nstart].x = bases[start].x + 0.5*dx;+      bases[nstart].y = bases[start].y + 0.5*dy;+      bases[nend].x = bases[end].x - 0.5*dx;+      bases[nend].y = bases[end].y - 0.5*dy;+      start = nstart;+      end = nend;+    }+    do {+      collision = false;+      construct_circle_segment(start,end);+      nstart = start + 1;+      if (nstart > nbase) nstart -= nbase + 1;+      dx = bases[nstart].x - bases[start].x;+      dy = bases[nstart].y - bases[start].y;+      a1 = atan2(dy,dx);+      if (a1 < 0.0) a1 += 2*pi;+      dac = a1 - astart;+      if (dac < 0.0) dac += 2*pi;+      if (dac > pi) collision = true;+      nend = end - 1;+      if (nend < 0) nend += nbase + 1;+      dx = bases[nend].x - bases[end].x;+      dy = bases[nend].y - bases[end].y;+      a2 = atan2(dy,dx);+      if (a2 < 0.0) a2 += 2*pi;+      dac = aend1 - a2;+      if (dac < 0.0) dac += 2*pi;+      if (dac > pi) collision = true;+      if (collision) {+	ac = minf2(aave,astart + 0.5);+	bases[nstart].x = bases[start].x + cos(ac);+	bases[nstart].y = bases[start].y + sin(ac);+	start = nstart;+	ac = maxf2(aave,aend2 - 0.5);+	bases[nend].x = bases[end].x + cos(ac);+	bases[nend].y = bases[end].y + sin(ac);+	end = nend;+	n -= 2;+      }+    } while    (collision && n > 1);+  }+}+++static void find_center_for_arc(int n,double b,double *hp,double *thetap)+/*+*   Given n points to be placed equidistantly and equiangularly on a+*   polygon which has a chord of length, b, find the distance, h, from the+*   midpoint of the chord for the center of polygon. Positive values+*   mean the center is within the polygon and the chord, whereas+*   negative values mean the center is outside the chord. Also, the+*   radial angle for each polygon side is returned in theta.+*+*   The procedure uses a bisection algorithm to find the correct+*   value for the center. Two equations are solved, the angles+*   around the center must add to 2*pi, and the sides of the polygon+*   excluding the chord must have a length of 1.+*/++{+  double h,hhi,hlow,r,disc,theta,e,phi;+  int iter;+#define maxiter 500++  hhi = (n+1) / pi;+  hlow = - hhi - b/(n+1.000001-b);  /* changed to prevent div by zero if (ih) */+  if (b<1) hlow = 0;  /* otherwise we might fail below (ih) */+  iter = 0;+  do {+    h = (hhi + hlow) / 2.0;+    r = sqrt(h*h + b*b/4.0);+    /*  if (r<0.5) {r = 0.5; h = 0.5*sqrt(1-b*b);} */+    disc = 1.0 - 0.5/(r*r);+    if (fabs(disc) > 1.0) {+      vrna_message_error("Unexpected large magnitude discriminant = %g %g", disc,r);+      exit(FATAL_ERROR);+    }+    theta = acos(disc);+    /*    theta = 2*acos(sqrt(1-1/(4*r*r))); */+    phi = acos(h/r);+    e = theta * (n+1) + 2*phi - 2*pi;+    if (e > 0.0) {+      hlow = h;+    }+    else {+      hhi = h;+    }+  } while    (fabs(e) > 0.0001 && ++iter < maxiter);+  if (iter >= maxiter) {+    vrna_message_warning("Iteration failed in find_center_for_arc");+    h = 0.0;+    theta = 0.0;+  }+  *hp = h;+  *thetap = theta;+}+
+ C/ViennaRNA/naview.h view
@@ -0,0 +1,24 @@+#ifndef VIENNA_RNA_PACKAGE_NAVIEW_H+#define VIENNA_RNA_PACKAGE_NAVIEW_H++/**+ *  @addtogroup   plotting_utils+ *+ *  @{+ *+ *  @file naview.h+ *+ */++/**+ *+ */+int naview_xy_coordinates(short *pair_table,+                          float *X,+                          float *Y);++/**+ * @}+ */++#endif
+ C/ViennaRNA/pair_mat.h view
@@ -0,0 +1,153 @@+#ifndef VIENNA_RNA_PACKAGE_PAIR_MAT_H+#define VIENNA_RNA_PACKAGE_PAIR_MAT_H++#include <ctype.h>+#include <ViennaRNA/utils.h>+#include <ViennaRNA/fold_vars.h>++#define NBASES 8+/*@notnull@*/++static const char Law_and_Order[] = "_ACGUTXKI";+static int BP_pair[NBASES][NBASES]=+/* _  A  C  G  U  X  K  I */+{{ 0, 0, 0, 0, 0, 0, 0, 0},+ { 0, 0, 0, 0, 5, 0, 0, 5},+ { 0, 0, 0, 1, 0, 0, 0, 0},+ { 0, 0, 2, 0, 3, 0, 0, 0},+ { 0, 6, 0, 4, 0, 0, 0, 6},+ { 0, 0, 0, 0, 0, 0, 2, 0},+ { 0, 0, 0, 0, 0, 1, 0, 0},+ { 0, 6, 0, 0, 5, 0, 0, 0}};++#define MAXALPHA 20       /* maximal length of alphabet */++static short alias[MAXALPHA+1];+static int pair[MAXALPHA+1][MAXALPHA+1];+/* rtype[pair[i][j]]:=pair[j][i] */+static int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};++#ifdef _OPENMP+#pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)+#endif++/* for backward compatibility */+#define ENCODE(c) encode_char(c)++static int encode_char(char c) {+  /* return numerical representation of base used e.g. in pair[][] */+  int code;+  if (energy_set>0) code = (int) (c-'A')+1;+  else {+    const char *pos;+    pos = strchr(Law_and_Order, c);+    if (pos==NULL) code=0;+    else code = (int) (pos-Law_and_Order);+    if (code>5) code = 0;+    if (code>4) code--; /* make T and U equivalent */+  }+  return code;+}++/*@+boolint +charint@*/+/*@null@*/+extern char *nonstandards;++static void make_pair_matrix(void)+{+   int i,j;++   if (energy_set==0) {+      for (i=0; i<5; i++) alias[i] = (short) i;+      alias[5] = 3; /* X <-> G */+      alias[6] = 2; /* K <-> C */+      alias[7] = 0; /* I <-> default base '@' */+      for (i=0; i<NBASES; i++) {+          for (j=0; j<NBASES; j++)+            pair[i][j] = BP_pair[i][j];+      }+      if (noGU) pair[3][4] = pair[4][3] =0;+      if (nonstandards!=NULL) {  /* allow nonstandard bp's */+         for (i=0; i<(int)strlen(nonstandards); i+=2)+            pair[encode_char(nonstandards[i])]+              [encode_char(nonstandards[i+1])]=7;+      }+      for (i=0; i<NBASES; i++) {+          for (j=0; j<NBASES; j++)+           rtype[pair[i][j]] = pair[j][i];+      }+   } else {+      for (i=0; i<=MAXALPHA; i++) {+         for (j=0; j<=MAXALPHA; j++)+            pair[i][j] = 0;+      }+      if (energy_set==1) {+         for (i=1; i<MAXALPHA;) {+            alias[i++] = 3;  /* A <-> G */+            alias[i++] = 2;  /* B <-> C */+         }+         for (i=1; i<MAXALPHA; i++) {+            pair[i][i+1] = 2;    /* AB <-> GC */+            i++;+            pair[i][i-1] = 1;    /* BA <-> CG */+         }+      }+      else if (energy_set==2) {+        for (i=1; i<MAXALPHA;) {+            alias[i++] = 1;  /* A <-> A*/+            alias[i++] = 4;  /* B <-> U */+         }+         for (i=1; i<MAXALPHA; i++) {+            pair[i][i+1] = 5;    /* AB <-> AU */+            i++;+            pair[i][i-1] = 6;    /* BA <-> UA */+         }+      }+      else if (energy_set==3) {+        for (i=1; i<MAXALPHA-2; ) {+          alias[i++] = 3;  /* A <-> G */+          alias[i++] = 2;  /* B <-> C */+          alias[i++] = 1;  /* C <-> A */+          alias[i++] = 4;  /* D <-> U */+        }+        for (i=1; i<MAXALPHA-2; i++) {+          pair[i][i+1] = 2;    /* AB <-> GC */+          i++;+          pair[i][i-1] = 1;    /* BA <-> CG */+          i++;+          pair[i][i+1] = 5;    /* CD <-> AU */+          i++;+          pair[i][i-1] = 6;    /* DC <-> UA */+        }+      }+      else vrna_message_error("What energy_set are YOU using??");+      for (i=0; i<=MAXALPHA; i++) {+        for (j=0; j<=MAXALPHA; j++)+          rtype[pair[i][j]] = pair[j][i];+      }+   }+}++static short *encode_sequence(const char *sequence, short how){+  unsigned int i,l = (unsigned int)strlen(sequence);+  short         *S = (short *) vrna_alloc(sizeof(short)*(l+2));++  switch(how){+    /* standard encoding as always used for S */+    case 0:   for(i=1; i<=l; i++) /* make numerical encoding of sequence */+                S[i]= (short) encode_char(toupper(sequence[i-1]));+              S[l+1] = S[1];+              S[0] = (short) l;+              break;+    /* encoding for mismatches of nostandard bases (normally used for S1) */+    case 1:   for(i=1; i<=l; i++)+                S[i] = alias[(short) encode_char(toupper(sequence[i-1]))];+              S[l+1] = S[1];+              S[0] = S[l];+              break;+  }++  return S;+}++#endif /* VIENNA_RNA_PACKAGE_PAIR_MAT_H */
+ C/ViennaRNA/params.c view
@@ -0,0 +1,889 @@+/*++                  c Ivo Hofacker++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <string.h>+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/params.h"+/**+*** \file params.c+*** <P>+*** This file provides functions that return temperature scaled energy parameters and+*** Boltzmann weights packed in datastructures+*** </P>+***/++/*------------------------------------------------------------------------*/+#define SCALE 10+/**+*** dangling ends should never be destabilizing, i.e. expdangle>=1<BR>+*** specific heat needs smooth function (2nd derivative)<BR>+*** we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2,+*** in the interval b<x<sqrt(3)/2+*/+#define SMOOTH(X) ((X)/SCALE<-1.2283697)?0:(((X)/SCALE>0.8660254)?(X):\+          SCALE*0.38490018*(sin((X)/SCALE-0.34242663)+1)*(sin((X)/SCALE-0.34242663)+1))++/* #define SMOOTH(X) ((X)<0 ? 0 : (X)) */++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE vrna_param_t p;+PRIVATE int id=-1;+/* variables for partition function */+PRIVATE vrna_exp_param_t pf;+PRIVATE int pf_id=-1;++#ifdef _OPENMP+#pragma omp threadprivate(id, pf_id)+#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE vrna_param_t      *get_scaled_params(vrna_md_t *md);+PRIVATE vrna_exp_param_t  *get_scaled_exp_params(vrna_md_t *md, double pfs);+PRIVATE vrna_exp_param_t  *get_exp_params_ali(vrna_md_t *md, unsigned int n_seq, double pfs);+PRIVATE void              rescale_params(vrna_fold_compound_t *vc);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC vrna_param_t *+vrna_params(vrna_md_t *md){++  if(md){+    return get_scaled_params(md);+  } else {+    vrna_md_t md;+    vrna_md_set_default(&md);+    return get_scaled_params(&md);+  }+}++PUBLIC vrna_exp_param_t *+vrna_exp_params(vrna_md_t *md){++  if(md){+    return  get_scaled_exp_params(md, -1.);+  } else {+    vrna_md_t md;+    vrna_md_set_default(&md);+    return get_scaled_exp_params(&md, -1.);+  }+}++PUBLIC vrna_exp_param_t *+vrna_exp_params_comparative(unsigned int n_seq, vrna_md_t *md){++  if(md){+    return  get_exp_params_ali(md, n_seq, -1.);+  } else {+    vrna_md_t md;+    vrna_md_set_default(&md);+    return get_exp_params_ali(&md, n_seq, -1.);+  }+}++PUBLIC vrna_param_t *+vrna_params_copy(vrna_param_t *par){++  vrna_param_t *copy = NULL;+  if(par){+    copy = (vrna_param_t *) vrna_alloc(sizeof(vrna_param_t));+    memcpy(copy, par, sizeof(vrna_param_t));+  }+  return copy;+}++PUBLIC vrna_exp_param_t *+vrna_exp_params_copy(vrna_exp_param_t *par){++  vrna_exp_param_t *copy = NULL;+  if(par){+    copy = (vrna_exp_param_t *) vrna_alloc(sizeof(vrna_exp_param_t));+    memcpy(copy, par, sizeof(vrna_exp_param_t));+  }+  return copy;+}++PUBLIC void+vrna_params_subst( vrna_fold_compound_t *vc,+                    vrna_param_t *parameters){++  if(vc){+    if(vc->params)+      free(vc->params);+    if(parameters){+      vc->params = vrna_params_copy(parameters);+    } else {+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:     /* fall through */++        case VRNA_FC_TYPE_COMPARATIVE:  vc->params = vrna_params(NULL);+                                      break;++        default:                      break;+      }+    }+  }+}++PUBLIC void+vrna_params_reset(vrna_fold_compound_t *vc,+                  vrna_md_t *md_p){++  if(vc){+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* fall through */++      case VRNA_FC_TYPE_COMPARATIVE:  if(vc->params)+                                      free(vc->params);+                                    vc->params = vrna_params(md_p);+                                    break;++      default:                      break;+    }+  }+}++PUBLIC void+vrna_exp_params_reset(vrna_fold_compound_t *vc,+                      vrna_md_t *md_p){++  if(vc){+    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* fall through */++      case VRNA_FC_TYPE_COMPARATIVE:  if(vc->exp_params)+                                      free(vc->exp_params);+                                    vc->exp_params = vrna_exp_params(md_p);+                                    break;++      default:                      break;+    }+  }+}++PUBLIC void+vrna_exp_params_subst(vrna_fold_compound_t *vc,+                      vrna_exp_param_t *params){++  if(vc){+    if(vc->exp_params)+      free(vc->exp_params);+    if(params){+      vc->exp_params = vrna_exp_params_copy(params);+    } else {+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:     vc->exp_params = vrna_exp_params(NULL);+                                      if(vc->cutpoint > 0)+                                        vc->exp_params->model_details.min_loop_size = 0;+                                      break;++        case VRNA_FC_TYPE_COMPARATIVE:  vc->exp_params = vrna_exp_params_comparative(vc->n_seq, NULL);+                                      break;++        default:                      break;+      }+    }+    /* fill additional helper arrays for scaling etc. */+    vrna_exp_params_rescale(vc, NULL);+  }+}++PUBLIC void+vrna_exp_params_rescale(vrna_fold_compound_t *vc,+                        double *mfe){++  vrna_exp_param_t  *pf;+  double            kT;+  vrna_md_t         *md;++  if(vc){+    +    if(!vc->exp_params){+      switch(vc->type){+        case VRNA_FC_TYPE_SINGLE:+          vc->exp_params = vrna_exp_params(&(vc->params->model_details));+          break;+        case VRNA_FC_TYPE_COMPARATIVE:+          vc->exp_params = vrna_exp_params_comparative(vc->n_seq, &(vc->params->model_details));+          break;+      }+    }++    pf = vc->exp_params;+    if(pf){+      kT = pf->kT;+      md = &(pf->model_details);++      if(vc->type == VRNA_FC_TYPE_COMPARATIVE)+        kT /= vc->n_seq;++      if(mfe){+        kT /= 1000.;+        pf->pf_scale = exp(-(md->sfact * *mfe)/ kT / vc->length);+      } else if(pf->pf_scale < 1.){  /* mean energy for random sequences: 184.3*length cal */+        pf->pf_scale = exp(-(-185+(pf->temperature-37.)*7.27)/kT);+      }+      if(pf->pf_scale < 1.)+        pf->pf_scale = 1.;+      rescale_params(vc);+    }+  }+}++/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/++PRIVATE vrna_param_t *+get_scaled_params(vrna_md_t *md){++  unsigned int i,j,k,l;+  double tempf;+  vrna_param_t *params;++  params  = (vrna_param_t *)vrna_alloc(sizeof(vrna_param_t));++  params->model_details = *md;  /* copy over the model details */+  params->temperature   = md->temperature;+  tempf                 = ((params->temperature+K0)/Tmeasure);++  for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)+    for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){+      double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * tempf;+      double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * tempf;+      params->gquad[i][j] = (int)GQuadAlpha_T*(i-1) + (int)(((double)GQuadBeta_T)*log(j - 2));+    }++  for (i=0; i<31; i++)+    params->hairpin[i]  = hairpindH[i] - (hairpindH[i] - hairpin37[i])*tempf;+  for (i=0; i<=MIN2(30,MAXLOOP); i++) {+    params->bulge[i]          = bulgedH[i] - (bulgedH[i] - bulge37[i]) * tempf;+    params->internal_loop[i]  = internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i]) * tempf;+  }+  params->lxc = lxc37*tempf;+  for (; i<=MAXLOOP; i++) {+    params->bulge[i] = params->bulge[30]+(int)(params->lxc*log((double)(i)/30.));+    params->internal_loop[i] = params->internal_loop[30]+(int)(params->lxc*log((double)(i)/30.));+  }++  params->ninio[2] = niniodH - (niniodH - ninio37) * tempf;++  params->TripleC = TripleCdH - (TripleCdH - TripleC37) * tempf;+  params->MultipleCA = MultipleCAdH - (MultipleCAdH - MultipleCA37) * tempf;+  params->MultipleCB = MultipleCBdH - (MultipleCBdH - MultipleCB37) * tempf;++  for (i=0; (i*7)<strlen(Tetraloops); i++)+    params->Tetraloop_E[i] = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*tempf;+  for (i=0; (i*5)<strlen(Triloops); i++)+    params->Triloop_E[i] =  TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*tempf;+  for (i=0; (i*9)<strlen(Hexaloops); i++)+    params->Hexaloop_E[i] =  HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*tempf;++  params->TerminalAU = TerminalAUdH - (TerminalAUdH - TerminalAU37) * tempf;++  params->DuplexInit = DuplexInitdH - (DuplexInitdH - DuplexInit37) *tempf;++  params->MLbase = ML_BASEdH - (ML_BASEdH - ML_BASE37) * tempf;++  for (i=0; i<=NBPAIRS; i++)+    params->MLintern[i] = ML_interndH - (ML_interndH - ML_intern37) * tempf;++  params->MLclosing = ML_closingdH - (ML_closingdH - ML_closing37) * tempf;+++  /* stacks    G(T) = H - [H - G(T0)]*T/T0 */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      params->stack[i][j] = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*tempf;++  /* mismatches */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<5; j++)+      for (k=0; k<5; k++) {+        int mm;+        params->mismatchI[i][j][k]    = mismatchIdH[i][j][k] - (mismatchIdH[i][j][k] - mismatchI37[i][j][k])*tempf;+        params->mismatchH[i][j][k]    = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*tempf;+        params->mismatch1nI[i][j][k]  = mismatch1nIdH[i][j][k]-(mismatch1nIdH[i][j][k]-mismatch1nI37[i][j][k])*tempf;/* interior nx1 loops */+        params->mismatch23I[i][j][k]  = mismatch23IdH[i][j][k]-(mismatch23IdH[i][j][k]-mismatch23I37[i][j][k])*tempf;/* interior 2x3 loops */+        if(md->dangles){+          mm                      = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*tempf;+          params->mismatchM[i][j][k]    = (mm > 0) ? 0 : mm;+          mm                      = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*tempf;+          params->mismatchExt[i][j][k]  = (mm > 0) ? 0 : mm;+        }+        else{+          params->mismatchM[i][j][k] = params->mismatchExt[i][j][k] = 0;+        }+      }++  /* dangles */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<5; j++) {+      int dd;+      dd = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*tempf;+      params->dangle5[i][j] = (dd>0) ? 0 : dd;  /* must be <= 0 */+      dd = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*tempf;+      params->dangle3[i][j] = (dd>0) ? 0 : dd;  /* must be <= 0 */+    }+  /* interior 1x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++)+          params->int11[i][j][k][l] = int11_dH[i][j][k][l] - (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*tempf;++  /* interior 2x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m;+          for (m=0; m<5; m++)+            params->int21[i][j][k][l][m] = int21_dH[i][j][k][l][m] - (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*tempf;+        }+  /* interior 2x2 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++)+              params->int22[i][j][k][l][m][n] = int22_dH[i][j][k][l][m][n] - (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*tempf;+        }++  strncpy(params->Tetraloops, Tetraloops, 281);+  strncpy(params->Triloops, Triloops, 241);+  strncpy(params->Hexaloops, Hexaloops, 361);++  params->id = ++id;+  return params;+}++PRIVATE vrna_exp_param_t *+get_scaled_exp_params(vrna_md_t *md,+                      double pfs){++  unsigned  int i, j, k, l;+  double        kT, TT;+  double        GT;+  vrna_exp_param_t     *pf;++  pf                = (vrna_exp_param_t *)vrna_alloc(sizeof(vrna_exp_param_t));+  pf->model_details = *md;+  pf->temperature   = md->temperature;+  pf->alpha         = md->betaScale;+  pf->kT = kT       = md->betaScale * (md->temperature + K0) * GASCONST;   /* kT in cal/mol  */+  pf->pf_scale      = pfs;+  TT                = (md->temperature + K0) / (Tmeasure);++  for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)+    for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){+      double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * TT;+      double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * TT;+      GT = ((double)GQuadAlpha_T)*((double)(i-1)) + ((double)GQuadBeta_T)*log(((double)j) - 2.);+      pf->expgquad[i][j] = exp( -GT*10./kT);+    }++  /* loop energies: hairpins, bulges, interior, mulit-loops */+  for (i=0; i<31; i++){+    GT  = hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;+    pf->exphairpin[i] = exp( -GT*10./kT);+  }++  for (i=0; i<=MIN2(30, MAXLOOP); i++) {+    GT =  bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;+    pf->expbulge[i] = exp( -GT*10./kT);+    GT =  internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;+    pf->expinternal[i] = exp( -GT*10./kT);+  }+  /* special case of size 2 interior loops (single mismatch) */+  if (james_rule) pf->expinternal[2] = exp ( -80*10./kT);++  pf->lxc = lxc37*TT;++  GT =  DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;+  pf->expDuplexInit = exp( -GT*10./kT);++  for (i=31; i<=MAXLOOP; i++) {+    GT = bulge37[30]*TT + (pf->lxc*log( i/30.));+    pf->expbulge[i] = exp( -GT*10./kT);+    GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));+    pf->expinternal[i] = exp( -GT*10./kT);+  }++  GT = niniodH - (niniodH - ninio37)*TT;+  for (j=0; j<=MAXLOOP; j++)+      pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kT);++  for (i=0; (i*7)<strlen(Tetraloops); i++) {+    GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;+    pf->exptetra[i] = exp( -GT*10./kT);+  }+  for (i=0; (i*5)<strlen(Triloops); i++) {+    GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;+    pf->exptri[i] = exp( -GT*10./kT);+  }+  for (i=0; (i*9)<strlen(Hexaloops); i++) {+    GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;+    pf->exphex[i] = exp( -GT*10./kT);+  }+  GT =  ML_closingdH - (ML_closingdH - ML_closing37)*TT;+  pf->expMLclosing = exp( -GT*10./kT);++  for (i=0; i<=NBPAIRS; i++) {+    GT =  ML_interndH - (ML_interndH - ML_intern37)*TT;+    /* if (i>2) GT += TerminalAU; */+    pf->expMLintern[i] = exp( -GT*10./kT);+  }+  GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;+  pf->expTermAU = exp(-GT*10./kT);++  GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;++  pf->expMLbase=exp(-10.*GT/kT);+++  /* if dangles==0 just set their energy to 0,+     don't let dangle energies become > 0 (at large temps),+     but make sure go smoothly to 0                        */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=4; j++) {+      if (md->dangles) {+        GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;+        pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kT);+        GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;+        pf->expdangle3[i][j] =  exp(SMOOTH(-GT)*10./kT);+      } else+        pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;+    }++  /* stacking energies */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++) {+      GT =  stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;+      pf->expstack[i][j] = exp( -GT*10./kT);+    }++  /* mismatch energies */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<5; j++)+      for (k=0; k<5; k++) {+        GT =  mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;+        pf->expmismatchI[i][j][k] = exp(-GT*10.0/kT);+        GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;+        pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kT);+        GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;+        pf->expmismatchH[i][j][k] = exp(-GT*10.0/kT);+        if (md->dangles) {+          GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;+          pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);+          GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;+          pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);+        }+        else{+          pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;+        }+        GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;+        pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kT);+      }++  /* interior lops of length 2 */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          GT = int11_dH[i][j][k][l] -+            (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;+          pf->expint11[i][j][k][l] = exp(-GT*10./kT);+        }+  /* interior 2x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m;+          for (m=0; m<5; m++) {+            GT = int21_dH[i][j][k][l][m] -+              (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;+            pf->expint21[i][j][k][l][m] = exp(-GT*10./kT);+          }+        }++  /* interior 2x2 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++) {+              GT = int22_dH[i][j][k][l][m][n] -+                (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;+              pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kT);+            }+        }++  strncpy(pf->Tetraloops, Tetraloops, 281);+  strncpy(pf->Triloops, Triloops, 241);+  strncpy(pf->Hexaloops, Hexaloops, 361);++  return pf;+}++PRIVATE vrna_exp_param_t *+get_exp_params_ali( vrna_md_t *md,+                    unsigned int n_seq,+                    double pfs){++  /* scale energy parameters and pre-calculate Boltzmann weights */+  unsigned int  i, j, k, l;+  double        kTn, TT;+  double        GT;+  vrna_exp_param_t     *pf;++  pf                = (vrna_exp_param_t *)vrna_alloc(sizeof(vrna_exp_param_t));+  pf->model_details = *md;+  pf->alpha         = md->betaScale;+  pf->temperature   = md->temperature;+  pf->pf_scale      = pfs;+  pf->kT = kTn      = ((double)n_seq)*md->betaScale*(md->temperature+K0)*GASCONST;   /* kT in cal/mol  */+  TT                = (md->temperature+K0)/(Tmeasure);+++   /* loop energies: hairpins, bulges, interior, mulit-loops */+  for (i=0; i<31; i++) {+    GT =  hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;+    pf->exphairpin[i] = exp( -GT*10./kTn);+  }+  /*add penalty for too short hairpins*/+  for (i=0; i<3; i++) {+    GT= 600/*Penalty*/*TT;+    pf->exphairpin[i] = exp( -GT*10./kTn);+  }++  for (i=0; i<=MIN2(30, MAXLOOP); i++) {+    GT =  bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;+    pf->expbulge[i] = exp( -GT*10./kTn);+    GT =  internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;+    pf->expinternal[i] = exp( -GT*10./kTn);+  }+  /* special case of size 2 interior loops (single mismatch) */+  if (james_rule) pf->expinternal[2] = exp ( -80*10./kTn);++  pf->lxc = lxc37*TT;++  GT =  DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;+  pf->expDuplexInit = exp( -GT*10./kTn);++  for (i=31; i<=MAXLOOP; i++) {+    GT = bulge37[30]*TT + (pf->lxc*log( i/30.));+    pf->expbulge[i] = exp( -GT*10./kTn);+    GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));+    pf->expinternal[i] = exp( -GT*10./kTn);+  }++  GT = niniodH - (niniodH - ninio37)*TT;+  for (j=0; j<=MAXLOOP; j++)+    pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kTn);++  for (i=0; (i*7)<strlen(Tetraloops); i++) {+    GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;+    pf->exptetra[i] = exp( -GT*10./kTn);+  }+  for (i=0; (i*5)<strlen(Triloops); i++) {+    GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;+    pf->exptri[i] = exp( -GT*10./kTn);+  }+  for (i=0; (i*9)<strlen(Hexaloops); i++) {+    GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;+    pf->exphex[i] = exp( -GT*10./kTn);+  }+  GT =  ML_closingdH - (ML_closingdH - ML_closing37)*TT;+  pf->expMLclosing = exp( -GT*10./kTn);++  for (i=0; i<=NBPAIRS; i++) { /* includes AU penalty */+    GT =  ML_interndH - (ML_interndH - ML_intern37)*TT;+    /* if (i>2) GT += TerminalAU; */+    pf->expMLintern[i] = exp( -GT*10./kTn);+  }+  GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;+  pf->expTermAU = exp(-GT*10./kTn);++  GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;+  pf->expMLbase=exp(-10.*GT/(kTn/n_seq));+++  /* if dangle_model==0 just set their energy to 0,+     don't let dangle energies become > 0 (at large temps),+     but make sure go smoothly to 0                        */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=4; j++) {+      if (md->dangles) {+        GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;+        pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kTn);+        GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;+        pf->expdangle3[i][j] =  exp(SMOOTH(-GT)*10./kTn);+      } else+        pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;+    }++  /* stacking energies */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++) {+      GT =  stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;+      pf->expstack[i][j] = exp( -GT*10./kTn);+    }++  /* mismatch energies */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<5; j++)+      for (k=0; k<5; k++) {+        GT =  mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;+        pf->expmismatchI[i][j][k] = exp(-GT*10.0/kTn);+        GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;+        pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kTn);+        GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;+        pf->expmismatchH[i][j][k] = exp(-GT*10.0/kTn);+        if (md->dangles) {+          GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;+          pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);+          GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;+          pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);+        }+        else{+          pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;+        }+        GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;+        pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kTn);+      }+++  /* interior lops of length 2 */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          GT = int11_dH[i][j][k][l] -+            (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;+          pf->expint11[i][j][k][l] = exp(-GT*10./kTn);+        }+  /* interior 2x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m;+          for (m=0; m<5; m++) {+            GT = int21_dH[i][j][k][l][m] -+              (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;+            pf->expint21[i][j][k][l][m] = exp(-GT*10./kTn);+          }+        }++  /* interior 2x2 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++) {+              GT = int22_dH[i][j][k][l][m][n] -+                (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;+              pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kTn);+            }+        }++  strncpy(pf->Tetraloops, Tetraloops, 281);+  strncpy(pf->Triloops, Triloops, 241);+  strncpy(pf->Hexaloops, Hexaloops, 361);++  return pf;+}++PRIVATE void+rescale_params(vrna_fold_compound_t *vc){++  int           i;+  vrna_exp_param_t  *pf = vc->exp_params;+  vrna_mx_pf_t      *m  = vc->exp_matrices;++  if(m && pf){+    m->scale[0] = 1.;+    m->scale[1] = (FLT_OR_DBL)(1./pf->pf_scale);+    m->expMLbase[0] = 1;+    m->expMLbase[1] = (FLT_OR_DBL)(pf->expMLbase / pf->pf_scale);+    for (i=2; i<=vc->length; i++) {+      m->scale[i] = m->scale[i/2]*m->scale[i-(i/2)];+      m->expMLbase[i] = (FLT_OR_DBL)pow(pf->expMLbase, (double)i) * m->scale[i];+    }+  }+}+++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC vrna_param_t *+scale_parameters(void){++  vrna_md_t md;+  set_model_details(&md);+  return vrna_params(&md);+}++PUBLIC vrna_param_t *+get_scaled_parameters(double temp,+                      vrna_md_t md){++  md.temperature = temp;+  return get_scaled_params(&md);+}++PUBLIC vrna_exp_param_t *+get_boltzmann_factors(double temp,+                      double betaScale,+                      vrna_md_t md,+                      double pfs){++  md.temperature  = temp;+  md.betaScale    = betaScale;+  pf_scale        = pfs;++  return get_scaled_exp_params(&md, pfs);+}++PUBLIC vrna_exp_param_t *+get_scaled_pf_parameters(void){++  vrna_md_t         md;+  vrna_exp_param_t  *pf;++  set_model_details(&md);++  pf = vrna_exp_params(&md);+  pf->pf_scale = pf_scale;++  return pf;+}++PUBLIC vrna_exp_param_t *+get_boltzmann_factors_ali(unsigned int n_seq,+                         double temp,+                         double betaScale,+                         vrna_md_t md,+                         double pfs){++  md.temperature  = temp;+  md.betaScale    = betaScale;+  pf_scale        = pfs;++  return get_exp_params_ali(&md, n_seq, pfs);+  +}++PUBLIC vrna_exp_param_t *+get_scaled_alipf_parameters(unsigned int n_seq){++  vrna_md_t  md;++  set_model_details(&md);++  return get_exp_params_ali(&md, n_seq, pf_scale);+}++PUBLIC vrna_exp_param_t *+get_boltzmann_factor_copy(vrna_exp_param_t *par){++  return vrna_exp_params_copy(par);+}++PUBLIC vrna_param_t *get_parameter_copy(vrna_param_t *par){++  return vrna_params_copy(par);+}++PUBLIC vrna_param_t *copy_parameters(void){+  vrna_param_t *copy;+  if (p.id != id){+    vrna_md_t md;+    set_model_details(&md);+    return vrna_params(&md);+  } else {+    copy = (vrna_param_t *) vrna_alloc(sizeof(vrna_param_t));+    memcpy(copy, &p, sizeof(vrna_param_t));+  }+  return copy;+}++PUBLIC vrna_param_t *set_parameters(vrna_param_t *dest){+  memcpy(&p, dest, sizeof(vrna_param_t));+  return &p;+}++PUBLIC vrna_exp_param_t *copy_pf_param(void){+  vrna_exp_param_t *copy;+  if (pf.id != pf_id){+    vrna_md_t md;+    set_model_details(&md);+    copy = vrna_exp_params(&md);+    copy->pf_scale = pf_scale;+    return copy;+  }+  else{+    copy = (vrna_exp_param_t *) vrna_alloc(sizeof(vrna_exp_param_t));+    memcpy(copy, &pf, sizeof(vrna_exp_param_t));+  }+  return copy;+}++PUBLIC vrna_exp_param_t *set_pf_param(vrna_param_t *dest){+  memcpy(&pf, dest, sizeof(vrna_exp_param_t));+  return &pf;+}++PUBLIC vrna_exp_param_t *scale_pf_parameters(void){+  vrna_md_t         md;+  vrna_exp_param_t  *pf;++  set_model_details(&md);++  pf = vrna_exp_params(&md);+  pf->pf_scale = pf_scale;++  return pf;+}++#endif+
+ C/ViennaRNA/params.h view
@@ -0,0 +1,479 @@+#ifndef VIENNA_RNA_PACKAGE_PARAMS_H+#define VIENNA_RNA_PACKAGE_PARAMS_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     params.h+ *  @ingroup  energy_parameters+ *  @brief    Functions to deal with sets of energy parameters+ */++/**+ *  @addtogroup energy_parameters+ *  @brief All relevant functions to retrieve and copy pre-calculated energy parameter sets as well as+ *  reading/writing the energy parameter set from/to file(s).+ *+ *  This module covers all relevant functions for pre-calculation of the energy parameters+ *  necessary for the folding routines provided by RNAlib. Furthermore, the energy parameter set+ *  in the RNAlib can be easily exchanged by a user-defined one. It is also possible to write the+ *  current energy parameter set into a text file.+ *  @{+ *  @ingroup  energy_parameters+ */++/** @brief Typename for the free energy parameter data structure #vrna_params */+typedef struct  vrna_param_s       vrna_param_t;+/** @brief Typename for the Boltzmann factor data structure #vrna_exp_params */+typedef struct  vrna_exp_param_s   vrna_exp_param_t;++#include <ViennaRNA/energy_const.h>+#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/model.h>++#define   VRNA_GQUAD_MAX_STACK_SIZE     7+#define   VRNA_GQUAD_MIN_STACK_SIZE     2+#define   VRNA_GQUAD_MAX_LINKER_LENGTH  15+#define   VRNA_GQUAD_MIN_LINKER_LENGTH  1+#define   VRNA_GQUAD_MIN_BOX_SIZE       ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))+#define   VRNA_GQUAD_MAX_BOX_SIZE       ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))++/**+ *  @brief The datastructure that contains temperature scaled energy parameters.+ */+struct vrna_param_s {+  int     id;+  int     stack[NBPAIRS+1][NBPAIRS+1];+  int     hairpin[31];+  int     bulge[MAXLOOP+1];+  int     internal_loop[MAXLOOP+1];+  int     mismatchExt[NBPAIRS+1][5][5];+  int     mismatchI[NBPAIRS+1][5][5];+  int     mismatch1nI[NBPAIRS+1][5][5];+  int     mismatch23I[NBPAIRS+1][5][5];+  int     mismatchH[NBPAIRS+1][5][5];+  int     mismatchM[NBPAIRS+1][5][5];+  int     dangle5[NBPAIRS+1][5];+  int     dangle3[NBPAIRS+1][5];+  int     int11[NBPAIRS+1][NBPAIRS+1][5][5];+  int     int21[NBPAIRS+1][NBPAIRS+1][5][5][5];+  int     int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];+  int     ninio[5];+  double  lxc;+  int     MLbase;+  int     MLintern[NBPAIRS+1];+  int     MLclosing;+  int     TerminalAU;+  int     DuplexInit;+  int     Tetraloop_E[200];+  char    Tetraloops[1401];+  int     Triloop_E[40];+  char    Triloops[241];+  int     Hexaloop_E[40];+  char    Hexaloops[1801];+  int     TripleC;+  int     MultipleCA;+  int     MultipleCB;+  int     gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]+                [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];++  double  temperature;            /**<  @brief  Temperature used for loop contribution scaling */++  vrna_md_t model_details;   /**<  @brief  Model details to be used in the recursions */+};++/**+ *  @brief  The data structure that contains temperature scaled Boltzmann weights of the energy parameters.+ */+struct vrna_exp_param_s {+  int     id;   /**<  @brief  An identifier for the data structure+                      @deprecated This attribute will be removed in version 3+                */+  double  expstack[NBPAIRS+1][NBPAIRS+1];+  double  exphairpin[31];+  double  expbulge[MAXLOOP+1];+  double  expinternal[MAXLOOP+1];+  double  expmismatchExt[NBPAIRS+1][5][5];+  double  expmismatchI[NBPAIRS+1][5][5];+  double  expmismatch23I[NBPAIRS+1][5][5];+  double  expmismatch1nI[NBPAIRS+1][5][5];+  double  expmismatchH[NBPAIRS+1][5][5];+  double  expmismatchM[NBPAIRS+1][5][5];+  double  expdangle5[NBPAIRS+1][5];+  double  expdangle3[NBPAIRS+1][5];+  double  expint11[NBPAIRS+1][NBPAIRS+1][5][5];+  double  expint21[NBPAIRS+1][NBPAIRS+1][5][5][5];+  double  expint22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];+  double  expninio[5][MAXLOOP+1];+  double  lxc;+  double  expMLbase;+  double  expMLintern[NBPAIRS+1];+  double  expMLclosing;+  double  expTermAU;+  double  expDuplexInit;+  double  exptetra[40];+  double  exptri[40];+  double  exphex[40];+  char    Tetraloops[1401];+  double  expTriloop[40];+  char    Triloops[241];+  char    Hexaloops[1801];+  double  expTripleC;+  double  expMultipleCA;+  double  expMultipleCB;+  double  expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]+                  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];++  double  kT;+  double  pf_scale;     /**<  @brief    Scaling factor to avoid over-/underflows */++  double  temperature;  /**<  @brief    Temperature used for loop contribution scaling */+  double  alpha;        /**<  @brief    Scaling factor for the thermodynamic temperature+                              @details  This allows for temperature scaling in Boltzmann+                                        factors independently from the energy contributions.+                                        The resulting Boltzmann factors are then computed by+                                        @f$ e^{-E/(\alpha \cdot K \cdot T)} @f$+                        */++  vrna_md_t model_details; /**<  @brief  Model details to be used in the recursions */++};+++/**+ *  @brief  Get a data structure containing prescaled free energy parameters+ *+ *  If a NULL pointer is passed for the model details parameter, the default+ *  model parameters are stored within the requested #vrna_param_t structure.+ *+ *  @see #vrna_md_t, vrna_md_set_default(), vrna_exp_params()+ *+ *  @param  md  A pointer to the model details to store inside the structure (Maybe NULL)+ *  @return     A pointer to the memory location where the requested parameters are stored+ */+vrna_param_t *+vrna_params(vrna_md_t *md);++/**+ *  @brief Get a copy of the provided free energy parameters+ *+ *  If NULL is passed as parameter, a default set of energy parameters is created+ *  and returned.+ *+ *  @see vrna_params(), #vrna_param_t+ *+ *  @param  par   The free energy parameters that are to be copied (Maybe NULL)+ *  @return       A copy or a default set of the (provided) parameters+ */+vrna_param_t *+vrna_params_copy(vrna_param_t *par);++/**+ *  @brief  Get a data structure containing prescaled free energy parameters+ *          already transformed to Boltzmann factors+ *+ *  This function returns a data structure that contains all necessary precomputed+ *  energy contributions for each type of loop.+ *+ *  In contrast to vrna_params(), the free energies within this data structure+ *  are stored as their Boltzmann factors, i.e.+ *+ *  @f$ exp(-E / kT) @f$+ *+ *  where @f$ E @f$ is the free energy.+ *+ *  If a NULL pointer is passed for the model details parameter, the default+ *  model parameters are stored within the requested #vrna_exp_param_t structure.+ *+ *  @see #vrna_md_t, vrna_md_set_default(), vrna_params(), vrna_rescale_pf_params()+ *+ *  @param  md  A pointer to the model details to store inside the structure (Maybe NULL)+ *  @return     A pointer to the memory location where the requested parameters are stored+ */+vrna_exp_param_t *+vrna_exp_params(vrna_md_t *md);++/**+ *  @brief  Get a data structure containing prescaled free energy parameters+ *          already transformed to Boltzmann factors (alifold version)+ *+ *  If a NULL pointer is passed for the model details parameter, the default+ *  model parameters are stored within the requested #vrna_exp_param_t structure.+ *+ *  @see #vrna_md_t, vrna_md_set_default(), vrna_exp_params(), vrna_params()+ *+ *  @param  n_seq   The number of sequences in the alignment+ *  @param  md      A pointer to the model details to store inside the structure (Maybe NULL)+ *  @return         A pointer to the memory location where the requested parameters are stored+ */+vrna_exp_param_t *+vrna_exp_params_comparative(unsigned int n_seq,+                            vrna_md_t *md);++/**+ *  @brief Get a copy of the provided free energy parameters (provided as Boltzmann factors)+ *+ *  If NULL is passed as parameter, a default set of energy parameters is created+ *  and returned.+ *+ *  @see vrna_exp_params(), #vrna_exp_param_t+ *+ *  @param  par   The free energy parameters that are to be copied (Maybe NULL)+ *  @return       A copy or a default set of the (provided) parameters+ */+vrna_exp_param_t *+vrna_exp_params_copy(vrna_exp_param_t *par);++/**+ *  @brief  Update/Reset energy parameters data structure within a #vrna_fold_compound_t+ *+ *  Passing NULL as second argument leads to a reset of the energy parameters within+ *  vc to their default values. Otherwise, the energy parameters provided will be copied+ *  over into vc.+ *+ *  @see vrna_params_reset(), #vrna_param_t, #vrna_md_t, vrna_params()+ *+ *  @param  vc    The #vrna_fold_compound_t that is about to receive updated energy parameters+ *  @param  par   The energy parameters used to substitute those within vc (Maybe NULL)+ */+void+vrna_params_subst( vrna_fold_compound_t *vc,+                    vrna_param_t *par);++/**+ *  @brief Update the energy parameters for subsequent partition function computations+ *+ *  This function can be used to properly assign new energy parameters for partition+ *  function computations to a #vrna_fold_compound_t. For this purpose, the data of the+ *  provided pointer `params`  will be copied into `vc` and a recomputation of the partition+ *  function scaling factor is issued, if the `pf_scale` attribute of `params` is less than `1.0`.+ *+ *  Passing NULL as second argument leads to a reset of the energy parameters within+ *  vc to their default values+ *+ *  @see vrna_exp_params_reset(), vrna_exp_params_rescale(), #vrna_exp_param_t, #vrna_md_t,+ *  vrna_exp_params()+ *+ *  @param  vc      The fold compound data structure+ *  @param  params  A pointer to the new energy parameters+ */+void+vrna_exp_params_subst(vrna_fold_compound_t *vc,+                      vrna_exp_param_t *params);++/**+ *  @brief Rescale Boltzmann factors for partition function computations+ *+ *  This function may be used to (automatically) rescale the Boltzmann factors used+ *  in partition function computations. Since partition functions over subsequences+ *  can easily become extremely large, the RNAlib internally rescales them to avoid+ *  numerical over- and/or underflow. Therefore, a proper scaling factor @f$s@f$ needs to+ *  be chosen that in turn is then used to normalize the corresponding+ *  partition functions @f$\hat{q}[i,j] = q[i,j] / s^{(j-i+1)}@f$.+ *+ *  This function provides two ways to automatically adjust the scaling+ *  factor.+ *  1. Automatic guess+ *  2. Automatic adjustment according to MFE+ *+ *  Passing `NULL` as second parameter activates the _automatic guess mode_. Here,+ *  the scaling factor is recomputed according to a mean free energy of `184.3*length` cal+ *  for random sequences.+ *  @note This recomputation only takes place if the `pf_scale` attribute of the+ *  `exp_params` data structure contained in `vc` has a value below `1.0`.+ *+ *  On the other hand, if the MFE for a sequence is known, it can be used to recompute+ *  a more robust scaling factor, since it represents the lowest free energy of the entire+ *  ensemble of structures, i.e. the highest Boltzmann factor. To activate this second+ *  mode of _automatic adjustment according to MFE_, a pointer to the MFE value needs to+ *  be passed as second argument. This value is then taken to compute the scaling factor+ *  as @f$ s = exp((sfact * MFE) / kT / length )@f$, where sfact is an additional+ *  scaling weight located in the vrna_md_t data structure of `exp_params` in `vc`.+ *+ *  The computed scaling factor @f$s@f$ will be stored as `pf_scale` attribute of the+ *  `exp_params` data structure in `vc`.+ *+ *  @see vrna_exp_params_subst(), vrna_md_t, vrna_exp_param_t, #vrna_fold_compound_t+ *+ *  @param  vc  The fold compound data structure+ *  @param  mfe A pointer to the MFE (in kcal/mol) or NULL+ */+void+vrna_exp_params_rescale(vrna_fold_compound_t *vc,+                        double *mfe);++/**+ *  @brief  Reset free energy parameters within a #vrna_fold_compound_t+ *          according to provided, or default model details+ *+ *  This function allows one to rescale free energy parameters for subsequent structure+ *  prediction or evaluation according to a set of model details, e.g. temperature+ *  values. To do so, the caller provides either a pointer to a set of model details+ *  to be used for rescaling, or NULL if global default setting should be used.+ *+ *  @see vrna_exp_params_reset(), vrna_params_subs()+ *  @param  vc    The fold compound data structure+ *  @param  md_p  A pointer to the new model details (or NULL for reset to defaults)+ */+void vrna_params_reset( vrna_fold_compound_t *vc,+                        vrna_md_t *md_p);++/**+ *  @brief  Reset Boltzmann factors for partition function computations+ *          within a #vrna_fold_compound_t according to provided, or+ *          default model details+ *+ *  This function allows one to rescale Boltzmann factors for subsequent partition+ *  function computations according to a set of model details, e.g. temperature+ *  values. To do so, the caller provides either a pointer to a set of model details+ *  to be used for rescaling, or NULL if global default setting should be used.+ *+ *  @see vrna_params_reset(), vrna_exp_params_subst(), vrna_exp_params_rescale()+ *  @param  vc    The fold compound data structure+ *  @param  md_p  A pointer to the new model details (or NULL for reset to defaults)+ */+void vrna_exp_params_reset( vrna_fold_compound_t *vc,+                            vrna_md_t *md_p);++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief Old typename of #vrna_param_s+ *  @deprecated Use #vrna_param_t instead!+*/+typedef struct vrna_param_s     paramT;++/**+ *  @brief Old typename of #vrna_exp_param_s+ *  @deprecated Use #vrna_exp_param_t instead!+*/+typedef struct vrna_exp_param_s pf_paramT;++DEPRECATED(vrna_param_t *get_parameter_copy(vrna_param_t *par));++/**+ *  get a data structure of type @ref vrna_exp_param_t which contains+ *  the Boltzmann weights of several energy parameters scaled+ *  according to the current temperature+ *+ *  @deprecated Use vrna_exp_params() instead!+ *+ *  @return The data structure containing Boltzmann weights for use in partition function calculations+ */+DEPRECATED(vrna_exp_param_t *get_scaled_pf_parameters(void));++/**+ *  @brief Get precomputed Boltzmann factors of the loop type+ *  dependent energy contributions with independent thermodynamic+ *  temperature+ *+ *  This function returns a data structure that contains+ *  all necessary precalculated Boltzmann factors for each+ *  loop type contribution.<br>+ *  In contrast to get_scaled_pf_parameters(), this function+ *  enables setting of independent temperatures for both, the+ *  individual energy contributions as well as the thermodynamic+ *  temperature used in+ *  @f$ exp(-\Delta G / kT) @f$+ *+ *  @deprecated Use vrna_exp_params() instead!+ *+ *  @see get_scaled_pf_parameters(), get_boltzmann_factor_copy()+ *+ *  @param  temperature   The temperature in degrees Celcius used for (re-)scaling the energy contributions+ *  @param  betaScale     A scaling value that is used as a multiplication factor for the absolute+ *                        temperature of the system+ *  @param  md            The model details to be used+ *  @param  pf_scale      The scaling factor for the Boltzmann factors+ *  @return               A set of precomputed Boltzmann factors+ */+DEPRECATED(vrna_exp_param_t *get_boltzmann_factors(double temperature, double betaScale, vrna_md_t md, double pf_scale));++/**+ *  @brief Get a copy of already precomputed Boltzmann factors+ *+ *  @deprecated Use vrna_exp_params_copy() instead!+ *+ *  @see get_boltzmann_factors(), get_scaled_pf_parameters()+ *+ *  @param  parameters  The input data structure that shall be copied+ *  @return             A copy of the provided Boltzmann factor data set+ */+DEPRECATED(vrna_exp_param_t *get_boltzmann_factor_copy(vrna_exp_param_t *parameters));++/**+ *  @brief Get precomputed Boltzmann factors of the loop type+ *  dependent energy contributions (alifold variant)+ *+ *  @deprecated Use vrna_exp_params_comparative() instead!+ *+ */+DEPRECATED(vrna_exp_param_t *get_scaled_alipf_parameters(unsigned int n_seq));++/**+ *  @brief Get precomputed Boltzmann factors of the loop type+ *  dependent energy contributions (alifold variant) with+ *  independent thermodynamic temperature+ *+ *  @deprecated Use vrna_exp_params_comparative() instead!+ *+ */+DEPRECATED(vrna_exp_param_t *get_boltzmann_factors_ali(unsigned int n_seq, double temperature, double betaScale, vrna_md_t md, double pf_scale));++/**+ * @brief Get precomputed energy contributions for all the known loop types+ *+ *  @note OpenMP: This function relies on several global model settings variables and thus is+ *        not to be considered threadsafe. See get_scaled_parameters() for a completely threadsafe+ *        implementation.+ *+ *  @deprecated Use vrna_params() instead!+ *+ * @return     A set of precomputed energy contributions+ */+DEPRECATED(vrna_param_t *scale_parameters(void));++/**+ * @brief Get precomputed energy contributions for all the known loop types+ *+ *  Call this function to retrieve precomputed energy contributions, i.e. scaled+ *  according to the temperature passed. Furthermore, this function assumes a+ *  data structure that contains the model details as well, such that subsequent+ *  folding recursions are able to retrieve the correct model settings+ *+ *  @deprecated Use vrna_params() instead!+ *+ *  @see #vrna_md_t, set_model_details()+ *+ *  @param temperature  The temperature in degrees Celcius+ *  @param md           The model details+ *  @return             precomputed energy contributions and model settings+ */+DEPRECATED(vrna_param_t *get_scaled_parameters(double temperature, vrna_md_t md));++DEPRECATED(vrna_param_t     *copy_parameters(void));+DEPRECATED(vrna_param_t     *set_parameters(vrna_param_t *dest));+DEPRECATED(vrna_exp_param_t *scale_pf_parameters(void));+DEPRECATED(vrna_exp_param_t *copy_pf_param(void));+DEPRECATED(vrna_exp_param_t *set_pf_param(vrna_param_t *dest));++#endif++/**+ *  @}+ */++++#endif
+ C/ViennaRNA/part_func.c view
@@ -0,0 +1,1241 @@+/*+                  partiton function for RNA secondary structures++                  Ivo L Hofacker + Ronny Lorenz+                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/mfe.h"+#include "ViennaRNA/part_func.h"++#ifdef _OPENMP+#include <omp.h>+#endif++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+PUBLIC  int         st_back = 0;++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++#ifdef  VRNA_BACKWARD_COMPAT++/* some backward compatibility stuff */+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;+PRIVATE int                 backward_compat           = 0;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void  pf_circ(vrna_fold_compound_t *vc);+PRIVATE void  pf_linear(vrna_fold_compound_t *vc);+PRIVATE void  alipf_linear(vrna_fold_compound_t *vc);+PRIVATE void  wrap_alipf_circ(vrna_fold_compound_t *vc, char *structure);++#ifdef  VRNA_BACKWARD_COMPAT++PRIVATE float+wrap_pf_fold( const char *sequence,+              char *structure,+              vrna_exp_param_t *parameters,+              int calculate_bppm,+              int is_constrained,+              int is_circular);++#endif++PRIVATE double+wrap_mean_bp_distance(FLT_OR_DBL *p,+                      int length,+                      int *index,+                      int turn);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC float+vrna_pf_fold( const char *seq,+              char *structure,+              vrna_plist_t **pl){++  float                 free_energy;+  double                mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);++  /* no need to backtrack MFE structure */+  md.backtrack = 0;++  if(!pl){ /* no need for pair probability computations if we do not store them somewhere */+    md.compute_bpp = 0;+  }++  vc  = vrna_fold_compound(seq, &md, 0);+  mfe = (double)vrna_pf(vc, NULL);+  vrna_exp_params_rescale(vc, &mfe);+  free_energy = vrna_pf(vc, structure);++  /* fill plist */+  if(pl){+    *pl = vrna_plist_from_probs(vc, /*cut_off:*/ 1e-6);+  }++  vrna_fold_compound_free(vc);++  return free_energy;+}++PUBLIC float+vrna_pf_circfold( const char *seq,+                  char *structure,+                  vrna_plist_t **pl){++  float                 free_energy;+  double                mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.circ = 1;++  /* no need to backtrack MFE structure */+  md.backtrack = 0;++  if(!pl){ /* no need for pair probability computations if we do not store them somewhere */+    md.compute_bpp = 0;+  }++  vc  = vrna_fold_compound(seq, &md, 0);+  mfe = (double)vrna_mfe(vc, NULL);+  vrna_exp_params_rescale(vc, &mfe);+  free_energy = vrna_pf(vc, structure);++  /* fill plist */+  if(pl){+    *pl = vrna_plist_from_probs(vc, /*cut_off:*/ 1e-6);+  }++  vrna_fold_compound_free(vc);++  return free_energy;+}++PUBLIC float+vrna_pf(vrna_fold_compound_t  *vc,+        char                  *structure){++  int               n;+  FLT_OR_DBL        Q;+  double            free_energy;+  vrna_md_t         *md;+  vrna_exp_param_t  *params;+  vrna_mx_pf_t      *matrices;++  free_energy = (float)(INF/100.);++  if(vc){+    /* make sure, everything is set up properly to start partition function computations */+    if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_PF)){+      vrna_message_warning("vrna_pf@part_func.c: Failed to prepare vrna_fold_compound");+      return free_energy;+    }++    n         = vc->length;+    params    = vc->exp_params;+    matrices  = vc->exp_matrices;+    md        = &(params->model_details);++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+    omp_set_dynamic(0);+#endif++#ifdef SUN4+    nonstandard_arithmetic();+#else+#ifdef HP9+    fpsetfastmode(1);+#endif+#endif++    /* call user-defined recursion status callback function */+    if(vc->stat_cb)+      vc->stat_cb(VRNA_STATUS_PF_PRE, vc->auxdata);++    switch(vc->type){+      case VRNA_FC_TYPE_SINGLE:     /* do the linear pf fold and fill all matrices  */+                                    pf_linear(vc);++                                    if(md->circ)+                                      pf_circ(vc); /* do post processing step for circular RNAs */++                                    break;++      case VRNA_FC_TYPE_COMPARATIVE:  /* do the linear pf fold and fill all matrices  */+                                    alipf_linear(vc);++                                    /* calculate post processing step for circular  */+                                    /* RNAs                                         */+                                    if(md->circ)+                                      wrap_alipf_circ(vc, structure);++                                    break;++      default:                      vrna_message_warning("vrna_pf@part_func.c: Unrecognized fold compound type");+                                    return free_energy;+                                    break;+    }+++    /* call user-defined recursion status callback function */+    if(vc->stat_cb)+      vc->stat_cb(VRNA_STATUS_PF_POST, vc->auxdata);++    /* calculate base pairing probability matrix (bppm)  */+    if(md->compute_bpp){+      vrna_pairing_probs(vc, structure);++#ifdef  VRNA_BACKWARD_COMPAT++      /*+      *  Backward compatibility:+      *  This block may be removed if deprecated functions+      *  relying on the global variable "pr" vanish from within the package!+      */+      pr = matrices->probs;+      /*+       {+        if(pr) free(pr);+        pr = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));+        memcpy(pr, probs, sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));+      }+      */++#endif++    }++    if (md->backtrack_type=='C')+      Q = matrices->qb[vc->iindx[1]-n];+    else if (md->backtrack_type=='M')+      Q = matrices->qm[vc->iindx[1]-n];+    else Q = (md->circ) ? matrices->qo : matrices->q[vc->iindx[1]-n];++    /* ensemble free energy in Kcal/mol              */+    if (Q<=FLT_MIN)+      vrna_message_warning("pf_scale too large");++    switch(vc->type){+      case VRNA_FC_TYPE_COMPARATIVE:  free_energy = (-log(Q)-n*log(params->pf_scale))*params->kT/(1000.0 * vc->n_seq);+                                    break;++      case VRNA_FC_TYPE_SINGLE:     /* fall through */++      default:                      free_energy = (-log(Q)-n*log(params->pf_scale))*params->kT/1000.0;+                                    break;+    }++#ifdef SUN4+    standard_arithmetic();+#else+#ifdef HP9+    fpsetfastmode(0);+#endif+#endif+  }++  return free_energy;+}++PRIVATE void+pf_linear(vrna_fold_compound_t *vc){++  char                *hard_constraints;+  int                 n, i,j, k, ij, d, *my_iindx, *jindx, with_gquad, turn,+                      with_ud, hc_decompose;+  FLT_OR_DBL          temp, Qmax, qbt1, *q, *qb, *qm, *qm1, *q1k, *qln;+  double              max_real;+  vrna_ud_t           *domains_up;+  vrna_md_t           *md;+  vrna_hc_t           *hc;+  vrna_mx_pf_t        *matrices;+  vrna_mx_pf_aux_el_t *aux_mx_el;+  vrna_mx_pf_aux_ml_t *aux_mx_ml;+  vrna_exp_param_t    *pf_params;++  n                 = vc->length;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  matrices          = vc->exp_matrices;+  pf_params         = vc->exp_params;+  hc                = vc->hc;+  domains_up        = vc->domains_up;+  q                 = matrices->q;+  qb                = matrices->qb;+  qm                = matrices->qm;+  qm1               = matrices->qm1;+  q1k               = matrices->q1k;+  qln               = matrices->qln;+  md                = &(pf_params->model_details);+  with_gquad        = md->gquad;+  turn              = md->min_loop_size;+  hard_constraints  = hc->matrix;++  with_ud           = (domains_up && domains_up->exp_energy_cb);+  Qmax              = 0;++  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  if (with_ud && domains_up->exp_prod_cb)+    domains_up->exp_prod_cb(vc, domains_up->data);++  if(with_gquad){+    free(vc->exp_matrices->G);+    vc->exp_matrices->G = get_gquad_pf_matrix(vc->sequence_encoding2, vc->exp_matrices->scale, vc->exp_params);+  }++  /* init auxiliary arrays for fast exterior/multibranch loops */+  aux_mx_el = vrna_exp_E_ext_fast_init(vc);+  aux_mx_ml = vrna_exp_E_ml_fast_init(vc);++  /*array initialization ; qb,qm,q+    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */+  for (d=0; d<=turn; d++)+    for (i=1; i<=n-d; i++) {+      j=i+d;+      ij = my_iindx[i]-j;+      qb[ij] = 0.0;+    }++  for (j = turn + 2; j <= n; j++) {+    for (i = j - turn - 1; i >= 1; i--) {+      /* construction of partition function of segment i,j */+      /* firstly that given i binds j : qb(i,j) */+      ij            = my_iindx[i] - j;+      hc_decompose  = hard_constraints[jindx[j] + i];+      qbt1          = 0;++      if(hc_decompose){+        /* process hairpin loop(s) */+        qbt1 += vrna_exp_E_hp_loop(vc, i, j);+        /* process interior loop(s) */+        qbt1 += vrna_exp_E_int_loop(vc, i, j);+        /* process multibranch loop(s) */+        qbt1 += vrna_exp_E_mb_loop_fast(vc, i, j, aux_mx_ml->qqm1);+      }+      qb[ij] = qbt1;++      /* Multibranch loop */+      qm[ij] = vrna_exp_E_ml_fast(vc, i, j, aux_mx_ml);++      if (qm1)+        qm1[jindx[j] + i] = aux_mx_ml->qqm[i]; /* for stochastic backtracking and circfold */++      /* Exterior loop */+      q[ij] = temp = vrna_exp_E_ext_fast(vc, i, j, aux_mx_el);++      if (temp>Qmax) {+        Qmax = temp;+        if (Qmax>max_real/10.)+          vrna_message_warning("Q close to overflow: %d %d %g", i,j,temp);+      }+      if (temp>=max_real) {+        vrna_message_error("overflow in pf_fold while calculating q[%d,%d]\n"+                                  "use larger pf_scale", i,j);+      }+    }++    /* rotate auxiliary arrays */+    vrna_exp_E_ext_fast_rotate(vc, aux_mx_el);+    vrna_exp_E_ml_fast_rotate(vc, aux_mx_ml);++  }++  /* prefill linear qln, q1k arrays */+  if(q1k && qln){+    for (k=1; k<=n; k++) {+      q1k[k] = q[my_iindx[1] - k];+      qln[k] = q[my_iindx[k] - n];+    }+    q1k[0] = 1.0;+    qln[n+1] = 1.0;+  }++  /* free memory occupied by auxiliary arrays for fast exterior/multibranch loops */+  vrna_exp_E_ml_fast_free(vc, aux_mx_ml);+  vrna_exp_E_ext_fast_free(vc, aux_mx_el);+}++/* calculate partition function for circular case */+/* NOTE: this is the postprocessing step ONLY     */+/* You have to call pf_linear first to calculate  */+/* complete circular case!!!                      */+PRIVATE void+pf_circ(vrna_fold_compound_t *vc){++  char              *ptype;+  short             *S1;+  int               u, p, q, k, l, turn, n, *my_iindx, *jindx, *rtype;+  FLT_OR_DBL        *scale, *qb, *qm, *qm1, *qm2, qo, qho, qio, qmo,+                    qbt1, qot, expMLclosing;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;++  n             = vc->length;+  matrices      = vc->exp_matrices;+  my_iindx      = vc->iindx;+  jindx         = vc->jindx;+  ptype         = vc->ptype;+  S1            = vc->sequence_encoding;+  pf_params     = vc->exp_params;+  qb            = matrices->qb;+  qm            = matrices->qm;+  qm1           = matrices->qm1;+  qm2           = matrices->qm2;+  scale         = matrices->scale;+  expMLclosing  = pf_params->expMLclosing;+  turn          = pf_params->model_details.min_loop_size;+  rtype         = &(pf_params->model_details.rtype[0]);+  qo = qho = qio = qmo = 0.;++  /* construct qm2 matrix from qm1 entries  */+  for(k=1; k<n-turn-1; k++){+    qot = 0.;+    for (u=k+turn+1; u<n-turn-1; u++)+      qot += qm1[jindx[u]+k]*qm1[jindx[n]+(u+1)];+    qm2[k] = qot;+   }++  for(p = 1; p < n; p++){+    for(q = p + turn + 1; q <= n; q++){+      int type;+      /* 1. get exterior hairpin contribution  */+      qbt1 = qb[my_iindx[p]-q] * vrna_exp_E_hp_loop(vc, q, p);+      qho += qbt1;++      u = n-q + p-1;+      if (u<turn) continue;+      type = ptype[jindx[q] + p];+      if (!type) continue;+       /* cause we want to calc the exterior loops, we need the reversed pair type from now on  */+      type=rtype[type];+++      /* 2. exterior interior loops, i "define" the (k,l) pair as "outer pair"  */+      /* so "outer type" is rtype[type[k,l]] and inner type is type[p,q]        */+      qot = 0.;+      for(k=q+1; k < n; k++){+        int ln1, lstart;+        ln1 = k - q - 1;+        if(ln1+p-1>MAXLOOP) break;+        lstart = ln1+p-1+n-MAXLOOP;+        if(lstart<k+turn+1) lstart = k + turn + 1;+        for(l=lstart;l <= n; l++){+          int ln2, type2;+          ln2 = (p - 1) + (n - l);++          if((ln1+ln2) > MAXLOOP) continue;++          type2 = ptype[jindx[l] + k];+          if(!type2) continue;+          qio += qb[my_iindx[p]-q] * qb[my_iindx[k]-l] * exp_E_IntLoop(ln2, ln1, rtype[type2], type, S1[l+1], S1[k-1], S1[p-1], S1[q+1], pf_params) * scale[ln1+ln2];+        }+      } /* end of kl double loop */+    }+  } /* end of pq double loop */++  /* 3. Multiloops  */+  for(k=turn+2; k<n-2*turn-3; k++)+    qmo += qm[my_iindx[1]-k] * qm2[k+1] * expMLclosing;++  /* add an additional pf of 1.0 to take the open chain into account too */+  qo = qho + qio + qmo + 1.0*scale[n];++  matrices->qo    = qo;+  matrices->qho   = qho;+  matrices->qio   = qio;+  matrices->qmo   = qmo;++}+++PUBLIC int+vrna_pf_float_precision(void){++  return (sizeof(FLT_OR_DBL) == sizeof(float));+}+++PRIVATE void+alipf_linear( vrna_fold_compound_t *vc){++  char                *hard_constraints;+  int                 i,j, ij, jij, d, turn, n, *my_iindx, *jindx, *pscore;+  FLT_OR_DBL          temp, Qmax, qbt1, *q, *qb, *qm, *qm1;+  double              kTn, max_real;+  vrna_exp_param_t    *pf_params;+  vrna_mx_pf_t        *matrices;+  vrna_mx_pf_aux_el_t *aux_mx_el;+  vrna_mx_pf_aux_ml_t *aux_mx_ml;+  vrna_md_t           *md;+  vrna_hc_t           *hc;++  n                 = vc->length;+  pf_params         = vc->exp_params;+  matrices          = vc->exp_matrices;+  hc                = vc->hc;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  pscore            = vc->pscore;     /* precomputed array of pair types */+  md                = &(pf_params->model_details);+  q                 = matrices->q;+  qb                = matrices->qb;+  qm                = matrices->qm;+  qm1               = matrices->qm1;+  hard_constraints  = hc->matrix;+  turn              = md->min_loop_size;+  kTn               = pf_params->kT/10.;   /* kT in cal/mol  */+  Qmax              = 0.;++  max_real          = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  /* init auxiliary arrays for fast exterior/multibranch loops */+  aux_mx_el = vrna_exp_E_ext_fast_init(vc);+  aux_mx_ml = vrna_exp_E_ml_fast_init(vc);++  /* array initialization ; qb,qm,q+     qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */++  for (d = 0; d <= turn; d++)+    for (i = 1; i <= n - d; i++) {+      j       = i + d;+      ij      = my_iindx[i]-j;+      qb[ij]  = 0.0;+    }++  for (j = turn + 2; j <= n; j++) {+    for (i = j - turn - 1; i >= 1; i--) {+      int psc;+      /* construction of partition function for segment i,j */+      /* calculate pf given that i and j pair: qb(i,j)      */+      ij  = my_iindx[i] - j;+      jij = jindx[j] + i;++      psc   = pscore[jij];+      qbt1  = 0.;++      if (hard_constraints[jij]) {+        /* process hairpin loop(s) */+        qbt1 += vrna_exp_E_hp_loop(vc, i, j);+        /* process interior loop(s) */+        qbt1 += vrna_exp_E_int_loop(vc, i, j);+        /* process multibranch loop(s) */+        qbt1 += vrna_exp_E_mb_loop_fast(vc, i, j, aux_mx_ml->qqm1);++        qbt1 *= exp(psc/kTn);+      }++      qb[ij] = qbt1;++      /* Multibranch loop */+      qm[ij] = vrna_exp_E_ml_fast(vc, i, j, aux_mx_ml);++      if (qm1)+        qm1[jindx[j] + i] = aux_mx_ml->qqm[i]; /* for stochastic backtracking and circfold */++      /* Exterior loop */+      q[ij] = temp = vrna_exp_E_ext_fast(vc, i, j, aux_mx_el);++      if (temp > Qmax) {+        Qmax = temp;+        if (Qmax > max_real/10.)+          vrna_message_warning("Q close to overflow: %d %d %g", i,j,temp);+      }+      if (temp >= max_real) {+        vrna_message_error("overflow in pf_fold while calculating q[%d,%d]\n"+                                  "use larger pf_scale", i,j);+      }+    }++    /* rotate auxiliary arrays */+    vrna_exp_E_ext_fast_rotate(vc, aux_mx_el);+    vrna_exp_E_ml_fast_rotate(vc, aux_mx_ml);+  }++  /* free memory occupied by auxiliary arrays for fast exterior/multibranch loops */+  vrna_exp_E_ml_fast_free(vc, aux_mx_ml);+  vrna_exp_E_ext_fast_free(vc, aux_mx_el);+}++/* calculate partition function for circular case   */+/* NOTE: this is the postprocessing step ONLY        */+/* You have to call alipf_linear first to calculate  */+/* circular case!!!                                  */++PRIVATE void+wrap_alipf_circ(vrna_fold_compound_t *vc,+                char *structure){++  char              **Ss, *hard_constraints;+  unsigned short    **a2s;+  short             **S, **S5, **S3;+  int               u, p, q, pq, k, l, s, *type, n_seq, n, *my_iindx, *jindx, *rtype;+  FLT_OR_DBL        qbt1, qot, qo, qho, qio, qmo, *qb, *qm, *qm1, *qm2, *scale,+                    expMLclosing;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  vrna_md_t         *md;+  vrna_hc_t         *hc;+  vrna_sc_t         **sc;++  n_seq             = vc->n_seq;+  n                 = vc->length;+  S                 = vc->S;+  S5                = vc->S5;     /* S5[s][i] holds next base 5' of i in sequence s */+  S3                = vc->S3;     /* Sl[s][i] holds next base 3' of i in sequence s */+  Ss                = vc->Ss;+  a2s               = vc->a2s;+  pf_params         = vc->exp_params;+  matrices          = vc->exp_matrices;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  hc                = vc->hc;+  sc                = vc->scs;+  qb                = matrices->qb;+  qm                = matrices->qm;+  qm1               = matrices->qm1;+  qm2               = matrices->qm2;+  scale             = matrices->scale;+  expMLclosing      = pf_params->expMLclosing;+  md                = &(pf_params->model_details);+  hard_constraints  = hc->matrix;+  rtype             = &(md->rtype[0]);+  qo = qho = qio = qmo = 0.;++  type  = (int *)vrna_alloc(sizeof(int) * n_seq);++  /* calculate the qm2 matrix  */+  for(k=1; k<n-TURN; k++){+    qot = 0.;+    for (u=k+TURN+1; u<n-TURN-1; u++)+      qot += qm1[jindx[u]+k]*qm1[jindx[n]+(u+1)];+    qm2[k] = qot;+  }++  for(p=1;p<n;p++){+    for(q=p+TURN+1;q<=n;q++){+      u = n-q + p-1;+      if (u<TURN) continue;+      pq  = jindx[q] + p;++      if(!hard_constraints[pq]) continue;++      for(s = 0; s < n_seq; s++){+        type[s] = md->pair[S[s][p]][S[s][q]];+        if (type[s]==0) type[s]=7;+      }++      /* 1. exterior hairpin contribution  */+      /* Note, that we do not scale Hairpin Energy by u+2 but by u cause the scale  */+      /* for the closing pair was already done in the forward recursion              */+      if(hard_constraints[pq] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){+        if(hc->up_hp[q+1] > u){+          for (qbt1=1,s=0; s<n_seq; s++) {+            int rt;+            char loopseq[10];+            u   = a2s[s][n] - a2s[s][q] + a2s[s][p] - 1;+            rt  = rtype[type[s]];++            if (u<9){+              strcpy(loopseq , Ss[s] + a2s[s][q] - 1);+              strncat(loopseq, Ss[s], a2s[s][p]);+            }+            qbt1 *= exp_E_Hairpin(u, rt, S3[s][q], S5[s][p], loopseq, pf_params);+          }+          if(sc)+            for(s = 0; s < n_seq; s++){+              if(sc[s]){+                if(sc[s]->exp_energy_up){+                  qbt1 *=   ((p > 1) ? sc[s]->exp_energy_up[1][a2s[s][p]-1] : 1.)+                          * ((q < n) ? sc[s]->exp_energy_up[a2s[s][q]+1][a2s[s][n] - a2s[s][q]] : 1.);+                }+              }+            }+          qho += qb[my_iindx[p]-q] * qbt1 * scale[u];+        }+      }+      /* 2. exterior interior loop contribution*/++      if(hard_constraints[pq] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+        for(k=q+1; k < n; k++){+          int ln1, lstart;+          ln1 = k - q - 1;+          if(ln1 + p - 1 > MAXLOOP)+            break;+          if(hc->up_int[q+1] < ln1)+            break;++          lstart = ln1+p-1+n-MAXLOOP;+          if(lstart<k+TURN+1) lstart = k + TURN + 1;+          for(l=lstart;l <= n; l++){+            int ln2, type_2;++            ln2 = (p - 1) + (n - l);++            if(!(hard_constraints[jindx[l]+k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP))+              continue;+            if((ln1+ln2) > MAXLOOP)+              continue;+            if(hc->up_int[l+1] < ln2)+              continue;++            FLT_OR_DBL qloop=1.;+            if (qb[my_iindx[k]-l]==0.){ qloop=0.; continue;}++            for (s=0; s<n_seq; s++){+              int ln1a = a2s[s][k] - 1 - a2s[s][q];+              int ln2a = a2s[s][n] - a2s[s][l] + a2s[s][p] - 1;+              int rt = rtype[type[s]];+              type_2 = md->pair[S[s][l]][S[s][k]];+              if (type_2 == 0) type_2 = 7;+              qloop *= exp_E_IntLoop(ln1a, ln2a, rt, type_2, S3[s][q], S5[s][p], S5[s][k], S3[s][l], pf_params);+            }+            if(sc)+              for(s = 0; s < n_seq; s++){+                int ln1a = a2s[s][k] - 1 - a2s[s][q];+                int ln2a = a2s[s][n] - a2s[s][l] + a2s[s][p] - 1;+                if(sc[s]){+                  if((ln1a+ln2a == 0) && (sc[s]->exp_energy_stack)){+                    if(S[s][p] && S[s][q] && S[s][k] && S[s][l]){ /* don't allow gaps in stack */+                      qloop *=    sc[s]->exp_energy_stack[a2s[s][p]]+                                * sc[s]->exp_energy_stack[a2s[s][q]]+                                * sc[s]->exp_energy_stack[a2s[s][k]]+                                * sc[s]->exp_energy_stack[a2s[s][l]];+                    }+                  }+                  if(sc[s]->exp_energy_up)+                    qloop *=    sc[s]->exp_energy_up[a2s[s][q] + 1][ln1a]+                              * ((l < n) ? sc[s]->exp_energy_up[a2s[s][l]+1][a2s[s][n] - a2s[s][l]] : 1.)+                              * ((p > 1) ? sc[s]->exp_energy_up[1][a2s[s][p]-1] : 1.);+                }+              }++            qio += qb[my_iindx[p]-q] * qb[my_iindx[k]-l] * qloop * scale[ln1+ln2];+          }+        } /* end of kl double loop */+      }+    }+  } /* end of pq double loop */++  /* 3. exterior multiloop contribution  */+  for(k=TURN+2; k<n-2*TURN-3; k++)+    qmo += qm[my_iindx[1]-k] * qm2[k+1] * pow(expMLclosing,n_seq);++  /* add additional pf of 1.0 to take open chain into account */+  qo = qho + qio + qmo;+  if(hc->up_ext[1] >= n)+     qo += 1.0 * scale[n];++  matrices->qo    = qo;+  matrices->qho   = qho;+  matrices->qio   = qio;+  matrices->qmo   = qmo;++  free(type);+}+++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++#ifdef  VRNA_BACKWARD_COMPAT++PRIVATE double+wrap_mean_bp_distance(FLT_OR_DBL *p,+                      int length,+                      int *index,+                      int turn){++  int         i,j;+  double      d = 0.;++  /* compute the mean base pair distance in the thermodynamic ensemble */+  /* <d> = \sum_{a,b} p_a p_b d(S_a,S_b)+     this can be computed from the pair probs p_ij as+     <d> = \sum_{ij} p_{ij}(1-p_{ij}) */++  for (i=1; i<=length; i++)+    for (j=i+turn+1; j<=length; j++)+      d += p[index[i]-j] * (1-p[index[i]-j]);++  return 2*d;+}++PRIVATE float+wrap_pf_fold( const char *sequence,+              char *structure,+              vrna_exp_param_t *parameters,+              int calculate_bppm,+              int is_constrained,+              int is_circular){++  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vc = NULL;++  /* we need vrna_exp_param_t datastructure to correctly init default hard constraints */+  if(parameters)+    md = parameters->model_details;+  else{+    set_model_details(&md); /* get global default parameters */+  }+  md.circ         = is_circular;+  md.compute_bpp  = calculate_bppm;++  vc = vrna_fold_compound(sequence, &md, VRNA_OPTION_DEFAULT);++  /* prepare exp_params and set global pf_scale */+  vc->exp_params = vrna_exp_params(&md);+  vc->exp_params->pf_scale = pf_scale;++  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound && backward_compat)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;+  iindx = backward_compat_compound->iindx;++  return vrna_pf(vc, structure);+}++PUBLIC vrna_plist_t *+stackProb(double cutoff){++  if(!(backward_compat_compound && backward_compat)){+    vrna_message_error("stackProb: run pf_fold() first!");+  } else if( !backward_compat_compound->exp_matrices->probs){+    vrna_message_error("stackProb: probs==NULL!");+  }++  return vrna_stack_prob(backward_compat_compound, cutoff);+}++PUBLIC char *+centroid( int length,+          double *dist) {++  if (pr==NULL)+    vrna_message_error("pr==NULL. You need to call pf_fold() before centroid()");++  return vrna_centroid_from_probs(length, dist, pr);+}+++PUBLIC double+mean_bp_dist(int length) {++  /* compute the mean base pair distance in the thermodynamic ensemble */+  /* <d> = \sum_{a,b} p_a p_b d(S_a,S_b)+     this can be computed from the pair probs p_ij as+     <d> = \sum_{ij} p_{ij}(1-p_{ij}) */++  int     i, j, *my_iindx;+  double  d = 0;++  if (pr==NULL)+    vrna_message_error("pr==NULL. You need to call pf_fold() before mean_bp_dist()");++  my_iindx = vrna_idx_row_wise(length);++  for (i=1; i<=length; i++)+    for (j=i+TURN+1; j<=length; j++)+      d += pr[my_iindx[i]-j] * (1-pr[my_iindx[i]-j]);++  free(my_iindx);+  return 2*d;+}++/* get the free energy of a subsequence from the q[] array */+PUBLIC double+get_subseq_F( int i,+              int j){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->q){+        int               *my_iindx   = backward_compat_compound->iindx;+        vrna_exp_param_t  *pf_params  = backward_compat_compound->exp_params;+        FLT_OR_DBL        *q          = backward_compat_compound->exp_matrices->q;+        return ((-log(q[my_iindx[i]-j])-(j-i+1)*log(pf_params->pf_scale))*pf_params->kT/1000.0);+      }++  vrna_message_error("call pf_fold() to fill q[] array before calling get_subseq_F()");+  return 0.; /* we will never get to this point */+}++++/*----------------------------------------------------------------------*/+PUBLIC double+expHairpinEnergy( int u,+                  int type,+                  short si1,+                  short sj1,+                  const char *string) {++/* compute Boltzmann weight of a hairpin loop, multiply by scale[u+2] */++  vrna_exp_param_t *pf_params = backward_compat_compound->exp_params;++  double q, kT;+  kT = pf_params->kT;   /* kT in cal/mol  */+  if(u <= 30)+    q = pf_params->exphairpin[u];+  else+    q = pf_params->exphairpin[30] * exp( -(pf_params->lxc*log( u/30.))*10./kT);+  if ((tetra_loop)&&(u==4)) {+    char tl[7]={0}, *ts;+    strncpy(tl, string, 6);+    if ((ts=strstr(pf_params->Tetraloops, tl)))+      return (pf_params->exptetra[(ts-pf_params->Tetraloops)/7]);+  }+  if ((tetra_loop)&&(u==6)) {+    char tl[9]={0}, *ts;+    strncpy(tl, string, 6);+    if ((ts=strstr(pf_params->Hexaloops, tl)))+      return  (pf_params->exphex[(ts-pf_params->Hexaloops)/9]);+  }+  if (u==3) {+    char tl[6]={0}, *ts;+    strncpy(tl, string, 5);+    if ((ts=strstr(pf_params->Triloops, tl)))+      return (pf_params->exptri[(ts-pf_params->Triloops)/6]);+    if (type>2)+      q *= pf_params->expTermAU;+  }+  else /* no mismatches for tri-loops */+    q *= pf_params->expmismatchH[type][si1][sj1];++  return q;+}++PUBLIC double+expLoopEnergy(int u1,+              int u2,+              int type,+              int type2,+              short si1,+              short sj1,+              short sp1,+              short sq1) {++/* compute Boltzmann weight of interior loop,+   multiply by scale[u1+u2+2] for scaling */+  double z=0;+  int no_close = 0;+  vrna_exp_param_t *pf_params = backward_compat_compound->exp_params;+++  if ((no_closingGU) && ((type2==3)||(type2==4)||(type==2)||(type==4)))+    no_close = 1;++  if ((u1==0) && (u2==0)) /* stack */+    z = pf_params->expstack[type][type2];+  else if (no_close==0) {+    if ((u1==0)||(u2==0)) { /* bulge */+      int u;+      u = (u1==0)?u2:u1;+      z = pf_params->expbulge[u];+      if (u2+u1==1) z *= pf_params->expstack[type][type2];+      else {+        if (type>2) z *= pf_params->expTermAU;+        if (type2>2) z *= pf_params->expTermAU;+      }+    }+    else {     /* interior loop */+      if (u1+u2==2) /* size 2 is special */+        z = pf_params->expint11[type][type2][si1][sj1];+      else if ((u1==1) && (u2==2))+        z = pf_params->expint21[type][type2][si1][sq1][sj1];+      else if ((u1==2) && (u2==1))+        z = pf_params->expint21[type2][type][sq1][si1][sp1];+      else if ((u1==2) && (u2==2))+        z = pf_params->expint22[type][type2][si1][sp1][sq1][sj1];+      else if (((u1==2)&&(u2==3))||((u1==3)&&(u2==2))){ /*2-3 is special*/+        z = pf_params->expinternal[5]*+          pf_params->expmismatch23I[type][si1][sj1]*+          pf_params->expmismatch23I[type2][sq1][sp1];+        z *= pf_params->expninio[2][1];+      }+      else if ((u1==1)||(u2==1)) {  /*1-n is special*/+        z = pf_params->expinternal[u1+u2]*+          pf_params->expmismatch1nI[type][si1][sj1]*+          pf_params->expmismatch1nI[type2][sq1][sp1];+        z *= pf_params->expninio[2][abs(u1-u2)];+      }+      else {+        z = pf_params->expinternal[u1+u2]*+          pf_params->expmismatchI[type][si1][sj1]*+          pf_params->expmismatchI[type2][sq1][sp1];+        z *= pf_params->expninio[2][abs(u1-u2)];+      }+    }+  }+  return z;+}++PUBLIC void+init_pf_circ_fold(int length){+/* DO NOTHING */+}++PUBLIC void+init_pf_fold(int length){+/* DO NOTHING */+}++/**+*** Allocate memory for all matrices and other stuff+**/+PUBLIC void+free_pf_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound  = NULL;+    backward_compat           = 0;+    iindx = NULL;+  }+}++PUBLIC FLT_OR_DBL *+export_bppm(void){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->probs)+        return backward_compat_compound->exp_matrices->probs;++  return NULL;+}++/*-------------------------------------------------------------------------*/+/* make arrays used for pf_fold available to other routines */+PUBLIC int+get_pf_arrays(short **S_p,+              short **S1_p,+              char **ptype_p,+              FLT_OR_DBL **qb_p,+              FLT_OR_DBL **qm_p,+              FLT_OR_DBL **q1k_p,+              FLT_OR_DBL **qln_p){++  if(backward_compat_compound){+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->qb){+        *S_p      = backward_compat_compound->sequence_encoding2;+        *S1_p     = backward_compat_compound->sequence_encoding;+        *ptype_p  = backward_compat_compound->ptype_pf_compat;+        *qb_p     = backward_compat_compound->exp_matrices->qb;+        *qm_p     = backward_compat_compound->exp_matrices->qm;+        *q1k_p    = backward_compat_compound->exp_matrices->q1k;+        *qln_p    = backward_compat_compound->exp_matrices->qln;+        return 1;+      }+  }+  return 0;+}++/*-----------------------------------------------------------------*/+PUBLIC float+pf_fold(const char *sequence,+        char *structure){++  return wrap_pf_fold(sequence, structure, NULL, do_backtrack, fold_constrained, 0);+}++PUBLIC float+pf_circ_fold( const char *sequence,+              char *structure){++  return wrap_pf_fold(sequence, structure, NULL, do_backtrack, fold_constrained, 1);+}++PUBLIC float+pf_fold_par(const char *sequence,+            char *structure,+            vrna_exp_param_t *parameters,+            int calculate_bppm,+            int is_constrained,+            int is_circular){++  return wrap_pf_fold(sequence, structure, parameters, calculate_bppm, is_constrained, is_circular);+}++PUBLIC char *+pbacktrack(char *seq){++  int n = (int)strlen(seq);+  return vrna_pbacktrack5(backward_compat_compound, n);+}++PUBLIC char *+pbacktrack5(char *seq,+            int length){++  /* the seq parameter must no differ to the one stored globally anyway, so we just ignore it */+  return vrna_pbacktrack5(backward_compat_compound, length);+}++PUBLIC char *+pbacktrack_circ(char *seq){++  char      *structure;+  vrna_md_t *md;++  structure = NULL;++  if(backward_compat_compound){+    md = &(backward_compat_compound->exp_params->model_details);+    if(md->circ && backward_compat_compound->exp_matrices->qm2){+      structure = vrna_pbacktrack(backward_compat_compound);+    }+  }++  return structure;+}++PUBLIC void+update_pf_params(int length){++  if(backward_compat_compound && backward_compat){+    vrna_md_t         md;+    set_model_details(&md);+    vrna_exp_params_reset(backward_compat_compound, &md);++    /* compatibility with RNAup, may be removed sometime */+    pf_scale = backward_compat_compound->exp_params->pf_scale;+  }+}++PUBLIC void+update_pf_params_par( int length,+                      vrna_exp_param_t *parameters){++  if(backward_compat_compound && backward_compat){+    vrna_md_t         md;+    if(parameters){+      vrna_exp_params_subst(backward_compat_compound, parameters);+    } else {+      set_model_details(&md);+      vrna_exp_params_reset(backward_compat_compound, &md);+    }++    /* compatibility with RNAup, may be removed sometime */+    pf_scale = backward_compat_compound->exp_params->pf_scale;+  }+}++PUBLIC char *+get_centroid_struct_gquad_pr( int length,+                              double *dist){++  return vrna_centroid(backward_compat_compound, dist);+}++PUBLIC void+assign_plist_gquad_from_pr( vrna_plist_t **pl,+                            int length, /* ignored */+                            double cut_off){++  if(!backward_compat_compound){+    *pl = NULL;+  } else if( !backward_compat_compound->exp_matrices->probs){+    *pl = NULL;+  } else {+    *pl = vrna_plist_from_probs(backward_compat_compound, cut_off);+  }+}++PUBLIC double+mean_bp_distance(int length){++  if(backward_compat_compound)+    if(backward_compat_compound->exp_matrices)+      if(backward_compat_compound->exp_matrices->probs)+        return vrna_mean_bp_distance(backward_compat_compound);++  vrna_message_error("mean_bp_distance: you need to call vrna_pf_fold first");+  return 0.; /* we will never get to this point */+}++PUBLIC double+mean_bp_distance_pr(int length,+                    FLT_OR_DBL *p){++  double d=0;+  int *index = vrna_idx_row_wise((unsigned int) length);++  if (p==NULL)+    vrna_message_error("p==NULL. You need to supply a valid probability matrix for mean_bp_distance_pr()");++  d = wrap_mean_bp_distance(p, length, index, TURN);++  free(index);+  return d;+}++#endif
+ C/ViennaRNA/part_func.h view
@@ -0,0 +1,489 @@+#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_H+#define VIENNA_RNA_PACKAGE_PART_FUNC_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+#include <ViennaRNA/centroid.h>+#include <ViennaRNA/equilibrium_probs.h>+#include <ViennaRNA/boltzmann_sampling.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     part_func.h+ *  @ingroup  pf_fold+ *  @brief    Partition function implementations+ * + *  This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to+ *  Partion function folding...+ */++/*+#################################################+# PARTITION FUNCTION COMPUTATION                #+#################################################+*/++/**+ *  @brief Compute the partition function @f$Q@f$ for a given RNA sequence, or sequence alignment+ *+ *  If @a structure is not a NULL pointer on input, it contains on+ *  return a string consisting of the letters " . , | { } ( ) " denoting+ *  bases that are essentially unpaired, weakly paired, strongly paired without+ *  preference, weakly upstream (downstream) paired, or strongly up-+ *  (down-)stream paired bases, respectively.+ *  If the parameter calculate_bppm is set to 0 base pairing probabilities will not+ *  be computed (saving CPU time), otherwise after calculations took place #pr will+ *  contain the probability that bases @a i and @a j pair.+ * + *  @ingroup pf_fold+ *+ *  @note This function is polymorphic. It accepts #vrna_fold_compound_t of type+ *        #VRNA_FC_TYPE_SINGLE, and #VRNA_FC_TYPE_COMPARATIVE.+ *+ *  @see #vrna_fold_compound_t, vrna_fold_compound(), vrna_pf_fold(), vrna_pf_circfold(),+ *        vrna_fold_compound_comparative(), vrna_pf_alifold(), vrna_pf_circalifold(),+ *        vrna_db_from_probs(), vrna_exp_params(), vrna_aln_pinfo()+ *+ *  @param[in,out]  vc              The fold compound data structure+ *  @param[in,out]  structure       A pointer to the character array where position-wise pairing propensity+ *                                  will be stored. (Maybe NULL)+ *  @return         The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+float vrna_pf(vrna_fold_compound_t *vc, char *structure);++/**+ *  @brief  Compute Partition function @f$Q@f$ (and base pair probabilities) for an RNA+ *          sequence using a comparative method+ *+ *  @ingroup pf_fold+ *+ *  This simplified interface to vrna_pf() computes the partition function and, if required,+ *  base pair probabilities for an RNA sequence using default options. Memory required for+ *  dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of+ *  this function, the recursively filled matrices are not available any more for any post-processing.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_pf(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  @see vrna_pf_circfold(), vrna_pf(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequence   RNA sequence+ *  @param structure  A pointer to the character array where position-wise pairing propensity+ *                    will be stored. (Maybe NULL)+ *  @param pl         A pointer to a list of #vrna_plist_t to store pairing probabilities (Maybe NULL)+ *  @return The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+float vrna_pf_fold(const char *sequence, char *structure, vrna_plist_t **pl);++/**+ *  @brief  Compute Partition function @f$Q@f$ (and base pair probabilities) for a circular+ *          RNA sequences using a comparative method+ *+ *  @ingroup pf_fold+ *+ *  This simplified interface to vrna_pf() computes the partition function and, if required,+ *  base pair probabilities for a circular RNA sequence using default options. Memory required for+ *  dynamic programming (DP) matrices will be allocated and free'd on-the-fly. Hence, after return of+ *  this function, the recursively filled matrices are not available any more for any post-processing.+ *+ *  @note In case you want to use the filled DP matrices for any subsequent post-processing step, or+ *  you require other conditions than specified by the default model details, use vrna_pf(),+ *  and the data structure #vrna_fold_compound_t instead.+ *+ *  Folding of circular RNA sequences is handled as a post-processing step of the forward+ *  recursions. See @cite hofacker:2006 for further details.+ *+ *  @see vrna_pf_fold(), vrna_pf(), vrna_fold_compound(), #vrna_fold_compound_t+ *+ *  @param sequence  A circular RNA sequence+ *  @param structure  A pointer to the character array where position-wise pairing propensity+ *                    will be stored. (Maybe NULL)+ *  @param pl         A pointer to a list of #vrna_plist_t to store pairing probabilities (Maybe NULL)+ *  @return The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+float vrna_pf_circfold(const char *sequence, char *structure, vrna_plist_t **pl);++/*+#################################################+# OTHER PARTITION FUNCTION RELATED DECLARATIONS #+#################################################+*/++/**+ *  @brief  Find out whether partition function computations are using+ *          single precision floating points+ *+ *  @see #FLT_OR_DBL+ *  @return  1 if single precision is used, 0 otherwise+ */+int vrna_pf_float_precision(void);++#ifdef  VRNA_BACKWARD_COMPAT++/*+#################################################+# DEPRECATED FUNCTIONS                          #+#################################################+*/++/**+ *  @brief Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking+ *+ *  Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking+ *  are filled in the forward recursions+ *+ *  @deprecated   set the @e uniq_ML flag in #vrna_md_t before passing it to vrna_fold_compound().+ *+ *  @ingroup subopt_stochbt+ *+ *  @see pbacktrack(), pbacktrack_circ+ */+extern  int st_back;++/**+ *  @brief Compute the partition function @f$Q@f$ for a given RNA sequence+ *+ *  If @a structure is not a NULL pointer on input, it contains on+ *  return a string consisting of the letters " . , | { } ( ) " denoting+ *  bases that are essentially unpaired, weakly paired, strongly paired without+ *  preference, weakly upstream (downstream) paired, or strongly up-+ *  (down-)stream paired bases, respectively.+ *  If #fold_constrained is not 0, the @a structure string is+ *  interpreted on input as a list of constraints for the folding. The+ *  character "x" marks bases that must be unpaired, matching brackets " ( ) "+ *  denote base pairs, all other characters are ignored. Any pairs+ *  conflicting with the constraint will be forbidden. This is usually sufficient+ *  to ensure the constraints are honored.+ *  If the parameter calculate_bppm is set to 0 base pairing probabilities will not+ *  be computed (saving CPU time), otherwise after calculations took place #pr will+ *  contain the probability that bases @a i and @a j pair.+ * + *  @ingroup pf_fold+ *+ *  @deprecated Use vrna_pf() instead+ *+ *  @note           The global array #pr is deprecated and the user who wants the calculated+ *                  base pair probabilities for further computations is advised to use the function+ *                  export_bppm()+ *  @post           After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.+ *                  Depending on whether the global variable #do_backtrack was set the base pair probabilities are already+ *                  computed and may be accessed for further usage via the export_bppm() function.+ *                  A call of free_pf_arrays() will free all memory allocated by this function.+ *                  Successive calls will first free previously allocated memory before starting the computation.+ *  @see            vrna_pf(), bppm_to_structure(), export_bppm(), vrna_exp_params(), free_pf_arrays()+ *  @param[in]      sequence        The RNA sequence input+ *  @param[in,out]  structure       A pointer to a char array where a base pair probability information can be stored in a+ *                                  pseudo-dot-bracket notation (may be NULL, too)+ *  @param[in]      parameters      Data structure containing the precalculated Boltzmann factors+ *  @param[in]      calculate_bppm  Switch to Base pair probability calculations on/off (0==off)+ *  @param[in]      is_constrained  Switch to indicate that a structure contraint is passed via the structure argument (0==off)+ *  @param[in]      is_circular     Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off)+ *  @return         The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+DEPRECATED(float   pf_fold_par(  const char *sequence,+                      char *structure,+                      vrna_exp_param_t *parameters,+                      int calculate_bppm,+                      int is_constrained,+                      int is_circular));++/**+ *  @brief Compute the partition function @f$Q@f$ of an RNA sequence+ * + *  If @a structure is not a NULL pointer on input, it contains on+ *  return a string consisting of the letters " . , | { } ( ) " denoting+ *  bases that are essentially unpaired, weakly paired, strongly paired without+ *  preference, weakly upstream (downstream) paired, or strongly up-+ *  (down-)stream paired bases, respectively.+ *  If #fold_constrained is not 0, the @a structure string is+ *  interpreted on input as a list of constraints for the folding. The+ *  character "x" marks bases that must be unpaired, matching brackets " ( ) "+ *  denote base pairs, all other characters are ignored. Any pairs+ *  conflicting with the constraint will be forbidden. This is usually sufficient+ *  to ensure the constraints are honored.+ *  If #do_backtrack has been set to 0 base pairing probabilities will not+ *  be computed (saving CPU time), otherwise #pr will contain the probability+ *  that bases @a i and @a j pair.+ * + *  @ingroup pf_fold+ *+ *  @note   The global array #pr is deprecated and the user who wants the calculated+ *          base pair probabilities for further computations is advised to use the function+ *          export_bppm().+ *  @note   @b OpenMP:+ *          This function is not entirely threadsafe. While the recursions are working on their+ *          own copies of data the model details for the recursions are determined from the global+ *          settings just before entering the recursions. Consider using pf_fold_par() for a+ *          really threadsafe implementation.+ *  @pre    This function takes its model details from the global variables provided in @e RNAlib+ *  @post   After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.+ *          Depending on whether the global variable #do_backtrack was set the base pair probabilities are already+ *          computed and may be accessed for further usage via the export_bppm() function.+ *          A call of free_pf_arrays() will free all memory allocated by this function.+ *          Successive calls will first free previously allocated memory before starting the computation.+ *  @see    pf_fold_par(), pf_circ_fold(), bppm_to_structure(), export_bppm()+ *  @param sequence   The RNA sequence input+ *  @param structure  A pointer to a char array where a base pair probability information can be stored in a pseudo-dot-bracket notation (may be NULL, too)+ *  @return           The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+DEPRECATED(float   pf_fold(const char *sequence,+                char *structure));++/**+ *  @brief Compute the partition function of a circular RNA sequence+ * + *  @ingroup pf_fold+ *+ *  @note           The global array #pr is deprecated and the user who wants the calculated+ *                  base pair probabilities for further computations is advised to use the function+ *                  export_bppm().+ *  @note           @b OpenMP:+ *                  This function is not entirely threadsafe. While the recursions are working on their+ *                  own copies of data the model details for the recursions are determined from the global+ *                  settings just before entering the recursions. Consider using pf_fold_par() for a+ *                  really threadsafe implementation.+ *  @pre            This function takes its model details from the global variables provided in @e RNAlib+ *  @post           After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.+ *                  Depending on whether the global variable #do_backtrack was set the base pair probabilities are already+ *                  computed and may be accessed for further usage via the export_bppm() function.+ *                  A call of free_pf_arrays() will free all memory allocated by this function.+ *                  Successive calls will first free previously allocated memory before starting the computation.+ *  @see            vrna_pf()+ *  @deprecated     Use vrna_pf() instead!+ *  @param[in]      sequence   The RNA sequence input+ *  @param[in,out]  structure  A pointer to a char array where a base pair probability information can be+ *                  stored in a pseudo-dot-bracket notation (may be NULL, too)+ *  @return         The Gibbs free energy of the ensemble (@f$G = -RT \cdot \log(Q) @f$) in kcal/mol+ */+DEPRECATED(float   pf_circ_fold( const char *sequence,+                      char *structure));++/**+ *  @brief Sample a secondary structure from the Boltzmann ensemble according its probability+ *+ *  @ingroup subopt_stochbt+ *  @pre    #st_back has to be set to 1 before calling pf_fold() or pf_fold_par()+ *  @pre    pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices+ *+ *  @param  sequence  The RNA sequence+ *  @return           A sampled secondary structure in dot-bracket notation+ */+DEPRECATED(char    *pbacktrack(char *sequence));++DEPRECATED(char    *pbacktrack5(char *sequence, int length));++/**+ *  @brief Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability+ * + *  This function does the same as @ref pbacktrack() but assumes the RNA molecule to be circular+ *+ *  @ingroup subopt_stochbt++ *  @pre    #st_back has to be set to 1 before calling pf_fold() or pf_fold_par()+ *  @pre    pf_fold_par() or pf_circ_fold() have to be called first to fill the partition function matrices+ *+ *  @deprecated Use vrna_pbacktrack() instead.+ *+ *  @param  sequence  The RNA sequence+ *  @return           A sampled secondary structure in dot-bracket notation+ */+DEPRECATED(char    *pbacktrack_circ(char *sequence));++/**+ *  @brief Free arrays for the partition function recursions+ *+ *  Call this function if you want to free all allocated memory associated with+ *  the partition function forward recursion.+ *  @note Successive calls of pf_fold(), pf_circ_fold() already check if they should free+ *  any memory from a previous run.+ *  @note <b>OpenMP notice:</b><br>+ *  This function should be called before leaving a thread in order to avoid leaking memory+ *  + *  @deprecated See vrna_fold_compound_t and its related functions for how to free memory+ *  occupied by the dynamic programming matrices+ *+ *  @ingroup pf_fold+ *+ *  @post   All memory allocated by pf_fold_par(), pf_fold() or pf_circ_fold() will be free'd+ *  @see    pf_fold_par(), pf_fold(), pf_circ_fold()+ */+DEPRECATED(void  free_pf_arrays(void));++/**+ *  @brief Recalculate energy parameters+ * + *  Call this function to recalculate the pair matrix and energy parameters+ *  after a change in folding parameters like #temperature+ *+ *  @deprecated Use vrna_exp_params_subst() instead+ *  @ingroup pf_fold+ *+ */+DEPRECATED(void  update_pf_params(int length));++/**+ *  @brief Recalculate energy parameters+ *+ *  @deprecated Use vrna_exp_params_subst() instead+ *  @ingroup pf_fold+ *+ */+DEPRECATED(void update_pf_params_par(int length, vrna_exp_param_t *parameters));++/**+ *  @brief Get a pointer to the base pair probability array+ *  @ingroup  pf_fold+ *+ *  Accessing the base pair probabilities for a pair (i,j) is achieved by+ *  @code+ *  FLT_OR_DBL *pr  = export_bppm();+ *  pr_ij           = pr[iindx[i]-j];+ *  @endcode+ *+ *  @pre      Call pf_fold_par(), pf_fold() or pf_circ_fold() first to fill the base pair probability array+ *+ *  @see pf_fold(), pf_circ_fold(), vrna_idx_row_wise()+ *+ *  @return A pointer to the base pair probability array+ */+DEPRECATED(FLT_OR_DBL  *export_bppm(void));+++/**+ *  @brief Get the pointers to (almost) all relavant computation arrays used in partition function computation+ *+ *  @ingroup    pf_fold+ *  @pre        In order to assign meaningful pointers, you have to call pf_fold_par() or pf_fold() first!+ *  @see        pf_fold_par(), pf_fold(), pf_circ_fold()+ *  @param[out] S_p       A pointer to the 'S' array (integer representation of nucleotides)+ *  @param[out] S1_p      A pointer to the 'S1' array (2nd integer representation of nucleotides)+ *  @param[out] ptype_p   A pointer to the pair type matrix+ *  @param[out] qb_p      A pointer to the Q<sup>B</sup> matrix+ *  @param[out] qm_p      A pointer to the Q<sup>M</sup> matrix+ *  @param[out] q1k_p     A pointer to the 5' slice of the Q matrix (@f$q1k(k) = Q(1, k)@f$)+ *  @param[out] qln_p     A pointer to the 3' slice of the Q matrix (@f$qln(l) = Q(l, n)@f$)+ *  @return     Non Zero if everything went fine, 0 otherwise+ */+DEPRECATED(int get_pf_arrays(short **S_p,+                  short **S1_p,+                  char **ptype_p,+                  FLT_OR_DBL **qb_p,+                  FLT_OR_DBL **qm_p,+                  FLT_OR_DBL **q1k_p,+                  FLT_OR_DBL **qln_p));++/**+ *  @brief Get the free energy of a subsequence from the q[] array+ */+DEPRECATED(double get_subseq_F(int i, int j));+++/**+ *  @brief Get the mean base pair distance of the last partition function computation+ * + *  @ingroup pf_fold+ *+ *  @deprecated Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!+ *  @see vrna_mean_bp_distance(), vrna_mean_bp_distance_pr()+ * + *  @param    length+ *  @return  mean base pair distance in thermodynamic ensemble+ */+DEPRECATED(double  mean_bp_distance(int length));++/**+ *  @brief Get the mean base pair distance in the thermodynamic ensemble+ * + *  This is a threadsafe implementation of @ref mean_bp_dist() !+ * + *  @f$<d> = \sum_{a,b} p_a p_b d(S_a,S_b)@f$\n+ *  this can be computed from the pair probs @f$p_ij@f$ as\n+ *  @f$<d> = \sum_{ij} p_{ij}(1-p_{ij})@f$+ * + *  @deprecated Use vrna_mean_bp_distance() or vrna_mean_bp_distance_pr() instead!+ * + *  @ingroup pf_fold+ *+ *  @param length The length of the sequence+ *  @param pr     The matrix containing the base pair probabilities+ *  @return       The mean pair distance of the structure ensemble+ */+DEPRECATED(double mean_bp_distance_pr(int length, FLT_OR_DBL *pr));++/**+ *  @brief  Get the probability of stacks+ *+ *  @deprecated   Use vrna_stack_prob() instead!+ */+DEPRECATED(vrna_plist_t *stackProb(double cutoff));+++/**+ *  @brief Allocate space for pf_fold()+ * + *  @deprecated This function is obsolete and will be removed soon!+ */+DEPRECATED(void init_pf_fold(int length));++/**+ *  @deprecated This function is deprecated and should not be used anymore as it is not threadsafe!+ *  @see get_centroid_struct_pl(), get_centroid_struct_pr()+ */+DEPRECATED(char *centroid(int length, double *dist));++/**+ *  @deprecated This function is deprecated and should not be used anymore as it is not threadsafe!+ *  @see vrna_centroid(), vrna_centroid_from_probs(), vrna_centroid_from_plist()+ */+DEPRECATED(char *get_centroid_struct_gquad_pr(int length,+                                  double *dist));++/**+ *  get the mean pair distance of ensemble+ * + *  @deprecated This function is not threadsafe and should not be used anymore. Use @ref mean_bp_distance() instead!+ */+DEPRECATED(double mean_bp_dist(int length));++/**+ *  @deprecated Use @ref exp_E_IntLoop() from loop_energies.h instead+ */+DEPRECATED(double expLoopEnergy(int u1,+                                int u2,+                                int type,+                                int type2,+                                short si1,+                                short sj1,+                                short sp1,+                                short sq1));++/**+ *  @deprecated Use exp_E_Hairpin() from loop_energies.h instead+ */+DEPRECATED(double expHairpinEnergy( int u,+                                    int type,+                                    short si1,+                                    short sj1,+                                    const char *string));++/* this doesn't work if free_pf_arrays() is called before */+DEPRECATED(void assign_plist_gquad_from_pr(vrna_plist_t **pl,+                                int length,+                                double cut_off));++#endif++#endif
+ C/ViennaRNA/part_func_co.c view
@@ -0,0 +1,1473 @@+/*+                  partiton function for RNA secondary structures++                  Ivo L Hofacker+                  Stephan Bernhart+                  Ronny Lorenz+                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include <limits.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/structure_utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/PS_dot.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/part_func_co.h"++#ifdef _OPENMP+#include <omp.h>+#endif++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+int     mirnatog      = 0;+double  F_monomer[2]  = {0,0}; /* free energies of the two monomers */++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/* some backward compatibility stuff */+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;+PRIVATE int                 backward_compat           = 0;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif+++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE void    pf_co(vrna_fold_compound_t *vc);+PRIVATE void    pf_co_bppm(vrna_fold_compound_t *vc, char *structure);+PRIVATE double  *Newton_Conc(double ZAB, double ZAA, double ZBB, double concA, double concB,double* ConcVec);+PRIVATE vrna_dimer_pf_t wrap_co_pf_fold(char *sequence,+                                char *structure,+                                vrna_exp_param_t *parameters,+                                int calculate_bppm,+                                int is_constrained);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++/*+*****************************************+* BEGIN backward compatibility wrappers *+*****************************************+*/++PRIVATE vrna_dimer_pf_t+wrap_co_pf_fold(char *sequence,+                char *structure,+                vrna_exp_param_t *parameters,+                int calculate_bppm,+                int is_constrained){++  int                 length;+  char                *seq;+  vrna_fold_compound_t  *vc;+  vrna_md_t           md;++  vc      = NULL;+  length  = strlen(sequence);++  /* we need vrna_exp_param_t datastructure to correctly init default hard constraints */+  if(parameters)+    md = parameters->model_details;+  else{+    set_model_details(&md); /* get global default parameters */+  }+  md.compute_bpp    = calculate_bppm;+  md.min_loop_size  = 0;++  seq = (char *)vrna_alloc(sizeof(char) * (length + 2));+  if(cut_point > -1){+    int i;+    for(i = 0; i < cut_point-1; i++)+      seq[i] = sequence[i];+    seq[i] = '&';+    for(;i<(int)length;i++)+      seq[i+1] = sequence[i];+  } else { /* this ensures the allocation of all cofold matrices via vrna_fold_compound_t */+    free(seq);+    seq = strdup(sequence);+  }++  vc = vrna_fold_compound(seq, &md, VRNA_OPTION_PF | VRNA_OPTION_HYBRID);++  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound = vc;+  backward_compat           = 1;+  iindx = backward_compat_compound->iindx;++  free(seq);+  return vrna_pf_dimer(vc, structure);+}++/*+*****************************************+* END backward compatibility wrappers   *+*****************************************+*/++PUBLIC vrna_dimer_pf_t+vrna_pf_dimer(vrna_fold_compound_t *vc,+              char *structure){++  int             n;+  FLT_OR_DBL      Q;+  vrna_dimer_pf_t         X;+  double          free_energy;+  char            *sequence;+  vrna_md_t       *md;+  vrna_exp_param_t  *params;+  vrna_mx_pf_t      *matrices;++  if(!vrna_fold_compound_prepare(vc, VRNA_OPTION_PF | VRNA_OPTION_HYBRID)){+    vrna_message_warning("vrna_pf_dimer@part_func_co.c: Failed to prepare vrna_fold_compound");+    X.FA = X.FB = X.FAB = X.F0AB = X.FcAB  = 0;+    return X;+  }++  params    = vc->exp_params;+  n         = vc->length;+  md        = &(params->model_details);+  matrices  = vc->exp_matrices;+  sequence  = vc->sequence;++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++#ifdef SUN4+  nonstandard_arithmetic();+#else+#ifdef HP9+  fpsetfastmode(1);+#endif+#endif++  /* call user-defined recursion status callback function */+  if(vc->stat_cb)+    vc->stat_cb(VRNA_STATUS_PF_PRE, vc->auxdata);++  pf_co(vc);++  /* call user-defined recursion status callback function */+  if(vc->stat_cb)+    vc->stat_cb(VRNA_STATUS_PF_POST, vc->auxdata);++  if (md->backtrack_type=='C')+    Q = matrices->qb[vc->iindx[1]-n];+  else if (md->backtrack_type=='M')+    Q = matrices->qm[vc->iindx[1]-n];+  else Q = matrices->q[vc->iindx[1]-n];++  /* ensemble free energy in Kcal/mol */+  if (Q<=FLT_MIN)+    vrna_message_warning("pf_scale too large");+  free_energy = (-log(Q)-n*log(params->pf_scale))*params->kT/1000.0;+  /* in case we abort because of floating point errors */+  if(n>1600)+    vrna_message_info(stderr, "free energy = %8.2f", free_energy);+  /*probability of molecules being bound together*/++  /*Computation of "real" Partition function*/+  /*Need that for concentrations*/+  if (vc->cutpoint > 0){+    double kT, QAB, QToT, Qzero;+    kT = params->kT/1000.0;+    Qzero = matrices->q[vc->iindx[1] - n];+    QAB = (matrices->q[vc->iindx[1] - n]- matrices->q[vc->iindx[1] - (vc->cutpoint - 1)] * matrices->q[vc->iindx[vc->cutpoint] - n]) * params->expDuplexInit;+    /*correction for symmetry*/+    if((n - (vc->cutpoint - 1) * 2) == 0){+      if((strncmp(sequence, sequence + vc->cutpoint - 1, vc->cutpoint - 1)) == 0){+        QAB/=2;+      }+    }++    QToT    = matrices->q[vc->iindx[1] - (vc->cutpoint - 1)] * matrices->q[vc->iindx[vc->cutpoint] - n] + QAB;+    X.FAB   = -kT * (log(QToT) + n * log(params->pf_scale));+    X.F0AB  = -kT * (log(Qzero)+ n * log(params->pf_scale));+    X.FcAB  = (QAB>1e-17) ? -kT * (log(QAB) + n * log(params->pf_scale)) : 999;+    X.FA    = -kT * (log(matrices->q[vc->iindx[1] - (vc->cutpoint - 1)]) + (vc->cutpoint - 1) * log(params->pf_scale));+    X.FB    = -kT * (log(matrices->q[vc->iindx[vc->cutpoint] - n]) + (n - vc->cutpoint + 1) * log(params->pf_scale));++    /* printf("QAB=%.9f\tQtot=%.9f\n",QAB/scale[n],QToT/scale[n]);*/+  }+  else {+    X.FA    = X.FB = X.FAB = X.F0AB = free_energy;+    X.FcAB  = 0;+  }++  /* backtracking to construct binding probabilities of pairs*/+  if(md->compute_bpp){+    pf_co_bppm(vc, structure);+    /*+    *  Backward compatibility:+    *  This block may be removed if deprecated functions+    *  relying on the global variable "pr" vanish from within the package!+    */+    pr = vc->exp_matrices->probs;+    /*+    {+      if(pr) free(pr);+      pr = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));+      memcpy(pr, probs, sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));+    }+    */+  }++#ifdef SUN4+  standard_arithmetic();+#else+#ifdef HP9+  fpsetfastmode(0);+#endif+#endif++  return X;+}++/* forward recursion of pf cofolding */+PRIVATE void+pf_co(vrna_fold_compound_t *vc){++  unsigned int      *sn;+  int               n, i,j,k,l, ij, kl, u,u1,u2,ii, type, type_2, tt, cp, turn, maxk, minl;+  FLT_OR_DBL        *qqm = NULL, *qqm1 = NULL, *qq = NULL, *qq1 = NULL;+  FLT_OR_DBL        temp, q_temp, Qmax=0;+  FLT_OR_DBL        qbt1, *tmp;+  FLT_OR_DBL        *q, *qb, *qm, *qm1;+  FLT_OR_DBL        *scale;+  FLT_OR_DBL        *expMLbase;+  short             *S1;+          short s5, s3;+  int               *my_iindx, *jindx;+  char              *ptype, *sequence;+  vrna_md_t         *md;+  vrna_hc_t         *hc;+  vrna_sc_t         *sc;+  FLT_OR_DBL        expMLclosing;+  int               noGUclosure;+  double            max_real;+  int               *rtype;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  int               hc_decompose;+  char              *hard_constraints;+  int               *hc_up_ext;+  int               *hc_up_hp;+  int               *hc_up_int;+  int               *hc_up_ml;++  sequence          = vc->sequence;+  S1                = vc->sequence_encoding;+  n                 = vc->length;+  cp                = vc->cutpoint;+  my_iindx          = vc->iindx;+  jindx             = vc->jindx;+  ptype             = vc->ptype;+  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  sn                = vc->strand_number;+  rtype             = &(md->rtype[0]);+  hc                = vc->hc;+  sc                = vc->sc;+  expMLclosing      = pf_params->expMLclosing;+  noGUclosure       = md->noGUclosure;+  matrices          = vc->exp_matrices;+  turn              = md->min_loop_size;++  q                 = matrices->q;+  qb                = matrices->qb;+  qm                = matrices->qm;+  qm1               = matrices->qm1;+  scale             = matrices->scale;+  expMLbase         = matrices->expMLbase;++  hard_constraints  = hc->matrix;+  hc_up_ext         = hc->up_ext;+  hc_up_hp          = hc->up_hp;+  hc_up_int         = hc->up_int;+  hc_up_ml          = hc->up_ml;++  max_real          = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  /* allocate memory for helper arrays */+  qq        = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  qq1       = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  qqm       = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+  qqm1      = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));++  /* hard code min_loop_size to 0, since we can not be sure yet that this is already the case */+  turn = 0;++  /*array initialization ; qb,qm,q+    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */++  /* for (d=0; d<=TURN; d++) */+  for (i=1; i<=n/*-d*/; i++) {+      ij      = my_iindx[i]-i;+      if(hc_up_ext[i]){+        q[ij] = scale[1];++        if(sc){+          if(sc->exp_energy_up)+            q[ij] *= sc->exp_energy_up[i][1];+          if(sc->exp_f)+            q[ij] *= sc->exp_f(i, i, i, i, VRNA_DECOMP_EXT_UP, sc->data);+        }+      } else {+        q[ij] = 0.;+      }++      qb[ij]  = qm[ij] = 0.0;+    }++  for (i=0; i<=n; i++)+    qq[i] = qq1[i] = qqm[i] = qqm1[i] = 0;++  for (j = turn + 2; j <= n; j++) {+    for (i = j - turn - 1; i >= 1; i--) {+      /* construction of partition function of segment i,j */+      /* firstly that given i binds j : qb(i,j) */+      u             = j - i - 1;+      ij            = my_iindx[i] - j;+      type          = (unsigned char)ptype[jindx[j] + i];+      hc_decompose  = hard_constraints[jindx[j] + i];+      qbt1          = 0;+      q_temp        = 0.;++      if(hc_decompose){+        /* process hairpin loop(s) */+        qbt1 += vrna_exp_E_hp_loop(vc, i, j);+        qbt1 += vrna_exp_E_int_loop(vc, i, j);+        qbt1 += vrna_exp_E_mb_loop_fast(vc, i, j, qqm1);++        qb[ij] = qbt1;+      } else  /* end if allowed to be paired */+        qb[ij] = 0.0;++      /* construction of qqm matrix containing final stem+         contributions to multiple loop partition function+         from segment i,j */+      qqm[i] = 0.;++      if(hc_up_ml[j]){+        if (sn[j] == sn[j - 1]) {+          q_temp  =  qqm1[i] * expMLbase[1];++          if(sc){+            if(sc->exp_energy_up)+              q_temp *= sc->exp_energy_up[j][1];++            if(sc->exp_f)+              q_temp *= sc->exp_f(i, j, i, j-1, VRNA_DECOMP_ML_ML, sc->data);+          }++          qqm[i] = q_temp;+        }+      }++      if(hc_decompose & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+        if ((sn[i] == sn[i - 1]) && (sn[j + 1] == sn[j])) {+          tt = type;++          if(tt == 0)+            tt = 7;++          qbt1    =   qb[ij];+          qbt1    *=  exp_E_MLstem(tt, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);+          if(sc){+            if(sc->exp_f)+              q_temp *= sc->exp_f(i, j, i, j, VRNA_DECOMP_ML_STEM, sc->data);+          }+          qqm[i]  +=  qbt1;+        }+      }++      if (qm1) qm1[jindx[j]+i] = qqm[i]; /* for stochastic backtracking */+++      /*construction of qm matrix containing multiple loop+        partition function contributions from segment i,j */+      temp  = 0.0;+      kl = my_iindx[i] - j + 1; /* ii-k=[i,k-1] */++      if (sc && sc->exp_f) {+        if (j >= cp) {+          for (k = j; k > MAX2(i, cp); k--, kl++) {+            q_temp = qm[kl] * qqm[k];+            q_temp *= sc->exp_f(i, j, k - 1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+            temp += q_temp;+          }+          for (; k > i; k--, kl++) {+            q_temp = qm[kl] * qqm[k];+            q_temp *= sc->exp_f(i, j, k - 1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+            temp += q_temp;+          }+        } else {+          for (k = j; k > i; k--, kl++) {+            q_temp = qm[kl] * qqm[k];+            q_temp *= sc->exp_f(i, j, k - 1, k, VRNA_DECOMP_ML_ML_ML, sc->data);+            temp += q_temp;+          }+        }+      } else { /* without soft-constraints */+        if (j >= cp) {+          for (k = j; k > MAX2(i, cp); k--, kl++)+            temp += qm[kl] * qqm[k];+          for (; k > i; k--, kl++)+            temp += qm[kl] * qqm[k];+        } else {+          for (k = j; k > i; k--, kl++)+            temp += qm[kl] * qqm[k];+        }+      }++      maxk = MIN2(i + hc_up_ml[i], j);+      if (i < cp) { /* we must not have the strand border within the unpaired segment */+        maxk = MIN2(maxk, cp - 1);+      }++      u = 1; /* length of unpaired stretch */++      if (sc) {+        for (k = i + 1; k <= maxk; k++, u++){+          q_temp = expMLbase[u] * qqm[k];++          if(sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[i][u];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, k, j, VRNA_DECOMP_ML_ML, sc->data);++          temp += q_temp;+        }+      } else { /* without soft-constraints */+        for (k = i + 1; k <= maxk; k++, u++)+          temp += expMLbase[u] * qqm[k];+      }++      qm[ij] = (temp + qqm[i]);++      /*auxiliary matrix qq for cubic order q calculation below */+      qbt1 = 0.;++      if(hc_decompose & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+        tt = type;++        if(tt == 0)+          tt = 7;+        s5 = ((i > 1) && (sn[i] == sn[i - 1])) ? S1[i - 1] : -1;+        s3 = ((j < n) && (sn[j + 1] == sn[j])) ? S1[j + 1] : -1;+        qbt1 =  qb[ij] * exp_E_ExtLoop(tt, s5, s3, pf_params);+        if(sc){+          if(sc->exp_f)+            qbt1 *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_STEM, sc->data);+        }+     }++      if(hc_up_ext[j]){+        q_temp = qq1[i] * scale[1];++        if(sc){+          if(sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[j][1];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, i, j-1, VRNA_DECOMP_EXT_EXT, sc->data);+        }++        qbt1 += q_temp;+      }+      qq[i] = qbt1;++       /*construction of partition function for segment i,j */+      temp = qq[i];++      /* the whole stretch [i,j] is unpaired */+      if(hc_up_ext[i] >= (j-i+1)){+        q_temp = 1.0 * scale[j-i+1];++        if(sc){+          if(sc->exp_energy_up)+            q_temp *= sc->exp_energy_up[i][j-i+1];++          if(sc->exp_f)+            q_temp *= sc->exp_f(i, j, i, j, VRNA_DECOMP_EXT_UP, sc->data);+        }++        temp += q_temp;+      }++      kl = my_iindx[i] - i;++      if (sc && sc->exp_f) {+        for (k=i; k<j; k++, kl--){+          q_temp = q[kl] * qq[k+1];+          q_temp *= sc->exp_f(i, j, k, k+1, VRNA_DECOMP_EXT_EXT_EXT, sc->data);+          temp += q_temp;+        }+      } else {+        for (k=i; k<j; k++, kl--)+          temp += q[kl] * qq[k+1];+      }++      q[ij] = temp;++      if (temp>Qmax) {+        Qmax = temp;+        if (Qmax>max_real/10.)+          vrna_message_warning("Q close to overflow: %d %d %g", i,j,temp);+      }+      if (temp>=max_real) {+        vrna_message_error("overflow in co_pf_fold while calculating q[%d,%d]\n"+                                  "use larger pf_scale", i,j);+      }+    }+    tmp = qq1;  qq1 =qq;  qq =tmp;+    tmp = qqm1; qqm1=qqm; qqm=tmp;+  }++  /* clean up */+  free(qq);+  free(qq1);+  free(qqm);+  free(qqm1);++}++/* backward recursion of pf cofolding */+PRIVATE void+pf_co_bppm(vrna_fold_compound_t *vc, char *structure){++  unsigned int      *sn;+  int               n, i,j,k,l, ij, kl, ii, ll, lj, u1, u2, type, type_2, tt, turn, ov=0, *my_iindx, *jindx, cp;+  FLT_OR_DBL        temp, Qmax=0, prm_MLb, tmp2, ppp;+  FLT_OR_DBL        prmt,prmt1, *expMLbase;+  FLT_OR_DBL        *tmp;+  FLT_OR_DBL        expMLclosing, *probs, *q1k, *qln, *q, *qb, *qm, *scale;+  double            max_real;+  vrna_exp_param_t  *pf_params;+  vrna_md_t         *md;+  short             *S, *S1, s5, s3;+  char              *ptype;+  vrna_hc_t         *hc;+  vrna_sc_t         *sc;+  vrna_mx_pf_t      *matrices;+  char              *sequence;+  char              *hard_constraints;+  int               *hc_up_ext;+  int               *hc_up_hp;+  int               *hc_up_int;+  int               *hc_up_ml;+  int               *rtype;++  sequence          = vc->sequence;+  n                 = vc->length;+  cp                = vc->cutpoint;+  pf_params         = vc->exp_params;+  md                = &(pf_params->model_details);+  expMLclosing      = pf_params->expMLclosing;+  S                 = vc->sequence_encoding2;+  S1                = vc->sequence_encoding;+  sn                = vc->strand_number;+  jindx             = vc->jindx;+  my_iindx          = vc->iindx;+  ptype             = vc->ptype;+  rtype             = &(md->rtype[0]);+  turn              = md->min_loop_size;++  matrices          = vc->exp_matrices;+  probs             = matrices->probs;+  scale             = matrices->scale;+  q1k               = matrices->q1k;+  qln               = matrices->qln;+  q                 = matrices->q;+  qb                = matrices->qb;+  qm                = matrices->qm;+  expMLbase         = matrices->expMLbase;++  hc                = vc->hc;+  sc                = vc->sc;++  hard_constraints  = hc->matrix;+  hc_up_ext         = hc->up_ext;+  hc_up_hp          = hc->up_hp;+  hc_up_int         = hc->up_int;+  hc_up_ml          = hc->up_ml;++  /* hard code min_loop_size to 0, since we can not be sure yet that this is already the case */+  turn = 0;++  max_real      = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;++  /* backtracking to construct binding probabilities of pairs*/+  if ((S != NULL) && (S1 != NULL)) {+    FLT_OR_DBL   *Qlout, *Qrout;+    FLT_OR_DBL *prm_l  = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+    FLT_OR_DBL *prm_l1 = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));+    FLT_OR_DBL *prml   = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*(n+2));++    Qmax  = 0;+    Qrout = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (n+2));+    Qlout = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * (cp+2));++    for (k=1; k<=n; k++) {+      q1k[k] = q[my_iindx[1] - k];+      qln[k] = q[my_iindx[k] - n];+    }+    q1k[0] = 1.0;+    qln[n+1] = 1.0;++    /* 1. exterior pair i,j and initialization of pr array */+    for (i=1; i<=n; i++) {+      for (j=i; j<=MIN2(i + turn, n); j++)+        probs[my_iindx[i]-j] = 0;++      for (j = i + turn + 1; j <= n; j++){+        ij = my_iindx[i]-j;+        if((hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP) && (qb[ij] > 0.)){+          type  = ptype[jindx[j] + i];++          if(type == 0)+            type = 7;++          s5 = ((i > 1) && (sn[i] == sn[i - 1])) ? S1[i - 1] : -1;+          s3 = ((j < n) && (sn[j + 1] == sn[j])) ? S1[j + 1] : -1;+          probs[ij] = q1k[i - 1] * qln[j + 1] / q1k[n];+          probs[ij] *= exp_E_ExtLoop(type, s5, s3, pf_params);+          if(sc){+            if(sc->exp_f){+              probs[ij] *= sc->exp_f(1, n, i, j, VRNA_DECOMP_EXT_STEM_OUTSIDE, sc->data);+            }+          }+        } else+          probs[ij] = 0;+      }+    }++    for(l = n; l > turn + 1; l--){++      /* 2. bonding k,l as substem of 2:loop enclosed by i,j */+      for(k = 1; k < l - turn; k++){+        kl      = my_iindx[k]-l;+        type_2  = (unsigned char)ptype[jindx[l] + k];+        type_2  = rtype[type_2];++        if(qb[kl]==0.) continue;++        if(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC){++          if(type_2 == 0)+            type_2 = 7;++          for(i = MAX2(1, k - MAXLOOP - 1); i <= k - 1; i++){+            u1 = k - i - 1;+            if(hc_up_int[i+1] < u1) continue;++            for(j = l + 1; j <= MIN2(l + MAXLOOP - k + i + 2, n); j++){+              u2 = j-l-1;+              if(hc_up_int[l+1] < u2) break;++              ij = my_iindx[i] - j;+              if(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){++                if ((sn[k] == sn[i]) && (sn[j] == sn[l])) {+                  type = (unsigned char)ptype[jindx[j] + i];+                  if(probs[ij] > 0){++                    if(type == 0)+                      type = 7;++                    tmp2  = probs[ij]+                            * scale[u1 + u2 + 2]+                            * exp_E_IntLoop(u1, u2, type, type_2, S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params);++                    if(sc){+                      if(sc->exp_energy_up)+                        tmp2 *=   sc->exp_energy_up[i+1][u1]+                                * sc->exp_energy_up[l+1][u2];++                      if(sc->exp_energy_bp)+                        tmp2 *=   sc->exp_energy_bp[ij];++                      if(sc->exp_energy_stack){+                        if((i+1 == k) && (j-1 == l)){+                          tmp2 *=   sc->exp_energy_stack[i]+                                  * sc->exp_energy_stack[k]+                                  * sc->exp_energy_stack[l]+                                  * sc->exp_energy_stack[j];+                        }+                      }++                      if(sc->exp_f)+                        tmp2 *= sc->exp_f(i, j, k, l, VRNA_DECOMP_PAIR_IL, sc->data);+                    }++                    probs[kl] += tmp2;+                  }+                }+              }+            }+          }+        }+      }++      /* 3. bonding k,l as substem of multi-loop enclosed by i,j */+      prm_MLb = 0.;+      if ((l < n) && (sn[l + 1] == sn[l]))+        for (k = 2; k < l - turn; k++) {+          kl    = my_iindx[k] - l;+          i     = k - 1;+          prmt  = prmt1 = 0.0;++          ii    = my_iindx[i];     /* ii-j=[i,j]     */+          ll    = my_iindx[l+1];   /* ll-j=[l+1,j] */+          tt    = (unsigned char)ptype[jindx[l+1] + i];+          tt    = rtype[tt];+          if (sn[k] == sn[i]) {+            if(hard_constraints[jindx[l+1] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){++              if(tt == 0)+                tt = 7;++              prmt1 = probs[ii-(l+1)]+                      * expMLclosing+                      * exp_E_MLstem(tt, S1[l], S1[i+1], pf_params);++              if(sc){+                /* which decompositions are covered here? => (i, l+1) -> enclosing pair, (k,l) -> enclosed pair, */+                if(sc->exp_energy_bp)+                  prmt1 *= sc->exp_energy_bp[ii - (l+1)];++/*+                if(sc->exp_f)+                  prmt1 *= sc->exp_f(i, l+1, k, l, , sc->data);+*/+              }+            }+            ij = my_iindx[i] - (l+2);+            lj = my_iindx[l+1]-(l+1);++            for(j = l + 2; j <= n; j++, ij--, lj--){+              if(hard_constraints[jindx[j] + i] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP){+                if (sn[j] == sn[j - 1]) { /*??*/+                  tt    =   (unsigned char)ptype[jindx[j] + i];+                  tt    =   rtype[tt];++                  if(tt == 0)+                    tt = 7;++                  /* which decomposition is covered here? =>+                    i + 1 = k < l < j:+                    (i,j)       -> enclosing pair+                    (k, l)      -> enclosed pair+                    (l+1, j-1)  -> multiloop part with at least one stem+                  */+                  ppp = probs[ii-j]+                        * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params)+                        * qm[ll-(j-1)];++                  if(sc){+                    if(sc->exp_energy_bp)+                      ppp *= sc->exp_energy_bp[ij];+/*+                    if(sc->exp_f)+                      ppp *= sc->exp_f(i, j, l+1, j-1, , sc->data);+*/+                  }+                  prmt += ppp;+                }+              }+            }+          }+          prmt *= expMLclosing;++          tt        =   ptype[jindx[l] + k];++          prml[ i]  =   prmt;++          /* l+1 is unpaired */+          if(hc->up_ml[l+1]){+            ppp = prm_l1[i] * expMLbase[1];+            if(sc){+              if(sc->exp_energy_up)+                ppp *= sc->exp_energy_up[l+1][1];++/*+              if(sc_exp_f)+                ppp *= sc->exp_f(, sc->data);+*/+            }+            prm_l[i] = ppp + prmt1;+          } else {+            prm_l[i] = prmt1;+          }++          /* i is unpaired */+          if(hc->up_ml[i]){+            ppp = prm_MLb*expMLbase[1];+            if(sc){+              if(sc->exp_energy_up)+                ppp *= sc->exp_energy_up[i][1];++/*+              if(sc->exp_f)+                ppp *= sc->exp_f(, sc->data);+*/+            }++            prm_MLb = ppp + prml[i];+            /* same as:    prm_MLb = 0;+               for (i=1; i<=k-1; i++) prm_MLb += prml[i]*expMLbase[k-i-1]; */++          } else {+            prm_MLb = prml[i];+          }+          prml[i] = prml[ i] + prm_l[i];++          if (qb[kl] == 0.) continue;++          if(hard_constraints[jindx[l] + k] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+            temp = prm_MLb;++            for (i=1;i<=k-2; i++) {+              if ((sn[i + 1] == sn[i]) && (sn[k] == sn[k - 1])) {+                temp += prml[i]*qm[my_iindx[i+1] - (k-1)];+              }+            }++            if(tt == 0)+              tt = 7;++            s5 = ((k > 1) && (sn[k] == sn[k - 1])) ? S1[k - 1] : -1;+            s3 = ((l < n) && (sn[l + 1] == sn[l])) ? S1[l + 1] : -1;+            temp *= exp_E_MLstem(tt, s5, s3, pf_params) * scale[2];+            probs[kl] += temp;++            if (probs[kl]>Qmax) {+              Qmax = probs[kl];+              if (Qmax>max_real/10.)+                vrna_message_warning("P close to overflow: %d %d %g %g",+                                            i, j, probs[kl], qb[kl]);+            }+            if (probs[kl]>=max_real) {+              ov++;+              probs[kl]=FLT_MAX;+            }+          }+        } /* end for (k=..) multloop*/+      else  /* set prm_l to 0 to get prm_l1 to be 0 */+        for (i=0; i<=n; i++) prm_l[i]=0;++      tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;++      /*computation of .(..(...)..&..). type features?*/+      if (cp<=0) continue;            /* no .(..(...)..&..). type features*/+      if ((l==n)||(l<=2)) continue;   /* no .(..(...)..&..). type features*/+      /*new version with O(n^3)??*/+      if (l>cp) {+        if (l<n) {+          int t,kt;+          for (t=n; t>l; t--) {+            for (k=1; k<cp; k++) {+              int samestrand;+              kt    = my_iindx[k]-t;++              samestrand = (sn[k + 1] == sn[k]) ? 1 : 0;+              type  = rtype[(unsigned char)ptype[jindx[t] + k]];++              if(type == 0)+                type = 7;++              temp  = probs[kt]+                      * exp_E_ExtLoop(type, S1[t-1], samestrand ? S1[k+1] : -1, pf_params)+                      * scale[2];++              if (l+1<t)+                temp    *=  q[my_iindx[l+1]-(t-1)];++              if (samestrand)+                temp    *=  q[my_iindx[k+1]-(cp-1)];++              Qrout[l]  +=  temp;+            }+          }+        }+        for (k=l-1; k>=cp; k--) {+          if (qb[my_iindx[k]-l]) {+            kl        =   my_iindx[k]-l;+            type      =   ptype[jindx[l] + k];+            temp      =   Qrout[l];++            if(type == 0)+              type = 7;++            temp      *=  exp_E_ExtLoop(type, (k>cp) ? S1[k-1] : -1, (l < n) ? S1[l+1] : -1, pf_params);+            if (k>cp)+              temp    *=  q[my_iindx[cp]-(k-1)];+            probs[kl] +=  temp;+          }+        }+      }+      else if (l==cp ) {+        int t, sk,s;+        for (t=2; t<cp;t++) {+          for (s=1; s<t; s++) {+            for (k=cp; k<=n; k++) {+              sk=my_iindx[s]-k;+              if (qb[sk]) {+                int samestrand;+                samestrand = (sn[k] == sn[k - 1]) ? 1 : 0;+                type      =   rtype[(unsigned char)ptype[jindx[k] + s]];++                if(type == 0)+                  type = 7;++                temp      =   probs[sk]+                              * exp_E_ExtLoop(type, samestrand ? S1[k - 1] : -1, S1[s + 1], pf_params)+                              * scale[2];+                if (s+1<t)+                  temp    *=  q[my_iindx[s+1]-(t-1)];+                if (samestrand)+                  temp    *=  q[my_iindx[cp]-(k-1)];+                Qlout[t]  +=  temp;+              }+            }+          }+        }+      }+      else if (l<cp) {+        for (k=1; k<l; k++) {+          if (qb[my_iindx[k]-l]) {+            type    =   ptype[jindx[l] + k];+            temp    =   Qlout[k];++            if(type == 0)+              type = 7;++            temp    *=  exp_E_ExtLoop(type, (k>1) ? S1[k-1] : -1, (l<(cp-1)) ? S1[l+1] : -1, pf_params);+            if (l+1<cp)+              temp  *=  q[my_iindx[l+1]-(cp-1)];+            probs[my_iindx[k]-l]  +=  temp;+          }+        }+      }+    }  /* end for (l=..)   */+    free(Qlout);+    free(Qrout);+    for (i=1; i<=n; i++)+      for (j=i+turn+1; j<=n; j++) {+        ij        =   my_iindx[i]-j;+        probs[ij] *=  qb[ij];+      }++    if (structure!=NULL){+      char *s = vrna_db_from_probs(probs, (unsigned int)n);+      memcpy(structure, s, n);+      structure[n] = '\0';+      free(s);+    }++    /* clean up */+    free(prm_l);+    free(prm_l1);+    free(prml);++  }   /* end if (do_backtrack)*/++  if(ov > 0)+    vrna_message_warning("%d overflows occurred while backtracking;\n"+                                "you might try a smaller pf_scale than %g\n",+                                ov, pf_params->pf_scale);+}++PUBLIC void+vrna_pf_dimer_probs(double FAB,+                    double FA,+                    double FB,+                    vrna_plist_t *prAB,+                    const vrna_plist_t *prA,+                    const vrna_plist_t *prB,+                    int Alength,+                    const vrna_exp_param_t *exp_params) {++  /*computes binding probabilities and dimer free energies*/+  int         i, j;+  double      pAB;+  double      mykT;+  const vrna_plist_t *lp2;+  vrna_plist_t       *lp1;+  int         offset;++  mykT = exp_params->kT/1000.;++  /* pair probabilities in pr are relative to the null model (without DuplexInit) */++  /*Compute probabilities pAB, pAA, pBB*/++  pAB = 1. - exp((1/mykT)*(FAB-FA-FB));++  /* compute pair probabilities given that it is a dimer */+  /* AB dimer */+  offset  = 0;+  lp2     = prA;+  if (pAB>0)+    for (lp1=prAB; lp1->j>0; lp1++) {+      float pp=0;+      i = lp1->i;+      j = lp1->j;+      while (offset+lp2->i < i && lp2->i>0) lp2++;+      if (offset+lp2->i == i)+        while ((offset+lp2->j) < j  && (lp2->j>0)) lp2++;+      if (lp2->j == 0) {lp2=prB; offset=Alength;}/* jump to next list */+      if ((offset+lp2->i==i) && (offset+lp2->j ==j)) {+        pp = lp2->p;+        lp2++;+      }+      lp1->p=(lp1->p-(1-pAB)*pp)/pAB;+      if(lp1->p < 0.){+        vrna_message_warning("vrna_co_pf_probs: numeric instability detected, probability below zero!");+        lp1->p = 0.;+      }+    }++  return;+}++PRIVATE double *+Newton_Conc(double KAB,+            double KAA,+            double KBB,+            double concA,+            double concB,+            double* ConcVec){++  double  TOL, EPS, xn, yn, det, cA, cB;+  int     i;++  i       = 0;+  /*Newton iteration for computing concentrations*/+  cA      = concA;+  cB      = concB;+  TOL     = 1e-6; /*Tolerance for convergence*/+  ConcVec = (double*)vrna_alloc(5*sizeof(double)); /* holds concentrations */+  do {+    /* det = (4.0 * KAA * cA + KAB *cB + 1.0) * (4.0 * KBB * cB + KAB *cA + 1.0) - (KAB *cB) * (KAB *cA); */+    det = 1 + 16. *KAA*KBB*cA*cB + KAB*(cA+cB) + 4.*KAA*cA + 4.*KBB*cB + 4.*KAB*(KBB*cB*cB + KAA*cA*cA);+    /* xn  = ( (2.0 * KBB * cB*cB + KAB *cA *cB + cB - concB) * (KAB *cA) -+       (2.0 * KAA * cA*cA + KAB *cA *cB + cA - concA) * (4.0 * KBB * cB + KAB *cA + 1.0) ) /det; */+    xn  = ( (2.0 * KBB * cB*cB + cB - concB) * (KAB *cA) - KAB*cA*cB*(4. * KBB*cB + 1.) -+	    (2.0 * KAA * cA*cA + cA - concA) * (4.0 * KBB * cB + KAB *cA + 1.0) ) /det;+    /* yn  = ( (2.0 * KAA * cA*cA + KAB *cA *cB + cA - concA) * (KAB *cB) -+       (2.0 * KBB * cB*cB + KAB *cA *cB + cB - concB) * (4.0 * KAA * cA + KAB *cB + 1.0) ) /det; */+    yn  = ( (2.0 * KAA * cA*cA + cA - concA) * (KAB *cB) - KAB*cA*cB*(4. * KAA*cA + 1.) -+            (2.0 * KBB * cB*cB + cB - concB) * (4.0 * KAA * cA + KAB *cB + 1.0) ) /det;+    EPS = fabs(xn/cA) + fabs(yn/cB);+    cA += xn;+    cB += yn;+    i++;+    if (i>10000) {+      vrna_message_warning("Newton did not converge after %d steps!!",i);+      break;+    }+  } while(EPS>TOL);++  ConcVec[0] = cA*cB*KAB ;/*AB concentration*/+  ConcVec[1] = cA*cA*KAA ;/*AA concentration*/+  ConcVec[2] = cB*cB*KBB ;/*BB concentration*/+  ConcVec[3] = cA;        /* A concentration*/+  ConcVec[4] = cB;        /* B concentration*/++  return ConcVec;+}++PUBLIC vrna_dimer_conc_t *+vrna_pf_dimer_concentrations(double FcAB,+                              double FcAA,+                              double FcBB,+                              double FEA,+                              double FEB,+                              const double *startconc,+                              const vrna_exp_param_t *exp_params){++  /*takes an array of start concentrations, computes equilibrium concentrations of dimers, monomers, returns array of concentrations in strucutre vrna_dimer_conc_t*/+  double            *ConcVec;+  int               i;+  vrna_dimer_conc_t *Concentration;+  double            KAA, KAB, KBB, kT;++  kT            = exp_params->kT/1000.;+  Concentration = (vrna_dimer_conc_t *)vrna_alloc(20*sizeof(vrna_dimer_conc_t));+ /* Compute equilibrium constants */+  /* again note the input free energies are not from the null model (without DuplexInit) */++  KAA = exp(( 2.0 * FEA - FcAA)/kT);+  KBB = exp(( 2.0 * FEB - FcBB)/kT);+  KAB = exp(( FEA + FEB - FcAB)/kT);+  /* printf("Kaa..%g %g %g\n", KAA, KBB, KAB); */+  for (i=0; ((startconc[i]!=0)||(startconc[i+1]!=0));i+=2) {+    ConcVec                 = Newton_Conc(KAB, KAA, KBB, startconc[i], startconc[i+1], ConcVec);+    Concentration[i/2].A0   = startconc[i];+    Concentration[i/2].B0   = startconc[i+1];+    Concentration[i/2].ABc  = ConcVec[0];+    Concentration[i/2].AAc  = ConcVec[1];+    Concentration[i/2].BBc  = ConcVec[2];+    Concentration[i/2].Ac   = ConcVec[3];+    Concentration[i/2].Bc   = ConcVec[4];++    if (!(((i+2)/2)%20))  {+      Concentration = (vrna_dimer_conc_t *)vrna_realloc(Concentration,((i+2)/2+20)*sizeof(vrna_dimer_conc_t));+    }+    free(ConcVec);+  }++  return Concentration;+}+++#if 0+/*+  stochastic backtracking in pf_fold arrays+  returns random structure S with Boltzman probabilty+  p(S) = exp(-E(S)/kT)/Z+*/+PRIVATE void+backtrack_qm1(vrna_fold_compound_t *vc,+              int i,+              int j,+              char *pstruc){++  /* i is paired to l, i<l<j; backtrack in qm1 to find l */+  int           ii, l, type, *jindx, *my_iindx, *rtype, turn;+  double        qt, r;+  FLT_OR_DBL    *qm, *qm1, *qb, *expMLbase;+  short         *S1;+  char          *ptype;+  vrna_md_t     *md;++  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;++  pf_params     = vc->exp_params;+  md            = &(pf_params->model_details);+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype;+  rtype         = &(md->rtype[0]);+  turn          = md->min_loop_size;++  matrices      = vc->exp_matrices;+  qb            = matrices->qb;+  qm            = matrices->qm;+  qm1           = matrices->qm1;+  expMLbase     = matrices->expMLbase;++  jindx         = vc->jindx;+  my_iindx      = vc->iindx;++  r   = vrna_urn() * qm1[jindx[j]+i];+  ii  = my_iindx[i];+  for (qt=0., l=i+turn+1; l<=j; l++) {+    type = ptype[jindx[l] + i];+    if (type)+      qt +=  qb[ii-l]*exp_E_MLstem(type, S1[i-1], S1[l+1], pf_params) * expMLbase[j-l];+    if (qt>=r) break;+  }+  if (l>j) vrna_message_error("backtrack failed in qm1");+  backtrack(vc, i,l, pstruc);+}++PRIVATE void+backtrack(vrna_fold_compound_t *vc,+          int i,+          int j,+          char *pstruc){++  int           *jindx, *my_iindx, *rtype, turn;+  FLT_OR_DBL    *qm, *qm1, *qb, *expMLbase, *scale;+  vrna_exp_param_t  *pf_params;+  vrna_mx_pf_t      *matrices;+  short         *S1;+  char          *ptype, *sequence;+  int           noGUclosure;+  vrna_md_t     *md;++  sequence      = vc->sequence;+  pf_params     = vc->exp_params;+  md            = &(pf_params->model_details);+  S1            = vc->sequence_encoding;+  ptype         = vc->ptype;+  rtype         = &(md->rtype[0]);+  turn          = md->min_loop_size;++  matrices      = vc->exp_matrices;+  qb            = matrices->qb;+  qm            = matrices->qm;+  qm1           = matrices->qm1;+  expMLbase     = matrices->expMLbase;+  scale         = matrices->scale;+  jindx         = vc->jindx;+  my_iindx      = vc->iindx;+  noGUclosure   = pf_params->model_details.noGUclosure;++  do {+    double r, qbt1;+    int k, l, type, u, u1;++    pstruc[i-1] = '('; pstruc[j-1] = ')';++    r     = vrna_urn() * qb[my_iindx[i]-j];+    type  = ptype[jindx[j] + i];+    u     = j - i - 1;+    /*hairpin contribution*/+    if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;+    else+      qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params)*scale[u+2];++    if (qbt1>r) return; /* found the hairpin we're done */++    for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-turn-2); k++) {+      u1 = k-i-1;+      for (l=MAX2(k+turn+1,j-1-MAXLOOP+u1); l<j; l++) {+        int type_2;+        type_2 = ptype[jindx[l] + k];+        if (type_2) {+          type_2  =   rtype[type_2];+          qbt1    +=  qb[my_iindx[k]-l] *+            exp_E_IntLoop(u1, j-l-1, type, type_2,+                          S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params)*scale[u1+j-l+1];+        }+        if (qbt1 > r) break;+      }+      if (qbt1 > r) break;+    }+    if (l<j) {+      i=k; j=l;+    }+    else break;+  } while (1);++  /* backtrack in multi-loop */+  {+    double r, qt;+    int k, ii, jj;++    i++; j--;+    /* find the first split index */+    ii = my_iindx[i]; /* ii-j=[i,j] */+    jj = jindx[j]; /* jj+i=[j,i] */+    for (qt=0., k=i+1; k<j; k++) qt += qm[ii-(k-1)]*qm1[jj+k];+    r = vrna_urn() * qt;+    for (qt=0., k=i+1; k<j; k++) {+      qt += qm[ii-(k-1)]*qm1[jj+k];+      if (qt>=r) break;+    }+    if (k>=j) vrna_message_error("backtrack failed, can't find split index ");++    backtrack_qm1(vc, k, j, pstruc);++    j = k-1;+    while (j>i) {+      /* now backtrack  [i ... j] in qm[] */+      jj  = jindx[j];+      ii  = my_iindx[i];+      r   = vrna_urn() * qm[ii - j];+      qt  = qm1[jj+i]; k=i;+      if (qt<r)+        for (k=i+1; k<=j; k++) {+          qt += (qm[ii-(k-1)]+expMLbase[k-i])*qm1[jj+k];+          if (qt >= r) break;+        }+      if (k>j) vrna_message_error("backtrack failed in qm");++      backtrack_qm1(vc, k,j, pstruc);++      if (k<i+turn) break; /* no more pairs */+      r = vrna_urn() * (qm[ii-(k-1)] + expMLbase[k-i]);+      if (expMLbase[k-i] >= r) break; /* no more pairs */+      j = k-1;+    }+  }+}++#endif++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC vrna_dimer_pf_t+co_pf_fold(char *sequence, char *structure){++  return wrap_co_pf_fold(sequence, structure, NULL, do_backtrack, fold_constrained);+}++PUBLIC vrna_dimer_pf_t+co_pf_fold_par( char *sequence,+                char *structure,+                vrna_exp_param_t *parameters,+                int calculate_bppm,+                int is_constrained){++  return wrap_co_pf_fold(sequence, structure, parameters, calculate_bppm, is_constrained);+}+++PUBLIC vrna_plist_t *+get_plist(vrna_plist_t *pl,+          int length,+          double cut_off){++  int i, j,n, count, *my_iindx;++  my_iindx = backward_compat_compound->iindx;+  /*get pair probibilities out of pr array*/+  count=0;+  n=2;+  for (i=1; i<length; i++) {+    for (j=i+1; j<=length; j++) {+      if (pr[my_iindx[i]-j]<cut_off) continue;+      if (count==n*length-1) {+        n*=2;+        pl=(vrna_plist_t *)vrna_realloc(pl,n*length*sizeof(vrna_plist_t));+      }+      pl[count].i=i;+      pl[count].j=j;+      pl[count++].p=pr[my_iindx[i]-j];+      /*      printf("gpl: %2d %2d %.9f\n",i,j,pr[my_iindx[i]-j]);*/+    }+  }+  pl[count].i=0;+  pl[count].j=0; /*->??*/+  pl[count++].p=0.;+  pl=(vrna_plist_t *)vrna_realloc(pl,(count)*sizeof(vrna_plist_t));+  return pl;+}++PUBLIC void+compute_probabilities(double FAB,+                      double FA,+                      double FB,+                      vrna_plist_t *prAB,+                      vrna_plist_t *prA,+                      vrna_plist_t *prB,+                      int Alength) {++  if(backward_compat_compound && backward_compat){+    vrna_pf_dimer_probs(FAB, FA, FB, prAB, (const vrna_plist_t *)prA, (const vrna_plist_t *)prB, Alength, (const vrna_exp_param_t *)backward_compat_compound->exp_params);+  }+}++PUBLIC vrna_dimer_conc_t *+get_concentrations( double FcAB,+                    double FcAA,+                    double FcBB,+                    double FEA,+                    double FEB,+                    double *startconc){++  return vrna_pf_dimer_concentrations(FcAB, FcAA, FcBB, FEA, FEB, (const double *)startconc, (const vrna_exp_param_t *)backward_compat_compound->exp_params);+}++PUBLIC void+init_co_pf_fold(int length){++ /* DO NOTHING */+}++PUBLIC void+free_co_pf_arrays(void){++  if(backward_compat_compound && backward_compat){+    vrna_fold_compound_free(backward_compat_compound);+    backward_compat_compound  = NULL;+    backward_compat           = 0;+  }+}++PUBLIC FLT_OR_DBL *+export_co_bppm(void){++  if(backward_compat_compound)+    return backward_compat_compound->exp_matrices->probs;+  else+    return NULL;+}++/*----------------------------------------------------------------------*/+PUBLIC void+update_co_pf_params(int length){++  if(backward_compat_compound && backward_compat){+    vrna_md_t         md;+    set_model_details(&md);+    vrna_exp_params_reset(backward_compat_compound, &md);++    /* compatibility with RNAup, may be removed sometime */+    pf_scale = backward_compat_compound->exp_params->pf_scale;+  }+}++PUBLIC void+update_co_pf_params_par(int length,+                        vrna_exp_param_t *parameters){++  if(backward_compat_compound && backward_compat){+    vrna_md_t         md;+    if(parameters){+      vrna_exp_params_subst(backward_compat_compound, parameters);+    } else {+      set_model_details(&md);+      vrna_exp_params_reset(backward_compat_compound, &md);+    }++    /* compatibility with RNAup, may be removed sometime */+    pf_scale = backward_compat_compound->exp_params->pf_scale;+  }+}+
+ C/ViennaRNA/part_func_co.h view
@@ -0,0 +1,358 @@+#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_CO_H+#define VIENNA_RNA_PACKAGE_PART_FUNC_CO_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     part_func_co.h+ *  @ingroup  pf_fold cofold pf_cofold+ *  @brief    Partition function for two RNA sequences+ */++/**+ *  @addtogroup pf_cofold+ *  @brief Partition Function Cofolding+ *+ *  To simplify the implementation the partition function computation is done+ *  internally in a null model that does not include the duplex initiation+ *  energy, i.e. the entropic penalty for producing a dimer from two+ *  monomers). The resulting free energies and pair probabilities are initially+ *  relative to that null model. In a second step the free energies can be+ *  corrected to include the dimerization penalty, and the pair probabilities+ *  can be divided into the conditional pair probabilities given that a re+ *  dimer is formed or not formed. See @cite bernhart:2006 for further details.+ *+ *  As for folding one RNA molecule, this computes the partition function+ *  of all possible structures and the base pair probabilities. Uses the+ *  same global #pf_scale variable to avoid overflows.+ *+ *  To simplify the implementation the partition function computation is done+ *  internally in a null model that does not include the duplex initiation+ *  energy, i.e. the entropic penalty for producing a dimer from two+ *  monomers). The resulting free energies and pair probabilities are initially+ *  relative to that null model. In a second step the free energies can be+ *  corrected to include the dimerization penalty, and the pair probabilities+ *  can be divided into the conditional pair probabilities given that a re+ *  dimer is formed or not formed.+ *+ *  After computing the partition functions of all possible dimeres one+ *  can compute the probabilities of base pairs, the concentrations out of+ *  start concentrations and sofar and soaway.+ *+ *  Dimer formation is inherently concentration dependent. Given the free+ *  energies of the monomers A and B and dimers AB, AA, and BB one can compute+ *  the equilibrium concentrations, given input concentrations of A and B, see+ *  e.g. Dimitrov & Zuker (2004)+ *+ *  @{+ *  @ingroup  pf_cofold+ */++/** @brief Typename for the data structure that stores the dimer partition functions, #vrna_dimer_pf_s, as returned by vrna_pf_dimer() */+typedef struct vrna_dimer_pf_s  vrna_dimer_pf_t;++/** @brief Typename for the data structure that stores the dimer concentrations, #vrna_dimer_conc_s, as required by vrna_pf_dimer_concentration() */+typedef struct vrna_dimer_conc_s  vrna_dimer_conc_t;+++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Backward compatibility typedef for #vrna_dimer_pf_s+ */+typedef struct vrna_dimer_pf_s    cofoldF;++/**+ *  @brief Backward compatibility typedef for #vrna_dimer_conc_s+ */+typedef struct vrna_dimer_conc_s  ConcEnt;++#endif++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>++/**+ *  @brief Toggles no intrabp in 2nd mol+ */+extern int    mirnatog;++/**+ *  @brief Free energies of the two monomers+ */+extern double F_monomer[2];++/**+ *  @brief  Data structure returned by vrna_pf_dimer()+ */+struct vrna_dimer_pf_s {+  /* free energies for: */+  double F0AB;  /**< @brief Null model without DuplexInit */+  double FAB;   /**< @brief all states with DuplexInit correction */+  double FcAB;  /**< @brief true hybrid states only */+  double FA;    /**< @brief monomer A */+  double FB;    /**< @brief monomer B */+};++/**+ *  @brief  Data structure for concentration dependency computations+ */+struct vrna_dimer_conc_s {+  double A0;    /**< @brief start concentration A */+  double B0;    /**< @brief start concentration B */+  double ABc;   /**< @brief End concentration AB */+  double AAc;+  double BBc;+  double Ac;+  double Bc;+};++/**+ *  @brief  Calculate partition function and base pair probabilities of+ *          nucleic acid/nucleic acid dimers+ *+ *  This is the cofold partition function folding.+ *+ *  @see    vrna_fold_compound() for how to retrieve the necessary data structure+ *+ *  @param  vc        the fold compound data structure+ *  @param  structure Will hold the structure or constraints+ *  @return           vrna_dimer_pf_t structure containing a set of energies needed for+ *                    concentration computations.+ */+vrna_dimer_pf_t+vrna_pf_dimer(vrna_fold_compound_t *vc,+              char *structure);++/**+ *  @brief Compute Boltzmann probabilities of dimerization without homodimers+ *+ *  Given the pair probabilities and free energies (in the null model) for a+ *  dimer AB and the two constituent monomers A and B, compute the conditional pair+ *  probabilities given that a dimer AB actually forms.+ *  Null model pair probabilities are given as a list as produced by+ *  vrna_plist_from_probs(), the dimer probabilities 'prAB' are modified in place.+ *+ *  @param FAB        free energy of dimer AB+ *  @param FA         free energy of monomer A+ *  @param FB         free energy of monomer B+ *  @param prAB       pair probabilities for dimer+ *  @param prA        pair probabilities monomer+ *  @param prB        pair probabilities monomer+ *  @param Alength    Length of molecule A+ *  @param exp_params The precomputed Boltzmann factors+ */+void  vrna_pf_dimer_probs(double FAB,+                          double FA,+                          double FB,+                          vrna_plist_t *prAB,+                          const vrna_plist_t *prA,+                          const vrna_plist_t *prB,+                          int Alength,+                          const vrna_exp_param_t *exp_params);++/**+ *  @brief Given two start monomer concentrations a and b, compute the+ *  concentrations in thermodynamic equilibrium of all dimers and the monomers.+ *+ *  This function takes an array  'startconc' of input concentrations with alternating+ *  entries for the initial concentrations of molecules A and B (terminated by+ *  two zeroes), then computes the resulting equilibrium concentrations+ *  from the free energies for the dimers. Dimer free energies should be the+ *  dimer-only free energies, i.e. the FcAB entries from the #vrna_dimer_pf_t struct.+ *+ *  @param FcAB       Free energy of AB dimer (FcAB entry)+ *  @param FcAA       Free energy of AA dimer (FcAB entry)+ *  @param FcBB       Free energy of BB dimer (FcAB entry)+ *  @param FEA        Free energy of monomer A+ *  @param FEB        Free energy of monomer B+ *  @param startconc  List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0]+ *  @param exp_params The precomputed Boltzmann factors+ *  @return vrna_dimer_conc_t array containing the equilibrium energies and start concentrations+ */+vrna_dimer_conc_t *vrna_pf_dimer_concentrations(double FcAB,+                                      double FcAA,+                                      double FcBB,+                                      double FEA,+                                      double FEB,+                                      const double *startconc,+                                      const vrna_exp_param_t *exp_params);++/**+ *  @}+ */++/*+#################################################+# DEPRECATED FUNCTIONS                          #+#################################################+*/++/**+ *  @brief Calculate partition function and base pair probabilities+ *+ *  This is the cofold partition function folding. The second molecule starts+ *  at the #cut_point nucleotide.+ *+ *  @note OpenMP: Since this function relies on the global parameters+ *        #do_backtrack, #dangles, #temperature and #pf_scale it is not+ *        threadsafe according to concurrent changes in these variables!+ *        Use co_pf_fold_par() instead to circumvent this issue.+ *+ *  @deprecated{Use vrna_pf_dimer() instead!}+ *+ *  @param  sequence  Concatenated RNA sequences+ *  @param  structure Will hold the structure or constraints+ *  @return           vrna_dimer_pf_t structure containing a set of energies needed for+ *                    concentration computations.+ */+DEPRECATED(vrna_dimer_pf_t co_pf_fold( char *sequence, char *structure));++/**+ *  @brief Calculate partition function and base pair probabilities+ *+ *  This is the cofold partition function folding. The second molecule starts+ *  at the #cut_point nucleotide.+ *+ *  @deprecated Use vrna_pf_dimer() instead!+ *+ *  @see get_boltzmann_factors(), co_pf_fold()+ *+ *  @param sequence       Concatenated RNA sequences+ *  @param structure      Pointer to the structure constraint+ *  @param parameters     Data structure containing the precalculated Boltzmann factors+ *  @param calculate_bppm Switch to turn Base pair probability calculations on/off (0==off)+ *  @param is_constrained Switch to indicate that a structure contraint is passed via the+ *                        structure argument (0==off)+ *  @return               vrna_dimer_pf_t structure containing a set of energies needed for+ *                        concentration computations.+ */+DEPRECATED(vrna_dimer_pf_t co_pf_fold_par(char *sequence, char *structure, vrna_exp_param_t *parameters, int calculate_bppm, int is_constrained));++/**+ *  DO NOT USE THIS FUNCTION ANYMORE+ *  @deprecated{ This function is deprecated and will be removed soon!}+ *  use assign_plist_from_pr() instead!+ */+DEPRECATED(vrna_plist_t  *get_plist( vrna_plist_t *pl,+                              int length,+                              double cut_off));++/**+ *  @brief Compute Boltzmann probabilities of dimerization without homodimers+ *+ *  Given the pair probabilities and free energies (in the null model) for a+ *  dimer AB and the two constituent monomers A and B, compute the conditional pair+ *  probabilities given that a dimer AB actually forms.+ *  Null model pair probabilities are given as a list as produced by+ *  assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place.+ *+ *  @deprecated{ Use vrna_pf_dimer_probs() instead!}+ *+ *  @param FAB      free energy of dimer AB+ *  @param FEA      free energy of monomer A+ *  @param FEB      free energy of monomer B+ *  @param prAB     pair probabilities for dimer+ *  @param prA      pair probabilities monomer+ *  @param prB      pair probabilities monomer+ *  @param Alength  Length of molecule A+ */+DEPRECATED(void compute_probabilities(double FAB, double FEA, double FEB, vrna_plist_t  *prAB, vrna_plist_t  *prA, vrna_plist_t  *prB, int Alength));++/**+ *  @brief Given two start monomer concentrations a and b, compute the+ *  concentrations in thermodynamic equilibrium of all dimers and the monomers.+ *+ *  This function takes an array  'startconc' of input concentrations with alternating+ *  entries for the initial concentrations of molecules A and B (terminated by+ *  two zeroes), then computes the resulting equilibrium concentrations+ *  from the free energies for the dimers. Dimer free energies should be the+ *  dimer-only free energies, i.e. the FcAB entries from the #vrna_dimer_pf_t struct.+ *+ *  @deprecated{ Use vrna_pf_dimer_concentrations() instead!}+ *+ *  @param FEAB       Free energy of AB dimer (FcAB entry)+ *  @param FEAA       Free energy of AA dimer (FcAB entry)+ *  @param FEBB       Free energy of BB dimer (FcAB entry)+ *  @param FEA        Free energy of monomer A+ *  @param FEB        Free energy of monomer B+ *  @param startconc  List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0]+ *  @return vrna_dimer_conc_t array containing the equilibrium energies and start concentrations+ */+DEPRECATED(vrna_dimer_conc_t *get_concentrations(double FEAB, double FEAA, double FEBB, double FEA, double FEB, double *startconc));++/**+ *  DO NOT USE THIS FUNCTION ANYMORE+ *  @deprecated{ This function is deprecated and will be removed soon!}+ */+DEPRECATED(void   init_co_pf_fold(int length));++/**+ *  @brief Get a pointer to the base pair probability array+ *+ *  Accessing the base pair probabilities for a pair (i,j) is achieved by+ *  @verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; @endverbatim+ *+ *  @deprecated This function is deprecated and will be removed soon! The base pair+ *              probability array is available through the #vrna_fold_compound_t data+ *              structure, and its associated #vrna_mx_pf_t member.+ *+ *  @see vrna_idx_row_wise()+ *  @return A pointer to the base pair probability array+ */+DEPRECATED(FLT_OR_DBL *export_co_bppm(void));++/**+ *  @brief Free the memory occupied by co_pf_fold()+ *+ *  @deprecated This function will be removed for the new API soon!+ *              See vrna_pf_dimer(), vrna_fold_compound(), and+ *              vrna_fold_compound_free() for an alternative+ */+DEPRECATED(void free_co_pf_arrays(void));++/**+ *  @brief Recalculate energy parameters+ *+ *  This function recalculates all energy parameters given+ *  the current model settings.+ *+ *  @deprecated   Use vrna_exp_params_subst() instead!+ *+ *  @param    length      Length of the current RNA sequence+ */+DEPRECATED(void update_co_pf_params(int length));++/**+ *  @brief Recalculate energy parameters+ *+ *  This function recalculates all energy parameters given+ *  the current model settings.+ *  It's second argument can either be NULL or a data structure+ *  containing the precomputed Boltzmann factors. In the first+ *  scenario, the necessary data structure will be created automatically+ *  according to the current global model settings, i.e. this+ *  mode might not be threadsafe.+ *  However, if the provided data structure is not NULL, threadsafety+ *  for the model parameters #dangles, #pf_scale and #temperature is regained, since their+ *  values are taken from this data structure during subsequent calculations.+ *+ *  @deprecated   Use vrna_exp_params_subst() instead!+ *+ *  @param    length      Length of the current RNA sequence+ *  @param    parameters  data structure containing the precomputed Boltzmann factors+ */+DEPRECATED(void update_co_pf_params_par(int length, vrna_exp_param_t *parameters));++#endif
+ C/ViennaRNA/part_func_up.c view
@@ -0,0 +1,1466 @@+/*+                  partiton function for RNA secondary structures++                  Ivo L Hofacker++                  Vienna RNA package+*/+/*+  $Log: part_func_up.c,v $+  Revision 1.4  2008/07/04 14:27:36  ivo+  Modify output (again)++  Revision 1.3  2008/05/08 14:11:55  ivo+  minor output changes++  Revision 1.2  2007/12/13 10:19:54  ivo+  major RNAup update from Ulli++  Revision 1.1  2007/04/30 15:13:13  ivo+  merge RNAup into package++  Revision 1.11  2006/07/17 11:11:43  ulim+  removed all globals from fold_vars.h,c, cleaned code++  Revision 1.10  2006/07/12 09:19:29  ulim+  global variables w, incr3 and incr5 are now local++  Revision 1.9  2006/07/11 12:45:02  ulim+  remove redundancy in function pf_interact(...)++  Revision 1.8  2006/03/08 15:26:37  ulim+  modified -o[1|2], added meaningful default++  Revision 1.5  2006/01/23 11:27:04  ulim+  include file into new package version. cleaned it++  Revision 1.2  2005/07/29 15:13:37  ulim+  put the function, calculating the probability of an unpaired region in+  an RNA and the function calculating the prob. of interaction between 2 RNAs+  in a seperate file (pf_two.c)++  Revision 1.1  2005/07/26 13:27:12  ulim+  Initial revision++  Revision 1.2  2005/07/01 13:14:57  ulim+  fixed error in scaling, included new commandline options -incr5, -incr3 to+  allow a variable number of unpaired positions 5' and 3' of the site of+  interaction between the two RNAs++  Revision 1.1  2005/04/19 08:16:38  ulim+  Initial revision+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>+#include <float.h>    /* #defines FLT_MAX ... */+#include <unistd.h>+#include "ViennaRNA/fold.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/part_func.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/part_func_up.h"+#include "ViennaRNA/duplex.h"+++#define CO_TURN 0+#define ZERO(A) (fabs(A) < DBL_EPSILON)+#define EQUAL(A,B) (fabs((A)-(B)) < 1000*DBL_EPSILON)+#define ISOLATED  256.0+/* #define NUMERIC 1 */++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE short       *S=NULL, *S1=NULL, *SS=NULL, *SS2=NULL;+PRIVATE vrna_exp_param_t   *Pf = NULL;/* use this structure for all the exp-arrays*/+PRIVATE FLT_OR_DBL  *qb=NULL, *qm=NULL, *prpr=NULL; /* add arrays for pf_unpaired()*/+PRIVATE FLT_OR_DBL  *probs=NULL;+PRIVATE FLT_OR_DBL  *q1k=NULL, *qln=NULL;+PRIVATE double      *qqm2=NULL, *qq_1m2=NULL, *qqm=NULL, *qqm1=NULL;+PRIVATE FLT_OR_DBL  *scale=NULL, *expMLbase=NULL;+PRIVATE char        *ptype=NULL; /* precomputed array of pair types */+PRIVATE int         init_length;  /* length in last call to init_pf_fold()*/+PRIVATE double      init_temp; /* temperature in last call to scale_pf_params */+PRIVATE int         *my_iindx = NULL;+/* make iptypes array for intermolecular constrains (ipidx for indexing)*/+++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE pu_out      *get_u_vals(pu_contrib *p_c,+                                int **unpaired_values,+                                char *select_contrib);++PRIVATE int         plot_free_pu_out( pu_out* res,+                                      interact *pint,+                                      char *ofile,+                                      char *head);++PRIVATE void        scale_stru_pf_params(unsigned int length);++PRIVATE void        init_pf_two(int length);++PRIVATE void        scale_int(const char *s,+                              const char *sl,+                              double *sc_int);++PRIVATE void        encode_seq( const char *s1,+                                const char *s2);++PRIVATE constrain   *get_ptypes_up(char *S,+                                const char *structure);++PRIVATE void        get_up_arrays(unsigned int length);++PRIVATE void        free_up_arrays(void);++PRIVATE void        set_encoded_seq(const char *sequence,+                                    short **S,+                                    short **S1);++PRIVATE void        get_interact_arrays(unsigned int n1,+                                        unsigned int n2,+                                        pu_contrib *p_c,+                                        pu_contrib *p_c2,+                                        int w,+                                        int incr5,+                                        int incr3,+                                        double ***p_c_S,+                                        double ***p_c2_S);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC pu_contrib *get_pu_contrib_struct(unsigned int n, unsigned int w){+  unsigned int i;+  pu_contrib  *pu = (pu_contrib *)vrna_alloc(sizeof(pu_contrib));+  pu->length      = n;+  pu->w           = w;+  /* contributions to probability of being unpaired witihin a(n)+   H hairpin,+   I interior loop,+   M muliloop,+   E exterior loop*/+  /* pu_test->X[i][j] where i <= j and i [1...n], j = [1...w[ */+  pu->H           = (double **)vrna_alloc(sizeof(double *) * (n + 1));+  pu->I           = (double **)vrna_alloc(sizeof(double *) * (n + 1));+  pu->M           = (double **)vrna_alloc(sizeof(double *) * (n + 1));+  pu->E           = (double **)vrna_alloc(sizeof(double *) * (n + 1));+  for(i=0;i<=n;i++){+    pu->H[i]  = (double *)vrna_alloc(sizeof(double) * (w + 1));+    pu->I[i]  = (double *)vrna_alloc(sizeof(double) * (w + 1));+    pu->M[i]  = (double *)vrna_alloc(sizeof(double) * (w + 1));+    pu->E[i]  = (double *)vrna_alloc(sizeof(double) * (w + 1));+  }+  return pu;+}++PUBLIC  void+free_pu_contrib(pu_contrib *pu){++  free_pu_contrib_struct(pu);+}++PUBLIC  void+free_pu_contrib_struct(pu_contrib *pu){++  unsigned int i;+  if(pu != NULL){+    for(i=0;i<=pu->length;i++){+      free(pu->H[i]);+      free(pu->I[i]);+      free(pu->M[i]);+      free(pu->E[i]);+    }+    free(pu->H);+    free(pu->I);+    free(pu->M);+    free(pu->E);+    free(pu);+  }+}++/* you have to call pf_fold(sequence, structure); befor pf_unstru */+PUBLIC pu_contrib *pf_unstru(char *sequence, int w){+  int           n, i, j, v, k, l, o, p, ij, kl, po, u, u1, d, type, type_2, tt;+  unsigned int  size;+  double        temp, tqm2;+  double        qbt1, *tmp, sum_l, *sum_M;+  double        *store_H, *store_Io, **store_I2o; /* hairp., interior contribs */+  double        *store_M_qm_o,*store_M_mlbase;    /* multiloop contributions */+  pu_contrib    *pu_test;++  sum_l           = 0.0;+  temp            = 0;+  n               = (int) strlen(sequence);+  sum_M           = (double *)  vrna_alloc((n+1) * sizeof(double));+  pu_test         = get_pu_contrib_struct((unsigned)n, (unsigned)w);+  size            = ((n+1)*(n+2))>>1;++  get_up_arrays((unsigned) n);+  init_pf_two(n);++  /* init everything */+  for (d=0; d<=TURN; d++)+    for (i=1; i<=n-d; i++){+      j=i+d;+      ij = my_iindx[i]-j;+      if(d < w) {+        pu_test->H[i][d]=pu_test->I[i][d]=pu_test->M[i][d]=pu_test->E[i][d]=0.;+      }+    }+++  for (i=0; i<size; i++)+    prpr[i]= probs[i];++  sum_M[0] = 0.;+  for (i=1; i<=n; i++){+    /* set auxillary arrays to 0, reuse qqm and qqm1, reuse qqm2 and qq_1m2*/+    sum_M[i] = qqm[i] = qqm1[i] = qqm2[i] = qq_1m2[i] = 0;+    for (j=i+TURN+1; j<=n; j++){+      ij = my_iindx[i]-j;+      /* i need the part_func of all structures outside bp[ij] */+      if(qb[ij] > 0.0) prpr[ij]= (probs[ij]/qb[ij]);+    }+  }++  /* alloc even more memory */+  store_I2o = (double **)vrna_alloc(sizeof(double *) * (n + 1)); /* for p,k */+  for(i=0;i<=n;i++)+    store_I2o[i] = (double *)vrna_alloc(sizeof(double) * (MAXLOOP + 2));++  /* expMLbase[i-p]*dangles_po */+  store_M_mlbase = (double *)vrna_alloc(sizeof(double) * (size + 1));++  /* 2. exterior bp (p,o) encloses unpaired region [i,i+w[*/+  for (o=TURN+2;o<=n; o++) {+    double sum_h;+    /*allocate space for arrays to store different contributions to H, I & M */+    store_H       = (double *)vrna_alloc(sizeof(double) * (o+2));+    /* unpaired between ]l,o[ */+    store_Io      = (double *)vrna_alloc(sizeof(double) * (o+2));+    /* qm[p+1,i-1]*dangles_po */+    store_M_qm_o  = (double *)vrna_alloc(sizeof(double) * (n+1));++    for (p=o-TURN-1; p>=1; p--) {+      /* construction of partition function of segment [p,o], given that+         an unpaired region [i,i+w[ exists within [p,o] */+      u = o-p-1;+      po = my_iindx[p]-o;+      type = ptype[po];+      if(type){++        /*hairpin contribution*/+        if (((type==3)||(type==4))&&no_closingGU)+          temp = 0.;+        else+          temp = prpr[po] * exp_E_Hairpin(u, type, S1[p+1], S1[o-1], sequence+p-1, Pf) * scale[u+2];+        /* all H contribs are collect for the longest unpaired region */+        store_H[p+1] = temp;++        /* interior loops with interior pair k,l and an unpaired region of+         length w between p and k || l and o*/+        for (k=p+1; k<=MIN2(p+MAXLOOP+1,o-TURN-2); k++) {+          u1    = k-p-1;+          sum_l = 0.;+          for (l=MAX2(k+TURN+1,o-1-MAXLOOP+u1); l<o; l++) {+            kl      = my_iindx[k]-l;+            type_2  = ptype[kl];+            if((l+1) < o) store_Io[l+1] += sum_l;++            temp=0.;+            if (type_2){+              type_2 = rtype[type_2];+              temp = prpr[po] * qb[kl] * exp_E_IntLoop(u1, o-l-1, type, type_2, S1[p+1], S1[o-1], S1[k-1], S1[l+1], Pf) *scale[u1+o-l+1];+              if((l+1) < o) store_Io[l+1] += temp; /* unpaired region between ]l,o[ */+              sum_l += temp;+            } /* end of if pair(k,l) */+          } /* end of l */+          /* unpaired in region ]p,k[  */+          for(i=p+1;i <= k-1;i++)+            store_I2o[i][MIN2(w-1,k-i-1)] += sum_l;+        } /* end of k */+      } /*end of if(type) test for bp (p,o) */++      /* multiple stem loop contribution+         calculate qm2[my_iindx[i]-j] in the course of the calculation+         of the multiple stem loop contribution:+         advantage: you save memory:+         instead of a (n+1)*n array for qqm2 you only need 2*n arrays+         disadvantage: you have to use two times the op-loop for the full+         multiloop contribution+         first op-loop: index o goes from 1...n and+                        index p from o-TURN-1 ... 1+         second op-loop: index o goes from n...1 and+                         index p from o+TURN+1 ... n !!+         HERE index o goes from 1...n and index p o-TURN-1 ... 1 ,+         we calculate the contributions to multiple stem loop+         where exp(i+w-1-p)*(qqm2 values between i+w and o-1)+         AND qm[iindex[p+1]-(i-1)]*exp(beta*w)*qm[iindex[i+w]-(o-1)]+         you have to recalculate of qqm matrix containing final stem+         contributions to multiple loop partition function+         from segment p,o */++      /* recalculate qqm[]+         qqm[p] := (contribution with exact one loop in region (p,o)*/+      qqm[p]  = qqm1[p] * expMLbase[1];+      if(type){+        qbt1    =   qb[po] * exp_E_MLstem(type, (p>1) ? S1[p-1] : -1, (o<n) ? S1[o+1] : -1, Pf);+        qqm[p]  +=  qbt1;+        /* reverse dangles for prpr[po]*... */+        temp    =   0.;+        tt      =   rtype[type];+        temp    =   prpr[po] * exp_E_MLstem(tt, S1[o-1], S1[p+1], Pf) * scale[2] * Pf->expMLclosing;+        for(i=p+1; i < o; i++) {+          int p1i = (p+1) < (i-1)  ? my_iindx[p+1]-(i-1)  : 0;+          /*unpaired region expMLbase[i-p] left of structured+            region qq_1m2[i+1]*/+          /* @expMLbase:  note distance of i-p == i-(p+1)+1 */+          store_M_mlbase[my_iindx[p+1]-i] += expMLbase[i-p] * temp * qq_1m2[i+1];+          /* structured region qm[p1i] left of unpaired region */+          /* contribition for unpaired region is added after the p-loop */+          store_M_qm_o[i] += qm[p1i] * temp;+        } /*end of for i ... */+      }++      for(tqm2 = 0., i=p+1; i < o; i++)+        tqm2  +=  qm[my_iindx[p]-i] * qqm[i+1];++      /* qqm2[p] contrib with at least 2 loops in region (p,o) */+      qqm2[p] = tqm2;+    } /* end for (p=..) */++    for(sum_h = 0., i=1; i < o; i++) {+      int max_v, vo;+      sum_h +=  store_H[i];+      max_v =   MIN2(w-1,o-i-1);+      for(v=max_v; v >= 0; v--){+        /* Hairpins */+        pu_test->H[i][v] += sum_h;/* store_H[i][v] + store_H[i][max_v]; */+        /* Interior loops: unpaired region between  ]l,o[ calculated here !*/+        /* unpaired region between ]p,k[ collected after after o-loop */+        if(v <= MIN2(max_v,MAXLOOP)) {+          pu_test->I[i][v] += store_Io[i]; /* ]l,o[ */+        }+        /* Multiloops:*/+        /* unpaired region [i,v] between structured regions ]p,i[ and ]v,o[. */+        /* store_M_qm_o[i] = part. funct over all structured regions ]p,i[ */+        vo = (i+v+1) <= (o-1) ? my_iindx[i+v+1]-(o-1): 0;+        pu_test->M[i][v] += store_M_qm_o[i]*expMLbase[v+1]*qm[vo];+      }+    }+    tmp = qqm1; qqm1=qqm; qqm=tmp;+    tmp = qqm2; qqm2=qq_1m2; qq_1m2=tmp;++    free(store_Io);+    free(store_H);+    free(store_M_qm_o);+  }/* end for (o=..) */++  for(i=1; i < n; i++) {+    int     max_v;+    double  sum_iv;+    sum_iv  = 0.;+    max_v   = MIN2(w-1,n-i);+    for(v=n; v >=0; v--) {+      if(v <= MIN2(max_v,MAXLOOP)) {+        /* all unpaired regions [i,v] between p and k in interior loops */+        /* notice v runs from max_v -> 0, sum_iv sums all int. l. contribs */+        /* for each x, v < x =< max_v, since they contribute to [i,v] */+        sum_iv            += store_I2o[i][v];+        pu_test->I[i][v]  += sum_iv;+      }+      /* all unpaired region [i,v] for a fixed v, given that */+      /* region ]v,o[ contains at least 2 structures qq_1m2[v+1]; */+      if(v >= i) {+        sum_M[v] += store_M_mlbase[my_iindx[i]-v];+        if(v-i<=max_v) {+          pu_test->M[i][v-i] += sum_M[v];+        }+      }+    }+  }++  for(i=0;i<=n;i++) {+    free(store_I2o[i]);+  }+  free(store_I2o);++  for (i=1; i<=n; i++) {+    /* set auxillary arrays to 0 */+    qqm[i] = qqm1[i] = qqm2[i] = qq_1m2[i] = 0;+  }++  /* 2. exterior bp (p,o) encloses unpaired region [i,j]+     HERE index o goes from n...1 and index p from o+TURN+1 ... n,+     that is, we add the one multiloop contribution that we+     could not calculate before  */++/* is free'ing plus allocating faster than looping over all entries an setting them to 0? */+#if 0+  free(store_M_mlbase);+  store_M_mlbase = (double *) vrna_alloc(sizeof(double) * (size + 1));+#else+  /* this should be the fastest way to set everything to 0 */+  memset(store_M_mlbase, 0, sizeof(double) * (size + 1));+#endif++  for (o=n-TURN-1;o>=1; o--) {+    for (p=o+TURN+1; p<=n; p++) {+      po    = my_iindx[o]-p;+      type  = ptype[po];+      /* recalculate of qqm matrix containing final stem+         contributions to multiple loop partition function+         from segment [o,p] */+      qqm[p] = qqm1[p] * expMLbase[1];+      if (type) {+        qbt1 = qb[po];+        qbt1 *= exp_E_MLstem(type, (o>1) ? S1[o-1] : -1, (p<n) ? S1[p+1] : -1, Pf);+        qqm[p] += qbt1;+        /* revers dangles for prpr[po]...  */+        temp=0.;+        tt=rtype[type];+        temp = prpr[po]*exp_E_MLstem(tt, S1[p-1], S1[o+1], Pf) * Pf->expMLclosing * scale[2];+      }+      tqm2=0.;+      for(i=o+1; i < p; i++) {+        tqm2+=qqm[i]*qm[my_iindx[i+1]-p];++        if(type !=0) {+          /* structured region qq_1m2[i-1] left of unpaired r. expMLbase[p-i]*/+          /* @expMLbase:  note distance of p-i == p+1-i+1 */+           store_M_mlbase[my_iindx[i]-p+1] +=  qq_1m2[i-1]*expMLbase[p-i]*temp;+        }+      }/*end of for i ....*/+      qqm2[p] = tqm2;+    }/* end for (p=..) */+    tmp = qqm1; qqm1=qqm; qqm=tmp;+    tmp = qqm2; qqm2=qq_1m2; qq_1m2=tmp;+  }/* end for (o=..) */+  /* now collect the missing multiloop contributions */+  for(i=0;i<=n;i++) { sum_M[i]=0.; }+  for(i=1; i<=n;i++) {+    int v_max = MIN2(w-1,n-i);+    for(v=n; v>=i; v--){+      sum_M[i]  += store_M_mlbase[my_iindx[i]-v];+      if ((v-i <= v_max) ) {+        pu_test->M[i][v-i] += sum_M[i];+      }+    }+  }++  /* 1. region [i,j] exterior to all loops */+  for (i=1; i<=n; i++) {+    for(j=i; j<MIN2(i+w,n+1);j++){+      ij=my_iindx[i]-j;+      temp=q1k[i-1]*1*scale[j-i+1]*qln[j+1]/q1k[n];+      pu_test->E[i][j-i]+=temp;++    }+  }++  free(sum_M);+  free(store_M_mlbase);+  free_up_arrays();+  return pu_test;+}+++PRIVATE void  get_interact_arrays(unsigned int n1,+                                  unsigned int n2,+                                  pu_contrib *p_c,+                                  pu_contrib *p_c2,+                                  int w,+                                  int incr5,+                                  int incr3,+                                  double ***p_c_S,+                                  double ***p_c2_S){++  unsigned int i;+  int pc_size, j;+  *p_c_S = (double **)vrna_alloc(sizeof(double *)*(n1+1));++  for (i=1; i<=n1; i++){+    pc_size = MIN2((w + incr5 + incr3), (int)n1);+    (*p_c_S)[i] = (double *)vrna_alloc(sizeof(double) * (pc_size + 1));+    for (j=0; j < pc_size; j++)+      (*p_c_S)[i][j] = p_c->H[i][j] + p_c->I[i][j] + p_c->M[i][j] + p_c->E[i][j];+  }++  if(p_c2 != NULL){+    (*p_c2_S) = (double **)vrna_alloc(sizeof(double *) * (n2 + 1));+    for (i=1; i<=n2; i++){+      pc_size = MIN2(w, (int)n2);+      (*p_c2_S)[i]  = (double *)vrna_alloc(sizeof(double) * (pc_size + 2));+      for (j=0; j < pc_size; j++)+        (*p_c2_S)[i][j] = p_c2->H[i][j] + p_c2->I[i][j] + p_c2->M[i][j] + p_c2->E[i][j];+    }+  }+}++/*------------------------------------------------------------------------*/+/* s1 is the longer seq */+PUBLIC interact *pf_interact( const char *s1,+                              const char *s2,+                              pu_contrib *p_c,+                              pu_contrib *p_c2,+                              int w,+                              char *cstruc,+                              int incr3,+                              int incr5){++  int         i, j, k,l,n1,n2,add_i5,add_i3, pc_size;+  double      temp, Z, rev_d, E, Z2,**p_c_S, **p_c2_S, int_scale;+  FLT_OR_DBL  ****qint_4, **qint_ik;+  /* PRIVATE double **pint; array for pf_up() output */+  interact    *Int;+  double      G_min, G_is,Gi_min;+  int         gi,gj,gk,gl,ci,cj,ck,cl,prev_k,prev_l;+  FLT_OR_DBL  **int_ik;+  double      Z_int, temp_int, temppfs;+  double      const_scale, const_T;+  constrain   *cc = NULL;  /* constrains for cofolding */+  char        *Seq, *i_long,*i_short,*pos=NULL; /* short seq appended to long one */+  /* int ***pu_jl; */ /* positions of interaction in the short RNA */++  G_min = G_is = Gi_min = 100.0;+  gi = gj = gk = gl = ci = cj = ck = cl = 0;++  n1      = (int) strlen(s1);+  n2      = (int) strlen(s2);+  prev_k  = 1;+  prev_l  = n2;++  i_long  = (char *) vrna_alloc(sizeof(char)*(n1+1));+  i_short = (char *) vrna_alloc(sizeof(char)*(n2+1));+  Seq     = (char *) vrna_alloc(sizeof(char)*(n1+n2+2));++  strcpy(Seq,s1);+  strcat(Seq,s2);++  set_encoded_seq(s1, &S, &S1);+  set_encoded_seq(s2, &SS, &SS2);++  cc = get_ptypes_up(Seq,cstruc);++  get_interact_arrays(n1, n2, p_c, p_c2, w, incr5, incr3, &p_c_S, &p_c2_S);++  /*array for pf_up() output */+  Int = (interact *) vrna_alloc(sizeof(interact)*1);+  Int->Pi = (double *) vrna_alloc(sizeof(double)*(n1+2));+  Int->Gi = (double *) vrna_alloc(sizeof(double)*(n1+2));++  /* use a different scaling for pf_interact*/+  scale_int(s2, s1, &int_scale);++  /* set the global scale array and the global variable pf_scale to the+     values used to scale the interaction, keep their former values !! */+  temppfs = pf_scale;+  pf_scale = int_scale;++  /* in order to scale expLoopEnergy correctly call*/+  /* we also pass twice the seq-length to avoid bogus access to scale[] array */+  scale_stru_pf_params((unsigned) 2*n1);++  qint_ik = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *) * (n1+1));+  for (i=1; i<=n1; i++) {+    qint_ik[i] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n1+1));+  }+/* int_ik */+  int_ik = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL *) * (n1+1));+  for (i=1; i<=n1; i++) {+    int_ik[i] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (n1+1));+  }+  Z_int=0.;+  /*  Gint = ( -log(int_ik[gk][gi])-( ((int) w/2)*log(pf_scale)) )*((Pf->temperature+K0)*GASCONST/1000.0); */+  const_scale = ((int) w/2)*log(pf_scale);+  const_T = (Pf->kT/1000.0);+  encode_seq(s1, s2);+  /* static  short *S~S1, *S1~SS1, *SS~S2, *SS2; */+  for (i=0; i<=n1; i++) {+    Int->Pi[i]=Int->Gi[i]=0.;+  }+  E=0.;+  Z=0.;++  if ( fold_constrained && cstruc != NULL) {+    pos = strchr(cstruc,'|');+    if(pos) {+      ci=ck=cl=cj=0;+      /* long seq              & short seq+         .........||..|||||....&....||||...  w = maximal interaction length+                 ck       ci       cj  cl    */+      strncpy(i_long,cstruc,n1);+      i_long[n1] = '\0';+      strncpy(i_short,&cstruc[n1],n2);+      i_short[n2] ='\0';+      pos = strchr(i_long,'|');+      if(pos) ck = (int) (pos-i_long)+1; /* k */+      pos = strrchr(i_long,'|');+      if(pos) ci = (int) (pos-i_long)+1; /* i */+      pos = strrchr(i_short,'|');+      if(pos) cl = (int) (pos-i_short)+1; /* l */+      pos = strchr(i_short,'|');+      if(pos) cj = (int) (pos-i_short)+1; /* j */++      if(ck > 0 && ci > 0 && ci-ck+1 > w) {+        vrna_message_warning("distance between constrains in longer seq, %d, larger than -w = %d",ci-ck+1,w);+        vrna_message_error("pf_interact: could not satisfy all constraints");+      }+      if(cj > 0 && cl > 0 && cl-cj+1 > w) {+        vrna_message_warning("distance between constrains in shorter seq, %d, larger than -w = %d",cl-cj+1,w);+        vrna_message_error("pf_interact: could not satisfy all constraints");+      }+    }++  } else if ( fold_constrained && cstruc == NULL) {+    vrna_message_error("option -C selected, but no constrained structure given\n");+  }+  if(fold_constrained) pos = strchr(cstruc,'|');++  /*  qint_4[i][j][k][l] contribution that region (k-i) in seq1 (l=n1)+      is paired to region (l-j) in seq 2(l=n2) that is+      a region closed by bp k-l  and bp i-j */+  qint_4 = (FLT_OR_DBL ****) vrna_alloc(sizeof(FLT_OR_DBL ***) * (n1+1));++  /* qint_4[i][j][k][l] */+  for (i=1; i<=n1; i++) {+    int end_k;+    end_k = i-w;+    if(fold_constrained && pos && ci) end_k= MAX2(i-w, ci-w);+    /* '|' constrains for long sequence: index i from 1 to n1 (5' to 3')*/+    /* interaction has to include 3' most '|' constrain, ci */+    if(fold_constrained && pos && ci && i==1 && i<ci)+      i= ci-w+1 > 1 ? ci-w+1 : 1;+    /* interaction has to include 5' most '|' constrain, ck*/+    if(fold_constrained && pos && ck && i > ck+w-1) break;++    /* note: qint_4[i] will be freed before we allocate qint_4[i+1] */+    qint_4[i] = (FLT_OR_DBL ***) vrna_alloc(sizeof(FLT_OR_DBL **) * (n2+1));+    for (j=n2; j>0; j--) {+      qint_4[i][j] = (FLT_OR_DBL **) vrna_alloc(sizeof(FLT_OR_DBL*) * (w+1));+      for (k=0; k<=w; k++) {+        qint_4[i][j][k] = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL) * (w+1));+      }+    }++     prev_k=1;+    for (j=n2; j>0; j--) {+      int type, type2,end_l;+      end_l = j+w;+      if(fold_constrained && pos && ci) end_l= MIN2(cj+w,j+w);+      /* '|' constrains for short sequence: index j from n2 to 1 (3' to 5')*/+      /* interaction has to include 5' most '|' constrain, cj */+      if(fold_constrained && pos && cj && j==n2 && j>cj)+        j = cj+w-1 > n2 ? n2 : cj+w-1;+      /* interaction has to include 3' most '|' constrain, cl*/+      if(fold_constrained && pos && cl && j < cl-w+1) break;+      type = cc->ptype[cc->indx[i]-(n1+j)];+      qint_4[i][j][0][0] = type ? Pf->expDuplexInit : 0;++      if (!type) continue;+      qint_4[i][j][0][0] *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, Pf);++      rev_d = exp_E_ExtLoop(rtype[type], (j>1) ? SS2[j-1] : -1, (i<n1) ? S1[i+1] : -1, Pf);++      /* add inc5 and incr3 */+      if((i-incr5) > 0 ) add_i5=i-incr5;+      else add_i5=1;+      add_i3=incr3;+      pc_size = MIN2((w+incr3+incr5),n1);+      if(incr3 < pc_size) add_i3=incr3;+      else add_i3=pc_size-1;++      /* only one bp (no interior loop) */+      if(p_c2 == NULL) {/* consider only structure of longer seq. */+        qint_ik[i][i]+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*scale[((int) w/2)];+        Z+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*scale[((int) w/2)];+      } else {/* consider structures of both seqs. */+        qint_ik[i][i]+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*p_c2_S[j][0]*scale[((int) w/2)];+        Z+=qint_4[i][j][0][0]*rev_d*p_c_S[add_i5][add_i3]*p_c2_S[j][0]*scale[((int) w/2)];+      }++/* int_ik */+      /* check deltaG_ges = deltaG_int + deltaG_unstr; */+      int_ik[i][i]+=qint_4[i][j][0][0]*rev_d*scale[((int) w/2)];+      Z_int+=qint_4[i][j][0][0]*rev_d*scale[((int) w/2)];+      temp_int=0.;++      temp=0.;+      prev_l = n2;+      for (k=i-1; k>end_k && k>0; k--) {+        if (fold_constrained && pos && cstruc[k-1] == '|' && k > prev_k)+          prev_k=k;+        for (l=j+1; l< end_l && l<=n2; l++) {+          int a,b,ia,ib,isw;+          double scalew, tt, intt;++          type2 = cc->ptype[cc->indx[k]-(n1+l)];+          /* '|' : l HAS TO be paired: not pair (k,x) where x>l allowed */+          if(fold_constrained && pos && cstruc[n1+l-1] == '|' && l < prev_l)+            prev_l=l; /*break*/+          if(fold_constrained && pos && (k<=ck || i>=ci) && !type2) continue;+          if(fold_constrained && pos && ((cstruc[k-1] == '|') || (cstruc[n1+l-1] == '|')) && !type2) break;++          if (!type2) continue;+          /* to save memory keep only qint_4[i-w...i][][][] in memory+             use indices qint_4[i][j][a={0,1,...,w-1}][b={0,1,...,w-1}] */+          a=i-k;/* k -> a from 1...w-1*/+          b=l-j;/* l -> b from 1...w-1 */++          /* scale everything to w/2 */+          isw = ((int) w/2);+          if ((a+b) < isw ){+            scalew = ( scale[isw - (a+b)] );+          } else if ( (a+b) > isw ) {+            scalew = 1/( scale[(a+b) - isw] );+          } else {+            scalew = 1;+          }++          if (i-k+l-j-2<=MAXLOOP) {+            if(k >= prev_k && l <= prev_l) { /* don't violate constrains */+              E = exp_E_IntLoop(i-k-1,l-j-1, type2, rtype[type],+                                S1[k+1], SS2[l-1], S1[i-1], SS2[j+1], Pf) *+                                scale[i-k+l-j]; /* add *scale[u1+u2+2] */++              qint_4[i][j][a][b] += ( qint_4[k][l][0][0]*E);++              /* use ia and ib to go from a....w-1 and from b....w-1  */+              ia=ib=1;+              while((a+ia)<w && i-(a+ia)>=1 && (b+ib)<w && (j+b+ib)<=n2) {+                int iaa,ibb;++                qint_4[i][j][a+ia][b+ib] += qint_4[k][l][ia][ib]*E;++                iaa=ia+1;+                while(a+iaa<w && i-(a+iaa)>=1) {+                  qint_4[i][j][a+iaa][b+ib] += qint_4[k][l][iaa][ib]*E;+                  ++iaa;+                }++                ibb=ib+1;+                while( (b+ibb)<w && (j+b+ibb)<=n2 ) {+                  qint_4[i][j][a+ia][b+ibb] += qint_4[k][l][ia][ibb]*E;+                  ++ibb;+                }+                ++ia;+                ++ib;+              }+            }+          }+          /* '|' constrain in long sequence */+          /* collect interactions starting before 5' most '|' constrain */+          if ( fold_constrained && pos && ci && i < ci) continue;+          /* collect interactions ending after 3' most '|' constrain*/+          if ( fold_constrained && pos && ck &&  k > ck) continue;+          /* '|' constrain in short sequence */+          /* collect interactions starting before 5' most '|' constrain */+          if ( fold_constrained && pos && cj && j > cj) continue;+          /* collect interactions ending after 3' most '|' constrain*/+          if ( fold_constrained && pos && cl && l < cl) continue;++          /* scale everything to w/2*/+          /* qint_ik[k][i] all interactions where k and i both are paired */+          /* substract incr5 from k */+          if(k-incr5 > 0) add_i5=k-incr5;+          else add_i5=1;+          /* add incr3 to i */+          pc_size = MIN2((w+incr3+incr5),n1);+          if(i-k+incr3 < pc_size) add_i3=i-k+incr3;+          else add_i3=pc_size-1;++          if(p_c2 == NULL) {/* consider only structure of longer seq. */+            tt = qint_4[i][j][a][b]*p_c_S[add_i5][add_i3]*scalew*rev_d;+          } else { /* consider structures of both seqs. */+            tt = qint_4[i][j][a][b]*p_c_S[add_i5][add_i3]*p_c2_S[j][b]*scalew*rev_d;+          }+          temp+= tt;+          qint_ik[k][i]+= tt;+          /* int_ik */+          /* check deltaG_ges = deltaG_int + deltaG_unstr; */+          intt = qint_4[i][j][a][b]*scalew*rev_d;+          temp_int += intt;+          int_ik[k][i]+= intt;+          G_is = (-log(tt)-const_scale)*(const_T);+          if (G_is < G_min || EQUAL(G_is,G_min)) {+            G_min = G_is;+            Gi_min =(-log(intt)-const_scale)*(const_T);+            gi=i;+            gj=j;+            gk=k;+            gl=l;+          }+        }+      }+      Z+=temp;+      /* int_ik */+      Z_int+=temp_int;+    }++    /* free qint_4 values not needed any more */+    if(i > w) {+      int bla;+      bla=i-w;+      if (fold_constrained && pos && ci && i-w < ci-w+1) continue;+      if (fold_constrained && pos && ci) bla = MAX2(ci-w+1,i-w);+      for (j=n2; j>0; j--) {+        for (k=0; k<=w; k++){+          free(qint_4[bla][j][k]);+        }+        free(qint_4[bla][j]);+      }+      free(qint_4[bla]);+      qint_4[bla] = NULL;+    }+  }+++  Z2=0.0;+  for (i=1; i<=n1; i++) {+    for (k=i; k<=n1 && k<i+w; k++) {+      Z2+=qint_ik[i][k];+      for(l=i;l<=k;l++) {+        /* Int->Pi[l]: prob that position l is within a paired region */+        /* qint_ik[i][k] as well as Z are scaled to scale[((int) w/2) */+        Int->Pi[l]+=qint_ik[i][k]/Z;+        /* Int->Gi[l]: minimal delta G at position [l] */+        Int->Gi[l]=MIN2(Int->Gi[l],+                       ( -log(qint_ik[i][k])-( ((int) w/2)*log(pf_scale)) )*+                       (Pf->kT/1000.0) );+      }+    }+  }+  if(n1 > w){+    int start_i,end_i;+    start_i = n1-w+1;+    end_i=n1;+    if (fold_constrained && pos && ci) {+      /* a break in the k loop might result in unfreed values */+      start_i = ci-w+1 < n1-w+1 ? ci-w+1 : n1-w+1;+      start_i = start_i > 0 ? start_i : 1;+      /* start_i = ck; */+      end_i = ck+w-1 > n1 ? n1 : ck+w-1;+    }+    for (i=start_i; i<=end_i; i++) {+      if(qint_4[i] == NULL ) continue;+      for (j=n2; j>0; j--) {+        for (k=0; k<=w; k++) {+          free(qint_4[i][j][k]);+        }+        free(qint_4[i][j]);+      }+      free(qint_4[i]);+    }+    free(qint_4);+  } else {+    int start_i,end_i;+    start_i = 1;+    end_i=n1;+    if (fold_constrained && pos) {+      start_i = ci-w+1 > 0 ? ci-w+1 : 1;+      end_i = ck+w-1 > n1 ? n1 : ck+w-1;+    }++    for (i=start_i; i<=end_i; i++) {+      for (j=n2; j>0; j--) {+        for (k=0; k<=w; k++) {+          free(qint_4[i][j][k]);+        }+        free(qint_4[i][j]);+      }+      free(qint_4[i]);+    }+    free(qint_4);+  }+  if(fold_constrained && (gi==0 || gk==0 ||  gl==0 || gj==0)) {+    vrna_message_error("pf_interact: could not satisfy all constraints");+  }+  /* fill structure interact */+  Int->length = n1;+  Int->i = gi;+  Int->j = gj;+  Int->k = gk;+  Int->l = gl;+  Int->Gikjl = G_min;+  Int->Gikjl_wo = Gi_min;++  free(i_long);+  free(i_short);++  for (i=1; i<=n1; i++) {+    free(int_ik[i]);+  }+  free(int_ik);+  for (i=1; i<=n1; i++) {+    free(qint_ik[i]);+  }+  free(qint_ik);++  /* reset the global variables pf_scale and scale to their original values */+  pf_scale = temppfs;/* reset pf_scale */+  scale_stru_pf_params((unsigned) n1);/* reset the scale array */+  free_pf_arrays(); /* for arrays for pf_fold(...) */++  if(expMLbase != NULL) {+    free(expMLbase);+    expMLbase = NULL;+  }+  if(scale != NULL) {+    free(scale);+    scale = NULL;+  }+  for (i=1; i<=n1; i++) {+    free(p_c_S[i]);+  }+  free(p_c_S);+  if(p_c2 != NULL) {+    for (i=1; i<=n2; i++) {+      free(p_c2_S[i]);+    }+    free(p_c2_S);+  }+  free(Seq);+  free(cc->indx);+  free(cc->ptype);+  free(cc);+  return(Int);+}+/*------------------------------------------------------------------------*/+/* use an extra scale for pf_interact, here sl is the longer sequence */+PRIVATE void scale_int(const char *s, const char *sl, double *sc_int){+  int       n,nl;+  duplexT   mfe;+  double    kT;++  n         = strlen(s);+  nl        = strlen(sl);++  free(expMLbase);+  free(scale);++  expMLbase = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*((nl+1)*2));+  scale     = (FLT_OR_DBL *) vrna_alloc(sizeof(FLT_OR_DBL)*((nl+1)*2));++  /* use RNA duplex to get a realistic estimate for the best possible+     interaction energy between the short RNA s and its target sl */+  mfe = duplexfold(s,sl);++  kT = Pf->kT/1000.0;   /* in Kcal */++  /* sc_int is similar to pf_scale: i.e. one time the scale */+  *sc_int = exp(-(mfe.energy)/kT/n);++  /* free the structure returned by duplexfold */+  free(mfe.structure);+}++/*----------------------------------------------------------------------*/+/* init_pf_two(n) :gets the arrays, that you need, from part_func.c */+/* get_pf_arrays(&S, &S1, &ptype, &qb, &qm, &q1k, &qln);*/+/* init_pf_fold(), update_pf_params, encode_char(), make_ptypes() are called by pf_fold() */+PRIVATE void init_pf_two(int length){+#ifdef SUN4+  nonstandard_arithmetic();+#else+#ifdef HP9+  fpsetfastmode(1);+#endif+#endif+  make_pair_matrix();++  /* gets the arrays, that we need, from part_func.c */+  if(!get_pf_arrays(&S, &S1, &ptype, &qb, &qm, &q1k, &qln))+    vrna_message_error("init_pf_two: pf_fold() has to be called before calling pf_unstru()\n");+  /* get a pointer to the base pair probs */+  probs = export_bppm();++  scale_stru_pf_params((unsigned) length);++  init_length=length;+  if(init_temp != Pf->temperature)+    vrna_message_error("init_pf_two: inconsistency with temperature");+}++PRIVATE void  get_up_arrays(unsigned int length){+  unsigned int l1 = length + 1;+  unsigned int l2 = length + 2;+  prpr      = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL)  * ((l1*l2)>>1));+  expMLbase = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL)  * l2);+  scale     = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL)  * l2);+  qqm2      = (double *)    vrna_alloc(sizeof(double)      * l2);+  qq_1m2    = (double *)    vrna_alloc(sizeof(double)      * l2);+  qqm       = (double *)    vrna_alloc(sizeof(double)      * l2);+  qqm1      = (double *)    vrna_alloc(sizeof(double)      * l2);+  my_iindx  = vrna_idx_row_wise(length);+}++PRIVATE void  free_up_arrays(void){+  if(prpr       != NULL){ free(prpr);       prpr      = NULL;}+  if(expMLbase  != NULL){ free(expMLbase);  expMLbase = NULL;}+  if(scale      != NULL){ free(scale);      scale     = NULL;}+  if(qqm        != NULL){ free(qqm);        qqm       = NULL;}+  if(qqm1       != NULL){ free(qqm1);       qqm1      = NULL;}+  if(qqm2       != NULL){ free(qqm2);       qqm2      = NULL;}+  if(qq_1m2     != NULL){ free(qq_1m2);     qq_1m2    = NULL;}+  if(my_iindx   != NULL){ free(my_iindx);   my_iindx  = NULL;}+}++PUBLIC void free_interact(interact *pin) {+  if(S != NULL && pin != NULL){+    free(S);+    S=NULL;+  }+  if(S1 != NULL && pin != NULL){+    free(S1);+    S1=NULL;+  }+  if(pin != NULL){+    free(pin->Pi);+    free(pin->Gi);+    free(pin);+    pin=NULL;+  }+}+/*---------------------------------------------------------------------------*/++PRIVATE void encode_seq(const char *s1, const char *s2) {+  unsigned int i,l;++  l = strlen(s1);+  /* S and S1 are freed by free_pf_arrays(); ! */+  S = (short *) vrna_alloc(sizeof(short)*(l+1));+  S1= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* S1 exists only for the special X K and I bases and energy_set!=0 */+  S[0] = l;+  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    S[i]= (short) encode_char(toupper(s1[i-1]));+    S1[i] = alias[S[i]];   /* for mismatches of nostandard bases */+  }+  if(s2 != NULL) {+    l = strlen(s2);+    /* SS2 exists only for the special X K and I bases and energy_set!=0 */+    SS[0] = l;+    for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+      SS[i]= (short) encode_char(toupper(s2[i-1]));+      SS2[i] = alias[SS[i]];   /* for mismatches of nostandard bases */+    }+  }+}++/*-------------------------------------------------------------------------*/+ /* scale energy parameters and pre-calculate Boltzmann weights:+  most of this is done in structure Pf see params.c,h (function:+  get_scaled_pf_parameters(), only arrays scale and expMLbase are handled here*/+PRIVATE void scale_stru_pf_params(unsigned int length)+{+  unsigned int i;+  double  kT;+++  /* Do this only at the first call for get_scaled_pf_parameters()+     and/or if temperature has changed*/+  if(init_temp != temperature) {+    if(Pf) free(Pf);+    vrna_md_t   md;+    set_model_details(&md);+    Pf=vrna_exp_params(&md);+  }++  init_temp = Pf->temperature;++  kT = Pf->kT;   /* kT in cal/mol  */++   /* scaling factors (to avoid overflows) */+  if (pf_scale == -1) { /* mean energy for random sequences: 184.3*length cal */+    pf_scale = exp(-(-185+(Pf->temperature-37.)*7.27)/kT);+    if (pf_scale<1) pf_scale=1;+  }+  Pf->pf_scale = pf_scale;+  scale[0] = 1.;+  scale[1] = 1./pf_scale;+  expMLbase[0] = 1;+  expMLbase[1] = Pf->expMLbase/pf_scale;+  for (i=2; i<=length+1; i++) {+    scale[i] = scale[i/2]*scale[i-(i/2)];+    expMLbase[i] = pow(Pf->expMLbase, (double)i) * scale[i];+  }+}+/*-------------------------------------------------------------------------*/+/* make a results structure containing all u-values & the header */+PUBLIC pu_out *get_u_vals(pu_contrib *p_c, int **unpaired_values, char *select_contrib) {+  int i, j, k, l, num_u_vals,count,contribs,size,w,len;+  int S,E,H,I,M;+  int off_S, off_E, off_H, off_I, off_M;+  /* double **p_cont,**p_cont_sh, dG_u; p_u AND its contributions */+  pu_out* u_results;++  len = p_c->length;++  /* number of different -u values */+  for (num_u_vals = 0, i = 1; i <= unpaired_values[0][0]; i++) {+    j = unpaired_values[i][0];+    do num_u_vals++; while(++j <= unpaired_values[i][1]);+  }+  /* check which contributions ([-c "SHIME"] ) are desired by the user,+     set the offset for each contribution */+  contribs = 0;+  S = E = H = I = M = 0;+  off_S = off_E = off_H = off_I = off_M = 0;+  if(strchr(select_contrib, 'S')) {+    S=1;+    off_S = contribs;+    ++contribs;+  }+  if(strchr(select_contrib, 'E')) {+    E=1;+    off_E = contribs;+    ++contribs;+  }+  if(strchr(select_contrib, 'H')) {+    H=1;+    off_H = contribs;+    ++contribs;+  }+  if(strchr(select_contrib, 'I')) {+    I=1;+    off_I = contribs;+    ++contribs;+  }+  if(strchr(select_contrib, 'M')) {+    M=1;+    off_M = contribs;+    ++contribs;+  }++  if(contribs > 5) {+    vrna_message_error("get_u_vals: error with contribs!");+  }+  /* allocate the results structure */+  u_results = (pu_out *) vrna_alloc(1*sizeof(pu_out));+  u_results->len = len; /* sequence length */+  /*num_u_vals differnet -u values, contribs [-c "SHIME"] */+  u_results->u_vals = num_u_vals;+  u_results->contribs = contribs;+  /* add 1 column for position within the sequence and+     add 1 column for the free energy of interaction values */+  /* header e.g. u3I (contribution for u3 interior loops */+  size = 1 + (num_u_vals*contribs) + 1;+  u_results->header = (char **) vrna_alloc((size+1)*sizeof(char*));+  for(i=0;i<(size+1);i++){+    u_results->header[i] = (char *) vrna_alloc(10*sizeof(char));+  }+  /* different free energies for all  -u and -c combinations */+  u_results->u_values = (double**) vrna_alloc((size+1) *sizeof(double*));+  for(i=0;i<(size+1);i++){+    /* position within the sequence  */+    u_results->u_values[i] = (double*) vrna_alloc((len+3)*sizeof(double));+  }+  /* write the position within the sequence in the u_results array+     at column zerro */+  sprintf(u_results->header[0],"pos");+  for(i=0;i<=len;i++){+    /* add the position*/+    u_results->u_values[0][i] = i;+  }+  /* go over the different -u values, u_vals[] listy of different -u values*/+  for (count = k = 1; k <= unpaired_values[0][0]; k++) {+    l = unpaired_values[k][0];+    do{+      int offset; /* offset for the respective -u value (depents on the number+                   of the -u value and on the numbers of contribs */++      offset = ((count - 1) * contribs) + 1; /* first colum is the position */+      /* set the current value of -u : here we call it w */+      w = l; /* set w to the actual -u value */+      if(w > len) break; /* corr caro */+      /* make the header - look which contribitions are wanted */+      if(S) sprintf(u_results->header[offset+off_S],"u%dS",w);+      if(E) sprintf(u_results->header[offset+off_E],"u%dE",w);+      if(H) sprintf(u_results->header[offset+off_H],"u%dH",w);+      if(I) sprintf(u_results->header[offset+off_I],"u%dI",w);+      if(M) sprintf(u_results->header[offset+off_M],"u%dM",w);++      if(p_c != NULL) {+        for (i=1; i<=len; i++) { /* for each position */+          /* w goes form j to i (intervall end at i) */+          for (j=i; j < MIN2((i+w),len+1); j++) { /* for each -u value < w+                                                this is not necessay ->+                                                calculate j from i and w+                                                : (j-i+1) == w */+            double blubb;+            /* if (j-i+1) == w we have the -u = w value wanted */+            if( (j-i+1) == w && i+w-1 <= len) {+              blubb = p_c->H[i][j-i]+p_c->I[i][j-i]+p_c->M[i][j-i]+p_c->E[i][j-i];++              /* printf("len %d  blubb %.3f \n",len, blubb); */+              if(S) u_results->u_values[offset+off_S][i+w-1]+=blubb;+              if(E) u_results->u_values[offset+off_E][i+w-1]+=p_c->E[i][j-i];+              if(H) u_results->u_values[offset+off_H][i+w-1]+=p_c->H[i][j-i];+              if(I) u_results->u_values[offset+off_I][i+w-1]+=p_c->I[i][j-i];+              if(M) u_results->u_values[offset+off_M][i+w-1]+=p_c->M[i][j-i];++            }+            if(i<w && (j-i+1) != w && i+w-1 > len &&  i+w-1 < len+3) {+              if(S) u_results->u_values[offset+off_S][i+w-1]=-1;+              if(E) u_results->u_values[offset+off_E][i+w-1]=-1;+              if(H) u_results->u_values[offset+off_H][i+w-1]=-1;+              if(I) u_results->u_values[offset+off_I][i+w-1]=-1;+              if(M) u_results->u_values[offset+off_M][i+w-1]=-1;+            }+          }+        }+      } else return(NULL); /* error */+      count++;+    } while(++l <= unpaired_values[k][1]);+  }+  return(u_results); /*success*/+}+/* plot the results structure */+/* when plotting the results for the target seq we add a header */+/* when plotting the results for the interaction partner u want no header,+   set s1 to NULL to avoid plotting the header */+/* currently we plot the free energies to a file: the probability of+   being unpaired for region [i,j], p_u[i,j], is related to the free+   energy to open region [i,j], dG_u[i,j] by:+   dG_u[i,j] = -log(p_u[i,j])*(temperature+K0)*GASCONST/1000.0; */+PUBLIC int plot_free_pu_out(pu_out* res, interact *pint, char *ofile, char *head) {+  int size,s,i,len;+  double dG_u;+  char nan[4], *time, dg[11];+  FILE *wastl;+  double  kT = Pf->kT;+  wastl = fopen(ofile,"a");+  if (wastl==NULL) {+    vrna_message_warning("p_cont: can't open %s for Up_plot", ofile);+    return(0);+  }+  sprintf(dg,"dG");++  /* printf("T=%.16f \n(temperature+K0)*GASCONST/1000.0 = %.16f\n",temperature,(temperature+K0)*GASCONST/1000.0); */++  /* write the header of the output file:  */+  /*  # timestamp commandlineaufruf   */+  /*  # length and name of first sequence (target) */+  /*  # first seq */+  /*  # length and name of second sequence (interaction partner) */+  /*  # second seq */+  /* the next line is the output for the target: colums+     position in target | dG_unpaired values for target | interaction energy */+  /*  # pos   u1S   u1H  dg */+  /*  values for target */+  /* if -b was choosen: the next lines are the dG_unpaired values for+     the interaction partner */+  /*  # pos   u1S   u1H  */+  /*  values for the interaction partner */++  /* print header, if nh is zerro */+  if(head){+    time = vrna_time_stamp();+    fprintf(wastl,"# %s\n", time);+    fprintf(wastl,"%s\n",head);+  }+  fprintf(wastl,"# ");+  /* }  else { fprintf(wastl," "); } close if before  */+  len  = res->len;+  size = res->u_vals * res->contribs;++  sprintf(nan,"NA");+  nan[2] = '\0';++  for(i=0;i<=len; i++) {+    for(s=0;s<=size+1;s++) { /* that is for different contribution */+      if ( i== 0 && s > size && pint != NULL)+        fprintf(wastl,"%8s  ",dg);+      if(i != 0) {+        if(s>0 && s<=size) {+          if(res->u_values[s][i] > 0.0) {+            dG_u = -log(res->u_values[s][i])*kT/1000.0;+            fprintf(wastl,"%8.3f  ",dG_u);+          } else { /* no p_u value was defined print nan*/+            fprintf(wastl,"%8s  ",nan);+          }++        } else if (s > size && pint != NULL) {+          fprintf(wastl,"%8.3f  ",pint->Gi[i]);+        } else if (s == 0) {+          fprintf(wastl,"%8.0f  ",res->u_values[s][i]);+        }+      } else {+        if(s>1) {+          fprintf(wastl,"%8s  ",res->header[s]);+        } else {+          fprintf(wastl,"%7s  ",res->header[s]);+        }+      }+    }+    fprintf(wastl,"\n");+  }+  fclose(wastl);+  /*free pu_out* res */+  if(res != NULL) {+    for(i=0;i<=(size+2);i++) {+      free(res->u_values[i]);+      free(res->header[i]);+    }+    free(res->u_values);+    free(res->header);+    free(res);+    res = NULL;+  }++  return(1); /* success */+}++PUBLIC int Up_plot(pu_contrib *p_c, pu_contrib *p_c_sh, interact *pint, char *ofile, int **unpaired_values, char *select_contrib, char *head, unsigned int mode) {+  pu_out *dada;+  int ret;+  /* check what case we have */++  /* upmode = 1 only one seq */+  /* if(p_c != NULL && pint == NULL) { */+  if(mode & RNA_UP_MODE_1){+    dada = get_u_vals(p_c,unpaired_values,select_contrib);+    ret = plot_free_pu_out(dada,NULL,ofile,head);++  /* upmode > 1 cofolding */+  /* } else if (p_c != NULL && pint != NULL) { */+  } else if(mode & RNA_UP_MODE_2) {+    dada = get_u_vals(p_c,unpaired_values,select_contrib);+    ret = plot_free_pu_out(dada,pint,ofile,head);++  /* upmode = 3  cofolding*/+  /* } else if (p_c == NULL && p_c_sh != NULL) { */+  }+  if(mode & RNA_UP_MODE_3) {+    dada  = get_u_vals(p_c,unpaired_values, select_contrib);+    ret   = plot_free_pu_out(dada, pint, ofile, head);++    dada = get_u_vals(p_c_sh, unpaired_values, select_contrib);+    ret = plot_free_pu_out(dada,NULL,ofile, NULL);+  }+  return(ret);+}++/*-------------------------------------------------------------------------*/+/* copy from part_func_co.c */+PRIVATE constrain *get_ptypes_up(char *Seq, const char *structure) {+  int n,i,j,k,l, length;+  constrain *con;+  short *s, *s1;++  length = strlen(Seq);+  make_pair_matrix();+  con = (constrain *) vrna_alloc(sizeof(constrain));+  con->indx = (int *) vrna_alloc(sizeof(int)*(length+1));+  for (i=1; i<=length; i++) {+    con->indx[i] = ((length+1-i)*(length-i))/2 +length+1;+  }+  con->ptype = (char *) vrna_alloc(sizeof(char)*((length+1)*(length+2)/2));++  set_encoded_seq((const char *)Seq, &s, &s1);++  n=s[0];+  for (k=1; k<=n-CO_TURN-1; k++)+    for (l=1; l<=2; l++) {+      int type,ntype=0,otype=0;+      i=k; j = i+CO_TURN+l; if (j>n) continue;+      type = pair[s[i]][s[j]];+      while ((i>=1)&&(j<=n)) {+        if ((i>1)&&(j<n)) ntype = pair[s[i-1]][s[j+1]];+        if (noLonelyPairs && (!otype) && (!ntype))+          type = 0; /* i.j can only form isolated pairs */+        con->ptype[con->indx[i]-j] = (char) type;+        otype =  type;+        type  = ntype;+        i--; j++;+      }+    }++  if (fold_constrained&&(structure!=NULL)) {+    int hx, *stack;+    char type;+    stack = (int *) vrna_alloc(sizeof(int)*(n+1));+    for(hx=0, j=1; j<=n; j++) {+      switch (structure[j-1]) {+      case 'x': /* can't pair */+        for (l=1; l<j-CO_TURN; l++) con->ptype[con->indx[l]-j] = 0;+        for (l=j+CO_TURN+1; l<=n; l++) con->ptype[con->indx[j]-l] = 0;+        break;+      case '(':+        stack[hx++]=j;+        /* fallthrough */+      case '<': /* pairs upstream */+        break;+      case ')':+        if (hx<=0) {+          vrna_message_error("1. unbalanced brackets in constraints\n%s", structure);+        }+        i = stack[--hx];+        type = con->ptype[con->indx[i]-j];+        /* don't allow pairs i<k<j<l */+        for (k=i; k<=j; k++)+          for (l=j; l<=n; l++) con->ptype[con->indx[k]-l] = 0;+        /* don't allow pairs k<i<l<j */+        for (k=1; k<=i; k++)+          for (l=i; l<=j; l++) con->ptype[con->indx[k]-l] = 0;+        con->ptype[con->indx[i]-j] = (type==0)?7:type;+      case '>': /* pairs downstream */+        break;+      }+    }+    if (hx!=0) {+      vrna_message_error("2. unbalanced brackets in constraint string\n%s", structure);+    }+    free(stack);+  }+  free(s);+  free(s1);+  return con;+}+PRIVATE  void  set_encoded_seq(const char *sequence, short **S, short **S1){+  unsigned int i,l;+  l = strlen(sequence);+  if(S!= NULL){+    *S  = (short *)vrna_alloc(sizeof(short) * (l + 2));+    for(i=1; i<=l; i++) /* make numerical encoding of sequence */+      (*S)[i]= (short) encode_char(toupper(sequence[i-1]));+    (*S)[l+1] = (*S)[1];+    (*S)[0]   = (short) l;+  }+  /* S1 exists only for the special X K and I bases and energy_set!=0 */+  if(S1 != NULL){+    *S1 = (short *)vrna_alloc(sizeof(short) * (l + 2));+    for(i=1; i<=l; i++) /* make numerical encoding of sequence */+      (*S1)[i]  = alias[(short) encode_char(toupper(sequence[i-1]))]; /* for mismatches of nostandard bases */+    /* for circular folding add first base at position n+1 and last base at position 0 in S1 */+    (*S1)[l+1]  = (*S1)[1];+    (*S1)[0]    = (*S1)[l];+  }+}
+ C/ViennaRNA/part_func_up.h view
@@ -0,0 +1,149 @@+#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_UP_H+#define VIENNA_RNA_PACKAGE_PART_FUNC_UP_H++#include <ViennaRNA/data_structures.h>++#define   RNA_UP_MODE_1   1U+#define   RNA_UP_MODE_2   2U+#define   RNA_UP_MODE_3   4U++/**+ *  @file     part_func_up.h+ *  @ingroup  pf_fold cofold pf_cofold+ *  @brief    Implementations for accessibility and RNA-RNA interaction as a stepwise process+ */++/**+ *  @addtogroup up_cofold+ *  @brief      RNA-RNA interaction as a stepwise process+ *+ * + *  In this approach to cofolding the interaction between two RNA molecules is+ *  seen as a stepwise process. In a first step, the target molecule has to+ *  adopt a structure in which a binding site is accessible. In a second step,+ *  the ligand molecule will hybridize with a region accessible to an+ *  interaction. Consequently the algorithm is designed as a two step process:+ *  The first step is the calculation of the probability+ *  that a region within the target is unpaired, or equivalently, the+ *  calculation of the free energy needed to expose a region. In the second step+ *  we compute the free energy of an interaction for every possible binding site.+ *  @{+ *  @ingroup  up_cofold+ */++/**+ *  @brief Calculate the partition function over all unpaired regions+ *  of a maximal length.+ * + *  You have to call function pf_fold() providing the same sequence before calling+ *  pf_unstru(). If you want to calculate unpaired regions for a constrained structure, set+ *  variable 'structure' in function 'pf_fold()' to the constrain string.+ *  It returns a #pu_contrib struct containing four arrays of dimension+ *  [i = 1 to length(sequence)][j = 0 to u-1] containing all possible contributions+ *  to the probabilities of unpaired regions of maximum length u.+ *  Each array in #pu_contrib contains one of the contributions to the+ *  total probability of being unpaired: The probability of being unpaired+ *  within an exterior loop is in array #pu_contrib->E, the probability+ *  of being unpaired within a hairpin loop is in array #pu_contrib->H,+ *  the probability of being unpaired within an interior loop is in array+ *  #pu_contrib->I and probability of being unpaired within a multi-loop+ *  is in array #pu_contrib->M. The total probability of being unpaired+ *  is the sum of the four arrays of #pu_contrib.+ * + *  This function frees everything allocated automatically. To+ *  free the output structure call free_pu_contrib().+ * + *  @param sequence+ *  @param max_w+ *  @return+ */+pu_contrib *pf_unstru(char *sequence,+                      int max_w);++/**+ *  @brief Calculates the probability of a local interaction between two sequences.+ * + *  The function considers the probability that the+ *  region of interaction is unpaired within 's1' and 's2'. The+ *  longer sequence has to be given as 's1'. The shorter sequence has to+ *  be given as 's2'. Function pf_unstru() has to be called+ *  for 's1' and 's2', where the probabilities of  being unpaired+ *  have to be given in 'p_c' and 'p_c2', respectively. If you do+ *  not want to include the probabilities of  being unpaired for 's2' set+ *  'p_c2' to NULL. If variable 'cstruc' is not NULL,+ *  constrained folding is done: The available constrains for intermolecular+ *  interaction are: '.' (no constrain), 'x' (the base has no intermolecular+ *  interaction) and '|' (the corresponding base has to be paired+ *  intermolecularily).\n+ *  The parameter 'w' determines the maximal length of the interaction. The+ *  parameters 'incr5' and 'incr3' allows inclusion of+ *  unpaired residues left ('incr5') and right ('incr3') of the region+ *  of interaction in 's1'. If the 'incr' options are used, function+ *  pf_unstru() has to be called with+ *  w=w+incr5+incr3 for the longer sequence 's1'.+ * + *  It returns a structure of type #interact which+ *  contains the probability of the best local interaction including residue i+ *  in Pi and the minimum free energy in Gi, where i is the position in sequence+ *  's1'. The member Gikjl of structure #interact is+ *  the best interaction between region [k,i] k<i in longer sequence+ *  's1' and region [j,l] j<l in 's2'. Gikjl_wo is Gikjl without the+ *  probability of beeing unpaired.\n+ *  Use free_interact() to free the returned structure, all+ *  other stuff is freed inside pf_interact().+ * + *  @param  s1+ *  @param  s2+ *  @param  p_c+ *  @param  p_c2+ *  @param  max_w+ *  @param  cstruc+ *  @param  incr3+ *  @param  incr5+ *  @return+ */+interact *pf_interact(const char *s1,+                      const char *s2,+                      pu_contrib *p_c,+                      pu_contrib *p_c2,+                      int max_w,+                      char *cstruc,+                      int incr3,+                      int incr5);++/**+ *  @brief Frees the output of function pf_interact().+ */+void free_interact(interact *pin);++/**+ *  @brief+ */+int Up_plot(pu_contrib *p_c,+            pu_contrib *p_c_sh,+            interact *pint,+            char *ofile,+            int **unpaired_values,+            char *select_contrib,+            char *head,+            unsigned int mode);++/**+ *  @brief+ */+pu_contrib  *get_pu_contrib_struct( unsigned int n,+                                    unsigned int w);++/**+ *  @brief Frees the output of function pf_unstru().+ */+void        free_pu_contrib_struct(pu_contrib *pu);++void+free_pu_contrib(pu_contrib *pu);++/**+ * @}+ */++#endif
+ C/ViennaRNA/perturbation_fold.c view
@@ -0,0 +1,493 @@++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include "perturbation_fold.h"+#include "eval.h"+#include "fold_vars.h"+#include "constraints.h"+#include "fold.h"+#include "part_func.h"+#include "utils.h"+#include "params.h"++#include <assert.h>+#include <math.h>+#include <stdio.h>+#include <stdlib.h>+#include <string.h>++#ifdef WITH_GSL+#include <gsl/gsl_multimin.h>+#endif++static void calculate_probability_unpaired(vrna_fold_compound_t *vc, double *probability)+{+  int length = vc->length;+  FLT_OR_DBL *probs = vc->exp_matrices->probs;+  int *iidx = vc->iindx;+  int i, j;++  for (i = 0; i <= length; ++i)+    probability[i] = 1;++  for (i = 1; i <= length; ++i)+    for (j = i + 1; j <= length; ++j)+    {+      probability[i] -= probs[iidx[i]-j];+      probability[j] -= probs[iidx[i]-j];+    }+}++static double calculate_norm(double *vector, int length)+{+  double sum = 0;+  int i;++  for (i = 1; i <= length; ++i)+    sum += vector[i] * vector[i];++  return sqrt(sum);+}++static void addSoftConstraint(vrna_fold_compound_t *vc, const double *epsilon, int length)+{+  vrna_sc_t *sc;+  int i, j;+  double kT = vc->exp_params->kT / 1000;++  sc = vrna_alloc(sizeof(vrna_sc_t));++  sc->exp_energy_up = vrna_alloc(sizeof(FLT_OR_DBL*) * (length + 2));+  sc->exp_energy_up[0] = vrna_alloc(1);+  for (i = 1; i <= length; ++i)+    sc->exp_energy_up[i] = vrna_alloc(sizeof(FLT_OR_DBL) * (length - i + 2));++  for (i = 1; i <= length; ++i)+  {+    sc->exp_energy_up[i][0] = 1;+    for (j = 1; j <= length - i + 1; ++j)+      sc->exp_energy_up[i][j] = sc->exp_energy_up[i][j-1] * exp(-(epsilon[i + j - 1]) / kT);+  }++  /* also add sc for MFE computation */+  sc->energy_up = vrna_alloc(sizeof(int*) * (length + 2));+  sc->energy_up[0] = vrna_alloc(sizeof(int));+  for (i = 1; i <= length; ++i)+    sc->energy_up[i] = vrna_alloc(sizeof(int) * (length - i + 2));++  for (i = 1; i <= length; ++i){+    sc->energy_up[i][0] = 0;+    for (j = 1; j <= length - i + 1; ++j)+      sc->energy_up[i][j] = sc->energy_up[i][j-1] + (epsilon[i + j - 1]*100.);+  }++  vc->sc = sc;+}++static double evaluate_objective_function_contribution(double value, int objective_function)+{+  if (objective_function == VRNA_OBJECTIVE_FUNCTION_QUADRATIC)+    return value * value;+  if (objective_function == VRNA_OBJECTIVE_FUNCTION_ABSOLUTE)+    return fabs(value);++  assert(0);+  return 0;+}++static double evaluate_perturbation_vector_score(vrna_fold_compound_t *vc, const double *epsilon, const double *q_prob_unpaired, double sigma_squared, double tau_squared, int objective_function)+{+  double kT, ret = 0;+  double ret2 = 0.;+  double *p_prob_unpaired;+  int i;+  int length = vc->length;++  /* calculate pairing probabilty in the pertubated energy model */+  p_prob_unpaired = vrna_alloc(sizeof(double) * (length + 1));++  addSoftConstraint(vc, epsilon, length);++  vc->exp_params->model_details.compute_bpp = 1;++  /* get new (constrained) MFE to scale pf computations properly */+  double mfe = (double)vrna_mfe(vc, NULL);+  vrna_exp_params_rescale(vc, &mfe);++  vrna_pf(vc, NULL);++  calculate_probability_unpaired(vc, p_prob_unpaired);++  vrna_sc_remove(vc);++  +  for (i = 1; i <= length; ++i)+  {+    /* add penalty for pertubation energies */+    ret += evaluate_objective_function_contribution(epsilon[i], objective_function) / tau_squared;++    /* add penalty for mismatches between observed and predicted probabilities */+    if (q_prob_unpaired[i] >= 0) /* ignore positions with missing data */+      ret2 += evaluate_objective_function_contribution(p_prob_unpaired[i] - q_prob_unpaired[i], objective_function) / sigma_squared;+  }++  vrna_message_info(stderr, "Score: pertubation: %g\tdiscrepancy: %g", ret, ret2);+  free(p_prob_unpaired);++  return ret + ret2;+}++static void pairing_probabilities_from_restricted_pf(vrna_fold_compound_t *vc, const double *epsilon, double *prob_unpaired, double **conditional_prob_unpaired)+{+  int length = vc->length;+  int i;++  addSoftConstraint(vc, epsilon, length);+  vc->exp_params->model_details.compute_bpp = 1;++  /* get new (constrained) MFE to scale pf computations properly */+  double mfe = (double)vrna_mfe(vc, NULL);+  vrna_exp_params_rescale(vc, &mfe);++  vrna_pf(vc, NULL);++  calculate_probability_unpaired(vc, prob_unpaired);++#ifdef _OPENMP+  #pragma omp parallel for private(i)+#endif+  for (i = 1; i <= length; ++i)+  {+    vrna_fold_compound_t *restricted_vc;+    char *hc_string;+    unsigned int constraint_options = VRNA_CONSTRAINT_DB+                                      | VRNA_CONSTRAINT_DB_PIPE+                                      | VRNA_CONSTRAINT_DB_DOT+                                      | VRNA_CONSTRAINT_DB_X+                                      | VRNA_CONSTRAINT_DB_ANG_BRACK+                                      | VRNA_CONSTRAINT_DB_RND_BRACK;++    hc_string = vrna_alloc(sizeof(char) * (length + 1));+    memset(hc_string, '.', length);+    hc_string[i - 1] = 'x';++    restricted_vc = vrna_fold_compound(vc->sequence, &(vc->exp_params->model_details), VRNA_OPTION_PF);+    vrna_constraints_add(restricted_vc, hc_string, constraint_options);+    free(hc_string);++    vrna_exp_params_subst(restricted_vc, vc->exp_params);++    vrna_pf(restricted_vc, NULL);+    calculate_probability_unpaired(restricted_vc, conditional_prob_unpaired[i]);++    restricted_vc->sc = NULL;+    vrna_fold_compound_free(restricted_vc);+  }++  vrna_sc_remove(vc);+}++static void pairing_probabilities_from_sampling(vrna_fold_compound_t *vc, const double *epsilon, int sample_size, double *prob_unpaired, double **conditional_prob_unpaired)+{+  double kT;+  int length = vc->length;+  int i, j, s;+  st_back = 1; /* is this really required? */++  addSoftConstraint(vc, epsilon, length);++  vc->exp_params->model_details.compute_bpp = 0;++  /* get new (constrained) MFE to scale pf computations properly */+  double mfe = (double)vrna_mfe(vc, NULL);+  vrna_exp_params_rescale(vc, &mfe);++  vrna_pf(vc, NULL);+++#ifdef _OPENMP+  #pragma omp parallel for private(s)+#endif+  for (s = 0; s < sample_size; ++s)+  {+    char *sample = vrna_pbacktrack(vc);++#ifdef _OPENMP+    #pragma omp critical+#endif+    {+      for (i = 1; i <= length; ++i)+      {+        if (sample[i-1] != '.')+          continue;++        ++prob_unpaired[i];++        for (j = 1; j <= length; ++j)+          if (sample[j-1] == '.')+            ++conditional_prob_unpaired[i][j];+      }+    }++    free(sample);+  }++  for (i = 1; i <= length; ++i)+  {+    if (prob_unpaired[i])+      for (j = 1; j <= length; ++j)+        conditional_prob_unpaired[i][j] /= prob_unpaired[i];++    prob_unpaired[i] /= sample_size;++    assert(prob_unpaired[i] >= 0 && prob_unpaired[i] <= 1);+  }++  vrna_sc_remove(vc);+}++static void allocateProbabilityArrays(double **unpaired, double ***conditional_unpaired, int length)+{+  int i;++  *unpaired = vrna_alloc(sizeof(double) * (length + 1));+  *conditional_unpaired = vrna_alloc(sizeof(double*) * (length + 1));++  for (i = 1; i <= length; ++i)+    (*conditional_unpaired)[i] = vrna_alloc(sizeof(double) * (length + 1));+}++static void freeProbabilityArrays(double *unpaired, double **conditional_unpaired, int length)+{+  int i;++  free(unpaired);+  for (i = 1; i <= length; ++i)+    free(conditional_unpaired[i]);+  free(conditional_unpaired);+}++static void evaluate_perturbation_vector_gradient(vrna_fold_compound_t *vc, const double *epsilon, const double *q_prob_unpaired, double sigma_squared, double tau_squared, int objective_function, int sample_size, double *gradient)+{+  double *p_prob_unpaired;+  double **p_conditional_prob_unpaired;+  int i, mu;+  int length = vc->length;+  double kT = vc->exp_params->kT / 1000;++  allocateProbabilityArrays(&p_prob_unpaired, &p_conditional_prob_unpaired, length);++  if (sample_size > 0)+    pairing_probabilities_from_sampling(vc, epsilon, sample_size, p_prob_unpaired, p_conditional_prob_unpaired);+  else+    pairing_probabilities_from_restricted_pf(vc, epsilon, p_prob_unpaired, p_conditional_prob_unpaired);++  for (mu = 1; mu <= length; ++mu)+  {+    double sum = 0;++    if (objective_function == VRNA_OBJECTIVE_FUNCTION_QUADRATIC)+    {+      for (i = 1; i <= length; ++i)+      {+        if (q_prob_unpaired[i] < 0) /* ignore positions with missing data */+          continue;++        sum += (p_prob_unpaired[i] - q_prob_unpaired[i])+               * p_prob_unpaired[i] * (p_prob_unpaired[mu] - p_conditional_prob_unpaired[i][mu])+               / sigma_squared;+      }++      gradient[mu] = 2 * (epsilon[mu] / tau_squared + sum/kT);+    }+    else if (objective_function == VRNA_OBJECTIVE_FUNCTION_ABSOLUTE)+    {+      for (i = 1; i <= length; ++i)+        if (q_prob_unpaired[i] >= 0 && p_prob_unpaired[i] != q_prob_unpaired[i])+          sum += (p_prob_unpaired[i] * (p_prob_unpaired[mu] - p_conditional_prob_unpaired[i][mu])) / kT+                 / sigma_squared+                 * (p_prob_unpaired[i] > q_prob_unpaired[i] ? 1. : -1.);++      if (epsilon[mu])+        sum += (epsilon[mu] > 0 ? 1. : -1.) / tau_squared;++      gradient[mu] = sum;+    }+  }++  freeProbabilityArrays(p_prob_unpaired, p_conditional_prob_unpaired, length);+}++#ifdef WITH_GSL+typedef struct parameters_gsl {+  vrna_fold_compound_t *vc;+  const double *q_prob_unpaired;+  double sigma_squared;+  double tau_squared;+  int objective_function;+  int sample_size;+} parameters_gsl;++static double f_gsl(const gsl_vector *x, void *params)+{+  parameters_gsl *p = params;++  return evaluate_perturbation_vector_score(p->vc, x->data, p->q_prob_unpaired, p->sigma_squared, p->tau_squared, p->objective_function);+}++static void df_gsl(const gsl_vector *x, void *params, gsl_vector *df)+{+  parameters_gsl *p = params;++  gsl_vector_set(df, 0, 0);+  evaluate_perturbation_vector_gradient(p->vc, x->data, p->q_prob_unpaired, p->sigma_squared, p->tau_squared, p->objective_function, p->sample_size, df->data);+}++static void fdf_gsl(const gsl_vector *x, void *params, double *f, gsl_vector *g)+{+  *f = f_gsl(x, params);+  df_gsl(x, params, g);+}+#endif /* WITH_GSL */++PUBLIC void+vrna_sc_minimize_pertubation(vrna_fold_compound_t *vc,+                              const double *q_prob_unpaired,+                              int objective_function,+                              double sigma_squared,+                              double tau_squared,+                              int algorithm,+                              int sample_size,+                              double *epsilon,+                              double initialStepSize,+                              double minStepSize,+                              double minImprovement,+                              double minimizerTolerance,+                              progress_callback callback){++  int iteration_count = 0;+  const int max_iterations = 100;+  int length = vc->length;++#ifdef WITH_GSL+  const gsl_multimin_fdfminimizer_type *minimizer_type = 0;++  struct {int type; const gsl_multimin_fdfminimizer_type *gsl_type;} algorithms[] = {{VRNA_MINIMIZER_CONJUGATE_FR, gsl_multimin_fdfminimizer_conjugate_fr},+                                                                                     {VRNA_MINIMIZER_CONJUGATE_PR, gsl_multimin_fdfminimizer_conjugate_pr},+                                                                                     {VRNA_MINIMIZER_VECTOR_BFGS, gsl_multimin_fdfminimizer_vector_bfgs},+                                                                                     {VRNA_MINIMIZER_VECTOR_BFGS2, gsl_multimin_fdfminimizer_vector_bfgs2},+                                                                                     {VRNA_MINIMIZER_STEEPEST_DESCENT, gsl_multimin_fdfminimizer_steepest_descent},+                                                                                     {0, NULL}};+  int i;+  for (i = 0; algorithms[i].type; ++i)+    if (algorithms[i].type == algorithm)+    {+      minimizer_type = algorithms[i].gsl_type;+      break;+    }++  if (minimizer_type)+  {+    parameters_gsl parameters;+    gsl_multimin_function_fdf fdf;+    gsl_multimin_fdfminimizer *minimizer;+    gsl_vector *vector;++    int status;++    parameters.vc = vc;+    parameters.q_prob_unpaired = q_prob_unpaired;+    parameters.sigma_squared = sigma_squared;+    parameters.tau_squared = tau_squared;+    parameters.objective_function = objective_function;+    parameters.sample_size = sample_size;++    fdf.n = length + 1;+    fdf.f = &f_gsl;+    fdf.df = &df_gsl;+    fdf.fdf = &fdf_gsl;+    fdf.params = (void*)&parameters;++    minimizer = gsl_multimin_fdfminimizer_alloc(minimizer_type, length + 1);+    vector = gsl_vector_calloc(length + 1);++    /* gsl_multimin_fdfminimizer_set(minimizer, &fdf, vector, 0.01, 1e-4); */+    gsl_multimin_fdfminimizer_set(minimizer, &fdf, vector, initialStepSize, minimizerTolerance);++    if (callback)+      callback(0, minimizer->f, minimizer->x->data);++    do+    {+      ++iteration_count;+      status = gsl_multimin_fdfminimizer_iterate(minimizer);++      if (callback)+        callback(iteration_count, minimizer->f, minimizer->x->data);++      if (status)+        break;++      status = gsl_multimin_test_gradient(minimizer->gradient, minimizerTolerance);+    }+    while (status == GSL_CONTINUE && iteration_count < max_iterations);++    memcpy(epsilon, minimizer->x->data, sizeof(double) * (length + 1));++    gsl_multimin_fdfminimizer_free(minimizer);+    gsl_vector_free(vector);++    return;+  }+#endif /* WITH_GSL */++  double improvement;+  const double min_improvement = minImprovement;++  double *new_epsilon = vrna_alloc(sizeof(double) * (length + 1));+  double *gradient = vrna_alloc(sizeof(double) * (length + 1));++  double score = evaluate_perturbation_vector_score(vc, epsilon, q_prob_unpaired, sigma_squared, tau_squared, objective_function);++  if (callback)+    callback(0, score, epsilon);++  do+  {+    double new_score;+    double step_size;++    ++iteration_count;++    evaluate_perturbation_vector_gradient(vc, epsilon, q_prob_unpaired, sigma_squared, tau_squared, objective_function, sample_size, gradient);++    /*    step_size = 0.5 / calculate_norm(gradient, length);*/+    step_size = initialStepSize;++    do+    {+      int i;+      for (i = 1; i <= length; ++i)+        new_epsilon[i] = epsilon[i] - step_size * gradient[i];++      new_score = evaluate_perturbation_vector_score(vc, new_epsilon, q_prob_unpaired, sigma_squared, tau_squared, objective_function);+      improvement = 1 - new_score / score;+      step_size /= 2;+    } while ((improvement < min_improvement) && (step_size >= minStepSize));++    if (new_score > score)+      break;++    if (callback)+      callback(iteration_count, new_score, new_epsilon);++    score = new_score;+    memcpy(epsilon, new_epsilon, sizeof(double) * (length+1));+  } while (improvement >= min_improvement && iteration_count < max_iterations);++  free(gradient);+  free(new_epsilon);+}+
+ C/ViennaRNA/perturbation_fold.h view
@@ -0,0 +1,151 @@+#ifndef VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H+#define VIENNA_RNA_PACKAGE_PERTURBATION_FOLD_H++#include "data_structures.h"++/**+ *  @file perturbation_fold.h+ *  @brief Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments+ *  @ingroup perturbation+ */++/**+ *  @addtogroup perturbation+ *  @brief Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments+ */++/**+ * @brief Use the sum of squared aberrations as objective function+ *+ * @f$ F(\vec\epsilon) = \sum_{i = 1}^n{ \frac{\epsilon_i^2}{\tau^2} } + \sum_{i = 1}^n{ \frac{(p_i(\vec\epsilon) - q_i)^2}{\sigma^2} } \to min @f$+ *+ * @ingroup perturbation+ */+#define VRNA_OBJECTIVE_FUNCTION_QUADRATIC 0++/**+ * @brief Use the sum of absolute aberrations as objective function+ *+ * @f$ F(\vec\epsilon) = \sum_{i = 1}^n{ \frac{|\epsilon_i|}{\tau^2} } + \sum_{i = 1}^n{ \frac{|p_i(\vec\epsilon) - q_i|}{\sigma^2} } \to min @f$+ *+ * @ingroup perturbation+ */+#define VRNA_OBJECTIVE_FUNCTION_ABSOLUTE 1++/**+ * @brief Use a custom implementation of the gradient descent algorithm to minimize the objective function+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_DEFAULT 0++/**+ * @brief Use the GNU Scientific Library implementation of the Fletcher-Reeves conjugate gradient algorithm to minimize the objective function+ *+ * Please note that this algorithm can only be used when the GNU Scientific Library is available on your system+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_CONJUGATE_FR 1++/**+ * @brief Use the GNU Scientific Library implementation of the Polak-Ribiere conjugate gradient algorithm to minimize the objective function+ *+ * Please note that this algorithm can only be used when the GNU Scientific Library is available on your system+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_CONJUGATE_PR 2++/**+ * @brief Use the GNU Scientific Library implementation of the vector Broyden-Fletcher-Goldfarb-Shanno algorithm to minimize the objective function+ *+ * Please note that this algorithm can only be used when the GNU Scientific Library is available on your system+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_VECTOR_BFGS 3++/**+ * @brief Use the GNU Scientific Library implementation of the vector Broyden-Fletcher-Goldfarb-Shanno algorithm to minimize the objective function+ *+ * Please note that this algorithm can only be used when the GNU Scientific Library is available on your system+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_VECTOR_BFGS2 4++/**+ * @brief Use the GNU Scientific Library implementation of the steepest descent algorithm to minimize the objective function+ *+ * Please note that this algorithm can only be used when the GNU Scientific Library is available on your system+ *+ * @ingroup perturbation+ */+#define VRNA_MINIMIZER_STEEPEST_DESCENT 5++/**+ * @brief Callback for following the progress of the minimization process+ *+ * @param iteration The number of the current iteration+ * @param score     The score of the objective function+ * @param epsilon   The perturbation vector yielding the reported score+ *+ * @ingroup perturbation+ */+typedef void (*progress_callback)(int iteration, double score, double *epsilon);++/**+ *  @brief Find a vector of perturbation energies that minimizes the discripancies between predicted and observed pairing probabilities and the amount of neccessary adjustments+ *+ *  Use an iterative minimization algorithm to find a vector of perturbation energies whose incorporation as soft constraints shifts the predicted+ *  pairing probabilities closer to the experimentally observed probabilities.+ *  The algorithm aims to minimize an objective function that penalizes discripancies between predicted and observed pairing probabilities and energy model adjustments,+ *  i.e. an appropriate vector of perturbation energies satisfies+ *  @f[+ *  F(\vec\epsilon) = \sum_{\mu}{ \frac{\epsilon_{\mu}^2}{\tau^2} } + \sum_{i =+ *  1}^n{ \frac{(p_i(\vec\epsilon) - q_i)^2}{\sigma^2} } \to \min.+ *  @f]+ *+ *  An initialized fold compound and an array containing the observed probability for each nucleotide to be unbound are required as input data.+ *  The parameters objective_function, sigma_squared and tau_squared are responsible for adjusting the aim of the objective function.+ *  Dependend on which type of objective function is selected, either squared or absolute aberrations are contributing to the objective function.+ *  The ratio of the parameters sigma_squared and tau_squared can be used to adjust the algorithm to find a solution either close to the thermodynamic prediction+ *  (sigma_squared >> tau_squared) or close to the experimental data (tau_squared >> sigma_squared).+ *  The minimization can be performed by makeing use of a custom gradient descent implementation or using one of the minimizing algorithms provided by the GNU Scientific Library.+ *  All algorithms require the evaluation of the gradient of the objective function, which includes the evaluation of conditional pairing probabilites.+ *  Since an exact evaluation is expensive, the probabilities can also be estimated from sampling by setting an appropriate sample size.+ *  The found vector of perturbation energies will be stored in the array epsilon.+ *  The progress of the minimization process can be tracked by implementing and passing a callback function.+ *+ *  @see For further details we refere to @cite washietl:2012.+ *  @ingroup perturbation+ *+ *  @param vc                 Pointer to a fold compound+ *  @param q_prob_unpaired    Pointer to an array containing the probability to be unpaired for each nucleotide+ *  @param objective_function The type of objective function to be used (VRNA_OBJECTIVE_FUNCTION_QUADRATIC / VRNA_OBJECTIVE_FUNCTION_LINEAR)+ *  @param sigma_squared      A factor used for weighting the objective function.+ *                            More weight on this factor will lead to a solution close to the null vector.+ *  @param tau_squared        A factor used for weighting the objective function.+ *                            More weight on this factor will lead to a solution close to the data provided in q_prob_unpaired.+ *  @param algorithm          The minimization algorithm (VRNA_MINIMIZER_*)+ *  @param sample_size        The number of sampled sequences used for estimating the pairing probabilities. A value <= 0 will lead to an exact evaluation.+ *  @param epsilon            A pointer to an array used for storing the calculated vector of perturbation energies+ *  @param callback           A pointer to a callback function used for reporting the current minimization progress+ *+ */+void vrna_sc_minimize_pertubation(vrna_fold_compound_t *vc,+                                  const double *q_prob_unpaired,+                                  int objective_function,+                                  double sigma_squared,+                                  double tau_squared,+                                  int algorithm,+                                  int sample_size,+                                  double *epsilon,+                                  double initialStepSize,+                                  double minStepSize,+                                  double minImprovement,+                                  double minimizerTolerance,+                                  progress_callback callback);++#endif
+ C/ViennaRNA/plex.c view
@@ -0,0 +1,3040 @@+/*+           compute the duplex structure of two RNA strands,+                allowing only inter-strand base pairs.+         see cofold() for computing hybrid structures without+                             restriction.+                             Ivo Hofacker+                          Vienna RNA package++*/+++/*+  library containing the function used in rnaplex+  the program rnaplex uses the following function+  Lduplexfold: finds high scoring segments+  it stores the end-position of these segments in an array+  and call then for each of these positions the duplexfold function+  which allows one to make backtracking for each of the high scoring position+  It allows one to find suboptimal partially overlapping (depends on a a parameter)+  duplexes between a long RNA and a shorter one.+  Contrarly to RNAduplex, the energy model is not in E~log(N),+  where N is the length of an interial loop but used an affine model,+  where the extension and begin parameter are fitted to the energy+  parameter used by RNAduplex. This allows one to check for duplex between a short RNA(20nt)+  and a long one at the speed of 1Mnt/s. At this speed the whole genome (3Gnt) can be analyzed for one siRNA+  in about 50 minutes.+  The algorithm is based on an idea by Durbin and Eddy:when the alginment reach a value larger than a+  given threshold this value is stored in an array. When the alignment score goes+  then under this threshold, the alignemnent begin from this value, in that way the backtracking allow us+  to find all non-overlapping high-scoring segments.+  For more information check "durbin, biological sequence analysis"+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/fold.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/ali_plex.h"+#include "ViennaRNA/loop_energies.h"+/* #################SIMD############### */++/* int subopt_sorted=0; */++#define PUBLIC+#define PRIVATE static++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */+#define ARRAY 32          /*array size*/+#define UNIT 100+#define MINPSCORE -2 * UNIT++/**+*** Macro that define indices for the Single Array approach defined in FLduplexfold_XS->gain of 20% in runtime+*** so that everything is done in a 1D array.+*** input is idx for i, j for j and the length of the query RNA+*** 1D is divided in 6 subarrays, one for each number of allowed state+*** The length of each subarray is 5*L. 5 the maximal stored distance on the target sequence,+*** L is the length of the query sequence+**/+#define LCI(i,j,l)      ((i     )*l + j)+#define LINI(i,j,l)     ((i +  5)*l + j)+#define LBXI(i,j,l)     ((i + 10)*l + j)+#define LBYI(i,j,l)     ((i + 15)*l + j)+#define LINIX(i,j,l)    ((i + 20)*l + j)+#define LINIY(i,j,l)    ((i + 25)*l + j)++PRIVATE void  encode_seqs(const char *s1, const char *s2);+PRIVATE short *encode_seq(const char *seq);+PRIVATE void  update_dfold_params(void);+/**+*** duplexfold(_XS)/backtrack(_XS) computes duplex interaction with standard energy and considers extension_cost+*** find_max(_XS)/plot_max(_XS) find suboptimals and MFE+*** fduplexfold(_XS) computes duplex in a plex way+**/+PRIVATE duplexT duplexfold(const char *s1, const char *s2, const int extension_cost);+PRIVATE char * backtrack(int i, int j, const int extension_cost);+PRIVATE void   find_max(const int *position, const int *position_j, const int delta, const int threshold, const int length, const char *s1, const char *s2, const int extension_cost, const int fast,const int il_a, const int il_b, const int b_a, const int b_b);+PRIVATE void   plot_max(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast,const int il_a, const int il_b, const int b_a, const int b_b);++/* PRIVATE duplexT duplexfold_XS(const char *s1, const char *s2,const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold); */+PRIVATE duplexT duplexfold_XS(const char *s1, const char *s2,const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold, const int i_flag, const int j_flag);+/* PRIVATE char *   backtrack_XS(int i, int j, const int** access_s1, const int** access_s2); */+PRIVATE char *backtrack_XS(int i, int j, const int **access_s1,const int **access_s2,const int i_flag, const int j_flag );+PRIVATE void find_max_XS(const int *position, const int *position_j,const int delta, const int threshold, const int alignment_length,+                         const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast,const int il_a, const int il_b, const int b_a, const int b_b);+PRIVATE void plot_max_XS(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast,const int il_a, const int il_b, const int b_a, const int b_b);+PRIVATE duplexT fduplexfold(const char *s1, const char *s2, const int extension_cost, const int il_a, const int il_b, const int b_a, const int b_b);+PRIVATE char *fbacktrack(int i, int j, const int extension_cost,const int il_a, const int il_b, const int b_a, const int b_b, int *dG);+PRIVATE duplexT fduplexfold_XS(const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold,const int il_a, const int il_b, const int b_a, const int b_b);+PRIVATE char * fbacktrack_XS(int i, int j, const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int il_a, const int il_b, const int b_a, const int b_b, int *dGe, int *dGeplex, int *dGx, int *dGy);++++/*@unused@*/++#define MAXSECTORS      500     /* dimension for a backtrack array */+#define LOCALITY        0.      /* locality parameter for base-pairs */++PRIVATE vrna_param_t *P = NULL;++/**+*** energy array used in fduplexfold and fduplexfold_XS+*** We do not use the 1D array here as it is not time critical+*** It also makes the code more readable+*** c -> stack;in -> interior loop;bx/by->bulge;inx/iny->1xn loops+**/++PRIVATE int   **c=NULL, **in=NULL, **bx=NULL, **by=NULL, **inx=NULL, **iny=NULL;++/**+*** S1, SS1, ... contains the encoded sequence for target and query+*** n1, n2, n3, n4 contains target and query length+**/++PRIVATE short  *S1=NULL, *SS1=NULL, *S2=NULL, *SS2=NULL;/*contains the sequences*/+PRIVATE int   n1,n2;    /* sequence lengths */+PRIVATE int n3, n4; /*sequence length for the duplex*/;+++/*-----------------------------------------------------------------------duplexfold_XS---------------------------------------------------------------------------*/++/**+*** duplexfold_XS is the pendant to the duplex function as defined in duplex.c+*** but takes the accessibility into account. It is similar to the MFE version of RNAup+*** The only approximation made is that target 3' end - query 5' end base pair is known+*** s1,s2 are the query and target sequence; access_s1, access_s2 are the accessibility+*** profiles, i_pos, j_pos are the coordinates of the closing pair.+**/++++PRIVATE duplexT duplexfold_XS(const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold, const int i_flag, const int j_flag) {+  int i, j,p,q, Emin=INF, l_min=0, k_min=0;+  char *struc;+  vrna_md_t   md;++  struc=NULL;+  duplexT mfe;+  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);++  set_model_details(&md);++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  for (i=0; i<=n3; i++){+    for(j=0;j<=n4;j++){+      c[i][j]=INF;+    }+  }+  encode_seqs(s1, s2);+  int type, type2, type3, E, k,l;+  i=n3-i_flag; j=1+j_flag;+  type = pair[S1[i]][S2[j]];+  if(!type){+    printf("Error during initialization of the duplex in duplexfold_XS\n");+    mfe.structure=NULL;+    mfe.energy = INF;+    return mfe;+  }+  c[i][j] = P->DuplexInit;+  /**  if (type>2) c[i][j] += P->TerminalAU;+  ***  c[i][j]+=P->dangle3[rtype[type]][SS1[i+1]];+  ***  c[i][j]+=P->dangle5[rtype[type]][SS2[j-1]];+  *** The three above lines are replaced by the line below+  **/+++  c[i][j] += E_ExtLoop(rtype[type], (j_flag ? SS2[j-1] : -1) , (i_flag ? SS1[i+1] : -1),  P);++/*   if(j_flag ==0 && i_flag==0){ */+/*     c[i][j] += E_ExtLoop(rtype[type], -1 , -1 , P); */+/*   }else if(j_flag ==0 && i_flag==1){ */+/*     c[i][j] += E_ExtLoop(rtype[type], -1 , SS1[i+1], P); */+/*   }else if(j_flag ==1 && i_flag==0){ */+/*     c[i][j] += E_ExtLoop(rtype[type], SS2[j-1] , -1, P); */+/*   }else { */+/*     c[i][j] += E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1], P); */+/*   } */+  /*  Just in case we have only one bp, we initialize ... */+  /*  k_min, l_min and Emin */+  k_min=i; l_min=j;Emin=c[i][j];+  for (k=i; k>1 ; k--) {+    if(k<i) c[k+1][0]=INF;+    for (l=j; l<=n4-1; l++) {+      if(!(k==i && l==j)){+        c[k][l]=INF;+      }+      type2 = pair[S1[k]][S2[l]];+      if (!type2) continue;+      for (p=k+1; p<= n3 - i_flag && p<k+MAXLOOP-1; p++) {+        for (q = l-1; q >= 1+j_flag; q--) {+          if (p-k+l-q-2>MAXLOOP) break;+          type3=pair[S1[p]][S2[q]];+          if(!type3) continue;+          E = E_IntLoop(p-k-1, l-q-1, type2, rtype[type3],SS1[k+1], SS2[l-1], SS1[p-1], SS2[q+1],P);+          c[k][l] = MIN2(c[k][l], c[p][q]+E);+        }+      }+      E = c[k][l];+      E+=access_s1[i-k+1][i_pos]+access_s2[l-1][j_pos+(l-1)-1];+      /**if (type2>2) E += P->TerminalAU;+      ***if (k>1) E += P->dangle5[type2][SS1[k-1]];+      ***if (l<n4) E += P->dangle3[type2][SS2[l+1]];+      *** Replaced by the line below+      **/+      E+=E_ExtLoop(type2, (k>1) ? SS1[k-1] : -1, (l<n4) ? SS2[l+1] : -1, P);++      if (E<Emin) {+        Emin=E; k_min=k; l_min=l;+      }+    }+  }++  if(Emin  > threshold){+    mfe.energy=INF;+    mfe.ddG=INF;+    mfe.structure=NULL;+    for (i=0; i<=n3; i++) free(c[i]);+    free(c);+    free(S1); free(S2); free(SS1); free(SS2);+    return mfe;+  } else{+    struc = backtrack_XS(k_min, l_min, access_s1, access_s2, i_flag, j_flag);+  }+++  /**+  *** find best dangles combination+  **/+  int dx_5, dx_3, dy_5, dy_3,dGx,dGy,bonus_x;+  dx_5=0; dx_3=0; dy_5=0; dy_3=0;dGx=0;dGy=0;bonus_x=0;+  /* x--------x */+  /*  |||||||| */+  /* x--------x */+   dGx = access_s1[i-k_min+1][i_pos];dx_3=0; dx_5=0;bonus_x=0;+   dGy = access_s2[l_min-j+1][j_pos + (l_min-1)];++  mfe.tb=i_pos -9 - i + k_min -1 -dx_5;+  mfe.te=i_pos -9 -1 + dx_3;+  mfe.qb=j_pos -9 -1 - dy_5;+  mfe.qe=j_pos + l_min -3 -9 + dy_3;+  mfe.ddG=(double) Emin * 0.01;+  mfe.dG1=(double) dGx*0.01 ;+  mfe.dG2=(double) dGy*0.01 ;++  mfe.energy= mfe.ddG - mfe.dG1 - mfe.dG2;++  mfe.structure = struc;+  for (i=0; i<=n3; i++) free(c[i]);+  free(c);+  free(S1); free(S2); free(SS1); free(SS2);+  return mfe;+}+++++++PRIVATE char *backtrack_XS(int i, int j, const int **access_s1,const int **access_s2, const int i_flag, const int j_flag) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;+  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  i0=i;/*MAX2(i-1,1);*/j0=j;/*MIN2(j+1,n4);*/+  while (i<=n3-i_flag && j>=1+j_flag) {+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    type = pair[S1[i]][S2[j]];+    if (!type) vrna_message_error("backtrack failed in fold duplex bli");+    for (k=i+1; k<=n3 && k>i-MAXLOOP-2; k++) {+      for (l=j-1; l>=1; l--) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        type2 = pair[S1[k]][S2[l]];+        if (!type2) continue;+        LE = E_IntLoop(k-i-1, j-l-1, type, rtype[type2], SS1[i+1], SS2[j-1], SS1[k-1], SS2[l+1],P);+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+#if 0+      if (i<n3) E -= P->dangle3[rtype[type]][SS1[i+1]];/* +access_s1[1][i+1]; */+      if (j>1)  E -= P->dangle5[rtype[type]][SS2[j-1]];/* +access_s2[1][j+1]; */+      if (type>2) E -= P->TerminalAU;+#endif+      E -= E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1], P);+      break;+      if (E != P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex bal");+      } else break;+    }+  }+  /* if (i<n3)  i++; */+  /* if (j>1)   j--; */+  struc = (char *) vrna_alloc(i-i0+1+j0-j+1+2);+  for (k=MAX2(i0,1); k<=i; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j; k<=j0; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i0-1,0)); strcat(struc, "&");+  strcat(struc, st2+j-1);+  free(st1); free(st2);+  return struc;+}+++/**+*** fduplexfold(_XS) computes the interaction based on the plex energy model.+*** Faster than duplex approach, but not standard model compliant+*** We use the standard matrix (c, in, etc..., because we backtrack)+**/++PRIVATE duplexT fduplexfold_XS(const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int i_pos, const int j_pos, const int threshold,const int il_a, const int il_b, const int b_a, const int b_b) {+  /**+  *** i,j recursion index+  *** Emin, i_min, j_min MFE position and energy+  *** mfe struc duplex structure+  **/+  int i, j, Emin, i_min, j_min,l1;+  duplexT mfe;+  char *struc;+  /**+  *** bext=b_a bulge extension parameter for linear model+  *** iopen=il_b interior opening for linear model+  *** iext_s=2*il_a asymmetric extension for interior loop+  *** iext_ass=60+il_a symmetric extension for interior loop+  *** min_colonne=INF; max score of a row+  *** i_length;+  *** max_pos; position of best hit during recursion on target+  *** max_pos_j; position of best hit during recursion on query+  *** temp; temp variable for min_colonne+  *** min_j_colonne; position of the minimum on query in row j+  *** max=INF; absolute MFE+  *** n3,n4 length of target and query+  *** DJ contains the accessibility penalty for the query sequence+  *** maxPenalty contains the maximum penalty+  **/+  int bopen=b_b;+  int bext=b_a;+  int iopen=il_b;+  int iext_s=2*il_a;/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  int temp=INF;+  int min_j_colonne;+  int max=INF;+  int **DJ;+  int maxPenalty[4];+  vrna_md_t   md;++  /**+  *** variable initialization+  **/+  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  /**+  *** array initialization+  **/+  c  = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  in = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  bx = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  by = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  inx= (int**) vrna_alloc(sizeof(int *) * (n3+1));+  iny= (int**) vrna_alloc(sizeof(int *) * (n3+1));+  /* #pragma omp parallel for */+  for (i=0; i<=n3; i++){+    c[i]  = (int *) vrna_alloc(sizeof(int) * (n4+1));+    in[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    bx[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    by[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    inx[i]= (int *) vrna_alloc(sizeof(int) * (n4+1));+    iny[i]= (int *) vrna_alloc(sizeof(int) * (n4+1));+  }+  for(i=0; i<n3; i++){+    for(j=0; j<n4; j++){+      in[i][j]=INF;/* no in before  1 */+      c[i][j] =INF; /* no bulge and no in before n2 */+      bx[i][j]=INF;/* no bulge before 1 */+      by[i][j]=INF;+      inx[i][j]=INF;/* no bulge before 1 */+      iny[i][j]=INF;+    }+  }+  /**+  *** sequence encoding+  **/+  encode_seqs(s1,s2);+  /**+  *** Compute max accessibility penalty for the query only once+  **/+  maxPenalty[0]=(int) -1*P->stack[2][2]/2;+  maxPenalty[1]=(int) -1*P->stack[2][2];+  maxPenalty[2]=(int) -3*P->stack[2][2]/2;+  maxPenalty[3]=(int) -2*P->stack[2][2];+++  DJ=(int **)   vrna_alloc(4*sizeof(int*));+  DJ[0]=(int *) vrna_alloc((1+n4)*sizeof(int));+  DJ[1]=(int *) vrna_alloc((1+n4)*sizeof(int));+  DJ[2]=(int *) vrna_alloc((1+n4)*sizeof(int));+  DJ[3]=(int *) vrna_alloc((1+n4)*sizeof(int));++  j=n4-9;+  while(--j>9){+    int jdiff=j_pos+j-11;+    /**+    *** Depending in which direction (i:1->n vs j:m->1) the accessibility is computed we get slightly different results.+    *** We reduce the discrepancies by taking the average of d^i_k and d^j_l+    **/+    DJ[0][j] = 0.5*(access_s2[5][jdiff+4] - access_s2[4][jdiff+4] + access_s2[5][jdiff]  -access_s2[4][jdiff-1]  );+    DJ[1][j] = 0.5*(access_s2[5][jdiff+5] - access_s2[4][jdiff+5] + access_s2[5][jdiff+1]-access_s2[4][jdiff]  ) + DJ[0][j];+    DJ[2][j] = 0.5*(access_s2[5][jdiff+6] - access_s2[4][jdiff+6] + access_s2[5][jdiff+2]-access_s2[4][jdiff+1]) + DJ[1][j];+    DJ[3][j] = 0.5*(access_s2[5][jdiff+7] - access_s2[4][jdiff+7] + access_s2[5][jdiff+3]-access_s2[4][jdiff+2]) + DJ[2][j];++++/*+    DJ[0][j] = access_s2[5][jdiff+4] - access_s2[4][jdiff+4]           ;+    DJ[1][j] = access_s2[5][jdiff+5] - access_s2[4][jdiff+5] + DJ[0][j];+    DJ[2][j] = access_s2[5][jdiff+6] - access_s2[4][jdiff+6] + DJ[1][j];+    DJ[3][j] = access_s2[5][jdiff+7] - access_s2[4][jdiff+7] + DJ[2][j];+    DJ[0][j] = MIN2(DJ[0][j],maxPenalty[0]);+    DJ[1][j] = MIN2(DJ[1][j],maxPenalty[1]);+    DJ[2][j] = MIN2(DJ[2][j],maxPenalty[2]);+    DJ[3][j] = MIN2(DJ[3][j],maxPenalty[3]);+*/+  }++  /**+  *** Start of the recursion+  *** first and last 10 nucleotides on target and query are dummy nucleotides+  *** allow to reduce number of if test+  **/+  i=11;+  i_length=n3-9;+  while(i < i_length) {+    int di1,di2,di3,di4;+    int idiff=i_pos-(n3-10-i);+    di1 = 0.5*(access_s1[5][idiff+4] - access_s1[4][idiff+4] + access_s1[5][idiff]   - access_s1[4][idiff-1]);+    di2 = 0.5*(access_s1[5][idiff+3] - access_s1[4][idiff+3] + access_s1[5][idiff-1] - access_s1[4][idiff-2]) + di1;+    di3 = 0.5*(access_s1[5][idiff+2] - access_s1[4][idiff+2] + access_s1[5][idiff-2] - access_s1[4][idiff-3]) + di2;+    di4 = 0.5*(access_s1[5][idiff+1] - access_s1[4][idiff+1] + access_s1[5][idiff-3] - access_s1[4][idiff-4]) + di3;+/*+    di1 =  access_s1[5][idiff]   - access_s1[4][idiff-1];+    di2 =  access_s1[5][idiff-1] - access_s1[4][idiff-2] + di1;+    di3 =  access_s1[5][idiff-2] - access_s1[4][idiff-3] + di2;+    di4 =  access_s1[5][idiff-3] - access_s1[4][idiff-4] + di3;+    di1=MIN2(di1,maxPenalty[0]);+    di2=MIN2(di2,maxPenalty[1]);+    di3=MIN2(di3,maxPenalty[2]);+    di4=MIN2(di4,maxPenalty[3]);+*/+    j=n4-9;+    min_colonne=INF;+    while (10 < --j) {+      int dj1,dj2,dj3,dj4;+      int jdiff=j_pos+j-11;+      dj1 = DJ[0][j];+      dj2 = DJ[1][j];+      dj3 = DJ[2][j];+      dj4 = DJ[3][j];+      int type, type2;+      type = pair[S1[i]][S2[j]];+      /**+      *** Start duplex+      **/+      /*+      c[i][j]=type ? P->DuplexInit + access_s1[1][idiff]+access_s2[1][jdiff] : INF;+      */+      c[i][j]=type ? P->DuplexInit: INF;+      /**+      *** update lin bx by linx liny matrix+      **/+      type2=pair[S2[j+1]][S1[i-1]];+      /**+      *** start/extend interior loop+      **/+      in[i][j]=MIN2(c[i - 1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s+di1+dj1,+                    in[i - 1][j]+iext_ass + di1);++      /**+      *** start/extend nx1 target+      *** use same type2 as for in+      **/+      inx[i][j]=MIN2(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s+di1+dj1,+                     inx[i-1][j]+iext_ass+di1);+      /**+      *** start/extend 1xn target+      *** use same type2 as for in+      **/+      iny[i][j]=MIN2(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s+di1+dj1,+                     iny[i][j+1]+iext_ass+dj1);+      /**+      *** extend interior loop+      **/+      in[i][j]=MIN2(in[i][j],in[i][j+1]+iext_ass + dj1);+      in[i][j]=MIN2(in[i][j],in[i - 1][j+1]+iext_s + di1 + dj1);+      /**+      *** start/extend bulge target+      **/+      type2=pair[S2[j]][S1[i-1]];+      bx[i][j]=MIN2(bx[i - 1][j]+bext + di1, c[i - 1][j]+bopen+bext+(type2>2?P->TerminalAU:0) + di1);+      /**+      *** start/extend bulge query+      **/+      type2=pair[S2[j+1]][S1[i]];+      by[i][j]=MIN2(by[i][j+1]+bext+dj1, c[i][j+1]+bopen+bext+(type2>2?P->TerminalAU:0)+dj1);+      /**+      ***end update recursion+      ***######################## Start stack extension##############################+      **/+      if(!type){continue;}+      c[i][j]+=E_ExtLoop(type, SS1[i-1], SS2[j+1],P);+      /**+      *** stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+1]]))+        c[i][j]=MIN2(c[i - 1][j+1]+P->stack[rtype[type]][type2]+di1+dj1, c[i][j]);+      /**+      *** 1x0 / 0x1 stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+2]]))+        c[i][j]=MIN2(c[i - 1][j+2]+P->bulge[1]+P->stack[rtype[type]][type2]+di1+dj2,c[i][j]);+      if((type2=pair[S1[i-2]][S2[j+1]]))+        c[i][j]=MIN2(c[i - 2][j+1]+P->bulge[1]+P->stack[type2][rtype[type]]+di2+dj1,c[i][j]);+      /**+      *** 1x1 / 2x2 stack extension+      **/+      if((type2=pair[S1[i-2]][S2[j+2]]))+        c[i][j]=MIN2(c[i - 2][j+2]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+di2+dj2, c[i][j]);+      if((type2 = pair[S1[i-3]][S2[j+3]]))+        c[i][j]=MIN2(c[i - 3][j+3]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di3+dj3,c[i][j]);+      /**+      *** 1x2 / 2x1 stack extension+      *** E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P) corresponds to+      *** P->int21[rtype[type]][type2][SS2[j+2]][SS1[i-1]][SS1[i-1]]+      **/+      if((type2 = pair[S1[i-3]][S2[j+2]]))+        c[i][j]=MIN2(c[i - 3][j+2]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+di3+dj2, c[i][j]);+      if((type2 = pair[S1[i-2]][S2[j+3]]))+        c[i][j]=MIN2(c[i - 2][j+3]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di2+dj3, c[i][j]);++      /**+      *** 2x3 / 3x2 stack extension+      **/+      if((type2 = pair[S1[i-4]][S2[j+3]]))+        c[i][j]=MIN2(c[i - 4][j+3]+P->internal_loop[5]+P->ninio[2]++                     P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di4+dj3, c[i][j]);+      if((type2 = pair[S1[i-3]][S2[j+4]]))+        c[i][j]=MIN2(c[i - 3][j+4]+P->internal_loop[5]+P->ninio[2]++                     P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di3+dj4, c[i][j]);++      /**+      *** So now we have to handle 1x3, 3x1, 3x3, and mxn m,n > 3+      **/+      /**+      *** 3x3 or more+      **/+      c[i][j]=MIN2(in[i - 3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*iext_s+di3+dj3, c[i][j]);+      /**+      *** 2xn or more+      **/+      c[i][j]=MIN2(in[i - 4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di4+dj2, c[i][j]);+      /**+      *** nx2 or more+      **/+      c[i][j]=MIN2(in[i - 2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di2+dj4, c[i][j]);+      /**+      *** nx1 n>2+      **/+      c[i][j]=MIN2(inx[i - 3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di3+dj1, c[i][j]);+      /**+      *** 1xn n>2+      **/+      c[i][j]=MIN2(iny[i - 1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+dj3+di1, c[i][j]);+      /**+      *** nx0 n>1+      **/+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      c[i][j]=MIN2(bx[i - 2][j+1]+di2+dj1+bext+bAU, c[i][j]);+      /**+      *** 0xn n>1+      **/+      c[i][j]=MIN2(by[i - 1][j+2]+di1+dj2+bext+bAU, c[i][j]);+      /*+      remove this line printf("%d\t",c[i][j]);+      */+      temp=min_colonne;+      min_colonne=MIN2(c[i][j]+ E_ExtLoop(rtype[type], SS2[j-1], SS1[i+1], P),min_colonne);+      if(temp>min_colonne){+        min_j_colonne=j;+      }+      /* ---------------------------------------------------------------------end update */+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    i++;+    /*+    remove this line printf("\n");+    */+  }+  Emin=max;+  if(Emin>threshold){+    free(S1); free(S2); free(SS1); free(SS2);+    for (i=0; i<=n3; i++) {+      free(c[i]);+      free(in[i]);+      free(bx[i]);+      free(by[i]);+      free(inx[i]);+      free(iny[i]);+    }+    for (i=0; i<=3; i++) {+      free(DJ[i]);+    }+    free(c);free(in);free(bx);free(by);free(inx);free(iny);free(DJ);+    mfe.energy=0;+    mfe.structure=NULL;+    return mfe;+  }+  i_min=max_pos;+  j_min=max_pos_j;+  int dGe, dGeplex, dGx, dGy;+  dGe=dGeplex=dGx=dGy=0;+  /* printf("MAX fduplexfold_XS %d\n",Emin); */+  struc = fbacktrack_XS(i_min, j_min, access_s1, access_s2, i_pos, j_pos,il_a, il_b,b_a,b_b,&dGe, &dGeplex, &dGx, &dGy);++  l1 = strchr(struc, '&')-struc;+  int size;+  size=strlen(struc)-1;+  int lengthx; int endx; int lengthy; int endy;+  lengthx=l1;+  lengthx-=(struc[0]=='.'?1:0);+  lengthx-=(struc[l1-1]=='.'?1:0);+  endx=(i_pos-(n3-i_min));+  lengthy=size-l1;+  lengthy-=(struc[size]=='.'?1:0);+  lengthy-=(struc[l1+1]=='.'?1:0);+  endy=j_pos+j_min+lengthy -22;+  if (i_min<n3-10) i_min++;+  if (j_min>11 ) j_min--;+  mfe.i = i_min;+  mfe.j = j_min;+  mfe.ddG = (double) Emin*0.01;+  mfe.structure = struc;+  mfe.energy_backtrack = (double) dGe * 0.01;+  mfe.energy = (double) dGeplex * 0.01;+  mfe.opening_backtrack_x = (double) dGx * 0.01;+  mfe.opening_backtrack_y = (double) dGy * 0.01;+  mfe.dG1=0;/* !remove access to complete access array (double) access_s1[lengthx][endx+10] * 0.01; */+  mfe.dG2=0;/* !remove access to complete access array (double) access_s2[lengthy][endy+10] * 0.01; */+  free(S1); free(S2); free(SS1); free(SS2);+  for (i=0; i<=n3; i++) {+    free(c[i]);+    free(in[i]);+    free(bx[i]);+    free(by[i]);+    free(inx[i]);+    free(iny[i]);+  }+  for (i=0; i<=3; i++) {+    free(DJ[i]);+  }+  free(DJ);+  free(c);free(in);free(bx);free(by);free(iny);free(inx);+  return mfe;+}++PRIVATE char *fbacktrack_XS(int i, int j, const int** access_s1, const int** access_s2, const int i_pos, const int j_pos,const int il_a, const int il_b, const int b_a, const int b_b, int *dG, int *dGplex, int *dGx, int *dGy) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;+  int bopen=b_b;+  int bext=b_a;+  int iopen=il_b;+  int iext_s=2*il_a;/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  i0=MIN2(i+1,n3-10); j0=MAX2(j-1,11);+  int state;+  state=1; /* we start backtracking from a a pair , i.e. c-matrix */+  /* state 1 -> base pair, c+     state 2 -> interior loop, in+     state 3 -> bx loop, bx+     state 4 -> by loop, by+  */+  traced=1;+  k=i; l=j; /* stores the i,j information for subsequence usage see * */+  int idiff,jdiff;+  /**+  *** (type>2?P->TerminalAU:0)+P->dangle3[rtype[type]][SS1[i+1]]+P->dangle5[rtype[type]][SS2[j-1]];+  **/++  int maxPenalty[4];+  vrna_md_t   md;++  set_model_details(&md);++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)){+    update_dfold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  maxPenalty[0]=(int) -1*P->stack[2][2]/2;+  maxPenalty[1]=(int) -1*P->stack[2][2];+  maxPenalty[2]=(int) -3*P->stack[2][2]/2;+  maxPenalty[3]=(int) -2*P->stack[2][2];++  type = pair[S1[i]][S2[j]];+  *dG+= E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1] , P);+  *dGplex=*dG;++  while (i>10 && j<=n4-9 && traced) {+    int di1,di2,di3,di4;+    idiff=i_pos-(n3-10-i);+    di1 = 0.5*(access_s1[5][idiff+4] - access_s1[4][idiff+4] + access_s1[5][idiff]   - access_s1[4][idiff-1]);+    di2 = 0.5*(access_s1[5][idiff+3] - access_s1[4][idiff+3] + access_s1[5][idiff-1] - access_s1[4][idiff-2]) + di1;+    di3 = 0.5*(access_s1[5][idiff+2] - access_s1[4][idiff+2] + access_s1[5][idiff-2] - access_s1[4][idiff-3]) + di2;+    di4 = 0.5*(access_s1[5][idiff+1] - access_s1[4][idiff+1] + access_s1[5][idiff-3] - access_s1[4][idiff-4]) + di3;+/*+    di1 = access_s1[5][idiff]   - access_s1[4][idiff-1];+    di2 = access_s1[5][idiff-1] - access_s1[4][idiff-2] + di1;+    di3 = access_s1[5][idiff-2] - access_s1[4][idiff-3] + di2;+    di4 = access_s1[5][idiff-3] - access_s1[4][idiff-4] + di3;+    di1=MIN2(di1,maxPenalty[0]);+    di2=MIN2(di2,maxPenalty[1]);+    di3=MIN2(di3,maxPenalty[2]);+    di4=MIN2(di4,maxPenalty[3]);+*/+    int dj1,dj2,dj3,dj4;+    jdiff=j_pos+j-11;+    dj1=0.5*(access_s2[5][jdiff+4] - access_s2[4][jdiff+4] + access_s2[5][jdiff]  -access_s2[4][jdiff-1]  );+    dj2=0.5*(access_s2[5][jdiff+5] - access_s2[4][jdiff+5] + access_s2[5][jdiff+1]-access_s2[4][jdiff]  ) + dj1;+    dj3=0.5*(access_s2[5][jdiff+6] - access_s2[4][jdiff+6] + access_s2[5][jdiff+2]-access_s2[4][jdiff+1]) + dj2;+    dj4=0.5*(access_s2[5][jdiff+7] - access_s2[4][jdiff+7] + access_s2[5][jdiff+3]-access_s2[4][jdiff+2]) + dj3;++++/*+    dj1 = access_s2[5][jdiff+4] - access_s2[4][jdiff+4];+    dj2 = access_s2[5][jdiff+5] - access_s2[4][jdiff+5] + dj1;+    dj3 = access_s2[5][jdiff+6] - access_s2[4][jdiff+6] + dj2;+    dj4 = access_s2[5][jdiff+7] - access_s2[4][jdiff+7] + dj3;+    dj1=MIN2(dj1,maxPenalty[0]);+    dj2=MIN2(dj2,maxPenalty[1]);+    dj3=MIN2(dj3,maxPenalty[2]);+    dj4=MIN2(dj4,maxPenalty[3]);+*/+    traced=0;+    switch(state){+    case 1:+      type = pair[S1[i]][S2[j]];+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      if(!type) vrna_message_error("backtrack failed in fold duplex");+      type2=pair[S1[i-1]][S2[j+1]];+      if(type2 && c[i][j]== (c[i - 1][j+1]+P->stack[rtype[type]][type2]+di1+dj1)){+        k=i-1;+        l=j+1;+        (*dG)+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di1;+        *dGy+=dj1;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-1]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 1][j+2]+P->bulge[1]+P->stack[rtype[type]][type2]+di1+dj2)){+        k=i-1;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di1;+        *dGy+=dj2;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-2]][S2[j+1]];+      if(type2 && c[i][j]==(c[i - 2][j+1]+P->bulge[1]+P->stack[type2][rtype[type]]+di2+dj1)){+        k=i-2;+        l=j+1;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di2;+        *dGy+=dj1;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-2]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 2][j+2]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+di2+dj2)){+        k=i-2;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di2;+        *dGy+=dj2;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 3][j+3]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di3+dj3)){+        k=i-3;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di3;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 3][j+2]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+di3+dj2)){+        k=i-3;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di3;+        *dGy+=dj2;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-2]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 2][j+3]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di2+dj3)){+        k=i-2;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di2;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-4]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 4][j+3]+P->internal_loop[5]+P->ninio[2]++                            P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di4+dj3)){+        k=i-4;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di2;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+4]];+      if(type2 && c[i][j]==(c[i - 3][j+4]+P->internal_loop[5]+P->ninio[2]++                            P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di3+dj4)){+        k=i-3;+        l=j+4;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di2;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+di3+dj3+2*iext_s)){+        k=i;+        l=j;+        *dGplex+=P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*iext_s;+        *dGx+=di3;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-3;+        j=j+3;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+di4+dj2+iext_s+2*iext_ass)){+        k=i;+        l=j;+        *dGplex+=P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass;+        *dGx+=di4;+        *dGy+=dj2;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-4;+        j=j+2;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+di2+dj4+iext_s+2*iext_ass)){+        k=i;+        l=j;+        *dGplex+=P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass;+        *dGx+=di2;+        *dGy+=dj4;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-2;+        j=j+4;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(inx[i - 3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di3+dj1)){+        k=i;+        l=j;+        *dGplex+=P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di3+dj1;+        *dGx+=di3;+        *dGy+=dj1;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-3;+        j=j+1;+        state=5;+        traced=1;+        break;+      }+      if(c[i][j]==(iny[i - 1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di1+dj3)){+        k=i;+        l=j;+        *dGplex+=P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di1+dj3;+        *dGx+=di1;+        *dGy+=dj3;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-1;+        j=j+3;+        state=6;+        traced=1;+        break;+      }+      if(c[i][j]==(bx[i - 2][j+1]+di2+dj1+bext+bAU)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        *dGplex+=bext+bAU;+        *dGx+=di2;+        *dGy+=dj1;+        i=i-2;+        j=j+1;+        state=3;+        traced=1;+        break;+      }+      if(c[i][j]==(by[i - 1][j+2]+di1+dj2+bext+bAU)){+        k=i;+        l=j;+        *dGplex+=bext+bAU;+        *dGx+=di1;+        *dGy+=dj2;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-1;+        j=j+2;+        state=4;+        traced=1;+        break;+      }+      break;+    case 2:+      if(in[i][j]==(in[i - 1][j+1]+iext_s + di1 + dj1)){+        i--;+        j++;+        *dGplex+=iext_s;+        *dGx+=di1;+        *dGy+=dj1;+        state=2;+        traced=1;+        break;+      }+      if(in[i][j]==(in[i - 1][j]+iext_ass + di1)){+        i=i-1;+        *dGplex+=iext_ass;+        *dGx+=di1;+        state=2;+        traced=1;+        break;+      }+      if(in[i][j]==(in[i][j+1]+iext_ass + dj1)){+        j++;+        state=2;+        *dGy+=dj1;+        *dGplex+=iext_ass;+        traced=1;+        break;+      }+      type2=pair[SS2[j+1]][SS1[i-1]];+      if(type2 && in[i][j]==(c[i - 1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s + di1 +dj1)){+        *dGplex+=P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s;+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di1;+        *dGy+=dj1;+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 3:+      if(bx[i][j]==(bx[i - 1][j]+bext+di1)){+        i--;+        *dGplex+=bext;+        *dGx+=di1;+        state=3;+        traced=1;+        break;+      }+      type2=pair[S2[j]][S1[i-1]];+      if(type2 && bx[i][j]==(c[i - 1][j]+bopen+bext+(type2>2?P->TerminalAU:0)+di1)){+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=bopen+bext+(type2>2?P->TerminalAU:0);+        *dGx+=di1;+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 4:+      if(by[i][j]==(by[i][j+1] + bext +dj1)){+        j++;+        *dGplex+=bext;+        state=4;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i]];+      if(type2 && by[i][j]==(c[i][j+1]+bopen+bext+(type2>2?P->TerminalAU:0) + dj1)){+        int temp; temp=k; k=i; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGplex+=bopen+bext+(type2>2?P->TerminalAU:0);+        *dGy+=dj1;+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 5:+      if(inx[i][j]==(inx[i-1][j]+iext_ass+di1)) {+        i--;+        *dGplex+=iext_ass;+        *dGx+=di1;+        state=5;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i-1]];+      if(type2 && inx[i][j]==(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s+di1+dj1)){+        *dGplex+=P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s;+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di1;+        *dGy+=dj1;+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 6:+      if(iny[i][j]==(iny[i][j+1]+iext_ass+dj1)) {+        j++;+        *dGplex+=iext_ass;+        *dGx+=dj1;+        state=6;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i-1]];+      if(type2 && iny[i][j]==(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s+di1+dj1)){+        *dGplex+=P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s;+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        *dGx+=di1;+        *dGy+=dj1;+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    }+  }+  if (!traced) {+    idiff=i_pos-(n3-10-i);+    jdiff=j_pos+j-11;+    E=c[i][j];+    /**+    *** if (i>1) {E -= P->dangle5[type][SS1[i-1]]; *dG+=P->dangle5[type][SS1[i-1]];*dGplex+=P->dangle5[type][SS1[i-1]];}+    *** if (j<n4){E -= P->dangle3[type][SS2[j+1]]; *dG+=P->dangle3[type][SS2[j+1]];*dGplex+=P->dangle3[type][SS2[j+1]];}+    *** if (type>2) {E -= P->TerminalAU; *dG+=P->TerminalAU;*dGplex+=P->TerminalAU;}+    **/+    int correction;+    correction = E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n4) ? SS2[j+1] : -1, P);+    *dG+=correction;+    *dGplex+=correction;+    E-=correction;++/*+ if (E != P->DuplexInit+access_s1[1][idiff]+access_s2[1][jdiff]) {+      vrna_message_error("backtrack failed in second fold duplex");+    }+*/+    if (E != P->DuplexInit) {+      vrna_message_error("backtrack failed in second fold duplex");+    }+    else{+      *dG+=P->DuplexInit;+      *dGplex+=P->DuplexInit;+      *dGx+=0;/* access_s1[1][idiff]; */+      *dGy+=0;/* access_s2[1][jdiff]; */+      st1[i-1]='(';+      st2[j-1]=')';+    }+  }+  if (i>11)  i--;+  if (j<n4-10) j++;+  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0));+  strcat(struc, "&");+  strcat(struc, st2+j0-1);+  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2);+  return struc;+}+++duplexT ** Lduplexfold_XS(const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int threshold, const int alignment_length, const int delta, const int fast, const int il_a, const int il_b, const int b_a, const int b_b)+{+  /**+  *** See variable definition in fduplexfold_XS+  **/+  int i, j;+  int bopen=b_b;+  int bext=b_a;+  int iopen=il_b;+  int iext_s=2*il_a;+  int iext_ass=50+il_a;+  int min_colonne=INF;+  int i_length;+  int max_pos;+  int max_pos_j;+  int min_j_colonne;+  int max=INF;+  int *position;+  int *position_j;+  int maxPenalty[4];+  int **DJ;+  /**+  *** 1D array corresponding to the standard 2d recursion matrix+  *** Makes the computation 20% faster+  **/+  int *SA;+  vrna_md_t   md;+  /**+  *** variable initialization+  **/+  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  /**+  *** Sequence encoding+  **/++  set_model_details(&md);++  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_dfold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  encode_seqs(s1,s2);+  /**+  *** Position of the high score on the target and query sequence+  **/+  position = (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  /**+  *** extension penalty, computed only once, further reduce the computation time+  **/+  maxPenalty[0]=(int) -1*P->stack[2][2]/2;+  maxPenalty[1]=(int) -1*P->stack[2][2];+  maxPenalty[2]=(int) -3*P->stack[2][2]/2;+  maxPenalty[3]=(int) -2*P->stack[2][2];++  DJ=(int **) vrna_alloc(4*sizeof(int*));+  DJ[0]=(int *) vrna_alloc(n2*sizeof(int));+  DJ[1]=(int *) vrna_alloc(n2*sizeof(int));+  DJ[2]=(int *) vrna_alloc(n2*sizeof(int));+  DJ[3]=(int *) vrna_alloc(n2*sizeof(int));+  j=n2-9;+  while(--j>10){+    DJ[0][j] = 0.5*(access_s2[5][j+4] - access_s2[4][j+4] + access_s2[5][j]  -access_s2[4][j-1]  );+    DJ[1][j] = 0.5*(access_s2[5][j+5] - access_s2[4][j+5] + access_s2[5][j+1]-access_s2[4][j]  ) + DJ[0][j];+    DJ[2][j] = 0.5*(access_s2[5][j+6] - access_s2[4][j+6] + access_s2[5][j+2]-access_s2[4][j+1]) + DJ[1][j];+    DJ[3][j] = 0.5*(access_s2[5][j+7] - access_s2[4][j+7] + access_s2[5][j+3]-access_s2[4][j+2]) + DJ[2][j];+/*+    DJ[0][j] = access_s2[5][j+4] - access_s2[4][j+4]           ;+    DJ[1][j] = access_s2[5][j+5] - access_s2[4][j+5] + DJ[0][j];+    DJ[2][j] = access_s2[5][j+6] - access_s2[4][j+6] + DJ[1][j];+    DJ[3][j] = access_s2[5][j+7] - access_s2[4][j+7] + DJ[2][j];+    DJ[0][j] = MIN2(DJ[0][j],maxPenalty[0]);+    DJ[1][j] = MIN2(DJ[1][j],maxPenalty[1]);+    DJ[2][j] = MIN2(DJ[2][j],maxPenalty[2]);+    DJ[3][j] = MIN2(DJ[3][j],maxPenalty[3]);+*/+  }+  /**+  *** instead of having 4 2-dim arrays we use a unique 1-dim array+  *** The mapping 2d -> 1D is done based ont the macro+  *** LCI(i,j,l)      ((i     )*l + j)+  *** LINI(i,j,l)     ((i +  5)*l + j)+  *** LBXI(i,j,l)     ((i + 10)*l + j)+  *** LBYI(i,j,l)     ((i + 15)*l + j)+  *** LINIX(i,j,l)    ((i + 20)*l + j)+  *** LINIY(i,j,l)    ((i + 25)*l + j)+  ***+  *** SA has a length of 5 (number of columns we look back) *+  ***                  * 6 (number of structures we look at) *+  ***                  * length of the sequence+  **/++  SA=(int *) vrna_alloc(sizeof(int)*5*6*(n2+5));+  for(j=n2+4;j>=0;j--) {+    SA[(j*30)   ]=SA[(j*30)+1   ]=SA[(j*30)+2   ]=SA[(j*30)+3   ]=SA[(j*30)+4   ]=INF;+    SA[(j*30)+5 ]=SA[(j*30)+1+5 ]=SA[(j*30)+2+5 ]=SA[(j*30)+3+5 ]=SA[(j*30)+4+5 ]=INF;+    SA[(j*30)+10]=SA[(j*30)+1+10]=SA[(j*30)+2+10]=SA[(j*30)+3+10]=SA[(j*30)+4+10]=INF;+    SA[(j*30)+15]=SA[(j*30)+1+15]=SA[(j*30)+2+15]=SA[(j*30)+3+15]=SA[(j*30)+4+15]=INF;+    SA[(j*30)+20]=SA[(j*30)+1+20]=SA[(j*30)+2+20]=SA[(j*30)+3+20]=SA[(j*30)+4+20]=INF;+    SA[(j*30)+25]=SA[(j*30)+1+25]=SA[(j*30)+2+25]=SA[(j*30)+3+25]=SA[(j*30)+4+25]=INF;+  }++  i=10 ;+  i_length= n1 - 9  ;+  while(i < i_length) {+    int di1,di2,di3,di4;+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    di1 = 0.5*(access_s1[5][i+4] - access_s1[4][i+4] + access_s1[5][i]   - access_s1[4][i-1]);+    di2 = 0.5*(access_s1[5][i+3] - access_s1[4][i+3] + access_s1[5][i-1] - access_s1[4][i-2]) + di1;+    di3 = 0.5*(access_s1[5][i+2] - access_s1[4][i+2] + access_s1[5][i-2] - access_s1[4][i-3]) + di2;+    di4 = 0.5*(access_s1[5][i+1] - access_s1[4][i+1] + access_s1[5][i-3] - access_s1[4][i-4]) + di3;+/*+    di1 = access_s1[5][i]   - access_s1[4][i-1];+    di2 = access_s1[5][i-1] - access_s1[4][i-2] + di1;+    di3 = access_s1[5][i-2] - access_s1[4][i-3] + di2;+    di4 = access_s1[5][i-3] - access_s1[4][i-4] + di3;+    di1=MIN2(di1,maxPenalty[0]);+    di2=MIN2(di2,maxPenalty[1]);+    di3=MIN2(di3,maxPenalty[2]);+    di4=MIN2(di4,maxPenalty[3]);+*/+    j=n2 - 9;+    while (--j > 9) {+      int dj1,dj2,dj3,dj4;+      dj1=DJ[0][j];+      dj2=DJ[1][j];+      dj3=DJ[2][j];+      dj4=DJ[3][j];+      int type2, type,temp;+      type  = pair[S1[i]][S2[j]];+      /**+      *** Start duplex+      **/+      /* SA[LCI(idx,j,n2)] = type ? P->DuplexInit + access_s1[1][i] + access_s2[1][j] : INF; */+      SA[LCI(idx,j,n2)] = type ? P->DuplexInit : INF;+      /**+      *** update lin bx by linx liny matrix+      **/+      type2=pair[S2[j+1]][S1[i-1]];+      /**+      *** start/extend interior loop+      **/+      SA[LINI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatchI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,+                              SA[LINI(idx_1,j,n2)]+iext_ass + di1);++      /**+      *** start/extend nx1 target+      *** use same type2 as for in+      **/+      SA[LINIX(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,+                               SA[LINIX(idx_1,j,n2)]+iext_ass + di1);+      /**+      *** start/extend 1xn target+      *** use same type2 as for in+      **/+      SA[LINIY(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+di1+dj1+iopen+iext_s,+                               SA[LINIY(idx,j+1,n2)]+iext_ass + dj1);+      /**+      *** extend interior loop+      **/+      SA[LINI(idx,j,n2)]=MIN2(SA[LINI(idx,j,n2)],SA[LINI(idx,j+1,n2)]+iext_ass + dj1);+      SA[LINI(idx,j,n2)]=MIN2(SA[LINI(idx,j,n2)],SA[LINI(idx_1,j+1,n2)]+iext_s + di1 + dj1);+      /**+      *** start/extend bulge target+      **/+      type2=pair[S2[j]][S1[i-1]];+      SA[LBXI(idx,j,n2)]=MIN2(SA[LBXI(idx_1,j,n2)]+bext + di1, SA[LCI(idx_1,j,n2)]+bopen+bext+(type2>2?P->TerminalAU:0) + di1);+      /**+      *** start/extend bulge query+      **/+      type2=pair[S2[j+1]][S1[i]];+      SA[LBYI(idx,j,n2)]=MIN2(SA[LBYI(idx,j+1,n2)]+bext + dj1 , SA[LCI(idx,j+1,n2)]+bopen+bext+(type2>2?P->TerminalAU:0)+ dj1);+      /**+      ***end update recursion+      **/+      if(!type){continue;}+      /**+      *** stack extension+      **/+      SA[LCI(idx,j,n2)]+= E_ExtLoop(type, SS1[i-1] , SS2[j+1], P);+      /**+      *** stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+1]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->stack[rtype[type]][type2]+di1+dj1, SA[LCI(idx,j,n2)]);+      /**+      *** 1x0 / 0x1 stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+2,n2)]+P->bulge[1]+P->stack[rtype[type]][type2]+di1+dj2, SA[LCI(idx,j,n2)]);+      if((type2=pair[S1[i-2]][S2[j+1]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+1,n2)]+P->bulge[1]+P->stack[type2][rtype[type]]+di2+dj1, SA[LCI(idx,j,n2)]);+      /**+      *** 1x1 / 2x2 stack extension+      **/+      if((type2=pair[S1[i-2]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+2,n2)]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+di2+dj2, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-3]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+3,n2)]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di3+dj3, SA[LCI(idx,j,n2)]);+      /**+      *** 1x2 / 2x1 stack extension+      *** E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P) corresponds to+      *** P->int21[rtype[type]][type2][SS2[j+2]][SS1[i-1]][SS1[i-1]]+      **/+      if((type2 = pair[S1[i-3]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+2,n2)]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+di3+dj2, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-2]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+3,n2)]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+di2+dj3, SA[LCI(idx,j,n2)]);+      /**+      *** 2x3 / 3x2 stack extension+      **/+      if((type2 = pair[S1[i-4]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_4,j+3,n2)]+P->internal_loop[5]+P->ninio[2]++                               P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di4+dj3, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-3]][S2[j+4]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+4,n2)]+P->internal_loop[5]+P->ninio[2]++                               P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+di3+dj4, SA[LCI(idx,j,n2)]);+      /**+      *** So now we have to handle 1x3, 3x1, 3x3, and mxn m,n > 3+      **/+      /**+      *** 3x3 or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_3,j+3,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*iext_s+di3+dj3,SA[LCI(idx,j,n2)]);+      /**+      *** 2xn or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_4,j+2,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di4+dj2, SA[LCI(idx,j,n2)]);+      /**+      *** nx2 or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_2,j+4,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+di2+dj4, SA[LCI(idx,j,n2)]);+      /**+      *** nx1 n>2+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINIX(idx_3,j+1,n2)]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+di3+dj1, SA[LCI(idx,j,n2)]);+      /**+      *** 1xn n>2+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINIY(idx_1,j+3,n2)]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+dj3+di1, SA[LCI(idx,j,n2)]);+      /**+      *** nx0 n>1+      **/+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      SA[LCI(idx,j,n2)]=MIN2(SA[LBXI(idx_2,j+1,n2)]+di2+dj1+bext+bAU,SA[LCI(idx,j,n2)]);+      /**+      *** 0xn n>1+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LBYI(idx_1,j+2,n2)]+di1+dj2+bext+bAU,SA[LCI(idx,j,n2)]);+      temp=min_colonne;+      /**+      *** (type>2?P->TerminalAU:0)++      *** P->dangle3[rtype[type]][SS1[i+1]]++      *** P->dangle5[rtype[type]][SS2[j-1]],+      **/+      /* remove this line printf("LCI %d:%d %d\t",i,j,SA[LCI(idx,j,n2)]); */+      /* remove this line printf("LI %d:%d %d\t",i,j, SA[LINI(idx,j,n2)]); */+      min_colonne=MIN2(SA[LCI(idx,j,n2)]+E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1] , P), min_colonne);++      if(temp>min_colonne){+        min_j_colonne=j;+      }++      /* ---------------------------------------------------------------------end update */+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    /* remove this line printf("\n"); */+    i++;+  }+  /* printf("MAX: %d",max); */+  free(S1); free(S2); free(SS1); free(SS2);free(SA);+  if(max<threshold){+    find_max_XS(position, position_j, delta, threshold, alignment_length, s1, s2, access_s1, access_s2, fast,il_a, il_b,b_a, b_b);+  }+  if(max<INF){+    plot_max_XS(max, max_pos, max_pos_j, alignment_length, s1, s2, access_s1, access_s2,fast, il_a, il_b, b_a, b_b);+  }+  for (i=0; i<=3; i++) {+    free(DJ[i]);+  }+  free(DJ);+  free(position);+  free(position_j);+  return NULL;+}++PRIVATE void find_max_XS(const int *position, const int *position_j,const int delta, const int threshold, const int alignment_length, const char *s1, const char *s2, const int **access_s1, const int **access_s2, const int fast,const int il_a, const int il_b, const int b_a, const int b_b){+  int pos=n1-9;+  if(fast==1){+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/100);+        pos=MAX2(10,pos+temp_min-delta);+      }+    }+  }+  else if(fast==2){+    pos=n1-9;+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* max_pos_j und pos entsprechen die realen position+            in der erweiterten sequenz.+           pos=1 -> position 1 in the sequence (and not 0 like in C)+           max_pos_j -> position 1 in the sequence ( not 0 like in C)+        */+        int alignment_length2; alignment_length2 = MIN2(n1,n2);+        int begin_t=MAX2(11, pos-alignment_length2+1);/* 10 */+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1); /* 10 */+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2 + 20));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2 + 20));+        strcpy(s3,"NNNNNNNNNN");strcpy(s4,"NNNNNNNNNN");+        strncat(s3, (s1+begin_t-1),  end_t - begin_t +1);+        strncat(s4, (s2+begin_q-1) , end_q - begin_q +1);+        strcat(s3,"NNNNNNNNNN");strcat(s4,"NNNNNNNNNN");+        s3[end_t -begin_t +1 +20 ]='\0';+        s4[end_q -begin_q +1 +20]='\0';+        duplexT test;+        test = fduplexfold_XS(s3, s4, access_s1, access_s2, end_t, begin_q,threshold, il_a, il_b, b_a, b_b);+        if(test.energy * 100 < threshold){+          int l1=strchr(test.structure, '&')-test.structure;+          printf(" %s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f] i:%d,j:%d <%5.2f>\n", test.structure,+                 begin_t-10+test.i-l1-10,+                 begin_t-10+test.i-1-10,+                 begin_q-10 + test.j-1-10 ,+                 (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2-10,+                 test.ddG, test.energy, test.opening_backtrack_x, test.opening_backtrack_y, test.energy_backtrack,+                 pos-10, max_pos_j-10, ((double) position[pos+delta])/100);+          pos=MAX2(10,pos+temp_min-delta);+          free(test.structure);+        }+        free(s3);free(s4);+      }+    }+  }+  else{+    pos=n1-9;+    while( pos-- > 10 ){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min; /* position on i */+        int max_pos_j;+        max_pos_j=position_j[pos+delta]; /* position on j */+        int begin_t=MAX2(11,pos-alignment_length);+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11,max_pos_j-1);+        int end_q  =MIN2(n2-10,max_pos_j+alignment_length-1);+        int i_flag;+        int j_flag;+        i_flag = (end_t   ==  pos+1?1:0);+        j_flag = (begin_q == max_pos_j-1?1:0);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+        strncpy(s3, (s1+begin_t),  end_t - begin_t+1);+        strncpy(s4, (s2+begin_q) , end_q - begin_q+1);+        s3[end_t -begin_t +1 ]='\0';+        s4[end_q -begin_q +1 ]='\0';+        duplexT test;+        test = duplexfold_XS(s3,s4,access_s1,access_s2,pos, max_pos_j,threshold,i_flag,j_flag);+        if(test.energy * 100 < threshold){+          printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) i:%d,j:%d <%5.2f>\n", test.structure,+                 test.tb,test.te,test.qb,test.qe, test.ddG, test.energy, test.dG1, test.dG2, pos-10, max_pos_j-10, ((double) position[pos+delta])/100);+          pos=MAX2(10,pos+temp_min-delta);+        }+        free(s3);free(s4);+        free(test.structure);+      }+    }+  }+}++#if 0+PRIVATE int compare(const void *sub1, const void *sub2) {+  int d;+  if (((duplexT *) sub1)->ddG > ((duplexT *) sub2)->ddG)+    return 1;+  if (((duplexT *) sub1)->ddG < ((duplexT *) sub2)->ddG)+    return -1;+  d = ((duplexT *) sub1)->i - ((duplexT *) sub2)->i;+  if (d!=0) return d;+  return  ((duplexT *) sub1)->j - ((duplexT *) sub2)->j;+}+#endif++PRIVATE void plot_max_XS(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int ** access_s1, const int ** access_s2, const int fast,const int il_a, const int il_b, const int b_a, const int b_b)+{+  if(fast==1){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n", max_pos-3, max_pos_j, ((double)max)/100);+  }+  else if(fast==2){+    int alignment_length2; alignment_length2 = MIN2(n1,n2);+    int begin_t=MAX2(11, max_pos-alignment_length2+1);/* 10 */+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1); /* 10 */+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2 + 20));+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2 + 20));+    strcpy(s3,"NNNNNNNNNN");strcpy(s4,"NNNNNNNNNN");+    strncat(s3, (s1+begin_t-1),  end_t - begin_t +1);+    strncat(s4, (s2+begin_q-1) , end_q - begin_q +1);+    strcat(s3,"NNNNNNNNNN");strcat(s4,"NNNNNNNNNN");+    s3[end_t -begin_t +1 +20 ]='\0';+    s4[end_q -begin_q +1 +20]='\0';+    duplexT test;+    test = fduplexfold_XS(s3, s4, access_s1, access_s2, end_t, begin_q, INF, il_a, il_b, b_a, b_b);+    int l1=strchr(test.structure, '&')-test.structure;+    printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) [%5.2f] i:%d,j:%d <%5.2f>\n", test.structure,+           begin_t-10+test.i-l1-10,+           begin_t-10+test.i-1-10,+           begin_q-10 + test.j-1-10 ,+           (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2-10,+           test.ddG, test.energy, test.opening_backtrack_x, test.opening_backtrack_y, test.energy_backtrack,+           max_pos-10, max_pos_j-10, (double) max/100);++    free(s3);free(s4);+    free(test.structure);+  }+  else{+    int begin_t=MAX2(11,max_pos-alignment_length);+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1);+    int end_q  =MIN2(n2-10,max_pos_j+alignment_length-1);+    int i_flag;+    int j_flag;+    i_flag = (end_t   == max_pos+1?1:0);+    j_flag = (begin_q == max_pos_j-1?1:0);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2)); /* +1 for \0 +1 for distance */+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));++    strncpy(s3, (s1+begin_t-1),  end_t - begin_t+1);/* -1 to go from  */+    strncpy(s4, (s2+begin_q-1) , end_q - begin_q+1);/* -1 to go from  */+    s3[end_t -begin_t +1 ]='\0';/*  */+    s4[end_q -begin_q +1 ]='\0';+    duplexT test;+    test = duplexfold_XS(s3,s4,access_s1,access_s2,max_pos, max_pos_j,INF,i_flag,j_flag);+    printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f) i:%d,j:%d <%5.2f>\n", test.structure,+           test.tb,test.te,test.qb,test.qe, test.ddG, test.energy, test.dG1, test.dG2, max_pos-10, max_pos_j - 10,(double) max/100);+    free(s3);free(s4);free(test.structure);+  }+}+++/*---------------------------------------------------------duplexfold----------------------------------------------------------------------------------*/+++PRIVATE duplexT duplexfold(const char *s1, const char *s2, const int extension_cost) {+  int i, j, l1, Emin=INF, i_min=0, j_min=0;+  char *struc;+  duplexT mfe;+  vrna_md_t md;++  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }++  c = (int **) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++) c[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  encode_seqs(s1, s2);+  for (i=1; i<=n3; i++) {+    for (j=n4; j>0; j--) {+      int type, type2, E, k,l;+      type = pair[S1[i]][S2[j]];+      c[i][j] = type ? P->DuplexInit +2 * extension_cost: INF;+      if (!type) continue;+      /**+      ***       if (i>1)  c[i][j] += P->dangle5[type][SS1[i-1]]+ extension_cost;+      ***       if (j<n4) c[i][j] += P->dangle3[type][SS2[j+1]]+ extension_cost;+      ***       if (type>2) c[i][j] += P->TerminalAU;+      **/+      c[i][j] += E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n4) ? SS2[j+1] : -1, P);+      for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+        for (l=j+1; l<=n4; l++) {+          if (i-k+l-j-2>MAXLOOP) break;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          E = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                        SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P)+(i-k+l-j)*extension_cost;+          c[i][j] = MIN2(c[i][j], c[k][l]+E);+        }+      }+      E = c[i][j];+      /**+      ***      if (i<n3) E += P->dangle3[rtype[type]][SS1[i+1]]+extension_cost;+      ***      if (j>1)  E += P->dangle5[rtype[type]][SS2[j-1]]+extension_cost;+      ***      if (type>2) E += P->TerminalAU;+      ***+      **/+      E += E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n3) ? SS1[i+1] : -1, P);+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      }+    }+  }+  struc = backtrack(i_min, j_min, extension_cost);+  if (i_min<n3) i_min++;+  if (j_min>1 ) j_min--;+  l1 = strchr(struc, '&')-struc;+  int size;+  size=strlen(struc)-1;+  Emin-= size * (extension_cost);+  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (double) Emin/100.;+  mfe.structure = struc;+  for (i=0; i<=n3; i++) free(c[i]);+  free(c);+  free(S1); free(S2); free(SS1); free(SS2);+  return mfe;+}++PRIVATE char *backtrack(int i, int j, const int extension_cost) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;++  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));++  i0=MIN2(i+1,n3); j0=MAX2(j-1,1);++  while (i>0 && j<=n4) {+    E = c[i][j]; traced=0;+    st1[i-1] = '(';+    st2[j-1] = ')';+    type = pair[S1[i]][S2[j]];+    if (!type) vrna_message_error("backtrack failed in fold duplex");+    for (k=i-1; k>0 && k>i-MAXLOOP-2; k--) {+      for (l=j+1; l<=n4; l++) {+        int LE;+        if (i-k+l-j-2>MAXLOOP) break;+        type2 = pair[S1[k]][S2[l]];+        if (!type2) continue;+        LE = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                       SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P)+(i-k+l-j)*extension_cost;+        if (E == c[k][l]+LE) {+          traced=1;+          i=k; j=l;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {++      E -=  E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n4) ? SS2[j+1] : -1, P);+      /**+      ***      if (i>1) E -= P->dangle5[type][SS1[i-1]]+extension_cost;+      ***      if (j<n4) E -= P->dangle3[type][SS2[j+1]]+extension_cost;+      ***      if (type>2) E -= P->TerminalAU;+      **/+      if (E != P->DuplexInit+2*extension_cost) {+        vrna_message_error("backtrack failed in fold duplex");+      } else break;+    }+  }+  if (i>1)  i--;+  if (j<n4) j++;++  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0));+  strcat(struc, "&");+  strcat(struc, st2+j0-1);+  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2);+  return struc;+}++PRIVATE duplexT fduplexfold(const char *s1, const char *s2, const int extension_cost,const int il_a, const int il_b, const int b_a, const int b_b) {+  int i, j, Emin, i_min, j_min,l1;+  duplexT mfe;+  char *struc;+  int bopen=b_b;+  int bext=b_a+extension_cost;+  int iopen=il_b;+  int iext_s=2*(il_a+extension_cost);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a+extension_cost;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  int temp=INF;+  int min_j_colonne;+  int max=INF;+  vrna_md_t md;+  /* FOLLOWING NEXT 4 LINE DEFINES AN ARRAY CONTAINING POSITION OF THE SUBOPT IN S1 */++  n3 = (int) strlen(s1);+  n4 = (int) strlen(s2);+  /* delta_check is the minimal distance allowed for two hits to be accepted */+  /* if both hits are closer, reject the smaller ( in term of position)  hits  */+  /* i want to implement a function that, given a position in a long sequence and a small sequence, */+  /* duplexfold them at this position and report the result at the command line */+  /* for this i first need to rewrite backtrack in order to remove the printf functio */+  /* END OF DEFINITION FOR NEEDED SUBOPT DATA  */+  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  /*local c array initialization---------------------------------------------*/+  c  = (int**)  vrna_alloc(sizeof(int *) * (n3+1));+  in = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  bx = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  by = (int**) vrna_alloc(sizeof(int *) * (n3+1));+  inx= (int**) vrna_alloc(sizeof(int *) * (n3+1));+  iny= (int**) vrna_alloc(sizeof(int *) * (n3+1));+  for (i=0; i<=n3; i++){+    c[i]  = (int *) vrna_alloc(sizeof(int) * (n4+1));+    in[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    bx[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    by[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    inx[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+    iny[i] = (int *) vrna_alloc(sizeof(int) * (n4+1));+  }+  /*-------------------------------------------------------------------------*/+  /*end of array initialisation----------------------------------*/+  /*maybe int *** would be better*/+  encode_seqs(s1,s2);+  /* ------------------------------------------matrix initialisierung */+  for(i=0; i<n3; i++){+    for(j=0; j<n4; j++){+      in[i][j]=INF;/* no in before  1 */+      c[i][j] =INF; /* no bulge and no in before n2 */+      bx[i][j]=INF;/* no bulge before 1 */+      by[i][j]=INF;+      inx[i][j]=INF;/* no bulge before 1 */+      iny[i][j]=INF;+    }+  }++  /*--------------------------------------------------------local array*/+++  /* -------------------------------------------------------------matrix initialisierung */+  i=11;+  i_length=n3-9;+  while(i < i_length) {+    j=n4-9;+    min_colonne=INF;+    while (10 < --j) {+      int type, type2;+      type = pair[S1[i]][S2[j]];+      /**+      *** Start duplex+      **/+      c[i][j]=type ? P->DuplexInit + 2*extension_cost : INF;+      /**+      *** update lin bx by linx liny matrix+      **/+      type2=pair[S2[j+1]][S1[i-1]];+      /**+      *** start/extend interior loop+      **/+      in[i][j]=MIN2(c[i - 1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s, in[i - 1][j]+iext_ass);+      /**+      *** start/extend nx1 target+      *** use same type2 as for in+      **/+      inx[i][j]=MIN2(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,+                     inx[i-1][j]+iext_ass);+      /**+      *** start/extend 1xn target+      *** use same type2 as for in+      **/+      iny[i][j]=MIN2(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,+                     iny[i][j+1]+iext_ass);+      /**+      *** extend interior loop+      **/+      in[i][j]=MIN2(in[i][j],in[i][j+1]+iext_ass);+      in[i][j]=MIN2(in[i][j],in[i - 1][j+1]+iext_s);+      /**+      *** start/extend bulge target+      **/+      type2=pair[S2[j]][S1[i-1]];+      bx[i][j]=MIN2(bx[i - 1][j]+bext, c[i - 1][j]+bopen+bext+(type2>2?P->TerminalAU:0));+      /**+      *** start/extend bulge query+      **/+      type2=pair[S2[j+1]][S1[i]];+      by[i][j]=MIN2(by[i][j+1]+bext, c[i][j+1]+bopen+bext+(type2>2?P->TerminalAU:0));+      /**+      ***end update recursion+      ***######################## Start stack extension##############################+      **/+      if(!type){continue;}+      c[i][j]+=E_ExtLoop(type, SS1[i-1] , SS2[j+1], P) + 2*extension_cost;+      /**+      *** stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+1]]))+        c[i][j]=MIN2(c[i - 1][j+1]+P->stack[rtype[type]][type2]+2*extension_cost, c[i][j]);+      /**+      *** 1x0 / 0x1 stack extension+      **/+      type2=pair[S1[i-1]][S2[j+2]];+      c[i][j]=MIN2(c[i - 1][j+2]+P->bulge[1]+P->stack[rtype[type]][type2]+3*extension_cost,c[i][j]);+      type2=pair[S1[i-2]][S2[j+1]];+      c[i][j]=MIN2(c[i - 2][j+1]+P->bulge[1]+P->stack[type2][rtype[type]]+3*extension_cost,c[i][j]);+      /**+      *** 1x1 / 2x2 stack extension+      **/+      type2=pair[S1[i-2]][S2[j+2]];+      c[i][j]=MIN2(c[i - 2][j+2]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+4*extension_cost, c[i][j]);+      type2 = pair[S1[i-3]][S2[j+3]];+      c[i][j]=MIN2(c[i - 3][j+3]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+6*extension_cost,c[i][j]);+      /**+      *** 1x2 / 2x1 stack extension+      *** E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P) corresponds to+      *** P->int21[rtype[type]][type2][SS2[j+2]][SS1[i-1]][SS1[i-1]]+      **/+      type2 = pair[S1[i-3]][S2[j+2]];+      c[i][j]=MIN2(c[i - 3][j+2]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+5*extension_cost, c[i][j]);+      type2 = pair[S1[i-2]][S2[j+3]];+      c[i][j]=MIN2(c[i - 2][j+3]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+5*extension_cost, c[i][j]);++      /**+      *** 2x3 / 3x2 stack extension+      **/+      if((type2 = pair[S1[i-4]][S2[j+3]]))+        c[i][j]=MIN2(c[i - 4][j+3]+P->internal_loop[5]+P->ninio[2]++                     P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost, c[i][j]);+      if((type2 = pair[S1[i-3]][S2[j+4]]))+        c[i][j]=MIN2(c[i - 3][j+4]+P->internal_loop[5]+P->ninio[2]++                     P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost, c[i][j]);+      /**+      *** So now we have to handle 1x3, 3x1, 3x3, and mxn m,n > 3+      **/+      /**+      *** 3x3 or more+      **/+      c[i][j]=MIN2(in[i - 3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*iext_s+2*extension_cost, c[i][j]);+      /**+      *** 2xn or more+      **/+      c[i][j]=MIN2(in[i - 4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, c[i][j]);+      /**+      *** nx2 or more+      **/+      c[i][j]=MIN2(in[i - 2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, c[i][j]);+      /**+      *** nx1 n>2+      **/+      c[i][j]=MIN2(inx[i - 3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, c[i][j]);+      /**+      *** 1xn n>2+      **/+      c[i][j]=MIN2(iny[i - 1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, c[i][j]);+      /**+      *** nx0 n>1+      **/+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      c[i][j]=MIN2(bx[i - 2][j+1]+2*extension_cost+bext+bAU, c[i][j]);+      /**+      *** 0xn n>1+      **/+      c[i][j]=MIN2(by[i - 1][j+2]+2*extension_cost+bext+bAU, c[i][j]);+      temp=min_colonne;+      min_colonne=MIN2(c[i][j]+E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1] , P) + 2*extension_cost, min_colonne);+      if(temp>min_colonne){+        min_j_colonne=j;+      }+      /* ---------------------------------------------------------------------end update */+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    i++;+  }+  Emin=max;+  i_min=max_pos;+  j_min=max_pos_j;+  int dGe;+  dGe=0;+  struc = fbacktrack(i_min, j_min, extension_cost, il_a, il_b, b_a, b_b,&dGe);+  if (i_min<n3-10) i_min++;+  if (j_min>11 ) j_min--;+  l1 = strchr(struc, '&')-struc;+  int size;+  size=strlen(struc)-1;+  Emin-= size * (extension_cost);+  mfe.i = i_min;+  mfe.j = j_min;+  mfe.energy = (double) Emin/100.;+  mfe.energy_backtrack = (double) dGe/100.;+  mfe.structure = struc;+  free(S1); free(S2); free(SS1); free(SS2);+  for (i=0; i<=n3; i++) {+    free(c[i]);+    free(in[i]);+    free(bx[i]);+    free(by[i]);+    free(inx[i]);+    free(iny[i]);+  }+  free(c);free(in);free(bx);free(by);free(inx);free(iny);+  return mfe;+}+++PRIVATE char *fbacktrack(int i, int j, const int extension_cost,const int il_a, const int il_b, const int b_a, const int b_b, int *dG) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;+  int bopen=b_b;+  int bext=b_a+extension_cost;+  int iopen=il_b;+  int iext_s=2*(il_a+extension_cost);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a+extension_cost;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  st1 = (char *) vrna_alloc(sizeof(char)*(n3+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n4+1));+  i0=MIN2(i+1,n3-10); j0=MAX2(j-1,11);+  int state;+  state=1; /* we start backtracking from a a pair , i.e. c-matrix */+  /* state 1 -> base pair, c+     state 2 -> interior loop, in+     state 3 -> bx loop, bx+     state 4 -> by loop, by+  */+  traced=1;+  k=i;l=j;+  type=pair[S1[i]][S2[j]];+  *dG+=E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1] , P);+  /*     (type>2?P->TerminalAU:0)+P->dangle3[rtype[type]][SS1[i+1]]+P->dangle5[rtype[type]][SS2[j-1]]; */+  while (i>10 && j<=n4-9 && traced) {+    traced=0;+    switch(state){+    case 1:+      type = pair[S1[i]][S2[j]];+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      if(!type) vrna_message_error("backtrack failed in fold duplex");+      type2=pair[S1[i-1]][S2[j+1]];+      if(type2 && c[i][j]== (c[i - 1][j+1]+P->stack[rtype[type]][type2]+2*extension_cost)){+        k=i-1;+        l=j+1;+        (*dG)+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-1]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 1][j+2]+P->bulge[1]+P->stack[rtype[type]][type2]+3*extension_cost)){+        k=i-1;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-2]][S2[j+1]];+      if(type2 && c[i][j]==(c[i - 2][j+1]+P->bulge[1]+P->stack[type2][rtype[type]]+3*extension_cost)){+        k=i-2;+        l=j+1;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2=pair[S1[i-2]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 2][j+2]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+4*extension_cost)){+        k=i-2;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 3][j+3]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+6*extension_cost)){+        k=i-3;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+2]];+      if(type2 && c[i][j]==(c[i - 3][j+2]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+5*extension_cost)){+        k=i-3;+        l=j+2;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-2]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 2][j+3]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+5*extension_cost)){+        k=i-2;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-4]][S2[j+3]];+      if(type2 && c[i][j]==(c[i - 4][j+3]+P->internal_loop[5]+P->ninio[2]++                            P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost)){+        k=i-4;+        l=j+3;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      type2 = pair[S1[i-3]][S2[j+4]];+      if(type2 && c[i][j]==(c[i - 3][j+4]+P->internal_loop[5]+P->ninio[2]++                            P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost)){+        k=i-3;+        l=j+4;+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 3][j+3]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*extension_cost+2*iext_s)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-3;+        j=j+3;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 4][j+2]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-4;+        j=j+2;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(in[i - 2][j+4]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-2;+        j=j+4;+        state=2;+        traced=1;+        break;+      }+      if(c[i][j]==(inx[i - 3][j+1]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-3;+        j=j+1;+        state=5;+        traced=1;+        break;+      }+      if(c[i][j]==(iny[i - 1][j+3]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-1;+        j=j+3;+        state=6;+        traced=1;+        break;+      }+      if(c[i][j]==(bx[i - 2][j+1]+2*extension_cost+bext+bAU)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-2;+        j=j+1;+        state=3;+        traced=1;+        break;+      }+      if(c[i][j]==(by[i - 1][j+2]+2*extension_cost+bext+bAU)){+        k=i;+        l=j;+        st1[i-1] = '(';+        st2[j-1] = ')';+        i=i-1;+        j=j+2;+        state=4;+        traced=1;+        break;+      }+      break;+    case 2:+      if(in[i][j]==(in[i - 1][j+1]+iext_s)){+        i--;+        j++;+        state=2;+        traced=1;+        break;+      }+      if(in[i][j]==(in[i - 1][j]+iext_ass)){+        i=i-1;+        state=2;+        traced=1;+        break;+      }+      if(in[i][j]==(in[i][j+1]+iext_ass)){+        j++;+        state=2;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i-1]];+      if(type2 && in[i][j]==(c[i - 1][j+1]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s)){+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 3:+      if(bx[i][j]==(bx[i - 1][j]+bext)){+        i--;+        state=3;+        traced=1;+        break;+      }+      type2=pair[S2[j]][S1[i-1]];+      if(type2 && bx[i][j]==(c[i - 1][j]+bopen+bext+(type2>2?P->TerminalAU:0))){+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 4:+      if(by[i][j]==(by[i][j+1] + bext)){+        j++;++        state=4;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i]];+      if(type2 && by[i][j]==(c[i][j+1]+bopen+bext+(type2>2?P->TerminalAU:0))){+        int temp; temp=k; k=i; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 5:+      if(inx[i][j]==(inx[i-1][j]+iext_ass)) {+        i--;+        state=5;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i-1]];+      if(type2 && inx[i][j]==(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s)){+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    case 6:+      if(iny[i][j]==(iny[i][j+1]+iext_ass)) {+        j++;+        state=6;+        traced=1;+        break;+      }+      type2=pair[S2[j+1]][S1[i-1]];+      if(type2 && iny[i][j]==(c[i-1][j+1]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s)){+        int temp; temp=k; k=i-1; i=temp;+        temp=l; l=j+1; j=temp;+        type=pair[S1[i]][S2[j]];+        *dG+=E_IntLoop(i-k-1, l-j-1, type2, rtype[type],SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+        i=k;+        j=l;+        state=1;+        traced=1;+        break;+      }+    }+  }+  if (!traced) {+    E=c[i][j];+    /**+    ***    if (i>1) {E -= P->dangle5[type][SS1[i-1]]+extension_cost; *dG+=P->dangle5[type][SS1[i-1]];}+    ***    if (j<n4){E -= P->dangle3[type][SS2[j+1]]+extension_cost; *dG+=P->dangle3[type][SS2[j+1]];}+    ***    if (type>2) {E -= P->TerminalAU; *dG+=P->TerminalAU;}+    **/+    int correction;+    correction = E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n4) ? SS2[j+1] : -1, P);+    *dG+=correction;+    E-=correction+2*extension_cost;+    if (E != P->DuplexInit+2*extension_cost) {+      vrna_message_error("backtrack failed in second fold duplex");+    }+    else{+      *dG+=P->DuplexInit;+      st1[i-1]='(';+      st2[j-1]=')';+    }+  }+  if (i>11)  i--;+  if (j<n4-10) j++;+  struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2);+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = '.';+  strcpy(struc, st1+MAX2(i-1,0));+  strcat(struc, "&");+  strcat(struc, st2+j0-1);+  /* printf("%s %3d,%-3d : %3d,%-3d\n", struc, i,i0,j0,j);  */+  free(st1); free(st2);+  return struc;+}+++duplexT ** Lduplexfold(const char *s1, const char *s2, const int threshold, const int extension_cost, const int alignment_length, const int delta, const int fast, const int il_a, const int il_b, const int b_a, const int b_b)+{+  /**+  *** See variable definition in fduplexfold_XS+  **/+  int i, j;+  int bopen=b_b;+  int bext=b_a+extension_cost;+  int iopen=il_b;+  int iext_s=2*(il_a+extension_cost);/* iext_s 2 nt nucleotide extension of interior loop, on i and j side */+  int iext_ass=50+il_a+extension_cost;/* iext_ass assymetric extension of interior loop, either on i or on j side. */+  int min_colonne=INF; /* enthaelt das maximum einer kolonne */+  int i_length;+  int max_pos;/* get position of the best hit */+  int max_pos_j;+  int temp=INF;+  int min_j_colonne;+  int max=INF;+  int *position; /* contains the position of the hits with energy > E */+  int *position_j;+  /**+  *** 1D array corresponding to the standard 2d recursion matrix+  *** Makes the computation 20% faster+  **/+  int *SA;+  vrna_md_t md;+  +  /**+  *** variable initialization+  **/+  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  /**+  *** Sequence encoding+  **/+  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    update_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  encode_seqs(s1,s2);+  /**+  *** Position of the high score on the target and query sequence+  **/+  position = (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  position_j= (int *) vrna_alloc((delta+n1+3+delta) * sizeof(int));+  /**+  *** instead of having 4 2-dim arrays we use a unique 1-dim array+  *** The mapping 2d -> 1D is done based ont the macro+  *** LCI(i,j,l)      ((i     )*l + j)+  *** LINI(i,j,l)     ((i +  5)*l + j)+  *** LBXI(i,j,l)     ((i + 10)*l + j)+  *** LBYI(i,j,l)     ((i + 15)*l + j)+  *** LINIX(i,j,l)    ((i + 20)*l + j)+  *** LINIY(i,j,l)    ((i + 25)*l + j)+  ***+  *** SA has a length of 5 (number of columns we look back) *+  ***                  * 6 (number of structures we look at) *+  ***                  * length of the sequence+  **/+  SA=(int *) vrna_alloc(sizeof(int)*5*6*(n2+5));+  for(j=n2+4;j>=0;j--) {+    SA[(j*30)   ]=SA[(j*30)+1   ]=SA[(j*30)+2   ]=SA[(j*30)+3   ]=SA[(j*30)+4   ]=INF;+    SA[(j*30)+5 ]=SA[(j*30)+1+5 ]=SA[(j*30)+2+5 ]=SA[(j*30)+3+5 ]=SA[(j*30)+4+5 ]=INF;+    SA[(j*30)+10]=SA[(j*30)+1+10]=SA[(j*30)+2+10]=SA[(j*30)+3+10]=SA[(j*30)+4+10]=INF;+    SA[(j*30)+15]=SA[(j*30)+1+15]=SA[(j*30)+2+15]=SA[(j*30)+3+15]=SA[(j*30)+4+15]=INF;+    SA[(j*30)+20]=SA[(j*30)+1+20]=SA[(j*30)+2+20]=SA[(j*30)+3+20]=SA[(j*30)+4+20]=INF;+    SA[(j*30)+25]=SA[(j*30)+1+25]=SA[(j*30)+2+25]=SA[(j*30)+3+25]=SA[(j*30)+4+25]=INF;+  }+  i=10;+  i_length= n1 - 9 ;+  while(i < i_length) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    j=n2-9;+    while (9 < --j) {+      int type, type2;+      type = pair[S1[i]][S2[j]];+      /**+      *** Start duplex+      **/+      SA[LCI(idx,j,n2)]=type ? P->DuplexInit + 2*extension_cost : INF;+      /**+      *** update lin bx by linx liny matrix+      **/+      type2=pair[S2[j+1]][S1[i-1]];+      /**+      *** start/extend interior loop+      **/+      SA[LINI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatchI[type2][SS2[j]][SS1[i]]+iopen+iext_s,+                              SA[LINI(idx_1,j,n2)]+iext_ass);+      /**+      *** start/extend nx1 target+      *** use same type2 as for in+      **/+      SA[LINIX(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,+                               SA[LINIX(idx_1,j,n2)]+iext_ass);+      /**+      *** start/extend 1xn target+      *** use same type2 as for in+      **/+      SA[LINIY(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->mismatch1nI[type2][SS2[j]][SS1[i]]+iopen+iext_s,+                               SA[LINIY(idx,j+1,n2)]+iext_ass);+      /**+      *** extend interior loop+      **/+      SA[LINI(idx,j,n2)]=MIN2(SA[LINI(idx,j,n2)],SA[LINI(idx,j+1,n2)]+iext_ass);+      SA[LINI(idx,j,n2)]=MIN2(SA[LINI(idx,j,n2)],SA[LINI(idx_1,j+1,n2)]+iext_s);+      /**+      *** start/extend bulge target+      **/+      type2=pair[S2[j]][S1[i-1]];+      SA[LBXI(idx,j,n2)]=MIN2(SA[LBXI(idx_1,j,n2)]+bext, SA[LCI(idx_1,j,n2)]+bopen+bext+(type2>2?P->TerminalAU:0));+      /**+      *** start/extend bulge query+      **/+      type2=pair[S2[j+1]][S1[i]];+      SA[LBYI(idx,j,n2)]=MIN2(SA[LBYI(idx,j+1,n2)]+bext, SA[LCI(idx,j+1,n2)]+bopen+bext+(type2>2?P->TerminalAU:0));+      /**+      ***end update recursion+      ***##################### Start stack extension ######################+      **/+      if(!type){continue;}+      /**+      *** stack extension+      **/+      SA[LCI(idx,j,n2)]+= E_ExtLoop(type, SS1[i-1] , SS2[j+1], P) + 2*extension_cost;+      /**+      *** stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+1]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+1,n2)]+P->stack[rtype[type]][type2]+2*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** 1x0 / 0x1 stack extension+      **/+      if((type2=pair[S1[i-1]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_1,j+2,n2)]+P->bulge[1]+P->stack[rtype[type]][type2]+3*extension_cost,SA[LCI(idx,j,n2)]);+      if((type2=pair[S1[i-2]][S2[j+1]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+1,n2)]+P->bulge[1]+P->stack[type2][rtype[type]]+3*extension_cost,SA[LCI(idx,j,n2)]);+      /**+      *** 1x1 / 2x2 stack extension+      **/+      if((type2=pair[S1[i-2]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+2,n2)]+P->int11[type2][rtype[type]][SS1[i-1]][SS2[j+1]]+4*extension_cost, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-3]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+3,n2)]+P->int22[type2][rtype[type]][SS1[i-2]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+6*extension_cost,SA[LCI(idx,j,n2)]);+      /**+      *** 1x2 / 2x1 stack extension+      *** E_IntLoop(1,2,type2, rtype[type],SS1[i-1], SS2[j+2], SS1[i-1], SS2[j+1], P) corresponds to+      *** P->int21[rtype[type]][type2][SS2[j+2]][SS1[i-1]][SS1[i-1]]+      **/+      if((type2 = pair[S1[i-3]][S2[j+2]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+2,n2)]+P->int21[rtype[type]][type2][SS2[j+1]][SS1[i-2]][SS1[i-1]]+5*extension_cost, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-2]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_2,j+3,n2)]+P->int21[type2][rtype[type]][SS1[i-1]][SS2[j+1]][SS2[j+2]]+5*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** 2x3 / 3x2 stack extension+      **/+      if((type2 = pair[S1[i-4]][S2[j+3]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_4,j+3,n2)]+P->internal_loop[5]+P->ninio[2]++                               P->mismatch23I[type2][SS1[i-3]][SS2[j+2]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost, SA[LCI(idx,j,n2)]);+      if((type2 = pair[S1[i-3]][S2[j+4]]))+        SA[LCI(idx,j,n2)]=MIN2(SA[LCI(idx_3,j+4,n2)]+P->internal_loop[5]+P->ninio[2]++                               P->mismatch23I[type2][SS1[i-2]][SS2[j+3]]+P->mismatch23I[rtype[type]][SS2[j+1]][SS1[i-1]]+7*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** So now we have to handle 1x3, 3x1, 3x3, and mxn m,n > 3+      **/+      /**+      *** 3x3 or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_3,j+3,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+2*iext_s+2*extension_cost,SA[LCI(idx,j,n2)]);+      /**+      *** 2xn or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_4,j+2,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** nx2 or more+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINI(idx_2,j+4,n2)]+P->mismatchI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_s+2*iext_ass+2*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** nx1 n>2+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINIX(idx_3,j+1,n2)]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** 1xn n>2+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LINIY(idx_1,j+3,n2)]+P->mismatch1nI[rtype[type]][SS1[i-1]][SS2[j+1]]+iext_ass+iext_ass+2*extension_cost, SA[LCI(idx,j,n2)]);+      /**+      *** nx0 n>1+      **/+      int bAU;+      bAU=(type>2?P->TerminalAU:0);+      SA[LCI(idx,j,n2)]=MIN2(SA[LBXI(idx_2,j+1,n2)]+2*extension_cost+bext+bAU,SA[LCI(idx,j,n2)]);+      /**+      *** 0xn n>1+      **/+      SA[LCI(idx,j,n2)]=MIN2(SA[LBYI(idx_1,j+2,n2)]+2*extension_cost+bext+bAU,SA[LCI(idx,j,n2)]);+      temp=min_colonne;++      min_colonne=MIN2(SA[LCI(idx,j,n2)]+E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1] , P) + 2*extension_cost, min_colonne);+      if(temp>min_colonne){+        min_j_colonne=j;+      }+    }+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+    }+    position[i+delta]=min_colonne;min_colonne=INF;+    position_j[i+delta]=min_j_colonne;+    i++;+  }+  /* printf("MAX: %d",max); */+  free(S1); free(S2); free(SS1); free(SS2);+  if(max<threshold){+    find_max(position, position_j, delta, threshold, alignment_length, s1, s2, extension_cost, fast, il_a, il_b, b_a, b_b);+  }+  if(max<INF){+    plot_max(max, max_pos, max_pos_j,alignment_length, s1, s2, extension_cost,fast, il_a, il_b, b_a, b_b);+  }+  free(SA);+  free(position);+  free(position_j);+  return NULL;+}+++++PRIVATE void find_max(const int *position, const int *position_j,const int delta, const int threshold, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast,const int il_a, const int il_b, const int b_a, const int b_b){+  int pos=n1-9;+  if(fast==1){+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        int max;+        max=position[pos+delta];+        printf("target upper bound %d: query lower bound %d  (%5.2f) \n", pos-10, max_pos_j-10, ((double)max)/100);+        pos=MAX2(10,pos+temp_min-delta);+      }+    }+  }+  else if(fast==2){+    pos=n1-9;+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* max_pos_j und pos entsprechen die realen position+           in der erweiterten sequenz.+           pos=1 -> position 1 in the sequence (and not 0 like in C)+           max_pos_j -> position 1 in the sequence ( not 0 like in C)+        */+        int alignment_length2; alignment_length2 = MIN2(n1,n2);+        int begin_t=MAX2(11, pos-alignment_length2+1);/* 10 */+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1); /* 10 */+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2 + 20));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2 + 20));+        strcpy(s3,"NNNNNNNNNN");strcpy(s4,"NNNNNNNNNN");+        strncat(s3, (s1+begin_t-1),  end_t - begin_t +1);+        strncat(s4, (s2+begin_q-1) , end_q - begin_q +1);+        strcat(s3,"NNNNNNNNNN");strcat(s4,"NNNNNNNNNN");+        s3[end_t -begin_t +1 +20 ]='\0';+        s4[end_q -begin_q +1 +20]='\0';+        duplexT test;+        test = fduplexfold(s3, s4, extension_cost,il_a, il_b, b_a, b_b);+        if(test.energy * 100 < threshold){+          int l1=strchr(test.structure, '&')-test.structure;+          printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f]  i:%d,j:%d <%5.2f>\n", test.structure,+                 begin_t-10+test.i-l1-10,+                 begin_t-10+test.i-1-10,+                 begin_q-10 + test.j-1-10 ,+                 (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2-10,+                 test.energy,test.energy_backtrack, pos-10, max_pos_j-10, ((double) position[pos+delta])/100);+          pos=MAX2(10,pos+temp_min-delta);+        }+        free(s3);free(s4);+        free(test.structure);+      }+    }+  }+#if 0+  else if(fast==3){+    pos=n1-9;+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* max_pos_j und pos entsprechen die realen position+           in der erweiterten sequenz.+           pos=1 -> position 1 in the sequence (and not 0 like in C)+           max_pos_j -> position 1 in the sequence ( not 0 like in C)+        */+        //Here we can start the reverse recursion for the+        //Starting from the reported pos / max_pos_j we start the recursion+        //We have to be careful with the fact that all energies are inverted.++        int alignment_length2;+        //Select the smallest interaction length in order to define the new interaction length+        alignment_length2 = MIN2(n1-pos + 1,max_pos_j - 1 + 1);+        //+        int begin_t=MAX2(11, pos-alignment_length2+1);/* 10 */+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1); /* 10 */+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2 + 20));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2 + 20));+        strcpy(s3,"NNNNNNNNNN");strcpy(s4,"NNNNNNNNNN");+        strncat(s3, (s1+begin_t-1),  end_t - begin_t +1);+        strncat(s4, (s2+begin_q-1) , end_q - begin_q +1);+        strcat(s3,"NNNNNNNNNN");strcat(s4,"NNNNNNNNNN");+        s3[end_t -begin_t +1 +20 ]='\0';+        s4[end_q -begin_q +1 +20]='\0';+        duplexT test;+        test = fduplexfold(s4, s3, extension_cost,il_a, il_b, b_a, b_b);+        if(test.energy * 100 < threshold){+          int structureLength=strlen(test.structure);+          int l1=strchr(test.structure, '&')-test.structure;+          int start_t,end_t,start_q,end_q;+++          /*reverse structure string*/+          char *reverseStructure = (char*) vrna_alloc(sizeof(char)*(structureLength+1));+          int posStructure;+          for(posStructure=l1+1; posStructure < structureLength; posStructure++){+            if(test.structure[posStructure]==')'){+              reverseStructure[posStructure-l1-1] = '(';+            }+            else{+              reverseStructure[posStructure-l1-1] = test.structure[posStructure];+            }+          }+          reverseStructure[structureLength-1-l1]='&';+          for(posStructure=0; posStructure<l1; posStructure++){+            if(test.structure[posStructure]=='('){+              reverseStructure[structureLength+posStructure-l1] = ')';+            }+            else{+              reverseStructure[structureLength+posStructure-l1] = test.structure[posStructure];+            }+          }+          reverseStructure[structureLength]='\0';+          //          l1=strchr(reverse.structure, '&')-test.structure;+++          printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f] i:%d,j:%d <%5.2f>\n", reverseStructure,+                 begin_t-10 + test.j-1-10,+                 (begin_t -11) + test.j + strlen(test.structure)-l1-2-10,+                 begin_q-10+test.i-l1-10,+                 begin_q-10+test.i-1-10,+                 test.energy,test.energy_backtrack,pos, max_pos_j, ((double) position[pos+delta])/100);+          pos=MAX2(10,pos+temp_min-delta);+        }+        free(s3);free(s4);+        free(test.structure);+      }+    }+  }+#endif+  else{+    pos=n1-9;+    while(10 < pos--){+      int temp_min=0;+      if(position[pos+delta]<(threshold)){+        int search_range;+        search_range=delta+1;+        while(--search_range){+          if(position[pos+delta-search_range]<=position[pos+delta-temp_min]){+            temp_min=search_range;+          }+        }+        pos-=temp_min;+        int max_pos_j;+        max_pos_j=position_j[pos+delta];+        /* max_pos_j und pos entsprechen die realen position+           in der erweiterten sequenz.+           pos=1 -> position 1 in the sequence (and not 0 like in C)+           max_pos_j -> position 1 in the sequence ( not 0 like in C)+        */+        int alignment_length2; alignment_length2 = MIN2(n1,n2);+        int begin_t=MAX2(11, pos-alignment_length2+1);/* 10 */+        int end_t  =MIN2(n1-10, pos+1);+        int begin_q=MAX2(11, max_pos_j-1); /* 10 */+        int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+        char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+        char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+        strncpy(s3, (s1+begin_t-1),  end_t - begin_t +1);+        strncpy(s4, (s2+begin_q-1) , end_q - begin_q +1);+        s3[end_t -begin_t +1 ]='\0';+        s4[end_q -begin_q +1 ]='\0';+        duplexT test;+        test = duplexfold(s3, s4, extension_cost);+        if(test.energy * 100 < threshold){+          int l1=strchr(test.structure, '&')-test.structure;+          printf("%s %3d,%-3d : %3d,%-3d (%5.2f)  i:%d,j:%d <%5.2f>\n", test.structure,+                 begin_t-10+test.i-l1,+                 begin_t-10+test.i-1,+                 begin_q-10 + test.j-1 ,+                 (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2,+                 test.energy, pos-10, max_pos_j-10, ((double) position[pos+delta])/100);+          pos=MAX2(10,pos+temp_min-delta);+        }+        free(s3);free(s4);+        free(test.structure);+      }+    }+  }+}+PRIVATE void plot_max(const int max, const int max_pos, const int max_pos_j, const int alignment_length, const char *s1, const char *s2, const int extension_cost, const int fast,const int il_a, const int il_b, const int b_a, const int b_b)+{+  if(fast==1){+    printf("target upper bound %d: query lower bound %d (%5.2f)\n", max_pos-10, max_pos_j-10, ((double)max)/100);+  }+  else if(fast==2){+    int alignment_length2; alignment_length2 = MIN2(n1,n2);+    int begin_t=MAX2(11, max_pos-alignment_length2+1);/* 10 */+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1); /* 10 */+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2 + 20));+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2 + 20));+    strcpy(s3,"NNNNNNNNNN");strcpy(s4,"NNNNNNNNNN");+    strncat(s3, (s1+begin_t-1),  end_t - begin_t +1);+    strncat(s4, (s2+begin_q-1) , end_q - begin_q +1);+    strcat(s3,"NNNNNNNNNN");strcat(s4,"NNNNNNNNNN");+    s3[end_t -begin_t +1 +20 ]='\0';+    s4[end_q -begin_q +1 +20]='\0';+    duplexT test;+    test = fduplexfold(s3, s4, extension_cost,il_a, il_b, b_a, b_b);+    int l1=strchr(test.structure, '&')-test.structure;+    printf("%s %3d,%-3d : %3d,%-3d (%5.2f) [%5.2f] i:%d,j:%d <%5.2f>\n", test.structure,+           begin_t-10+test.i-l1-10,+           begin_t-10+test.i-1-10,+           begin_q-10 + test.j-1-10 ,+           (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2-10,+           test.energy, test.energy_backtrack,max_pos-10, max_pos_j-10,((double) max)/100);+    free(s3);free(s4);free(test.structure);+  }+  else{+    duplexT test;+    int alignment_length2; alignment_length2 = MIN2(n1,n2);+    int begin_t=MAX2(11, max_pos-alignment_length2+1);+    int end_t  =MIN2(n1-10, max_pos+1);+    int begin_q=MAX2(11, max_pos_j-1);+    int end_q  =MIN2(n2-10, max_pos_j+alignment_length2-1);+    char *s3 = (char*) vrna_alloc(sizeof(char)*(end_t - begin_t +2));+    char *s4 = (char*) vrna_alloc(sizeof(char)*(end_q - begin_q +2));+    strncpy(s3, (s1+begin_t-1),  end_t - begin_t + 1);+    strncpy(s4, (s2+begin_q-1) , end_q - begin_q +1 );+    s3[end_t -begin_t +1 ]='\0';+    s4[end_q -begin_q +1 ]='\0';+    test = duplexfold(s3, s4, extension_cost);+    int l1=strchr(test.structure, '&')-test.structure;+    printf("%s %3d,%-3d : %3d,%-3d (%5.2f) i:%d,j:%d <%5.2f>\n", test.structure,+           begin_t-10+test.i-l1,+           begin_t-10+test.i-1,+           begin_q-10 +test.j-1 ,+           (begin_q -11) + test.j + (int)strlen(test.structure)-l1-2,+           test.energy, max_pos-10, max_pos_j -10, ((double) max)/100);+    free(s3);free(s4);free(test.structure);+  }+}+++PRIVATE void update_dfold_params(void)+{+  vrna_md_t md;+  if(P)+    free(P);+  set_model_details(&md);+  P = vrna_params(&md);+  make_pair_matrix();+}++PRIVATE void encode_seqs(const char *s1, const char *s2) {+  unsigned int i,l;++  l = strlen(s1);+  S1 = encode_seq(s1);+  SS1= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS1 exists only for the special X K and I bases and energy_set!=0 */++  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS1[i] = alias[S1[i]];   /* for mismatches of nostandard bases */+  }++  l = strlen(s2);+  S2 = encode_seq(s2);+  SS2= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS2 exists only for the special X K and I bases and energy_set!=0 */++  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS2[i] = alias[S2[i]];   /* for mismatches of nostandard bases */+  }+}++PRIVATE short * encode_seq(const char *sequence) {+  unsigned int i,l;+  short *S;+  l = strlen(sequence);+  S = (short *) vrna_alloc(sizeof(short)*(l+2));+  S[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    S[i]= (short) encode_char(toupper(sequence[i-1]));++  /* for circular folding add first base at position n+1 */+  S[l+1] = S[1];++  return S;+}++int arraySize(duplexT** array)+{+  int site_count=0;+  while(array[site_count]!=NULL){+    site_count++;+  }+  return site_count;+}++void freeDuplexT(duplexT** array)+{+  int size=arraySize(array);+  while(--size){+    free(array[size]->structure);+    free(array[size]);+  }+  free(array[0]->structure);+  free(array);+}
+ C/ViennaRNA/plex.h view
@@ -0,0 +1,80 @@+#ifndef VIENNA_RNA_PACKAGE_PLEX_H+#define VIENNA_RNA_PACKAGE_PLEX_H++#include <ViennaRNA/data_structures.h>+++extern int subopt_sorted;++/**+*** Lduplexfold Computes duplexes between two single sequences+**/+duplexT** Lduplexfold(const char *s1,+                      const char *s2,+                      const int threshold,+                      const int extension_cost,+                      const int alignment_length,+                      const int delta,+                      const int fast,+                      const int il_a,+                      const int il_b,+                      const int b_a,+                      const int b_b);++/**+*** Lduplexfold_XS Computes duplexes between two single sequences with accessibility+**/+duplexT** Lduplexfold_XS( const char*s1,+                          const char* s2,+                          const int **access_s1,+                          const int **access_s2,+                          const int threshold,+                          const int delta,+                          const int alignment_length,+                          const int fast,+                          const int il_a,+                          const int il_b,+                          const int b_a,+                          const int b_b);/* , const int target_dead, const int query_dead); */++/**+*** Lduplexfold_C Computes duplexes between two single sequences and takes constraint into account+**/+duplexT** Lduplexfold_C(const char *s1,+                        const char *s2,+                        const int threshold,+                        const int extension_cost,+                        const int alignment_length,+                        const int delta,+                        const int fast,+                        const char* structure,+                        const int il_a,+                        const int il_b,+                        const int b_a,+                        const int b_b);++/**+*** Lduplexfold_CXS Computes duplexes between two single sequences and takes constraint as well as accessibility into account+**/++duplexT** Lduplexfold_CXS(const char*s1,+                          const char* s2,+                          const int **access_s1,+                          const int **access_s2,+                          const int threshold,+                          const int delta,+                          const int alignment_length,+                          const int fast,+                          const char* structure,+                          const int il_a,+                          const int il_b,+                          const int b_a,+                          const int b_b); /*, const int target_dead, const int query_dead); */+++++int      arraySize(duplexT** array);+void     freeDuplexT(duplexT** array);++#endif
+ C/ViennaRNA/plex_functions.c view
@@ -0,0 +1,307 @@+/*+           compute potentially pseudoknotted structures of an RNA sequence+                             Ivo Hofacker+                          Vienna RNA package+*/++/*+  library containing the function used in PKplex+  it generates pseudoknotted structures by letting the sequence form a duplex structure with itself+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include <time.h>++#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"++#include "ViennaRNA/pair_mat.h"++#include "ViennaRNA/fold.h"+#include "ViennaRNA/PKplex.h"++#undef  MAXLOOP+#define MAXLOOP 10++PRIVATE void  update_dfold_params(void);+PRIVATE void  duplexfold_XS(const char *s1, int **access_s1, const int threshold, const int max_interaction_length);+PRIVATE char  *backtrack_XS(int kk, int ll, const int ii, const int jj, const int max_interaction_length);+PRIVATE void  make_ptypes(const char *structure);++PRIVATE vrna_param_t  *P = NULL;+PRIVATE int     ***c3 = NULL;      /* energy array used in duplexfold */+PRIVATE short   *S1 = NULL, *SS1 = NULL;+PRIVATE int     n1;+PRIVATE char    *ptype = NULL;     /* precomputed array of pair types */+PRIVATE int     *indx = NULL;      /* index for moving in the triangle matrices ptype[] */++PUBLIC  dupVar  *PlexHits = NULL;+PUBLIC  int     PlexHitsArrayLength = 100;+PUBLIC  int     NumberOfHits        = 0;+PUBLIC  int     verbose             = 0;++/*-----------------------------------------------------------------------duplexfold_XS---------------------------------------------------------------------------*/++PRIVATE void  duplexfold_XS(const char *s1,+                            int **access_s1,+                            const int threshold,+                            const int max_interaction_length){++  int i, j, k, l, p, q, Emin=INF, l_min=0, k_min=0, j_min=0;+  int type, type2, type3, E, tempK;+  char *struc;+  int length = (int) strlen(s1);+  struc=NULL;++  c3 = (int ***) vrna_alloc(sizeof(int **) * (length));+  for (i=0; i<length; i++){+    c3[i] = (int **) vrna_alloc(sizeof(int *) * max_interaction_length);+    for (j=0; j<max_interaction_length; j++) {+      c3[i][j]=(int *) vrna_alloc(sizeof(int) * max_interaction_length);+    }+  }++  i = length - 9;++  while( i-- > 11 ){+    Emin=INF;+    j_min=0;+    l_min=0;+    k_min=0;++    /* init all matrix elements to INF */+    for (j=0; j < length; j++){+      for(k=0;k<max_interaction_length;k++){+        for(l=0;l<max_interaction_length;l++){+          c3[j][k][l]=INF;+        }+      }+    }+    char string[10] = {'\0'};+    /* matrix starting values for (i,j)-basepairs */+    for(j=i+4; j<n1-10; j++) {+      type=ptype[indx[j]+i];+      if (type) {+        c3[j-11][max_interaction_length-1][0] = P->DuplexInit;+        c3[j-11][max_interaction_length-1][0] += E_Hairpin(j-i-1, type,  SS1[i+1], SS1[j-1], string, P);+/*        c3[j-11][max_interaction_length-1][0] += E_ExtLoop(type, SS1[i+1], SS1[j-1], P); */+/*           c3[j-11][max_interaction_length-1][0] += E_ExtLoop(rtype[type], SS1[j-1], SS1[i+1], P); */+       }+    }++    int i_pos_begin=MAX2(9, i-max_interaction_length); /* why 9 ??? */++    /* fill matrix */+    for(k=i-1; k>i_pos_begin; k--) {+      tempK=max_interaction_length-i+k-1;+      for(l = i + 5; l < n1 - 9; l++) { /* again, why 9 less then the sequence length ? */+        type2 = ptype[indx[l] + k];+        if(!type2) continue;+        for(p = k + 1; (p <= i) && (p <= k + MAXLOOP + 1); p++){+          for(q = l - 1; (q>=i+4) && (q >= l - MAXLOOP - 1); q--){+            if (p - k + l - q - 2 > MAXLOOP) break;+            type3 = ptype[indx[q] + p];+            if(!type3) continue;+            E = E_IntLoop(p - k - 1, l - q - 1, type2, rtype[type3], SS1[k + 1], SS1[l - 1], SS1[p - 1], SS1[q + 1], P);+            for(j = MAX2(i + 4, l - max_interaction_length + 1); j <= q; j++){+              type = ptype[indx[j]+i];+              if (type){+                c3[j-11][tempK][l-j] = MIN2(c3[j-11][tempK][l-j], c3[j-11][max_interaction_length-i+p-1][q-j]+E);+              }+            }/* next j */+          }/* next q */+        }/* next p */+      }/* next l */+    }/* next k */++    /* read out matrix minimum */+    for(j=i+4; j<n1-10; j++) {+      type=ptype[indx[j]+i];+      if (!type) continue;+      int j_pos_end=MIN2(n1-9,j+max_interaction_length);+      for (k=i-1; k>i_pos_begin; k--) {+        for (l=j+1; l<j_pos_end; l++) {+          type2=ptype[indx[l]+k];+          if (!type2) continue;+          E = c3[j-11][max_interaction_length-i+k-1][l-j];+/*           printf("[%d,%d][%d,%d]\t%6.2f\t%6.2f\t%6.2f\n", i, k, l, j, E/100., access_s1[i-k+1][i]/100., access_s1[l-j+1][l]/100.); */+          E+=access_s1[i-k+1][i]+access_s1[l-j+1][l];+          E+=E_ExtLoop(type2,((k>i_pos_begin+1)? SS1[k-1]:-1),((l<j_pos_end-1)? SS1[l+1]:-1),P);+          E+=E_ExtLoop(rtype[type], SS1[j-1], SS1[i+1], P);+          if (E<Emin) {+            Emin=E; k_min=k; l_min=l;+            j_min=j;+          }+        }+      }+    }++    if(Emin  < threshold){+      struc = backtrack_XS(k_min, l_min, i, j_min, max_interaction_length);++      /* lets take care of the dangles */+      /* find best combination */+      int dx_5, dx_3, dy_5, dy_3,dGx,dGy,bonus_x, bonus_y;+      dx_5 = dx_3 = dy_5 = dy_3 = dGx = dGy = bonus_x = bonus_y = 0;+      dGx = access_s1[i-k_min+1][i];+      dGy = access_s1[l_min-j_min+1][l_min];+      PlexHits[NumberOfHits].tb=k_min -10 -dx_5;+      PlexHits[NumberOfHits].te=i -10 + dx_3;+      PlexHits[NumberOfHits].qb=j_min -10 - dy_5;+      PlexHits[NumberOfHits].qe=l_min -10 + dy_3;+      PlexHits[NumberOfHits].ddG=(double) Emin * 0.01;+      PlexHits[NumberOfHits].dG1=(double) dGx*0.01 ;+      PlexHits[NumberOfHits].dG2=(double) dGy*0.01 ;+      PlexHits[NumberOfHits].energy = PlexHits[NumberOfHits].ddG - PlexHits[NumberOfHits].dG1 - PlexHits[NumberOfHits].dG2;+      PlexHits[NumberOfHits].structure = struc;++      /* output: */+      if(PlexHits[NumberOfHits].energy * 100 < threshold){+        if (verbose) printf("%s %3d,%-3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f)\n", PlexHits[NumberOfHits].structure, PlexHits[NumberOfHits].tb, PlexHits[NumberOfHits].te, PlexHits[NumberOfHits].qb, PlexHits[NumberOfHits].qe, PlexHits[NumberOfHits].ddG, PlexHits[NumberOfHits].energy, PlexHits[NumberOfHits].dG1, PlexHits[NumberOfHits].dG2);+        NumberOfHits++;+        if(NumberOfHits==PlexHitsArrayLength-1){+          PlexHitsArrayLength*=2;+          PlexHits = (dupVar *) vrna_realloc(PlexHits,sizeof(dupVar)*PlexHitsArrayLength);+        }+      }+    }+  }++  for (i=0; i<(n1-20); i++) {+    for (j=0; j<max_interaction_length; j++) {+      free(c3[i][j]);+    }+    free(c3[i]);+  }+  free(c3);+}+++PRIVATE char *backtrack_XS(int k, int l, const int i, const int j, const int max_interaction_length) {+  /* backtrack structure going backwards from i, and forwards from j+     return structure in bracket notation with & as separator */+  int p, q, type, type2, E, traced, i0, j0;+  char *st1, *st2, *struc;+  st1 = (char *) vrna_alloc(sizeof(char)*(i-k+2));+  st1[i-k+1]='\0';+  st2 = (char *) vrna_alloc(sizeof(char)*(l-j+2));+  st2[l-j+1]='\0';++  i0=k; j0=l;+  while (k<=i && l>=j) {+    E = c3[j-11][max_interaction_length-i+k-1][l-j]; traced=0;+    st1[k-i0] = '(';+    st2[l-j] = ')';++    type=ptype[indx[l]+k];+    if (!type) vrna_message_error("backtrack failed in fold duplex bli");+    for (p=k+1; p<=i; p++) {+      for (q=l-1; q>=j; q--) {+        int LE;+        if (p-k+l-q-2>MAXLOOP) break;+        type2=ptype[indx[q]+p];+        if (!type2) continue;+         LE = E_IntLoop(p-k-1, l-q-1, type, rtype[type2], SS1[k+1], SS1[l-1], SS1[p-1], SS1[q+1], P);+         if (E == c3[j-11][max_interaction_length-i+p-1][q-j]+LE) {+          traced=1;+           k=p; l=q;+          break;+        }+      }+      if (traced) break;+    }+    if (!traced) {+      E-=E_ExtLoop(type2, ((k<i)?SS1[k+1]:-1), ((l>j-1)? SS1[l-1]:-1), P);+      break;+      if (E != P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex bal");+      } else break;+    }+  }+  struc = (char *) vrna_alloc(k-i0+1+j0-l+1+2);++  for (p=0; p<=i-i0; p++){+    if (!st1[p]) st1[p] = '.';+  }++  for (p=0; p<=j0-j; p++) {+    if (!st2[p]) {+      st2[p] = '.';+    }+  }++  strcpy(struc, st1);+  strcat(struc, "&");+  strcat(struc, st2);+  free(st1); free(st2);+  return struc;+}++PUBLIC  dupVar  **PKLduplexfold_XS( const char *s1,+                                    int **access_s1,+                                    const int threshold,+                                    const int max_interaction_length,+                                    const int delta){++  if ((!P) || (fabs(P->temperature - temperature)>1e-6))+    update_dfold_params();++  n1 = (int) strlen(s1);+  S1 = encode_sequence(s1, 0);+  SS1 = encode_sequence(s1, 1);++  indx  = vrna_idx_col_wise(n1);+  ptype = (char *) vrna_alloc(sizeof(char)*((n1*(n1+1))/2+2));+  make_ptypes(s1);++  P->DuplexInit=0;+  duplexfold_XS(s1,access_s1,threshold, max_interaction_length);+  free(S1); free(SS1);+  free(indx); free(ptype);+  return NULL;+}++/*---------------------------------UTILS------------------------------------------*/++PRIVATE void update_dfold_params(void){+  vrna_md_t md;+  if(P)+    free(P);+  set_model_details(&md);+  P = vrna_params(&md);+  make_pair_matrix();+}++/*---------------------------------------------------------------------------*/++PRIVATE void make_ptypes(const char *structure) {+  int n,i,j,k,l;++  n=S1[0];+  for (k=1; k<n-TURN; k++)+    for (l=1; l<=2; l++) {+      int type,ntype=0,otype=0;+      i=k; j = i+TURN+l; if (j>n) continue;+      type = pair[S1[i]][S1[j]];+      while ((i>=1)&&(j<=n)) {+        if ((i>1)&&(j<n)) ntype = pair[S1[i-1]][S1[j+1]];+        if (noLonelyPairs && (!otype) && (!ntype))+          type = 0; /* i.j can only form isolated pairs */+        ptype[indx[j]+i] = (char) type;+        otype =  type;+        type  = ntype;+        i--; j++;+      }+    }+}
+ C/ViennaRNA/plot_aln.c view
@@ -0,0 +1,600 @@+/*+        PostScript output for Sequence / Structure Alignments++                 c  Ivo Hofacker, Peter F Stadler, Ronny Lorenz+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <string.h>+#include <ctype.h>+#include "ViennaRNA/model.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/plot_aln.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++int PS_color_aln(const char *structure, const char *filename,+                 const char *seqs[], const char *names[]) {+  /* produce PS sequence alignment color-annotated by consensus structure */++  int N,i,j,k,x,y,tmp,columnWidth;+  char *tmpBuffer,*ssEscaped,*ruler, *cons;+  char c;+  float fontWidth, fontHeight, imageHeight, imageWidth,tmpColumns;+  int length, maxName, maxNum, currPos;+  float lineStep,blockStep,consStep,ssStep,rulerStep,nameStep,numberStep;+  float maxConsBar,startY,namesX,seqsX, currY;+  float score,barHeight,xx,yy;+  int match,block;+  FILE *outfile;+  short *pair_table;+  char * colorMatrix[6][3] = {+    {"0.0 1", "0.0 0.6",  "0.0 0.2"},  /* red    */+    {"0.16 1","0.16 0.6", "0.16 0.2"}, /* ochre  */+    {"0.32 1","0.32 0.6", "0.32 0.2"}, /* turquoise */+    {"0.48 1","0.48 0.6", "0.48 0.2"}, /* green  */+    {"0.65 1","0.65 0.6", "0.65 0.2"}, /* blue   */+    {"0.81 1","0.81 0.6", "0.81 0.2"} /* violet */+  };++  const char *alnPlotHeader =+        "%%!PS-Adobe-3.0 EPSF-3.0\n"+        "%%%%BoundingBox: %i %i %i %i\n"+        "%%%%EndComments\n"+        "%% draws Vienna RNA like colored boxes\n"+        "/box { %% x1 y1 x2 y2 hue saturation\n"+        "  gsave\n"+        "  dup 0.3 mul 1 exch sub sethsbcolor\n"+        "  exch 3 index sub exch 2 index sub rectfill\n"+        "  grestore\n"+        "} def\n"+        "%% draws a box in current color\n"+        "/box2 { %% x1 y1 x2 y2\n"+        "  exch 3 index sub exch 2 index sub rectfill\n"+        "} def\n"+        "/string { %% (Text) x y\n"+        " 6 add\n"+        " moveto\n"+        "  show\n"+        "} def\n"+        "0 %i translate\n"+        "1 -1 scale\n"+        "/Courier findfont\n"+        "[10 0 0 -10 0 0] makefont setfont\n";++  vrna_md_t     md;++  set_model_details(&md);++  outfile = fopen(filename, "w");++  if (outfile == NULL) {+    vrna_message_warning("can't open file %s - not doing alignment plot\n", filename);+    return 0;+  }++  columnWidth=60;            /* Display long alignments in blocks of this size */+  fontWidth=6;               /* Font metrics */+  fontHeight=6.5;+  lineStep=fontHeight+2;     /* distance between lines */+  blockStep=3.5*fontHeight;  /* distance between blocks */+  consStep=fontHeight*0.5;   /* distance between alignment and conservation curve */+  ssStep=2;                  /* distance between secondary structure line and sequences */+  rulerStep=2;               /* distance between sequences and ruler */+  nameStep=3*fontWidth;             /* distance between names and sequences */+  numberStep=fontWidth;      /* distance between sequeces and numbers */+  maxConsBar=2.5*fontHeight; /* Height of conservation curve */+  startY=2;                     /* "y origin" */+  namesX=fontWidth;             /* "x origin" */++  /* Number of columns of the alignment */+  length=strlen(seqs[0]);++  /* Allocate memory for various strings, length*2 is (more than)+         enough for all of them */+  tmpBuffer = (char *) vrna_alloc((unsigned) MAX2(length*2,columnWidth)+1);+  ssEscaped=(char *) vrna_alloc((unsigned) length*2);+  ruler=(char *) vrna_alloc((unsigned) length*2);++  pair_table=vrna_ptable(structure);+  /* Get length of longest name and count sequences in alignment*/++  for (i=maxName=N=0; names[i] != NULL; i++) {+    N++;+    tmp=strlen(names[i]);+    if (tmp>maxName)  maxName=tmp;+  }+++  /* x-coord. where sequences start */+  seqsX=namesX+maxName*fontWidth+nameStep;++  /* calculate number of digits of the alignment length */+  snprintf(tmpBuffer,length, "%i",length);+  maxNum=strlen(tmpBuffer);+++  /* Calculate bounding box */+  tmpColumns=columnWidth;+  if (length<columnWidth){+        tmpColumns=length;+  }+  imageWidth=ceil(namesX+(maxName+tmpColumns+maxNum)*fontWidth+2*nameStep+fontWidth+numberStep);+  imageHeight=startY+ceil((float)length/columnWidth)*((N+2)*lineStep+blockStep+consStep+ssStep+rulerStep);++  /* Write postscript header including correct bounding box */+  fprintf(outfile,alnPlotHeader,0,0,(int)imageWidth,(int)imageHeight,(int)imageHeight);++  /* Create ruler and secondary structure lines */+  i=0;+  /* Init all with dots */+  for (i=0;i<(length);i++){+        ruler[i]='.';+  }+  i=0;+  for (i=0;i<length;i++){+        /* Write number every 10th position, leave out block breaks */+        if ((i+1)%10==0 && (i+1)%columnWidth!=0){+          snprintf(tmpBuffer,length,"%i",i+1);+          strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer));+        }+  }+  ruler[length]='\0';++  /* Draw color annotation first */+  /* Repeat for all pairs */+  for (i=1; i<=length; i++) {+    if ((j=pair_table[i])>i) {+      /* Repeat for open and closing position */+      for (k=0;k<2;k++){+        int pairings, nonpair, s, col;+        int ptype[8] = {0,0,0,0,0,0,0,0};+        char *color;+        col = (k==0)?i-1:j-1;+        block=ceil((float)(col+1)/columnWidth);+        xx=seqsX+(col-(block-1)*columnWidth)*fontWidth;+        /* Repeat for each sequence */+        for (s=pairings=nonpair=0; s<N; s++) {+          ptype[md.pair[vrna_nucleotide_encode(seqs[s][i-1], &md)][vrna_nucleotide_encode(seqs[s][j-1], &md)]]++;+        }+        for (pairings=0,s=1; s<=7; s++) {+          if (ptype[s]) pairings++;+        }+        nonpair=ptype[0];+        if (nonpair <=2) {+          color = colorMatrix[pairings-1][nonpair];+          for (s=0; s<N; s++) {+            yy=startY+(block-1)*(lineStep*(N+2)+blockStep+consStep+rulerStep)+ssStep*(block)+(s+1)*lineStep;++            /* Color according due color information in pi-array, only if base pair is possible */+            if (md.pair[vrna_nucleotide_encode(seqs[s][i-1], &md)][vrna_nucleotide_encode(seqs[s][j-1], &md)]) {++              fprintf(outfile, "%.1f %.1f %.1f %.1f %s box\n",+                      xx,yy-1,xx+fontWidth,yy+fontHeight+1,color);+            }+          }+        }+      }+    }+  }+  free(pair_table);++  /* Process rest of the output in blocks of columnWidth */++  currY=startY;+  currPos=0;++  cons =  consensus(seqs);++  while (currPos<length) {++    /* Display secondary structure line */+    fprintf(outfile,"0 setgray\n");+    strncpy(tmpBuffer,structure+currPos,columnWidth);+    tmpBuffer[columnWidth]='\0';++    x=0;y=0;+    while ((c=tmpBuffer[x])){+      if (c=='.'){+        ssEscaped[y++]='.';+      } else {+        ssEscaped[y++]='\\';+        ssEscaped[y++]=c;+      }+      x++;+    }+    ssEscaped[y]='\0';++    fprintf(outfile, "(%s) %.1f %.1f string\n", ssEscaped,seqsX,currY);+    currY+=ssStep+lineStep;++    /* Display names, sequences and numbers */++    for (i=0; i<N; i++) {++      strncpy(tmpBuffer,seqs[i]+currPos,columnWidth);+      tmpBuffer[columnWidth]='\0';++      match=0;+      for (j=0;j<(currPos+strlen(tmpBuffer));j++){+        if (seqs[i][j] != '-') match++;+      }++      fprintf(outfile, "(%s) %.1f %.1f string\n", names[i],namesX,currY);+      fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);+      fprintf(outfile, "(%i) %.1f %.1f string\n", match,seqsX+fontWidth*(strlen(tmpBuffer))+numberStep,currY);+      currY+=lineStep;+    }+    currY+=rulerStep;+    strncpy(tmpBuffer,ruler+currPos,columnWidth);+    tmpBuffer[columnWidth]='\0';+    fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);++    currY+=lineStep;+    currY+=consStep;++    /*Display conservation bar*/++    fprintf(outfile,"0.6 setgray\n");+    for (i=currPos;(i<currPos+columnWidth && i<length);i++){+      match=0;+      for (j=0;j<N;j++){+        if (cons[i] == seqs[j][i]) match++;+        if (cons[i]=='U' && seqs[j][i]=='T') match++;+        if (cons[i]=='T' && seqs[j][i]=='U') match++;+      }+      score=(float)(match-1)/(N-1);++      if (cons[i] == '-' ||+          cons[i] == '_' ||+          cons[i] == '.'){+        score=0;+      }++      barHeight=maxConsBar*score;+      if (barHeight==0){+        barHeight=1;+      }++      xx=seqsX+(i-(columnWidth*currPos/columnWidth))*fontWidth;++      fprintf(outfile,"%.1f %.1f %.1f %.1f box2\n",+              xx,+              currY+maxConsBar-barHeight,+              xx+fontWidth,+              currY+maxConsBar);+    }++    currY+=blockStep;+    currPos+=columnWidth;+  }+  free(cons);++  fprintf(outfile,"showpage\n");+  fclose(outfile);++  free(tmpBuffer);+  free(ssEscaped);free(ruler);++  return 0;++}++int aliPS_color_aln(const char *structure, const char *filename, +                    const char *seqs[], const char *names[]) {+  /* produce PS sequence alignment color-annotated by consensus structure */++  int N,i,j,k,x,y,tmp,columnWidth;+  char *tmpBuffer,*ssEscaped,*ruler, *cons;+  char c;+  float fontWidth, fontHeight, imageHeight, imageWidth,tmpColumns;+  int length, maxName, maxNum, currPos;+  float lineStep,blockStep,consStep,ssStep,rulerStep,nameStep,numberStep;+  float maxConsBar,startY,namesX,seqsX, currY;+  float score,barHeight,xx,yy;+  int match,block;+  FILE *outfile;+  short *pair_table;+  char * colorMatrix[6][3] = {+    {"0.0 1", "0.0 0.6",  "0.0 0.2"},  /* red    */+    {"0.16 1","0.16 0.6", "0.16 0.2"}, /* ochre  */+    {"0.32 1","0.32 0.6", "0.32 0.2"}, /* turquoise */+    {"0.48 1","0.48 0.6", "0.48 0.2"}, /* green  */+    {"0.65 1","0.65 0.6", "0.65 0.2"}, /* blue   */+    {"0.81 1","0.81 0.6", "0.81 0.2"} /* violet */+  };++  const char *alnPlotHeader =+        "%%!PS-Adobe-3.0 EPSF-3.0\n"+        "%%%%BoundingBox: %i %i %i %i\n"+        "%%%%EndComments\n"+        "%% draws Vienna RNA like colored boxes\n"+        "/box { %% x1 y1 x2 y2 hue saturation\n"+        "  gsave\n"+        "  dup 0.3 mul 1 exch sub sethsbcolor\n"+        "  exch 3 index sub exch 2 index sub rectfill\n"+        "  grestore\n"+        "} def\n"+        "%% draws a box in current color\n"+        "/box2 { %% x1 y1 x2 y2\n"+        "  exch 3 index sub exch 2 index sub rectfill\n"+        "} def\n"+        "/string { %% (Text) x y\n"+        " 6 add\n"+        " moveto\n"+        "  show\n"+        "} def\n"+        "0 %i translate\n"+        "1 -1 scale\n"+        "/Courier findfont\n"+        "[10 0 0 -10 0 0] makefont setfont\n";+        +  vrna_md_t md;++  set_model_details(&md);++  outfile = fopen(filename, "w");+  if (outfile == NULL) {+    vrna_message_warning("can't open file %s - not doing alignment plot\n", filename);+    return 0;+  }+  +  columnWidth=100;            /* Display long alignments in blocks of this size */+  fontWidth=6;               /* Font metrics */+  fontHeight=6.5;+  lineStep=fontHeight+2;     /* distance between lines */+  blockStep=3.5*fontHeight;  /* distance between blocks */+  consStep=fontHeight*0.5;   /* distance between alignment and conservation curve */+  ssStep=2;                  /* distance between secondary structure line and sequences */+  rulerStep=2;               /* distance between sequences and ruler */+  nameStep=3*fontWidth;             /* distance between names and sequences */+  numberStep=fontWidth;      /* distance between sequeces and numbers */+  maxConsBar=2.5*fontHeight; /* Height of conservation curve */+  startY=2;                     /* "y origin" */+  namesX=fontWidth;             /* "x origin" */++  /* Number of columns of the alignment */+  length=strlen(seqs[0]);++  /* Allocate memory for various strings, length*2 is (more than)+         enough for all of them */+  tmpBuffer = (char *) vrna_alloc((unsigned) columnWidth + length*2 );+  ssEscaped=(char *) vrna_alloc((unsigned) length*2 );+  ruler=(char *) vrna_alloc((unsigned) length*2  );+/*   char * structur; */+/*   structur = (char*) vrna_alloc((length+1)*sizeof(char)); */+/*   structur = strdup(structure); */+/*   for(i=0; i<length;i++){ */+/*     if(structur[i] == '<') structur[i]='('; */+/*     if(structur[i] == '>') structur[i]=')'; */+/*   } */+/*   structur[length]='\0';    */+/*   printf("%s \n", structur); */+   pair_table=vrna_pt_ali_get(structure);+  /* Get length of longest name and count sequences in alignment*/++  for (i=maxName=N=0; names[i] != NULL; i++) {+    N++;+    tmp=strlen(names[i]);+    if (tmp>maxName)  maxName=tmp;+  }++  +  /* x-coord. where sequences start */+  seqsX=namesX+maxName*fontWidth+nameStep; ++  /* calculate number of digits of the alignment length */+  snprintf(tmpBuffer,length, "%i",length);+  maxNum=strlen(tmpBuffer);+  ++  /* Calculate bounding box */+  tmpColumns=columnWidth;+  if (length<columnWidth){+        tmpColumns=length;+  }+  imageWidth=ceil(namesX+(maxName+tmpColumns+maxNum)*fontWidth+2*nameStep+fontWidth+numberStep);+  imageHeight=startY+ceil((float)length/columnWidth)*((N+2)*lineStep+blockStep+consStep+ssStep+rulerStep);++  /* Write postscript header including correct bounding box */+  fprintf(outfile,alnPlotHeader,0,0,(int)imageWidth,(int)imageHeight,(int)imageHeight);++  /* Create ruler and secondary structure lines */+  i=0;+  /* Init all with dots */+  for (i=0;i<(length);i++){+        ruler[i]='.';+  }+  i=0;+  for (i=0;i<length;i++){+        /* Write number every 10th position, leave out block breaks */+        if ((i+1)%10==0 && (i+1)%columnWidth!=0){+          snprintf(tmpBuffer,length,"%i",i+1);+          strncpy(ruler+i,tmpBuffer,strlen(tmpBuffer));+        }+  }+  ruler[length]='\0';+  +  /* Draw color annotation first */+  /* Repeat for all pairs */+  for (i=1; i<=length; i++) {+    if ((j=pair_table[i])>i) {+      /* Repeat for open and closing position */+      for (k=0;k<2;k++){+        int pairings, nonpair, s, col;+        int ptype[8] = {0,0,0,0,0,0,0,0};+        char *color;+        col = (k==0)?i-1:j-1;+        block=ceil((float)(col+1)/columnWidth);+        xx=seqsX+(col-(block-1)*columnWidth)*fontWidth;+        /* Repeat for each sequence */+        for (s=pairings=nonpair=0; s<N; s++) {+          ptype[md.pair[vrna_nucleotide_encode(seqs[s][i-1], &md)][vrna_nucleotide_encode(seqs[s][j-1], &md)]]++;+        }+        for (pairings=0,s=1; s<=7; s++) {+          if (ptype[s]) pairings++;+        }+        nonpair=ptype[0];+        if (nonpair <=2) {+          color = colorMatrix[pairings-1][nonpair];+          for (s=0; s<N; s++) {+            yy=startY+(block-1)*(lineStep*(N+2)+blockStep+consStep+rulerStep)+ssStep*(block)+(s+1)*lineStep;+            +            /* Color according due color information in pi-array, only if base pair is possible */+            if (md.pair[vrna_nucleotide_encode(seqs[s][i-1], &md)][vrna_nucleotide_encode(seqs[s][j-1], &md)]) {++              fprintf(outfile, "%.1f %.1f %.1f %.1f %s box\n",+                      xx,yy-1,xx+fontWidth,yy+fontHeight+1,color);+            }+          }+        }+      }+    }+  }+  free(pair_table);++  /* Process rest of the output in blocks of columnWidth */++  currY=startY;+  currPos=0;++  cons =  consensus(seqs);+  +  while (currPos<length) {++    /* Display secondary structure line */+    fprintf(outfile,"0 setgray\n");+    strncpy(tmpBuffer,structure+currPos,columnWidth);+    tmpBuffer[columnWidth]='\0';+    +    x=0;y=0;+    while ((c=tmpBuffer[x])){+      if (c=='.'){+        ssEscaped[y++]='.';+      } else {+        ssEscaped[y++]='\\';+        ssEscaped[y++]=c;+      }                         +      x++;+    }+    ssEscaped[y]='\0';+    +    fprintf(outfile, "(%s) %.1f %.1f string\n", ssEscaped,seqsX,currY);+    currY+=ssStep+lineStep;+    +    /* Display names, sequences and numbers */++    for (i=0; i<N; i++) {+      +      strncpy(tmpBuffer,seqs[i]+currPos,columnWidth);+      tmpBuffer[columnWidth]='\0';+      +      match=0;+      for (j=0;j<(currPos+strlen(tmpBuffer));j++){+        if (seqs[i][j] != '-') match++;+      }+      +      fprintf(outfile, "(%s) %.1f %.1f string\n", names[i],namesX,currY);+      fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);+      fprintf(outfile, "(%i) %.1f %.1f string\n", match,seqsX+fontWidth*(strlen(tmpBuffer))+numberStep,currY);+      currY+=lineStep;+    }+    currY+=rulerStep;+    strncpy(tmpBuffer,ruler+currPos,columnWidth);+    tmpBuffer[columnWidth]='\0';+    fprintf(outfile, "(%s) %.1f %.1f string\n", tmpBuffer,seqsX,currY);+    +    currY+=lineStep;+    currY+=consStep;+    +    /*Display conservation bar*/+    +    fprintf(outfile,"0.6 setgray\n");+    for (i=currPos;(i<currPos+columnWidth && i<length);i++){+      match=0;+      for (j=0;j<N;j++){+        if (cons[i] == seqs[j][i]) match++;+        if (cons[i]=='U' && seqs[j][i]=='T') match++;+        if (cons[i]=='T' && seqs[j][i]=='U') match++;+      }+      score=(float)(match-1)/(N-1);+      +      if (cons[i] == '-' ||+          cons[i] == '_' ||+          cons[i] == '.'){+        score=0;+      }+      +      barHeight=maxConsBar*score;+      if (barHeight==0){+        barHeight=1;+      }+      +      xx=seqsX+(i-(columnWidth*currPos/columnWidth))*fontWidth;+      +      fprintf(outfile,"%.1f %.1f %.1f %.1f box2\n",+              xx,+              currY+maxConsBar-barHeight,+              xx+fontWidth,+              currY+maxConsBar);+    }+    +    currY+=blockStep;+    currPos+=columnWidth;+  }+  free(cons);+  fprintf(outfile,"showpage\n");+  fclose(outfile);+  free(tmpBuffer);+  free(ssEscaped);free(ruler);+  +  return 0;++}++#ifdef VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/+++#endif+
+ C/ViennaRNA/plot_aln.h view
@@ -0,0 +1,53 @@+#ifndef VIENNA_RNA_PACKAGE_PLOT_ALN_H+#define VIENNA_RNA_PACKAGE_PLOT_ALN_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file     plot_aln.h+ *  @ingroup  plotting_utils+ *  @brief    Various functions for plotting Sequence / Structure Alignments+ */++/**+ *  @{+ *  @ingroup  plotting_utils+ */++/**+ *  @brief Produce PostScript sequence alignment color-annotated by consensus+ *  structure+*/+int PS_color_aln( const char *structure,+                  const char *filename,+                  const char *seqs[],+                  const char *names[]);++/**+ *  PS_color_aln for duplexes+*/+int aliPS_color_aln(const char *structure,+                    const char *filename, +                    const char *seqs[],+                    const char *names[]); ++#ifdef VRNA_BACKWARD_COMPAT++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/plot_layouts.c view
@@ -0,0 +1,161 @@+/**+ * This file is a container for all plotting layout algorithms+ *+ *  c Ronny Lorenz+ *    The ViennaRNA Package+ */++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/plot_layouts.h"++#ifdef _OPENMP+#include <omp.h>+#endif++#define PUBLIC+#define PRIVATE static++PUBLIC  int     rna_plot_type = 1;  /* 0 = simple, 1 = naview, 2 = circular plot */++PRIVATE float   *angle;+PRIVATE int     *loop_size, *stack_size;+PRIVATE int     lp, stk;++PRIVATE void  loop(int i, int j, short *pair_table);++#ifdef _OPENMP+/* NOTE: all threadprivate variables are uninitialized when entering a thread! */+#pragma omp threadprivate(angle, loop_size, stack_size, lp, stk)+#endif++/*---------------------------------------------------------------------------*/++PUBLIC int simple_xy_coordinates(short *pair_table, float *x, float *y)+{+  float INIT_ANGLE=0.;     /* initial bending angle */+  float INIT_X = 100.;     /* coordinate of first digit */+  float INIT_Y = 100.;     /* see above */+  float RADIUS =  15.;++  int i, length;+  float  alpha;++  length = pair_table[0];+  angle =      (float*) vrna_alloc( (length+5)*sizeof(float) );+  loop_size  =   (int*) vrna_alloc( 16+(length/5)*sizeof(int) );+  stack_size =   (int*) vrna_alloc( 16+(length/5)*sizeof(int) );+  lp = stk = 0;+  loop(0, length+1, pair_table);+  loop_size[lp] -= 2;     /* correct for cheating with function loop */++  alpha = INIT_ANGLE;+  x[0]  = INIT_X;+  y[0]  = INIT_Y;++  for (i = 1; i <= length; i++) {+    x[i] = x[i-1]+RADIUS*cos(alpha);+    y[i] = y[i-1]+RADIUS*sin(alpha);+    alpha += PI-angle[i+1];+  }+  free(angle);+  free(loop_size);+  free(stack_size);++  return length;++}++/*---------------------------------------------------------------------------*/++PRIVATE void loop(int i, int j, short *pair_table)+             /* i, j are the positions AFTER the last pair of a stack; i.e+                i-1 and j+1 are paired. */+{+  int    count = 2;   /* counts the VERTICES of a loop polygon; that's+                           NOT necessarily the number of unpaired bases!+                           Upon entry the loop has already 2 vertices, namely+                           the pair i-1/j+1.  */++  int    r = 0, bubble = 0; /* bubble counts the unpaired digits in loops */++  int    i_old, partner, k, l, start_k, start_l, fill, ladder;+  int    begin, v, diff;+  float  polygon;++  short *remember;++  remember = (short *) vrna_alloc((3+(j-i)/5)*2*sizeof(short));++  i_old = i-1, j++;         /* j has now been set to the partner of the+                               previous pair for correct while-loop+                               termination.  */+  while (i != j) {+    partner = pair_table[i];+    if ((!partner) || (i==0))+      i++, count++, bubble++;+    else {+      count += 2;+      k = i, l = partner;    /* beginning of stack */+      remember[++r] = k;+      remember[++r] = l;+      i = partner+1;         /* next i for the current loop */++      start_k = k, start_l = l;+      ladder = 0;+      do {+        k++, l--, ladder++;        /* go along the stack region */+      }+      while ((pair_table[k] == l) && (pair_table[k] > k));++      fill = ladder-2;+      if (ladder >= 2) {+        angle[start_k+1+fill] += PIHALF;   /*  Loop entries and    */+        angle[start_l-1-fill] += PIHALF;   /*  exits get an        */+        angle[start_k]        += PIHALF;   /*  additional PI/2.    */+        angle[start_l]        += PIHALF;   /*  Why ? (exercise)    */+        if (ladder > 2) {+          for (; fill >= 1; fill--) {+            angle[start_k+fill] = PI;    /*  fill in the angles  */+            angle[start_l-fill] = PI;    /*  for the backbone    */+          }+        }+      }+      stack_size[++stk] = ladder;+      if(k <= l)+        loop(k, l, pair_table);+    }+  }+  polygon = PI*(count-2)/(float)count; /* bending angle in loop polygon */+  remember[++r] = j;+  begin = i_old < 0 ? 0 : i_old;+  for (v = 1; v <= r; v++) {+    diff  = remember[v]-begin;+    for (fill = 0; fill <= diff; fill++)+      angle[begin+fill] += polygon;+    if (v > r)+      break;+    begin = remember[++v];+  }+  loop_size[++lp] = bubble;+  free(remember);+}++/*---------------------------------------------------------------------------*/++PUBLIC int simple_circplot_coordinates(short *pair_table, float *x, float *y){+  unsigned int  length = (unsigned int) pair_table[0];+  unsigned int  i;+  float         d = 2*PI/length;+  for(i=0; i < length; i++){+    x[i] = cos(i * d - PI/2);+    y[i] = sin(i * d - PI/2);+  }+  return length;+}
+ C/ViennaRNA/plot_layouts.h view
@@ -0,0 +1,121 @@+/**+ *  @file     plot_layouts.h+ *  @ingroup  plotting_utils+ *  @brief    Secondary structure plot layout algorithms+ */++/**+ *  @{+ *  @ingroup   plotting_utils+ *+ */+#ifndef VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H+#define VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/naview.h>++#ifndef PI+#define  PI       3.141592654+#endif+#define  PIHALF       PI/2.+++/**+ *  @brief Definition of Plot type <i>simple</i>+ *+ *  This is the plot type definition for several RNA structure plotting functions telling+ *  them to use <b>Simple</b> plotting algorithm+ *+ *  @see rna_plot_type, vrna_file_PS_rnaplot_a(), vrna_file_PS_rnaplot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()+ */+#define VRNA_PLOT_TYPE_SIMPLE     0++/**+ *  @brief Definition of Plot type <i>Naview</i>+ *+ *  This is the plot type definition for several RNA structure plotting functions telling+ *  them to use <b>Naview</b> plotting algorithm+ *+ *  @see rna_plot_type, vrna_file_PS_rnaplot_a(), vrna_file_PS_rnaplot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()+ */+#define VRNA_PLOT_TYPE_NAVIEW     1++/**+ *  @brief Definition of Plot type <i>Circular</i>+ *+ *  This is the plot type definition for several RNA structure plotting functions telling+ *  them to produce a <b>Circular plot</b>+ *+ *  @see rna_plot_type, vrna_file_PS_rnaplot_a(), vrna_file_PS_rnaplot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()+ */+#define VRNA_PLOT_TYPE_CIRCULAR   2++/**+ *  @brief this is a workarround for the SWIG Perl Wrapper RNA plot function+ *  that returns an array of type COORDINATE+ */+typedef struct {+  float X; /* X coords */+  float Y; /* Y coords */+} COORDINATE;++/**+ *  @brief Switch for changing the secondary structure layout algorithm+ *+ *  Current possibility are 0 for a simple radial drawing or 1 for the modified+ *  radial drawing taken from the @e naview program of @cite bruccoleri:1988.+ *+ *  @note To provide thread safety please do not rely on this global variable in future implementations+ *  but pass a plot type flag directly to the function that decides which layout algorithm it may use!+ *+ *  @see #VRNA_PLOT_TYPE_SIMPLE, #VRNA_PLOT_TYPE_NAVIEW, #VRNA_PLOT_TYPE_CIRCULAR+ *+ */+extern int rna_plot_type;++/**+ *  @brief Calculate nucleotide coordinates for secondary structure plot the <i>Simple way</i>+ *+ *  @see make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), vrna_file_PS_rnaplot_a(),+ *  vrna_file_PS_rnaplot, svg_rna_plot()+ *+ *  @param  pair_table  The pair table of the secondary structure+ *  @param  X           a pointer to an array with enough allocated space to hold the x coordinates+ *  @param  Y           a pointer to an array with enough allocated space to hold the y coordinates+ *  @return             length of sequence on success, 0 otherwise+ */+int simple_xy_coordinates(short *pair_table,+                          float *X,+                          float *Y);++/**+ *  @brief Calculate nucleotide coordinates for <i>Circular Plot</i>+ *+ *  This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.+ *+ *  @note In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate+ *  a second tangential point @f$P^t@f$ in addition to the actual R<sup>2</sup> coordinates.+ *  the simplest way to do so may be to compute a radius scaling factor @f$rs@f$ in the interval @f$[0,1]@f$ that+ *  weights the proportion of base pair span to the actual length of the sequence. This scaling factor+ *  can then be used to calculate the coordinates for @f$P^t@f$, i.e. @f$ P^{t}_x[i] = X[i] * rs@f$+ *  and @f$P^{t}_y[i] = Y[i] * rs@f$.+ *+ *  @see make_pair_table(), rna_plot_type, simple_xy_coordinates(), naview_xy_coordinates(), vrna_file_PS_rnaplot_a(),+ *  vrna_file_PS_rnaplot, svg_rna_plot()+ *+ *  @param  pair_table  The pair table of the secondary structure+ *  @param  x           a pointer to an array with enough allocated space to hold the x coordinates+ *  @param  y           a pointer to an array with enough allocated space to hold the y coordinates+ *  @return             length of sequence on success, 0 otherwise+ */+int simple_circplot_coordinates(short *pair_table,+                                float *x,+                                float *y);++/**+ * @}+ */+++#endif
+ C/ViennaRNA/plot_structure.c view
@@ -0,0 +1,1256 @@+/*+        PostScript and other output formats for RNA secondary structure plots++                 c  Ivo Hofacker, Peter F Stadler, Ronny Lorenz+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <string.h>+#include <ctype.h>+#include "ViennaRNA/model.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/aln_util.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/plot_layouts.h"+#include "ViennaRNA/plot_structure.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++#ifndef PI+#define  PI       3.141592654+#endif+#define  PIHALF       PI/2.+#define SIZE 452.++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+static const char *RNAss_head =+"%%BeginProlog\n"+"/RNAplot 100 dict def\n"+"RNAplot begin\n"+"/fsize  14 def\n"+"/outlinecolor {0.2 setgray} bind def\n"+"/paircolor    {0.2 setgray} bind def\n"+"/seqcolor     {0   setgray} bind def\n"+"/cshow  { dup stringwidth pop -2 div fsize -3 div rmoveto show} bind def\n"+"/min { 2 copy gt { exch } if pop } bind def\n"+"/max { 2 copy lt { exch } if pop } bind def\n"+"/arccoords { % i j arccoords\n"+"  % puts optimal x1 y1 x2 y2 coordinates used in bezier curves from i to j\n"+"  % onto the stack\n"+"  dup 3 -1 roll dup 4 -1 roll lt dup dup 5 2 roll {exch} if\n"+"  dup 3 -1 roll dup 3 -1 roll exch sub 1 sub dup\n"+"  4 -2 roll 5 -1 roll {exch} if 4 2 roll\n"+"  sequence length dup 2 div exch 3 1 roll lt \n"+"  {exch 5 -1 roll pop 4 -2 roll exch 4 2 roll}\n"+"  { 4 2 roll 5 -1 roll dup 6 1 roll {exch} if\n"+"    4 -2 roll exch pop dup 3 -1 roll dup 4 1 roll\n"+"    exch add 4 -1 roll dup 5 1 roll sub 1 sub\n"+"    5 -1 roll not {4 -2 roll exch 4 2 roll} if\n"+"  }ifelse\n"+"   % compute the scalingfactor and prepare (1-sf) and sf*r\n"+"  2 mul exch cpr 3 1 roll div dup\n"+"  3 -1 roll mul exch 1 exch sub exch\n"+"   % compute the coordinates\n"+"  3 -1 roll 1 sub coor exch get aload pop % get coord for i\n"+"  4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate y1\n"+"  4 -1 roll dup 5 1 roll mul 3 -1 roll dup 4 1 roll add exch % calculate x1\n"+"  5 -1 roll 1 sub coor exch get aload pop % get coord for j\n"+"  % duplicate j coord\n"+"  dup 3 -1 roll dup 4 1 roll exch 8 2 roll\n"+"  6 -1 roll dup 7 1 roll mul 5 -1 roll dup 6 1 roll add exch % calculate y2\n"+"  6 -1 roll mul 5 -1 roll add exch % calculate x2\n"+"  6 -2 roll % reorder\n"+"} bind def\n"+"/drawoutline {\n"+"  gsave outlinecolor newpath\n"+"  coor 0 get aload pop 0.8 0 360 arc % draw 5' circle of 1st sequence\n"+"  currentdict /cutpoint known        % check if cutpoint is defined\n"+"  {coor 0 cutpoint getinterval\n"+"   {aload pop lineto} forall         % draw outline of 1st sequence\n"+"   coor cutpoint 1 add get aload pop\n"+"   2 copy moveto 0.8 0 360 arc       % draw 5' circle of 2nd sequence\n"+"   coor cutpoint 1 add coor length cutpoint 1 add sub getinterval\n"+"   {aload pop lineto} forall}        % draw outline of 2nd sequence\n"+"  {coor {aload pop lineto} forall}   % draw outline as a whole\n"+"  ifelse\n"+"  stroke grestore\n"+"} bind def\n"+"/drawpairs {\n"+"  paircolor\n"+"  0.7 setlinewidth\n"+"  [9 3.01] 9 setdash\n"+"  newpath\n"+"  pairs {aload pop\n"+"      currentdict (cpr) known\n"+"      { exch dup\n"+"        coor  exch 1 sub get aload pop moveto\n"+"        exch arccoords curveto\n"+"      }\n"+"      { coor exch 1 sub get aload pop moveto\n"+"        coor exch 1 sub get aload pop lineto\n"+"      }ifelse\n"+"  } forall\n"+"  stroke\n"+"} bind def\n"+"% draw bases\n"+"/drawbases {\n"+"  [] 0 setdash\n"+"  seqcolor\n"+"  0\n"+"  coor {\n"+"    aload pop moveto\n"+"    dup sequence exch 1 getinterval cshow\n"+"    1 add\n"+"  } forall\n"+"  pop\n"+"} bind def\n\n"+"/init {\n"+"  /Helvetica findfont fsize scalefont setfont\n"+"  1 setlinejoin\n"+"  1 setlinecap\n"+"  0.8 setlinewidth\n"+"  % find the coordinate range\n"+"  /xmax -1000 def /xmin 10000 def\n"+"  /ymax -1000 def /ymin 10000 def\n"+"  coor {\n"+"      aload pop\n"+"      dup ymin lt {dup /ymin exch def} if\n"+"      dup ymax gt {/ymax exch def} {pop} ifelse\n"+"      dup xmin lt {dup /xmin exch def} if\n"+"      dup xmax gt {/xmax exch def} {pop} ifelse\n"+"  } forall\n"+"  /size {xmax xmin sub ymax ymin sub max} bind def\n"+"  /width {xmax xmin sub} bind def\n"+"  /height {ymax ymin sub} bind def\n"+"  10 10 translate\n"+"  680 size 10 add div dup scale\n"+"  size width sub width xmin sub xmax sub add 2 div 5 add\n"+"  size height sub height ymin sub ymax sub add 2 div 5 add\n"+"  translate\n"+"} bind def\n"+"end\n";++static const char *anote_macros =+"RNAplot begin\n"+"% extra definitions for standard anotations\n"+"/min { 2 copy gt { exch } if pop } bind def\n"+"/BLACK { 0 0 0 } def\n"+"/RED   { 1 0 0 } def\n"+"/GREEN { 0 1 0 } def\n"+"/BLUE  { 0 0 1 } def\n"+"/WHITE { 1 1 1 } def\n"+"/LabelFont { % font size LabelFont\n"+"  exch findfont exch fsize mul scalefont setfont\n"+"} bind def\n"+"/Label { % i dx dy (text) Label\n"+"  % write text at base i plus offset dx, dy\n"+"  4 3 roll 1 sub coor exch get aload pop moveto\n"+"  3 1 roll fsize mul exch fsize mul exch rmoveto\n"+"  show\n"+"} bind def\n"+"/cmark { % i cmark   draw circle around base i\n"+"  newpath 1 sub coor exch get aload pop\n"+"  fsize 2 div 0 360 arc stroke\n"+"} bind def\n"+"/gmark { % i j c gmark\n"+"  % draw basepair i,j with c counter examples in gray\n"+"  gsave\n"+"  3 min [0 0.33 0.66 0.9] exch get setgray\n"+"  1 sub dup coor exch get aload pop moveto\n"+"  sequence exch 1 getinterval cshow\n"+"  1 sub dup coor exch get aload pop moveto\n"+"  sequence exch 1 getinterval cshow\n"+"  grestore\n"+"} bind def\n"+"/segmark { % f i j lw r g b segmark\n"+"  % mark segment [i,j] with outline width lw and color rgb\n"+"  % use omark and Fomark instead\n"+"  gsave\n"+"  setrgbcolor setlinewidth\n"+"  newpath\n"+"  1 sub exch 1 sub dup\n"+"  coor exch get aload pop moveto\n"+"  currentdict (cpr) known\n"+"  {\n"+"    3 -1 roll dup 4 1 roll dup\n"+"    {\n"+"      3 1 roll dup 3 -1 roll dup\n"+"      4 1 roll exch 5 2 roll exch\n"+"    }\n"+"    {\n"+"      3 1 roll exch\n"+"    } ifelse\n"+"    1 exch { coor exch get aload pop lineto } for\n"+"    {\n"+"      dup 3 1 roll 1 add exch 1 add arccoords pop pop\n"+"      4 2 roll 5 -1 roll coor exch get aload pop curveto\n"+"    } if\n"+"  }\n"+"  {\n"+"    exch 1 exch {\n"+"      coor exch get aload pop lineto\n"+"    } for\n"+"  } ifelse\n"+"  { closepath fill } if  stroke\n"+"  grestore\n"+"} bind def\n"+"/omark { % i j lw r g b omark\n"+"  % stroke segment [i..j] with linewidth lw, color rgb\n"+"  false 7 1 roll segmark\n"+"} bind def\n"+"/Fomark { % i j r g b Fomark\n"+"  % fill segment [i..j] with color rgb\n"+"  % should precede drawbases\n"+"  1 4 1 roll true 7 1 roll segmark\n"+"} bind def\n"+"/BFmark{ % i j k l r g b BFmark\n"+"  % fill block between pairs (i,j) and (k,l) with color rgb\n"+"  % should precede drawbases\n"+"  gsave\n"+"  setrgbcolor\n"+"  newpath\n"+"  currentdict (cpr) known\n"+"  {\n"+"    dup 1 sub coor exch get aload pop moveto % move to l\n"+"    dup 1 sub 4 -1 roll dup 5 1 roll 1 sub 1 exch\n"+"    { coor exch get aload pop lineto } for % lines from l to j\n"+"    3 -1 roll 4 -1 roll dup 5 1 roll arccoords curveto % curve from j to i\n"+"    exch dup 4 -1 roll 1 sub exch 1 sub 1 exch\n"+"    { coor exch get aload pop lineto } for % lines from i to k\n"+"    exch arccoords curveto% curve from k to l\n"+"  }\n"+"  {  exch 4 3 roll exch 1 sub exch 1 sub dup\n"+"     coor exch get aload pop moveto\n"+"     exch 1 exch { coor exch get aload pop lineto } for\n"+"     exch 1 sub exch 1 sub dup\n"+"     coor exch get aload pop lineto\n"+"     exch 1 exch { coor exch get aload pop lineto } for\n"+"  } ifelse\n"+"    closepath fill stroke\n"+"   grestore\n"+"} bind def\n"+"/hsb {\n"+"  dup 0.3 mul 1 exch sub sethsbcolor\n"+"} bind def\n"+"/colorpair { % i j hue sat colorpair\n"+"  % draw basepair i,j in color\n"+"  % 1 index 0.00 ne {\n"+"  gsave\n"+"  newpath\n"+"  hsb\n"+"  fsize setlinewidth\n"+"  currentdict (cpr) known\n"+"  {\n"+"    exch dup\n"+"    coor  exch 1 sub get aload pop moveto\n"+"    exch arccoords curveto\n"+"  }\n"+"  { 1 sub coor exch get aload pop moveto\n"+"    1 sub coor exch get aload pop lineto\n"+"  } ifelse\n"+"   stroke\n"+"   grestore\n"+"   % } if\n"+"} bind def\n"+ "end\n\n";++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE char **annote(const char *structure, const char *AS[]);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC int+vrna_file_PS_rnaplot( const char *string,+                      const char *structure,+                      const char *ssfile,+                      vrna_md_t  *md_p){++  return vrna_file_PS_rnaplot_a(string, structure, ssfile, NULL, NULL, md_p);+}++PUBLIC int+vrna_file_PS_rnaplot_a( const char *seq,+                        const char *structure,+                        const char *ssfile,+                        const char *pre,+                        const char *post,+                        vrna_md_t  *md_p){++  float  xmin, xmax, ymin, ymax;+  int    i, length;+  int    ee, gb, ge, Lg, l[3];+  float *X, *Y;+  FILE  *xyplot;+  short *pair_table, *pair_table_g;+  char  *c, *string;+  vrna_md_t   md;++  if(!md_p){+    set_model_details(&md);+    md_p  = &md;+  }+    +  string = strdup(seq);+  length = strlen(string);++  xyplot = fopen(ssfile, "w");+  if (xyplot == NULL) {+    vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+    return 0;+  }++  pair_table = vrna_ptable(structure);+  pair_table_g = vrna_ptable(structure);++  ge=0;+  while ( (ee=parse_gquad(structure+ge, &Lg, l)) >0 ) {+    ge += ee;+    gb=ge-Lg*4-l[0]-l[1]-l[2]+1;+    /* add pseudo-base pair encloding gquad */+    for (i=0; i<Lg; i++) {+      pair_table_g[ge-i]=gb+i;+      pair_table_g[gb+i]=ge-i;+    }+  } +      +  X = (float *) vrna_alloc((length+1)*sizeof(float));+  Y = (float *) vrna_alloc((length+1)*sizeof(float));+  switch(rna_plot_type){+    case VRNA_PLOT_TYPE_SIMPLE:   i = simple_xy_coordinates(pair_table_g, X, Y);+                                  break;+    case VRNA_PLOT_TYPE_CIRCULAR: {+                                    int radius = 3*length;+                                    i = simple_circplot_coordinates(pair_table_g, X, Y);+                                    for (i = 0; i < length; i++) {+                                      X[i] *= radius;+                                      X[i] += radius;+                                      Y[i] *= radius;+                                      Y[i] += radius;+                                    }+                                  }+                                  break;+    default:                      i = naview_xy_coordinates(pair_table_g, X, Y);+                                  break;+  }+  if(i!=length)+    vrna_message_warning("strange things happening in PS_rna_plot...");++  xmin = xmax = X[0];+  ymin = ymax = Y[0];+  for (i = 1; i < length; i++) {+     xmin = X[i] < xmin ? X[i] : xmin;+     xmax = X[i] > xmax ? X[i] : xmax;+     ymin = Y[i] < ymin ? Y[i] : ymin;+     ymax = Y[i] > ymax ? Y[i] : ymax;+  }++  fprintf(xyplot,+          "%%!PS-Adobe-3.0 EPSF-3.0\n"+          "%%%%Creator: ViennaRNA-%s\n"+          "%%%%CreationDate: %s"+          "%%%%Title: RNA Secondary Structure Plot\n"+          "%%%%BoundingBox: 0 0 700 700\n"+          "%%%%DocumentFonts: Helvetica\n"+          "%%%%Pages: 1\n"+          "%%%%EndComments\n\n"+          "%%Options: %s\n", VERSION, vrna_time_stamp(), vrna_md_option_string(md_p));+  fprintf(xyplot, "%% to switch off outline pairs of sequence comment or\n"+          "%% delete the appropriate line near the end of the file\n\n");+  fprintf(xyplot, "%s", RNAss_head);++  if (pre || post) {+    fprintf(xyplot, "%s", anote_macros);+  }+  fprintf(xyplot, "%%%%EndProlog\n");++  fprintf(xyplot, "RNAplot begin\n"+          "%% data start here\n");++  /* cut_point */+  if ((c = strchr(structure, '&'))) {+    int cutpoint;+    cutpoint = c - structure;+    string[cutpoint] = ' '; /* replace & with space */+    fprintf(xyplot, "/cutpoint %d def\n", cutpoint);+  }++  /* sequence */+  fprintf(xyplot,"/sequence (\\\n");+  i=0;+  while (i<length) {+    fprintf(xyplot, "%.255s\\\n", string+i);  /* no lines longer than 255 */+    i+=255;+  }+  fprintf(xyplot,") def\n");+  /* coordinates */+  fprintf(xyplot, "/coor [\n");+  for (i = 0; i < length; i++)+    fprintf(xyplot, "[%3.8f %3.8f]\n", X[i], Y[i]);+  fprintf(xyplot, "] def\n");+  /* correction coordinates for quadratic beziers in case we produce a circplot */+  if(rna_plot_type == VRNA_PLOT_TYPE_CIRCULAR)+    fprintf(xyplot, "/cpr %6.2f def\n", (float)3*length);+  /* base pairs */+  fprintf(xyplot, "/pairs [\n");+  for (i = 1; i <= length; i++)+    if (pair_table[i]>i)+      fprintf(xyplot, "[%d %d]\n", i, pair_table[i]);+  /* add gquad pairs */+  ge=0;+  while ( (ee=parse_gquad(structure+ge, &Lg, l)) >0 ) {+    int k;+    fprintf(xyplot, "%% gquad\n");+    ge += ee;+    gb=ge-Lg*4-l[0]-l[1]-l[2]+1; /* add pseudo-base pair encloding gquad */+    for (k=0; k<Lg; k++) {+      int ii, jj, il;+      for (il=0, ii=gb+k; il<3; il++) {+        jj = ii+l[il]+Lg;+        fprintf(xyplot, "[%d %d]\n", ii, jj);+        ii = jj;+      }+      jj = gb+k;+      fprintf(xyplot, "[%d %d]\n", jj, ii);+    }+  }++  fprintf(xyplot, "] def\n\n");++  fprintf(xyplot, "init\n\n");+  /* draw the data */+  if (pre) {+    fprintf(xyplot, "%% Start Annotations\n");+    fprintf(xyplot, "%s\n", pre);+    fprintf(xyplot, "%% End Annotations\n");+  }+  fprintf(xyplot,+          "%% switch off outline pairs or bases by removing these lines\n"+          "drawoutline\n"+          "drawpairs\n"+          "drawbases\n");++  if (post) {+    fprintf(xyplot, "%% Start Annotations\n");+    fprintf(xyplot, "%s\n", post);+    fprintf(xyplot, "%% End Annotations\n");+  }+  fprintf(xyplot, "%% show it\nshowpage\n");+  fprintf(xyplot, "end\n");+  fprintf(xyplot, "%%%%EOF\n");++  fclose(xyplot);++  free(string);+  free(pair_table);+  free(pair_table_g);+  free(X); free(Y);+  return 1; /* success */+}++/* options for gml output:+   uppercase letters: print sequence labels+   lowercase letters: no sequence lables+   graphics information:+   x X  simple xy plot+   (nothing else implemented at present)+   default:           no graphics data at all+*/++PUBLIC int gmlRNA(char *string, char *structure, char *ssfile, char option)+{+  FILE *gmlfile;+  int i;+  int length;+  short *pair_table;+  float *X, *Y;++  gmlfile = fopen(ssfile, "w");+  if (gmlfile == NULL) {+     vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+     return 0;+  }++  length = strlen(string);++  pair_table = vrna_ptable(structure);++  switch(option){+  case 'X' :+  case 'x' :+    /* Simple XY Plot */+    X = (float *) vrna_alloc((length+1)*sizeof(float));+    Y = (float *) vrna_alloc((length+1)*sizeof(float));+    if (rna_plot_type == 0)+      i = simple_xy_coordinates(pair_table, X, Y);+    else+      i = naview_xy_coordinates(pair_table, X, Y);++    if(i!=length)+      vrna_message_warning("strange things happening in gmlRNA ...");+    break;+  default:+    /* No Graphics Information */+    X = NULL;+    Y = NULL;+  }++  fprintf(gmlfile,+          "# Vienna RNA Package %s\n"+          "# GML Output\n"+          "# CreationDate: %s\n"+          "# Name: %s\n"+          "# Options: %s\n", VERSION, vrna_time_stamp(), ssfile, option_string());+  fprintf(gmlfile,+          "graph [\n"+          " directed 0\n");+  for (i=1; i<=length; i++){+     fprintf(gmlfile,+          " node [ id %d ", i);+     if (option) fprintf(gmlfile,+          "label \"%c\"",string[i-1]);+     if ((option == 'X')||(option=='x'))+       fprintf(gmlfile,+               "\n  graphics [ x %9.4f y %9.4f ]\n", X[i-1], Y[i-1]);+     fprintf(gmlfile," ]\n");+  }+  for (i=1; i<length; i++)+    fprintf(gmlfile,+            "edge [ source %d target %d ]\n", i, i+1);+  for (i=1; i<=length; i++) {+     if (pair_table[i]>i)+        fprintf(gmlfile,+                "edge [ source %d target %d ]\n", i, pair_table[i]);+  }+  fprintf(gmlfile, "]\n");+  fclose(gmlfile);++  free(pair_table);+  free(X); free(Y);+  return 1; /* success */+}++++int PS_rna_plot_snoop_a(char *string, char *structure, char *ssfile, int *relative_access, const char *seqs[])+{+  int    i, length;+  float *X, *Y;+  FILE  *xyplot;+  short *pair_table;+  short *pair_table_snoop;++  length = strlen(string);++  xyplot = fopen(ssfile, "w");+  if (xyplot == NULL) {+    vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+    return 0;+  }++  pair_table = vrna_ptable(structure);+  pair_table_snoop = vrna_pt_snoop_get(structure);++  X = (float *) vrna_alloc((length+1)*sizeof(float));+  Y = (float *) vrna_alloc((length+1)*sizeof(float));+  if (rna_plot_type == 0)+    i = simple_xy_coordinates(pair_table, X, Y);+  else+    i = naview_xy_coordinates(pair_table, X, Y);+  if(i!=length)+    vrna_message_warning("strange things happening in PS_rna_plot...");+/*   printf("cut_point %d\n", cut_point); */++/*   for (i = 1; i < length; i++) { */+/*     printf("%d X %f Y %f \n", i, X[i], Y[i]); */+/*     xmin = X[i] < xmin ? X[i] : xmin; */+/*     xmax = X[i] > xmax ? X[i] : xmax; */+/*     ymin = Y[i] < ymin ? Y[i] : ymin; */+/*     ymax = Y[i] > ymax ? Y[i] : ymax; */+/*   } */+  /* localize centre of the interaction bucket. Geometry */+  +  for (i = 1; i < cut_point; i++) {  /* interior loop of size 0 */+    if(pair_table_snoop[i] != 0){ +      X[i-1]=X[pair_table_snoop[i]-1]; +      Y[i-1]=Y[pair_table_snoop[i]-1]; +    }+    else if(pair_table_snoop[i-1] && pair_table_snoop[i+1]){ /* interior loop of size 1 */+      X[i-1]=X[pair_table_snoop[i-1] -1-1];+      Y[i-1]=Y[pair_table_snoop[i-1] -1-1];+    } +    else if(pair_table_snoop[i-1] && pair_table_snoop[i+2]){ /* interior loop of size 2 */+      if(pair_table_snoop[i-1] - pair_table_snoop[i+2] ==2){+        X[i-1]=X[pair_table_snoop[i-1]-2];+        Y[i-1]=Y[pair_table_snoop[i-1]-2];+        X[i]=X[pair_table_snoop[i+2]];+        Y[i]=Y[pair_table_snoop[i+2]];+        i++;+      }+      else if(pair_table[pair_table_snoop[i-1]-1]){+        X[i-1]=X[pair_table_snoop[i-1]-2];+        Y[i-1]=Y[pair_table_snoop[i-1]-2];+        X[i]=X[pair_table[pair_table_snoop[i-1]-1]-1];+        Y[i]=Y[pair_table[pair_table_snoop[i-1]-1]-1];+        i++;+      }+      else if(pair_table[pair_table_snoop[i-1]-2]){+        X[i-1]=X[pair_table_snoop[i-1]-3];+        Y[i-1]=Y[pair_table_snoop[i-1]-3];+        X[i]=X[pair_table[pair_table_snoop[i-1]-2]-1];+        Y[i]=Y[pair_table[pair_table_snoop[i-1]-2]-1];+        i++;+      }+      else if(pair_table[pair_table_snoop[i-1]-3]){+        X[i-1]=X[pair_table_snoop[i-1]-4];+        Y[i-1]=Y[pair_table_snoop[i-1]-4];+        X[i]=X[pair_table[pair_table_snoop[i-1]-3]-1];+        Y[i]=Y[pair_table[pair_table_snoop[i-1]-3]-1];+        i++;+      }+      else{+        X[i-1]=X[pair_table_snoop[i-1]-2];+        Y[i-1]=Y[pair_table_snoop[i-1]-2];+        X[i]=X[pair_table_snoop[i+2]];+        Y[i]=Y[pair_table_snoop[i+2]];+        i++;+      }+    }+    else if(pair_table_snoop[i-1] && pair_table_snoop[i+3]){ /* interior loop of size 2 */+      if(pair_table[pair_table_snoop[i-1]-1]){+        X[i-1]=0.5*(X[pair_table_snoop[i-1]-1]+X[pair_table_snoop[i-1]-2]);+        Y[i-1]=0.5*(Y[pair_table_snoop[i-1]-1]+Y[pair_table_snoop[i-1]-2]);+        X[i]=  0.5*(X[pair_table[pair_table_snoop[i-1]-1]-1]+X[pair_table_snoop[i-1]-2]);+        Y[i]=  0.5*(Y[pair_table[pair_table_snoop[i-1]-1]-1]+Y[pair_table_snoop[i-1]-2]);+        X[i+1]=0.5*(X[pair_table[pair_table_snoop[i-1]-1]-2]+X[pair_table[pair_table_snoop[i-1]-1]-1]);+        Y[i+1]=0.5*(Y[pair_table[pair_table_snoop[i-1]-1]-2]+Y[pair_table[pair_table_snoop[i-1]-1]-1]);+        i++;i++;++      }+      else if(pair_table[pair_table_snoop[i-1]-2]){+        X[i-1]=0.5*(X[pair_table_snoop[i-1]-2]+X[pair_table_snoop[i-1]-3]);+        Y[i-1]=0.5*(Y[pair_table_snoop[i-1]-2]+Y[pair_table_snoop[i-1]-3]);+        X[i]=  0.5*(X[pair_table[pair_table_snoop[i-1]-2]-1]+X[pair_table_snoop[i-1]-3]);+        Y[i]=  0.5*(Y[pair_table[pair_table_snoop[i-1]-2]-1]+Y[pair_table_snoop[i-1]-3]);+        X[i+1]=0.5*(X[pair_table[pair_table_snoop[i-1]-2]-2]+X[pair_table[pair_table_snoop[i-1]-2]-1]);+        Y[i+1]=0.5*(Y[pair_table[pair_table_snoop[i-1]-2]-2]+Y[pair_table[pair_table_snoop[i-1]-2]-1]);+        i++;i++;+      }+      else if(pair_table[pair_table_snoop[i-1]-3]){+        X[i-1]=0.5*(X[pair_table_snoop[i-1]-3]+X[pair_table_snoop[i-1]-4]);+        Y[i-1]=0.5*(Y[pair_table_snoop[i-1]-3]+Y[pair_table_snoop[i-1]-4]);+        X[i]=  0.5*(X[pair_table[pair_table_snoop[i-1]-3]-1]+X[pair_table_snoop[i-1]-4]);+        Y[i]=  0.5*(Y[pair_table[pair_table_snoop[i-1]-3]-1]+Y[pair_table_snoop[i-1]-4]);+        X[i+1]=0.5*(X[pair_table[pair_table_snoop[i-1]-3]-2]+X[pair_table[pair_table_snoop[i-1]-3]-1]);+        Y[i+1]=0.5*(Y[pair_table[pair_table_snoop[i-1]-3]-2]+Y[pair_table[pair_table_snoop[i-1]-3]-1]);+        i++;i++;+      }+      else{+        X[i-1]=X[pair_table_snoop[i-1]-2];+        Y[i-1]=Y[pair_table_snoop[i-1]-2];+        X[i]=X[pair_table_snoop[i-1]-2];+        Y[i]=Y[pair_table_snoop[i-1]-2];+        X[i+1]=X[pair_table_snoop[i-1]-2];+        Y[i+1]=Y[pair_table_snoop[i-1]-2];+        i++;i++;+      }+    }+  }+  double xC;+  double yC;+  float X0=-1,Y0=-1,X1=-1,Y1=-1,X2=-1,Y2=-1;+/*   int c1,c2,c3; */+  for(i=1;i<cut_point; i++){+    if(pair_table_snoop[i]){+      X0=X[pair_table_snoop[i]-1];Y0=Y[pair_table_snoop[i]-1];+  /*     c1=pair_table_snoop[i]; */+      i++;+      break;+    }+  }+  for(;i<cut_point; i++){+    if(pair_table_snoop[i]){+      X1=X[pair_table_snoop[i]-1];Y1=Y[pair_table_snoop[i]-1];+    /*   c2=pair_table_snoop[i]; */+      i++;+      break;+    }+  }+  for(;i<cut_point; i++){+    if(pair_table_snoop[i]){+      X2=X[pair_table_snoop[i]-1];Y2=Y[pair_table_snoop[i]-1];+    /*   c3=pair_table_snoop[i]; */+      i++;+      break;+    }+  }+/*   for(i=cut_point-2;i>pair_table_snoop[c1]; i--){ */+/*     if(pair_table_snoop[i]){ */+/*       X1=X[pair_table_snoop[i]-1];Y1=Y[pair_table_snoop[i]-1]; */+/*       c2=pair_table_snoop[i]; */+/*       i++; */+/*       break; */+/*     } */+/*   } */+/*   for(i=pair_table_snoop[c1]+1;i<pair_table_snoop[c2]; i++){ */+/*     if(pair_table_snoop[i]){ */+/*       X2=X[pair_table_snoop[i]-1];Y2=Y[pair_table_snoop[i]-1]; */+/*       c3=pair_table_snoop[i]; */+/*       i++; */+/*       break; */+/*     } */+/*   } */ + if(X0 < 0 || X1 < 0 || X2 < 0){+   printf("Could not get the center of the binding bucket. No ps file will be produced!\n");+   fclose(xyplot);+   free(pair_table);+   free(pair_table_snoop);+   free(X);free(Y);+   pair_table=NULL;pair_table_snoop=NULL;X=NULL;Y=NULL;+   return 0;+ }+  double alpha   =   (X0 -X1)/(Y1-Y0);+  double alpha_p =   (X1 -X2)/(Y2-Y1);+  double b =         (Y0+Y1 -alpha*(X0+X1))*0.5;+  double b_p =       (Y1+Y2 -alpha_p*(X1+X2))*0.5;+  /*    if(abs(alpha -alpha_p) > 0.0000001){ */+  xC  =  (b_p - b) / (alpha - alpha_p);+  yC  =  alpha * xC + b;+  for (i = 1; i < cut_point; i++) {  +     X[i-1] = X[i-1] + 0.25*(xC-X[i-1]);  +     Y[i-1] = Y[i-1] + 0.25*(yC-Y[i-1]);  +  }  ++  fprintf(xyplot,+          "%%!PS-Adobe-3.0 EPSF-3.0\n"+          "%%%%Creator: ViennaRNA-%s\n"+          "%%%%CreationDate: %s"+          "%%%%Title: RNA Secondary Structure Plot\n"+          "%%%%BoundingBox: 0 0 700 700\n"+          "%%%%DocumentFonts: Helvetica\n"+          "%%%%Pages: 1\n"+          "%%%%EndComments\n\n"+          "%%Options: %s\n", VERSION, vrna_time_stamp(), option_string());+  fprintf(xyplot, "%% to switch off outline pairs of sequence comment or\n"+          "%% delete the appropriate line near the end of the file\n\n");+  fprintf(xyplot, "%s", RNAss_head);+  char **A;+  fprintf(xyplot, "%s", anote_macros);+  if(seqs){+    fprintf(xyplot, "%s", anote_macros);+    A = annote(structure, (const char**) seqs);+  }+  fprintf(xyplot, "%%%%EndProlog\n");+  +  fprintf(xyplot, "RNAplot begin\n"+          "%% data start here\n");+  /* cut_point */+  if (cut_point > 0 && cut_point <= strlen(string))+    fprintf(xyplot, "/cutpoint %d def\n", cut_point-1);+  /* sequence */+  fprintf(xyplot,"/sequence (\\\n");+  i=0;+  while (i<length) {+    fprintf(xyplot, "%.255s\\\n", string+i);  /* no lines longer than 255 */+    i+=255;+  }+  fprintf(xyplot,") def\n");+  /* coordinates */+  fprintf(xyplot, "/coor [\n");+  for (i = 0; i < length; i++)+    fprintf(xyplot, "[%3.3f %3.3f]\n", X[i], Y[i]);+  fprintf(xyplot, "] def\n");+  /* base pairs */+  fprintf(xyplot, "/pairs [\n");+  for (i = 1; i <= length; i++)+    if (pair_table[i]>i)+      fprintf(xyplot, "[%d %d]\n", i, pair_table[i]);+  for (i = 1; i <= length; i++)+    if (pair_table_snoop[i]>i)+      fprintf(xyplot, "[%d %d]\n", i, pair_table_snoop[i]);+  fprintf(xyplot, "] def\n\n");+  if(relative_access){+    fprintf(xyplot,"/S [\n");+    for(i=0;i<cut_point-1; i++){+      fprintf(xyplot, " %f\n", (float)relative_access[i]/100);+    }+    fprintf(xyplot,"]\n bind def\n");+    fprintf(xyplot,"/invert false def\n");+    fprintf(xyplot,"/range 0.8 def\n");+    fprintf(xyplot,"/drawreliability {\n"                      +                   "/Smax 2.6 def\n"                         +                   "  0        \n"                              +                   "  coor 0 cutpoint getinterval {\n"+                   "    aload pop\n"+                   "    S 3 index get\n"+                   "    Smax div range mul\n"     +                   "    invert {range exch sub} if\n"  +                   "    1 1 sethsbcolor\n"+                   "    newpath\n"+                   "    fsize 2.5 div 0 360 arc\n"+                   "    fill\n"+                   "    1 add\n"+                   "  } forall\n"+                   "\n"+                   "} bind def\n"); +  }+  fprintf(xyplot, "init\n\n");+  /*raw the data */+  if (seqs) { +     fprintf(xyplot, "%% Start Annotations\n"); +     fprintf(xyplot, "%s\n", A[0]); +     fprintf(xyplot, "%% End Annotations\n"); +   } +++  fprintf(xyplot,"%%switch off outline pairs or bases by removing these lines\n");+  if(relative_access){+    fprintf(xyplot,"drawreliability\n");+  }+  fprintf(xyplot,+          "drawoutline\n"+          "drawpairs\n"+          "drawbases\n");+  /* fprintf(xyplot, "%d cmark\n",c1); */+  /* fprintf(xyplot, "%d cmark\n",c2); */+  /* fprintf(xyplot, "%d cmark\n",c3); */+  if (seqs) { +     fprintf(xyplot, "%% Start Annotations\n"); +     fprintf(xyplot, "%s\n", A[1]); +     fprintf(xyplot, "%% End Annotations\n"); +   } +  fprintf(xyplot, "%% show it\nshowpage\n");+  fprintf(xyplot, "end\n");+  fprintf(xyplot, "%%%%EOF\n");++  fclose(xyplot);+  if(seqs){free(A[0]);free(A[1]);free(A);}+  free(pair_table);free(pair_table_snoop);+  free(X); free(Y);+  return 1; /* success */+}+++PRIVATE char **annote(const char *structure, const char *AS[]) {+  char *ps, *colorps, **A;+  int i, n, s, pairings, maxl;+  short *ptable;+  char * colorMatrix[6][3] = {+    {"0.0 1", "0.0 0.6",  "0.0 0.2"},  /* red    */+    {"0.16 1","0.16 0.6", "0.16 0.2"}, /* ochre  */+    {"0.32 1","0.32 0.6", "0.32 0.2"}, /* turquoise */+    {"0.48 1","0.48 0.6", "0.48 0.2"}, /* green  */+    {"0.65 1","0.65 0.6", "0.65 0.2"}, /* blue   */+    {"0.81 1","0.81 0.6", "0.81 0.2"} /* violet */+  };++  vrna_md_t   md;+  set_model_details(&md);++  n = strlen(AS[0]);+  maxl = 1024;++  A = (char **) vrna_alloc(sizeof(char *)*2);+  ps = (char *) vrna_alloc(maxl);+  colorps = (char *) vrna_alloc(maxl);+  ptable = vrna_pt_ali_get(structure);+  for (i=1; i<=n; i++) {+    char pps[64], ci='\0', cj='\0';+    int j, type, pfreq[8] = {0,0,0,0,0,0,0,0}, vi=0, vj=0;+    if ((j=ptable[i])<i) continue;+    for (s=0; AS[s]!=NULL; s++) {+      type = md.pair[vrna_nucleotide_encode(AS[s][i-1], &md)][vrna_nucleotide_encode(AS[s][j-1], &md)];+      pfreq[type]++;+      if (type) {+        if (AS[s][i-1] != ci) { ci = AS[s][i-1]; vi++;}+        if (AS[s][j-1] != cj) { cj = AS[s][j-1]; vj++;}+      }+    }+    for (pairings=0,s=1; s<=7; s++) {+      if (pfreq[s]) pairings++;+    }++    if ((maxl - strlen(ps) < 192) || ((maxl - strlen(colorps)) < 64)) {+      maxl *= 2;+      ps = realloc(ps, maxl);+      colorps = realloc(colorps, maxl);+      if ((ps==NULL) || (colorps == NULL))+          vrna_message_error("out of memory in realloc");+    }++    if (pfreq[0]<=2) {+      snprintf(pps, 64, "%d %d %s colorpair\n",+               i,j, colorMatrix[pairings-1][pfreq[0]]);+      strcat(colorps, pps);+    }++    if (pfreq[0]>0) {+      snprintf(pps, 64, "%d %d %d gmark\n", i, j, pfreq[0]);+      strcat(ps, pps);+    }+    if (vi>1) {+      snprintf(pps, 64, "%d cmark\n", i);+      strcat(ps, pps);+    }+    if (vj>1) {+      snprintf(pps, 64, "%d cmark\n", j);+      strcat(ps, pps);+    }+  }+  free(ptable);+  A[0]=colorps;+  A[1]=ps;+  return A;+}++/*--------------------------------------------------------------------------*/+++int svg_rna_plot(char *string, char *structure, char *ssfile)+{+  float  xmin, xmax, ymin, ymax, size;+  int    i, length;+  float *X, *Y, *R = NULL, *CX = NULL, *CY = NULL;+  FILE  *xyplot;+  short *pair_table;++  length = strlen(string);++  xyplot = fopen(ssfile, "w");+  if (xyplot == NULL) {+    vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+    return 0;+  }++  pair_table = vrna_ptable(structure);++  X = (float *) vrna_alloc((length+1)*sizeof(float));+  Y = (float *) vrna_alloc((length+1)*sizeof(float));++  switch(rna_plot_type){+    case VRNA_PLOT_TYPE_SIMPLE:   i = simple_xy_coordinates(pair_table, X, Y);+                                  break;+    case VRNA_PLOT_TYPE_CIRCULAR: {+                                    int radius = 3*length;+                                    int dr = 0;+                                    R = (float *) vrna_alloc((length+1)*sizeof(float));+                                    CX = (float *) vrna_alloc((length+1)*sizeof(float));+                                    CY = (float *) vrna_alloc((length+1)*sizeof(float));+                                    i = simple_circplot_coordinates(pair_table, X, Y);+                                    for (i = 0; i < length; i++) {+                                      if(i+1 < pair_table[i+1]){+                                        dr = (pair_table[i+1]-i+1 <= (length/2 + 1)) ? pair_table[i+1]-i : i + length - pair_table[i+1];+                                        R[i] = 1. - (2.*dr/(float)length);+                                      }+                                      else if(pair_table[i+1]){+                                        R[i] = R[pair_table[i+1]-1];+                                      }+                                      else{+                                        R[i] = 1.0;+                                      }+                                      CX[i] = X[i] * radius * R[i] + radius;+                                      CY[i] = Y[i] * radius * R[i] + radius;+                                      X[i] *= radius;+                                      X[i] += radius;+                                      Y[i] *= radius;+                                      Y[i] += radius;+                                    }+                                  }+                                  break;+    default:                      i = naview_xy_coordinates(pair_table, X, Y);+                                  break;+  }++  if(i!=length)+    vrna_message_warning("strange things happening in PS_rna_plot...");+++  xmin = xmax = X[0];+  ymin = ymax = Y[0];+  for (i = 1; i < length; i++) {+     xmin = X[i] < xmin ? X[i] : xmin;+     xmax = X[i] > xmax ? X[i] : xmax;+     ymin = Y[i] < ymin ? Y[i] : ymin;+     ymax = Y[i] > ymax ? Y[i] : ymax;+  }+  for (i = 0; i < length; i++)+    Y[i] = ymin+ymax - Y[i]; /* mirror coordinates so they look as in PS */++  if(rna_plot_type == VRNA_PLOT_TYPE_CIRCULAR)+    for (i = 0; i < length; i++){+      CY[i] = ymin+ymax - CY[i]; /* mirror coordinates so they look as in PS */+    }+   +  size = MAX2((xmax-xmin),(ymax-ymin));+  size += 15; /* add some so the bounding box isn't too tight */++  fprintf(xyplot,+          "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"yes\"?>\n"+          "<svg xmlns=\"http://www.w3.org/2000/svg\" height=\"452\" width=\"452\">\n");+  fprintf(xyplot,+          "<script type=\"text/ecmascript\">\n"+          "      <![CDATA[\n"+          "        var shown = 1;\n"+          "        function click() {\n"+          "             var seq = document.getElementById(\"seq\");\n"+          "             if (shown==1) {\n"+          "               seq.setAttribute(\"style\", \"visibility: hidden\");\n"+          "               shown = 0;\n"+          "             } else {\n"+          "               seq.setAttribute(\"style\", \"visibility: visible\");\n"+          "               shown = 1;\n"+          "             }\n"+          "         }\n"+          "        ]]>\n"+          "</script>\n");+  fprintf(xyplot,+          "  <rect style=\"stroke: white; fill: white\" height=\"452\" x=\"0\" y=\"0\" width=\"452\" onclick=\"click(evt)\" />\n"+          "  <g transform=\"scale(%7f,%7f) translate(%7f,%7f)\">\n",+          SIZE/size, SIZE/size, (size-xmin-xmax)/2, (size-ymin-ymax)/2);++  fprintf(xyplot,+          "    <polyline style=\"stroke: black; fill: none; stroke-width: 1.5\" id=\"outline\" points=\"\n");+  for (i = 0; i < length; i++)+    fprintf(xyplot, "      %3.3f,%3.3f\n", X[i], Y[i]);+  fprintf(xyplot,"    \" />\n");++  fprintf(xyplot,"    <g style=\"stroke: black; stroke-width: 1; fill: none;\" id=\"pairs\">\n");+  for (i = 1; i <= length; i++) {+    int j;+    if ((j=pair_table[i])>i){+      if(rna_plot_type == VRNA_PLOT_TYPE_CIRCULAR)+        fprintf(xyplot,+                "      <path id=\"%d,%d\" d=\"M %6.15f %6.15f C %6.15f,%6.15f %6.15f,%6.15f %6.15f %6.15f\" />\n",+                i,j, X[i-1], Y[i-1], CX[i-1], CY[i-1], CX[j-1], CY[j-1], X[j-1], Y[j-1]);+      else+        fprintf(xyplot,+                "      <line id=\"%d,%d\" x1=\"%6.5f\" y1=\"%6.5f\" x2=\"%6.5f\" y2=\"%6.5f\" />\n",+                i,j, X[i-1], Y[i-1], X[j-1], Y[j-1]);+    }+  }+  fprintf(xyplot, "    </g>\n");+  fprintf(xyplot, "    <g style=\"font-family: SansSerif\" transform=\"translate(-4.6, 4)\" id=\"seq\">\n");+  for (i = 0; i < length; i++)+    fprintf(xyplot, "      <text x=\"%.3f\" y=\"%.3f\">%c</text>\n", X[i], Y[i], string[i]);+  fprintf(xyplot, "    </g>\n");+  fprintf(xyplot, "  </g>\n");+  fprintf(xyplot, "</svg>\n");++  fclose(xyplot);++  free(pair_table);+  free(X); free(Y);+  if(R) free(R);+  if(CX) free(CX);+  if(CY) free(CY);+  return 1; /* success */+}++/*--------------------------------------------------------------------------*/++PUBLIC int ssv_rna_plot(char *string, char *structure, char *ssfile)+{           /* produce input for the SStructView java applet */+  FILE *ssvfile;+  int i, bp;+  int length;+  short *pair_table;+  float *X, *Y;+  float xmin, xmax, ymin, ymax;++  ssvfile = fopen(ssfile, "w");+  if (ssvfile == NULL) {+     vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+     return 0;+  }+  length = strlen(string);+  pair_table = vrna_ptable(structure);++  /* make coordinates */+  X = (float *) vrna_alloc((length+1)*sizeof(float));+  Y = (float *) vrna_alloc((length+1)*sizeof(float));++  if (rna_plot_type == 0)+    i = simple_xy_coordinates(pair_table, X, Y);+  else+    i = naview_xy_coordinates(pair_table, X, Y);+  if (i!=length)+    vrna_message_warning("strange things happening in ssv_rna_plot...");++  /* make coords nonegative */+  xmin = xmax = X[0];+  ymin = ymax = Y[0];+  for (i = 1; i < length; i++) {+     xmin = X[i] < xmin ? X[i] : xmin;+     xmax = X[i] > xmax ? X[i] : xmax;+     ymin = Y[i] < ymin ? Y[i] : ymin;+     ymax = Y[i] > ymax ? Y[i] : ymax;+  }+  if (xmin<1) {+    for (i = 0; i <= length; i++)+      X[i] -= xmin-1;+    xmin = 1;+  }+  if (ymin<1) {+    for (i = 0; i <= length; i++)+      Y[i] -= ymin-1;+    ymin = 1;+  }+#if 0+  {+    float size, xoff, yoff;+    float JSIZE = 500; /* size of the java applet window */+    /* rescale coordinates, center on square of size HSIZE */+    size = MAX2((xmax-xmin),(ymax-ymin));+    xoff = (size - xmax + xmin)/2;+    yoff = (size - ymax + ymin)/2;+    for (i = 0; i <= length; i++) {+      X[i] = (X[i]-xmin+xoff)*(JSIZE-10)/size + 5;+      Y[i] = (Y[i]-ymin+yoff)*(JSIZE-10)/size + 5;+    }+  }+#endif+  /* */++  fprintf(ssvfile,+          "# Vienna RNA Package %s\n"+          "# SStructView Output\n"+          "# CreationDate: %s\n"+          "# Name: %s\n"+          "# Options: %s\n", VERSION, vrna_time_stamp(), ssfile, option_string());+  for (i=1; i<=length; i++)+    fprintf(ssvfile, "BASE\t%d\t%c\t%d\t%d\n",+            i, string[i-1], (int) (X[i-1]+0.5), (int) (Y[i-1]+0.5));+  for (bp=1, i=1; i<=length; i++)+    if (pair_table[i]>i)+      fprintf(ssvfile, "BASE-PAIR\tbp%d\t%d\t%d\n", bp++, i, pair_table[i]);+  fclose(ssvfile);++  free(pair_table);+  free(X); free(Y);+  return 1; /* success */+}++/*---------------------------------------------------------------------------*/+PUBLIC int xrna_plot(char *string, char *structure, char *ssfile)+{           /* produce input for XRNA RNA drawing program */+  FILE *ss_file;+  int i;+  int length;+  short *pair_table;+  float *X, *Y;++  ss_file = fopen(ssfile, "w");+  if (ss_file == NULL) {+    vrna_message_warning("can't open file %s - not doing xy_plot", ssfile);+    return 0;+  }++  length = strlen(string);+  pair_table = vrna_ptable(structure);++  /* make coordinates */+  X = (float *) vrna_alloc((length+1)*sizeof(float));+  Y = (float *) vrna_alloc((length+1)*sizeof(float));++  if (rna_plot_type == 0)+    i = simple_xy_coordinates(pair_table, X, Y);+  else+    i = naview_xy_coordinates(pair_table, X, Y);+  if (i!=length)+    vrna_message_warning("strange things happening in xrna_plot...");++  fprintf(ss_file,+          "# Vienna RNA Package %s, XRNA output\n"+          "# CreationDate: %s\n"+          "# Options: %s\n", VERSION, vrna_time_stamp(), option_string());+  for (i=1; i<=length; i++)+    /* XRNA likes to have coordinate mirrored, so we use (-X, Y) */+    fprintf(ss_file, "%d %c %6.2f %6.2f %d %d\n", i, string[i-1],+            -X[i-1], Y[i-1], (pair_table[i]?1:0), pair_table[i]);+  fclose(ss_file);++  free(pair_table);+  free(X); free(Y);+  return 1; /* success */+}++#ifdef VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC int+PS_rna_plot(char *string,+            char *structure,+            char *ssfile){++  return vrna_file_PS_rnaplot((const char*)string,+                              (const char*)structure,+                              (const char*) ssfile,+                              NULL);+}++PUBLIC int+PS_rna_plot_a(char *string,+              char *structure,+              char *ssfile,+              char *pre,+              char *post){++  return vrna_file_PS_rnaplot_a((const char*)string,+                                (const char*)structure,+                                (const char*)ssfile,+                                (const char*)pre,+                                (const char*)post,+                                NULL);+}++PUBLIC int+PS_rna_plot_a_gquad(char *string,+                    char *structure,+                    char *ssfile,+                    char *pre,+                    char *post){++  return vrna_file_PS_rnaplot_a((const char*)string,+                                (const char*)structure,+                                (const char*)ssfile,+                                (const char*)pre,+                                (const char*)post,+                                NULL);+}++#endif+
+ C/ViennaRNA/plot_structure.h view
@@ -0,0 +1,168 @@+#ifndef VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H+#define VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H++#include <ViennaRNA/model.h>+#include <ViennaRNA/plot_layouts.h>++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++/**+ *  @file plot_structure.h+ *  @ingroup   plotting_utils+ *  @brief Various functions for plotting RNA secondary structures+ */++/**+ *  @{+ *  @ingroup   plotting_utils+ */++/* write PostScript drawing of structure to file with annotation */+int PS_rna_plot_snoop_a(char *string,+                        char *structure,+                        char *ssfile,+                        int *relative_access,+                        const char *seqs[]);++/**+ *  @brief Produce a secondary structure graph in PostScript and write it to 'filename'.+ *+ *  Note that this function has changed from previous versions+ *  and now expects the structure to be plotted in dot-bracket notation as an+ *  argument. It does not make use of the global #base_pair array anymore.+ *+ *  @param seq        The RNA sequence+ *  @param structure  The secondary structure in dot-bracket notation+ *  @param file       The filename of the postscript output+ *  @param md_p       Model parameters used to generate a commandline option string in the output (Maybe NULL)+ *  @return           1 on success, 0 otherwise+ */+int vrna_file_PS_rnaplot( const char *seq,+                          const char *structure,+                          const char *file,+                          vrna_md_t  *md_p);++/**+ *  @brief Produce a secondary structure graph in PostScript including additional+ *  annotation macros and write it to 'filename'+ *+ *  Same as vrna_file_PS_rnaplot() but adds extra PostScript macros for various+ *  annotations (see generated PS code). The 'pre' and 'post'+ *  variables contain PostScript code that is verbatim copied in the+ *  resulting PS file just before and after the structure plot.+ *  If both arguments ('pre' and 'post') are NULL, no additional macros will+ *  be printed into the PostScript.+ *+ *  @param seq     The RNA sequence+ *  @param structure  The secondary structure in dot-bracket notation+ *  @param file       The filename of the postscript output+ *  @param pre        PostScript code to appear before the secondary structure plot+ *  @param post       PostScript code to appear after the secondary structure plot+ *  @param md_p       Model parameters used to generate a commandline option string in the output (Maybe NULL)+ *  @return           1 on success, 0 otherwise+ */+int vrna_file_PS_rnaplot_a( const char *seq,+                            const char *structure,+                            const char *file,+                            const char *pre,+                            const char *post,+                            vrna_md_t  *md_p);++/**+ *  @brief Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file+ *+ *  If 'option' is an uppercase letter the RNA sequence is used to label nodes, if 'option' equals+ *  @a 'X' or @a 'x' the resulting file will coordinates for an initial layout of the graph.+ *+ *  @param  string    The RNA sequence+ *  @param  structure The secondary structure in dot-bracket notation+ *  @param  ssfile    The filename of the gml output+ *  @param  option    The option flag+ *  @return           1 on success, 0 otherwise+ */+int gmlRNA( char *string,+            char *structure,+            char *ssfile,+            char option);++/**+ *  @brief  Produce a secondary structure graph in SStructView format+ *+ *  Write coord file for SStructView+ *+ *  @param  string    The RNA sequence+ *  @param  structure The secondary structure in dot-bracket notation+ *  @param  ssfile    The filename of the ssv output+ *  @return           1 on success, 0 otherwise+ */+int ssv_rna_plot( char *string,+                  char *structure,+                  char *ssfile);++/**+ *  @brief Produce a secondary structure plot in SVG format and write it to a file+ *+ *  @param string     The RNA sequence+ *  @param structure  The secondary structure in dot-bracket notation+ *  @param ssfile     The filename of the svg output+ *  @return           1 on success, 0 otherwise+ */+int svg_rna_plot( char *string,+                  char *structure,+                  char *ssfile);++/**+ *  @brief Produce a secondary structure plot for further editing in XRNA+ *+ *  @param string     The RNA sequence+ *  @param structure  The secondary structure in dot-bracket notation+ *  @param ssfile     The filename of the xrna output+ *  @return           1 on success, 0 otherwise+ */+int xrna_plot(char *string,+              char *structure,+              char *ssfile);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Produce a secondary structure graph in PostScript and write it to 'filename'.+ *+ *  @deprecated   Use vrna_file_PS_rnaplot() instead!+ */+DEPRECATED(int PS_rna_plot(char *string, char *structure, char *file));++/**+ *  @brief Produce a secondary structure graph in PostScript including additional+ *  annotation macros and write it to 'filename'+ *+ *  @deprecated   Use vrna_file_PS_rnaplot_a() instead!+ */+DEPRECATED(int PS_rna_plot_a(char *string, char *structure, char *file, char *pre, char *post));++/**+ *  @brief Produce a secondary structure graph in PostScript including additional+ *  annotation macros and write it to 'filename' (detect and draw g-quadruplexes)+ *+ *  @deprecated   Use vrna_file_PS_rnaplot_a() instead!+ */+DEPRECATED(int PS_rna_plot_a_gquad(char *string, char *structure, char *ssfile, char *pre, char *post));++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/profiledist.h view
@@ -0,0 +1,62 @@+#ifndef VIENNA_RNA_PACKAGE_PROFILEDIST_H+#define VIENNA_RNA_PACKAGE_PROFILEDIST_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++#include <ViennaRNA/data_structures.h>++/** \file profiledist.h  */++/**+ *  \brief Align the 2 probability profiles T1, T2\n+ * + *  This is like a Needleman-Wunsch alignment,+ *  we should really use affine gap-costs ala Gotoh+ */+float profile_edit_distance(const float *T1,+                            const float *T2);++/**+ *  \brief condense pair probability matrix into a vector containing probabilities+ *  for unpaired, upstream paired and downstream paired.+ * + *  This resulting probability profile is used as input for profile_edit_distance+ * + *  \param bppm   A pointer to the base pair probability matrix+ *  \param length The length of the sequence+ *  \returns      The bp profile+ */+float *Make_bp_profile_bppm(FLT_OR_DBL *bppm,+                            int length);++/**+ *  \brief print string representation of probability profile+ */+void  print_bppm(const float *T);++/**+ *  \brief free space allocated in Make_bp_profile+ * + *  Backward compatibility only. You can just use plain free()+ */+void  free_profile(float *T);++/**+ *  \note This function is NOT threadsafe+ * + *  \see Make_bp_profile_bppm()+ * + *  \deprecated This function is deprecated and will be removed soon! See \ref Make_bp_profile_bppm() for a replacement+ * + */+DEPRECATED(float *Make_bp_profile(int length));++#endif
+ C/ViennaRNA/read_epars.c view
@@ -0,0 +1,1079 @@+/*+                  read energy parameters from a file++                      Stephan Kopp, Ivo Hofacker+                          Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <string.h>+#include <math.h>+#include <stdarg.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_const.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/read_epars.h"++#define PUBLIC+#define PRIVATE   static+#define PARSET 20++#define DEF -50+#define NST 0++PRIVATE FILE *fp;++PRIVATE void  display_array(int *p, int size, int line, FILE *fp);+PRIVATE char  *get_array1(int *arr, int size);+PRIVATE void  ignore_comment(char *line);+PRIVATE void  check_symmetry(void);+PRIVATE void  update_nst(int array[NBPAIRS+1][NBPAIRS+1][5][5][5][5]);++/**+*** read a 1dimensional array from file+*** \param array  a pointer to the first element in the array+*** \param dim    the size of the array+*** \param shift  the first position the new values will be written in+**/+PRIVATE void  rd_1dim(int *array, int dim, int shift);+PRIVATE void  rd_1dim_slice(int *array, int dim, int shift, int post);+PRIVATE void  rd_2dim(int *array,+                      int dim1, int dim2,+                      int shift1, int shift2);+PRIVATE void  rd_2dim_slice(int *array,+                      int dim1, int dim2,+                      int shift1, int shift2,+                      int post1, int post2);+PRIVATE void  rd_3dim(int *array,+                      int dim1, int dim2, int dim3,+                      int shift1, int shift2, int shift3);+PRIVATE void  rd_3dim_slice(int *array,+                      int dim1, int dim2, int dim3,+                      int shift1, int shift2, int shift3,+                      int post1, int post2, int post3);+PRIVATE void  rd_4dim(int *array,+                      int dim1, int dim2, int dim3, int dim4,+                      int shift1, int shift2, int shift3, int shift4);+PRIVATE void  rd_4dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4,+                      int shift1, int shift2, int shift3, int shift4,+                      int post1, int post2, int post3, int post4);+PRIVATE void  rd_5dim(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5,+                      int shift1, int shift2, int shift3, int shift4, int shift5);+PRIVATE void  rd_5dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5,+                      int shift1, int shift2, int shift3, int shift4, int shift5,+                      int post1, int post2, int post3, int post4, int post5);+PRIVATE void  rd_6dim(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5, int dim6,+                      int shift1, int shift2, int shift3, int shift4, int shift5, int shift6);+PRIVATE void  rd_6dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5, int dim6,+                      int shift1, int shift2, int shift3, int shift4, int shift5, int shift6,+                      int post1, int post2, int post3, int post4, int post5, int post6);+PRIVATE void  rd_Tetraloop37(void);+PRIVATE void  rd_Triloop37(void);+PRIVATE void  rd_Hexaloop37(void);++/*------------------------------------------------------------*/+PUBLIC void read_parameter_file(const char fname[]){+  char        *line, ident[256];+  enum parset type;+  int         r;++  if (!(fp=fopen(fname,"r"))) {+    vrna_message_warning("\nread_parameter_file:\n"+                                "\t\tcan't open file %s\n"+                                "\t\tusing default parameters instead.",+                                fname);+    return;+  }++  if (!(line = vrna_read_line(fp))) {+    vrna_message_warning(" File %s is improper.\n", fname);+    fclose(fp);+    return;+  }++  if (strncmp(line,"## RNAfold parameter file v2.0",30)!=0) {+    vrna_message_warning( "Missing header line in file.\n"+                          "May be this file has not v2.0 format.\n"+                          "Use INTERRUPT-key to stop.");+  }+  free(line);++  while((line=vrna_read_line(fp))) {++    r = sscanf(line, "# %255s", ident);+    if (r==1) {+      type = gettype(ident);+      switch (type){+        case QUIT:    break;+        case S:       rd_2dim(&(stack37[0][0]), NBPAIRS+1, NBPAIRS+1, 1, 1);+                      break;+        case S_H:     rd_2dim(&(stackdH[0][0]), NBPAIRS+1, NBPAIRS+1, 1, 1);+                      break;+        case HP:      rd_1dim(&(hairpin37[0]), 31, 0);+                      break;+        case HP_H:    rd_1dim(&(hairpindH[0]), 31, 0);+                      break;+        case B:       rd_1dim(&(bulge37[0]), 31, 0);+                      break;+        case B_H:     rd_1dim(&(bulgedH[0]), 31, 0);+                      break;+        case IL:      rd_1dim(&(internal_loop37[0]), 31, 0);+                      break;+        case IL_H:    rd_1dim(&(internal_loopdH[0]), 31, 0);+                      break;+        case MME:     rd_3dim(&(mismatchExt37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MME_H:   rd_3dim(&(mismatchExtdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMH:     rd_3dim(&(mismatchH37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMH_H:   rd_3dim(&(mismatchHdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI:     rd_3dim(&(mismatchI37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI_H:   rd_3dim(&(mismatchIdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI1N:   rd_3dim(&(mismatch1nI37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI1N_H: rd_3dim(&(mismatch1nIdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI23:   rd_3dim(&(mismatch23I37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMI23_H: rd_3dim(&(mismatch23IdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMM:     rd_3dim(&(mismatchM37[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case MMM_H:   rd_3dim(&(mismatchMdH[0][0][0]),+                          NBPAIRS+1, 5, 5,+                          1, 0, 0);+                      break;+        case INT11:   rd_4dim(&(int11_37[0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5,+                          1, 1, 0, 0);+                      break;+        case INT11_H: rd_4dim(&(int11_dH[0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5,+                          1, 1, 0, 0);+                      break;+        case INT21:   rd_5dim(&(int21_37[0][0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5, 5,+                          1, 1, 0, 0, 0);+                      break;+        case INT21_H: rd_5dim(&(int21_dH[0][0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5, 5,+                          1, 1, 0, 0, 0);+                      break;+        case INT22:   rd_6dim_slice(&(int22_37[0][0][0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5, 5, 5,+                          1, 1, 1, 1, 1, 1,+                          1, 1, 0, 0, 0, 0);+                      update_nst(int22_37);+                      break;+        case INT22_H: rd_6dim_slice(&(int22_dH[0][0][0][0][0][0]),+                          NBPAIRS+1, NBPAIRS+1, 5, 5, 5, 5,+                          1, 1, 1, 1, 1, 1,+                          1, 1, 0, 0, 0, 0);+                      update_nst(int22_dH);+                      break;+        case D5:      rd_2dim(&(dangle5_37[0][0]), NBPAIRS+1, 5, 1, 0);+                      break;+        case D5_H:    rd_2dim(&(dangle5_dH[0][0]), NBPAIRS+1, 5, 1, 0);+                      break;+        case D3:      rd_2dim(&(dangle3_37[0][0]), NBPAIRS+1, 5, 1, 0);+                      break;+        case D3_H:    rd_2dim(&(dangle3_dH[0][0]), NBPAIRS+1, 5, 1, 0);+                      break;+        case ML:      {+                        int values[6];+                        rd_1dim(&values[0], 6, 0);+                        ML_BASE37     = values[0];+                        ML_BASEdH     = values[1];+                        ML_closing37  = values[2];+                        ML_closingdH  = values[3];+                        ML_intern37   = values[4];+                        ML_interndH   = values[5];+                      }+                      break;+        case NIN:     {+                        int values[3];+                        rd_1dim(&values[0], 3, 0);+                        ninio37 = values[0];+                        niniodH = values[1];+                        MAX_NINIO  = values[2];+                      }+                      break;+        case MISC:    {+                        int values[4];+                        rd_1dim(&values[0], 4, 0);+                        DuplexInit37 = values[0];+                        DuplexInitdH = values[1];+                        TerminalAU37 = values[2];+                        TerminalAUdH = values[3];+                      }+                      break;+        case TL:      rd_Tetraloop37();+                      break;+        case TRI:     rd_Triloop37();+                      break;+        case HEX:     rd_Hexaloop37();+                      break;+        default:      /* do nothing but complain */+                      vrna_message_warning("read_epars: Unknown field identifier in `%s'", line);+      }+    } /* else ignore line */+    free(line);+  }+  fclose(fp);++  check_symmetry();+  return;+}++/*------------------------------------------------------------*/++PRIVATE void display_array(int *p, int size, int nl, FILE *fp)+{+  int i;++  for (i=1; i<=size; i++, p++) {+    switch(*p)+      {+      case  INF: fprintf(fp,"   INF"); break;+      case -INF: fprintf(fp,"  -INf"); break;+      case  DEF: fprintf(fp,"   DEF"); break;+      default:   fprintf(fp,"%6d",  *p); break;+      }+    if ((i%nl)==0) fprintf(fp,"\n");+  }+  if (size%nl) fprintf(fp,"\n");+  return;+}++/*------------------------------------------------------------*/++PRIVATE char *get_array1(int *arr, int size)+{+  int    i, p, pos, pp, r, last;+  char  *line, buf[16];+++  i = last = 0;+  while( i<size ) {+    line = vrna_read_line(fp);+    if (!line) vrna_message_error("unexpected end of file in get_array1");+    ignore_comment(line);+    pos=0;+    while ((i<size)&&(sscanf(line+pos,"%15s%n", buf, &pp)==1)) {+      pos += pp;+      if (buf[0]=='*') {i++; continue;}+      else if (buf[0]=='x') { /* should only be used for loop parameters */+        if (i==0) vrna_message_error("can't extrapolate first value");+        p = arr[last] + (int) (0.5+ lxc37*log(((double) i)/(double)(last)));+      }+      else if (strcmp(buf,"DEF") == 0) p = DEF;+      else if (strcmp(buf,"INF") == 0) p = INF;+      else if (strcmp(buf,"NST") == 0) p = NST;+      else {+        r=sscanf(buf,"%d", &p);+        if (r!=1) {+          return line+pos;+          vrna_message_error("can't interpret `%s' in get_array1", buf);+          exit(1);+        }+        last = i;+      }+      arr[i++]=p;+    }+    free(line);+  }++  return NULL;+}++PRIVATE void rd_1dim(int *array, int dim, int shift){+  rd_1dim_slice(array, dim, shift, 0);+}++PRIVATE void rd_1dim_slice(int *array, int dim, int shift, int post){+  char *cp;+  cp   = get_array1(array+shift, dim-shift-post);++  if (cp) {+    vrna_message_error("\nrd_1dim: %s", cp);+    exit(1);+  }+  return;+}++PRIVATE void  rd_2dim(int *array, int dim1, int dim2, int shift1, int shift2){+  rd_2dim_slice(array, dim1, dim2, shift1, shift2, 0, 0);+}++PRIVATE void  rd_2dim_slice(int *array,+                      int dim1, int dim2,+                      int shift1, int shift2,+                      int post1, int post2){+  int i;+  int delta_pre   = shift1 + shift2;+  int delta_post  = post1 + post2;++  if(delta_pre + delta_post == 0){+    rd_1dim(array, dim1 * dim2, 0);+    return;+  }+  for (i=shift1; i<dim1 - post1; i++)+    rd_1dim_slice(array + (i*dim2), dim2, shift2, post2);+  return;+}++PRIVATE void  rd_3dim(int *array, int dim1, int dim2, int dim3, int shift1, int shift2, int shift3){+  rd_3dim_slice(array,+                dim1, dim2, dim3,+                shift1, shift2, shift3,+                0, 0, 0);+}++PRIVATE void  rd_3dim_slice(int *array,+                            int dim1, int dim2, int dim3,+                            int shift1, int shift2, int shift3,+                            int post1, int post2, int post3){+  int    i;+  int delta_pre   = shift1 + shift2 + shift3;+  int delta_post  = post1 + post2 + post3;++  if(delta_pre + delta_post == 0){+    rd_1dim(array, dim1 * dim2 * dim3, 0);+    return;+  }+  for (i=shift1; i<dim1 - post1; i++){+    rd_2dim_slice(array + (i * dim2 * dim3),+            dim2, dim3,+            shift2, shift3,+            post2, post3);+  }+  return;+}++PRIVATE void  rd_4dim(int *array,+                      int dim1, int dim2, int dim3, int dim4,+                      int shift1, int shift2, int shift3, int shift4){+  rd_4dim_slice(array,+                dim1, dim2, dim3, dim4,+                shift1, shift2, shift3, shift4,+                0, 0, 0, 0);+}++PRIVATE void  rd_4dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4,+                      int shift1, int shift2, int shift3, int shift4,+                      int post1, int post2, int post3, int post4){+  int i;+  int delta_pre   = shift1 + shift2 + shift3 + shift4;+  int delta_post  = post1 + post2 + post3 + post4;++  if(delta_pre + delta_post == 0){+    rd_1dim(array, dim1 * dim2 * dim3 * dim4, 0);+    return;+  }+  for(i=shift1; i<dim1 - post1; i++){+    rd_3dim_slice(array + (i * dim2 * dim3 * dim4),+            dim2, dim3, dim4,+            shift2, shift3, shift4,+            post2, post3, post4);+  }+  return;+}++PRIVATE void  rd_5dim(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5,+                      int shift1, int shift2, int shift3, int shift4, int shift5){+  rd_5dim_slice(array,+                dim1, dim2, dim3, dim4, dim5,+                shift1, shift2, shift3, shift4, shift5,+                0, 0, 0, 0, 0);+}++PRIVATE void  rd_5dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5,+                      int shift1, int shift2, int shift3, int shift4, int shift5,+                      int post1, int post2, int post3, int post4, int post5){+  int i;+  int delta_pre   = shift1 + shift2 + shift3 + shift4 + shift5;+  int delta_post  = post1 + post2 + post3 + post4 + post5;++  if(delta_pre + delta_post == 0){+    rd_1dim(array, dim1 * dim2 * dim3 * dim4 * dim5, 0);+    return;+  }+  for(i=shift1; i<dim1 - post1; i++)+    rd_4dim_slice(array + (i * dim2 * dim3 * dim4 * dim5),+            dim2, dim3, dim4, dim5,+            shift2, shift3, shift4, shift5,+            post2, post3, post4, post5);+  return;+}++/**+*** \param dim1   The size of the first dimension+*** \param shift1 The pre shift for the first dimension+**/+PRIVATE void  rd_6dim(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5, int dim6,+                      int shift1, int shift2, int shift3, int shift4, int shift5, int shift6){+  rd_6dim_slice(array,+                dim1, dim2, dim3, dim4, dim5, dim6,+                shift1, shift2, shift3, shift4, shift5, shift6,+                0, 0, 0, 0, 0, 0);+}++PRIVATE void  rd_6dim_slice(int *array,+                      int dim1, int dim2, int dim3, int dim4, int dim5, int dim6,+                      int shift1, int shift2, int shift3, int shift4, int shift5, int shift6,+                      int post1, int post2, int post3, int post4, int post5, int post6){+  int i;+  int delta_pre   = shift1 + shift2 + shift3 + shift4 + shift5 + shift6;+  int delta_post  = post1 + post2 + post3 + post4 + post5 + post6;++  if(delta_pre + delta_post == 0){+    rd_1dim(array, dim1 * dim2 * dim3 * dim4 * dim5 * dim6, 0);+    return;+  }+  for(i=shift1; i<dim1 - post1; i++)+    rd_5dim_slice(array + (i * dim2 * dim3 * dim4 * dim5 * dim6),+            dim2, dim3, dim4, dim5, dim6,+            shift2, shift3, shift4, shift5, shift6,+            post2, post3, post4, post5, post6);+  return;+}+++/*------------------------------------------------------------*/+PRIVATE void  rd_Tetraloop37(void)+{+  int    i, r;+  char   *buf;++  i=0;+  /* erase old tetraloop entries */+  memset(&Tetraloops, 0, 281);+  memset(&Tetraloop37, 0, sizeof(int)*40);+  memset(&TetraloopdH, 0, sizeof(int)*40);+  do {+    buf = vrna_read_line(fp);+    if (buf==NULL) break;+    r = sscanf(buf,"%6s %d %d", &Tetraloops[7*i], &Tetraloop37[i], &TetraloopdH[i]);+    strcat(Tetraloops, " ");+    free(buf);+    i++;+  } while((r==3)&&(i<40));+  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_Hexaloop37(void)+{+  int    i, r;+  char   *buf;++  i=0;+  /* erase old hexaloop entries */+  memset(&Hexaloops, 0, 361);+  memset(&Hexaloop37, 0, sizeof(int)*40);+  memset(&HexaloopdH, 0, sizeof(int)*40);+  do {+    buf = vrna_read_line(fp);+    if (buf==NULL) break;+    r = sscanf(buf,"%8s %d %d", &Hexaloops[9*i], &Hexaloop37[i], &HexaloopdH[i]);+    strcat(Hexaloops, " ");+    free(buf);+    i++;+  } while((r==3)&&(i<40));+  return;+}++/*------------------------------------------------------------*/+PRIVATE void  rd_Triloop37(void)+{+  int    i, r;+  char   *buf;++  i=0;+  /* erase old hexaloop entries */+  memset(&Triloops,   0, 241);+  memset(&Triloop37,  0, sizeof(int)*40);+  memset(&TriloopdH,  0, sizeof(int)*40);+  do {+    buf = vrna_read_line(fp);+    if (buf==NULL) break;+    r = sscanf(buf,"%5s %d %d", &Triloops[6*i], &Triloop37[i], &TriloopdH[i]);+    strcat(Triloops, " ");+    free(buf);+    i++;+  } while((r==3)&&(i<40));+  return;+}++/*------------------------------------------------------------*/+++PRIVATE void ignore_comment(char * line)+{+  /* excise C style comments */+  /* only one comment per line, no multiline comments */+  char *cp1, *cp2;++  if ((cp1=strstr(line, "/*"))) {+    cp2 = strstr(cp1, "*/");+    if (cp2==NULL)+      vrna_message_error("unclosed comment in parameter file");+    /* can't use strcpy for overlapping strings */+    for (cp2+=2; *cp2!='\0'; cp2++, cp1++)+      *cp1 = *cp2;+    *cp1 = '\0';+  }++  return;+}+/*------------------------------------------------------------*/++PUBLIC char *settype(enum parset s){+  switch(s){+    case        S:  return "stack";+    case      S_H:  return "stack_enthalpies";+    case       HP:  return "hairpin";+    case     HP_H:  return "hairpin_enthalpies";+    case        B:  return "bulge";+    case      B_H:  return "bulge_enthalpies";+    case       IL:  return "interior";+    case     IL_H:  return "interior_enthalpies";+    case      MME:  return "mismatch_exterior";+    case    MME_H:  return "mismatch_exterior_enthalpies";+    case      MMH:  return "mismatch_hairpin";+    case    MMH_H:  return "mismatch_hairpin_enthalpies";+    case      MMI:  return "mismatch_interior";+    case    MMI_H:  return "mismatch_interior_enthalpies";+    case    MMI1N:  return "mismatch_interior_1n";+    case  MMI1N_H:  return "mismatch_interior_1n_enthalpies";+    case    MMI23:  return "mismatch_interior_23";+    case  MMI23_H:  return "mismatch_interior_23_enthalpies";+    case      MMM:  return "mismatch_multi";+    case    MMM_H:  return "mismatch_multi_enthalpies";+    case       D5:  return "dangle5";+    case     D5_H:  return "dangle5_enthalpies";+    case       D3:  return "dangle3";+    case     D3_H:  return "dangle3_enthalpies";+    case    INT11:  return "int11";+    case  INT11_H:  return "int11_enthalpies";+    case    INT21:  return "int21";+    case  INT21_H:  return "int21_enthalpies";+    case    INT22:  return "int22";+    case  INT22_H:  return "int22_enthalpies";+    case       ML:  return "ML_params";+    case      NIN:  return "NINIO";+    case      TRI:  return "Triloops";+    case       TL:  return "Tetraloops";+    case      HEX:  return "Hexaloops";+    case     QUIT:  return "END";+    case     MISC:  return "Misc";+    default: vrna_message_error("\nThe answer is: 42\n");+  }+  return "";+}+/*------------------------------------------------------------*/++PUBLIC enum parset gettype(const char *ident){+  if      (strcmp(ident,"stack") == 0)                            return S;+  else if (strcmp(ident,"stack_enthalpies") == 0)                 return S_H;+  else if (strcmp(ident,"hairpin") == 0)                          return HP;+  else if (strcmp(ident,"hairpin_enthalpies") == 0)               return HP_H;+  else if (strcmp(ident,"bulge") == 0)                            return B;+  else if (strcmp(ident,"bulge_enthalpies") == 0)                 return B_H;+  else if (strcmp(ident,"interior") == 0)                         return IL;+  else if (strcmp(ident,"interior_enthalpies") == 0)              return IL_H;+  else if (strcmp(ident,"mismatch_exterior") == 0)                return MME;+  else if (strcmp(ident,"mismatch_exterior_enthalpies") == 0)     return MME_H;+  else if (strcmp(ident,"mismatch_hairpin") == 0)                 return MMH;+  else if (strcmp(ident,"mismatch_hairpin_enthalpies") == 0)      return MMH_H;+  else if (strcmp(ident,"mismatch_interior") == 0)                return MMI;+  else if (strcmp(ident,"mismatch_interior_enthalpies") == 0)     return MMI_H;+  else if (strcmp(ident,"mismatch_interior_1n") == 0)             return MMI1N;+  else if (strcmp(ident,"mismatch_interior_1n_enthalpies") == 0)  return MMI1N_H;+  else if (strcmp(ident,"mismatch_interior_23") == 0)             return MMI23;+  else if (strcmp(ident,"mismatch_interior_23_enthalpies") == 0)  return MMI23_H;+  else if (strcmp(ident,"mismatch_multi") == 0)                   return MMM;+  else if (strcmp(ident,"mismatch_multi_enthalpies") == 0)        return MMM_H;+  else if (strcmp(ident,"int11") == 0)                            return INT11;+  else if (strcmp(ident,"int11_enthalpies") == 0)                 return INT11_H;+  else if (strcmp(ident,"int21") == 0)                            return INT21;+  else if (strcmp(ident,"int21_enthalpies") == 0)                 return INT21_H;+  else if (strcmp(ident,"int22") == 0)                            return INT22;+  else if (strcmp(ident,"int22_enthalpies") == 0)                 return INT22_H;+  else if (strcmp(ident,"dangle5")== 0)                           return D5;+  else if (strcmp(ident,"dangle5_enthalpies")== 0)                return D5_H;+  else if (strcmp(ident,"dangle3")== 0)                           return D3;+  else if (strcmp(ident,"dangle3_enthalpies")== 0)                return D3_H;+  else if (strcmp(ident,"ML_params")== 0)                         return ML;+  else if (strcmp(ident,"NINIO") == 0)                            return NIN;+  else if (strcmp(ident,"Triloops") == 0)                         return TRI;+  else if (strcmp(ident,"Tetraloops") == 0)                       return TL;+  else if (strcmp(ident,"Hexaloops") == 0)                        return HEX;+  else if (strcmp(ident,"Misc") == 0)                             return MISC;+  else if (strcmp(ident,"END") == 0)                              return QUIT;+  else return UNKNOWN;+}++/*---------------------------------------------------------------*/++PUBLIC void write_parameter_file(const char fname[]){+  FILE *outfp;+  int c;+  char *pnames[] = {"NP", "CG", "GC", "GU", "UG", "AU", "UA", " @"};+  char bnames[] = "@ACGU";+  outfp = fopen(fname, "w");+  if (!outfp) {+    vrna_message_error("can't open file %s", fname);+    exit(1);+  }+  fprintf(outfp,"## RNAfold parameter file v2.0\n");++  fprintf(outfp,"\n# %s\n", settype(S));+  fprintf(outfp,"/*  CG    GC    GU    UG    AU    UA    @  */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(stack37[c]+1,NBPAIRS,NBPAIRS, outfp);++  fprintf(outfp,"\n# %s\n", settype(S_H));+  fprintf(outfp,"/*  CG    GC    GU    UG    AU    UA    @  */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(stackdH[c]+1,NBPAIRS,NBPAIRS, outfp);++  fprintf(outfp,"\n# %s\n", settype(MMH));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchH37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMH_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchHdH[k][i],5,5, outfp);++  }++  fprintf(outfp,"\n# %s\n", settype(MMI));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchI37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMI_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchIdH[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMI1N));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatch1nI37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMI1N_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatch1nIdH[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMI23));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatch23I37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMI23_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatch23IdH[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMM));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchM37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MMM_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchMdH[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MME));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchExt37[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(MME_H));+  { int i,k;+  for (k=1; k<NBPAIRS+1; k++)+    for (i=0; i<5; i++)+      display_array(mismatchExtdH[k][i],5,5, outfp);+  }++  fprintf(outfp,"\n# %s\n", settype(D5));+  fprintf(outfp,"/*  @     A     C     G     U   */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(dangle5_37[c], 5, 5, outfp);++  fprintf(outfp,"\n# %s\n", settype(D5_H));+  fprintf(outfp,"/*  @     A     C     G     U   */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(dangle5_dH[c], 5, 5, outfp);++  fprintf(outfp,"\n# %s\n", settype(D3));+  fprintf(outfp,"/*  @     A     C     G     U   */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(dangle3_37[c], 5, 5, outfp);++  fprintf(outfp,"\n# %s\n", settype(D3_H));+  fprintf(outfp,"/*  @     A     C     G     U   */\n");+  for (c=1; c<NBPAIRS+1; c++)+    display_array(dangle3_dH[c], 5, 5, outfp);+++  /* dont print "no pair" entries for interior loop arrays */+  fprintf(outfp,"\n# %s\n", settype(INT11));+  { int i,k,l;+  for (k=1; k<NBPAIRS+1; k++)+    for (l=1; l<NBPAIRS+1; l++) {+      fprintf(outfp, "/* %2s..%2s */\n", pnames[k], pnames[l]);+      for (i=0; i<5; i++)+        display_array(int11_37[k][l][i], 5, 5, outfp);+    }+  }++  fprintf(outfp,"\n# %s\n", settype(INT11_H));+  { int i,k,l;+  for (k=1; k<NBPAIRS+1; k++)+    for (l=1; l<NBPAIRS+1; l++) {+      fprintf(outfp, "/* %2s..%2s */\n", pnames[k], pnames[l]);+      for (i=0; i<5; i++)+        display_array(int11_dH[k][l][i],5,5, outfp);+    }+  }++  fprintf(outfp,"\n# %s\n", settype(INT21));+  { int p1, p2, i, j;+  for (p1=1; p1<NBPAIRS+1; p1++)+    for (p2=1; p2<NBPAIRS+1; p2++)+      for (i=0; i<5; i++) {+        fprintf(outfp, "/* %2s.%c..%2s */\n",+                pnames[p1], bnames[i], pnames[p2]);+        for (j=0; j<5; j++)+          display_array(int21_37[p1][p2][i][j],5,5, outfp);+      }+  }++  fprintf(outfp,"\n# %s\n", settype(INT21_H));+  { int p1, p2, i, j;+  for (p1=1; p1<NBPAIRS+1; p1++)+    for (p2=1; p2<NBPAIRS+1; p2++)+      for (i=0; i<5; i++) {+        fprintf(outfp, "/* %2s.%c..%2s */\n",+                pnames[p1], bnames[i], pnames[p2]);+        for (j=0; j<5; j++)+          display_array(int21_dH[p1][p2][i][j],5,5, outfp);+      }+  }++  fprintf(outfp,"\n# %s\n", settype(INT22));+  { int p1, p2, i, j, k;+  for (p1=1; p1<NBPAIRS; p1++)+    for (p2=1; p2<NBPAIRS; p2++)+      for (i=1; i<5; i++)+        for (j=1; j<5; j++) {+          fprintf(outfp, "/* %2s.%c%c..%2s */\n",+                  pnames[p1], bnames[i], bnames[j], pnames[p2]);+          for (k=1; k<5; k++)+            display_array(int22_37[p1][p2][i][j][k]+1,4,5, outfp);+        }+  }++  fprintf(outfp,"\n# %s\n", settype(INT22_H));+  { int p1, p2, i, j, k;+  for (p1=1; p1<NBPAIRS; p1++)+    for (p2=1; p2<NBPAIRS; p2++)+      for (i=1; i<5; i++)+        for (j=1; j<5; j++) {+          fprintf(outfp, "/* %2s.%c%c..%2s */\n",+                  pnames[p1], bnames[i], bnames[j], pnames[p2]);+          for (k=1; k<5; k++)+            display_array(int22_dH[p1][p2][i][j][k]+1,4,5, outfp);+        }+  }++  fprintf(outfp,"\n# %s\n", settype(HP));+  display_array(hairpin37, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(HP_H));+  display_array(hairpindH, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(B));+  display_array(bulge37, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(B_H));+  display_array(bulgedH, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(IL));+  display_array(internal_loop37, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(IL_H));+  display_array(internal_loopdH, 31, 10, outfp);++  fprintf(outfp,"\n# %s\n", settype(ML));+  fprintf(outfp,"/* F = cu*n_unpaired + cc + ci*loop_degree (+TermAU) */\n");+  fprintf(outfp,"/*\t    cu\t cu_dH\t    cc\t cc_dH\t    ci\t ci_dH  */\n");+  fprintf(outfp,"\t%6d\t%6d\t%6d\t%6d\t%6d\t%6d\n", ML_BASE37, ML_BASEdH, ML_closing37, ML_closingdH, ML_intern37, ML_interndH);++  fprintf(outfp,"\n# %s\n", settype(NIN));+  fprintf(outfp,"/* Ninio = MIN(max, m*|n1-n2| */\n"+              "/*\t    m\t  m_dH     max  */\n"+              "\t%6d\t%6d\t%6d\n", ninio37, niniodH, MAX_NINIO);++  fprintf(outfp,"\n# %s\n", settype(MISC));+  fprintf(outfp,"/* all parameters are pairs of 'energy enthalpy' */\n");+  fprintf(outfp,"/*    DuplexInit     TerminalAU      LXC */\n");+  fprintf(outfp,"   %6d %6d %6d  %6d %3.6f %6d\n", DuplexInit37, DuplexInitdH, TerminalAU37, TerminalAUdH, lxc37, 0);++  fprintf(outfp,"\n# %s\n", settype(HEX));+  for (c=0; c< strlen(Hexaloops)/9; c++)+    fprintf(outfp,"\t%.8s %6d %6d\n", Hexaloops+c*9, Hexaloop37[c], HexaloopdH[c]);++  fprintf(outfp,"\n# %s\n", settype(TL));+  for (c=0; c< strlen(Tetraloops)/7; c++)+    fprintf(outfp,"\t%.6s %6d %6d\n", Tetraloops+c*7, Tetraloop37[c], TetraloopdH[c]);++  fprintf(outfp,"\n# %s\n", settype(TRI));+  for (c=0; c< strlen(Triloops)/6; c++)+    fprintf(outfp,"\t%.5s %6d %6d\n", Triloops+c*6, Triloop37[c], TriloopdH[c]);++  fprintf(outfp,"\n# %s\n", settype(QUIT));+  fclose(outfp);+}++PRIVATE void check_symmetry(void) {+  int i,j,k,l;++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      if (stack37[i][j] != stack37[j][i])+        vrna_message_warning("stacking energies not symmetric");++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      if (stackdH[i][j] != stackdH[j][i])+        vrna_message_warning("stacking enthalpies not symmetric");+++  /* interior 1x1 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++)+          if (int11_37[i][j][k][l] != int11_37[j][i][l][k])+            vrna_message_warning("int11 energies not symmetric (%d,%d,%d,%d) (%d vs. %d)",+                                        i, j, k, l, int11_37[i][j][k][l], int11_37[j][i][l][k]);++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++)+          if (int11_dH[i][j][k][l] != int11_dH[j][i][l][k])+            vrna_message_warning("int11 enthalpies not symmetric");++  /* interior 2x2 loops */+  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++)+              if (int22_37[i][j][k][l][m][n] != int22_37[j][i][m][n][k][l])+                vrna_message_warning("int22 energies not symmetric");+        }++  for (i=0; i<=NBPAIRS; i++)+    for (j=0; j<=NBPAIRS; j++)+      for (k=0; k<5; k++)+        for (l=0; l<5; l++) {+          int m,n;+          for (m=0; m<5; m++)+            for (n=0; n<5; n++)+              if (int22_dH[i][j][k][l][m][n] != int22_dH[j][i][m][n][k][l])+                vrna_message_warning("int22 enthalpies not symmetric: %d %d %d %d %d %d",+                                            i,j,k,l,m,n);+        }+}++/* update nonstandard nucleotide/basepair involved contributions for int22 */+PRIVATE void update_nst(int array[NBPAIRS+1][NBPAIRS+1][5][5][5][5]){+  int    i, j, k, l, m, n;+  int max, max2, max3, max4, max5, max6;++  /* get maxima for one nonstandard nucleotide */+  for (i=1; i<NBPAIRS; i++){+    for (j=1; j<NBPAIRS; j++){+      for (k=1; k<5; k++){+        for (l=1; l<5; l++){+          for (m=1; m<5; m++){+            max = max2 = max3 = max4 = -INF; /* max of {CGAU} */+            for(n=1;n<5;n++){+              max   = MAX2(max,   array[i][j][k][l][m][n]);+              max2  = MAX2(max2,  array[i][j][k][l][n][m]);+              max3  = MAX2(max3,  array[i][j][k][n][l][m]);+              max4  = MAX2(max4,  array[i][j][n][k][l][m]);+            }+            array[i][j][k][l][m][0] = max;+            array[i][j][k][l][0][m] = max2;+            array[i][j][k][0][l][m] = max3;+            array[i][j][0][k][l][m] = max4;+          }+        }+      }+    }+  }+  /* get maxima for two nonstandard nucleotides */+  for (i=1; i<NBPAIRS; i++){+    for (j=1; j<NBPAIRS; j++){+      for (k=1; k<5; k++){+        for (l=1; l<5; l++){+          max = max2 = max3 = max4 = max5 = max6 = -INF; /* max of {CGAU} */+          for (m=1; m<5; m++){+            max   = MAX2(max,   array[i][j][k][l][m][0]);+            max2  = MAX2(max2,  array[i][j][k][m][0][l]);+            max3  = MAX2(max3,  array[i][j][m][0][k][l]);+            max4  = MAX2(max4,  array[i][j][0][k][l][m]);+            max5  = MAX2(max5,  array[i][j][0][k][m][l]);+            max6  = MAX2(max6,  array[i][j][k][0][l][m]);+          }+          array[i][j][k][l][0][0] = max;+          array[i][j][k][0][0][l] = max2;+          array[i][j][0][0][k][l] = max3;+          array[i][j][k][0][l][0] = max6;+          array[i][j][0][k][0][l] = max5;+          array[i][j][0][k][l][0] = max4;+        }+      }+    }+  }+  /* get maxima for three nonstandard nucleotides */+  for (i=1; i<NBPAIRS; i++){+    for (j=1; j<NBPAIRS; j++){+      for (k=1; k<5; k++){+        max = max2 = max3 = max4 = -INF; /* max of {CGAU} */+        for (l=1; l<5; l++){+          /* should be arbitrary where index l resides in last 3 possible locations */+          max   = MAX2(max,   array[i][j][k][l][0][0]);+          max2  = MAX2(max2,  array[i][j][0][k][l][0]);+          max3  = MAX2(max3,  array[i][j][0][0][k][l]);+          max4  = MAX2(max4,  array[i][j][0][0][l][k]);+        }+        array[i][j][k][0][0][0] = max;+        array[i][j][0][k][0][0] = max2;+        array[i][j][0][0][k][0] = max3;+        array[i][j][0][0][0][k] = max4;+      }+    }+  }+  /* get maxima for 4 nonstandard nucleotides */+  for (i=1; i<NBPAIRS; i++){+    for (j=1; j<NBPAIRS; j++){+      max = -INF; /* max of {CGAU} */+      for (k=1; k<5; k++){+        max   = MAX2(max,   array[i][j][k][0][0][0]);+      }+      array[i][j][0][0][0][0] = max;+    }+  }++  /* now compute contributions for nonstandard base pairs ... */+  /* first, 1 nonstandard bp */+  for (i=1; i<NBPAIRS; i++){+    for (k=0; k<5; k++){+      for (l=0; l<5; l++){+        for (m=0; m<5; m++){+          for(n=0;n<5;n++){+            max = max2 = -INF;+            for(j=1;j<NBPAIRS;j++){+              max   = MAX2(max, array[i][j][k][l][m][n]);+              max2  = MAX2(max2, array[j][i][k][l][m][n]);+            }+            array[i][NBPAIRS][k][l][m][n] = max;+            array[NBPAIRS][i][k][l][m][n] = max2;+          }+        }+      }+    }+  }++  /* now 2 nst base pairs */+  for (k=0; k<5; k++){+    for (l=0; l<5; l++){+      for (m=0; m<5; m++){+        for(n=0;n<5;n++){+          max = -INF;+          for(j=1;j<NBPAIRS;j++){+            max   = MAX2(max, array[NBPAIRS][j][k][l][m][n]);+          }+          array[NBPAIRS][NBPAIRS][k][l][m][n] = max;+        }+      }+    }+  }++}
+ C/ViennaRNA/read_epars.h view
@@ -0,0 +1,62 @@+#ifndef VIENNA_RNA_PACKAGE_READ_EPARS_H+#define VIENNA_RNA_PACKAGE_READ_EPARS_H++/**+ *  @file     read_epars.h+ *  @ingroup  energy_parameters+ *  @brief    Read and write energy parameter files+ */++/**+ *  @addtogroup energy_parameters_rw+ *  @brief  Read and Write energy parameter sets from and to text files+ *+ *  A default set of parameters, identical to the one described in+ *  @cite mathews:2004 and @cite turner:2010, is compiled into the library.+ *+ *  @{+ *  @ingroup  energy_parameters_rw+ */++/**+ *  @brief+ *+ */+enum parset {+  UNKNOWN= -1, QUIT,+  S, S_H, HP, HP_H, B, B_H, IL, IL_H, MMH, MMH_H, MMI, MMI_H,+  MMI1N, MMI1N_H, MMI23, MMI23_H, MMM, MMM_H, MME, MME_H, D5, D5_H, D3, D3_H,+  INT11, INT11_H, INT21, INT21_H, INT22, INT22_H, ML, TL,+  TRI, HEX, NIN, MISC};++/**+ *  @brief Read energy parameters from a file+ * + *  @param fname  The path to the file containing the energy parameters+ */+void  read_parameter_file(const char fname[]);++/**+ *  @brief Write energy parameters to a file+ * + *  @param fname  A filename (path) for the file where the current energy parameters will be written to+ */+void  write_parameter_file(const char fname[]);++/**+ *  @brief+ *+ */+enum  parset gettype(const char *ident);++/**+ *  @brief+ *+ */+char  *settype(enum parset s);++/**+ *  @}+ */++#endif
+ C/ViennaRNA/ribo.c view
@@ -0,0 +1,1134 @@++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdlib.h>+#include <stdio.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/ribo.h"++static float dm_12_5[7][7]={{0,0,0,0,0,0,0},+{0, 3.092536, 3.375764, 1.374085, 0.681999, 2.357501, 2.759147},+{0, 3.375764, 3.223949, 1.077220, 0.713622, 2.742085, 2.325847},+{0, 1.374085, 1.077220, 0.801987, -0.251514, 0.289428, 0.641530},+{0, 0.681999, 0.713622, -0.251514, 1.203844, -0.228733, 0.292522},+{0, 2.357501, 2.742085, 0.289428, -0.228733, 1.511221, 1.958625},+{0, 2.759147, 2.325847, 0.641530, 0.292522, 1.958625, 1.948208}};+static float dm_12_6[7][7]={{0,0,0,0,0,0,0},+{0, 3.092373, 3.375631, 1.374059, 0.681938, 2.357565, 2.759217},+{0, 3.375631, 3.223782, 1.077212, 0.713641, 2.742133, 2.325829},+{0, 1.374059, 1.077212, 0.801954, -0.251326, 0.289489, 0.641712},+{0, 0.681938, 0.713641, -0.251326, 1.203723, -0.228872, 0.292526},+{0, 2.357565, 2.742133, 0.289489, -0.228872, 1.511158, 1.958685},+{0, 2.759217, 2.325829, 0.641712, 0.292526, 1.958685, 1.948130}};+static float dm_12_7[7][7]={{0,0,0,0,0,0,0},+{0, 3.053179, 3.352207, 1.390738, 0.684033, 2.353429, 2.765638},+{0, 3.352207, 3.188833, 1.115659, 0.689646, 2.742801, 2.338308},+{0, 1.390738, 1.115659, 0.803823, -0.192463, 0.312652, 0.698703},+{0, 0.684033, 0.689646, -0.192463, 1.107424, -0.189709, 0.302683},+{0, 2.353429, 2.742801, 0.312652, -0.189709, 1.453439, 1.907102},+{0, 2.765638, 2.338308, 0.698703, 0.302683, 1.907102, 1.850447}};+static float dm_12_8[7][7]={{0,0,0,0,0,0,0},+{0, 3.049303, 3.270569, 1.417231, 0.666003, 2.313534, 2.891832},+{0, 3.270569, 3.186336, 1.047878, 0.717329, 2.806323, 2.360206},+{0, 1.417231, 1.047878, 0.718061, -0.168063, 0.238106, 0.821674},+{0, 0.666003, 0.717329, -0.168063, 0.995556, 0.010346, 0.171852},+{0, 2.313534, 2.806323, 0.238106, 0.010346, 1.361999, 1.906834},+{0, 2.891832, 2.360206, 0.821674, 0.171852, 1.906834, 1.745436}};+static float dm_12_9[7][7]={{0,0,0,0,0,0,0},+{0, 3.165100, 3.153340, 1.293645, 0.683711, 2.215911, 3.082474},+{0, 3.153340, 3.304615, 1.071703, 0.672898, 2.978487, 2.330174},+{0, 1.293645, 1.071703, 0.684991, -0.294258, 0.196122, 0.756948},+{0, 0.683711, 0.672898, -0.294258, 1.089387, 0.034000, 0.046088},+{0, 2.215911, 2.978487, 0.196122, 0.034000, 1.457778, 1.997389},+{0, 3.082474, 2.330174, 0.756948, 0.046088, 1.997389, 1.860867}};+static float dm_12_10[7][7]={{0,0,0,0,0,0,0},+{0, 3.316050, 3.080141, 1.198316, 0.719889, 2.155618, 3.134309},+{0, 3.080141, 3.404347, 1.108233, 0.637222, 2.938360, 2.294410},+{0, 1.198316, 1.108233, 0.657620, -0.563942, 0.269879, 0.776661},+{0, 0.719889, 0.637222, -0.563942, 1.170892, 0.077878, -0.014940},+{0, 2.155618, 2.938360, 0.269879, 0.077878, 1.631701, 2.093486},+{0, 3.134309, 2.294410, 0.776661, -0.014940, 2.093486, 2.008351}};+static float dm_12_11[7][7]={{0,0,0,0,0,0,0},+{0, 4.453617, 3.036904, 0.865118, 0.725919, 2.140436, 3.324865},+{0, 3.036904, 4.352423, 0.749665, 0.059865, 2.923511, 2.308393},+{0, 0.865118, 0.749665, 0.722300, -1.323178, 0.374187, 0.426083},+{0, 0.725919, 0.059865, -1.323178, 1.727563, -0.428759, 0.330746},+{0, 2.140436, 2.923511, 0.374187, -0.428759, 2.428389, 2.233568},+{0, 3.324865, 2.308393, 0.426083, 0.330746, 2.233568, 2.821057}};+static float dm_13_5[7][7]={{0,0,0,0,0,0,0},+{0, 2.533782, 3.282896, 1.521364, 0.752652, 2.264693, 2.589635},+{0, 3.282896, 2.711135, 0.952877, 1.215201, 2.545641, 2.334410},+{0, 1.521364, 0.952877, 0.827991, 0.183827, 0.378211, 0.794884},+{0, 0.752652, 1.215201, 0.183827, 0.819462, 0.368008, 0.475756},+{0, 2.264693, 2.545641, 0.378211, 0.368008, 1.007668, 1.732095},+{0, 2.589635, 2.334410, 0.794884, 0.475756, 1.732095, 1.315666}};+static float dm_13_6[7][7]={{0,0,0,0,0,0,0},+{0, 2.533730, 3.282872, 1.521367, 0.752640, 2.264708, 2.589641},+{0, 3.282872, 2.711079, 0.952872, 1.215222, 2.545643, 2.334410},+{0, 1.521367, 0.952872, 0.827971, 0.183877, 0.378217, 0.794922},+{0, 0.752640, 1.215222, 0.183877, 0.819423, 0.368018, 0.475753},+{0, 2.264708, 2.545643, 0.378217, 0.368018, 1.007640, 1.732099},+{0, 2.589641, 2.334410, 0.794922, 0.475753, 1.732099, 1.315634}};+static float dm_13_7[7][7]={{0,0,0,0,0,0,0},+{0, 2.517035, 3.288237, 1.534295, 0.752649, 2.264114, 2.587804},+{0, 3.288237, 2.694998, 0.956805, 1.227789, 2.542543, 2.336350},+{0, 1.534295, 0.956805, 0.820438, 0.200329, 0.379706, 0.803818},+{0, 0.752649, 1.227789, 0.200329, 0.797982, 0.376972, 0.476299},+{0, 2.264114, 2.542543, 0.379706, 0.376972, 0.988104, 1.718544},+{0, 2.587804, 2.336350, 0.803818, 0.476299, 1.718544, 1.288938}};+static float dm_13_8[7][7]={{0,0,0,0,0,0,0},+{0, 2.455141, 3.267199, 1.550791, 0.740489, 2.281213, 2.624344},+{0, 3.267199, 2.639092, 0.938981, 1.263224, 2.561521, 2.363191},+{0, 1.550791, 0.938981, 0.771171, 0.200008, 0.376450, 0.811315},+{0, 0.740489, 1.263224, 0.200008, 0.754473, 0.422913, 0.493286},+{0, 2.281213, 2.561521, 0.376450, 0.422913, 0.922402, 1.721243},+{0, 2.624344, 2.363191, 0.811315, 0.493286, 1.721243, 1.225387}};+static float dm_13_9[7][7]={{0,0,0,0,0,0,0},+{0, 2.379212, 3.195011, 1.477942, 0.732266, 2.283994, 2.699509},+{0, 3.195011, 2.577100, 0.912791, 1.272057, 2.625508, 2.371223},+{0, 1.477942, 0.912791, 0.737835, 0.193712, 0.381625, 0.838647},+{0, 0.732266, 1.272057, 0.193712, 0.719631, 0.491776, 0.516184},+{0, 2.283994, 2.625508, 0.381625, 0.491776, 0.889747, 1.759331},+{0, 2.699509, 2.371223, 0.838647, 0.516184, 1.759331, 1.193323}};+static float dm_13_10[7][7]={{0,0,0,0,0,0,0},+{0, 2.280425, 3.074698, 1.281893, 0.750335, 2.294618, 2.818548},+{0, 3.074698, 2.501446, 0.902613, 1.237324, 2.733365, 2.420051},+{0, 1.281893, 0.902613, 0.663356, 0.025119, 0.436734, 0.946242},+{0, 0.750335, 1.237324, 0.025119, 0.634862, 0.635376, 0.587841},+{0, 2.294618, 2.733365, 0.436734, 0.635376, 0.851475, 1.822634},+{0, 2.818548, 2.420051, 0.946242, 0.587841, 1.822634, 1.133656}};+static float dm_13_11[7][7]={{0,0,0,0,0,0,0},+{0, 2.049420, 3.065598, 1.147184, 0.984070, 2.286178, 2.745107},+{0, 3.065598, 2.349472, 0.907685, 1.527069, 2.637071, 2.291610},+{0, 1.147184, 0.907685, 0.583508, 0.290374, 0.432797, 0.907368},+{0, 0.984070, 1.527069, 0.290374, 0.528508, 0.783625, 0.671962},+{0, 2.286178, 2.637071, 0.432797, 0.783625, 0.749801, 1.701156},+{0, 2.745107, 2.291610, 0.907368, 0.671962, 1.701156, 0.981579}};+static float dm_13_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.904683, 3.147814, 1.383470, 0.788061, 2.230640, 2.516545},+{0, 3.147814, 2.158800, 1.031644, 1.913906, 2.492254, 1.996584},+{0, 1.383470, 1.031644, 0.332441, 0.746301, 0.435514, 0.879258},+{0, 0.788061, 1.913906, 0.746301, 0.496698, 0.960208, 0.630473},+{0, 2.230640, 2.492254, 0.435514, 0.960208, 0.830695, 1.541673},+{0, 2.516545, 1.996584, 0.879258, 0.630473, 1.541673, 0.887994}};+static float dm_14_5[7][7]={{0,0,0,0,0,0,0},+{0, 2.294989, 3.205559, 1.584266, 0.734475, 2.289599, 2.535028},+{0, 3.205559, 2.485328, 0.891295, 1.466901, 2.470993, 2.328167},+{0, 1.584266, 0.891295, 0.759635, 0.320177, 0.322250, 0.907780},+{0, 0.734475, 1.466901, 0.320177, 0.770910, 0.521607, 0.411958},+{0, 2.289599, 2.470993, 0.322250, 0.521607, 0.900558, 1.829543},+{0, 2.535028, 2.328167, 0.907780, 0.411958, 1.829543, 1.149384}};+static float dm_14_6[7][7]={{0,0,0,0,0,0,0},+{0, 2.294961, 3.205540, 1.584268, 0.734469, 2.289603, 2.535026},+{0, 3.205540, 2.485292, 0.891288, 1.466911, 2.470989, 2.328168},+{0, 1.584268, 0.891288, 0.759627, 0.320205, 0.322258, 0.907802},+{0, 0.734469, 1.466911, 0.320205, 0.770895, 0.521619, 0.411961},+{0, 2.289603, 2.470989, 0.322258, 0.521619, 0.900543, 1.829549},+{0, 2.535026, 2.328168, 0.907802, 0.411961, 1.829549, 1.149367}};+static float dm_14_7[7][7]={{0,0,0,0,0,0,0},+{0, 2.284183, 3.205463, 1.589806, 0.733327, 2.290173, 2.534179},+{0, 3.205463, 2.474571, 0.891349, 1.473391, 2.469534, 2.329742},+{0, 1.589806, 0.891349, 0.754092, 0.329639, 0.323746, 0.913721},+{0, 0.733327, 1.473391, 0.329639, 0.760515, 0.527766, 0.413001},+{0, 2.290173, 2.469534, 0.323746, 0.527766, 0.890631, 1.825071},+{0, 2.534179, 2.329742, 0.913721, 0.413001, 1.825071, 1.136190}};+static float dm_14_8[7][7]={{0,0,0,0,0,0,0},+{0, 2.235726, 3.181914, 1.595503, 0.722770, 2.300997, 2.546218},+{0, 3.181914, 2.427845, 0.875999, 1.494647, 2.473461, 2.342035},+{0, 1.595503, 0.875999, 0.724803, 0.342682, 0.323718, 0.932708},+{0, 0.722770, 1.494647, 0.342682, 0.734102, 0.566070, 0.421129},+{0, 2.300997, 2.473461, 0.323718, 0.566070, 0.855249, 1.842018},+{0, 2.546218, 2.342035, 0.932708, 0.421129, 1.842018, 1.098536}};+static float dm_14_9[7][7]={{0,0,0,0,0,0,0},+{0, 2.169213, 3.125506, 1.561668, 0.710360, 2.315725, 2.570925},+{0, 3.125506, 2.366074, 0.850145, 1.506427, 2.491705, 2.351458},+{0, 1.561668, 0.850145, 0.699815, 0.342923, 0.328538, 0.974691},+{0, 0.710360, 1.506427, 0.342923, 0.708392, 0.630838, 0.430721},+{0, 2.315725, 2.491705, 0.328538, 0.630838, 0.830805, 1.888777},+{0, 2.570925, 2.351458, 0.974691, 0.430721, 1.888777, 1.064891}};+static float dm_14_10[7][7]={{0,0,0,0,0,0,0},+{0, 2.121401, 3.097557, 1.560258, 0.689908, 2.317536, 2.630291},+{0, 3.097557, 2.307448, 0.784748, 1.536794, 2.544322, 2.395549},+{0, 1.560258, 0.784748, 0.636637, 0.281228, 0.337831, 0.965036},+{0, 0.689908, 1.536794, 0.281228, 0.656827, 0.697208, 0.440900},+{0, 2.317536, 2.544322, 0.337831, 0.697208, 0.832763, 1.933003},+{0, 2.630291, 2.395549, 0.965036, 0.440900, 1.933003, 1.020585}};+static float dm_14_11[7][7]={{0,0,0,0,0,0,0},+{0, 2.073657, 3.129452, 1.652733, 0.683925, 2.335236, 2.616220},+{0, 3.129452, 2.249754, 0.745361, 1.637265, 2.557071, 2.392472},+{0, 1.652733, 0.745361, 0.597976, 0.222713, 0.343902, 0.889990},+{0, 0.683925, 1.637265, 0.222713, 0.624604, 0.786781, 0.435623},+{0, 2.335236, 2.557071, 0.343902, 0.786781, 0.831075, 1.905111},+{0, 2.616220, 2.392472, 0.889990, 0.435623, 1.905111, 0.955225}};+static float dm_14_12[7][7]={{0,0,0,0,0,0,0},+{0, 2.029277, 3.087264, 1.718185, 0.587838, 2.396044, 2.545040},+{0, 3.087264, 2.177344, 0.725318, 1.676438, 2.547083, 2.447849},+{0, 1.718185, 0.725318, 0.542734, 0.219786, 0.369477, 0.869417},+{0, 0.587838, 1.676438, 0.219786, 0.608994, 0.859758, 0.368574},+{0, 2.396044, 2.547083, 0.369477, 0.859758, 0.842019, 2.027160},+{0, 2.545040, 2.447849, 0.869417, 0.368574, 2.027160, 0.909170}};+static float dm_14_13[7][7]={{0,0,0,0,0,0,0},+{0, 2.000248, 3.122593, 1.864659, 0.494490, 2.479114, 2.554107},+{0, 3.122593, 2.129482, 0.626369, 1.637370, 2.548600, 2.565048},+{0, 1.864659, 0.626369, 0.454571, 0.172183, 0.351022, 0.794287},+{0, 0.494490, 1.637370, 0.172183, 0.671707, 0.748383, 0.198126},+{0, 2.479114, 2.548600, 0.351022, 0.748383, 0.846495, 2.353506},+{0, 2.554107, 2.565048, 0.794287, 0.198126, 2.353506, 0.877777}};+static float dm_15_5[7][7]={{0,0,0,0,0,0,0},+{0, 2.185017, 3.256348, 1.588804, 0.666905, 2.355718, 2.520031},+{0, 3.256348, 2.374070, 0.850906, 1.551282, 2.511878, 2.371123},+{0, 1.588804, 0.850906, 0.689517, 0.366678, 0.267602, 0.985305},+{0, 0.666905, 1.551282, 0.366678, 0.702683, 0.582839, 0.372196},+{0, 2.355718, 2.511878, 0.267602, 0.582839, 0.778425, 1.871858},+{0, 2.520031, 2.371123, 0.985305, 0.372196, 1.871858, 1.031343}};+static float dm_15_6[7][7]={{0,0,0,0,0,0,0},+{0, 2.184997, 3.256344, 1.588807, 0.666901, 2.355725, 2.520032},+{0, 3.256344, 2.374049, 0.850901, 1.551289, 2.511879, 2.371126},+{0, 1.588807, 0.850901, 0.689501, 0.366694, 0.267601, 0.985320},+{0, 0.666901, 1.551289, 0.366694, 0.702666, 0.582848, 0.372191},+{0, 2.355725, 2.511879, 0.267601, 0.582848, 0.778413, 1.871866},+{0, 2.520032, 2.371126, 0.985320, 0.372191, 1.871866, 1.031328}};+static float dm_15_7[7][7]={{0,0,0,0,0,0,0},+{0, 2.178225, 3.255949, 1.591734, 0.666172, 2.356327, 2.519434},+{0, 3.255949, 2.367187, 0.850656, 1.554802, 2.511035, 2.372193},+{0, 1.591734, 0.850656, 0.685901, 0.372252, 0.268459, 0.988985},+{0, 0.666172, 1.554802, 0.372252, 0.696898, 0.586767, 0.372815},+{0, 2.356327, 2.511035, 0.268459, 0.586767, 0.772770, 1.869928},+{0, 2.519434, 2.372193, 0.988985, 0.372815, 1.869928, 1.024003}};+static float dm_15_8[7][7]={{0,0,0,0,0,0,0},+{0, 2.141127, 3.237374, 1.592766, 0.658485, 2.364123, 2.524356},+{0, 3.237374, 2.330108, 0.840158, 1.565238, 2.512924, 2.380899},+{0, 1.592766, 0.840158, 0.665322, 0.384438, 0.266965, 1.010245},+{0, 0.658485, 1.565238, 0.384438, 0.677947, 0.617501, 0.377062},+{0, 2.364123, 2.512924, 0.266965, 0.617501, 0.748457, 1.886645},+{0, 2.524356, 2.380899, 1.010245, 0.377062, 1.886645, 0.998685}};+static float dm_15_9[7][7]={{0,0,0,0,0,0,0},+{0, 2.082602, 3.194686, 1.571476, 0.645533, 2.377215, 2.534602},+{0, 3.194686, 2.272916, 0.822962, 1.573341, 2.520912, 2.393028},+{0, 1.571476, 0.822962, 0.640049, 0.397585, 0.269078, 1.050093},+{0, 0.645533, 1.573341, 0.397585, 0.651218, 0.668684, 0.385365},+{0, 2.377215, 2.520912, 0.269078, 0.668684, 0.720559, 1.929423},+{0, 2.534602, 2.393028, 1.050093, 0.385365, 1.929423, 0.964692}};+static float dm_15_10[7][7]={{0,0,0,0,0,0,0},+{0, 2.011980, 3.208890, 1.586936, 0.614653, 2.410291, 2.569991},+{0, 3.208890, 2.192435, 0.783958, 1.618693, 2.560039, 2.439652},+{0, 1.586936, 0.783958, 0.566237, 0.382907, 0.271841, 1.006087},+{0, 0.614653, 1.618693, 0.382907, 0.581074, 0.728724, 0.387583},+{0, 2.410291, 2.560039, 0.271841, 0.728724, 0.689985, 1.958203},+{0, 2.569991, 2.439652, 1.006087, 0.387583, 1.958203, 0.901393}};+static float dm_15_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.960846, 3.364729, 1.711101, 0.580163, 2.436976, 2.568375},+{0, 3.364729, 2.127484, 0.757940, 1.724525, 2.572193, 2.449286},+{0, 1.711101, 0.757940, 0.506015, 0.306759, 0.248888, 0.900846},+{0, 0.580163, 1.724525, 0.306759, 0.515784, 0.796313, 0.387969},+{0, 2.436976, 2.572193, 0.248888, 0.796313, 0.651734, 1.900198},+{0, 2.568375, 2.449286, 0.900846, 0.387969, 1.900198, 0.825616}};+static float dm_15_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.905112, 3.368458, 1.738759, 0.521209, 2.469970, 2.532597},+{0, 3.368458, 2.057336, 0.733674, 1.764054, 2.567498, 2.475677},+{0, 1.738759, 0.733674, 0.452960, 0.356533, 0.263124, 0.915940},+{0, 0.521209, 1.764054, 0.356533, 0.468384, 0.825416, 0.393747},+{0, 2.469970, 2.567498, 0.263124, 0.825416, 0.620497, 1.933061},+{0, 2.532597, 2.475677, 0.915940, 0.393747, 1.933061, 0.776274}};+static float dm_15_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.764334, 3.521734, 1.844636, 0.465089, 2.475371, 2.501349},+{0, 3.521734, 1.899254, 0.652013, 1.866354, 2.519286, 2.498764},+{0, 1.844636, 0.652013, 0.373857, 0.494613, 0.240469, 1.003296},+{0, 0.465089, 1.866354, 0.494613, 0.346332, 0.823497, 0.447243},+{0, 2.475371, 2.519286, 0.240469, 0.823497, 0.468987, 1.894554},+{0, 2.501349, 2.498764, 1.003296, 0.447243, 1.894554, 0.650703}};+static float dm_15_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.753217, 3.560554, 1.890084, 0.497526, 2.482621, 2.508029},+{0, 3.560554, 1.886087, 0.571603, 1.903238, 2.518939, 2.505216},+{0, 1.890084, 0.571603, 0.375259, 0.535512, 0.227112, 1.009415},+{0, 0.497526, 1.903238, 0.535512, 0.355054, 0.732221, 0.497356},+{0, 2.482621, 2.518939, 0.227112, 0.732221, 0.453713, 1.824189},+{0, 2.508029, 2.505216, 1.009415, 0.497356, 1.824189, 0.649442}};+static float dm_16_5[7][7]={{0,0,0,0,0,0,0},+{0, 2.096356, 3.297512, 1.643277, 0.627608, 2.425850, 2.531892},+{0, 3.297512, 2.277720, 0.776768, 1.578330, 2.507998, 2.381738},+{0, 1.643277, 0.776768, 0.652789, 0.376193, 0.205475, 1.050591},+{0, 0.627608, 1.578330, 0.376193, 0.635057, 0.695045, 0.328657},+{0, 2.425850, 2.507998, 0.205475, 0.695045, 0.647026, 1.971812},+{0, 2.531892, 2.381738, 1.050591, 0.328657, 1.971812, 0.893562}};+static float dm_16_6[7][7]={{0,0,0,0,0,0,0},+{0, 2.096346, 3.297510, 1.643276, 0.627604, 2.425854, 2.531894},+{0, 3.297510, 2.277709, 0.776764, 1.578331, 2.508000, 2.381737},+{0, 1.643276, 0.776764, 0.652783, 0.376197, 0.205477, 1.050597},+{0, 0.627604, 1.578331, 0.376197, 0.635048, 0.695048, 0.328658},+{0, 2.425854, 2.508000, 0.205477, 0.695048, 0.647022, 1.971820},+{0, 2.531894, 2.381737, 1.050597, 0.328658, 1.971820, 0.893558}};+static float dm_16_7[7][7]={{0,0,0,0,0,0,0},+{0, 2.092914, 3.296980, 1.644541, 0.627228, 2.426164, 2.531487},+{0, 3.296980, 2.274181, 0.776531, 1.579823, 2.507496, 2.382211},+{0, 1.644541, 0.776531, 0.650930, 0.378902, 0.205995, 1.052513},+{0, 0.627228, 1.579823, 0.378902, 0.632483, 0.697137, 0.329046},+{0, 2.426164, 2.507496, 0.205995, 0.697137, 0.644461, 1.971311},+{0, 2.531487, 2.382211, 1.052513, 0.329046, 1.971311, 0.890302}};+static float dm_16_8[7][7]={{0,0,0,0,0,0,0},+{0, 2.073428, 3.286494, 1.644950, 0.623462, 2.430093, 2.532505},+{0, 3.286494, 2.254339, 0.771248, 1.583832, 2.507212, 2.385719},+{0, 1.644950, 0.771248, 0.640496, 0.385785, 0.205764, 1.064654},+{0, 0.623462, 1.583832, 0.385785, 0.622568, 0.714265, 0.331069},+{0, 2.430093, 2.507212, 0.205764, 0.714265, 0.632331, 1.982670},+{0, 2.532505, 2.385719, 1.064654, 0.331069, 1.982670, 0.877393}};+static float dm_16_9[7][7]={{0,0,0,0,0,0,0},+{0, 2.040939, 3.265472, 1.637410, 0.615748, 2.438042, 2.535927},+{0, 3.265472, 2.221433, 0.760900, 1.588059, 2.509252, 2.391099},+{0, 1.637410, 0.760900, 0.625103, 0.394320, 0.206172, 1.085801},+{0, 0.615748, 1.588059, 0.394320, 0.606102, 0.744667, 0.334067},+{0, 2.438042, 2.509252, 0.206172, 0.744667, 0.614764, 2.010608},+{0, 2.535927, 2.391099, 1.085801, 0.334067, 2.010608, 0.856570}};+static float dm_16_10[7][7]={{0,0,0,0,0,0,0},+{0, 1.929517, 3.299150, 1.679136, 0.598406, 2.478683, 2.546578},+{0, 3.299150, 2.091719, 0.711831, 1.702824, 2.519268, 2.443818},+{0, 1.679136, 0.711831, 0.530571, 0.408434, 0.197624, 1.036293},+{0, 0.598406, 1.702824, 0.408434, 0.495823, 0.861514, 0.331873},+{0, 2.478683, 2.519268, 0.197624, 0.861514, 0.535526, 2.017192},+{0, 2.546578, 2.443818, 1.036293, 0.331873, 2.017192, 0.751594}};+static float dm_16_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.790624, 3.419792, 1.804745, 0.585040, 2.511724, 2.507394},+{0, 3.419792, 1.936325, 0.655038, 1.866549, 2.481327, 2.473116},+{0, 1.804745, 0.655038, 0.440211, 0.419147, 0.190157, 0.999819},+{0, 0.585040, 1.866549, 0.419147, 0.384589, 0.972519, 0.349591},+{0, 2.511724, 2.481327, 0.190157, 0.972519, 0.439998, 1.950823},+{0, 2.507394, 2.473116, 0.999819, 0.349591, 1.950823, 0.634690}};+static float dm_16_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.738485, 3.413306, 1.823292, 0.565589, 2.524720, 2.483688},+{0, 3.413306, 1.875156, 0.624931, 1.902547, 2.464176, 2.477746},+{0, 1.823292, 0.624931, 0.407593, 0.460985, 0.201735, 1.024667},+{0, 0.565589, 1.902547, 0.460985, 0.347262, 1.021166, 0.354417},+{0, 2.524720, 2.464176, 0.201735, 1.021166, 0.409784, 1.969276},+{0, 2.483688, 2.477746, 1.024667, 0.354417, 1.969276, 0.597237}};+static float dm_16_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.664768, 3.405759, 1.848635, 0.546367, 2.518192, 2.460663},+{0, 3.405759, 1.785451, 0.567988, 1.961108, 2.436129, 2.469090},+{0, 1.848635, 0.567988, 0.373320, 0.524553, 0.220489, 1.071079},+{0, 0.546367, 1.961108, 0.524553, 0.294419, 1.099707, 0.370092},+{0, 2.518192, 2.436129, 0.220489, 1.099707, 0.364109, 1.982751},+{0, 2.460663, 2.469090, 1.071079, 0.370092, 1.982751, 0.552731}};+static float dm_16_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.586401, 3.322065, 1.884482, 0.570145, 2.512906, 2.427617},+{0, 3.322065, 1.692728, 0.531570, 1.996685, 2.415287, 2.448701},+{0, 1.884482, 0.531570, 0.352236, 0.601762, 0.215346, 1.113649},+{0, 0.570145, 1.996685, 0.601762, 0.269440, 1.208804, 0.368633},+{0, 2.512906, 2.415287, 0.215346, 1.208804, 0.308130, 2.023351},+{0, 2.427617, 2.448701, 1.113649, 0.368633, 2.023351, 0.509060}};+static float dm_16_15[7][7]={{0,0,0,0,0,0,0},+{0, 1.663168, 3.308261, 1.850005, 0.549647, 2.516260, 2.489382},+{0, 3.308261, 1.762303, 0.472887, 1.999308, 2.452056, 2.487940},+{0, 1.850005, 0.472887, 0.321624, 0.611101, 0.250077, 1.031153},+{0, 0.549647, 1.999308, 0.611101, 0.328556, 1.140290, 0.273025},+{0, 2.516260, 2.452056, 0.250077, 1.140290, 0.460515, 2.003803},+{0, 2.489382, 2.487940, 1.031153, 0.273025, 2.003803, 0.593446}};+static float dm_17_5[7][7]={{0,0,0,0,0,0,0},+{0, 2.007833, 3.291241, 1.663891, 0.607307, 2.464689, 2.554022},+{0, 3.291241, 2.181349, 0.736718, 1.592793, 2.504274, 2.379900},+{0, 1.663891, 0.736718, 0.616428, 0.445344, 0.161487, 1.114375},+{0, 0.607307, 1.592793, 0.445344, 0.571508, 0.773714, 0.288043},+{0, 2.464689, 2.504274, 0.161487, 0.773714, 0.544800, 2.054002},+{0, 2.554022, 2.379900, 1.114375, 0.288043, 2.054002, 0.814483}};+static float dm_17_6[7][7]={{0,0,0,0,0,0,0},+{0, 2.007829, 3.291242, 1.663892, 0.607308, 2.464688, 2.554020},+{0, 3.291242, 2.181345, 0.736719, 1.592796, 2.504272, 2.379900},+{0, 1.663892, 0.736719, 0.616427, 0.445344, 0.161487, 1.114376},+{0, 0.607308, 1.592796, 0.445344, 0.571507, 0.773715, 0.288042},+{0, 2.464688, 2.504272, 0.161487, 0.773715, 0.544799, 2.054004},+{0, 2.554020, 2.379900, 1.114376, 0.288042, 2.054004, 0.814482}};+static float dm_17_7[7][7]={{0,0,0,0,0,0,0},+{0, 2.006511, 3.290918, 1.664311, 0.607172, 2.464800, 2.553839},+{0, 3.290918, 2.179982, 0.736617, 1.593288, 2.504065, 2.380066},+{0, 1.664311, 0.736617, 0.615720, 0.446361, 0.161718, 1.115108},+{0, 0.607172, 1.593288, 0.446361, 0.570613, 0.774548, 0.288223},+{0, 2.464800, 2.504065, 0.161718, 0.774548, 0.543905, 2.053924},+{0, 2.553839, 2.380066, 1.115108, 0.288223, 2.053924, 0.813353}};+static float dm_17_8[7][7]={{0,0,0,0,0,0,0},+{0, 1.997746, 3.285639, 1.664262, 0.605619, 2.466015, 2.554194},+{0, 3.285639, 2.170945, 0.734627, 1.594479, 2.504060, 2.380880},+{0, 1.664262, 0.734627, 0.611204, 0.449825, 0.161638, 1.120324},+{0, 0.605619, 1.594479, 0.449825, 0.566330, 0.782686, 0.288928},+{0, 2.466015, 2.504060, 0.161638, 0.782686, 0.538801, 2.060339},+{0, 2.554194, 2.380880, 1.120324, 0.288928, 2.060339, 0.807944}};+static float dm_17_9[7][7]={{0,0,0,0,0,0,0},+{0, 1.982793, 3.276596, 1.661720, 0.602603, 2.468779, 2.554925},+{0, 3.276596, 2.155408, 0.730430, 1.596575, 2.504169, 2.382555},+{0, 1.661720, 0.730430, 0.603805, 0.454813, 0.162205, 1.129925},+{0, 0.602603, 1.596575, 0.454813, 0.558528, 0.796813, 0.290137},+{0, 2.468779, 2.504169, 0.162205, 0.796813, 0.530589, 2.073034},+{0, 2.554925, 2.382555, 1.129925, 0.290137, 2.073034, 0.798318}};+static float dm_17_10[7][7]={{0,0,0,0,0,0,0},+{0, 1.832394, 3.307697, 1.711062, 0.587652, 2.500571, 2.542166},+{0, 3.307697, 1.983636, 0.677419, 1.738092, 2.497012, 2.437609},+{0, 1.711062, 0.677419, 0.494725, 0.489828, 0.154804, 1.109600},+{0, 0.587652, 1.738092, 0.489828, 0.434240, 0.948956, 0.303653},+{0, 2.500571, 2.497012, 0.154804, 0.948956, 0.429058, 2.071173},+{0, 2.542166, 2.437609, 1.109600, 0.303653, 2.071173, 0.671361}};+static float dm_17_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.633896, 3.402351, 1.834789, 0.578697, 2.521230, 2.483018},+{0, 3.402351, 1.765915, 0.619865, 1.929028, 2.436812, 2.470046},+{0, 1.834789, 0.619865, 0.383602, 0.561116, 0.161953, 1.095287},+{0, 0.578697, 1.929028, 0.561116, 0.306100, 1.098171, 0.336383},+{0, 2.521230, 2.436812, 0.161953, 1.098171, 0.313977, 2.003038},+{0, 2.483018, 2.470046, 1.095287, 0.336383, 2.003038, 0.532942}};+static float dm_17_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.595425, 3.398979, 1.849409, 0.570570, 2.521120, 2.468389},+{0, 3.398979, 1.722025, 0.598918, 1.955315, 2.423195, 2.464611},+{0, 1.849409, 0.598918, 0.364362, 0.591967, 0.170305, 1.116927},+{0, 0.570570, 1.955315, 0.591967, 0.283012, 1.131490, 0.342010},+{0, 2.521120, 2.423195, 0.170305, 1.131490, 0.296061, 2.010796},+{0, 2.468389, 2.464611, 1.116927, 0.342010, 2.010796, 0.511111}};+static float dm_17_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.549012, 3.376494, 1.861681, 0.554571, 2.504364, 2.452632},+{0, 3.376494, 1.665273, 0.557068, 1.995296, 2.410242, 2.446184},+{0, 1.861681, 0.557068, 0.344309, 0.638901, 0.190280, 1.155475},+{0, 0.554571, 1.995296, 0.638901, 0.253950, 1.182863, 0.350164},+{0, 2.504364, 2.410242, 0.190280, 1.182863, 0.281259, 2.030459},+{0, 2.452632, 2.446184, 1.155475, 0.350164, 2.030459, 0.492848}};+static float dm_17_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.495463, 3.333516, 1.880225, 0.561395, 2.499855, 2.437629},+{0, 3.333516, 1.603946, 0.541227, 2.013724, 2.402244, 2.432190},+{0, 1.880225, 0.541227, 0.328083, 0.699849, 0.185966, 1.189426},+{0, 0.561395, 2.013724, 0.699849, 0.236830, 1.224252, 0.355651},+{0, 2.499855, 2.402244, 0.185966, 1.224252, 0.250988, 2.050938},+{0, 2.437629, 2.432190, 1.189426, 0.355651, 2.050938, 0.468514}};+static float dm_17_15[7][7]={{0,0,0,0,0,0,0},+{0, 1.445032, 3.277640, 1.899860, 0.579524, 2.495022, 2.453726},+{0, 3.277640, 1.540316, 0.514869, 2.009604, 2.432139, 2.400556},+{0, 1.899860, 0.514869, 0.290900, 0.783431, 0.190682, 1.228429},+{0, 0.579524, 2.009604, 0.783431, 0.228588, 1.227334, 0.350982},+{0, 2.495022, 2.432139, 0.190682, 1.227334, 0.254986, 2.050370},+{0, 2.453726, 2.400556, 1.228429, 0.350982, 2.050370, 0.451843}};+static float dm_17_16[7][7]={{0,0,0,0,0,0,0},+{0, 1.488960, 3.203613, 1.823525, 0.490317, 2.511323, 2.529750},+{0, 3.203613, 1.582014, 0.402531, 1.848617, 2.505082, 2.396065},+{0, 1.823525, 0.402531, 0.270031, 0.719134, 0.275540, 1.315131},+{0, 0.490317, 1.848617, 0.719134, 0.249862, 1.211044, 0.369940},+{0, 2.511323, 2.505082, 0.275540, 1.211044, 0.401915, 2.139891},+{0, 2.529750, 2.396065, 1.315131, 0.369940, 2.139891, 0.524210}};+static float dm_18_5[7][7]={{0,0,0,0,0,0,0},+{0, 1.959599, 3.270973, 1.671129, 0.574402, 2.470822, 2.567678},+{0, 3.270973, 2.124333, 0.699437, 1.586377, 2.503971, 2.367755},+{0, 1.671129, 0.699437, 0.602529, 0.514746, 0.131217, 1.191973},+{0, 0.574402, 1.586377, 0.514746, 0.543897, 0.783468, 0.266230},+{0, 2.470822, 2.503971, 0.131217, 0.783468, 0.523535, 2.125332},+{0, 2.567678, 2.367755, 1.191973, 0.266230, 2.125332, 0.795089}};+static float dm_18_6[7][7]={{0,0,0,0,0,0,0},+{0, 1.959599, 3.270973, 1.671129, 0.574402, 2.470822, 2.567678},+{0, 3.270973, 2.124333, 0.699437, 1.586377, 2.503971, 2.367755},+{0, 1.671129, 0.699437, 0.602529, 0.514746, 0.131217, 1.191973},+{0, 0.574402, 1.586377, 0.514746, 0.543897, 0.783468, 0.266230},+{0, 2.470822, 2.503971, 0.131217, 0.783468, 0.523535, 2.125332},+{0, 2.567678, 2.367755, 1.191973, 0.266230, 2.125332, 0.795089}};+static float dm_18_7[7][7]={{0,0,0,0,0,0,0},+{0, 1.959107, 3.270822, 1.671269, 0.574356, 2.470852, 2.567602},+{0, 3.270822, 2.123822, 0.699405, 1.586546, 2.503884, 2.367804},+{0, 1.671269, 0.699405, 0.602271, 0.515123, 0.131315, 1.192250},+{0, 0.574356, 1.586546, 0.515123, 0.543584, 0.783791, 0.266309},+{0, 2.470852, 2.503884, 0.131315, 0.783791, 0.523221, 2.125324},+{0, 2.567602, 2.367804, 1.192250, 0.266309, 2.125324, 0.794693}};+static float dm_18_8[7][7]={{0,0,0,0,0,0,0},+{0, 1.954893, 3.267998, 1.671033, 0.573675, 2.471278, 2.567651},+{0, 3.267998, 2.119451, 0.698449, 1.587072, 2.503825, 2.367971},+{0, 1.671033, 0.698449, 0.600163, 0.516924, 0.131274, 1.194926},+{0, 0.573675, 1.587072, 0.516924, 0.541618, 0.787988, 0.266654},+{0, 2.471278, 2.503825, 0.131274, 0.787988, 0.520857, 2.128706},+{0, 2.567651, 2.367971, 1.194926, 0.266654, 2.128706, 0.792170}};+static float dm_18_9[7][7]={{0,0,0,0,0,0,0},+{0, 1.945124, 3.264181, 1.671424, 0.571213, 2.472533, 2.567351},+{0, 3.264181, 2.109123, 0.695302, 1.589162, 2.502780, 2.369180},+{0, 1.671424, 0.695302, 0.595101, 0.519845, 0.132914, 1.201167},+{0, 0.571213, 1.589162, 0.519845, 0.536309, 0.796405, 0.268040},+{0, 2.472533, 2.502780, 0.132914, 0.796405, 0.515207, 2.135443},+{0, 2.567351, 2.369180, 1.201167, 0.268040, 2.135443, 0.785257}};+static float dm_18_10[7][7]={{0,0,0,0,0,0,0},+{0, 1.778806, 3.290372, 1.729008, 0.558489, 2.496256, 2.542594},+{0, 3.290372, 1.919078, 0.640136, 1.742877, 2.490111, 2.425930},+{0, 1.729008, 0.640136, 0.481526, 0.559858, 0.122004, 1.188502},+{0, 0.558489, 1.742877, 0.559858, 0.408793, 0.965121, 0.290692},+{0, 2.496256, 2.490111, 0.122004, 0.965121, 0.406294, 2.135398},+{0, 2.542594, 2.425930, 1.188502, 0.290692, 2.135398, 0.650811}};+static float dm_18_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.541260, 3.359887, 1.863305, 0.552149, 2.512117, 2.465080},+{0, 3.359887, 1.659552, 0.577262, 1.954784, 2.419679, 2.467978},+{0, 1.863305, 0.577262, 0.355424, 0.658994, 0.133093, 1.173777},+{0, 0.552149, 1.954784, 0.658994, 0.268144, 1.152204, 0.340224},+{0, 2.512117, 2.419679, 0.133093, 1.152204, 0.278844, 2.069528},+{0, 2.465080, 2.467978, 1.173777, 0.340224, 2.069528, 0.496656}};+static float dm_18_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.515109, 3.355111, 1.873865, 0.547484, 2.509063, 2.454676},+{0, 3.355111, 1.629923, 0.562408, 1.973041, 2.410124, 2.462343},+{0, 1.873865, 0.562408, 0.343602, 0.682667, 0.137341, 1.188539},+{0, 0.547484, 1.973041, 0.682667, 0.253609, 1.175520, 0.346154},+{0, 2.509063, 2.410124, 0.137341, 1.175520, 0.268542, 2.074538},+{0, 2.454676, 2.462343, 1.188539, 0.346154, 2.074538, 0.483464}};+static float dm_18_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.473845, 3.334992, 1.883878, 0.535323, 2.497538, 2.439103},+{0, 3.334992, 1.582030, 0.528874, 2.002078, 2.397872, 2.448436},+{0, 1.883878, 0.528874, 0.327587, 0.725281, 0.148692, 1.223566},+{0, 0.535323, 2.002078, 0.725281, 0.230794, 1.216739, 0.355996},+{0, 2.497538, 2.397872, 0.148692, 1.216739, 0.256653, 2.092929},+{0, 2.439103, 2.448436, 1.223566, 0.355996, 2.092929, 0.466494}};+static float dm_18_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.438699, 3.305116, 1.892865, 0.534599, 2.498865, 2.427961},+{0, 3.305116, 1.541486, 0.516396, 2.013794, 2.391791, 2.443225},+{0, 1.892865, 0.516396, 0.314606, 0.768388, 0.147398, 1.244406},+{0, 0.534599, 2.013794, 0.768388, 0.219136, 1.239877, 0.363050},+{0, 2.498865, 2.391791, 0.147398, 1.239877, 0.245018, 2.106483},+{0, 2.427961, 2.443225, 1.244406, 0.363050, 2.106483, 0.452624}};+static float dm_18_15[7][7]={{0,0,0,0,0,0,0},+{0, 1.402188, 3.243491, 1.873197, 0.523749, 2.513206, 2.440632},+{0, 3.243491, 1.493880, 0.479570, 2.003177, 2.410569, 2.437229},+{0, 1.873197, 0.479570, 0.286984, 0.854376, 0.156044, 1.259959},+{0, 0.523749, 2.003177, 0.854376, 0.211875, 1.261759, 0.358950},+{0, 2.513206, 2.410569, 0.156044, 1.261759, 0.268410, 2.128211},+{0, 2.440632, 2.437229, 1.259959, 0.358950, 2.128211, 0.448424}};+static float dm_18_16[7][7]={{0,0,0,0,0,0,0},+{0, 1.399936, 3.187488, 1.813113, 0.458372, 2.536421, 2.523106},+{0, 3.187488, 1.481063, 0.386274, 1.879206, 2.472031, 2.470590},+{0, 1.813113, 0.386274, 0.260196, 0.908918, 0.241168, 1.252977},+{0, 0.458372, 1.879206, 0.908918, 0.212976, 1.264362, 0.319339},+{0, 2.536421, 2.472031, 0.241168, 1.264362, 0.364359, 2.184745},+{0, 2.523106, 2.470590, 1.252977, 0.319339, 2.184745, 0.485249}};+static float dm_18_17[7][7]={{0,0,0,0,0,0,0},+{0, 1.267458, 3.104292, 1.954389, 0.508102, 2.474593, 2.482510},+{0, 3.104292, 1.332773, 0.384678, 1.918735, 2.426904, 2.409497},+{0, 1.954389, 0.384678, 0.231292, 1.095239, 0.222912, 1.303908},+{0, 0.508102, 1.918735, 1.095239, 0.194026, 1.349575, 0.325298},+{0, 2.474593, 2.426904, 0.222912, 1.349575, 0.302607, 2.167885},+{0, 2.482510, 2.409497, 1.303908, 0.325298, 2.167885, 0.414809}};+static float dm_19_5[7][7]={{0,0,0,0,0,0,0},+{0, 1.925029, 3.259785, 1.678082, 0.532879, 2.480385, 2.567162},+{0, 3.259785, 2.081752, 0.661029, 1.587558, 2.507624, 2.352855},+{0, 1.678082, 0.661029, 0.587688, 0.564095, 0.115803, 1.245217},+{0, 0.532879, 1.587558, 0.564095, 0.523708, 0.804297, 0.259865},+{0, 2.480385, 2.507624, 0.115803, 0.804297, 0.509191, 2.180337},+{0, 2.567162, 2.352855, 1.245217, 0.259865, 2.180337, 0.778683}};+static float dm_19_6[7][7]={{0,0,0,0,0,0,0},+{0, 1.925029, 3.259785, 1.678082, 0.532879, 2.480385, 2.567162},+{0, 3.259785, 2.081752, 0.661029, 1.587558, 2.507624, 2.352855},+{0, 1.678082, 0.661029, 0.587688, 0.564095, 0.115803, 1.245217},+{0, 0.532879, 1.587558, 0.564095, 0.523708, 0.804297, 0.259865},+{0, 2.480385, 2.507624, 0.115803, 0.804297, 0.509191, 2.180337},+{0, 2.567162, 2.352855, 1.245217, 0.259865, 2.180337, 0.778683}};+static float dm_19_7[7][7]={{0,0,0,0,0,0,0},+{0, 1.924817, 3.259699, 1.678128, 0.532863, 2.480398, 2.567133},+{0, 3.259699, 2.081532, 0.661015, 1.587619, 2.507590, 2.352872},+{0, 1.678128, 0.661015, 0.587581, 0.564243, 0.115852, 1.245339},+{0, 0.532863, 1.587619, 0.564243, 0.523585, 0.804442, 0.259908},+{0, 2.480398, 2.507590, 0.115852, 0.804442, 0.509065, 2.180349},+{0, 2.567133, 2.352872, 1.245339, 0.259908, 2.180349, 0.778524}};+static float dm_19_8[7][7]={{0,0,0,0,0,0,0},+{0, 1.921707, 3.257254, 1.677579, 0.532391, 2.480555, 2.567179},+{0, 3.257254, 2.078298, 0.660245, 1.587790, 2.507604, 2.352655},+{0, 1.677579, 0.660245, 0.586053, 0.565436, 0.115818, 1.247825},+{0, 0.532391, 1.587790, 0.565436, 0.522217, 0.807816, 0.260351},+{0, 2.480555, 2.507604, 0.115818, 0.807816, 0.507451, 2.183255},+{0, 2.567179, 2.352655, 1.247825, 0.260351, 2.183255, 0.776767}};+static float dm_19_9[7][7]={{0,0,0,0,0,0,0},+{0, 1.914948, 3.253973, 1.677337, 0.531084, 2.481010, 2.566882},+{0, 3.253973, 2.071131, 0.658362, 1.589059, 2.507048, 2.352997},+{0, 1.677337, 0.658362, 0.582634, 0.567513, 0.117022, 1.252162},+{0, 0.531084, 1.589059, 0.567513, 0.518726, 0.814061, 0.261409},+{0, 2.481010, 2.507048, 0.117022, 0.814061, 0.503793, 2.188359},+{0, 2.566882, 2.352997, 1.252162, 0.261409, 2.188359, 0.772214}};+static float dm_19_10[7][7]={{0,0,0,0,0,0,0},+{0, 1.742218, 3.274206, 1.736365, 0.520548, 2.506409, 2.538636},+{0, 3.274206, 1.874376, 0.601999, 1.751372, 2.493109, 2.410477},+{0, 1.736365, 0.601999, 0.469932, 0.605555, 0.101804, 1.237622},+{0, 0.520548, 1.751372, 0.605555, 0.394004, 0.990584, 0.288953},+{0, 2.506409, 2.493109, 0.101804, 0.990584, 0.393873, 2.187079},+{0, 2.538636, 2.410477, 1.237622, 0.288953, 2.187079, 0.636158}};+static float dm_19_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.468048, 3.334714, 1.879583, 0.513847, 2.525290, 2.448642},+{0, 3.334714, 1.575000, 0.532017, 1.991892, 2.413770, 2.459092},+{0, 1.879583, 0.532017, 0.330291, 0.714265, 0.121153, 1.217842},+{0, 0.513847, 1.991892, 0.714265, 0.242569, 1.209724, 0.357392},+{0, 2.525290, 2.413770, 0.121153, 1.209724, 0.254157, 2.113204},+{0, 2.448642, 2.459092, 1.217842, 0.357392, 2.113204, 0.465079}};+static float dm_19_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.447264, 3.331175, 1.887623, 0.510032, 2.522588, 2.440064},+{0, 3.331175, 1.551640, 0.520175, 2.006256, 2.406278, 2.453450},+{0, 1.887623, 0.520175, 0.321641, 0.733595, 0.124449, 1.227696},+{0, 0.510032, 2.006256, 0.733595, 0.232046, 1.228902, 0.363719},+{0, 2.522588, 2.406278, 0.124449, 1.228902, 0.246735, 2.116614},+{0, 2.440064, 2.453450, 1.227696, 0.363719, 2.116614, 0.455445}};+static float dm_19_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.413676, 3.312147, 1.892690, 0.497363, 2.513815, 2.427618},+{0, 3.312147, 1.512635, 0.491529, 2.029384, 2.398107, 2.440346},+{0, 1.892690, 0.491529, 0.309708, 0.770725, 0.131677, 1.255730},+{0, 0.497363, 2.029384, 0.770725, 0.215276, 1.262537, 0.375238},+{0, 2.513815, 2.398107, 0.131677, 1.262537, 0.238420, 2.134600},+{0, 2.427618, 2.440346, 1.255730, 0.375238, 2.134600, 0.443272}};+static float dm_19_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.390424, 3.289395, 1.895911, 0.494394, 2.515601, 2.419213},+{0, 3.289395, 1.485413, 0.482937, 2.038817, 2.393102, 2.437050},+{0, 1.895911, 0.482937, 0.301201, 0.802783, 0.131369, 1.267332},+{0, 0.494394, 2.038817, 0.802783, 0.208219, 1.278597, 0.381488},+{0, 2.515601, 2.393102, 0.131369, 1.278597, 0.233137, 2.145289},+{0, 2.419213, 2.437050, 1.267332, 0.381488, 2.145289, 0.435049}};+static float dm_19_15[7][7]={{0,0,0,0,0,0,0},+{0, 1.359065, 3.252756, 1.879860, 0.477404, 2.530994, 2.422584},+{0, 3.252756, 1.444344, 0.446651, 2.034691, 2.393761, 2.436293},+{0, 1.879860, 0.446651, 0.279248, 0.878068, 0.136700, 1.277241},+{0, 0.477404, 2.034691, 0.878068, 0.203105, 1.302254, 0.369173},+{0, 2.530994, 2.393761, 0.136700, 1.302254, 0.254187, 2.176724},+{0, 2.422584, 2.436293, 1.277241, 0.369173, 2.176724, 0.429742}};+static float dm_19_16[7][7]={{0,0,0,0,0,0,0},+{0, 1.319235, 3.187463, 1.883259, 0.425750, 2.549595, 2.483464},+{0, 3.187463, 1.390041, 0.356901, 1.935186, 2.431514, 2.438827},+{0, 1.883259, 0.356901, 0.250462, 1.025379, 0.218729, 1.267437},+{0, 0.425750, 1.935186, 1.025379, 0.196407, 1.314921, 0.319083},+{0, 2.549595, 2.431514, 0.218729, 1.314921, 0.318075, 2.206259},+{0, 2.483464, 2.438827, 1.267437, 0.319083, 2.206259, 0.438250}};+static float dm_19_17[7][7]={{0,0,0,0,0,0,0},+{0, 1.160111, 3.036527, 2.090520, 0.506996, 2.523007, 2.425038},+{0, 3.036527, 1.210398, 0.370582, 1.975521, 2.395384, 2.342602},+{0, 2.090520, 0.370582, 0.208600, 1.267580, 0.187575, 1.340450},+{0, 0.506996, 1.975521, 1.267580, 0.167525, 1.417493, 0.331364},+{0, 2.523007, 2.395384, 0.187575, 1.417493, 0.245059, 2.119651},+{0, 2.425038, 2.342602, 1.340450, 0.331364, 2.119651, 0.347729}};+static float dm_19_18[7][7]={{0,0,0,0,0,0,0},+{0, 1.088965, 3.033821, 2.120758, 0.473214, 2.457352, 2.432026},+{0, 3.033821, 1.133849, 0.379829, 2.009372, 2.419403, 2.321236},+{0, 2.120758, 0.379829, 0.179593, 1.357010, 0.233102, 1.418578},+{0, 0.473214, 2.009372, 1.357010, 0.153161, 1.425354, 0.285522},+{0, 2.457352, 2.419403, 0.233102, 1.425354, 0.262864, 2.054949},+{0, 2.432026, 2.321236, 1.418578, 0.285522, 2.054949, 0.338514}};+static float dm_20_5[7][7]={{0,0,0,0,0,0,0},+{0, 1.897075, 3.279011, 1.691793, 0.504730, 2.480118, 2.562844},+{0, 3.279011, 2.039856, 0.633859, 1.632167, 2.502239, 2.351187},+{0, 1.691793, 0.633859, 0.568358, 0.603584, 0.107146, 1.236087},+{0, 0.504730, 1.632167, 0.603584, 0.501897, 0.828959, 0.259130},+{0, 2.480118, 2.502239, 0.107146, 0.828959, 0.486634, 2.206702},+{0, 2.562844, 2.351187, 1.236087, 0.259130, 2.206702, 0.747065}};+static float dm_20_6[7][7]={{0,0,0,0,0,0,0},+{0, 1.897075, 3.279011, 1.691793, 0.504730, 2.480118, 2.562844},+{0, 3.279011, 2.039856, 0.633859, 1.632167, 2.502239, 2.351187},+{0, 1.691793, 0.633859, 0.568358, 0.603584, 0.107146, 1.236087},+{0, 0.504730, 1.632167, 0.603584, 0.501897, 0.828959, 0.259130},+{0, 2.480118, 2.502239, 0.107146, 0.828959, 0.486634, 2.206702},+{0, 2.562844, 2.351187, 1.236087, 0.259130, 2.206702, 0.747065}};+static float dm_20_7[7][7]={{0,0,0,0,0,0,0},+{0, 1.896975, 3.278955, 1.691795, 0.504726, 2.480131, 2.562842},+{0, 3.278955, 2.039753, 0.633848, 1.632190, 2.502228, 2.351194},+{0, 1.691795, 0.633848, 0.568300, 0.603635, 0.107161, 1.236152},+{0, 0.504726, 1.632190, 0.603635, 0.501838, 0.829046, 0.259144},+{0, 2.480131, 2.502228, 0.107161, 0.829046, 0.486574, 2.206739},+{0, 2.562842, 2.351194, 1.236152, 0.259144, 2.206739, 0.746992}};+static float dm_20_8[7][7]={{0,0,0,0,0,0,0},+{0, 1.893588, 3.276862, 1.690784, 0.504129, 2.480570, 2.563086},+{0, 3.276862, 2.036224, 0.632813, 1.632784, 2.502765, 2.351393},+{0, 1.690784, 0.632813, 0.566635, 0.604567, 0.107215, 1.237196},+{0, 0.504129, 1.632784, 0.604567, 0.500459, 0.833358, 0.259465},+{0, 2.480570, 2.502765, 0.107215, 0.833358, 0.484631, 2.209749},+{0, 2.563086, 2.351393, 1.237196, 0.259465, 2.209749, 0.744986}};+static float dm_20_9[7][7]={{0,0,0,0,0,0,0},+{0, 1.884748, 3.272721, 1.689032, 0.502174, 2.481643, 2.563448},+{0, 3.272721, 2.026963, 0.630025, 1.634741, 2.503505, 2.351925},+{0, 1.689032, 0.630025, 0.562287, 0.606772, 0.108251, 1.240282},+{0, 0.502174, 1.634741, 0.606772, 0.496494, 0.843309, 0.260392},+{0, 2.481643, 2.503505, 0.108251, 0.843309, 0.479544, 2.217089},+{0, 2.563448, 2.351925, 1.240282, 0.260392, 2.217089, 0.739346}};+static float dm_20_10[7][7]={{0,0,0,0,0,0,0},+{0, 1.724070, 3.286052, 1.745294, 0.494028, 2.511104, 2.531181},+{0, 3.286052, 1.845625, 0.575819, 1.789622, 2.488166, 2.403681},+{0, 1.745294, 0.575819, 0.464041, 0.655968, 0.086096, 1.231891},+{0, 0.494028, 1.789622, 0.655968, 0.386445, 0.993640, 0.286030},+{0, 2.511104, 2.488166, 0.086096, 0.993640, 0.381186, 2.210917},+{0, 2.531181, 2.403681, 1.231891, 0.286030, 2.210917, 0.619655}};+static float dm_20_11[7][7]={{0,0,0,0,0,0,0},+{0, 1.366924, 3.326755, 1.917379, 0.486377, 2.535956, 2.402764},+{0, 3.326755, 1.458409, 0.487252, 2.081863, 2.377195, 2.464398},+{0, 1.917379, 0.487252, 0.291262, 0.818906, 0.121663, 1.238422},+{0, 0.486377, 2.081863, 0.818906, 0.204468, 1.272391, 0.381068},+{0, 2.535956, 2.377195, 0.121663, 1.272391, 0.212433, 2.115436},+{0, 2.402764, 2.464398, 1.238422, 0.381068, 2.115436, 0.410852}};+static float dm_20_12[7][7]={{0,0,0,0,0,0,0},+{0, 1.349682, 3.322530, 1.923718, 0.483384, 2.534184, 2.393804},+{0, 3.322530, 1.439522, 0.479792, 2.090923, 2.369673, 2.461525},+{0, 1.923718, 0.479792, 0.284782, 0.836368, 0.126042, 1.246251},+{0, 0.483384, 2.090923, 0.836368, 0.197208, 1.286660, 0.385916},+{0, 2.534184, 2.369673, 0.126042, 1.286660, 0.206645, 2.118761},+{0, 2.393804, 2.461525, 1.246251, 0.385916, 2.118761, 0.403098}};+static float dm_20_13[7][7]={{0,0,0,0,0,0,0},+{0, 1.325594, 3.311550, 1.928873, 0.475383, 2.528168, 2.382278},+{0, 3.311550, 1.412034, 0.461445, 2.106893, 2.361332, 2.453619},+{0, 1.928873, 0.461445, 0.277185, 0.862477, 0.132110, 1.265629},+{0, 0.475383, 2.106893, 0.862477, 0.186437, 1.309775, 0.393588},+{0, 2.528168, 2.361332, 0.132110, 1.309775, 0.200886, 2.128515},+{0, 2.382278, 2.453619, 1.265629, 0.393588, 2.128515, 0.394595}};+static float dm_20_14[7][7]={{0,0,0,0,0,0,0},+{0, 1.311939, 3.299898, 1.933137, 0.471935, 2.529169, 2.375251},+{0, 3.299898, 1.395992, 0.455706, 2.114821, 2.356211, 2.451006},+{0, 1.933137, 0.455706, 0.271715, 0.884807, 0.131733, 1.269681},+{0, 0.471935, 2.114821, 0.884807, 0.182317, 1.320966, 0.396050},+{0, 2.529169, 2.356211, 0.131733, 1.320966, 0.199041, 2.134307},+{0, 2.375251, 2.451006, 1.269681, 0.396050, 2.134307, 0.389641}};+static float dm_20_15[7][7]={{0,0,0,0,0,0,0},+{0, 1.290169, 3.289532, 1.928987, 0.454296, 2.557077, 2.372959},+{0, 3.289532, 1.366891, 0.412695, 2.119268, 2.344543, 2.452420},+{0, 1.928987, 0.412695, 0.254556, 0.948114, 0.109102, 1.276760},+{0, 0.454296, 2.119268, 0.948114, 0.179089, 1.351415, 0.361892},+{0, 2.557077, 2.344543, 0.109102, 1.351415, 0.225454, 2.170825},+{0, 2.372959, 2.452420, 1.276760, 0.361892, 2.170825, 0.384073}};+static float dm_20_16[7][7]={{0,0,0,0,0,0,0},+{0, 1.241983, 3.298278, 2.020828, 0.408475, 2.597074, 2.370026},+{0, 3.298278, 1.298912, 0.321238, 2.068440, 2.315534, 2.439604},+{0, 2.020828, 0.321238, 0.220983, 1.147124, 0.213801, 1.254817},+{0, 0.408475, 2.068440, 1.147124, 0.172898, 1.335235, 0.279635},+{0, 2.597074, 2.315534, 0.213801, 1.335235, 0.296732, 2.123562},+{0, 2.370026, 2.439604, 1.254817, 0.279635, 2.123562, 0.381151}};+static float dm_20_17[7][7]={{0,0,0,0,0,0,0},+{0, 1.031083, 3.146699, 2.295330, 0.511540, 2.584730, 2.277981},+{0, 3.146699, 1.064679, 0.357052, 2.105656, 2.264165, 2.292508},+{0, 2.295330, 0.357052, 0.171546, 1.497354, 0.225501, 1.336781},+{0, 0.511540, 2.105656, 1.497354, 0.136152, 1.441587, 0.273770},+{0, 2.584730, 2.264165, 0.225501, 1.441587, 0.196237, 1.955911},+{0, 2.277981, 2.292508, 1.336781, 0.273770, 1.955911, 0.267176}};+static float dm_20_18[7][7]={{0,0,0,0,0,0,0},+{0, 0.943522, 3.116469, 2.274659, 0.422065, 2.542425, 2.299795},+{0, 3.116469, 0.970661, 0.354446, 2.179069, 2.278761, 2.269135},+{0, 2.274659, 0.354446, 0.148767, 1.494225, 0.206332, 1.496611},+{0, 0.422065, 2.179069, 1.494225, 0.128695, 1.562489, 0.209998},+{0, 2.542425, 2.278761, 0.206332, 1.562489, 0.230554, 1.946200},+{0, 2.299795, 2.269135, 1.496611, 0.209998, 1.946200, 0.272444}};+static float dm_20_19[7][7]={{0,0,0,0,0,0,0},+{0, 0.900882, 2.994246, 2.284230, 0.220253, 2.658395, 2.356499},+{0, 2.994246, 0.929797, 0.286242, 2.159140, 2.277679, 2.304699},+{0, 2.284230, 0.286242, 0.130488, 1.356211, 0.237656, 1.714175},+{0, 0.220253, 2.159140, 1.356211, 0.130093, 1.740519, 0.194186},+{0, 2.658395, 2.277679, 0.237656, 1.740519, 0.250414, 1.898882},+{0, 2.356499, 2.304699, 1.714175, 0.194186, 1.898882, 0.292298}};+++float **get_ribosum(const char **Alseq, int n_seq, int length){+  int i, j,k;+  float ident=0;+  int pairnum=0;+  float minimum=1;+  float maximum=0.;+  int min;+  int max;+  float **ribo;++  ribo=(float **)vrna_alloc(7*sizeof(float *));+  for (i=0; i<7; i++) {+    ribo[i]=(float *)vrna_alloc(7*sizeof(float));+  }+  for(j=0; j<n_seq-1; j++)+    for(k=j+1; k<n_seq; k++) {+      ident=length-vrna_hamming_distance(Alseq[k],Alseq[j]);+      if ((ident/(length))<minimum) minimum=ident/(float)(length);+      if ((ident/(length))>maximum) maximum=ident/(float)(length);+    }+  /*+2.5 for ALWAYS round up*/+  minimum*=100;+  maximum*=100;+  minimum+=0.5;+  maximum+=0.5;+  if (n_seq==1 || minimum>100.45){+    for (i=0; i<7; i++)+      for (j=0; j<7;j++)+        ribo[i][j]= 0.;+    return ribo;+  }+  min=(int) minimum/5;+  max=(int) maximum/5;++  if (max<12) max=12;+  if (min<5) min=5;+  if (min>=max) min=max-1;+  switch (max) {+  case 12:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_12_11[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 13:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_13_12[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 14:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_14_13[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 15:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_15_14[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 16:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_14[i][j];+    break;+    case 15:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_16_15[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 17:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_14[i][j];+    break;+    case 15:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_15[i][j];+      break;+    case 16:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_17_16[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 18:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_14[i][j];+    break;+    case 15:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_15[i][j];+      break;+    case 16:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_16[i][j];+      break;+    case 17:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_18_17[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+   case 19:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_14[i][j];+      break;+    case 15:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_15[i][j];+      break;+    case 16:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_16[i][j];+      break;+    case 17:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_17[i][j];+      break;+    case 18:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_19_18[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  case 20:+    switch (min) {+    case 5:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_5[i][j];+      break;+    case 6:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_6[i][j];+      break;+    case 7:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_7[i][j];+      break;+    case 8:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_8[i][j];+      break;+    case 9:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_9[i][j];+      break;+    case 10:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_10[i][j];+      break;+    case 11:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_11[i][j];+      break;+    case 12:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_12[i][j];+      break;+    case 13:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_13[i][j];+      break;+    case 14:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_14[i][j];+    break;+    case 15:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_15[i][j];+      break;+    case 16:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_16[i][j];+      break;+    case 17:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_17[i][j];+      break;+    case 18:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_18[i][j];+      break;+    case 19:+      for (i=0; i<7; i++) for (j=0; j<7;j++) ribo[i][j]=dm_20_19[i][j];+      break;+    default:+      vrna_message_error("da hats was grobes im dmchoose\n");+    }+    break;+  default:+    vrna_message_error("da hats was grobes im dmchoose\n");+  }+  return ribo;+}++PUBLIC float **readribosum(char *name){++  float **dm;+  char *line;+  FILE *fp;+  int i=0;+  int who=0;+  float a,b,c,d,e,f;+  int translator[7]={0,5,1,2,3,6,4};++  fp=fopen(name,"r");+  dm=(float **)vrna_alloc(7*sizeof(float*));+  for (i=0; i<7;i++) {+    dm[i]=(float *)vrna_alloc(7*sizeof(float));+  }+  while(1) { /*bisma hoit fertisch san*/+    line=vrna_read_line(fp);+    if (*line=='#') continue;+    i=0;+    i=sscanf(line,"%f %f %f %f %f %f",&a,&b,&c,&d,&e,&f);+    if (i==0) break;+    dm[translator[++who]][translator[1]]=a;+    dm[translator[who]][translator[2]]=b;+    dm[translator[who]][translator[3]]=c;+    dm[translator[who]][translator[4]]=d;+    dm[translator[who]][translator[5]]=e;+    dm[translator[who]][translator[6]]=f;+    free(line);+    if (who==6) break;+  }+  fclose(fp);+  return dm;+}+
+ C/ViennaRNA/ribo.h view
@@ -0,0 +1,33 @@+#ifndef VIENNA_RNA_PACKAGE_RIBOSUM_H+#define VIENNA_RNA_PACKAGE_RIBOSUM_H++/**+ *  @file ribo.h+ *  @ingroup   file_utils+ *  @brief  Parse RiboSum Scoring Matrices for Covariance Scoring of Alignments+ */++/**+ *  @{+ *  @ingroup   file_utils+ */++/**+ *  @brief Retrieve a RiboSum Scoring Matrix for a given Alignment+ *  \ingroup consensus_fold+ * + */+float **get_ribosum(const char **Alseq,+                    int n_seq,+                    int length);++/**+ *  \brief Read a RiboSum or other user-defined Scoring Matrix and Store into global Memory+ * + */+float   **readribosum(char *name);++/**+ *  @}+ */+#endif
+ C/ViennaRNA/snofold.c view
@@ -0,0 +1,1103 @@+/*+                  minimum free energy+                  RNA secondary structure prediction++                  c Ivo Hofacker, Chrisoph Flamm+                  original implementation by+                  Walter Fontana++                  Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/structure_utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/snofold.h"+#include "ViennaRNA/loop_energies.h"++#ifdef __GNUC__+#define INLINE inline+#else+#define INLINE+#endif++#define PAREN++#define PUBLIC+#define PRIVATE static++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */++/*@unused@*/+PRIVATE void  get_arrays(unsigned int size);+/* PRIVATE int   stack_energy(int i, const char *string); */+PRIVATE void  make_ptypes(const short *S, const char *structure);+PRIVATE void encode_seq(const char *sequence);+PRIVATE void  backtrack(const char *sequence, int s);+PRIVATE int   fill_arrays(const char *sequence, const int max_asymm, const int threshloop,+                          const int min_s2, const int max_s2, const int half_stem, const int max_half_stem);+/*@unused@*/+++/* alifold */+PRIVATE void alisnoinitialize_fold(const int length);+PRIVATE void make_pscores(const short *const* S, const char *const* AS,int n_seq, const char *structure);+PRIVATE int   *pscore;  /* precomputed array of pair types */+PRIVATE short **Sali;+PRIVATE int alifill_arrays(const char **string, const int max_asymm, const int threshloop, +                           const int min_s2, const int max_s2, const int half_stem, +                           const int max_half_stem);+PRIVATE void aliget_arrays(unsigned int size);+PRIVATE short * aliencode_seq(const char *sequence);+PRIVATE int alibacktrack(const char **strings, int s);++#define UNIT 100+#define MINPSCORE -2 * UNIT+/* end alifold */++#define MAXSECTORS      500     /* dimension for a backtrack array */+#define LOCALITY        0.      /* locality parameter for base-pairs */++#define MIN2(A, B)      ((A) < (B) ? (A) : (B))+#define MAX2(A, B)      ((A) > (B) ? (A) : (B))+#define SAME_STRAND(I,J) (((I)>=cut_point)||((J)<cut_point))++PRIVATE vrna_param_t *P = NULL;++PRIVATE int *indx = NULL; /* index for moving in the triangle matrices c[] and fMl[]*/++PRIVATE int   *c = NULL;       /* energy array, given that i-j pair */+PRIVATE int   *cc = NULL;      /* linear array for calculating canonical structures */+PRIVATE int   *cc1 = NULL;     /*   "     "        */+PRIVATE int   *Fmi = NULL;     /* holds row i of fML (avoids jumps in memory) */+PRIVATE int   *DMLi = NULL;    /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */+PRIVATE int   *DMLi1 = NULL;   /*             MIN(fML[i+1,k]+fML[k+1,j])  */+PRIVATE int   *DMLi2 = NULL;   /*             MIN(fML[i+2,k]+fML[k+1,j])  */+PRIVATE char  *ptype = NULL;   /* precomputed array of pair types */+PRIVATE short *S = NULL, *S1 = NULL;+PRIVATE int    init_length=-1;+PRIVATE int    *mLoop = NULL; /*contains the minimum of c for a xy range*/+PRIVATE folden **foldlist = NULL;+PRIVATE folden **foldlist_XS = NULL;++PRIVATE int     *BP = NULL; /* contains the structure constrainsts: BP[i]+                        -1: | = base must be paired+                        -2: < = base must be paired with j<i+                        -3: > = base must be paired with j>i+                        -4: x = base must not pair+                        positive int: base is paired with int      */+++static sect sector[MAXSECTORS]; /* stack of partial structures for backtracking */++PRIVATE char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";+/* needed by cofold/eval */+/* PRIVATE int cut_in_loop(int i); */+/* PRIVATE int min_hairpin = TURN; */++/* some definitions to take circfold into account...        */+/* PRIVATE int   *fM2 = NULL;*/        /* fM2 = multiloop region with exactly two stems, extending to 3' end        */+PUBLIC        int   Fc, FcH, FcI, FcM; /* parts of the exterior loop energies                        */+/*--------------------------------------------------------------------------*/++void snoinitialize_fold(const int length)+{+  unsigned int n;+  if (length<1) vrna_message_error("snoinitialize_fold: argument must be greater 0");+  if (init_length>0) snofree_arrays(length);+  get_arrays((unsigned) length);+  init_length=length;+  for (n = 1; n <= (unsigned) length; n++)+    indx[n] = (n*(n-1)) >> 1;        /* n(n-1)/2 */++  snoupdate_fold_params();+}++PRIVATE void alisnoinitialize_fold(const int length)+{+  unsigned int n;+  if (length<1) vrna_message_error("snoinitialize_fold: argument must be greater 0");+  if (init_length>0) snofree_arrays(length);+  aliget_arrays((unsigned) length);+  make_pair_matrix();+  init_length=length;+  for (n = 1; n <= (unsigned) length; n++)+    indx[n] = (n*(n-1)) >> 1;        /* n(n-1)/2 */+  snoupdate_fold_params();+}  +++/*--------------------------------------------------------------------------*/++PRIVATE void get_arrays(unsigned int size)+{+  indx = (int *) vrna_alloc(sizeof(int)*(size+1));+  c     = (int *) vrna_alloc(sizeof(int)*((size*(size+1))/2+2));+  mLoop = (int *) vrna_alloc(sizeof(int)*((size*(size+1))/2+2));++  ptype = (char *) vrna_alloc(sizeof(char)*((size*(size+1))/2+2));+  cc    = (int *) vrna_alloc(sizeof(int)*(size+2));+  cc1   = (int *) vrna_alloc(sizeof(int)*(size+2));+  Fmi   = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi  = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi1  = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi2  = (int *) vrna_alloc(sizeof(int)*(size+1));+  if (base_pair) free(base_pair);+  base_pair = (vrna_bp_stack_t *) vrna_alloc(sizeof(vrna_bp_stack_t)*(1+size/2));+  /* extra array(s) for circfold() */+}++PRIVATE void aliget_arrays(unsigned int size)+{+  indx = (int *) vrna_alloc(sizeof(int)*(size+1));+  c     = (int *) vrna_alloc(sizeof(int)*((size*(size+1))/2+2));+  mLoop = (int *) vrna_alloc(sizeof(int)*((size*(size+1))/2+2));+  pscore = (int *) vrna_alloc(sizeof(int)*((size*(size+1))/2+2));+  ptype = (char *) vrna_alloc(sizeof(char)*((size*(size+1))/2+2));+  cc    = (int *) vrna_alloc(sizeof(int)*(size+2));+  cc1   = (int *) vrna_alloc(sizeof(int)*(size+2));+  Fmi   = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi  = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi1  = (int *) vrna_alloc(sizeof(int)*(size+1));+  DMLi2  = (int *) vrna_alloc(sizeof(int)*(size+1));+  if (base_pair) free(base_pair);+  base_pair = (vrna_bp_stack_t *) vrna_alloc(sizeof(vrna_bp_stack_t)*(1+size/2));+  /* extra array(s) for circfold() */+}+++++/*--------------------------------------------------------------------------*/+++void snofree_arrays(const int length)+{+  free(indx); free(c);free(cc); free(cc1);+  free(ptype);free(mLoop);+  int i;+  for(i=length;i>-1;i--){+    while(foldlist[i]!=NULL){+      folden *n = foldlist[i];+      foldlist[i] = foldlist[i]->next;+      free(n);+    }+    free(foldlist[i]);+  }+  free(foldlist);+  for(i=length;i>-1;i--){+    while(foldlist_XS[i]!=NULL){+      folden *n = foldlist_XS[i];+      foldlist_XS[i] = foldlist_XS[i]->next;+      free(n);+    }+    free(foldlist_XS[i]);+  }+  free(foldlist_XS);+  free(base_pair); base_pair=NULL; free(Fmi);+  free(DMLi); free(DMLi1);free(DMLi2);+  free(BP);+  init_length=0;+}++void alisnofree_arrays(const int length)+{+  free(indx); free(c);free(cc); free(cc1);+  free(ptype);free(mLoop);free(pscore);+  int i;+  for(i=length-1;i>-1;i--){+    while(foldlist[i]!=NULL){+      folden *n = foldlist[i];+      foldlist[i] = foldlist[i]->next;+      free(n);+    }+    free(foldlist[i]);+  }+  free(foldlist);+  free(base_pair); base_pair=NULL; free(Fmi);+  free(DMLi); free(DMLi1);free(DMLi2);+  free(BP);+  init_length=0;+}++/*--------------------------------------------------------------------------*/++void snoexport_fold_arrays(int **indx_p, int **mLoop_p, int **cLoop,  folden ***fold_p, folden ***fold_p_XS) {+  /* make the DP arrays available to routines such as subopt() */+  *indx_p = indx; *mLoop_p = mLoop;+  *cLoop = c; *fold_p = foldlist;*fold_p_XS=foldlist_XS;+}++/* void alisnoexport_fold_arrays(int **indx_p, int **mLoop_p, int **cLoop, folden ***fold_p, int **pscores) { */+/*   /\* make the DP arrays available to routines such as subopt() *\/ */+/*   *indx_p = indx; *mLoop_p = mLoop; */+/*   *cLoop = c; *fold_p = foldlist; */+/*   *pscores=pscore; */+/* } */++/*--------------------------------------------------------------------------*/+++++++++++int snofold(const char *string, char *structure, const int max_assym, const int threshloop, +              const int min_s2, const int max_s2, const int half_stem, const int max_half_stem) {+  int length, energy, bonus, bonus_cnt, s;+  +  /* Variable initialization */+  bonus = 0;+  bonus_cnt = 0;+  s     = 0;+  length = (int) strlen(string);+  +  S   = encode_sequence(string, 0);+  S1  = encode_sequence(string, 1);++  +  /* structure = (char *) vrna_alloc((unsigned) length+1); */+  +  if (length>init_length) snoinitialize_fold(length);+  else if (fabs(P->temperature - temperature)>1e-6) snoupdate_fold_params();++  ++  /* encode_seq(string); */+  BP  = (int *)vrna_alloc(sizeof(int)*(length+2));+  make_ptypes(S, structure);+  energy=fill_arrays(string, max_assym, threshloop, min_s2, max_s2, half_stem, max_half_stem);+  backtrack(string, s);++  free(structure);+  free(S); free(S1); /* free(BP); */+  return energy;+}++PRIVATE void make_pscores(const short *const* S, const char *const* AS,+                          int n_seq, const char *structure) {+  /* calculate co-variance bonus for each pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */+#define NONE -10000 /* score for forbidden pairs */+  int n,i,j,k,l,s,score;+  int dm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                       {0,0,2,2,1,2,2} /* CG */,+                {0,2,0,1,2,2,2} /* GC */,+                {0,2,1,0,2,1,2} /* GU */,+                {0,1,2,2,0,2,1} /* UG */,+                {0,2,2,1,2,0,2} /* AU */,+                {0,2,2,2,1,2,0} /* UA */};+  n=Sali[0][0];  /* length of seqs */+  for (i=1; i<n; i++) {+    for (j=i+1; (j<i+TURN+1) && (j<=n); j++)+      pscore[indx[j]+i] = NONE;+    for (j=i+TURN+1; j<=n; j++) {+      int pfreq[8]={0,0,0,0,0,0,0,0};+      for (s=0; s<n_seq; s++) {+        int type;+        if (Sali[s][i]==0 && Sali[s][j]==0) type = 7; /* gap-gap  */+        else {+          if ((AS[s][i] == '~')||(AS[s][j] == '~')) type = 7;+          else type = pair[Sali[s][i]][Sali[s][j]];+        }++        pfreq[type]++;+      }+      if (pfreq[0]*2>n_seq) { pscore[indx[j]+i] = NONE; continue;}+      for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+        for (l=k+1; l<=6; l++)+          /* scores for replacements between pairtypes    */+          /* consistent or compensatory mutations score 1 or 2  */+          score += pfreq[k]*pfreq[l]*dm[k][l];+      /* counter examples score -1, gap-gap scores -0.25   */+      pscore[indx[j]+i] = cv_fact *+        ((UNIT*score)/n_seq - nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));+    }+  }++  if (noLonelyPairs) /* remove unwanted pairs */+    for (k=1; k<n-TURN-1; k++)+      for (l=1; l<=2; l++) {+        int type,ntype=0,otype=0;+        i=k; j = i+TURN+l;+        type = pscore[indx[j]+i];+        while ((i>=1)&&(j<=n)) {+          if ((i>1)&&(j<n)) ntype = pscore[indx[j+1]+i-1];+          if ((otype<-4*UNIT)&&(ntype<-4*UNIT))  /* worse than 2 counterex */+            pscore[indx[j]+i] = NONE; /* i.j can only form isolated pairs */+          otype =  type;+          type  = ntype;+          i--; j++;+        }+      }+++  if (fold_constrained&&(structure!=NULL)) {+    int psij, hx, hx2, *stack, *stack2;+    stack = (int *) vrna_alloc(sizeof(int)*(n+1));+    stack2 = (int *) vrna_alloc(sizeof(int)*(n+1));++    for(hx=hx2=0, j=1; j<=n; j++) {+      switch (structure[j-1]) {+      case 'x': /* can't pair */+        for (l=1; l<j-TURN; l++) pscore[indx[j]+l] = NONE;+        for (l=j+TURN+1; l<=n; l++) pscore[indx[l]+j] = NONE;+        break;+      case '(':+        stack[hx++]=j;+        /* fallthrough */+      case '[':+        stack2[hx2++]=j;+        /* fallthrough */+      case '<': /* pairs upstream */+        for (l=1; l<j-TURN; l++) pscore[indx[j]+l] = NONE;+        break;+      case ']':+        if (hx2<=0) {+          vrna_message_error("unbalanced brackets in constraints\n%s", structure);+        }+        i = stack2[--hx2];+        pscore[indx[j]+i]=NONE;+        break;+      case ')':+        if (hx<=0) {+          vrna_message_error("unbalanced brackets in constraints\n%s", structure);+        }+        i = stack[--hx];+        psij = pscore[indx[j]+i]; /* store for later */+        for (k=j; k<=n; k++)+          for (l=i; l<=j; l++)+            pscore[indx[k]+l] = NONE;+        for (l=i; l<=j; l++)+          for (k=1; k<=i; k++)+            pscore[indx[l]+k] = NONE;+        for (k=i+1; k<j; k++)+          pscore[indx[k]+i] = pscore[indx[j]+k] = NONE;+        pscore[indx[j]+i] = (psij>0) ? psij : 0;+        /* fallthrough */+      case '>': /* pairs downstream */+        for (l=j+TURN+1; l<=n; l++) pscore[indx[l]+j] = NONE;+        break;+      }+    }+    if (hx!=0) {+      vrna_message_error("unbalanced brackets in constraint string\n%s", structure);+    }+    free(stack); free(stack2);+  }+}++float alisnofold(const char **strings, const int max_assym, const int threshloop, +              const int min_s2, const int max_s2, const int half_stem, const int max_half_stem) {+  int s,n_seq, length, energy;+  char * structure;+  length = (int) strlen(strings[0]);+  /* structure = (char *) vrna_alloc((unsigned) length+1); */+  structure = NULL;+  if (length>init_length) alisnoinitialize_fold(length);+  if (fabs(P->temperature - temperature)>1e-6) snoupdate_fold_params();+  for (s=0; strings[s]!=NULL; s++);+  n_seq = s;+  Sali = (short **) vrna_alloc(n_seq*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(strings[s]) != length) vrna_message_error("uneqal seqence lengths");+    Sali[s] = aliencode_seq(strings[s]);+  }+  make_pscores((const short **) Sali, (const char *const *) strings, n_seq, structure);+  energy=alifill_arrays(strings, max_assym, threshloop, min_s2, max_s2, half_stem, max_half_stem);+  alibacktrack((const char **)strings, 0);+  for (s=0; s<n_seq; s++) free(Sali[s]);+  free(Sali);+  /* free(structure); */+  /*  free(S)*/; free(S1); /* free(BP); */+  return (float) energy/100.;+}++PRIVATE int alifill_arrays(const char **strings, const int max_asymm, const int threshloop, +                           const int min_s2, const int max_s2, const int half_stem, +                           const int max_half_stem) {++  int   i, j, length, energy;+  /* int   decomp, new_fML; */+  int   *type, type_2;+  int   bonus,n_seq,s;++  +  for (n_seq=0; strings[n_seq]!=NULL; n_seq++);+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  length = strlen(strings[0]);+  bonus=0;+  /*   max_separation = (int) ((1.-LOCALITY)*(double)(length-2));*/ /* not in use */+  +    /* for (i=(j>TURN?(j-TURN):1); i<j; i++) { */+    /* } */+    for (i = (length)-TURN-1; i >= 1; i--) { /* i,j in [1..length] */+      for (j = i+TURN+1; j <= length; j++) {+        int p, q, ij,psc;+        ij = indx[j]+i;+        for (s=0; s<n_seq; s++) {+          type[s] = pair[Sali[s][i]][Sali[s][j]];+          if (type[s]==0) type[s]=7;+        }+        psc = pscore[indx[j]+i];+        if (psc>=MINPSCORE) {   /* we have a pair */+        int new_c=0, stackEnergy=INF; /* seems that new_c immer den minimum von cij enthaelt */+        /* hairpin ----------------------------------------------*/+        +        for (new_c=s=0; s<n_seq; s++)+          new_c += E_Hairpin(j-i-1,type[s],Sali[s][i+1],Sali[s][j-1],strings[s]+i-1,P);+        /*--------------------------------------------------------      +          check for elementary structures involving more than one+          closing pair (interior loop).+          --------------------------------------------------------*/      +        +        for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {+          int minq = j-i+p-MAXLOOP-2;+          if (minq<p+1+TURN) minq = p+1+TURN;+          for (q = minq; q < j; q++) {+            if (pscore[indx[q]+p]<MINPSCORE) continue;+            if(abs((p-i) - (j-q)) > max_asymm) continue;+            for (energy = s=0; s<n_seq; s++) {+              type_2 = pair[Sali[s][q]][Sali[s][p]]; /* q,p not p,q! */+              if (type_2 == 0) type_2 = 7;+              energy += E_IntLoop(p-i-1, j-q-1, type[s], type_2,+                                  Sali[s][i+1], Sali[s][j-1],+                                  Sali[s][p-1], Sali[s][q+1],P);+            }+            new_c = MIN2(energy+c[indx[q]+p], new_c);+            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */+            +          } /* end q-loop */+        } /* end p-loop */+        +        /* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */+        +        new_c = MIN2(new_c, cc1[j-1]+stackEnergy);+        cc[j] = new_c - psc; /* add covariance bonnus/penalty */+        c[ij]=cc[j];+        } /* end >> if (pair) << */+        else c[ij] = INF;+        /* done with c[i,j], now compute fML[i,j] */+        /* free ends ? -----------------------------------------*/+        +      }++    {+      int *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+    }+  }+  foldlist = (folden**) vrna_alloc((length)*sizeof(folden*));++  for(i=0; i< length; i++){+    foldlist[i]=(folden*) vrna_alloc(sizeof(folden));+    foldlist[i]->next=NULL;+    foldlist[i]->k=INF+1;+    foldlist[i]->energy=INF;++  }+  folden* head; /* we save the stem loop information in a list like structure */++  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */+    int max_k, min_k;+    max_k = MIN2(length-min_s2,i+max_half_stem+1);+    min_k = MAX2(i+half_stem+1, length-max_s2);+    for (j = i+TURN+1; j <= length; j++) {+      int ij,a,b;+      ij = indx[j]+i;+      for(a=0; a< MISMATCH ;a++){+        for(b=0; b< MISMATCH ; b++){+          mLoop[ij]=MIN2(mLoop[ij],  c[indx[j-a]+i+b]);++        }+      }+      if(mLoop[ij]>=n_seq*threshloop){+        mLoop[ij]=INF;        +      }+      else{+        if(j>=min_k-1 && j < max_k){ /* comment if out to recover the known behaviour */+          head = (folden*) vrna_alloc(sizeof(folden));+          head->k=j;+          head->energy=mLoop[ij];+          head->next=foldlist[i];+          foldlist[i] = head;++        }+      }+    }+    +  }+  free(type);+  return mLoop[indx[length]+1];/* mLoop;  */+}++PRIVATE int alibacktrack(const char **strings, int s) {++  /*------------------------------------------------------------------+    trace back through the "c", "f5" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This is fast, since only few structure elements are recalculated.+    ------------------------------------------------------------------*/++  /* normally s=0.+     If s>0 then s items have been already pushed onto the sector stack */+  int   i, j, length, energy;/* , new; */+  int   type_2;+  int   bonus,n_seq,*type;  int   b=0,cov_en = 0;++  length = strlen(strings[0]);+  for (n_seq=0; strings[n_seq]!=NULL; n_seq++);+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  if (s==0) {+    sector[++s].i = 1;+    sector[s].j = length;+    sector[s].ml = 2 ; +  }+  while (s>0) {+    int ml, ss, cij, traced, i1, j1, p, q;+    int canonical = 1;     /* (i,j) closes a canonical structure */+    i  = sector[s].i;+    j  = sector[s].j;+    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to+                              occur in the fML- (1) or in the f-array (0) */+    if (ml==2) {+      base_pair[++b].i = i;+      base_pair[b].j   = j;+      goto repeat1;+    }++    if (j < i+TURN+1) continue; /* no more pairs in this interval */+++  repeat1:++    /*----- begin of "repeat:" -----*/+    if (canonical)  cij = c[indx[j]+i];+    for (ss=0; ss<n_seq; ss++) {+      type[ss] = pair[Sali[ss][i]][Sali[ss][j]];+      if (type[ss]==0) type[ss] = 7;+    }+    bonus = 0;+    +    if (noLonelyPairs)+      if (cij == c[indx[j]+i]) {+        /* (i.j) closes canonical structures, thus+           (i+1.j-1) must be a pair                */+        for (ss=0; ss<n_seq; ss++) {+          type_2 = pair[Sali[ss][j-1]][Sali[ss][i+1]];  /* j,i not i,j */+          if (type_2==0) type_2 = 7;+          cij -= P->stack[type[ss]][type_2];+        }+        cij += pscore[indx[j]+i];+        base_pair[++b].i = i+1;+        base_pair[b].j   = j-1;+        cov_en += pscore[indx[j-1]+i+1];+        i++; j--;+        canonical=0;+        goto repeat1;+      }+    canonical = 1;+    cij += pscore[indx[j]+i];+    {int cc=0;+      for (ss=0; ss<n_seq; ss++)+        cc += E_Hairpin(j-i-1, type[ss], Sali[ss][i+1], Sali[ss][j-1], strings[ss]+i-1,P);+      if (cij == cc) /* found hairpin */+        continue;+    }+    for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1); p++) {+      int minq;+      minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+TURN) minq = p+1+TURN;+      for (q = j-1; q >= minq; q--) {+        for (ss=energy=0; ss<n_seq; ss++) {+          type_2 = pair[Sali[ss][q]][Sali[ss][p]];  /* q,p not p,q */+          if (type_2==0) type_2 = 7;+          energy += E_IntLoop(p-i-1, j-q-1, type[ss], type_2,+                               Sali[ss][i+1], Sali[ss][j-1],+                              Sali[ss][p-1], Sali[ss][q+1],P);+        }+        traced = (cij == energy+c[indx[q]+p]);+        if (traced) {+          base_pair[++b].i = p;+          base_pair[b].j   = q;+          cov_en += pscore[indx[q]+p];+          i = p, j = q;+          goto repeat1;+        }+      }+    }++    /* end of repeat: --------------------------------------------------*/++    /* (i.j) must close a multi-loop */+    /* tt = rtype[type]; */+/*     mm = bonus+P->MLclosing+P->MLintern[tt]; */+/*     d5 = P->dangle5[tt][S1[j-1]]; */+/*     d3 = P->dangle3[tt][S1[i+1]]; */+    i1 = i+1; j1 = j-1;+    sector[s+1].ml  = sector[s+2].ml = 1;+    +/*      if (k<=j-3-TURN) { /\\* found the decomposition *\\/ *\/ */+/*       sector[++s].i = i1; */+/*       sector[s].j   = k; */+/*       sector[++s].i = k+1; */+/*       sector[s].j   = j1; */+/*     } /\* else { *\/ */+/*       vrna_message_error("backtracking failed in repeat"); */+/*     } */+    +  }+  base_pair[0].i = b;    /* save the total number of base pairs */+  free(type);+  return cov_en;+}++PRIVATE int fill_arrays(const char *string, const int max_asymm, const int threshloop, +                        const int min_s2, const int max_s2, const int half_stem, const int max_half_stem) {++  int   i, j,  length, energy;+  /*   int   decomp;*/ /*, new_fML; */+  int   no_close, type, type_2;+  int   bonus;+  int min_c;+  +  min_c=INF;+  length = (int) strlen(string);+  bonus=0;+  /*   max_separation = (int) ((1.-LOCALITY)*(double)(length-2)); */ /* not in use */+++  ++  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */+    /* printf("i=%d\t",i);  */+    for (j = i+TURN+1; j <= length; j++) {+/*         printf("j=%d,",j); */+      int p, q, ij;+      ij = indx[j]+i;+      type = ptype[ij];+      bonus = 0;+      energy = INF;++      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;+      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;+      if ((BP[i]==-4)||(BP[j]==-4)) type=0;++      no_close = (((type==3)||(type==4))&&no_closingGU);++      /* if (j-i-1 > max_separation) type = 0; */ /* forces locality degree */++      if (type) {   /* we have a pair */+        int new_c=0, stackEnergy=INF; /* seems that new_c immer den minimum von cij enthaelt */+        /* hairpin ----------------------------------------------*/++        if (no_close) new_c = FORBIDDEN;+        else+          new_c = E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], string+i-1,P); /* computes hair pin structure for subsequence i...j */++        /*--------------------------------------------------------      +          check for elementary structures involving more than one+          closing pair (interior loop).+          --------------------------------------------------------*/      ++        for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {+          int minq = j-i+p-MAXLOOP-2;+          if (minq<p+1+TURN) minq = p+1+TURN;+          for (q = minq; q < j; q++) {+            +            if(abs((p-i) - (j-q)) > max_asymm) continue;+            type_2 = ptype[indx[q]+p];++            if (type_2==0) continue;+            type_2 = rtype[type_2];++            if (no_closingGU)+              if (no_close||(type_2==3)||(type_2==4))+                if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */++            energy = E_IntLoop(p-i-1, j-q-1, type, type_2,+                               S1[i+1], S1[j-1], S1[p-1], S1[q+1],P);+            new_c = MIN2(energy+c[indx[q]+p], new_c);+            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */++          } /* end q-loop */+        } /* end p-loop */+++++        /* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */+++        new_c = MIN2(new_c, cc1[j-1]+stackEnergy);+        cc[j] = new_c;+        c[ij] = new_c;+        /*         min_c=MIN2(min_c, c[ij]); */++      } /* end >> if (pair) << */++      else c[ij] = INF;+++      /* done with c[i,j], now compute fML[i,j] */+      /* free ends ? -----------------------------------------*/++    }++    {+      int *FF; /* rotate the auxilliary arrays */+      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;+      FF = cc1; cc1=cc; cc=FF;+      for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }+    }+  }+  foldlist = (folden**) vrna_alloc((length+1)*sizeof(folden*));+  foldlist_XS = (folden**) vrna_alloc((length+1)*sizeof(folden*));+  /* linked list initialization*/+  for(i=0; i<=length; i++){+    foldlist[i]=(folden*) vrna_alloc(sizeof(folden));+    foldlist[i]->next=NULL;+    foldlist[i]->k=INF+1;+    foldlist[i]->energy=INF;+    foldlist_XS[i]=(folden*) vrna_alloc(sizeof(folden));+    foldlist_XS[i]->next=NULL;+    foldlist_XS[i]->k=INF+1;+    foldlist_XS[i]->energy=INF;+  }+  folden* head; /* we save the stem loop information in a list like structure */+  folden* head_XS;+  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */+    int max_k, min_k;+    max_k = MIN2(length-min_s2,i+max_half_stem+1);+    min_k = MAX2(i+half_stem+1, length-max_s2);+++    for (j = i+TURN+1; j <= length; j++) {+        int ij,a,b;+              ij = indx[j]+i;+            for(a=0; a< MISMATCH ;a++){+          for(b=0; b< MISMATCH ; b++){+              mLoop[ij]=MIN2(mLoop[ij],  c[indx[j-a]+i+b]);+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j-2]+i]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j]+i+1]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j-1]+i+1]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j-2]+i+1]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j]+i+2]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j-1]+i+2]); */+            /* #mLoop[ij]=MIN2(mLoop[ij], c[indx[j-2]+i+2]); */+          }+        }+        min_c = MIN2(mLoop[ij] ,min_c);+        +        if(mLoop[ij]>=threshloop){+          mLoop[ij]=INF;        +        }+        else{+          if(j>=min_k-1 && j <= max_k){ /* comment if out to recover the known behaviour */+            head = (folden*) vrna_alloc(sizeof(folden));+            head->k=j;+            head->energy=mLoop[ij];+            head->next=foldlist[i];+            foldlist[i] = head;+            head_XS = (folden*) vrna_alloc(sizeof(folden));+            head_XS->k=i;+            head_XS->energy=mLoop[ij];+            head_XS->next=foldlist_XS[j];+            foldlist_XS[j] = head_XS;            +          }+        }+    }+    +  }+/*   int count=0; */+/*    for(i=0; i< length; i++){  */+/*      folden *temp;  */+/*      temp = foldlist[i];  */+/*      while(temp->next){  */+/*        count++; */+/*        printf("count %d: i%d j%d energy %d \n", count, i, temp->k, temp->energy);  */+/*        temp=temp->next;  */+/*      }      */+/*    }  */+/*    printf("Count %d \n", count); */+/*    count=0; */+/*    for(i=length-1; i>=0; i--){  */+/*      folden *temp;  */+/*      temp = foldlist_XS[i];  */+/*      while(temp->next){  */+/*        count++; */+/*        printf("count %d: i%d j%d energy %d \n", count, temp->k,i, temp->energy);  */+/*        temp=temp->next;  */+/*      }      */+/*    }  */+/*    printf("Count %d \n", count); */+/*    return mLoop[indx[length]+1]; */ /* mLoop; */+   return min_c;+  /* printf("\nmin_array = %d\n", min_c); */+  /* return f5[length]; */+}+++++PRIVATE void backtrack(const char *string, int s) {++  /*------------------------------------------------------------------+    trace back through the "c", "f5" and "fML" arrays to get the+    base pairing list. No search for equivalent structures is done.+    This is fast, since only few structure elements are recalculated.+    ------------------------------------------------------------------*/++  /* normally s=0.+     If s>0 then s items have been already pushed onto the sector stack */+  int   i, j, /*k,*/ length, energy, new;+  int   no_close, type, type_2;/* , tt; */+  int   bonus;+  int   b=0;++  length = strlen(string);+  if (s==0) {+    sector[++s].i = 1;+    sector[s].j = length;+    sector[s].ml = 2 ; +  }+  while (s>0) {+    int ml, cij, traced, i1, j1, /*d3, d5, mm,*/ p, q;+    int canonical = 1;     /* (i,j) closes a canonical structure */+    i  = sector[s].i;+    j  = sector[s].j;+    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to+                              occur in the fML- (1) or in the f-array (0) */+    if (ml==2) {+      base_pair[++b].i = i;+      base_pair[b].j   = j;+      goto repeat1;+    }++    if (j < i+TURN+1) continue; /* no more pairs in this interval */+++  repeat1:++    /*----- begin of "repeat:" -----*/+    if (canonical)  cij = c[indx[j]+i];+    type = ptype[indx[j]+i];+    bonus = 0;+    if (fold_constrained) {+      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;+      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;+    }+    if (noLonelyPairs)+      if (cij == c[indx[j]+i]) {+        /* (i.j) closes canonical structures, thus+           (i+1.j-1) must be a pair                */+        type_2 = ptype[indx[j-1]+i+1]; type_2 = rtype[type_2];+        cij -= P->stack[type][type_2] + bonus;+        base_pair[++b].i = i+1;+        base_pair[b].j   = j-1;+        i++; j--;+        canonical=0;+        goto repeat1;+      }+    canonical = 1;+    no_close = (((type==3)||(type==4))&&no_closingGU&&(bonus==0));+    if (no_close) {+      if (cij == FORBIDDEN) continue;+    } else+      if (cij == E_Hairpin(j-i-1, type, S1[i+1], S1[j-1],string+i-1,P)+bonus)+        continue;+    for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1); p++) {+      int minq;+      minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+TURN) minq = p+1+TURN;+      for (q = j-1; q >= minq; q--) {+        type_2 = ptype[indx[q]+p];+        if (type_2==0) continue;+        type_2 = rtype[type_2];+        if (no_closingGU)+          if (no_close||(type_2==3)||(type_2==4))+            if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */+        energy = E_IntLoop(p-i-1, j-q-1, type, type_2,+                           S1[i+1], S1[j-1], S1[p-1], S1[q+1],P);+        new = energy+c[indx[q]+p]+bonus;+        traced = (cij == new);+        if (traced) {+          base_pair[++b].i = p;+          base_pair[b].j   = q;+          i = p, j = q;+          goto repeat1;+        }+      }+    }++    /* end of repeat: --------------------------------------------------*/++    /* (i.j) must close a multi-loop */+/*     tt = rtype[type]; */+/*     mm = bonus+P->MLclosing+P->MLintern[tt]; */+/*     d5 = P->dangle5[tt][S1[j-1]]; */+/*     d3 = P->dangle3[tt][S1[i+1]]; */+    i1 = i+1; j1 = j-1;+    sector[s+1].ml  = sector[s+2].ml = 1;++/*      if (k<=j-3-TURN) { */ /* found the decomposition */+/*       sector[++s].i = i1; */+/*       sector[s].j   = k; */+/*       sector[++s].i = k+1; */+/*       sector[s].j   = j1; */+/*     } else { */+/*         vrna_message_error("backtracking failed in repeat"); */+/*     } */+/*  */+  }++  base_pair[0].i = b;    /* save the total number of base pairs */+}++char *snobacktrack_fold_from_pair(const char *sequence, int i, int j) {+  char *structure;+  sector[1].i  = i;+  sector[1].j  = j;+  sector[1].ml = 2;+  base_pair[0].i=0;+  encode_seq(sequence);+  backtrack(sequence, 1);+  structure = vrna_db_from_bp_stack(base_pair, strlen(sequence));+  free(S);free(S1);+  return structure;+}++char *alisnobacktrack_fold_from_pair(const char **strings, int i, int j, int *cov) {+  char *structure;+  int n_seq, s, length;+  length = (int) strlen(strings[0]);+  for (s=0; strings[s]!=NULL; s++);+  n_seq = s;+  sector[1].i  = i;+  sector[1].j  = j;+  sector[1].ml = 2;+  base_pair[0].i=0;+  /* encode_seq(sequence); */+  Sali = (short **) vrna_alloc(n_seq*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if (strlen(strings[s]) != length) vrna_message_error("uneqal seqence lengths");+    Sali[s] = aliencode_seq(strings[s]);+  }+  *cov=alibacktrack(strings, 1);+  structure = vrna_db_from_bp_stack(base_pair, length);+  free(S);free(S1);+  for (s=0; s<n_seq; s++) {+    free(Sali[s]);+  }+  free(Sali);+  return structure;+}++++/*---------------------------------------------------------------------------*/+++/*---------------------------------------------------------------------------*/+++/*--------------------------------------------------------------------------*/+++/*---------------------------------------------------------------------------*/+++PRIVATE void encode_seq(const char *sequence) {+  unsigned int i,l;++  l = strlen(sequence);+  S = (short *) vrna_alloc(sizeof(short)*(l+2));+  S1= (short *) vrna_alloc(sizeof(short)*(l+2));+  /* S1 exists only for the special X K and I bases and energy_set!=0 */+  S[0] = (short) l;++  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    S[i]= (short) encode_char(toupper(sequence[i-1]));+    S1[i] = alias[S[i]];   /* for mismatches of nostandard bases */+  }+  /* for circular folding add first base at position n+1 and last base at+        position 0 in S1        */+  S[l+1] = S[1]; S1[l+1]=S1[1]; S1[0] = S1[l];+}++PRIVATE short * aliencode_seq(const char *sequence) {+  unsigned int i,l;+  short *Stemp;+  l = strlen(sequence);+  Stemp = (short *) vrna_alloc(sizeof(short)*(l+2));+  Stemp[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    Stemp[i]= (short) encode_char(toupper(sequence[i-1]));++  /* for circular folding add first base at position n+1 */+  /* Stemp[l+1] = Stemp[1]; */++  return Stemp;+}++/*---------------------------------------------------------------------------*/++PUBLIC void snoupdate_fold_params(void)+{+  vrna_md_t md;+  if(P)+    free(P);+  set_model_details(&md);+  P = vrna_params(&md);+  make_pair_matrix();+  if (init_length < 0) init_length=0;+}++/*---------------------------------------------------------------------------*/++PRIVATE void make_ptypes(const short *S, const char *structure) {+  int n,i,j,k,l;++  n=S[0];+  for (k=1; k<n-TURN; k++)+    for (l=1; l<=2; l++) {+      int type,ntype=0,otype=0;+      i=k; j = i+TURN+l; if (j>n) continue;+      type = pair[S[i]][S[j]];+      while ((i>=1)&&(j<=n)) {+        if ((i>1)&&(j<n)) ntype = pair[S[i-1]][S[j+1]];+        if (noLonelyPairs && (!otype) && (!ntype))+          type = 0; /* i.j can only form isolated pairs */+        ptype[indx[j]+i] = (char) type;+        otype =  type;+        type  = ntype;+        i--; j++;+      }+    }++  if (fold_constrained&&(structure!=NULL)) {+    constrain_ptypes(structure, (unsigned int)n, ptype, BP, TURN, 0);+  }+}
+ C/ViennaRNA/snofold.h view
@@ -0,0 +1,58 @@+/* function from fold.c */+#ifndef VIENNA_RNA_PACKAGE_SNOFOLD_H+#define VIENNA_RNA_PACKAGE_SNOFOLD_H++#include <ViennaRNA/data_structures.h>++/* Normal fold */++/**+*** snofold is the stem folding array for RNAsnoop+**/+int  snofold( const char *sequence,+		char *structure,+                const int max_assym,+                const int threshold, +                const int min_s2,+                const int max_s2,+                const int half_stem,+                const int max_half_stem);+/**+*** Free arrays and structure related to snofold+**/++void   snofree_arrays(const int length);  /* free arrays for mfe folding */+void   snoinitialize_fold(int length);    /* allocate arrays for folding */+void   snoupdate_fold_params(void);       /* recalculate parameters */+int    snoloop_energy(short *ptable,+                      short *s,+                      short *s1,+                      int i);+void   snoexport_fold_arrays( int **indx_p,+                              int **mLoop_p,+                              int **cLoop,+                              folden ***fold_p,+                              folden ***fold_p_XS);+char * snobacktrack_fold_from_pair( const char *sequence,+                                    int i,+                                    int j);+/* alifold */+float alisnofold( const char **strings,+                  const int max_assym,+                  const int threshloop, +                  const int min_s2,+                  const int max_s2,+                  const int half_stem,+                  const int max_half_stem);+void  alisnofree_arrays(const int length);+char  *alisnobacktrack_fold_from_pair(const char **sequence,+                                      int i,+                                      int j,+                                      int *cov);+extern double cv_fact /* =1 */;+extern double nc_fact /* =1 */;++/* max number of mismatch >>>>>..((   )).>>>> */+#define MISMATCH 3++#endif
+ C/ViennaRNA/snoop.c view
@@ -0,0 +1,2621 @@+/*                +           compute the duplex structure of two RNA strands,+                allowing only inter-strand base pairs.+         see cofold() for computing hybrid structures without+                             restriction.++                             Ivo Hofacker+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/snofold.h"+#include "ViennaRNA/pair_mat.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/snoop.h"+#include "ViennaRNA/PS_dot.h"+/* #include "ViennaRNA/fold.h" */+#include "ViennaRNA/duplex.h"+#include "ViennaRNA/loop_energies.h"+++#define STACK_BULGE1  1   /* stacking energies for bulges of size 1 */+#define NEW_NINIO     1   /* new asymetry penalty */++++PRIVATE void  encode_seqs(const char *s1, const char *s2);+PRIVATE short *encode_seq(const char *seq);++PRIVATE void find_max_snoop(const char *s1, const char *s2, const int max, +                            const int alignment_length, const int* position, +                            const int delta, const int distance,  const int penalty, +                            const int threshloop, const int threshLE, const int threshRE, +                            const int threshDE, const int threshTE, const int threshSE, const int threshD,+                            const int half_stem, const int max_half_stem,  const int min_s2, +                            const int max_s2, const int min_s1, const int  max_s1, const int min_d1, const int min_d2, const char* name, const int fullStemEnergy);++PRIVATE void find_max_snoop_XS(const char *s1, const char *s2, const int **access_s1, const int max, +                               const int alignment_length, const int* position, const int *position_j,+                               const int delta, const int distance,  const int penalty, +                               const int threshloop, const int threshLE, const int threshRE, +                               const int threshDE, const int threshTE, const int threshSE, const int threshD,+                               const int half_stem, const int max_half_stem,  const int min_s2, +                               const int max_s2, const int min_s1, const int  max_s1, const int min_d1, const int min_d2, const char *name, const int fullStemEnergy);++++++PRIVATE char * alisnoop_backtrack(int i, int j, const char ** s2, +                                  int* Duplex_El, int* Duplex_Er, int* Loop_E, int *Loop_D, int *u, +                                  int *pscd, int *psct, int *pscg,+                                  const int penalty, const int threshloop, +                                  const int threshLE, const int threshRE, const int threshDE, const int threshD,+                                  const int half_stem, const int max_half_stem, +                                  const int min_s2, const int max_s2, const int min_s1, +                                  const int max_s1, const int min_d1, const int min_d2,+                                  const short **S1, const short **S2);++   +PRIVATE char * snoop_backtrack(int i, int j, const char* s2, int* Duplex_El, int* Duplex_Er, int* Loop_E, int *Loop_D, int *u, +                               const int penalty, const int threshloop, const int threshLE, const int threshRE, const int threshDE, +                               const int threshD,+                               const int half_stem, const int max_half_stem, +                               const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2);++PRIVATE char * snoop_backtrack_XS(int i, int j, const char* s2, int* Duplex_El, int* Duplex_Er, int* Loop_E, int *Loop_D, int *u, +                               const int penalty, const int threshloop, const int threshLE, const int threshRE, const int threshDE, +                               const int threshD,+                               const int half_stem, const int max_half_stem, +                               const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2);+++++PRIVATE int compare(const void *sub1, const void *sub2);+PRIVATE int covscore(const int *types, int n_seq);+PRIVATE short * aliencode_seq(const char *sequence);++PUBLIC  int snoop_subopt_sorted=0; /* from subopt.c, default 0 */+++/*@unused@*/+++++#define MAXLOOP_L        3+#define MIN2(A, B)      ((A) < (B) ? (A) : (B))+#define MAX2(A, B)      ((A) > (B) ? (A) : (B))+#define ASS                1+PRIVATE vrna_param_t *P = NULL;++PRIVATE int   **c = NULL;      /* energy array, given that i-j pair */+PRIVATE int   **r = NULL;+PRIVATE int   **lc = NULL;      /* energy array, given that i-j pair */+PRIVATE int   **lr = NULL;+PRIVATE int   **c_fill = NULL;+PRIVATE int   **r_fill = NULL;+PRIVATE int   **lpair = NULL;+++PRIVATE short  *S1 = NULL, *SS1 = NULL, *S2 = NULL, *SS2 = NULL;+PRIVATE short *S1_fill = NULL, *SS1_fill = NULL, *S2_fill = NULL, *SS2_fill = NULL;+PRIVATE int   n1,n2;    /* sequence lengths */++extern int cut_point;++PRIVATE int delay_free=0;+/*--------------------------------------------------------------------------*/++snoopT alisnoopfold(const char **s1, const char **s2, +                    const int penalty, const int threshloop, +                    const int threshLE, const int threshRE, const int threshDE, const int threshD,+                    const int half_stem, const int max_half_stem, +                    const int min_s2, const int max_s2, const int min_s1, +                    const int max_s1, const int min_d1, const int min_d2) {+  +  int s,n_seq;+  int i, j, E, l1,Emin=INF, i_min=0, j_min=0;+  char *struc;+  snoopT mfe;+  int *indx;+  int *mLoop;+  int *cLoop;+  folden  **foldlist; folden **foldlist_XS;+  int Duplex_El, Duplex_Er,pscd,psct,pscg;+  int Loop_D;+  int u;+  int Loop_E;+  short **Sali1,**Sali2;+  int *type,*type2,*type3;+  vrna_md_t md;+  Duplex_El=0;Duplex_Er=0;Loop_E=0; Loop_D=0;pscd=0;psct=0;pscg=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS); +  n1 = (int) strlen(s1[0]);+  n2 = (int) strlen(s2[0]);+  +  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; s2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in aliduplexfold()\n");+  +  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  c = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  r = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=0; i<=n1; i++) {+          c[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        r[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                c[i][j]=INF;+                r[i][j]=INF;+        }+  }+  Sali1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  Sali2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if ((int)strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if ((int)strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    Sali1[s] = aliencode_seq(s1[s]);+    Sali2[s] = aliencode_seq(s2[s]);+  }+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  type2 = (int *) vrna_alloc(n_seq*sizeof(int));+  type3 = (int *) vrna_alloc(n_seq*sizeof(int));+  /*   encode_seqs(s1, s2); */+  for (i=6; i<=n1-5; i++) {+    int U; U=0;+    for (s=0; s<n_seq; s++) {+      U+=Sali1[s][i-2];+    }+    U = (U==(n_seq)*4?1:0);+    for (j=n2-min_d2; j>min_d1; j--) {+      int type4, k,l,psc,psc2,psc3;+      for (s=0; s<n_seq; s++) {+        type[s] = pair[Sali1[s][i]][Sali2[s][j]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      c[i][j] = (psc>=MINPSCORE) ? (n_seq*P->DuplexInit) : INF;+      if (psc<MINPSCORE) continue;+      if(/*  pair[Sali1[i+1]][Sali2[j-1]] &&  */+         U && j < max_s1 && j > min_s1 &&  +         j > n2 - max_s2 - max_half_stem && +         j < n2 -min_s2 -half_stem ) { /*constraint on s2 and i*/+        folden *temp;+        temp=foldlist[j+1];+        while(temp->next){+          int k = temp->k;+          for (s=0; s<n_seq; s++) {+            type2[s]= pair[Sali1[s][i-3]][Sali2[s][k+1]];+            type3[s]= pair[Sali1[s][i-4]][Sali2[s][k+1]];+          }+          psc2 = covscore(type2, n_seq);+          psc3 = covscore(type3, n_seq);+          if(psc2 > MINPSCORE){+            r[i][j]=MIN2(r[i][j],c[i-3][k+1]+temp->energy);+          }+          if(psc3 > MINPSCORE){+            r[i][j]=MIN2(r[i][j],c[i-4][k+1]+temp->energy);+          }+          temp=temp->next;+        }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      for (s=0; s<n_seq; s++) {+        c[i][j] += E_ExtLoop(type[s], Sali1[s][i-1],Sali2[s][j+1],P);+      }+      for (k=i-1; k>0 && (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2 ; l++) {+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS ) continue;+          for (E=s=0; s<n_seq; s++) { +            type4 = pair[Sali1[s][k]][Sali2[s][l]];+            if (type4==0) type4=7;+            E += E_IntLoop(i-k-1, l-j-1, type4, rtype[type[s]],+                           Sali1[s][k+1], Sali2[s][l-1], Sali1[s][i-1], Sali2[s][j+1],P);+          }+          c[i][j] = MIN2(c[i][j], c[k][l] + E);+          r[i][j] = MIN2(r[i][j], r[k][l] + E);+        }+      }+      c[i][j]-=psc;+      r[i][j]-=psc;+      E = r[i][j]; +      for (s=0; s<n_seq; s++) {+        E+= E_ExtLoop(rtype[type[s]], Sali2[s][j-1], Sali1[s][i+1], P);+        /**+        *** if (i<n1) E += P->dangle3[rtype[type[s]]][Sali1[s][i+1]];+        *** if (j>1)  E += P->dangle5[rtype[type[s]]][Sali2[s][j-1]];+        *** if (type[s]>2) E += P->TerminalAU;+        **/+      }+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      } +    }+  }+  if(Emin > 0){+          printf("no target found under the constraints chosen\n");+        for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+        free(c);+        free(r);+        for(s=0; s<n_seq;s++){+          free(Sali1[s]);+          free(Sali2[s]);+        }+        free(Sali1); free(Sali2);+        free(S2); free(SS1); free(SS2);free(type);free(type2);free(type3);+        mfe.energy=INF;+        mfe.structure=NULL;+        return mfe;+  }+  struc = alisnoop_backtrack(i_min, j_min,(const char**) s2, +                             &Duplex_El, &Duplex_Er, &Loop_E, +                             &Loop_D, &u, &pscd, &psct, &pscg,+                             penalty, threshloop, threshLE, +                             threshRE,threshDE, threshD,+                             half_stem, max_half_stem, min_s2, +                             max_s2, min_s1, max_s1, min_d1, +                             min_d2,(const short**) Sali1,(const short**) Sali2);+  /* if (i_min<n1-5) i_min++; */+  /* if (j_min>6 ) j_min--; */+  l1 = strchr(struc, '&')-struc;+  mfe.i = i_min-5;+  mfe.j = j_min-5;+  mfe.u = u -5;+  mfe.Duplex_Er = (float) Duplex_Er/100;+  mfe.Duplex_El = (float) Duplex_El/100;+  mfe.Loop_D = (float) Loop_D/100;+  mfe.Loop_E = (float) Loop_E/100;+  mfe.energy = (float) Emin/100 ;+  /* mfe.fullStemEnergy = (float) fullStemEnergy/100; */+  mfe.pscd = pscd;+  mfe.psct = psct;+  mfe.structure = struc;+  for(s=0; s<n_seq;s++){+    free(Sali1[s]);free(Sali2[s]);+  }+  free(Sali1);free(Sali2);free(type);free(type2);free(type3);++  if (!delay_free) {+    for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+    free(c);+    free(r);+    free(S2); free(SS1); free(SS2);+  }+  return mfe;+}++PUBLIC snoopT *alisnoop_subopt(const char **s1, const char **s2, int delta, int w, +                              const int penalty, const int threshloop, +                               const int threshLE, const int threshRE, const int threshDE, const int threshTE, const int threshSE, const int threshD,+                              const int distance, const int half_stem, const int max_half_stem,+                               const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2) {+++  short **Sali1, **Sali2;+  /* printf("%d %d\n", min_s2, max_s2); */+  int i,j,s,n_seq, n1, n2, E, n_subopt=0, n_max;+  char *struc;+  snoopT mfe;+  snoopT *subopt;+  int thresh;+  int *type;+  int Duplex_El, Duplex_Er, Loop_E,pscd,psct,pscg;+  int Loop_D;+  Duplex_El=0; Duplex_Er=0; Loop_E=0;Loop_D=0;pscd=0;psct=0;pscg=0;+  int u;+  u=0;+  n_max=16;+  subopt = (snoopT *) vrna_alloc(n_max*sizeof(snoopT));+  delay_free=1;+  mfe = alisnoopfold(s1, s2, penalty, threshloop, threshLE, threshRE, threshDE,threshD,+                  half_stem, max_half_stem,+                     min_s2, max_s2, min_s1, max_s1, min_d1, min_d2);+  if(mfe.energy > 0){+          free(subopt);+        delay_free=0;+        return NULL;+  }+  thresh = MIN2((int) ((mfe.Duplex_Er + mfe.Duplex_El + mfe.Loop_E)*100+0.1 + 410) + delta, threshTE );+ /* subopt[n_subopt++]=mfe; */+  free(mfe.structure);+  n1 = (int)strlen(s1[0]);+  n2 = (int)strlen(s2[0]);+  for (s=0; s1[s]!=NULL; s++);+  n_seq = s;+  Sali1 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  Sali2 = (short **) vrna_alloc((n_seq+1)*sizeof(short *));+  for (s=0; s<n_seq; s++) {+    if ((int)strlen(s1[s]) != n1) vrna_message_error("uneqal seqence lengths");+    if ((int)strlen(s2[s]) != n2) vrna_message_error("uneqal seqence lengths");+    Sali1[s] = aliencode_seq(s1[s]);+    Sali2[s] = aliencode_seq(s2[s]);+  }+  Sali1[n_seq]=NULL;  Sali2[n_seq]=NULL;+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  for (i=n1; i>1; i--){+    for (j=1; j<=n2; j++) {+      int  ii,jj, Ed,psc,skip;+      for (s=0; s<n_seq; s++) {+        type[s] = pair[Sali2[s][j]][Sali1[s][i]];+      }+      psc = covscore(type, n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s]=7;+      if (psc<MINPSCORE) continue;+      E = Ed = r[i][j];+      for  (s=0; s<n_seq; s++) {+        /*         if (i<n1-5) Ed += P->dangle3[type[s]][Sali1[s][i+1]]; */+        /*       if (j>6)  Ed += P->dangle5[type[s]][Sali2[s][j-1]]; */+        if (type[s]>2) Ed += P->TerminalAU;+      }+      if (Ed>thresh) continue;+      /* too keep output small, remove hits that are dominated by a+         better one close (w) by. For simplicity we do test without+         adding dangles, which is slightly inaccurate. +      */ +      w=1;+      for (skip=0, ii=MAX2(i-w,1); (ii<=MIN2(i+w,n1)) && type; ii++) { +        for (jj=MAX2(j-w,1); jj<=MIN2(j+w,n2); jj++)+          if (r[ii][jj]<E) {skip=1; break;}+      }+      if (skip){continue;}+      psct=0;+      pscg=0;+      struc = alisnoop_backtrack(i,j,s2, &Duplex_El, +                                 &Duplex_Er, &Loop_E, &Loop_D, &u, &pscd, &psct,&pscg, +                                 penalty, threshloop,threshLE,threshRE,threshDE, threshD,+                                 half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2,(const short int**) Sali1,(const int short **) Sali2);+              +      if (Duplex_Er > threshRE || Duplex_El > threshLE || Loop_D > threshD ||+         (Duplex_Er + Duplex_El) > threshDE || +         (Duplex_Er + Duplex_El + Loop_E) > threshTE ||+         (Duplex_Er + Duplex_El + Loop_E + Loop_D + 410) > threshSE) {+                 /* printf(" Duplex_Er %d threshRE %d Duplex_El %d threshLE %d \n" */+                /*        " Duplex_Er + Duplex_El %d  threshDE %d \n" */+                /*        " Duplex_Er + Duplex_El + Loop_E %d  threshTE %d \n" */+                /*        " Duplex_Er + Duplex_El + Loop_E + Loop_D %d  threshSE %d \n",  */+                /*          Duplex_Er , threshRE , Duplex_El ,threshLE, */+                /*          Duplex_Er + Duplex_El, threshDE, */+                /*          Duplex_Er + Duplex_El+  Loop_E , threshTE, */+                /*          Duplex_Er + Duplex_El+  Loop_E + Loop_D, threshSE);  */+                 Duplex_Er=0; +                Duplex_El=0;+                Loop_E = 0;+                Loop_D = 0;+                u=0,+                free(struc);+                continue;+        }++      if (n_subopt+1>=n_max) {+        n_max *= 2;+        subopt = (snoopT *) vrna_realloc(subopt, n_max*sizeof(snoopT));+      }+      +      subopt[n_subopt].i = i-5;+      subopt[n_subopt].j = j-5;+      subopt[n_subopt].u = u-5;+      subopt[n_subopt].Duplex_Er = Duplex_Er * 0.01;+      subopt[n_subopt].Duplex_El = Duplex_El * 0.01;+      subopt[n_subopt].Loop_E = Loop_E * 0.01;+      subopt[n_subopt].Loop_D = Loop_D * 0.01;+      subopt[n_subopt].energy = (Duplex_Er +Duplex_El + Loop_E + Loop_D + 410) * 0.01 ;+      subopt[n_subopt].pscd = pscd * 0.01;+      subopt[n_subopt].psct = -psct * 0.01;+      subopt[n_subopt++].structure = struc;+      +      /* i=u; */+      Duplex_Er=0; Duplex_El=0; Loop_E=0; Loop_D=0;u=0;pscd=0;psct=0;+    }+  }+  +  for (i=0; i<=n1; i++) {free(c[i]);free(r[i]);}+  free(c);free(r);+  for (s=0; s<n_seq; s++) {+    free(Sali1[s]); free(Sali2[s]);+  }+  free(Sali1); free(Sali2); free(type);+  +  if (snoop_subopt_sorted) +    qsort(subopt, n_subopt, sizeof(snoopT), compare);+  subopt[n_subopt].i =0;+  subopt[n_subopt].j =0;+  subopt[n_subopt].structure = NULL;+  return subopt;+}++++++++PRIVATE char *alisnoop_backtrack(int i, int j, const char ** snoseq, int *Duplex_El, +                                 int *Duplex_Er, int *Loop_E, int *Loop_D, int *u, +                                 int *pscd, int *psct, int *pscg,+                                 const int penalty, const int threshloop, const int threshLE, +                                 const int threshRE, const int threshDE, const int threshD, const int half_stem, +                                 const int max_half_stem, +                                 const int min_s2, const int max_s2, const int min_s1, +                                 const int max_s1, +                                 const int min_d1, const int min_d2,const short **Sali1, const short **Sali2) {+  /* backtrack structure going backwards from i, and forwards from j +     return structure in bracket notation with & as separator */+  int k, l, *type,*type2,*type3,type4, E, traced, i0, j0,s,n_seq,psc;+  int traced_r=0; /* flag for following backtrack in c or r */+  char *st1, *st2, *struc;+  char *struc_loop;+  n1 = (int) Sali1[0][0];+  n2 = (int) Sali2[0][0];+  +  for (s=0; Sali1[s]!=NULL; s++);+  n_seq = s;+  for (s=0; Sali2[s]!=NULL; s++);+  if (n_seq != s) vrna_message_error("unequal number of sequences in alibacktrack()\n");+  +  st1 = (char *) vrna_alloc(sizeof(char)*(n1+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n2+1));+  type = (int *) vrna_alloc(n_seq*sizeof(int));+  type2 = (int *) vrna_alloc(n_seq*sizeof(int));+  type3 = (int *) vrna_alloc(n_seq*sizeof(int));+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  i0=i; j0=j; /* MIN2(i+1,n1); j0=MAX2(j-1,1);!modified */+  for (s=0; s<n_seq; s++) {+    type[s] = pair[Sali1[s][i]][Sali2[s][j]];+    if(type[s]==0) type[s] = 7;+    *Duplex_Er += E_ExtLoop(rtype[type[s]], (j>1) ? Sali2[s][j-1] : -1, (i<n1) ? Sali1[s][i+1] : -1, P);+    /**+    *** if (i<n1)   *Duplex_Er += P->dangle3[rtype[type[s]]][Sali1[s][i+1]];+    *** if (j>1)    *Duplex_Er += P->dangle5[rtype[type[s]]][Sali2[s][j-1]];+    *** if (type[s]>2) *Duplex_Er += P->TerminalAU;+    **/+  }+  while (i>0 && j<=n2-min_d2 ) {+    if(!traced_r) {+      E = r[i][j]; traced=0;+      st1[i-1] = '<';+      st2[j-1] = '>'; +      for (s=0; s<n_seq; s++) {+        type[s] = pair[Sali1[s][i]][Sali2[s][j]];+      }+      psc = covscore(type,n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s] = 7;+      E += psc;+      *pscd +=psc;+      for (k=i-1; k>0 && (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2 ; l++) {+          int LE;+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS) continue;+          for (s=LE=0; s<n_seq; s++) {+            type4 = pair[Sali1[s][k]][Sali2[s][l]];+            if (type4==0) type4=7;+            LE += E_IntLoop(i-k-1, l-j-1, type4, rtype[type[s]], Sali1[s][k+1], Sali2[s][l-1], Sali1[s][i-1], Sali2[s][j+1],P);+          }+          if (E == r[k][l]+LE) {+            traced=1; +            i=k; j=l;+            *Duplex_Er+=LE;+            break;+          }+        }+        if (traced) break;+      }+      if(!traced){+        int U=0;+        for (s=0; s<n_seq; s++) {+          U+=Sali1[s][i-2];+        }+        U = (U==(n_seq)*4?1:0);+        if(/*  pair[Sali1[i+1]][Sali2[j-1]] && */   /* only U's are allowed */+            U && j < max_s1 && j > min_s1 && +            j > n2 - max_s2 - max_half_stem && +            j < n2 -min_s2 -half_stem ) {+          int min_k, max_k;+          max_k = MIN2(n2-min_s2,j+max_half_stem+1);+          min_k = MAX2(j+half_stem+1, n2-max_s2);+          folden * temp;+          temp=foldlist[j+1];+          while(temp->next) {+            int psc2, psc3;+            int k = temp->k;+            for (s=0; s<n_seq; s++) {+              type2[s]= pair[Sali1[s][i-3]][Sali2[s][k+1]];+              type3[s]= pair[Sali1[s][i-4]][Sali2[s][k+1]];+            }+            psc2 = covscore(type2, n_seq);+            psc3 = covscore(type3, n_seq);+            if(psc2>MINPSCORE /*&& pair[Sali1[i-4]][Sali2[k+2]]*/    ){  /* introduce structure from RNAfold */+              if(E==c[i-3][k+1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i-3]= '|';+                *u=i-2;+                int a,b;+                /* int fix_ij=indx[k-1+1]+j+1; */+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[k-1-a+1]+j+1+b;+                    if(cLoop[ij]==temp->energy) {+                      /* int bla; */+                      struc_loop=alisnobacktrack_fold_from_pair(snoseq, j+1+b, k-a-1+1,psct);+                    a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_r=1;+                i=i-3;j=k+1;+                break;+              }+            }+             if (psc3>MINPSCORE  /*&& pair[Sali1[i-5]][Sali2[k+2]]*/){  /* introduce structure from RNAfold */+              if(E==c[i-4][k+1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i-3]= '|';+                *u=i-2;+                int a,b;+                /* int fix_ij=indx[k-1+1]+j+1; */+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[k-1-a+1]+j+1+b;+                    if(cLoop[ij]==temp->energy) {+                      /* int bla; */+                      struc_loop=alisnobacktrack_fold_from_pair(snoseq, j+1+b, k-a-1+1,psct);+                      a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_r=1;+                i=i-4;j=k+1;+                break;+              }+            } /* else if */+            temp=temp->next;+          } /* while temp-> next */+        } /* test on j  */+      }/* traced? */+    }/* traced_r? */+    else{+      E = c[i][j]; traced=0;+      st1[i-1] = '<';+      st2[j-1] = '>'; +      for (s=0; s<n_seq; s++) {+        type[s] = pair[Sali1[s][i]][Sali2[s][j]];+      }+      psc = covscore(type,n_seq);+      for (s=0; s<n_seq; s++) if (type[s]==0) type[s] = 7;+      E += psc;+      *pscd+=psc;+      if (!type) vrna_message_error("backtrack failed in fold duplex c");+      for (k=i-1; (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2; l++) {+          int LE;+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS) continue;+          for (s=LE=0; s<n_seq; s++) {+            type4 = pair[Sali1[s][k]][Sali2[s][l]];+            if (type4==0) type4=7;+            LE += E_IntLoop(i-k-1, l-j-1, type4, rtype[type[s]], Sali1[s][k+1], Sali2[s][l-1], Sali1[s][i-1], Sali2[s][j+1],P);+          }+          if (E == c[k][l]+LE) {+            traced=1; +            i=k; j=l;+            *Duplex_El+=LE;+            break;+          }+        }+        if (traced) break;+      }+    }+    if (!traced) { +      for (s=0; s<n_seq; s++) {+        int correction;+        correction = E_ExtLoop(type[s], (i>1) ? Sali1[s][i-1] : -1, (j<n2) ? Sali2[s][j+1] : -1, P);+        *Duplex_El += correction;+        E          -= correction;+        /**+        *** if (i>1)    {E -= P->dangle5[type[s]][Sali1[s][i-1]]; *Duplex_El +=P->dangle5[type[s]][Sali1[s][i-1]];}+        *** if (j<n2)   {E -= P->dangle3[type[s]][Sali2[s][j+1]]; *Duplex_El +=P->dangle3[type[s]][Sali2[s][j+1]];}+        *** if (type[s]>2) {E -= P->TerminalAU;                      *Duplex_El +=P->TerminalAU;}+        **/+      }+      if (E != n_seq * P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex end");+      } else break;+    }+  }+/*   if (i>1)  i--;  */+/*   if (j<n2) j++;  */+  /* struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2); */ /* declare final duplex structure */+  struc = (char *) vrna_alloc(i0-i+1+n2-1+1+2); /* declare final duplex structure */+  char * struc2;+  struc2 = (char *) vrna_alloc(n2+1);+  /* char * struct_const; */+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  /* for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = struc_loop[k-1];*/ /* '.'; normal */+  /*  char * struct_const; */+  /*  struct_const = (char *) vrna_alloc(sizeof(char)*(n2+1));   */+  for (k=1; k<=n2; k++) {+    if (!st2[k-1]) st2[k-1] = struc_loop[k-1];/* '.'; */+    struc2[k-1] = st2[k-1];/* '.'; */+    /*      if (k>=j0 && k<=j){ */+    /*              struct_const[k-1]='x'; */+    /*      } */+    /*      else{ */+    /*              if(k<j0) {struct_const[k-1]='<';} */+    /*              if(k>j) {struct_const[k-1]='>';} */+    /*      } */+  }++  /*   char duplexseq_1[j0+1]; */+  /* char duplexseq_2[n2-j+3]; */+  if(j<n2){+    char **duplexseq_1, **duplexseq_2;+    duplexseq_1 = (char**) vrna_alloc((n_seq+1) * sizeof(char*));+    duplexseq_2 = (char**) vrna_alloc((n_seq+1) * sizeof(char*));+    for(s=0; s<n_seq; s++){+      duplexseq_1[s] = (char*) vrna_alloc((j0)*sizeof(char)); /* modfied j0+1 */+      duplexseq_2[s] = (char*) vrna_alloc((n2-j+2)*sizeof(char)); /* modified j+3 */+      strncpy(duplexseq_1[s], snoseq[s], j0-1); /* modified j0 */+      strcpy(duplexseq_2[s], snoseq[s] + j); /* modified j-1 */+      duplexseq_1[s][j0-1]='\0'; /* modified j0 */+      duplexseq_2[s][n2-j+1]='\0';/* modified j+2 */+    }+    duplexseq_1[n_seq]=NULL;+    duplexseq_2[n_seq]=NULL;+    duplexT temp;+    temp=aliduplexfold((const char**)duplexseq_1, (const char**)duplexseq_2);+    *Loop_D =  MIN2(0,-410 + (int) 100 * temp.energy*n_seq);+    if(*Loop_D){+      int l1,ibegin, iend, jbegin, jend;+      l1=strchr(temp.structure, '&')-temp.structure;+      ibegin=temp.i-l1;+      iend  =temp.i-1;+      jbegin=temp.j;+      jend  =temp.j+(int)strlen(temp.structure)-l1-2-1;+      for(k=ibegin+1; k<=iend+1; k++){+        struc2[k-1]=temp.structure[k-ibegin-1];+      }+      for(k=jbegin+j; k<=jend+j; k++){+        struc2[k-1]=temp.structure[l1+k-j-jbegin+1];+      }+    }+    for(s=0; s<n_seq; s++){+      free(duplexseq_1[s]);+      free(duplexseq_2[s]);+    }+    free(duplexseq_1);free(duplexseq_2);+    free(temp.structure);+  }+  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&"); +  /* strcat(struc, st2); */+  strncat(struc, struc2+5, (int)strlen(struc2)-10);+  free(struc2);+  free(struc_loop);+  free(st1); free(st2);+  free(type);free(type2);free(type3);+  /* free_arrays(); */+  return struc;+}++++++++void Lsnoop_subopt(const char *s1, const char *s2, int delta, int w, +                   const int penalty, const int threshloop, +                   const int threshLE, const int threshRE, const int threshDE, const int threshTE,const int threshSE,const int threshD,+                   const int distance,+                   const int half_stem, const int max_half_stem,+                   const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int alignment_length, const char* name, const int fullStemEnergy)+{++ int min_colonne=INF;+ int max_pos;+ int max;max=INF;+ /* int temp; */+ /* int nsubopt=10; */+ n1 = (int) strlen(s1);+ n2 = (int) strlen(s2);+ int *position;+ position = (int*) vrna_alloc((n1+3)*sizeof(int));+++  /* int Eminj, Emin_l; */+  int i, j; /* l1, Emin=INF, i_min=0, j_min=0; */+  /* char *struc; */+  /* snoopT mfe; */+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  /* int u; */+  int Loop_E;+  vrna_md_t md;++  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop, &foldlist, &foldlist_XS); +  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  lc = (int **) vrna_alloc(sizeof(int *) * (5));+  lr = (int **) vrna_alloc(sizeof(int *) * (5));+  for (i=0; i<5; i++) {+          lc[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        lr[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                lc[i][j]=INF;+                lr[i][j]=INF;+        }+  }+  encode_seqs(s1, s2);+  for (i=1; i<=n1; i++) {+      int idx=i%5;+      int idx_1=(i-1)%5;+      int idx_2=(i-2)%5;+      int idx_3=(i-3)%5;+      int idx_4=(i-4)%5;+    for (j=n2-min_d2; j>min_d1; j--) {+      int type, type2, k;+      type = pair[S1[i]][S2[j]];+      lc[idx][j] = (type) ? P->DuplexInit + 2*penalty : INF;+      lr[idx][j] = INF;+      if(!type) continue;+      if( /*pair[S1[i+1]][S2[j-1]]   &&  check that we have a solid base stack after the mLoop */+          j < max_s1 && j > min_s1 &&  +          j > n2 - max_s2 - max_half_stem && +          j < n2 -min_s2 -half_stem && S1[i-2]==4) { /*constraint on s2 and i*/+        int min_k, max_k;+        max_k = MIN2(n2-min_s2,j+max_half_stem+1);+        min_k = MAX2(j+half_stem+1, n2-max_s2);+        for(k=min_k; k <= max_k ; k++){         +          if(mLoop[indx[k-1]+j+1] < 0){+                }+          if(pair[S1[i-3]][S2[k]] /*genau zwei ungepaarte nucleotiden --NU--*/+             && mLoop[indx[k-1]+j+1] < threshloop){  +            lr[idx][j]=MIN2(lr[idx][j], lc[idx_3][k]+mLoop[indx[k-1]+j+1]);+          }+          else if(pair[S1[i-4]][S2[k]] &&  mLoop[indx[k-1]+j+1] < threshloop){/*--NUN--*/+            lr[idx][j]=MIN2(lr[idx][j], lc[idx_4][k]+mLoop[indx[k-1]+j+1]);+          }+              }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      lc[idx][j] += E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, P);+      /**+      *** if (i>1)    lc[idx][j] += P->dangle5[type][SS1[i-1]];+      *** if (j<n2)   lc[idx][j] += P->dangle3[type][SS2[j+1]];+      *** if (type>2) lc[idx][j] += P->TerminalAU;+      **/+      +      if(j<n2 && i>1){+        type2=pair[S1[i-1]][S2[j+1]];+              if(type2>0){+          lc[idx][j]=MIN2(lc[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+2*penalty, lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+2*penalty, lr[idx][j]);+              }+      }+      if(j<n2-1 && i>2){+        type2=pair[S1[i-2]][S2[j+2]];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+4*penalty, lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+4*penalty, lr[idx][j]);+        }+      }+      if(j<n2-2 && i>3){+        type2 = pair[S1[i-3]][S2[j+3]];+        if(type2>0){+          lc[idx][j]=MIN2(lc[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+6*penalty,lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+6*penalty,lr[idx][j]);+              }+      }+      /**+      *** (type>2?P->TerminalAU:0)+(i<(n1)?P->dangle3[rtype[type]][SS1[i+1]]+penalty:0)+(j>1?P->dangle5[rtype[type]][SS2[j-1]]+penalty:0)+      **/+      min_colonne=MIN2(lr[idx][j]+E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P), min_colonne);+      }+      position[i]=min_colonne;+      if(max>=min_colonne){+        max=min_colonne;+        max_pos=i;+      }+      min_colonne=INF;+ }+ +  free(S1); free(S2); free(SS1); free(SS2);+  if(max<threshTE){+        find_max_snoop(s1, s2, max, alignment_length, position, delta, +                       distance, penalty, threshloop, threshLE, threshRE, threshDE, +                       threshTE, threshSE, threshD, half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2,name, fullStemEnergy);+   }+  for (i=1; i<5; i++) {free(lc[i]);free(lr[i]);}+  free(lc[0]);free(lr[0]);+  free(lc);free(lr);+  free(position);+  +}  ++++void Lsnoop_subopt_list(const char *s1, const char *s2, int delta, int w, +                        const int penalty, const int threshloop, +                        const int threshLE, const int threshRE, const int threshDE, const int threshTE,const int threshSE,const int threshD,+                        const int distance,+                        const int half_stem, const int max_half_stem,+                        const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int alignment_length,const char *name,const int fullStemEnergy)+{+ + int min_colonne=INF;+ int max_pos;+ int max;max=INF;+ /* int temp; */+ /* int nsubopt=10; */+ n1 = (int) strlen(s1);+ n2 = (int) strlen(s2);+ int *position;+ position = (int*) vrna_alloc((n1+3)*sizeof(int));+++ /* int Eminj, Emin_l; */+  int i, j;/*  l1, Emin=INF, i_min=0, j_min=0; */+  /* char *struc; */+  /* snoopT mfe; */+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  /* int u; */+  int Loop_E;+  vrna_md_t md;++  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop, &foldlist,  &foldlist_XS); ++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  lpair = (int **) vrna_alloc(sizeof(int *) * (6));+  lc    = (int **) vrna_alloc(sizeof(int *) * (6));+  lr    = (int **) vrna_alloc(sizeof(int *) * (6));+  for (i=0; i<6; i++) {+          lc[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        lr[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        lpair[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                lc[i][j]=INF;+                lr[i][j]=INF;+                lpair[i][j]=0;+        }+  }+  encode_seqs(s1, s2);+  int lim_maxj=n2-min_d2 ;+  int lim_minj=min_d1;+  int lim_maxi=n1;+  for (i=5; i<=lim_maxi; i++) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;++    for (j=lim_maxj; j>lim_minj; j--) {+      int type, type2;/*  E, k,l; */+      type = pair[S1[i]][S2[j]];+      lpair[idx][j] = type;+      lc[idx][j] = (type) ? P->DuplexInit + 2*penalty : INF;+      lr[idx][j] = INF;+      if(!type) continue;+      if( /*pair[S1[i+1]][S2[j-1]] && Be sure it binds*/+          j < max_s1 && j > min_s1 &&  +          j > n2 - max_s2 - max_half_stem && +          j < n2 -min_s2 -half_stem && S1[i-2]==4 ) { /*constraint on s2 and i*/+        int min_k, max_k;+        max_k = MIN2(n2-min_s2,j+max_half_stem+1);+        min_k = MAX2(j+half_stem+1, n2-max_s2);+        folden * temp;+        temp=foldlist[j+1];+        while(temp->next){+          int k = temp->k;+          /* if(k >= min_k-1 && k < max_k){ comment to recover normal behaviour */+          if(lpair[idx_3][k+1] /*&& lpair[idx_4][k+2]*/){+            lr[idx][j]=MIN2(lr[idx][j], lc[idx_3][k+1]+temp->energy);/*--NU--*/+          }+          /*else*/ if(lpair[idx_4][k+1]){/*--NUN--*/+            lr[idx][j]=MIN2(lr[idx][j], lc[idx_4][k+1]+temp->energy);+          }+            /*  } */+          temp=temp->next;+        }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      lc[idx][j] += E_ExtLoop(type,  SS1[i-1] , SS2[j+1] , P);+      /**+      ***      lc[idx][j] += P->dangle5[type][SS1[i-1]];+      ***      lc[idx][j] += P->dangle3[type][SS2[j+1]];+      ***      if (type>2) lc[idx][j] += P->TerminalAU;+      **/+      /*       if(j<n2 && i>1){ */+      /* type2=pair[S1[i-1]][S2[j+1]]; */+        type2=lpair[idx_1][j+1];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+2*penalty, lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+2*penalty, lr[idx][j]);+        }+        /* } */+        /*       if(j<n2-1 && i>2){ */+        /* type2=pair[S1[i-2]][S2[j+2]]; */+        type2=lpair[idx_2][j+2];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P), lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P), lr[idx][j]);+          /*         } */+      }+        /*       if(j<n2-2 && i>3){ */+        /* type2 = pair[S1[i-3]][S2[j+3]]; */+        type2 =lpair[idx_3][j+3];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+6*penalty,lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+6*penalty,lr[idx][j]);+          /*         } */+      }+      /* min_colonne=MIN2(lr[idx][j]+(type>2?P->TerminalAU:0)+P->dangle3[rtype[type]][SS1[i+1]]+P->dangle5[rtype[type]][SS2[j-1]], min_colonne); */+      int bla;+      bla=lr[idx][j]+E_ExtLoop(rtype[type], SS2[j-1] , SS1[i+1], P)+2*penalty;+      min_colonne=MIN2(bla, min_colonne);+    }+    position[i]=min_colonne;+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      }+    min_colonne=INF;+ }+ +  free(S1); free(S2); free(SS1); free(SS2);+  if(max<threshTE){+      find_max_snoop(s1, s2, max, alignment_length, position, +                     delta, distance, penalty, threshloop, +                     threshLE, threshRE, threshDE, threshTE, threshSE, threshD,+                     half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2,name, fullStemEnergy);+   }+  for (i=1; i<6; i++) {free(lc[i]);free(lr[i]);free(lpair[i]);}+  free(lc[0]);free(lr[0]);free(lpair[0]);+  free(lc);free(lr);free(lpair);+  free(position);+}  +++PRIVATE void find_max_snoop(const char *s1, const char *s2,const int max,  const int alignment_length, const int* position, const int delta, +                            const int distance, const int penalty, const int threshloop,  const int threshLE, const int threshRE, +                            const int threshDE, const int threshTE, const int threshSE, const int threshD, +                            const int half_stem, const int max_half_stem, const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const char* name, const int fullStemEnergy)+{+  int count=0;+  int pos=n1+1;+  int threshold = MIN2(threshTE , max + delta );+  /* printf("threshTE %d max %d\n", threshTE, max); */+  /* #pragma omp parallel for */+  /*   for(pos=n1+1;pos>distance;pos--){ */+  while(pos-- > 5){+    int temp_min=0;+    if(position[pos]<(threshold)){+      int search_range;+      search_range=distance+1;+      while(--search_range){+        if(position[pos-search_range]<=position[pos-temp_min]){+          temp_min=search_range;+        }+      }+      pos-=temp_min;+      int begin=MAX2(6, pos-alignment_length+1);+      char *s3 = (char*) vrna_alloc(sizeof(char)*(pos-begin+3+12));+      strcpy(s3, "NNNNN");+      strncat(s3, (s1+begin-1), pos-begin+2);+      strcat(s3,"NNNNN\0");+      /* printf("%s s3\n", s3);  */+      snoopT test;+      test = snoopfold(s3, s2, penalty, threshloop, threshLE, threshRE, threshDE, threshD, half_stem, max_half_stem, min_s2, max_s2, min_s1, +                       max_s1, min_d1, min_d2,fullStemEnergy);+      if(test.energy==INF){+        free(s3);+        continue;+      }+      if(test.Duplex_El > threshLE * 0.01 || test.Duplex_Er > threshRE * 0.01  ||+         test.Loop_D > threshD * 0.01 || (test.Duplex_Er + test.Duplex_El) > threshDE * 0.01 ||+         (test.Duplex_Er + test.Duplex_El + test.Loop_E + test.Loop_D + 410) > threshSE*0.01) {+        free(test.structure);free(s3);+        continue;+      }+      int l1;+      l1 = strchr(test.structure, '&')-test.structure;+      +      int shift=0;+      if(test.i > (int)strlen(s3)-10){+        test.i--;+        l1--; +      }+      if(test.i-l1<0){+        l1--;+        shift++;+      }+      char *target_struct =  (char*) vrna_alloc(sizeof(char) * (strlen(test.structure)+1));+      strncpy(target_struct, test.structure+shift, l1);+      strncat(target_struct, test.structure + (strchr(test.structure, '&')-+                                               test.structure), (int)strlen(test.structure) - (strchr(test.structure, '&')-+                                                                                          test.structure));+      strcat(target_struct,"\0");+      char *target; +      target = (char *) vrna_alloc(l1+1);+      strncpy(target, (s3+test.i+5-l1), l1);+      target[l1]='\0';+      char *s4;+      s4 = (char*) vrna_alloc(sizeof(char) *(strlen(s2)-9));+      strncpy(s4, s2+5, (int)strlen(s2)-10);+      s4[(int)strlen(s2)-10]='\0';+      printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + 4.1 ) (%5.2f) \n%s&%s\n", +             target_struct,begin + test.i-5-l1,begin + test.i -6 , begin + test.u -6, +             test.j+1, test.j + (int)(strrchr(test.structure,'>') - strchr(test.structure,'>'))+1 ,+             test.Loop_D + test.Duplex_El + test.Duplex_Er + test.Loop_E + 4.10, test.Duplex_El,+             test.Duplex_Er, test.Loop_E, test.Loop_D,test.fullStemEnergy, target,s4);+      if(name){+        char *temp_seq;+        char *temp_struc;+        char psoutput[100];+        temp_seq = (char*) vrna_alloc(sizeof(char)*(l1+n2-9));+        temp_struc = (char*) vrna_alloc(sizeof(char)*(l1+n2-9));+        strcpy(temp_seq, target);+        strcat(temp_seq, s4);+        strncpy(temp_struc, target_struct, l1);+        strcat(temp_struc, target_struct+l1+1);+        temp_seq[n2+l1-10]='\0';+        temp_struc[n2+l1-10]='\0';+        cut_point = l1+1;+        char str[16];char upos[16];+        strcpy(psoutput,"sno_");+        sprintf(str,"%d",count);+        strcat(psoutput,str);+        sprintf(upos,"%d",begin + test.u - 6);+        strcat(psoutput,"_u_");+        strcat(psoutput,upos);+        strcat(psoutput,"_");+        strcat(psoutput,name);+        strcat(psoutput,".ps\0");+        PS_rna_plot_snoop_a(temp_seq, temp_struc, psoutput, NULL, NULL);+        cut_point = -1;+        free(temp_seq);+        free(temp_struc);+        count++;+        /* free(psoutput); */+      }+      free(s4);+      free(test.structure);+      free(target_struct);+      free(target);+      free(s3);+    }+  }+  +}+++++++++snoopT snoopfold(const char *s1, const char *s2, +                 const int penalty, const int threshloop, const int threshLE, const int threshRE, const int threshDE,+                 const int threshD,+                 const int half_stem, const int max_half_stem, +                 const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int fullStemEnergy) {+  /* int Eminj, Emin_l; */+  int i, j, l1, Emin=INF, i_min=0, j_min=0;+  char *struc;+  snoopT mfe;+  int *indx;+  int *mLoop;+  int *cLoop;+  folden** foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  int u;+  int Loop_E;+  vrna_md_t md;+  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  +  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  c = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  r = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=0; i<=n1; i++) {+          c[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        r[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                c[i][j]=INF;+                r[i][j]=INF;+        }+  }+  encode_seqs(s1, s2);+  for (i=6; i<=n1-5; i++) {+    for (j=n2-min_d2; j>min_d1; j--) {+      int type, type2, E, k,l;+      type = pair[S1[i]][S2[j]];+      c[i][j] = (type ) ? P->DuplexInit : INF;+      if(!type) continue;+      if(/*  pair[S1[i+1]][S2[j-1]] &&  */+         j < max_s1 && j > min_s1 &&  +         j > n2 - max_s2 - max_half_stem && +         j < n2 -min_s2 -half_stem && S1[i-2]==4  ) { /*constraint on s2 and i*/+        int min_k, max_k;+        max_k = MIN2(n2-min_s2,j+max_half_stem);+        min_k = MAX2(j+half_stem, n2-max_s2);+        folden * temp;+        temp=foldlist[j+1];+        while(temp->next){+          int k = temp->k;+          /* if(k >= min_k-1 && k < max_k){ uncomment to recovernormal behaviour */+          if(pair[S1[i-3]][S2[k+1]] /*&& pair[S1[i-4]][S2[k+2]]*/ ){+            r[i][j]=MIN2(r[i][j], c[i-3][k+1]+temp->energy);+          }+          /*else*/ if(pair[S1[i-4]][S2[k+1]] /*&& pair[S1[i-5]][S2[k+2]]*/ ){+            r[i][j]=MIN2(r[i][j], c[i-4][k+1]+temp->energy);+          }+          /* } */+          temp=temp->next;+        }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      /**+      *** c[i][j] += P->dangle5[type][SS1[i-1]];+      *** c[i][j] += P->dangle3[type][SS2[j+1]];+      *** if (type>2) c[i][j] += P->TerminalAU;+      **/+      c[i][j]+=E_ExtLoop(type, SS1[i-1] , SS2[j+1], P);+      for (k=i-1; k>0 && (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2 ; l++) {+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS ) continue;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          E = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                        SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+          c[i][j] = MIN2(c[i][j], c[k][l]+E+(i-k+l-j)*penalty);+          r[i][j] = MIN2(r[i][j], r[k][l]+E+(i-k+l-j)*penalty);+        }+      }+      E = r[i][j]; +      /**+      *** if (i<n1) E += P->dangle3[rtype[type]][SS1[i+1]];              +      *** if (j>1)  E += P->dangle5[rtype[type]][SS2[j-1]]; +      *** f (type>2) E += P->TerminalAU;+      **/+      E+=E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      } +    }+  }+  if(Emin > 0){+          printf("no target found under the constraints chosen\n");+        for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+        free(c);+        free(r);+        free(S1); free(S2); free(SS1); free(SS2);+        mfe.energy=INF;+        return mfe;+  }+  struc = snoop_backtrack(i_min, j_min,s2, &Duplex_El, &Duplex_Er, &Loop_E, &Loop_D, +                          &u, penalty, threshloop, threshLE, threshRE,threshDE, threshD,+                            half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2);+/*   if (i_min<n1-5) i_min++; */+/*   if (j_min>1 ) j_min--; */+  l1 = strchr(struc, '&')-struc;+  mfe.i = i_min-5;+  mfe.j = j_min-5;+  mfe.u = u -5;+  mfe.Duplex_Er = (float) Duplex_Er/100;+  mfe.Duplex_El = (float) Duplex_El/100;+  mfe.Loop_D = (float) Loop_D/100;+  mfe.Loop_E = (float) Loop_E/100;+  mfe.energy = (float) Emin/100 ;+  mfe.fullStemEnergy = (float) fullStemEnergy/100;+  mfe.structure = struc;+  if (!delay_free) {+    for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+    free(c);+    free(r);+    free(S1); free(S2); free(SS1); free(SS2);+  }+  return mfe;+}++PRIVATE int snoopfold_XS_fill(const char *s1, const char *s2, const int **access_s1,+                 const int penalty, const int threshloop, const int threshLE, const int threshRE, const int threshDE,+                 const int threshD,+                 const int half_stem, const int max_half_stem, +                 const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2) {+  /* int Eminj, Emin_l; */+  int i, j, Emin=INF, i_min=0, j_min=0;+  /* char *struc; */+  /* snoopT mfe; */+  int *indx;+  int *mLoop;+  int *cLoop;+  folden** foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  /* int u; */+  int Loop_E;+  vrna_md_t   md;+  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  +  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  c_fill = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  r_fill = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=0; i<=n1; i++) {+          c_fill[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        r_fill[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                c_fill[i][j]=INF;+                r_fill[i][j]=INF;+        }+  }+  encode_seqs(s1, s2);++  int di[5];+  di[0]=0;  +  for (i=6; i<=n1-5; i++) {+    di[1]=access_s1[5][i]   - access_s1[4][i-1];           +    di[2]=access_s1[5][i-1] - access_s1[4][i-2] + di[1];+    di[3]=access_s1[5][i-2] - access_s1[4][i-3] + di[2];+    di[4]=access_s1[5][i-3] - access_s1[4][i-4] + di[3];+    di[1]=MIN2(di[1],165);+    di[2]=MIN2(di[2],330);+    di[3]=MIN2(di[3],495);+    di[4]=MIN2(di[4],660);+    for (j=n2-min_d2; j>min_d1; j--) {+      int type, type2, E, k,l;+      type = pair[S1[i]][S2[j]];+      c_fill[i][j] = (type ) ? P->DuplexInit : INF;+      if(!type) continue;+      if(/*  pair[S1[i+1]][S2[j-1]] &&  */+         j < max_s1 && j > min_s1 &&  +         j > n2 - max_s2 - max_half_stem && +         j < n2 -min_s2 -half_stem && S1[i-2]==4  ) { /*constraint on s2 and i*/+        int min_k, max_k;+        max_k = MIN2(n2-min_s2,j+max_half_stem);+        min_k = MAX2(j+half_stem, n2-max_s2);+        folden * temp;+        temp=foldlist[j+1];+        while(temp->next){+          int k = temp->k;+          /* if(k >= min_k-1 && k < max_k){ uncomment to recovernormal behaviour */+          if(pair[S1[i-3]][S2[k+1]] /*&& pair[S1[i-4]][S2[k+2]]*/ ){+            r_fill[i][j]=MIN2(r_fill[i][j], c_fill[i-3][k+1]+temp->energy+ di[3]);+          }+          /*else*/ if(pair[S1[i-4]][S2[k+1]] /*&& pair[S1[i-5]][S2[k+2]]*/ ){+            r_fill[i][j]=MIN2(r_fill[i][j], c_fill[i-4][k+1]+temp->energy + di[4]);+          }+          /* } */+          temp=temp->next;+        }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      /**+      *** c_fill[i][j] += P->dangle5[type][SS1[i-1]];+      *** c_fill[i][j] += P->dangle3[type][SS2[j+1]];+      *** if (type>2) c_fill[i][j] += P->TerminalAU;+      **/+      c_fill[i][j]+= E_ExtLoop(type, SS1[i-1], SS2[j+1],P);+      for (k=i-1; k>0 && (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2 ; l++) {+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS ) continue;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          E = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                        SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+          c_fill[i][j] = MIN2(c_fill[i][j], c_fill[k][l]+E+di[i-k]);+          r_fill[i][j] = MIN2(r_fill[i][j], r_fill[k][l]+E+di[i-k]);+        }+      }+      E = r_fill[i][j]; +      /**+      ***  if (i<n1) E += P->dangle3[rtype[type]][SS1[i+1]];              +      ***  if (j>1)  E += P->dangle5[rtype[type]][SS2[j-1]]; +      *** if (type>2) E += P->TerminalAU;+      **/+      E+= E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+      if (E<Emin) {+        Emin=E; i_min=i; j_min=j;+      } +    }+  }+  return Emin;+}++++PUBLIC snoopT *snoop_subopt(const char *s1, const char *s2, int delta, int w, +                            const int penalty, const int threshloop, +                            const int threshLE, const int threshRE, const int threshDE, const int threshTE, const int threshSE, const int threshD,+                            const int distance, const int half_stem, const int max_half_stem,+                            const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int fullStemEnergy) {++++  /* printf("%d %d\n", min_s2, max_s2); */+  int i,j, n1, n2, E, n_subopt=0, n_max;+  char *struc;+  snoopT mfe;+  snoopT *subopt;+  int thresh;++  int Duplex_El, Duplex_Er, Loop_E;+  int Loop_D;+  Duplex_El=0; Duplex_Er=0; Loop_E=0;Loop_D=0;+  int u;+  u=0;+  n_max=16;+  subopt = (snoopT *) vrna_alloc(n_max*sizeof(snoopT));+  delay_free=1;+  mfe = snoopfold(s1, s2, penalty, threshloop, threshLE, threshRE, threshDE,threshD,+                  half_stem, max_half_stem,+                  min_s2, max_s2, min_s1, max_s1, min_d1, min_d2, fullStemEnergy);++++  if(mfe.energy > 0){+          free(subopt);+        delay_free=0;+        return NULL;+  }+  thresh = MIN2((int) ((mfe.Duplex_Er + mfe.Duplex_El + mfe.Loop_E)*100+0.1 + 410) + delta, threshTE );+ /* subopt[n_subopt++]=mfe; */+  free(mfe.structure);+  +  n1 = (int)strlen(s1); n2=(int)strlen(s2);+  for (i=n1; i>0; i--) {+    for (j=1; j<=n2; j++) {+      int type, Ed;+      type = pair[S2[j]][S1[i]];+      if (!type) continue;+      E = Ed = r[i][j];+      /**+      *** if (i<n1) Ed += P->dangle3[type][SS1[i+1]]; +      *** if (j>1)  Ed += P->dangle5[type][SS2[j-1]]; +      *** if (type>2) Ed += P->TerminalAU;+      **/+      Ed+= E_ExtLoop(type, (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+      if (Ed>thresh) continue;+      /* too keep output small, remove hits that are dominated by a+         better one close (w) by. For simplicity we do test without+         adding dangles, which is slightly inaccurate. +      */ +      /* w=1; */+/*       for (ii=MAX2(i-w,1); (ii<=MIN2(i+w,n1)) && type; ii++) {  */+/*         for (jj=MAX2(j-w,1); jj<=MIN2(j+w,n2); jj++) */+/*           if (r[ii][jj]<E) {type=0; break;} */+/*       } */+      if (!type) continue;++      struc = snoop_backtrack(i,j,s2, &Duplex_El, &Duplex_Er, &Loop_E, &Loop_D, &u, penalty, threshloop,threshLE,threshRE,threshDE,threshD, +                        half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2);+      if (Duplex_Er > threshRE || Duplex_El > threshLE || Loop_D > threshD ||+         (Duplex_Er + Duplex_El) > threshDE || +         (Duplex_Er + Duplex_El + Loop_E) > threshTE ||+         (Duplex_Er + Duplex_El + Loop_E + Loop_D + 410) > threshSE) {+                 /* printf(" Duplex_Er %d threshRE %d Duplex_El %d threshLE %d \n" */+                /*        " Duplex_Er + Duplex_El %d  threshDE %d \n" */+                /*        " Duplex_Er + Duplex_El + Loop_E %d  threshTE %d \n" */+                /*        " Duplex_Er + Duplex_El + Loop_E + Loop_D %d  threshSE %d \n",  */+                /*          Duplex_Er , threshRE , Duplex_El ,threshLE, */+                /*          Duplex_Er + Duplex_El, threshDE, */+                /*          Duplex_Er + Duplex_El+  Loop_E , threshTE, */+                /*          Duplex_Er + Duplex_El+  Loop_E + Loop_D, threshSE);  */+                 Duplex_Er=0; +                Duplex_El=0;+                Loop_E = 0;+                Loop_D = 0;+                u=0,+                free(struc);+                continue;+        }++      if (n_subopt+1>=n_max) {+        n_max *= 2;+        subopt = (snoopT *) vrna_realloc(subopt, n_max*sizeof(snoopT));+      }+      subopt[n_subopt].i = i-5;+      subopt[n_subopt].j = j-5;+      subopt[n_subopt].u = u-5;+      subopt[n_subopt].Duplex_Er = Duplex_Er * 0.01;+      subopt[n_subopt].Duplex_El = Duplex_El * 0.01;+      subopt[n_subopt].Loop_E = Loop_E * 0.01;+      subopt[n_subopt].Loop_D = Loop_D * 0.01;+      subopt[n_subopt].energy = (Duplex_Er +Duplex_El + Loop_E + Loop_D + 410) * 0.01 ;+      subopt[n_subopt].fullStemEnergy = (float) fullStemEnergy * 0.01;+      subopt[n_subopt++].structure = struc;++      Duplex_Er=0; Duplex_El=0; Loop_E=0; Loop_D=0;u=0;+    }+  }+  +  for (i=0; i<=n1; i++) {free(c[i]);free(r[i]);}+  free(c);free(r);+  free(S1); free(S2); free(SS1); free(SS2);+  delay_free=0;++  if (snoop_subopt_sorted) qsort(subopt, n_subopt, sizeof(snoopT), compare);+  subopt[n_subopt].i =0;+  subopt[n_subopt].j =0;+  subopt[n_subopt].structure = NULL;+  return subopt;+}++PUBLIC void snoop_subopt_XS(const char *s1, const char *s2, const int **access_s1, int delta, int w, +                            const int penalty, const int threshloop, +                            const int threshLE, const int threshRE, const int threshDE, const int threshTE, const int threshSE, const int threshD,+                            const int distance, const int half_stem, const int max_half_stem,+                            const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int alignment_length, const char *name, const int fullStemEnergy) {++++  /* printf("%d %d\n", min_s2, max_s2); */+  int i,j, E,  n_max;+  /* char *struc; */+  /* snoopT mfe; */++  int thresh;++  int Duplex_El, Duplex_Er, Loop_E;+  int Loop_D;+  Duplex_El=0; Duplex_Er=0; Loop_E=0;Loop_D=0;+  int u;+  u=0;+  n_max=16;+  delay_free=1;+  int Emin = snoopfold_XS_fill(s1, s2, access_s1,penalty, threshloop, threshLE, threshRE, threshDE,threshD,+                               half_stem, max_half_stem,+                               min_s2, max_s2, min_s1, max_s1, min_d1, min_d2);+  if(Emin > 0){+    delay_free=0;+  }+  thresh = MIN2(-100, threshTE +alignment_length*30);  +  /*   n1=(int)strlen(s1);  */+  /*   n2=(int)strlen(s2); */+  +  int n3=(int)strlen(s1);+  int n4=(int)strlen(s2);+  S1_fill = (short*)vrna_alloc(sizeof(short)*(n3+2));+  S2_fill = (short*)vrna_alloc(sizeof(short)*(n4+2));+  SS1_fill = (short*)vrna_alloc(sizeof(short)*(n3+1));+  SS2_fill = (short*)vrna_alloc(sizeof(short)*(n4+1));+  memcpy(S1_fill, S1, sizeof(short)*n3+2);+  memcpy(S2_fill, S2, sizeof(short)*n4+2);+  memcpy(SS1_fill, SS1, sizeof(short)*n3+1);+  memcpy(SS2_fill, SS2, sizeof(short)*n4+1);+  free(S1);free(S2);free(SS1);free(SS2);+  int count=0;+  for (i=n3-5; i>0; i--) {+    for (j=1; j<=n4; j++) {+      int type, Ed;+      type = pair[S2_fill[j]][S1_fill[i]];+      if (!type) continue;+      E = Ed = r_fill[i][j];+      /**+      ***if (i<n3) Ed += P->dangle3[type][SS1_fill[i+1]]; +      ***if (j>1)  Ed += P->dangle5[type][SS2_fill[j-1]]; +      ***if (type>2) Ed += P->TerminalAU;+      **/+      Ed+=E_ExtLoop(type, (j > 1) ? SS2[j-1] : -1, (i<n3) ? SS1[i+1] : -1, P);+      if (Ed>thresh) continue;+      +      /* to keep output small, remove hits that are dominated by a+         better one close (w) by. For simplicity we do test without+         adding dangles, which is slightly inaccurate. +      */ +/*       w=10;  */+/*       for (ii=MAX2(i-w,1); (ii<=MIN2(i+w,n3-5)) && type; ii++) {   */+/*         for (jj=MAX2(j-w,1); jj<=MIN2(j+w,n4-5); jj++)  */+/*           if (r_fill[ii][jj]<E) {type=0; break;}  */+/*       }  */+/*       i=ii;j=jj; */+      if (!type) continue;+      int begin=MAX2(5, i-alignment_length);+      int end  =MIN2(n3-5, i-1); +      char *s3 = (char*) vrna_alloc(sizeof(char)*(end-begin+2)+5);+      strncpy(s3, (s1+begin), end - begin +1);+      strcat(s3,"NNNNN\0");+      int n5 = (int)strlen(s3);+      snoopT test = snoopfold_XS(s3, s2, access_s1, i, j ,penalty, +                          threshloop, threshLE, threshRE, +                          threshDE, threshD, half_stem, +                          max_half_stem, min_s2, max_s2, min_s1, +                                 max_s1, min_d1, min_d2,fullStemEnergy);+      if(test.energy==INF){+        free(s3);+        continue;+      }+      if( test.Duplex_El > threshLE * 0.01 ||test.Duplex_Er > threshRE * 0.01  || +          test.Loop_D > threshD * 0.01 || (test.Duplex_Er + test.Duplex_El) > threshDE * 0.01 || +          (test.Duplex_Er + test.Duplex_El + test.Loop_E) > threshTE*0.01 || (test.Duplex_Er + test.Duplex_El + test.Loop_E + test.Loop_D + 410) > threshSE*0.01) +        { +          free(test.structure);free(s3); +          continue; +        }+      char *s4; +      s4 = (char*) vrna_alloc(sizeof(char) *(n4-9)); +      strncpy(s4, s2+5, n4-10); +      s4[n4-10]='\0';+      +      char *s5 = vrna_alloc(sizeof(char) * n5-test.i+2-5);+      strncpy(s5,s3+test.i-1,n5-test.i+1-5);+      s5[n5-test.i+1-5]='\0';+      float dE = ((float) (access_s1[n5-test.i+1-5][i]))*0.01;+      printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + %5.2f + 4.10)  (%5.2f)\n%s&%s\n" ,  +             test.structure, i  -  (n5 - test.i) ,i - 5, i - (n5 - test.u ),+             j-5, j-5 + (int)(strrchr(test.structure,'>') - strchr(test.structure,'>')), +             test.Loop_D + test.Duplex_El + test.Duplex_Er + test.Loop_E + 4.10+dE, test.Duplex_El, +             test.Duplex_Er, test.Loop_E, test.Loop_D,dE , test.fullStemEnergy, s5,s4);+      if(name){+        int begin_t, end_t, begin_q, end_q, and, pipe,k; +        char psoutput[100];+        begin_q=0;+        end_q=n4-10;+        begin_t=0;+        end_t=n5-test.i+ 1-5;+        and=end_t+1;+        pipe=test.u -test.i + 1;+        cut_point = end_t +1 ;+        char *catseq, *catstruct;/*  *fname;  */+        catseq = (char*) vrna_alloc(n5 + end_q -begin_q +2);+        catstruct = (char*) vrna_alloc(n5 + end_q -begin_q +2);+        strcpy(catseq, s5);+        strncpy(catstruct, test.structure, end_t);+        strcat(catseq, s4);+        strncat(catstruct, test.structure+end_t+1, end_q-begin_q+1);+        catstruct[end_t - begin_t + end_q-begin_q+2]='\0';+        catseq[end_t - begin_t + end_q-begin_q+2]='\0';+        int *relative_access;+        relative_access = vrna_alloc(sizeof(int)*strlen(s5));+        relative_access[0] = access_s1[1][i - (n5  - test.i) + 5];+        for(k=1;k<(int)strlen(s5);k++){+          relative_access[k] =  access_s1[k+1][i - (n5  - test.i) + k + 5] -  access_s1[k][i - (n5  - test.i) + k + 4];+        }+        char str[16];char upos[16];+        strcpy(psoutput,"sno_XS_");+        sprintf(str,"%d",count);+        strcat(psoutput,str);+        sprintf(upos,"%d",i - (n5 - test.u ));+        strcat(psoutput,"_u_");+        strcat(psoutput,upos);+        strcat(psoutput,"_");+        strcat(psoutput,name);+        strcat(psoutput,".ps\0");+        PS_rna_plot_snoop_a(catseq, catstruct, psoutput,relative_access,NULL);+        free(catseq);free(catstruct);free(relative_access);+        count++;+      }+      free(s3);free(s4);free(s5);free(test.structure);+    }+  }  +  for (i=0; i<=n3; i++) {free(c_fill[i]);free(r_fill[i]);}+  free(c_fill);free(r_fill);+  free(S1_fill); free(S2_fill); free(SS1_fill); free(SS2_fill);+  delay_free=0;+}+++++PRIVATE char *snoop_backtrack(int i, int j, const char* snoseq, +                              int *Duplex_El, int *Duplex_Er, +                              int *Loop_E, int *Loop_D, int *u, +                              const int penalty, const int threshloop, +                              const int threshLE, const int threshRE, const int threshDE, const int threshD,+                              const int half_stem, const int max_half_stem, +                              const int min_s2, const int max_s2, const int min_s1, +                              const int max_s1, const int min_d1, const int min_d2) {+  /* backtrack structure going backwards from i, and forwards from j +     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  int traced_r=0; /* flag for following backtrack in c or r */+  char *st1, *st2, *struc;+  char *struc_loop;++  st1 = (char *) vrna_alloc(sizeof(char)*(n1+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n2+1));+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  type=pair[S1[i]][S2[j]];+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  i0=i; j0=j;+  /**+  *** if (i<n1)   *Duplex_Er += P->dangle3[rtype[type]][SS1[i+1]];+  *** if (j>1)    *Duplex_Er += P->dangle5[rtype[type]][SS2[j-1]];+  *** if (type>2) *Duplex_Er += P->TerminalAU;+  **/+  *Duplex_Er += E_ExtLoop(rtype[type], (j > 1) ? SS2[j-1] : -1, (i<n1) ? SS1[i+1] : -1, P);+  while (i>0 && j<=n2-min_d2 ) {+    if(!traced_r) {+      E = r[i][j]; traced=0;+      st1[i-1] = '<';+      st2[j-1] = '>'; +      type = pair[S1[i]][S2[j]];+      if (!type) vrna_message_error("backtrack failed in fold duplex r");+      for (k=i-1; k>0 && (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2 ; l++) {+          int LE;+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS) continue;+          +          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          LE = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                         SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+          if (E == r[k][l]+LE+(i-k+l-j)*penalty) {+            traced=1; +            i=k; j=l;+            *Duplex_Er+=LE;+            break;+          }+        }+        if (traced) break;+      }+      if(!traced){+        if(/*  pair[S1[i+1]][S2[j-1]] && */  +            j < max_s1 && j > min_s1 && +            j > n2 - max_s2 - max_half_stem && +            j < n2 -min_s2 -half_stem && +            S1[i-2]==4) {+          int min_k, max_k;+          max_k = MIN2(n2-min_s2,j+max_half_stem+1);+          min_k = MAX2(j+half_stem+1, n2-max_s2);+          folden * temp;+          temp=foldlist[j+1];+          while(temp->next) {+            int k = temp->k;+            if(pair[S1[i-3]][S2[k+1]] /*&& pair[S1[i-4]][S2[k+2]]*/    ){  /* introduce structure from RNAfold */+              if(E==c[i-3][k+1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i-3]= '|';+                *u=i-2;+                int a,b;+                /* int fix_ij=indx[k-1+1]+j+1; */+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[k-1-a+1]+j+1+b;+                    if(cLoop[ij]==temp->energy) {+                      struc_loop=snobacktrack_fold_from_pair(snoseq, j+1+b, k-a-1+1);+                    a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_r=1;+                i=i-3;j=k+1;+                break;+              }+            }+            /*else*/ if (pair[S1[i-4]][S2[k+1]] /*&& pair[S1[i-5]][S2[k+2]]*/){  /* introduce structure from RNAfold */+              if(E==c[i-4][k+1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i-3]= '|';+                *u=i-2;+                int a,b;+                /* int fix_ij=indx[k-1+1]+j+1; */+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[k-1-a+1]+j+1+b;+                    if(cLoop[ij]==temp->energy) {+                      struc_loop=snobacktrack_fold_from_pair(snoseq, j+1+b, k-a-1+1);+                      a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_r=1;+                i=i-4;j=k+1;+                break;+              }+            } /* else if */+            temp=temp->next;+          } /* while temp-> next */+        } /* test on j  */+      }/* traced? */+    }/* traced_r? */+    else{+      E = c[i][j]; traced=0;+      st1[i-1] = '<';+      st2[j-1] = '>'; +      type = pair[S1[i]][S2[j]];+      if (!type) vrna_message_error("backtrack failed in fold duplex c");+      for (k=i-1; (i-k)<MAXLOOP_L; k--) {+        for (l=j+1; l<=n2; l++) {+          int LE;+          if (i-k+l-j>2*MAXLOOP_L-2) break;+          if (abs(i-k-l+j) >= ASS) continue;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          LE = E_IntLoop(i-k-1, l-j-1, type2, rtype[type],+                         SS1[k+1], SS2[l-1], SS1[i-1], SS2[j+1],P);+          if (E == c[k][l]+LE+(i-k+l-j)*penalty) {+            traced=1; +            i=k; j=l;+            *Duplex_El+=LE;+            break;+          }+        }+        if (traced) break;+      }+    }+    if (!traced) { +      int correction;+      correction = E_ExtLoop(type, (i>1) ? SS1[i-1] : -1, (j<n2) ? SS2[j+1] : -1, P);+      E-=correction;+      *Duplex_El+=correction;+      /**+      *** if (i>1)    {E -= P->dangle5[type][SS1[i-1]]; *Duplex_El +=P->dangle5[type][SS1[i-1]];}+      *** if (j<n2)   {E -= P->dangle3[type][SS2[j+1]]; *Duplex_El +=P->dangle3[type][SS2[j+1]];}+      *** if (type>2) {E -= P->TerminalAU;                    *Duplex_El +=P->TerminalAU;}+      **/+      if (E != P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex end");+      } else break;+    }+  }+/*   if (i>1)  i--; */+/*   if (j<n2) j++; */  +  /* struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2); */ /* declare final duplex structure */+  struc = (char *) vrna_alloc(i0-i+1+n2-1+1+2); /* declare final duplex structure */+  char * struc2;+  struc2 = (char *) vrna_alloc(n2+1);+  /* char * struct_const; */+  for (k=MAX2(i,1); k<=i0; k++) if (!st1[k-1]) st1[k-1] = '.';+  /* for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = struc_loop[k-1];*/ /* '.'; normal */+  /*  char * struct_const; */+  /*  struct_const = (char *) vrna_alloc(sizeof(char)*(n2+1));   */+  for (k=1; k<=n2; k++) {+    if (!st2[k-1]) st2[k-1] = struc_loop[k-1];/* '.'; */+    struc2[k-1] = st2[k-1];/* '.'; */+    /*      if (k>=j0 && k<=j){ */+    /*              struct_const[k-1]='x'; */+    /*      } */+    /*      else{ */+    /*              if(k<j0) {struct_const[k-1]='<';} */+    /*              if(k>j) {struct_const[k-1]='>';} */+    /*      } */+  }+  char duplexseq_1[j0];+  char duplexseq_2[n2-j+2];+  if(j<n2){+    strncpy(duplexseq_1, snoseq, j0-1);+    strcpy(duplexseq_2, snoseq + j);+    duplexseq_1[j0-1]='\0';+    duplexseq_2[n2-j+1]='\0';+    duplexT temp;+    temp=duplexfold(duplexseq_1, duplexseq_2);+    *Loop_D =  MIN2(0,-410 + (int) 100 * temp.energy);+    if(*Loop_D){+      int l1,ibegin, iend, jbegin, jend;+      l1=strchr(temp.structure, '&')-temp.structure;+      ibegin=temp.i-l1;+      iend  =temp.i-1;+      jbegin=temp.j;+      jend  =temp.j+(int)strlen(temp.structure)-l1-2-1;+      for(k=ibegin+1; k<=iend+1; k++){+        struc2[k-1]=temp.structure[k-ibegin-1];+      }+      for(k=jbegin+j; k<=jend+j; k++){+        struc2[k-1]=temp.structure[l1+k-j-jbegin+1];+      } +    }+    free(temp.structure);+  } +  strcpy(struc, st1+MAX2(i-1,0)); strcat(struc, "&"); +  /* strcat(struc, st2); */+  strncat(struc, struc2+5, (int)strlen(struc2)-10);+  free(struc2);+  free(struc_loop);+  free(st1); free(st2);+  /* free_arrays(); */+  return struc;+}++void Lsnoop_subopt_list_XS(const char *s1, const char *s2,  const int **access_s1, int delta, int w, +                        const int penalty, const int threshloop, +                        const int threshLE, const int threshRE, const int threshDE, const int threshTE,const int threshSE,const int threshD,+                        const int distance,+                        const int half_stem, const int max_half_stem,+                           const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int alignment_length, const char *name, const int fullStemEnergy)+{+ + int min_colonne=INF;+ int max_pos;+ int max;max=INF;+ /* int temp; */+ /* int nsubopt=10; */+ n1 = (int) strlen(s1);+ n2 = (int) strlen(s2);+ int *position;+ int *position_j;+ int min_j_colonne;+ int max_pos_j=INF; + position = (int*) vrna_alloc((n1+3)*sizeof(int));+ position_j = (int*) vrna_alloc((n1+3)*sizeof(int));++ /* int Eminj, Emin_l; */+  int i, j;/*  l1, Emin=INF, i_min=0, j_min=0; */+  /* char *struc; */+  /* snoopT mfe; */+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  /* int u; */+  int Loop_E;+  vrna_md_t md;++  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop, &foldlist, &foldlist_XS); ++  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  lpair = (int **) vrna_alloc(sizeof(int *) * (6));+  lc    = (int **) vrna_alloc(sizeof(int *) * (6));+  lr    = (int **) vrna_alloc(sizeof(int *) * (6));+  for (i=0; i<6; i++) {+          lc[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        lr[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        lpair[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                lc[i][j]=INF;+                lr[i][j]=INF;+                lpair[i][j]=0;+        }+  }+  encode_seqs(s1, s2);+  int lim_maxj=n2-min_d2 ;+  int lim_minj=min_d1;+  int lim_maxi=n1-5;+  for (i=5; i<=lim_maxi; i++) {+    int idx=i%5;+    int idx_1=(i-1)%5;+    int idx_2=(i-2)%5;+    int idx_3=(i-3)%5;+    int idx_4=(i-4)%5;+    int di1, di2, di3, di4;+    di1 = access_s1[5][i]   - access_s1[4][i-1];           +    di2 =access_s1[5][i-1] - access_s1[4][i-2] + di1;+    di3 = access_s1[5][i-2] - access_s1[4][i-3] + di2;+    di4 = access_s1[5][i-3] - access_s1[4][i-4] + di3;+    di1=MIN2(di1,165);+    di2=MIN2(di2,330);+    di3=MIN2(di3,495);+    di4=MIN2(di4,660);+    for (j=lim_maxj; j>lim_minj; j--) {+      int type, type2;/*  E, k,l; */+      type = pair[S1[i]][S2[j]];+      lpair[idx][j] = type;+      lc[idx][j] = (type) ? P->DuplexInit + access_s1[1][i] : INF;+      lr[idx][j] = INF;+      if(!type) continue;+      if( /*pair[S1[i+1]][S2[j-1]] && Be sure it binds*/+          j < max_s1 && j > min_s1 &&  +          j > n2 - max_s2 - max_half_stem && +          j < n2 -min_s2 -half_stem && S1[i-2]==4 ) { /*constraint on s2 and i*/+        int min_k, max_k;+        max_k = MIN2(n2-min_s2,j+max_half_stem+1);+        min_k = MAX2(j+half_stem+1, n2-max_s2);+        folden * temp;+        temp=foldlist[j+1];+        while(temp->next){+          int k = temp->k;+          /* if(k >= min_k-1 && k < max_k){ comment to recover normal behaviour */+          if(lpair[idx_3][k+1] && lc[idx_3][k+1] /*+di3*/ < 411 /*&& lpair[idx_4][k+2]*/){ /*  remove second condition */+            lr[idx][j]=MIN2(lr[idx][j], di3 + lc[idx_3][k+1]+temp->energy);/*--NU--*/+          }+          /*else*/ if(lpair[idx_4][k+1] && /*di4 +*/ lc[idx_4][k+1] < 411  ){/*--NUN--*/ /*  remove second condition  */+            lr[idx][j]=MIN2(lr[idx][j], di4 + lc[idx_4][k+1]+temp->energy);+          }+            /*  } */+          temp=temp->next;+        }+      }+      /* dangle 5'SIDE relative to the mRNA  */+      /**+      *** lc[idx][j] += P->dangle5[type][SS1[i-1]];+      *** lc[idx][j] += P->dangle3[type][SS2[j+1]];+      *** if (type>2) lc[idx][j] += P->TerminalAU;+      **/+      lc[idx][j]+=E_ExtLoop(type, SS1[i-1] ,  SS2[j+1] , P);+      /*       if(j<n2 && i>1){ */+      /* type2=pair[S1[i-1]][S2[j+1]]; */+        type2=lpair[idx_1][j+1];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+di1, lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_1][j+1]+E_IntLoop(0,0,type2, rtype[type],SS1[i], SS2[j], SS1[i-1], SS2[j+1], P)+di1, lr[idx][j]);+        }+        type2=lpair[idx_2][j+2];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+di2, lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_2][j+2]+E_IntLoop(1,1,type2, rtype[type],SS1[i-1], SS2[j+1], SS1[i-1], SS2[j+1], P)+di2, lr[idx][j]);+         +      }+        type2 =lpair[idx_3][j+3];+        if(type2>0 ){+          lc[idx][j]=MIN2(lc[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+di3,lc[idx][j]);+          lr[idx][j]=MIN2(lr[idx_3][j+3]+E_IntLoop(2,2,type2, rtype[type],SS1[i-2], SS2[j+2], SS1[i-1], SS2[j+1], P)+di3,lr[idx][j]);++      }+      int bla;+      int temp2;+      temp2=min_colonne;+      bla=lr[idx][j] + E_ExtLoop(rtype[type], SS2[j-1], SS1[i+1] , P);+        /**+        *** (type>2?P->TerminalAU:0)+P->dangle3[rtype[type]][SS1[i+1]]+P->dangle5[rtype[type]][SS2[j-1]];+        **/+      min_colonne=MIN2(bla, min_colonne);+      if(temp2>min_colonne){+        min_j_colonne=j;+      }+    }+    position[i]=min_colonne;+    if(max>=min_colonne){+      max=min_colonne;+      max_pos=i;+      max_pos_j=min_j_colonne;+      }+    position_j[i]=min_j_colonne;+    min_colonne=INF;+ }+  free(S1); free(S2); free(SS1); free(SS2);++  if(max<threshTE + 30*alignment_length){+    find_max_snoop_XS(s1, s2, access_s1,max,alignment_length, position, position_j,+                     delta, distance, penalty, threshloop, +                     threshLE, threshRE, threshDE, threshTE, threshSE, threshD,+                      half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2,name,fullStemEnergy);+   }+  for (i=1; i<6; i++) {free(lc[i]);free(lr[i]);free(lpair[i]);}+  free(lc[0]);free(lr[0]);free(lpair[0]);+  free(lc);free(lr);free(lpair);+  free(position);free(position_j);+}  +++PRIVATE void find_max_snoop_XS(const char *s1, const char *s2, const int **access_s1, +                               const int max,  const int alignment_length, +                               const int* position, const int* position_j, const int delta, +                               const int distance, const int penalty, const int threshloop,  const int threshLE, const int threshRE, +                               const int threshDE, const int threshTE, const int threshSE, const int threshD, +                               const int half_stem, const int max_half_stem, const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const char *name, const int fullStemEnergy){+  int count=0;+  int n3=(int)strlen(s1);+  int n4=(int)strlen(s2);+  int pos=n1-4;+  int max_pos_j;+  int threshold = MIN2(threshTE + alignment_length*30, -100);+  /* printf("threshTE %d max %d\n", threshTE, max); */+  /* #pragma omp parallel for */+  /*   for(pos=n1+1;pos>distance;pos--){ */+  while(pos-->5){+    int temp_min=0;+    if(position[pos]<(threshold)){+      int search_range;+      search_range=distance+1;+      while(--search_range){+        if(position[pos-search_range]<=position[pos-temp_min]){+          temp_min=search_range;+        }+      }+      pos-=temp_min;+      max_pos_j=position_j[pos];+      int begin=MAX2(5, pos-alignment_length);+      int end  =MIN2(n3-5, pos-1); +      char *s3 = (char*) vrna_alloc(sizeof(char)*(end-begin+2)+5);+      strncpy(s3, (s1+begin), end - begin +1);+      strcat(s3,"NNNNN\0");++      int n5 = (int)strlen(s3);+      snoopT test;+      test = snoopfold_XS(s3, s2, access_s1, pos, max_pos_j ,penalty, +                          threshloop, threshLE, threshRE, +                          threshDE, threshD, half_stem, +                          max_half_stem, min_s2, max_s2, min_s1, +                          max_s1, min_d1, min_d2, fullStemEnergy);+      if(test.energy==INF){+        free(s3);+        continue;+      }+      if( test.Duplex_El > threshLE * 0.01 ||test.Duplex_Er > threshRE * 0.01  || +         test.Loop_D > threshD * 0.01 || (test.Duplex_Er + test.Duplex_El) > threshDE * 0.01 || +         (test.Duplex_Er + test.Duplex_El + test.Loop_E) > threshTE*0.01 || (test.Duplex_Er + test.Duplex_El + test.Loop_E + test.Loop_D + 410) > threshSE*0.01) { +        free(test.structure);free(s3); +        continue; +      }+      +      char *s4; +      s4 = (char*) vrna_alloc(sizeof(char) *(n4-9)); +      strncpy(s4, s2+5, n4-10); +      s4[n4-10]='\0';++      char *s5 = vrna_alloc(sizeof(char) * n5-test.i+2-5);+      strncpy(s5,s3+test.i-1,n5-test.i+1-5);+      s5[n5-test.i+1-5]='\0';+      float dE = ((float) (access_s1[n5-test.i+1-5][pos]))*0.01;+      printf("%s %3d,%-3d;%3d : %3d,%-3d (%5.2f = %5.2f + %5.2f + %5.2f + %5.2f + %5.2f + 4.10) (%5.2f)\n%s&%s\n" ,  +             test.structure, pos  -  (n5 - test.i) ,pos - 5, pos - (n5 - test.u ),+             max_pos_j-5, max_pos_j-5 + (int)(strrchr(test.structure,'>') - strchr(test.structure,'>')), +             test.Loop_D + test.Duplex_El + test.Duplex_Er + test.Loop_E + 4.10+dE, test.Duplex_El, +             test.Duplex_Er, test.Loop_E, test.Loop_D,dE ,test.fullStemEnergy, s5,s4);+      if(name){+        int begin_t, end_t, begin_q, end_q, and, pipe, i; +        char psoutput[100];+        begin_q=0;+        end_q=n4-10;+        begin_t=0;+        end_t=n5-test.i+ 1-5;+        and=end_t+1;+        pipe=test.u -test.i + 1;+        cut_point = end_t +1 ;+        char *catseq, *catstruct;/*  *fname;  */+        catseq = (char*) vrna_alloc(n5 + end_q -begin_q +2);+        catstruct = (char*) vrna_alloc(n5 + end_q -begin_q +2);+        strcpy(catseq, s5);+        strncpy(catstruct, test.structure, end_t);+        strcat(catseq, s4);+        strncat(catstruct, test.structure+end_t+1, end_q-begin_q+1);+        catstruct[end_t - begin_t + end_q-begin_q+2]='\0';+        catseq[end_t - begin_t + end_q-begin_q+2]='\0';+        int *relative_access;+        relative_access = vrna_alloc(sizeof(int)*strlen(s5));++        relative_access[0] = access_s1[1][pos - (n5  - test.i) + 5];+        for(i=1;i<(int)strlen(s5);i++){+          relative_access[i] =  access_s1[i+1][pos - (n5  - test.i) + i + 5] -  access_s1[i][pos - (n5  - test.i) + i + 4];+        }+        char str[16];+        char upos[16];+        strcpy(psoutput,"sno_XS_");+        sprintf(str,"%d",count);+        strcat(psoutput,str);+        sprintf(upos,"%d",pos - (n5 - test.u ));+        strcat(psoutput,"_u_");+        strcat(psoutput,upos);+        strcat(psoutput,"_");+        strcat(psoutput,name);+        strcat(psoutput,".ps\0");+        PS_rna_plot_snoop_a(catseq, catstruct, psoutput,relative_access,NULL);+        free(catseq);free(catstruct);free(relative_access);+        count++;+      }+      free(s3);free(s4);free(s5);free(test.structure);+    }+  }+}++snoopT snoopfold_XS(const char *s1, const char *s2, const int **access_s1, const int pos_i, const int pos_j,+                 const int penalty, const int threshloop, const int threshLE, const int threshRE, const int threshDE,+                 const int threshD,+                 const int half_stem, const int max_half_stem, +                    const int min_s2, const int max_s2, const int min_s1, const int max_s1, const int min_d1, const int min_d2, const int fullStemEnergy) {+  /*   int Eminj, Emin_l; */+  int a,b,i, j, Emin=INF, a_min=0, b_min=0;+  char *struc;+  snoopT mfe;+  int *indx;+  int *mLoop;+  int *cLoop;+  folden** foldlist, **foldlist_XS;+  int Duplex_El, Duplex_Er;+  int Loop_D;+  int u;+  int Loop_E;+  vrna_md_t md;++  Duplex_El=0;Duplex_Er=0;Loop_E=0, Loop_D=0;+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  n1 = (int) strlen(s1);+  n2 = (int) strlen(s2);+  +  set_model_details(&md);+  if ((!P) || (fabs(P->temperature - temperature)>1e-6)) {+    snoupdate_fold_params();+    if(P)+      free(P);+    P = vrna_params(&md);+    make_pair_matrix();+  }+  +  c = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  r = (int **) vrna_alloc(sizeof(int *) * (n1+1));+  for (i=0; i<=n1; i++) {+          c[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        r[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+        for(j=n2; j>-1; j--){+                c[i][j]=INF;+                r[i][j]=INF;+        }+  }+  encode_seqs(s1, s2);+  i=n1-5;+  j=pos_j;+  /* printf("tar: %s\nsno: %s\n ", s1, s2); */+  /* printf("pos_i %d pos_j %d\n", pos_i, pos_j); */+  /* printf("type %d n1 %d n2 %d S1[n1] %d S2[n2] %d", pair[S1[i]][S2[j]], n1, n2, S1[n1], S2[n2]); */+  int type, type2, E, p,q;    +  r[i][j] = P->DuplexInit; +  /* r[i][j] += P->dangle3[rtype[type]][SS1[i+1]] + P->dangle5[rtype[type]][SS2[j-1]];  */+  +  if(pair[S1[i]][S2[j]]>2) r[i][j]+=P->TerminalAU;+  for(a=i-1; a>0;a--){ /* i-1 */+    r[a+1][0]=INF;+    for(b=j+1; b<=n2-min_d2;b++){ /* j+1 */+      r[a][b]=INF;+      type = pair[S1[a]][S2[b]]; +       if(!type) continue; +       if(S1[a+1]==4){ +         folden * temp; +         temp=foldlist_XS[b-1]; +         while(temp->next) {     +           int k = temp->k; +           if(pair[S1[a+3]][S2[k-1]] && k< max_s1 && k > min_s1 && k > n2 - max_s2 - max_half_stem &&  k < n2 -min_s2 -half_stem /*&& r[a+3][k-1] + access_s1[i-(a+3)+1][pos_i] < 411*/) { /* remove last condition last condition is to check if the interaction is stable enough */+             c[a][b]=MIN2(c[a][b], r[a+3][k-1]+temp->energy); +           }+           temp=temp->next;+         }+       }+       if(S1[a+2]==4){+         folden * temp; +         temp=foldlist_XS[b-1]; +         while(temp->next){ +           int k = temp->k; +           if(pair[S1[a+4]][S2[k-1]] &&  k< max_s1 && k > min_s1 && k > n2 - max_s2 - max_half_stem &&  k < n2 -min_s2 -half_stem /*&& r[a+4][k-1] + access_s1[i-(a+4)+1][pos_i] < 411 */ ) { /* remove last condition  */+             c[a][b]=MIN2(c[a][b], r[a+4][k-1]+temp->energy); +           }+           temp=temp->next;+         }+       }+       for(p=a+1; p<n1 && (p-a) < MAXLOOP_L; p++) { /* p < n1 */+         for (q=b-1; q > 1  ; q--) {  /* q > 1 */+           if (p-a+b-q>2*MAXLOOP_L-2) break; +           if (abs((p-a)-(b-q)) >= ASS ) continue; +           type2 = pair[S1[p]][S2[q]]; +           if (!type2) continue; +           E = E_IntLoop(p-a-1, b-q-1, type2, rtype[type],SS1[a+1], SS2[b-1], SS1[p-1], SS2[q+1],P); +           c[a][b] = MIN2(c[a][b], c[p][q]+E); +           r[a][b] = MIN2(r[a][b], r[p][q]+E); +         }+       }+       E = c[a][b];  +       if (type>2) E += P->TerminalAU;  +       /*        E +=P->dangle5[rtype[type]][SS1[i+1]]; */+       /* E +=P->dangle5[rtype[type]][SS2[j-1]];  */+       E+=access_s1[i-a+1][pos_i]; +       if (E<Emin) { +         Emin=E; a_min=a; b_min=b; +       }  +    }+  }+  if(Emin > 0){ +    printf("no target found under the constraints chosen\n");+    for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+    free(c);+    free(r); +    free(S1); free(S2); free(SS1); free(SS2);+    mfe.energy=INF;+    return mfe;+  }  +  type2=pair[S1[a_min]][S2[b_min]];+  if(type2>2) Emin +=P->TerminalAU;+  mfe.energy = ((float) (Emin))/100;+  struc = snoop_backtrack_XS(a_min, b_min,s2, &Duplex_El, &Duplex_Er, &Loop_E, &Loop_D, +                             &u, penalty, threshloop, threshLE, threshRE,threshDE, threshD, +                             half_stem, max_half_stem, min_s2, max_s2, min_s1, max_s1, min_d1, min_d2); ++  mfe.i = a_min;+  mfe.j = b_min;+  mfe.u = u;+  mfe.Duplex_Er = (float) Duplex_Er/100;+  mfe.Duplex_El = (float) Duplex_El/100;+  mfe.Loop_D = (float) Loop_D/100;+  mfe.Loop_E = (float) Loop_E/100;+  mfe.energy = (float) Emin/100 ;+  mfe.fullStemEnergy = (float) fullStemEnergy/100;+  mfe.structure = struc;+  return mfe;+}++PRIVATE char *snoop_backtrack_XS(int i, int j, const char* snoseq, +                              int *Duplex_El, int *Duplex_Er, +                              int *Loop_E, int *Loop_D, int *u, +                              const int penalty, const int threshloop, +                              const int threshLE, const int threshRE, const int threshDE, const int threshD,+                              const int half_stem, const int max_half_stem, +                              const int min_s2, const int max_s2, const int min_s1, +                              const int max_s1, const int min_d1, const int min_d2) {+  /* backtrack structure going backwards from i, and forwards from j +     return structure in bracket notation with & as separator */+  int k, l, type, type2, E, traced, i0, j0;+  int traced_c=0; /* flag for following backtrack in c or r */+  char *st1, *st2, *struc;+  char *struc_loop;++  st1 = (char *) vrna_alloc(sizeof(char)*(n1+1));+  st2 = (char *) vrna_alloc(sizeof(char)*(n2+1));+  int *indx;+  int *mLoop;+  int *cLoop;+  folden **foldlist, **foldlist_XS;+  type=pair[S1[i]][S2[j]];+  snoexport_fold_arrays(&indx, &mLoop, &cLoop,&foldlist, &foldlist_XS ); +  i0=i;j0=j;+  /*   i0=MAX2(i,1); j0=MIN2(j+1,n2); */+  while (i<=n1 && j>=1 ) {+    if(!traced_c) {+      E = c[i][j]; traced=0;+      st1[i] = '<';+      st2[j-1] = '>'; +      type = pair[S1[i]][S2[j]];+      if (!type) vrna_message_error("backtrack failed in fold duplex c");+      for (k=i+1; k>0 && (k-i)<MAXLOOP_L; k++) {+        for (l=j-1; l>=1 ; l--) {+          int LE;+          if (k-i+j-l>2*MAXLOOP_L-2) break;+          if (abs(k-i-j+l) >= ASS) continue;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          LE = E_IntLoop(k-i-1, j-l-1, type2, rtype[type],+                         SS1[i+1], SS2[j-1], SS1[k-1], SS2[l+1],P);+          if (E == c[k][l]+LE) {+            traced=1; +            i=k; j=l;+            *Duplex_El+=LE;+            break;+          }+        }+        if (traced) break;+      }+      if(!traced){+        if(S1[i+1]==4) {+          folden * temp;+          temp=foldlist_XS[j-1];+          while(temp->next) {+            int k = temp->k;+            if(pair[S1[i+3]][S2[k-1]] && k< max_s1 && k > min_s1 && k > n2 - max_s2 - max_half_stem &&  k < n2 -min_s2 -half_stem ) {+              if(E==r[i+3][k-1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i+1]= '|';+                st1[i+2]='.';+                *u=i+1;+                int a,b;+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[j-1-a]+k+b;+                    if(cLoop[ij]==temp->energy) {+                      struc_loop=snobacktrack_fold_from_pair(snoseq, k+b, j-1-a); +                      a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_c=1;+                i=i+3;j=k-1;+                break;+              }+            }+            temp=temp->next;+          }+        }+        if (S1[i+2]==4){  /* introduce structure from RNAfold */+          folden * temp;+          temp=foldlist_XS[j-1];+          while(temp->next) {+            int k = temp->k;+            if(pair[S1[i+4]][S2[k-1]] && k< max_s1 && k > min_s1 && k > n2 - max_s2 - max_half_stem &&  k < n2 -min_s2 -half_stem ) {+              if(E==r[i+4][k-1]+temp->energy){+                *Loop_E=temp->energy;+                st1[i+2]= '|';+                st1[i+1]=st1[i+3]='.';+                *u=i+2;+                int a,b;+                for(a=0; a< MISMATCH ;a++){+                  for(b=0; b< MISMATCH ; b++){+                    int ij=indx[j-1-a]+k+b;+                    if(cLoop[ij]==temp->energy) {+                      struc_loop=snobacktrack_fold_from_pair(snoseq, k+b, j-a-1);+                      a=INF; b=INF;        +                    }+                  }+                }+                traced=1;+                traced_c=1;+                i=i+4;j=k-1;+                break;+              }+            }+            temp=temp->next;+          }+        }+      }/* traced? */+    }/* traced_r? */+    else{+      E = r[i][j]; traced=0;+      st1[i] = '<';+      st2[j-1] = '>'; +      type = pair[S1[i]][S2[j]];+      if (!type) vrna_message_error("backtrack failed in fold duplex r");+      for (k=i+1; k>0 && (k-i)<MAXLOOP_L; k++) {+        for (l=j-1; l>=1 ; l--) {+          int LE;+          if (k-i+j-l>2*MAXLOOP_L-2) break;+          if (abs(k-i-j+l) >= ASS) continue;+          type2 = pair[S1[k]][S2[l]];+          if (!type2) continue;+          LE = E_IntLoop(k-i-1, j-l-1, type2, rtype[type],+                         SS1[i+1], SS2[j-1], SS1[k-1], SS2[l+1],P);+          if (E == r[k][l]+LE) {+            traced=1; +            i=k; j=l;+            *Duplex_Er+=LE;+            break;+          }+        }+        if (traced) break;+      }+    }+    if (!traced) { +/*       if (i>1)    {E -= P->dangle5[type][SS1[i-1]]; *Duplex_El +=P->dangle5[type][SS1[i-1]];} */+/*       if (j<n2)   {E -= P->dangle3[type][SS2[j+1]]; *Duplex_El +=P->dangle3[type][SS2[j+1]];} */+      if (type>2) {E -= P->TerminalAU;        *Duplex_Er +=P->TerminalAU;}+      if (E != P->DuplexInit) {+        vrna_message_error("backtrack failed in fold duplex end");+      } else break;+    }+  }++  +  /* struc = (char *) vrna_alloc(i0-i+1+j-j0+1+2); */ /* declare final duplex structure */+  struc = (char *) vrna_alloc(i-i0+1+n2); /* declare final duplex structure */+  char * struc2;+  struc2 = (char *) vrna_alloc(n2+1);+  /* char * struct_const; */++  for (k=MIN2(i0,1); k<=i; k++) if (!st1[k-1]) st1[k-1] = '.';+  /* for (k=j0; k<=j; k++) if (!st2[k-1]) st2[k-1] = struc_loop[k-1];*/ /* '.'; normal */+  /*  char * struct_const; */+  /*  struct_const = (char *) vrna_alloc(sizeof(char)*(n2+1));   */+  for (k=1; k<=n2; k++) {+    if (!st2[k-1]) st2[k-1] = struc_loop[k-1];/* '.'; */+    struc2[k-1] = st2[k-1];/* '.'; */+    /*      if (k>=j0 && k<=j){ */+    /*              struct_const[k-1]='x'; */+    /*      } */+    /*      else{ */+    /*              if(k<j0) {struct_const[k-1]='<';} */+    /*              if(k>j) {struct_const[k-1]='>';} */+    /*      } */+  }+  char duplexseq_1[j];+  char duplexseq_2[n2-j0+2];+  if(j0<n2){+    strncpy(duplexseq_1, snoseq, j-1);+    strcpy(duplexseq_2, snoseq + j0);+    duplexseq_1[j-1]='\0';+    duplexseq_2[n2-j0+1]='\0';+    duplexT temp;+    temp=duplexfold(duplexseq_1, duplexseq_2);+    *Loop_D =  MIN2(0,-410 + (int) 100 * temp.energy);+    if(*Loop_D){+      int l1,ibegin, iend, jbegin, jend;+      l1=strchr(temp.structure, '&')-temp.structure;+      ibegin=temp.i-l1;+      iend  =temp.i-1;+      jbegin=temp.j;+      jend  =temp.j+(int)strlen(temp.structure)-l1-2-1;+      for(k=ibegin+1; k<=iend+1; k++){+        struc2[k-1]=temp.structure[k-ibegin-1];+      }+      for(k=jbegin+j0; k<=jend+j0; k++){+        struc2[k-1]=temp.structure[l1+k-j0-jbegin+1];+      } +    }+    free(temp.structure);+  } +  strcpy(struc, st1+MAX2(i0,1)); strcat(struc, "&"); +  /* strcat(struc, st2); */+  strncat(struc, struc2+5, (int)strlen(struc2)-10);+  free(struc2);+  free(struc_loop);+  free(st1); free(st2);+  +    for (i=0; i<=n1; i++) {free(r[i]);free(c[i]);}+    free(c);+    free(r);+    free(S1);free(S2);free(SS1);free(SS2);+    /* free_arrays(); */+  return struc;+}++PRIVATE int covscore(const int *types, int n_seq) {+  /* calculate co-variance bonus for a pair depending on  */+  /* compensatory/consistent mutations and incompatible seqs */+  /* should be 0 for conserved pairs, >0 for good pairs      */+#define NONE -10000 /* score for forbidden pairs */+  int k,l,s,score, pscore;+  int dm[7][7]={{0,0,0,0,0,0,0}, /* hamming distance between pairs */+                {0,0,2,2,1,2,2} /* CG */,+                {0,2,0,1,2,2,2} /* GC */,+                {0,2,1,0,2,1,2} /* GU */,+                {0,1,2,2,0,2,1} /* UG */,+                {0,2,2,1,2,0,2} /* AU */,+                {0,2,2,2,1,2,0} /* UA */};+  +  int pfreq[8]={0,0,0,0,0,0,0,0};+  for (s=0; s<n_seq; s++)+    pfreq[types[s]]++;++  if (pfreq[0]*2>n_seq) return NONE;+  for (k=1,score=0; k<=6; k++) /* ignore pairtype 7 (gap-gap) */+    for (l=k+1; l<=6; l++)+      /* scores for replacements between pairtypes    */+      /* consistent or compensatory mutations score 1 or 2  */+      score += pfreq[k]*pfreq[l]*dm[k][l];+  +  /* counter examples score -1, gap-gap scores -0.25   */+  pscore = cv_fact * +    ((UNIT*score)/n_seq - nc_fact*UNIT*(pfreq[0] + pfreq[7]*0.25));+  return pscore;+}++/*---------------------------------------------------------------------------*/++PRIVATE short * aliencode_seq(const char *sequence) {+  unsigned int i,l;+  short *Stemp;+  l = strlen(sequence);+  Stemp = (short *) vrna_alloc(sizeof(short)*(l+2));+  Stemp[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    Stemp[i]= (short) encode_char(toupper(sequence[i-1]));++  /* for circular folding add first base at position n+1 */+  /* Stemp[l+1] = Stemp[1]; */++  return Stemp;+}++PRIVATE short * encode_seq(const char *sequence) {+  unsigned int i,l;+  short *S;+  l = strlen(sequence);+extern double nc_fact;+  S = (short *) vrna_alloc(sizeof(short)*(l+2));+  S[0] = (short) l;++  /* make numerical encoding of sequence */+  for (i=1; i<=l; i++)+    S[i]= (short) encode_char(toupper(sequence[i-1]));+  /* for circular folding add first base at position n+1 */+  S[l+1] = S[1];++  return S;+}++PRIVATE void encode_seqs(const char *s1, const char *s2) {+  unsigned int i,l;++  l = strlen(s1);+  S1 = encode_seq(s1);+  SS1= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS1 exists only for the special X K and I bases and energy_set!=0 */+  +  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS1[i] = alias[S1[i]];   /* for mismatches of nostandard bases */+  }++  l = strlen(s2);+  S2 = encode_seq(s2);+  SS2= (short *) vrna_alloc(sizeof(short)*(l+1));+  /* SS2 exists only for the special X K and I bases and energy_set!=0 */+  +  for (i=1; i<=l; i++) { /* make numerical encoding of sequence */+    SS2[i] = alias[S2[i]];   /* for mismatches of nostandard bases */+  }+}++PRIVATE int compare(const void *sub1, const void *sub2) {+  int d;+  if (((snoopT *) sub1)->energy > ((snoopT *) sub2)->energy)+    return 1;+  if (((snoopT *) sub1)->energy < ((snoopT *) sub2)->energy)+    return -1;+  d = ((snoopT *) sub1)->i - ((snoopT *) sub2)->i;+  if (d!=0) return d;+  return  ((snoopT *) sub1)->j - ((snoopT *) sub2)->j;+}+++
+ C/ViennaRNA/snoop.h view
@@ -0,0 +1,284 @@+#ifndef VIENNA_RNA_PACKAGE_SNOOP_H+#define VIENNA_RNA_PACKAGE_SNOOP_H++#include <ViennaRNA/data_structures.h>+/** +*** computes snoRNA-RNA interactions in RNAduplex manner+**/++snoopT snoopfold( const char *s1,+                  const char *s2, +                  const int penalty,+                  const int threshloop, +                  const int threshLE,+                  const int threshRE,+                  const int threshDE,+                  const int threshD,+                  const int half_stem,+                  const int max_half_stem,+                  const int min_s2,+                  const int max_s2,+                  const int min_s1,+                  const int max_s1,+                  const int min_d1,+                  const int min_d2,+		  const int fullStemEnergy);++/** +*** computes snoRNA-RNA suboptimal interactions in RNAduplex manner+**/+++snoopT *snoop_subopt( const char *s1,+                      const char *s2,+                      int delta,+                      int w,+                      const int penalty,+                      const int threshloop, +                      const int threshLE,+                      const int threshRE,+                      const int threshDE,+                      const int threshTE,+                      const int threshSE,+                      const int threshD,+                      const int distance,+                      const int half_stem,+                      const int max_half_stem,+                      const int min_s2,+                      const int max_s2,+                      const int min_s1,+                      const int max_s1,+                      const int min_d1,+                      const int min_d2,+		      const int fullStemEnergy);++/** +*** computes snoRNA-RNA suboptimal interactions in a RNAplex manner+**/++++void Lsnoop_subopt( const char *s1,+                    const char *s2,+                    int delta,+                    int w, +                    const int penalty,+                    const int threshloop, +                    const int threshLE,+                    const int threshRE,+                    const int threshDE,+                    const int threshTE,+                    const int threshSE,+                    const int threshD,+                    const int distance,+                    const int half_stem,+                    const int max_half_stem,+                    const int min_s2,+                    const int max_s2,+                    const int min_s1,+                    const int max_s1,+                    const int min_d1,+                    const int min_d2,+                    const int alignment_length,+                    const char* name,+		    const int fullStemEnergy);++/** +*** computes snoRNA-RNA suboptimal interactions in a RNAplex manner. The stem energy is saved into a list of struct, leading to a runtime improvement of 20%+**/++++void Lsnoop_subopt_list ( const char *s1,+                          const char *s2,+                          int delta,+                          int w, +                          const int penalty,+                          const int threshloop, +                          const int threshLE,+                          const int threshRE,+                          const int threshDE,+                          const int threshTE,+                          const int threshSE,+                          const int threshD,+                          const int distance,+                          const int half_stem,+                          const int max_half_stem,+                          const int min_s2,+                          const int max_s2,+                          const int min_s1,+                          const int max_s1,+                          const int min_d1,+                          const int min_d2,+                          const int alignment_length,+                          const char *name,+			  const int fullStemEnergy);++/** +*** computes snoRNA-RNA suboptimal interactions in a RNAplex manner. The stem energy is saved into a list of struct, leading to a runtime improvement of 20%. It considers accessibility+**/+++void Lsnoop_subopt_list_XS (const char *s1,+                            const char *s2,+                            const int **access_s1,+                            int delta,+                            int w, +                            const int penalty,+                            const int threshloop, +                            const int threshLE,+                            const int threshRE,+                            const int threshDE,+                            const int threshTE,+                            const int threshSE,+                            const int threshD,+                            const int distance,+                            const int half_stem,+                            const int max_half_stem,+                            const int min_s2,+                            const int max_s2,+                            const int min_s1,+                            const int max_s1,+                            const int min_d1,+                            const int min_d2,+                            const int alignment_length,+                            const char *name,+			    const int fullStemEnergy);+++/** +*** computes snoRNA-RNA suboptimal interactions in a RNAduplex manner, and considers accessibility+**/+++void snoop_subopt_XS (const char *s1,+                      const char *s2,+                      const int **access_s1,+                      int delta,+                      int w, +                      const int penalty,+                      const int threshloop, +                      const int threshLE,+                      const int threshRE,+                      const int threshDE,+                      const int threshTE,+                      const int threshSE,+                      const int threshD,+                      const int distance,+                      const int half_stem,+                      const int max_half_stem,+                      const int min_s2,+                      const int max_s2,+                      const int min_s1,+                      const int max_s1,+                      const int min_d1,+                      const int min_d2,+                      const int alignment_length,+                      const char *name,+		      const int fullStemEnergy);++/**+*** aliduplex-like alignment version of snoop_subopt+ **/++snoopT *alisnoop_subopt(const char **s1,+                        const char **s2,+                        int delta,+                        int w,+                        const int penalty,+                        const int threshloop, +                        const int threshLE,+                        const int threshRE,+                        const int threshDE,+                        const int threshTE,+                        const int threshSE,+                        const int threshD,+                        const int distance,+                        const int half_stem,+                        const int max_half_stem,+                        const int min_s2,+                        const int max_s2,+                        const int min_s1,+                        const int max_s1,+                        const int min_d1,+                        const int min_d2);++/**+*** RNAplex-like Alignment version of snoop_subopt+ **/++++snoopT *aliLsnoop_subopt_list ( const char **s1,+                                const char **s2,+                                int delta,+                                int w, +                                const int penalty,+                                const int threshloop, +                                const int threshLE,+                                const int threshRE,+                                const int threshDE,+                                const int threshTE,+                                const int threshSE,+                                const int threshD,+                                const int distance,+                                const int half_stem,+                                const int max_half_stem,+                                const int min_s2,+                                const int max_s2,+                                const int min_s1,+                                const int max_s1,+                                const int min_d1,+                                const int min_d2,+                                const int alignment_length);+/**+*** RNAaliduplex-like version of snoopfold+**/+++snoopT alisnoopfold(const char **s1,+                    const char **s2, +                    const int penalty,+                    const int threshloop,+                    const int threshLE,+                    const int threshRE,+                    const int threshDE,+                    const int threshD,+                    const int half_stem,+                    const int max_half_stem,+                    const int min_s2,+                    const int max_s2,+                    const int min_s1,+                    const int max_s1,+                    const int min_d1,+                    const int min_d2);+/**+*** RNAduplex-like version of snoopfold with accessibility information+**/ ++snoopT snoopfold_XS(const char *s1,+                    const char *s2,+                    const int **access_s1,+                    const int pos,+                    const int max_pos_j,+                    const int penalty,+                    const int threshloop, +                    const int threshLE,+                    const int threshRE,+                    const int threshDE,+                    const int threshD,+                    const int half_stem,+                    const int max_half_stem,+                    const int min_s2,+                    const int max_s2,+                    const int min_s1,+                    const int max_s1,+                    const int min_d1,+                    const int min_d2,+		    const int fullStemEnergy);+++++extern int snoop_subopt_sorted;+#endif
+ C/ViennaRNA/string_utils.c view
@@ -0,0 +1,340 @@+/*+                               string_utils.c++                 c  Ivo L Hofacker and Walter Fontana+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <errno.h>+#include <time.h>+#include <string.h>+#include <sys/types.h>+#include <stdint.h>+#include <stdarg.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/string_utils.h"++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++#ifndef HAVE_STRDUP+char *strdup(const char *s) {+  char *dup;++  dup = vrna_alloc(strlen(s)+1);+  strcpy(dup, s);+  return(dup);+}+#endif++PUBLIC char *+vrna_strdup_printf(const char *format, ...){++  char *result;+  va_list argp;++  va_start(argp, format);+  result = vrna_strdup_vprintf(format, argp);+  va_end(argp); /* Each va_start() or va_copy() needs a va_end() */++  return result;+}++PUBLIC char *+vrna_strdup_vprintf(const char *format, va_list argp){++  char    *result;+  int     r;++  result  = NULL;++#ifndef HAVE_VASPRINTF+  int     count;+  va_list copy;+  va_copy(copy, argp);++  r = -1;++  /* retrieve the number of characters that the string requires */+#ifdef _WIN32+  /*+    vsnprintf() in Windows is not ANSI compliant, although it's+    "...included for compliance to the ANSI standard"+    Thus, we use _vscprintf() that explicitly counts characters+  */+  count = _vscprintf(format, argp);+#else+  count = vsnprintf(NULL, 0, format, argp);+#endif++  if((count >= 0) && (count < INT_MAX)){+    char *buf = (char *)vrna_alloc(sizeof(char) * (count + 1));+    if(buf == NULL)+      r = -1;+    else if((r = vsnprintf(buf, count + 1, format, copy)) < 0)+      free(buf);+    else+      result = buf;+  }++  va_end(copy);  /* Each va_start() or va_copy() needs a va_end() */+#else+  /* the default is to use vasprintf() if available */+  r = vasprintf(&result, format, argp);+#endif++  /* check for any memory allocation error indicated by r == -1 */+  if(r == -1){+    vrna_message_warning("vrna_strdup_printf: memory allocation failure!");+    result = NULL;+  }++  return result;+}+++PUBLIC int+vrna_strcat_printf(char **dest, const char *format, ...){++  int r;+  va_list argp;++  va_start(argp, format);+  r = vrna_strcat_vprintf(dest, format, argp);+  va_end(argp); /* Each va_start() or va_copy() needs a va_end() */++  return r;+}+++PUBLIC int+vrna_strcat_vprintf(char **dest, const char *format, va_list args){++  char    *buf;+  int     r, l1, l2;+  size_t  old_count, new_count;++  if((!dest) || (!format))+    return -1;++  va_list copy;+  va_copy(copy, args);++  r         = -1;+  buf       = *dest;+  old_count = (buf) ? strlen(buf) : 0;++  /* retrieve the number of characters that the string requires */+#ifdef _WIN32+  /*+    vsnprintf() in Windows is not ANSI compliant, although it's+    "...included for compliance to the ANSI standard"+    Thus, we use _vscprintf() that explicitly counts characters+  */+  new_count = _vscprintf(format, args);+#else+  new_count = vsnprintf(NULL, 0, format, args);+#endif++  /* determine longer and shorter part of new string for INT overflow protection */+  if(old_count > new_count){+    l1 = old_count;+    l2 = new_count;+  } else {+    l1 = new_count;+    l2 = old_count;+  }++  if((new_count > 0) && (l1 < SIZE_MAX) && ((SIZE_MAX - l1) > l2)){+    buf = (char *)vrna_realloc(buf, sizeof(char) * (old_count + new_count + 1));+    if(buf == NULL)+      r = -1;+    else if((r = vsnprintf(buf + old_count, new_count + 1, format, copy)) < 0)+      free(buf);+    else {+      *dest = buf;+      r = old_count + new_count;+    }+  } else if(new_count == 0){+    /* we do not treat empty format string as error */+    r = (int)old_count;+  }++  va_end(copy);  /* Each va_start() or va_copy() needs a va_end() */++  /* check for any memory allocation error indicated by r == -1 */+  if(r == -1){+    vrna_message_warning("vrna_strcat_printf: memory allocation failure!");+    *dest = NULL;+  }++  return r;+}+++PUBLIC char *+vrna_random_string(int l, const char symbols[]){++  char *r;+  int   i, rn, base;++  base = (int) strlen(symbols);+  r = (char *) vrna_alloc(sizeof(char)*(l+1));++  for (i = 0; i < l; i++) {+    rn = (int) (vrna_urn()*base);  /* [0, base-1] */+    r[i] = symbols[rn];+  }+  r[l] = '\0';+  return r;+}++/*-----------------------------------------------------------------*/++PUBLIC int+vrna_hamming_distance(const char *s1,+                      const char *s2){++  int h=0;++  for (; *s1 && *s2; s1++, s2++)+    if (*s1 != *s2) h++;+  return h;+}++PUBLIC int+vrna_hamming_distance_bound(const char *s1,+                            const char *s2,+                            int boundary){++  int h=0;++  for (; *s1 && *s2 && boundary; s1++, s2++, boundary--)+    if (*s1 != *s2) h++;+  return h;+}++PUBLIC  void+vrna_seq_toRNA(char *sequence){++  unsigned int i;+  if(sequence){+    for(i = 0; sequence[i]; i++){+      if(sequence[i] == 'T') sequence[i] = 'U';+      if(sequence[i] == 't') sequence[i] = 'u';+    }+  }+}++PUBLIC void+vrna_seq_toupper(char *sequence){++  unsigned int i;+  if(sequence){+    for(i=0;sequence[i];i++)+      sequence[i] = toupper(sequence[i]);+  }+}++PUBLIC char *+vrna_cut_point_insert(const char *string,+                      int cp){++  char *ctmp;+  int len;++  if(cp > 0){+    len = strlen(string);+    ctmp = (char *)vrna_alloc((len+2) * sizeof(char));+    /* first sequence */+    (void) strncpy(ctmp, string, cp-1);+    /* spacer */+    ctmp[cp-1] = '&';+    /* second sequence */+    (void) strcat(ctmp, string+cp-1);+  } else {+    ctmp = strdup(string);+  }+  return ctmp;+}++PUBLIC char *+vrna_cut_point_remove(const char *string,+                      int *cp){++  char *pos, *copy = NULL;++  *cp = -1;++  if(string){+    copy = (char *) vrna_alloc(strlen(string)+1);+    (void) sscanf(string, "%s", copy);+    pos = strchr(copy, '&');+    if (pos) {+      *cp = (int)(pos - copy) + 1;+      if (*cp >= strlen(copy)) *cp = -1;+      if (strchr(pos+1, '&')) vrna_message_error("more than one cut-point in input");+      for (;*pos;pos++) *pos = *(pos+1); /* splice out the & */+    }+  }++  return copy;+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC void+str_uppercase(char *sequence){++  vrna_seq_toupper(sequence);+}++PUBLIC void+str_DNA2RNA(char *sequence){++  vrna_seq_toRNA(sequence);+}++PUBLIC char *+random_string(int l, const char symbols[]){++  return vrna_random_string(l, symbols);+}++PUBLIC int+hamming(const char *s1,+        const char *s2){++  return vrna_hamming_distance(s1, s2);+}++PUBLIC int+hamming_bound(const char *s1,+              const char *s2,+              int boundary){++  return vrna_hamming_distance_bound(s1, s2, boundary);+}++#endif
+ C/ViennaRNA/string_utils.h view
@@ -0,0 +1,259 @@+#ifndef VIENNA_RNA_PACKAGE_STRING_UTILS_H+#define VIENNA_RNA_PACKAGE_STRING_UTILS_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     string_utils.h+ *  @ingroup  utils+ *  @brief    General utility- and helper-functions for RNA sequence and structure strings used throughout the ViennaRNA Package+ */++/**+ *  @{+ *  @ingroup   string_utils+ */++#include <stdarg.h>+#include <ViennaRNA/data_structures.h>++/**+ * @brief Stringify a macro after expansion+ */+#define XSTR(s) STR(s)++/**+ * @brief Stringify a macro argument+ */+#define STR(s) #s++#ifndef FILENAME_MAX_LENGTH++/**+ *  @brief Maximum length of filenames that are generated by our programs+ *+ *  This definition should be used throughout the complete ViennaRNA package+ *  wherever a static array holding filenames of output files is declared.+ */+#define FILENAME_MAX_LENGTH   80++/**+ *  @brief Maximum length of id taken from fasta header for filename generation+ *+ *  this has to be smaller than FILENAME_MAX_LENGTH since in most cases,+ *  some suffix will be appended to the ID+ */+#define FILENAME_ID_LENGTH    42++#endif++#ifdef HAVE_CONFIG_H+#include <config.h>+#ifndef HAVE_STRDUP+char *strdup(const char *s);+#endif+#endif++/**+ *  @brief Safely create a formatted string+ *+ *  This function is a safe implementation for creating a formatted character array,+ *  similar to @em sprintf.+ *  Internally, it uses the @em asprintf function if available to dynamically allocate+ *  a large enough character array to store the supplied content. If @em asprintf is+ *  not available, mimic it's behavior using @em vsnprintf.+ *+ *  @note The returned pointer of this function should always be passed to @em free() to+ *  release the allocated memory+ *+ *  @see vrna_strdup_vprintf(), vrna_strcat_printf()+ *+ *  @param  format  The format string (See also asprintf)+ *  @param  ...     The list of variables used to fill the format string+ *  @return         The formatted, null-terminated string, or NULL if something has gone wrong+ */+char *vrna_strdup_printf(const char *format, ...);+++/**+ *  @brief Safely create a formatted string+ *+ *  This function is the @em va_list version of vrna_strdup_printf()+ *+ *  @note The returned pointer of this function should always be passed to @em free() to+ *  release the allocated memory+ *+ *  @see vrna_strdup_printf(), vrna_strcat_printf(), vrna_strcat_vprintf()+ *+ *  @param  format  The format string (See also asprintf)+ *  @param  ...     The list of variables used to fill the format string+ *  @return         The formatted, null-terminated string, or NULL if something has gone wrong+ */+char *vrna_strdup_vprintf(const char *format, va_list argp);+++/**+ *  @brief Safely append a formatted string to another string+ *+ *  This function is a safe implementation for appending a formatted character array,+ *  similar to a cobination of @em strcat and @em sprintf.+ *  The function automatically allocates enough memory to store both, the previous+ *  content stored at @p dest and the appended format string. If the @p dest pointer+ *  is NULL, the function allocate memory only for the format string.+ *  The function returns the number of characters in the resulting string or -1+ *  in case of an error.+ *+ *  @see vrna_strcat_vprintf(), vrna_strdup_printf(), vrna_strdup_vprintf()+ *+ *  @param  dest    The address of a char *pointer where the formatted string is to be appended+ *  @param  format  The format string (See also sprintf)+ *  @param  ...     The list of variables used to fill the format string+ *  @return         The number of characters in the final string, or -1 on error+ */+int vrna_strcat_printf(char **dest, const char *format, ...);+++/**+ *  @brief Safely append a formatted string to another string+ *+ *  This function is the @em va_list version of vrna_strcat_printf()+ *+ *  @see vrna_strcat_printf(), vrna_strdup_printf(), vrna_strdup_vprintf()+ *+ *  @param  dest    The address of a char *pointer where the formatted string is to be appended+ *  @param  format  The format string (See also sprintf)+ *  @param  ...     The list of variables used to fill the format string+ *  @return         The number of characters in the final string, or -1 on error+ */+int vrna_strcat_vprintf(char **dest, const char *format, va_list args);+++/**+ *  @brief Create a random string using characters from a specified symbol set+ *+ *  @param l        The length of the sequence+ *  @param symbols  The symbol set+ *  @return         A random string of length 'l' containing characters from the symbolset+ */+char  *vrna_random_string(int l, const char symbols[]);++/**+ *  @brief Calculate hamming distance between two sequences+ *+ *  @param s1   The first sequence+ *  @param s2   The second sequence+ *  @return     The hamming distance between s1 and s2+ */+int vrna_hamming_distance(const char *s1, const char *s2);++/**+ *  @brief Calculate hamming distance between two sequences up to a specified length+ *+ *  This function is similar to vrna_hamming_distance() but instead of comparing both sequences+ *  up to their actual length only the first 'n' characters are taken into account+ *  @param  s1  The first sequence+ *  @param  s2  The second sequence+ *  @param  n   The length of the subsequences to consider (starting from the 5' end)+ *  @return     The hamming distance between s1 and s2+ */+int vrna_hamming_distance_bound(const char *s1, const char *s2, int n);++/**+ *  @brief Convert an input sequence (possibly containing DNA alphabet characters) to RNA alphabet+ *+ *  This function substitudes <i>T</i> and <i>t</i> with <i>U</i> and <i>u</i>, respectively+ * + *  @param sequence The sequence to be converted+ */+void vrna_seq_toRNA(char *sequence);++/**+ *  @brief Convert an input sequence to uppercase+ * + *  @param sequence The sequence to be converted+ */+void vrna_seq_toupper(char *sequence);++/**+ *  @brief Add a separating '&' character into a string according to cut-point position+ *+ *  If the cut-point position is less or equal to zero, this function just+ *  returns a copy of the provided string. Otherwise, the cut-point character+ *  is set at the corresponding position+ *+ *  @param  string    The original string+ *  @param  cp        The cut-point position+ *  @return           A copy of the provided string including the cut-point character+ */+char *vrna_cut_point_insert(const char *string,+                            int cp);++/**+ *  @brief  Remove a separating '&' character from a string+ *+ *  This function removes the cut-point indicating '&' character from a string+ *  and memorizes its position in a provided integer variable. If not '&' is+ *  found in the input, the integer variable is set to -1. The function returns+ *  a copy of the input string with the '&' being sliced out.+ *+ *  @param  string  The original string+ *  @param  cp      The cut-point position+ *  @return         A copy of the input string with the '&' being sliced out+ */+char *vrna_cut_point_remove(const char *string,+                            int *cp);++/**+ *  @}+ */++#ifdef  VRNA_BACKWARD_COMPAT++/**+ *  @brief Convert an input sequence to uppercase+ *  @deprecated   Use vrna_seq_toupper() instead!+ */+DEPRECATED(void  str_uppercase(char *sequence));++/**+ *  @brief Convert a DNA input sequence to RNA alphabet+ *+ *  @deprecated Use vrna_seq_toRNA() instead!+ */+DEPRECATED(void str_DNA2RNA(char *sequence));++/**+ *  @brief Create a random string using characters from a specified symbol set+ *+ *  @deprecated Use vrna_random_string() instead!+ */+DEPRECATED(char *random_string(int l, const char symbols[]));++/**+ *  @brief Calculate hamming distance between two sequences+ *+ *  @deprecated Use vrna_hamming_distance() instead!+ */+DEPRECATED(int hamming(const char *s1, const char *s2));++/**+ *  @brief Calculate hamming distance between two sequences up to a specified length+ *+ *  @deprecated Use vrna_hamming_distance_bound() instead!+ */+DEPRECATED(int hamming_bound(const char *s1, const char *s2, int n));++#endif++#endif
+ C/ViennaRNA/stringdist.c view
@@ -0,0 +1,434 @@+/*+		String alignment for RNA secondary structures+		      Peter F Stadler, Ivo Hofacker+			   Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include <math.h>+#include "ViennaRNA/edit_cost.h"+#include "ViennaRNA/dist_vars.h"+#include "ViennaRNA/utils.h"+++#define PUBLIC+#define PRIVATE        static++PUBLIC  float      string_edit_distance(swString *T1, swString *T2);+PUBLIC  swString  *Make_swString(char *string);+PUBLIC  void       print_swString(swString *x);+PUBLIC  void       print_alignment_list(void);++PRIVATE void       sprint_aligned_swStrings(swString *T1, swString *T2);+PRIVATE float      StrEditCost(int i, int j, swString *T1, swString *T2);+PRIVATE void       DeCode(char *string, int k, int *tp, float *w);+PRIVATE int        decode(char *id);+PRIVATE void       encode(int type, char label[]);+PRIVATE int       *alignment[2]; /* contains information from backtracking+				    alignment[0][n] is the node in tree2+				    matching node n in tree1               */+++/*---------------------------------------------------------------------------*/++PUBLIC float string_edit_distance(swString *T1, swString *T2)++{+    float  **distance;+    short    **i_point, **j_point;++    int           i, j, i1, j1, pos, length1,length2;+    float         minus, plus, change, temp;++    if (cost_matrix==0) EditCost = &UsualCost;+    else EditCost = &ShapiroCost;++    length1 = T1[0].sign;+    length2 = T2[0].sign;++    distance = (float **)  vrna_alloc((length1 +1)*sizeof(float *));+    if(edit_backtrack){+       i_point  = (short **)  vrna_alloc((length1 +1)*sizeof(short *));+       j_point  = (short **)  vrna_alloc((length1 +1)*sizeof(short *));+    }+    for(i=0; i<= length1; i++){+       distance[i] = (float *) vrna_alloc( (length2+1)*sizeof(float));+       if(edit_backtrack){+	  i_point[i]  = (short *) vrna_alloc( (length2+1)*sizeof(short));+	  j_point[i]  = (short *) vrna_alloc( (length2+1)*sizeof(short));+       }+    }++    for(i = 1; i <= length1; i++) {+       if (edit_backtrack){+	  i_point[i][0] = i-1;+	  j_point[i][0] = 0;+       }+       distance[i][0] = distance[i-1][0]+StrEditCost(i,0,T1,T2);+    }+    for(j = 1; j <= length2; j++) {+       if (edit_backtrack){+	  j_point[0][j] = j-1;+	  i_point[0][j] = 0;+       }+       distance[0][j] = distance[0][j-1]+StrEditCost(0,j,T1,T2);+    }++    for (i = 1; i <= length1; i++) {+       for (j = 1; j <= length2 ; j++) {+          minus  = distance[i-1][j]  + StrEditCost(i,0,T1,T2);+          plus   = distance[i][j-1]  + StrEditCost(0,j,T1,T2);+          change = distance[i-1][j-1]+ StrEditCost(i,j,T1,T2);++          distance[i][j] = MIN3(minus, plus, change);+          /* printf("%g ", distance[i][j]); */++          if(edit_backtrack){+             if(distance[i][j] == change) {+                i_point[i][j]=i-1; j_point[i][j]=j-1;  }+             else if(distance[i][j] == plus) {+                i_point[i][j]=i  ; j_point[i][j]=j-1;  }+             else {+                i_point[i][j]=i-1; j_point[i][j]=j  ;  }+          }+       }+       /* printf("\n"); */+    }+    /* printf("\n"); */+    temp = distance[length1][length2];+    for(i=0;i<=length1;i++)+       free(distance[i]);+    free(distance);++    if(edit_backtrack){+       if(alignment[0]!= NULL) free(alignment[0]);+       if(alignment[1]!= NULL) free(alignment[1]);+       alignment[0] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));+       alignment[1] = (int *) vrna_alloc((length1+length2+1)*sizeof(int));++       pos = length1+length2;+       i   = length1;+       j   = length2;+       while( (i>0)||(j>0) ) {+          i1 = i_point[i][j];+          j1 = j_point[i][j];+          if( ((i-i1)==1)&&((j-j1)==1) )  {  /* substitution    */+              alignment[0][pos] = i;+              alignment[1][pos] = j;+          }+          if( ((i-i1)==1)&&(j==j1) )      {  /* Deletion in [1] */+              alignment[0][pos] = i;+              alignment[1][pos] = 0;+          }+          if( (i==i1)&&((j-j1)==1)  )      {  /* Deletion in [0] */+              alignment[0][pos] = 0;+              alignment[1][pos] = j;+          }+          pos--;+          i = i1;+          j = j1;+       }+       for(i=pos+1; i<=length1+length2; i++){+          alignment[0][i-pos] = alignment[0][i];+          alignment[1][i-pos] = alignment[1][i];+       }+       alignment[0][0] = length1+length2-pos;   /* length of alignment */++       for(i=0; i<=length1; i++){+          free(i_point[i]); free(j_point[i]);+       }+       free(i_point); free(j_point);+       sprint_aligned_swStrings(T1,T2);++    }++    return temp;+}+++/*---------------------------------------------------------------------------*/++PRIVATE float StrEditCost(int i, int j, swString *T1, swString *T2)+{+    float  c, diff, cd, min, a, b, dist;++    if(i==0) {+       cd   =  (float) (*EditCost)[0][T2[j].type];+       diff =  T2[j].weight;+       dist =  cd*diff;+    }+    else+    if(j==0) {+       cd   =  (float) (*EditCost)[T1[i].type][0];+       diff =  T1[i].weight;+       dist =  cd*diff;+    }+    else+    if( ((T1[i].sign)*(T2[j].sign)) > 0) {+       c = (float) (*EditCost)[T1[i].type][T2[j].type];+       diff = (float) fabs((a=T1[i].weight) - (b=T2[j].weight));+       min = MIN2(a,b);+       if (min == a) cd = (float) (*EditCost)[0][T2[j].type];+       else          cd = (float) (*EditCost)[T1[i].type][0];+       dist = c * min + cd * diff;+    }+    else dist = (float) DIST_INF;+    return dist;+}++/*---------------------------------------------------------------------------*/++PUBLIC swString *Make_swString(char *string)+{+   int i=0, j=0, k=0;+   int tp, len, l, length;+   float w;+   swString  *S;++   length = strlen(string);++   for(i=0; i<length; i++) {+      if( (string[i]=='(') || (string[i]==')') ) j++;+      if(string[i]=='.') j+=2;+   }++   len = j;++   S= (swString *) vrna_alloc(sizeof(swString)*(len+1));+   S[0].sign = j; /* number of entries */+   S[0].weight= 0.0;+   S[0].type=     0;++   i=0;+   j=1;+   while(i<length){+      switch(string[i]){+       case '(' :+          S[j].sign = 1;+          l=1;+          k=i;+          while (l>0) {+             k++;+             if(string[k] == '(' ) l++;+             if(string[k] == ')' ) l--;+          }+          DeCode(string,k,&tp,&w);+          S[j].type   = tp;+          S[j].weight = w/2.0;+	  j++;+          break;+       case ')' :+          k=i;+          S[j].sign = -1;+          DeCode(string,k,&tp,&w);+          S[j].type = tp;+          S[j].weight = w/2.0;+	  j++;+          break;+       case '.' :+          S[j].sign = 1;+          S[j].type = 1;+          S[j].weight = 0.5;+          j++;+          S[j].sign = -1;+          S[j].type =  1;+          S[j].weight = 0.5;+	  j++;+          break;+      }+      i++;+   }+   return S;+}++/*---------------------------------------------------------------------------*/++PRIVATE void DeCode(char *string, int k, int *tp, float *w)+   /* retrieves type and weigth for a node closed  by a bracket at position k */+{+   int i,j,l,m;+   char  label[20], id[20] ;+   i=k;+   label[0] = '\0';+   while(i>=0){+      i--;+      if( (string[i]=='(')||(string[i]==')')||(string[i]=='.') ) break;+      else {+         label[k-i-1] = string[i]; label[k-i] = '\0';+      }+   }+   l=strlen(label);+   if (l==0) {           /* Dot-Bracket notation */+     *w  = 1.0;+     *tp =   2;+   }+   else{+     for (i=0; i<l; i++) {+       if (!isalpha(label[l-i-1])) break;+       id[i] = label[l-i-1];+      }+      id[i] = '\0';+      *tp=decode(id);+      l=l-i-1;+      if(l>=0){+         for(j=0; j<=l; j++)+            id[j] = label[l-j];+         label[l+1] ='\0';+         m=-1;+         sscanf(label,"%d",&m);+         *w= (float) m;+         if(m==-1) {+            vrna_message_warning("Non-integer weight in DeCode ignored");+            *w=1.0;+         }+      }+      else+         *w=1.0;+   }+}++/*---------------------------------------------------------------------------*/++PRIVATE int decode(char *id)+{+    int   n, quit, i;+    char  label[100], *code;++    n = 0;++    quit = 0;+    code = coding;++    while (!quit) {+        for (i = 0; code[i] != sep; i++) {+            if (code[i] == '\0') {+                quit = 1;+                break;+            }+            label[i] = code[i];+        }+        label[i] = '\0';+        if (strcmp(id, label) == 0) return (n);+        code += (i+1);+        n++;+    }++    vrna_message_error("Syntax error: node identifier \"%s\" not found "+                              "in coding string \"%s\"\n"+                              "Exiting",+                              id, coding);+    exit(0);+}+++/*---------------------------------------------------------------------------*/++PRIVATE void encode( int type, char label[])++{+    int   i, l;++    l = 0;+    for (i = 0; i < type; i++) {+        while (coding[l] != sep && coding[l]) l++;+        l++;+    }++    for (i = 0; coding[l+i] != sep; i++) {+        if (coding[l+i] == '\0') break;+        label[i] = coding[l+i];+    }+    label[i] = '\0';+}++/*---------------------------------------------------------------------------*/++PRIVATE void sprint_aligned_swStrings(swString *T1, swString *T2)+{+   int i, j, l0, l1, ltmp=0, weights;+   char label[10], *a0, *a1, tmp0[20], tmp1[20];++   weights = 0;+   for (i=1; i<=T1[0].sign; i++) weights = (weights||(T1[i].weight!=0.5));+   for (i=1; i<=T2[0].sign; i++) weights = (weights||(T2[i].weight!=0.5));++   a0 = (char *) vrna_alloc(alignment[0][0]*4+2);+   a1 = (char *) vrna_alloc(alignment[0][0]*4+2);+   for(i=1; i<= alignment[0][0]; i++){+      tmp0[0] = '\0'; l0=0;+      if(alignment[0][i] > 0) {+         encode(T1[alignment[0][i]].type, label);+         if(T1[alignment[0][i]].sign > 0) {+            tmp0[0] = '(';+            tmp0[1] = '\0';+         }+         strcat(tmp0,label);+	 if (weights)+	    sprintf(tmp0+strlen(tmp0), "%d",+		    (int)(2*T1[alignment[0][i]].weight));++         if(T1[alignment[0][i]].sign < 0) strcat(tmp0, ")");+	 l0 = strlen(tmp0);+      }+      tmp1[0]= '\0'; l1=0;+      if(alignment[1][i] > 0) {+         encode(T2[alignment[1][i]].type, label);+         if(T2[alignment[1][i]].sign > 0) {+            tmp1[0] = '(';+            tmp1[1] = '\0';+         }+         strcat(tmp1,label);+	 if (weights)+	    sprintf(tmp1+strlen(tmp1), "%d",+		    (int)(2*T2[alignment[1][i]].weight));++	 if(T2[alignment[1][i]].sign < 0) strcat(tmp1, ")");+         l1 = strlen(tmp1);+      }+      ltmp = MAX2(l0,l1);+      for (j=l0; j<ltmp; j++) tmp0[j] = '_';+      for (j=l1; j<ltmp; j++) tmp1[j] = '_';+      tmp0[ltmp] = '\0'; tmp1[ltmp] = '\0';++      strcat(a0,tmp0); strcat(a1,tmp1);+      ltmp = strlen(a0);+   }+   if (aligned_line[0]!= NULL) { free(aligned_line[0]); aligned_line[0]= NULL;}+   if (aligned_line[1]!= NULL) { free(aligned_line[1]); aligned_line[1]= NULL;}+   aligned_line[0] = strdup(a0);+   free(a0);+   aligned_line[1] = strdup(a1);+   free(a1);+}++/*---------------------------------------------------------------------------*/+++PUBLIC void print_swString(swString *x)+{+   int i;+   for (i=0; i<=x[0].sign; i++)+      printf("(%d,%d,%f\n) ", x[i].type, x[i].sign, x[i].weight );+   printf("\n");+}++/*---------------------------------------------------------------------------*/++PUBLIC void print_alignment_list(void)+{+   int i;+   printf("\n");+   for (i=1; i<= alignment[0][0]; i++)+      printf("%3d ",alignment[0][i]);+      printf("\n");+   for (i=1; i<= alignment[0][0]; i++)+      printf("%3d ",alignment[1][i]);+   printf("\n");+}
+ C/ViennaRNA/stringdist.h view
@@ -0,0 +1,30 @@+#ifndef VIENNA_RNA_PACKAGE_STRING_DIST_H+#define VIENNA_RNA_PACKAGE_STRING_DIST_H++/**+ *  \file stringdist.h+ *  \brief Functions for String Alignment+ */++#include <ViennaRNA/dist_vars.h>+++/**+ *  \brief Convert a structure into a format suitable for string_edit_distance().+ * + *  \param string+ *  \return+ */+swString *Make_swString(char *string);++/**+ *  \brief Calculate the string edit distance of T1 and T2.+ * + *  \param  T1+ *  \param  T2+ *  \return+ */+float     string_edit_distance( swString *T1,+                                swString *T2);++#endif
+ C/ViennaRNA/structure_utils.c view
@@ -0,0 +1,1253 @@+/*+    structure_utils.c++    Various functions to convert, parse, encode secondary structures++    c  Ivo L Hofacker, Walter Fontana, Ronny Lorenz+                Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <math.h>++#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/structure_utils.h"++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE vrna_plist_t *+wrap_get_plist( vrna_mx_pf_t *matrices,+                int length,+                int *index,+                short *S,+                vrna_exp_param_t *pf_params,+                double cut_off);++PRIVATE vrna_plist_t *+wrap_plist( vrna_fold_compound_t *vc,+            double cut_off);++PRIVATE void assign_elements_pair(short *pt, int i, int j, char *elements);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++PUBLIC char *+vrna_db_pack(const char *struc){++  /* 5:1 compression using base 3 encoding */+  int i,j,l,pi;+  unsigned char *packed;++  l = (int) strlen(struc);+  packed = (unsigned char *) vrna_alloc(((l+4)/5+1)*sizeof(unsigned char));++  j=i=pi=0;+  while (i<l) {+    register int p;+    for (p=pi=0; pi<5; pi++) {+      p *= 3;+      switch (struc[i]) {+      case '(':+      case '\0':+        break;+      case '.':+        p++;+        break;+      case ')':+        p += 2;+        break;+      default: vrna_message_error("pack_structure: illegal character in structure");+      }+      if (i<l) i++;+    }+    packed[j++] = (unsigned char) (p+1); /* never use 0, so we can use+                                            strcmp()  etc. */+  }+  packed[j] = '\0';      /* for str*() functions */+  return (char *) packed;+}++PUBLIC char *+vrna_db_unpack(const char *packed){++  /* 5:1 compression using base 3 encoding */+  int i,j,l;+  char *struc;+  unsigned const char *pp;+  char code[3] = {'(', '.', ')'};++  l = (int) strlen(packed);+  pp = (const unsigned char *) packed;+  struc = (char *) vrna_alloc((l*5+1)*sizeof(char));   /* up to 4 byte extra */++  for (i=j=0; i<l; i++) {+    register int p, c, k;++    p = (int) pp[i] - 1;+    for (k=4; k>=0; k--) {+      c = p % 3;+      p /= 3;+      struc[j+k] = code[c];+    }+    j += 5;+  }+  struc[j--] = '\0';+  while (struc[j] == '(') /* strip trailing ( */+    struc[j--] = '\0';++  return struc;+}++PUBLIC short *+vrna_ptable(const char *structure){++    /* returns array representation of structure.+       table[i] is 0 if unpaired or j if (i.j) pair.  */+   short i,j,hx;+   short length;+   short *stack;+   short *table;++   length = (short) strlen(structure);+   stack = (short *) vrna_alloc(sizeof(short)*(length+1));+   table = (short *) vrna_alloc(sizeof(short)*(length+2));+   table[0] = length;++   for (hx=0, i=1; i<=length; i++) {+      switch (structure[i-1]) {+       case '(':+         stack[hx++]=i;+         break;+       case ')':+         j = stack[--hx];+         if (hx<0) {+            vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+         }+         table[i]=j;+         table[j]=i;+         break;+       default:   /* unpaired base, usually '.' */+         table[i]= 0;+         break;+      }+   }+   if (hx!=0) {+      vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+   }+   free(stack);+   return(table);+}++PUBLIC short *+vrna_pt_pk_get(const char *structure){++   short i,j,hx, hx2;+   short length;+   short *stack;+   short *stack2;+   short *table;++   length = (short) strlen(structure);+   stack  = (short *) vrna_alloc(sizeof(short)*(length+1));+   stack2 = (short *) vrna_alloc(sizeof(short)*(length+1));+   table  = (short *) vrna_alloc(sizeof(short)*(length+2));+   table[0] = length;++   for (hx=0, hx2=0, i=1; i<=length; i++) {+      switch (structure[i-1]) {+       case '(':+         stack[hx++]=i;+         break;+       case ')':+         j = stack[--hx];+         if (hx<0) {+            vrna_message_error("%s\nunbalanced '()' brackets in make_pair_table_pk", structure);+         }+         table[i]=j;+         table[j]=i;+         break;+       case '[':+         stack2[hx2++]=i;+         break;+       case ']':+         j = stack2[--hx2];+         if (hx2<0) {+            vrna_message_error("%s\nunbalanced '[]' brackets in make_pair_table_pk", structure);+         }+         table[i]=j;+         table[j]=i;+         break;+       default:   /* unpaired base, usually '.' */+         table[i]= 0;+         break;+      }+   }+   if (hx!=0) {+      vrna_message_error("%s\nunbalanced '()' brackets in make_pair_table_pk", structure);+   } else if (hx2!=0) {+      vrna_message_error("%s\nunbalanced '[]' brackets in make_pair_table_pk", structure);+   }+   free(stack);+   free(stack2);+   return(table);+}+++PUBLIC short *+vrna_pt_snoop_get(const char *structure){++    /* returns array representation of structure.+       table[i] is 0 if unpaired or j if (i.j) pair.  */+   short i,j,hx;+   short length;+   short *stack;+   short *table;++   length = (short) strlen(structure);+   stack = (short *) vrna_alloc(sizeof(short)*(length+1));+   table = (short *) vrna_alloc(sizeof(short)*(length+2));+   table[0] = length;++   for (hx=0, i=1; i<=length; i++) {+     switch (structure[i-1]) {+     case '<':+       stack[hx++]=i;+       break;+     case '>':+       j = stack[--hx];+       if (hx<0) {+         vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+       }+       table[i]=j;+       table[j]=i;+       break;+     default:   /* unpaired base, usually '.' */+       table[i]= table[i];+       break;+     }+   }+   if (hx!=0) {+     vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+   }+   free(stack);+   return table ;+}++++PUBLIC short *+vrna_pt_ali_get(const char *structure){++    /* returns array representation of structure.+       table[i] is 0 if unpaired or j if (i.j) pair.  */+   short i,j,hx;+   short length;+   short *stack;+   short *table;++   length = (short) strlen(structure);+   stack = (short *) vrna_alloc(sizeof(short)*(length+1));+   table = (short *) vrna_alloc(sizeof(short)*(length+2));+   table[0] = length;++   for (hx=0, i=1; i<=length; i++) {+      switch (structure[i-1]) {+       case '(':+         stack[hx++]=i;+         break;+       case ')':+         j = stack[--hx];+         if (hx<0) {+            vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+         }+         table[i]=j;+         table[j]=i;+         break;+       default:   /* unpaired base, usually '.' */+         table[i]= 0;+         break;+      }+   }+   for (hx=0, i=1; i<=length; i++) {+      switch (structure[i-1]) {+       case '<':+         stack[hx++]=i;+         break;+       case '>':+         j = stack[--hx];+         if (hx<0) {+            vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+         }+         table[i]=j;+         table[j]=i;+         break;+       default:   /* unpaired base, usually '.' */+         table[i]= table[i];+         break;+      }+   }+   for (hx=0, i=1; i<=length; i++) {+     switch (structure[i-1]) {+     case '[':+       stack[hx++]=i;+       break;+     case ']':+       j = stack[--hx];+       if (hx<0) {+         vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+       }+       table[i]=j;+       table[j]=i;+       break;+     default:   /* unpaired base, usually '.' */+       break;+     }+   }+   if (hx!=0) {+      vrna_message_error("%s\nunbalanced brackets in make_pair_table", structure);+   }+   free(stack);+   return(table);+}++PUBLIC short *+vrna_ptable_copy(const short *pt){+  short *table = (short *)vrna_alloc(sizeof(short) * (pt[0]+2));+  memcpy(table, pt, sizeof(short)*(pt[0]+2));+  return table;+}+++PUBLIC int *+vrna_loopidx_from_ptable(const short *pt){++  /* number each position by which loop it belongs to (positions start+     at 1) */+  int i,hx,l,nl;+  int length;+  int *stack = NULL;+  int *loop = NULL;++  length = pt[0];+  stack  = (int *) vrna_alloc(sizeof(int)*(length+1));+  loop   = (int *) vrna_alloc(sizeof(int)*(length+2));+  hx=l=nl=0;++  for (i=1; i<=length; i++) {+    if ((pt[i] != 0) && (i < pt[i])) { /* ( */+      nl++; l=nl;+      stack[hx++]=i;+    }+    loop[i]=l;++    if ((pt[i] != 0) && (i > pt[i])) { /* ) */+      --hx;+      if (hx>0)+        l = loop[stack[hx-1]];  /* index of enclosing loop   */+      else l=0;                 /* external loop has index 0 */+      if (hx<0) {+        vrna_message_error("unbalanced brackets in make_pair_table");+      }+    }+  }+  loop[0] = nl;+  free(stack);+  return (loop);+}++PUBLIC char *+vrna_db_from_ptable(short *pt){++  int i;+  char *dotbracket = NULL;+  if(pt){+    dotbracket = (char *)vrna_alloc((pt[0]+1)*sizeof(char));+    memset(dotbracket, '.', pt[0]);++    for(i=1; i<=pt[0]; i++){+      if(pt[i] > i){+        dotbracket[i-1] = '(';+        dotbracket[pt[i]-1] = ')';+      }+    }+    dotbracket[i-1] = '\0';+  }+  return dotbracket;+}++/*---------------------------------------------------------------------------*/++PUBLIC int+vrna_bp_distance(const char *str1, const char *str2){++  /* dist = {number of base pairs in one structure but not in the other} */+  /* same as edit distance with pair_open pair_close as move set */+   int dist;+   short i,l;+   short *t1, *t2;++   dist = 0;+   t1 = vrna_ptable(str1);+   t2 = vrna_ptable(str2);++   l = (t1[0]<t2[0])?t1[0]:t2[0];    /* minimum of the two lengths */++   for (i=1; i<=l; i++)+     if (t1[i]!=t2[i]) {+       if (t1[i]>i) dist++;+       if (t2[i]>i) dist++;+     }+   free(t1); free(t2);+   return dist;+}++/* get a matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j+*  access it via iindx!!!+*/+PUBLIC unsigned int *+vrna_refBPcnt_matrix( const short *reference_pt,+                      unsigned int turn){++  unsigned int i,j,k,ij,length;+  int *iindx;+  unsigned int *array;+  unsigned int size;+  length = (unsigned int)reference_pt[0];+  size  = ((length+1)*(length+2))/2;+  iindx = vrna_idx_row_wise(length);+  array = (unsigned int *) vrna_alloc(sizeof(unsigned int)*size);    /* matrix containing number of basepairs of reference structure1 in interval [i,j] */;+  for (k=0; k<=turn; k++)+    for (i=1; i<=length-k; i++) {+      j=i+k;+      ij = iindx[i]-j;+      array[ij] = 0;+    }++  for (i = length-turn-1; i >= 1; i--)+    for (j = i+turn+1; j <= length; j++){+      int bps;+      ij = iindx[i]-j;+      bps = array[ij+1];+      if((i<=(unsigned int)reference_pt[j]) && ((unsigned int)reference_pt[j] < j))+        bps++;+      array[ij] = bps;+    }+  free(iindx);+  return array;+}+++PUBLIC unsigned int *+vrna_refBPdist_matrix(const short *pt1,+                      const short *pt2,+                      unsigned int turn){++  unsigned int *array;+  unsigned int n, size, i, j, ij, d;+  n = (unsigned int)pt1[0];+  size = ((n+1)*(n+2))/2;+  array = (unsigned int *)vrna_alloc(sizeof(unsigned int) * size);+  int *iindx = vrna_idx_row_wise(n);+  for(i = n - turn - 1; i>=1; i--){+    d = 0;+    for(j = i+turn+1; j <= n; j++){+      ij = iindx[i]-j;+      d = array[ij+1];+      if(pt1[j] != pt2[j]){+        if(i <= (unsigned int)pt1[j] && (unsigned int)pt1[j] < j){+          /* we got an additional base pair in reference structure 1 */+          d++;+        }+        if(i <= (unsigned int)pt2[j] && (unsigned int)pt2[j] < j){+          /* we got another base pair in reference structure 2 */+          d++;+        }+      }+      array[ij] = d;++    }+  }+  free(iindx);+  return array;+}++PUBLIC char+vrna_bpp_symbol(const float *x){++/*  if( ((x[1]-x[2])*(x[1]-x[2]))<0.1&&x[0]<=0.677) return '|'; */+  if( x[0] > 0.667 )  return '.';+  if( x[1] > 0.667 )  return '(';+  if( x[2] > 0.667 )  return ')';+  if( (x[1]+x[2]) > x[0] ) {+    if( (x[1]/(x[1]+x[2])) > 0.667) return '{';+    if( (x[2]/(x[1]+x[2])) > 0.667) return '}';+    else return '|';+  }+  if( x[0] > (x[1]+x[2]) ) return ',';+  return ':';+}++PUBLIC char *+vrna_db_from_probs(const FLT_OR_DBL *p,+                    unsigned int length){++  int    i, j, *index;+  float  P[3];   /* P[][0] unpaired, P[][1] upstream p, P[][2] downstream p */+  char  *s;++  index = vrna_idx_row_wise(length);+  s     = (char *)vrna_alloc(sizeof(char) * (length + 1));++  for( j=1; j<=length; j++ ) {+    P[0] = 1.0;+    P[1] = P[2] = 0.0;+    for( i=1; i<j; i++) {+      P[2] += (float)p[index[i]-j];    /* j is paired downstream */+      P[0] -= (float)p[index[i]-j];    /* j is unpaired */+    }+    for( i=j+1; i<=length; i++ ) {+      P[1] += (float)p[index[j]-i];    /* j is paired upstream */+      P[0] -= (float)p[index[j]-i];    /* j is unpaired */+    }+    s[j-1] = vrna_bpp_symbol(P);+  }+  s[length] = '\0';+  free(index);++  return s;+}++PUBLIC void+vrna_letter_structure(char *structure,+                      vrna_bp_stack_t *bp,+                      unsigned int length){++  int   n, k, x, y;+  char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";++  memset(structure, '.', length);+  structure[length] = '\0';++  for (n = 0, k = 1; k <= bp[0].i; k++) {+    y = bp[k].j;+    x = bp[k].i;+    if (x-1 > 0 && y+1 <= length) {+      if (structure[x-2] != ' ' && structure[y] == structure[x-2]) {+        structure[x-1] = structure[x-2];+        structure[y-1] = structure[x-1];+        continue;+      }+    }+    if (structure[x] != ' ' && structure[y-2] == structure[x]) {+      structure[x-1] = structure[x];+      structure[y-1] = structure[x-1];+      continue;+    }+    n++;+    structure[x-1] = alpha[n-1];+    structure[y-1] = alpha[n-1];+  }+}++/*---------------------------------------------------------------------------*/++PUBLIC char *+vrna_db_from_bp_stack(vrna_bp_stack_t *bp,+                      unsigned int length){++  int k, i, j, temp;+  char *structure;++  structure = vrna_alloc(sizeof(char) * (length + 1));++  if(length > 0)+    memset(structure, '.', length);++  structure[length] = '\0';++  for (k = 1; k <= bp[0].i; k++) {+    i=bp[k].i;+    j=bp[k].j;+    if (i>length) i-=length;+    if (j>length) j-=length;+    if (i>j) {+      temp=i; i=j; j=temp;+    }+    if(i == j){ /* Gquad bonds are marked as bp[i].i == bp[i].j */+      structure[i-1] = '+';+    } else { /* the following ones are regular base pairs */+      structure[i-1] = '(';+      structure[j-1] = ')';+    }+  }+  return structure;+}++PUBLIC vrna_plist_t *+vrna_plist( const char *struc,+            float pr){++  /* convert bracket string to plist */+  short *pt;+  int i, k = 0, size, n;+  vrna_plist_t *gpl, *ptr, *pl;++  size  = strlen(struc);+  n     = 2;++  pt  = vrna_ptable(struc);+  pl = (vrna_plist_t *)vrna_alloc(n*size*sizeof(vrna_plist_t));+  for(i = 1; i < size; i++){+    if(pt[i]>i){+      (pl)[k].i      = i;+      (pl)[k].j      = pt[i];+      (pl)[k].p      = pr;+      (pl)[k++].type = 0;+    }+  }++  gpl = get_plist_gquad_from_db(struc, pr);+  for(ptr = gpl; ptr->i != 0; ptr++){+    if (k == n * size - 1){+      n *= 2;+      pl = (vrna_plist_t *)vrna_realloc(pl, n * size * sizeof(vrna_plist_t));+    }+    (pl)[k].i      = ptr->i;+    (pl)[k].j      = ptr->j;+    (pl)[k].p       = ptr->p;+    (pl)[k++].type = ptr->type;+  }+  free(gpl);++  (pl)[k].i      = 0;+  (pl)[k].j      = 0;+  (pl)[k].p      = 0.;+  (pl)[k++].type = 0.;+  free(pt);+  pl = (vrna_plist_t *)vrna_realloc(pl, k * sizeof(vrna_plist_t));++  return pl;+}++PUBLIC vrna_plist_t *+vrna_plist_from_probs(vrna_fold_compound_t *vc,+                    double cut_off){++  if(!vc){+    vrna_message_error("vrna_pl_get_from_pr: run vrna_pf_fold first!");+  } else if( !vc->exp_matrices->probs){+    vrna_message_error("vrna_pl_get_from_pr: probs==NULL!");+  }++  return wrap_plist(vc, cut_off);+}++PUBLIC  char *+vrna_db_from_plist(vrna_plist_t *pairs,+              unsigned int n){++  vrna_plist_t *ptr;+  char  *structure = NULL;+  int   i;++  if(n > 0){+    structure = (char *)vrna_alloc(sizeof(char) * (n+1));+    memset(structure, '.', n);+    structure[n] = '\0';++    for(ptr = pairs; (*ptr).i; ptr++){+      if(((*ptr).i < n) && ((*ptr).j <= n)){+        structure[(*ptr).i - 1] = '(';+        structure[(*ptr).j - 1] = ')';+      }+    }+  }+  return structure;+}+++PUBLIC int+vrna_plist_append(vrna_plist_t        **target,+                  const vrna_plist_t  *list){++  int                 size1, size2;+  const vrna_plist_t  *ptr;++  if((target) && (list)){+    size1 = size2 = 0;++    if(*target)+      for(ptr = *target; ptr->i; size1++, ptr++);++    for(ptr = list; ptr->i; size2++, ptr++);++    *target = (vrna_plist_t *)vrna_realloc(*target, sizeof(vrna_plist_t) * (size1 + size2 + 1));++    if(*target){+      memcpy(*target + size1, list, sizeof(vrna_plist_t) * size2);+      (*target)[size1 + size2].i = (*target)[size1 + size2].j = 0;+      return 1;+    }+  }++  return 0;+}+++PRIVATE vrna_plist_t *+wrap_get_plist( vrna_mx_pf_t *matrices,+                int length,+                int *index,+                short *S,+                vrna_exp_param_t *pf_params,+                double cut_off){++  int i, j, k, n, count, gquad;+  FLT_OR_DBL  *probs, *G, *scale;+  vrna_plist_t         *pl;++  probs     = matrices->probs;+  G         = matrices->G;+  scale     = matrices->scale;+  gquad     = pf_params->model_details.gquad;++  count = 0;+  n     = 2;++  /* first guess of the size needed for pl */+  pl = (vrna_plist_t *)vrna_alloc(n*length*sizeof(vrna_plist_t));++  for (i=1; i<length; i++) {+    for (j=i+1; j<=length; j++) {+      /* skip all entries below the cutoff */+      if (probs[index[i]-j] < (FLT_OR_DBL)cut_off) continue;++      /* do we need to allocate more memory? */+      if (count == n * length - 1){+        n *= 2;+        pl = (vrna_plist_t *)vrna_realloc(pl, n * length * sizeof(vrna_plist_t));+      }++      /* check for presence of gquadruplex */+      if(gquad && (S[i] == 3) && (S[j] == 3)){+        /* add probability of a gquadruplex at position (i,j)+           for dot_plot+        */+        (pl)[count].i      = i;+        (pl)[count].j      = j;+        (pl)[count].p      = (float)probs[index[i] - j];+        (pl)[count++].type = 1;+        /* now add the probabilies of it's actual pairing patterns */+        vrna_plist_t *inner, *ptr;+        inner = get_plist_gquad_from_pr(S, i, j, G, probs, scale, pf_params);+        for(ptr=inner; ptr->i != 0; ptr++){+            if (count == n * length - 1){+              n *= 2;+              pl = (vrna_plist_t *)vrna_realloc(pl, n * length * sizeof(vrna_plist_t));+            }+            /* check if we've already seen this pair */+            for(k = 0; k < count; k++)+              if(((pl)[k].i == ptr->i) && ((pl)[k].j == ptr->j))+                break;+            (pl)[k].i      = ptr->i;+            (pl)[k].j      = ptr->j;+            (pl)[k].type = 0;+            if(k == count){+              (pl)[k].p  = ptr->p;+              count++;+            } else+              (pl)[k].p  += ptr->p;+        }+      } else {+          (pl)[count].i      = i;+          (pl)[count].j      = j;+          (pl)[count].p      = (float)probs[index[i] - j];+          (pl)[count++].type = 0;+      }+    }+  }+  /* mark the end of pl */+  (pl)[count].i    = 0;+  (pl)[count].j    = 0;+  (pl)[count].type = 0;+  (pl)[count++].p  = 0.;+  /* shrink memory to actual size needed */+  pl = (vrna_plist_t *)vrna_realloc(pl, count * sizeof(vrna_plist_t));++  return pl;+}++PRIVATE vrna_plist_t *+wrap_plist( vrna_fold_compound_t *vc,+            double cut_off){++  short             *S;+  int               i, j, k, n, m, count, gquad, length, *index;+  FLT_OR_DBL        *probs, *G, *scale;+  vrna_plist_t      *pl;+  vrna_mx_pf_t      *matrices;+  vrna_exp_param_t  *pf_params;++  S         = vc->sequence_encoding2;+  index     = vc->iindx;+  length    = vc->length;+  pf_params = vc->exp_params;+  matrices  = vc->exp_matrices;+  probs     = matrices->probs;+  G         = matrices->G;+  scale     = matrices->scale;+  gquad     = pf_params->model_details.gquad;++  count = 0;+  n     = 2;++  /* first guess of the size needed for pl */+  pl = (vrna_plist_t *)vrna_alloc(n*length*sizeof(vrna_plist_t));++  for (i=1; i<length; i++) {+    for (j=i+1; j<=length; j++) {++      /* skip all entries below the cutoff */+      if(probs[index[i]-j] < (FLT_OR_DBL)cut_off)+        continue;++      /* do we need to allocate more memory? */+      if (count == n * length - 1){+        n *= 2;+        pl = (vrna_plist_t *)vrna_realloc(pl, n * length * sizeof(vrna_plist_t));+      }++      /* check for presence of gquadruplex */+      if(gquad && (S[i] == 3) && (S[j] == 3)){+        /* add probability of a gquadruplex at position (i,j)+           for dot_plot+        */+        (pl)[count].i      = i;+        (pl)[count].j      = j;+        (pl)[count].p      = (float)probs[index[i] - j];+        (pl)[count++].type = VRNA_PLIST_TYPE_GQUAD;+        /* now add the probabilies of it's actual pairing patterns */+        vrna_plist_t *inner, *ptr;+        inner = get_plist_gquad_from_pr(S, i, j, G, probs, scale, pf_params);+        for(ptr=inner; ptr->i != 0; ptr++){+            if (count == n * length - 1){+              n *= 2;+              pl = (vrna_plist_t *)vrna_realloc(pl, n * length * sizeof(vrna_plist_t));+            }+            /* check if we've already seen this pair */+            for(k = 0; k < count; k++)+              if(((pl)[k].i == ptr->i) && ((pl)[k].j == ptr->j))+                break;+            (pl)[k].i      = ptr->i;+            (pl)[k].j      = ptr->j;+            (pl)[k].type = VRNA_PLIST_TYPE_BASEPAIR;+            if(k == count){+              (pl)[k].p  = ptr->p;+              count++;+            } else+              (pl)[k].p  += ptr->p;+        }+      } else {+          (pl)[count].i      = i;+          (pl)[count].j      = j;+          (pl)[count].p      = (float)probs[index[i] - j];+          (pl)[count++].type = VRNA_PLIST_TYPE_BASEPAIR;+      }+    }+  }++  /* check unstructured domains */+  if(vc->domains_up){+    vrna_ud_t *domains_up;+    domains_up = vc->domains_up;++    if(domains_up->probs_get)+      for(i = 1; i <= length; i++)+        for(m = 0; m < domains_up->motif_count; m++){+          FLT_OR_DBL pp;+          j = i + domains_up->motif_size[m] - 1;+          pp = 0.;+          pp += domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP, m, domains_up->data);+          pp += domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP, m, domains_up->data);+          pp += domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP, m, domains_up->data);+          pp += domains_up->probs_get(vc, i, j, VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP, m, domains_up->data);+          if(pp >= (FLT_OR_DBL)cut_off){++            /* do we need to allocate more memory? */+            if (count == n * length - 1){+              n *= 2;+              pl = (vrna_plist_t *)vrna_realloc(pl, n * length * sizeof(vrna_plist_t));+            }++            (pl)[count].i      = i;+            (pl)[count].j      = j;+            (pl)[count].p      = (float)pp;+            (pl)[count++].type = VRNA_PLIST_TYPE_UD_MOTIF;+          }+        }+  }++  /* mark the end of pl */+  (pl)[count].i    = 0;+  (pl)[count].j    = 0;+  (pl)[count].type = 0;+  (pl)[count++].p  = 0.;+  /* shrink memory to actual size needed */+  pl = (vrna_plist_t *)vrna_realloc(pl, count * sizeof(vrna_plist_t));++  return pl;+}++PUBLIC vrna_hx_t *+vrna_hx_from_ptable(short *pt){++  int i, k, n, l, s, *stack;+  vrna_hx_t *list;++  n = pt[0];+  l = 0;+  s = 1;+  list  = (vrna_hx_t *)vrna_alloc(sizeof(vrna_hx_t) * n/2);+  stack = (int *)vrna_alloc(sizeof(int) * n/2);++  stack[s] = 1;++  do{+    for(i = stack[s--]; i <= n; i++){+      if(pt[i] > (short)i){  /* found a base pair */+        k = i;+        /* go through stack */+        for(;pt[k+1] == pt[k] - 1; k++);+        list[l].start  = i;+        list[l].end    = pt[i];+        list[l].length = k - i + 1;+        list[l].up5 = list[l].up3 = 0;+        l++;+        stack[++s] = pt[i] + 1;+        stack[++s] = k + 1;+        break;+      } else if(pt[i]) { /* end of region */+        break;+      }+    }+  } while (s > 0);++  list = vrna_realloc(list, (l+1)*sizeof(vrna_hx_t));+  list[l].start = list[l].end = list[l].length = list[l].up5 = list[l].up3 = 0;++  free(stack);+  return list;+}++PUBLIC vrna_hx_t *+vrna_hx_merge(const vrna_hx_t *list, int maxdist){+  int merged, i, j, s, neighbors, n;+  vrna_hx_t *merged_list;++  for(n=0; list[n].length > 0; n++); /* check size of list */++  merged_list = (vrna_hx_t *)vrna_alloc(sizeof(vrna_hx_t) * (n+1));+  memcpy(merged_list, list, sizeof(vrna_hx_t) * (n+1));++  s = n+1;++  do{+    merged = 0;+    for(i = 1; merged_list[i].length > 0; i++){+      /*+        GOAL: merge two consecutive helices i and i-1, if i-1+        subsumes i, and not more than i+      */++      /* 1st, check for neighbors */+      neighbors = 0;+      for(j = i + 1; merged_list[j].length > 0; j++){+        if(merged_list[j].start > merged_list[i-1].end) break;+        if(merged_list[j].start < merged_list[i].end) continue;+        neighbors = 1;+      }+      if(neighbors) continue;++      /* check if we may merge i with i-1 */+      if(merged_list[i].end < merged_list[i-1].end){+        merged_list[i-1].up5 += merged_list[i].start+                                - merged_list[i-1].start+                                - merged_list[i-1].length+                                - merged_list[i-1].up5+                                + merged_list[i].up5;+        merged_list[i-1].up3 += merged_list[i-1].end+                                - merged_list[i-1].length+                                - merged_list[i-1].up3+                                - merged_list[i].end+                                + merged_list[i].up3;+        merged_list[i-1].length += merged_list[i].length;+        /* splice out helix i */+        memmove(merged_list+i, merged_list+i+1, sizeof(vrna_hx_t)*(n-i));+        s--;+        merged = 1;+        break;+      }+    }+  } while(merged);++  merged_list = vrna_realloc(merged_list, sizeof(vrna_hx_t) * s);++  return merged_list;+}+++PUBLIC char *+vrna_db_to_element_string(const char *structure){++  char    *elements;+  int     n, i;+  short   *pt;++  elements = NULL;++  if(structure){+    n         = (int)strlen(structure);+    pt        = vrna_ptable(structure);+    elements  = (char *)vrna_alloc(sizeof(char) * (n + 1));++    for(i = 1; i <= n; i++){+      if(!pt[i])  /* mark nucleotides in exterior loop */+        elements[i-1] = 'e';+      else {+        assign_elements_pair(pt, i, pt[i], elements);+        i = pt[i];+      }+    }++    elements[n] = '\0';+    free(pt);+  }++  return elements;+}++PRIVATE void+assign_elements_pair(short *pt, int i, int j, char *elements){++  int p, k, num_pairs;++  num_pairs = 0;+  /* first, determine the number of pairs (i,j) is enclosing */+  for(k = i + 1; k < j; k++){+    if(k < pt[k]){+      num_pairs++;+      k = pt[k];+    }+  }++  switch(num_pairs){+    case 0:   /* hairpin loop */+              elements[i - 1] = elements[j - 1] = 'H';+              for(k = i + 1; k < j; k++)+                elements[k-1] = 'h';+              break;++    case 1:   /* interior loop */+              elements[i - 1] = elements[j - 1] = 'I';+              for(k = i + 1; k < j; k++){+                if(!pt[k])+                  elements[k-1] = 'i';+                else {+                  p = k;+                  k = pt[k];+                }+              }+              assign_elements_pair(pt, p, pt[p], elements);+              break;++    default:  /* multibranch loop */+              elements[i - 1] = elements[j - 1] = 'M';+              for(k = i + 1; k < j; k++){+                if(!pt[k])+                  elements[k-1] = 'm';+                else {+                  assign_elements_pair(pt, k, pt[k], elements);+                  k = pt[k];+                }+              }+              break;+  }+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/+++PUBLIC char *+pack_structure(const char *struc){++  return vrna_db_pack(struc);+}++PUBLIC char *+unpack_structure(const char *packed){++  return vrna_db_unpack(packed);+}++PUBLIC void+parenthesis_structure(char *structure,+                      vrna_bp_stack_t *bp,+                      int length){++  char *s = vrna_db_from_bp_stack(bp, length);+  strncpy(structure, s, length + 1);+  free(s);+}++PUBLIC void+letter_structure( char *structure,+                  vrna_bp_stack_t *bp,+                  int length){++  vrna_letter_structure(structure, bp, length);+}++PUBLIC void+parenthesis_zuker(char *structure,+                  vrna_bp_stack_t *bp,+                  int length){++  char *s = vrna_db_from_bp_stack(bp, length);+  strncpy(structure, s, length + 1);+  free(s);+}++PUBLIC void+assign_plist_from_pr( vrna_plist_t **pl,+                      FLT_OR_DBL *probs,+                      int length,+                      double cut_off){++  int              *index;+  vrna_mx_pf_t     *matrices;+  vrna_md_t        md;+  vrna_exp_param_t *pf_params;++  index     = vrna_idx_row_wise(length);+  matrices  = (vrna_mx_pf_t *)vrna_alloc(sizeof(vrna_mx_pf_t));++  set_model_details(&md);+  md.gquad        = 0;+  pf_params       = vrna_exp_params(&md);+  matrices->probs = probs;++  *pl = wrap_get_plist( matrices,+                        length,+                        index,+                        NULL,+                        pf_params,+                        cut_off);++  free(index);+  free(pf_params);+  free(matrices);+}++PUBLIC void+assign_plist_from_db( vrna_plist_t **pl,+                      const char *struc,+                      float pr){++  *pl = vrna_plist(struc, pr);+}++PUBLIC short *+make_pair_table(const char *structure){++  return vrna_ptable(structure);+}++PUBLIC short *+copy_pair_table(const short *pt){++  return vrna_ptable_copy(pt);+}++PUBLIC short *+make_pair_table_pk(const char *structure){++  return vrna_pt_pk_get(structure);+}++PUBLIC short *+make_pair_table_snoop(const char *structure){++  return vrna_pt_snoop_get(structure);+}++PUBLIC short *+alimake_pair_table(const char *structure){++  return vrna_pt_ali_get(structure);+}++PUBLIC int *+make_loop_index_pt(short *pt){++  return vrna_loopidx_from_ptable((const short*)pt);+}++PUBLIC int+bp_distance(const char *str1, const char *str2){++  return vrna_bp_distance(str1, str2);+}++PUBLIC unsigned int *+make_referenceBP_array( short *reference_pt,+                        unsigned int turn){++  return vrna_refBPcnt_matrix((const short *)reference_pt, turn);+}++PUBLIC unsigned int *+compute_BPdifferences(short *pt1,+                      short *pt2,+                      unsigned int turn){++  return vrna_refBPdist_matrix((const short *)pt1, (const short *)pt2, turn);+}++PUBLIC char+bppm_symbol(const float *x){++  return vrna_bpp_symbol(x);+}++PUBLIC void+bppm_to_structure(char *structure,+                  FLT_OR_DBL *p,+                  unsigned int length){++  char *s = vrna_db_from_probs((const FLT_OR_DBL *)p, length);+  memcpy(structure, s, length);+  structure[length] = '\0';+  free(s);+}++#endif
+ C/ViennaRNA/structure_utils.h view
@@ -0,0 +1,449 @@+#ifndef VIENNA_RNA_PACKAGE_STRUCT_UTILS_H+#define VIENNA_RNA_PACKAGE_STRUCT_UTILS_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     structure_utils.h+ *  @ingroup  utils+ *  @brief    Various utility- and helper-functions for secondary structure parsing, converting, etc.+ */++/**+ *  @{+ *  @ingroup   struct_utils+ */++/**+ *  @brief Convenience typedef for data structure #vrna_hx_s+ */+typedef struct vrna_hx_s  vrna_hx_t;++#include <stdio.h>++#include <ViennaRNA/data_structures.h>++/**+ *  @brief  Data structure representing an entry of a helix list+ */+struct vrna_hx_s {+  unsigned int start;+  unsigned int end;+  unsigned int length;+  unsigned int up5;+  unsigned int up3;+};++/**+ *  @brief Pack secondary secondary structure, 5:1 compression using base 3 encoding+ *+ *  Returns a binary string encoding of the secondary structure using+ *  a 5:1 compression scheme. The string is NULL terminated and can+ *  therefore be used with standard string functions such as strcmp().+ *  Useful for programs that need to keep many structures in memory.+ *+ *  @see  vrna_db_unpack()+ *  @param struc    The secondary structure in dot-bracket notation+ *  @return         The binary encoded structure+ */+char *vrna_db_pack(const char *struc);++/**+ *  @brief Unpack secondary structure previously packed with vrna_db_pack()+ *+ *  Translate a compressed binary string produced by vrna_db_pack() back into+ *  the familiar dot-bracket notation.+ *+ *  @see  vrna_db_pack()+ *  @param packed   The binary encoded packed secondary structure+ *  @return         The unpacked secondary structure in dot-bracket notation+ */+char *vrna_db_unpack(const char *packed);++/**+ *  @brief Create a pair table of a secondary structure+ *+ *  Returns a newly allocated table, such that table[i]=j if (i.j) pair+ *  or 0 if i is unpaired, table[0] contains the length of the structure.+ *+ *  @param  structure The secondary structure in dot-bracket notation+ *  @return           A pointer to the created pair_table+ */+short *vrna_ptable(const char *structure);+++/**+ *  @brief Create a pair table of a secondary structure (pseudo-knot version)+ *+ *  Returns a newly allocated table, such that table[i]=j if (i.j) pair+ *  or 0 if i is unpaired, table[0] contains the length of the structure.+ *+ *  In contrast to vrna_ptable() this function also recognizes the base pairs+ *  denoted by '[' and ']' brackets.+ *+ *  @param  structure The secondary structure in (extended) dot-bracket notation+ *  @return           A pointer to the created pair_table+ */+short *vrna_pt_pk_get(const char *structure);++/**+ *  @brief Get an exact copy of a pair table+ *+ *  @param pt The pair table to be copied+ *  @return   A pointer to the copy of 'pt' + */+short *vrna_ptable_copy(const short *pt);++/**+ * @brief Create a pair table of a secondary structure (snoop align version)+ *+ */+short *vrna_pt_ali_get(const char *structure);++/**+ * @brief Create a pair table of a secondary structure (snoop version)+ *+ *  returns a newly allocated table, such that:  table[i]=j if (i.j) pair or+ *  0 if i is unpaired, table[0] contains the length of the structure.+ *  The special pseudoknotted H/ACA-mRNA structure is taken into account.+ */+short *vrna_pt_snoop_get(const char *structure);++/**+ *  @brief Get a loop index representation of a structure+ */+int *vrna_loopidx_from_ptable(const short *pt);++/**+ *  @brief Convert a pair table into dot-parenthesis notation+ *+ *  @param pt The pair table to be copied+ *  @return   A char pointer to the dot-bracket string+ */+char *vrna_db_from_ptable(short *pt);+++/**+ *  @brief Compute the "base pair" distance between two secondary structures s1 and s2.+ * + *  The sequences should have the same length.+ *  dist = number of base pairs in one structure but not in the other+ *  same as edit distance with open-pair close-pair as move-set+ * + *  @param str1   First structure in dot-bracket notation+ *  @param str2   Second structure in dot-bracket notation+ *  @return       The base pair distance between str1 and str2+ */+int vrna_bp_distance( const char *str1,+                      const char *str2);++/**+ *  @brief Make a reference base pair count matrix+ *+ *  Get an upper triangular matrix containing the number of basepairs of a reference+ *  structure for each interval [i,j] with i<j. Access it via iindx!!!+ */+unsigned int  *vrna_refBPcnt_matrix(const short *reference_pt,+                                    unsigned int turn);++/**+ *  @brief Make a reference base pair distance matrix+ *+ *  Get an upper triangular matrix containing the base pair distance of two+ *  reference structures for each interval [i,j] with i<j. Access it via iindx!!!+ *+ */+unsigned int  *vrna_refBPdist_matrix( const short *pt1,+                                      const short *pt2,+                                      unsigned int turn);++/**+ *  @brief Create a dot-bracket like structure string from base pair probability matrix+ */+char *vrna_db_from_probs( const FLT_OR_DBL *pr,+                          unsigned int length);++/**+ *  @brief Get a pseudo dot bracket notation for a given probability information+ */+char vrna_bpp_symbol(const float *x);++/**+ *  @brief Create a dot-backet/parenthesis structure from backtracking stack+ *+ *  This function is capable to create dot-bracket structures from suboptimal+ *  structure prediction sensu M. Zuker+ *+ *  @param bp     Base pair stack containing the traced base pairs+ *  @param length The length of the structure+ *  @return       The secondary structure in dot-bracket notation as+ *                provided in the input+ */+char *vrna_db_from_bp_stack(vrna_bp_stack_t *bp,+                            unsigned int length);++void vrna_letter_structure( char *structure,+                            vrna_bp_stack_t *bp,+                            unsigned int length);++/**+ *  @brief Create a #vrna_plist_t from a dot-bracket string+ * + *  The dot-bracket string is parsed and for each base pair an+ *  entry in the plist is created. The probability of each pair in+ *  the list is set by a function parameter.+ * + *  The end of the plist is marked by sequence positions i as well as j+ *  equal to 0. This condition should be used to stop looping over its+ *  entries+ * + *  @param struc  The secondary structure in dot-bracket notation+ *  @param pr     The probability for each base pair used in the plist+ *  @return       The plist array+ */+vrna_plist_t *vrna_plist(const char *struc, float pr);++/**+ *  @brief Create a #vrna_plist_t from base pair probability matrix+ * + *  The probability matrix provided via the #vrna_fold_compound_t is parsed+ *  and all pair probabilities above the given threshold are used to create+ *  an entry in the plist+ * + *  The end of the plist is marked by sequence positions i as well as j+ *  equal to 0. This condition should be used to stop looping over its+ *  entries+ * + *  @ingroup            pf_fold+ *  @param[in]  vc        The fold compound+ *  @param[in]  cut_off   The cutoff value+ *  @return               A pointer to the plist that is to be created+ */+vrna_plist_t *vrna_plist_from_probs(vrna_fold_compound_t *vc, double cut_off);++/**+ *  @brief  Convert a list of base pairs into dot-bracket notation+ *+ *  @see vrna_plist()+ *  @param  pairs   A #vrna_plist_t containing the pairs to be included in+ *                  the dot-bracket string+ *  @param  n       The length of the structure (number of nucleotides)+ *  @return         The dot-bracket string containing the provided base pairs+ */+char *vrna_db_from_plist(vrna_plist_t *pairs, unsigned int n);++char *vrna_db_to_element_string(const char *structure);++vrna_hx_t *vrna_hx_from_ptable(short *pt);+vrna_hx_t *vrna_hx_merge(const vrna_hx_t *list, int maxdist);++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++/**+ *  @brief Create a #vrna_plist_t from a dot-bracket string+ * + *  The dot-bracket string is parsed and for each base pair an+ *  entry in the plist is created. The probability of each pair in+ *  the list is set by a function parameter.+ * + *  The end of the plist is marked by sequence positions i as well as j+ *  equal to 0. This condition should be used to stop looping over its+ *  entries+ * + *  @deprecated   Use vrna_plist() instead+ * + *  @param pl     A pointer to the #vrna_plist_t that is to be created+ *  @param struc  The secondary structure in dot-bracket notation+ *  @param pr     The probability for each base pair+ */+DEPRECATED(void assign_plist_from_db(vrna_plist_t **pl, const char *struc, float pr));++/**+ *  @brief Pack secondary secondary structure, 5:1 compression using base 3 encoding+ *+ *  Returns a binary string encoding of the secondary structure using+ *  a 5:1 compression scheme. The string is NULL terminated and can+ *  therefore be used with standard string functions such as strcmp().+ *  Useful for programs that need to keep many structures in memory.+ *+ *  @deprecated     Use vrna_db_pack() as a replacement+ *  @param struc    The secondary structure in dot-bracket notation+ *  @return         The binary encoded structure+ */+DEPRECATED(char *pack_structure(const char *struc));++/**+ *  @brief Unpack secondary structure previously packed with pack_structure()+ *+ *  Translate a compressed binary string produced by pack_structure() back into+ *  the familiar dot-bracket notation.+ *+ *  @deprecated     Use vrna_db_unpack() as a replacement+ *  @param packed   The binary encoded packed secondary structure+ *  @return         The unpacked secondary structure in dot-bracket notation+ */+DEPRECATED(char *unpack_structure(const char *packed));++/**+ *  @brief Create a pair table of a secondary structure+ *+ *  Returns a newly allocated table, such that table[i]=j if (i.j) pair+ *  or 0 if i is unpaired, table[0] contains the length of the structure.+ *+ *  @deprecated Use vrna_ptable() instead+ *+ *  @param  structure The secondary structure in dot-bracket notation+ *  @return           A pointer to the created pair_table+ */+DEPRECATED(short *make_pair_table(const char *structure));++DEPRECATED(short *make_pair_table_pk(const char *structure));++/**+ *  @brief Get an exact copy of a pair table+ *+ *  @deprecated Use vrna_ptable_copy() instead+ *+ *  @param pt The pair table to be copied+ *  @return   A pointer to the copy of 'pt' + */+DEPRECATED(short *copy_pair_table(const short *pt));++/**+*** Pair table for snoop align+***+*** @deprecated Use vrna_pt_ali_get() instead!+**/+DEPRECATED(short *alimake_pair_table(const char *structure));++/**+*** returns a newly allocated table, such that:  table[i]=j if (i.j) pair or+*** 0 if i is unpaired, table[0] contains the length of the structure.+*** The special pseudoknotted H/ACA-mRNA structure is taken into account.+*** @deprecated Use vrna_pt_snoop_get() instead!+**/+DEPRECATED(short *make_pair_table_snoop(const char *structure));++DEPRECATED(int *make_loop_index_pt(short *pt));++/**+ *  @brief Compute the "base pair" distance between two secondary structures s1 and s2.+ * + *  The sequences should have the same length.+ *  dist = number of base pairs in one structure but not in the other+ *  same as edit distance with open-pair close-pair as move-set+ *+ *  @deprecated   Use vrna_bp_distance instead+ *  @param str1   First structure in dot-bracket notation+ *  @param str2   Second structure in dot-bracket notation+ *  @return       The base pair distance between str1 and str2+ */+DEPRECATED(int bp_distance(const char *str1, const char *str2));++/**+ *  @brief Make a reference base pair count matrix+ *+ *  Get an upper triangular matrix containing the number of basepairs of a reference+ *  structure for each interval [i,j] with i<j. Access it via iindx!!!+ *+ *  @deprecated Use vrna_refBPcnt_matrix() instead+ */+DEPRECATED(unsigned int  *make_referenceBP_array(short *reference_pt,+                                      unsigned int turn));+/**+ *  @brief Make a reference base pair distance matrix+ *+ *  Get an upper triangular matrix containing the base pair distance of two+ *  reference structures for each interval [i,j] with i<j. Access it via iindx!!!+ *+ *  @deprecated Use vrna_refBPdist_matrix() instead+ */+DEPRECATED(unsigned int  *compute_BPdifferences( short *pt1,+                                      short *pt2,+                                      unsigned int turn));++/**+ *  @brief Create a vrna_plist_t from a probability matrix+ * + *  The probability matrix given is parsed and all pair probabilities above+ *  the given threshold are used to create an entry in the plist+ * + *  The end of the plist is marked by sequence positions i as well as j+ *  equal to 0. This condition should be used to stop looping over its+ *  entries+ * + *  @note This function is threadsafe+ *  @deprecated Use vrna_plist_from_probs() instead!+ *+ *  @ingroup            pf_fold+ *  @param[out] pl      A pointer to the vrna_plist_t that is to be created+ *  @param[in]  probs   The probability matrix used for creating the plist+ *  @param[in]  length  The length of the RNA sequence+ *  @param[in]  cutoff  The cutoff value+ */+DEPRECATED(void  assign_plist_from_pr( vrna_plist_t **pl,+                            FLT_OR_DBL *probs,+                            int length,+                            double cutoff));++/**+ *  @brief Create a dot-backet/parenthesis structure from backtracking stack+ *+ *  @deprecated use vrna_parenthesis_structure() instead+ * + *  @note This function is threadsafe+ */+DEPRECATED(void parenthesis_structure(char *structure,+                                      vrna_bp_stack_t *bp,+                                      int length));++/**+ *  @brief Create a dot-backet/parenthesis structure from backtracking stack+ *  obtained by zuker suboptimal calculation in cofold.c+ * + *  @deprecated use vrna_parenthesis_zuker instead+ * + *  @note This function is threadsafe+ */+DEPRECATED(void parenthesis_zuker(char *structure,+                                  vrna_bp_stack_t *bp,+                                  int length));++DEPRECATED(void letter_structure( char *structure,+                                  vrna_bp_stack_t *bp,+                                  int length));++/**+ *  @brief Create a dot-bracket like structure string from base pair probability matrix+ *  @deprecated Use vrna_db_from_probs() instead!+ */+DEPRECATED(void  bppm_to_structure(char *structure, FLT_OR_DBL *pr, unsigned int length));++/**+ *  @brief Get a pseudo dot bracket notation for a given probability information+ *  @deprecated Use vrna_bpp_symbol() instead!+ */+DEPRECATED(char    bppm_symbol(const float *x));++#endif++/**+ * @}+ */++#endif
+ C/ViennaRNA/structured_domains.h view
@@ -0,0 +1,31 @@+#ifndef VIENNA_RNA_PACKAGE_STRUCTURAL_DOMAINS_H+#define VIENNA_RNA_PACKAGE_STRUCTURAL_DOMAINS_H++/**+ *  @file structured_domains.h+ *  @ingroup domains_struc+ *+ *  @brief  This module provides interfaces that deal with additional structured domains in the folding grammar.+ */++/**+ *  @addtogroup domains_struc+ *+ *  @brief  Add and modify structured domains to the RNA folding grammar+ *+ *  This module provides the tools to add and modify structured domains to the production rules of the RNA folding grammar.+ *  Usually this functionality is utilized for incorporating self-enclosed structural modules that exhibit a more or less+ *  complex base pairing pattern.+ *+ */+++typedef struct vrna_structured_domains_s  vrna_sd_t;+++struct vrna_structured_domains_s {+++};++#endif
+ C/ViennaRNA/subopt.c view
@@ -0,0 +1,2070 @@+/*+   suboptimal folding - Stefan Wuchty, Walter Fontana & Ivo Hofacker++                       Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <unistd.h>+#include <ctype.h>+#include <string.h>+#include <math.h>+#include "ViennaRNA/fold.h"+#include "ViennaRNA/constraints.h"+#include "ViennaRNA/utils.h"+#include "ViennaRNA/energy_par.h"+#include "ViennaRNA/fold_vars.h"+#include "list.h"+#include "ViennaRNA/eval.h"+#include "ViennaRNA/params.h"+#include "ViennaRNA/loop_energies.h"+#include "ViennaRNA/cofold.h"+#include "ViennaRNA/gquad.h"+#include "ViennaRNA/subopt.h"++/* hack */+#include "ViennaRNA/color_output.inc"++#ifdef _OPENMP+#include <omp.h>+#endif++#define true              1+#define false             0+#define ON_SAME_STRAND(I,J,C)  (((I)>=(C))||((J)<(C)))++/**+ *  @brief  Sequence interval stack element used in subopt.c+ */+typedef struct INTERVAL {+    int i;+    int j;+    int array_flag;+} INTERVAL;++typedef struct {+    char *structure;+    LIST *Intervals;+    int partial_energy;+    int is_duplex;+    /* int best_energy;   */ /* best attainable energy */+} STATE;++typedef struct {+  LIST          *Intervals;+  LIST          *Stack;+  int           nopush;+} subopt_env;+++struct old_subopt_dat {++  unsigned long max_sol;+  unsigned long n_sol;+  SOLUTION      *SolutionList;+  FILE          *fp;+};++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+PUBLIC  int     subopt_sorted=0;                           /* output sorted by energy */+PUBLIC  int     density_of_states[MAXDOS+1];+PUBLIC  double  print_energy = 9999; /* printing threshold for use with logML */++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/++/* some backward compatibility stuff */+PRIVATE int                 backward_compat           = 0;+PRIVATE vrna_fold_compound_t  *backward_compat_compound = NULL;++#ifdef _OPENMP++#pragma omp threadprivate(backward_compat_compound, backward_compat)++#endif++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++#ifdef VRNA_BACKWARD_COMPAT++PRIVATE SOLUTION *+wrap_subopt(char *seq,+            char *structure,+            vrna_param_t *parameters,+            int delta,+            int is_constrained,+            int is_circular,+            FILE *fp);+#endif++PRIVATE void      make_pair(int i, int j, STATE *state);++/* mark a gquadruplex in the resulting dot-bracket structure */+PRIVATE void      make_gquad(int i, int L, int l[3], STATE *state);++PRIVATE INTERVAL  *make_interval (int i, int j, int ml);+/*@out@*/ PRIVATE STATE *make_state(/*@only@*/LIST *Intervals,+                                    /*@only@*/ /*@null@*/ char *structure,+                                    int partial_energy, int is_duplex, int length);+PRIVATE STATE     *copy_state(STATE * state);+PRIVATE void      print_state(STATE * state);+//PRIVATE void      UNUSED print_stack(LIST * list);+/*@only@*/ PRIVATE LIST *make_list(void);+PRIVATE void      push(LIST * list, /*@only@*/ void *data);+PRIVATE void      *pop(LIST * list);+PRIVATE int       best_attainable_energy(vrna_fold_compound_t *vc, STATE * state);+PRIVATE void      scan_interval(vrna_fold_compound_t *vc, int i, int j, int array_flag, int threshold, STATE * state, subopt_env *env);+PRIVATE void      free_interval_node(/*@only@*/ INTERVAL * node);+PRIVATE void      free_state_node(/*@only@*/ STATE * node);+PRIVATE void      push_back(LIST *Stack, STATE * state);+PRIVATE char*     get_structure(STATE * state);+PRIVATE int       compare(const void *solution1, const void *solution2);+PRIVATE void      make_output(SOLUTION *SL, int cp, FILE *fp);+PRIVATE void      repeat(vrna_fold_compound_t *vc, int i, int j, STATE * state, int part_energy, int temp_energy, int best_energy, int threshold, subopt_env *env);+PRIVATE void      repeat_gquad(vrna_fold_compound_t *vc, int i, int j, STATE *state, int part_energy, int temp_energy, int best_energy, int threshold, subopt_env *env);+++PRIVATE void      old_subopt_print( const char *structure, float energy, void *data);+PRIVATE void      old_subopt_store( const char *structure, float energy, void *data);++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++++/*---------------------------------------------------------------------------*/+/*List routines--------------------------------------------------------------*/+/*---------------------------------------------------------------------------*/++PRIVATE void+make_pair(int i, int j, STATE *state)+{+  state->structure[i-1] = '(';+  state->structure[j-1] = ')';+}++PRIVATE void+make_gquad(int i, int L, int l[3], STATE *state)+{+  int x;+  for(x = 0; x < L; x++){+    state->structure[i - 1 + x] = '+';+    state->structure[i - 1 + x + L + l[0]] = '+';+    state->structure[i - 1 + x + 2*L + l[0] + l[1]] = '+';+    state->structure[i - 1 + x + 3*L + l[0] + l[1] + l[2]] = '+';+  }+}++/*---------------------------------------------------------------------------*/++PRIVATE INTERVAL *+make_interval(int i, int j, int array_flag)+{+  INTERVAL *interval;++  interval = lst_newnode(sizeof(INTERVAL));+  interval->i = i;+  interval->j = j;+  interval->array_flag = array_flag;+  return interval;+}++/*---------------------------------------------------------------------------*/++PRIVATE void+free_interval_node(INTERVAL * node)+{+  lst_freenode(node);+}++/*---------------------------------------------------------------------------*/++PRIVATE void+free_state_node(STATE * node)+{+  free(node->structure);+  if (node->Intervals)+    lst_kill(node->Intervals, lst_freenode);+  lst_freenode(node);+}++/*---------------------------------------------------------------------------*/++PRIVATE STATE *+make_state(LIST * Intervals,+           char *structure,+           int partial_energy,+           int is_duplex,+           int length)+{+  STATE *state;++  state = lst_newnode(sizeof(STATE));++  if (Intervals)+    state->Intervals = Intervals;+  else+    state->Intervals = lst_init();+  if (structure)+    state->structure = structure;+  else {+    int i;+    state->structure = (char *) vrna_alloc(length+1);+    for (i=0; i<length; i++)+      state->structure[i] = '.';+  }++  state->partial_energy = partial_energy;++  return state;+}++/*---------------------------------------------------------------------------*/++PRIVATE STATE *+copy_state(STATE * state)+{+  STATE *new_state;+  void *after;+  INTERVAL *new_interval, *next;++  new_state = lst_newnode(sizeof(STATE));+  new_state->Intervals = lst_init();+  new_state->partial_energy = state->partial_energy;+  /* new_state->best_energy = state->best_energy; */++  if (state->Intervals->count) {+    after = LST_HEAD(new_state->Intervals);+    for ( next = lst_first(state->Intervals); next; next = lst_next(next))+      {+        new_interval = lst_newnode(sizeof(INTERVAL));+        *new_interval = *next;+        lst_insertafter(new_state->Intervals, new_interval, after);+        after = new_interval;+      }+  }+  new_state->structure = strdup(state->structure);+  if (!new_state->structure) vrna_message_error("out of memory");+  return new_state;+}++/*---------------------------------------------------------------------------*/++/*@unused @*/ PRIVATE void+print_state(STATE * state)+{+  INTERVAL *next;++  if (state->Intervals->count)+    {+      printf("%d intervals:\n", state->Intervals->count);+      for (next = lst_first(state->Intervals); next; next = lst_next(next))+        {+          printf("[%d,%d],%d ", next->i, next->j, next->array_flag);+        }+      printf("\n");+    }+  printf("partial structure: %s\n", state->structure);+  printf("\n");+  printf(" partial_energy: %d\n", state->partial_energy);+  /* printf(" best_energy: %d\n", state->best_energy); */+  (void) fflush(stdout);+}++/*---------------------------------------------------------------------------*/++/*@unused @*/ PRIVATE void+print_stack(LIST * list)+{+  void *rec;++  printf("================\n");+  printf("%d states\n", list->count);+  for (rec = lst_first(list); rec; rec = lst_next(rec))+    {+      printf("state-----------\n");+      print_state(rec);+    }+  printf("================\n");+}++/*---------------------------------------------------------------------------*/++PRIVATE LIST *+make_list(void)+{+  return lst_init();+}++/*---------------------------------------------------------------------------*/++PRIVATE void+push(LIST * list, void *data)+{+  lst_insertafter(list, data, LST_HEAD(list));+}++/* PRIVATE void */+/* push_stack(STATE *state) { */ /* keep the stack sorted by energy */+/*   STATE *after, *next; */+/*   nopush = false; */+/*   next = after = LST_HEAD(Stack); */+/*   while ( next = lst_next(next)) { */+/*     if ( next->best_energy >= state->best_energy ) break; */+/*     after = next; */+/*   } */+/*   lst_insertafter(Stack, state, after); */+/* } */++/*---------------------------------------------------------------------------*/++PRIVATE void *+pop(LIST * list)+{+  void *data;++  data = lst_deletenext(list, LST_HEAD(list));+  return data;+}++/*---------------------------------------------------------------------------*/+/*auxiliary routines---------------------------------------------------------*/+/*---------------------------------------------------------------------------*/++PRIVATE int+best_attainable_energy( vrna_fold_compound_t *vc,+                        STATE *state){++  /* evaluation of best possible energy attainable within remaining intervals */++  register int sum;+  INTERVAL        *next;+  vrna_md_t       *md;+  vrna_mx_mfe_t   *matrices;+  int             *indx;++  md        = &(vc->params->model_details);+  matrices  = vc->matrices;+  indx      = vc->jindx;++  sum = state->partial_energy;  /* energy of already found elements */++  for (next = lst_first(state->Intervals); next; next = lst_next(next))+    {+      if (next->array_flag == 0)+        sum += (md->circ) ? matrices->Fc : matrices->f5[next->j];+      else if (next->array_flag == 1)+        sum += matrices->fML[indx[next->j] + next->i];+      else if (next->array_flag == 2)+        sum += matrices->c[indx[next->j] + next->i];+      else if (next->array_flag == 3)+        sum += matrices->fM1[indx[next->j] + next->i];+      else if (next->array_flag == 4)+        sum += matrices->fc[next->i];+      else if (next->array_flag == 5)+        sum += matrices->fc[next->j];+      else if (next->array_flag == 6)+        sum += matrices->ggg[indx[next->j] + next->i];+    }++  return sum;+}++/*---------------------------------------------------------------------------*/++PRIVATE void+push_back(LIST *Stack, STATE * state)+{+  push(Stack, copy_state(state));+  return;+}++/*---------------------------------------------------------------------------*/++PRIVATE char*+get_structure(STATE * state)+{+  char* structure;++  structure = strdup(state->structure);+  return structure;+}++/*---------------------------------------------------------------------------*/+PRIVATE int+compare(const void *solution1, const void *solution2)+{+  if (((SOLUTION *) solution1)->energy > ((SOLUTION *) solution2)->energy)+    return 1;+  if (((SOLUTION *) solution1)->energy < ((SOLUTION *) solution2)->energy)+    return -1;+  return strcmp(((SOLUTION *) solution1)->structure,+                ((SOLUTION *) solution2)->structure);+}++/*---------------------------------------------------------------------------*/++PRIVATE void make_output(SOLUTION *SL, int cp, FILE *fp)  /* prints stuff */+{+  SOLUTION *sol;++  for (sol = SL; sol->structure!=NULL; sol++){+    char *e_string = vrna_strdup_printf(" %6.2f", sol->energy);+    print_structure(fp, sol->structure, e_string);+    free(e_string);+  }+}++PRIVATE STATE *+derive_new_state( int i,+                  int j,+                  STATE *s,+                  int e,+                  int flag){++  STATE     *s_new  = copy_state(s);+  INTERVAL  *ival   = make_interval(i, j, flag);+  push(s_new->Intervals, ival);++  s_new->partial_energy += e;++  return s_new;+}++PRIVATE void+fork_state( int i,+            int j,+            STATE *s,+            int e,+            int flag,+            subopt_env *env){++  STATE *s_new = derive_new_state(i, j, s, e, flag);+  push(env->Stack, s_new);+  env->nopush = false;+}++PRIVATE void+fork_int_state( int i, int j,+                int p, int q,+                STATE *s,+                int e,+                subopt_env *env){++  STATE *s_new = derive_new_state(p, q, s, e, 2);+  make_pair(i, j, s_new);+  make_pair(p, q, s_new);+  push(env->Stack, s_new);+  env->nopush = false;+}++PRIVATE void+fork_state_pair(int i,+                int j,+                STATE *s,+                int e,+                subopt_env *env){++  STATE     *new_state;++  new_state = copy_state(s);+  make_pair(i, j, new_state);+  new_state->partial_energy += e;+  push(env->Stack, new_state);+  env->nopush = false;+}++PRIVATE void+fork_two_states_pair( int i,+                      int j,+                      int k,+                      STATE *s,+                      int e,+                      int flag1,+                      int flag2,+                      subopt_env *env){++  INTERVAL  *interval1, *interval2;+  STATE     *new_state;++  new_state = copy_state(s);+  interval1 = make_interval(i+1, k-1, flag1);+  interval2 = make_interval(k, j-1, flag2);+  if (k-i < j-k) { /* push larger interval first */+    push(new_state->Intervals, interval1);+    push(new_state->Intervals, interval2);+  } else {+    push(new_state->Intervals, interval2);+    push(new_state->Intervals, interval1);+  }+  make_pair(i, j, new_state);+  new_state->partial_energy += e;++  push(env->Stack, new_state);+  env->nopush = false;+}+++PRIVATE void+fork_two_states(int i,+                int j,+                int p,+                int q,+                STATE *s,+                int e,+                int flag1,+                int flag2,+                subopt_env *env){++  INTERVAL  *interval1, *interval2;+  STATE     *new_state;++  new_state = copy_state(s);+  interval1 = make_interval(i, j, flag1);+  interval2 = make_interval(p, q, flag2);++  if((j - i) < (q - p)){+    push(new_state->Intervals, interval1);+    push(new_state->Intervals, interval2);+  } else {+    push(new_state->Intervals, interval2);+    push(new_state->Intervals, interval1);+  }+  new_state->partial_energy += e;++  push(env->Stack, new_state);+  env->nopush = false;+}++/*---------------------------------------------------------------------------*/+/* start of subopt backtracking ---------------------------------------------*/+/*---------------------------------------------------------------------------*/++PUBLIC SOLUTION *+vrna_subopt(vrna_fold_compound_t *vc,+            int delta,+            int sorted,+            FILE *fp){++  SOLUTION      *SolutionList;+  unsigned long max_sol, n_sol;+  struct old_subopt_dat data;++  data.SolutionList = NULL;+  data.max_sol      = 128;+  data.n_sol        = 0;+  data.fp           = fp;++  if(vc){+    /* SolutionList stores the suboptimal structures found */++    data.SolutionList = (SOLUTION *) vrna_alloc(data.max_sol*sizeof(SOLUTION));++    /* end initialize ------------------------------------------------------- */++    if (fp) {+      float min_en;+      char  *SeQ, *energies = NULL;+      if(vc->cutpoint > 0)+        min_en = vrna_mfe_dimer(vc, NULL);+      else+        min_en = vrna_mfe(vc, NULL);++      SeQ = vrna_cut_point_insert(vc->sequence, vc->cutpoint);+      energies = vrna_strdup_printf(" %6.2f %6.2f", min_en, (float)delta/100.);+      print_structure(fp, SeQ, energies);+      free(SeQ);+      free(energies);++      vrna_mx_mfe_free(vc);+    }+    /* call subopt() */+    vrna_subopt_cb(vc, delta, (!sorted && fp) ? &old_subopt_print : &old_subopt_store, (void *)&data);++    if(sorted){+      /* sort structures by energy */+      if(data.n_sol > 0)+        qsort(data.SolutionList, data.n_sol - 1, sizeof(SOLUTION), compare);+      if(fp)+        make_output(data.SolutionList, vc->cutpoint, fp);+    }++    if(fp){ /* we've printed everything -- free solutions */+      SOLUTION *sol;+      for(sol = data.SolutionList; sol->structure != NULL; sol++)+        free(sol->structure);+      free(data.SolutionList);+      data.SolutionList = NULL;+    }+  }++  return data.SolutionList;+}++PUBLIC void+vrna_subopt_cb( vrna_fold_compound_t *vc,+                int delta,+                vrna_subopt_callback *cb,+                void *data){++  subopt_env    *env;+  STATE         *state;+  INTERVAL      *interval;+  int           maxlevel, count, partial_energy, old_dangles, logML, dangle_model, length, circular, threshold, cp;+  double        structure_energy, min_en, eprint;+  char          *struc, *structure, *sequence;+  float         correction;+  vrna_param_t  *P;+  vrna_md_t     *md;+  int           minimal_energy;+  int           Fc;+  int           *f5;++  vrna_fold_compound_prepare(vc, VRNA_OPTION_MFE | VRNA_OPTION_HYBRID);++  sequence            = vc->sequence;+  length              = vc->length;+  cp                  = vc->cutpoint;+  P                   = vc->params;+  md                  = &(P->model_details);++  /* do mfe folding to get fill arrays and get ground state energy  */+  /* in case dangles is neither 0 or 2, set dangles=2 while folding */++  circular    = md->circ;+  logML       = md->logML;+  old_dangles = dangle_model = md->dangles;++  if(md->uniq_ML != 1)  /* failsafe mechanism to enforce valid fM1 array */+    md->uniq_ML = 1;++  /* temporarily set dangles to 2 if necessary */+  if((md->dangles != 0) && (md->dangles != 2))+    md->dangles = 2;++  struc = (char *)vrna_alloc(sizeof(char) * (length + 1));++  if(circular){+    min_en = vrna_mfe(vc, struc);+    Fc  = vc->matrices->Fc;+    f5    = vc->matrices->f5;++    /* restore dangle model */+    md->dangles = old_dangles;+    /* re-evaluate in case we're using logML etc */+    min_en = vrna_eval_structure(vc, struc);+  } else {+    min_en = vrna_mfe_dimer(vc, struc);++    f5    = vc->matrices->f5;++    /* restore dangle model */+    md->dangles = old_dangles;+    /* re-evaluate in case we're using logML etc */+    min_en = vrna_eval_structure(vc, struc);+  }++  free(struc);+  eprint = print_energy + min_en;++  correction = (min_en < 0) ? -0.1 : 0.1;++  /* Initialize ------------------------------------------------------------ */++  maxlevel = 0;+  count = 0;+  partial_energy = 0;++  /* Initialize the stack ------------------------------------------------- */++  minimal_energy = (circular) ? Fc : f5[length];+  threshold = minimal_energy + delta;+  if(threshold > INF){+    vrna_message_warning("Energy range too high, limiting to reasonable value");+    threshold = INF-EMAX;+  }++  /* init env data structure */+  env = (subopt_env *)vrna_alloc(sizeof(subopt_env));+  env->Stack      = NULL;+  env->nopush     = true;+  env->Stack      = make_list();                                                   /* anchor */+  env->Intervals  = make_list();                                   /* initial state: */+  interval   = make_interval(1, length, 0);          /* interval [1,length,0] */+  push(env->Intervals, interval);+  env->nopush = false;+  state  = make_state(env->Intervals, NULL, partial_energy,0, length);+  /* state->best_energy = minimal_energy; */+  push(env->Stack, state);+  env->nopush = false;++  /* end initialize ------------------------------------------------------- */+++  while (1) {                    /* forever, til nothing remains on stack */++    maxlevel = (env->Stack->count > maxlevel ? env->Stack->count : maxlevel);++    if (LST_EMPTY (env->Stack))                   /* we are done! clean up and quit */+      {+        /* fprintf(stderr, "maxlevel: %d\n", maxlevel); */++        lst_kill(env->Stack, free_state_node);++        cb(NULL, 0, data); /* NULL (last time to call callback function */++        break;+      }++    /* pop the last element ---------------------------------------------- */++    state = pop(env->Stack);                       /* current state to work with */++    if (LST_EMPTY(state->Intervals))+      {+        int e;+        /* state has no intervals left: we got a solution */++        count++;+        structure = get_structure(state);+        structure_energy = state->partial_energy / 100.;++#ifdef CHECK_ENERGY+        structure_energy = vrna_eval_structure(vc, structure);++        if (!logML)+          if ((double) (state->partial_energy / 100.) != structure_energy) {+            vrna_message_error("%s %6.2f %6.2f",+                                      structure,+                                      state->partial_energy / 100.,+                                      structure_energy );+            exit(1);+          }+#endif+        if (logML || (dangle_model==1) || (dangle_model==3)) { /* recalc energy */+          structure_energy = vrna_eval_structure(vc, structure);+        }++        e = (int) ((structure_energy-min_en)*10. - correction); /* avoid rounding errors */+        if (e>MAXDOS) e=MAXDOS;+        density_of_states[e]++;+        if(structure_energy <= eprint){+          char *outstruct = vrna_cut_point_insert(structure, cp);+          cb((const char *)outstruct, structure_energy, data);+          free(outstruct);+        }+        free(structure);+      }+    else {+      /* get (and remove) next interval of state to analyze */++      interval = pop(state->Intervals);+      scan_interval(vc, interval->i, interval->j, interval->array_flag, threshold, state, env);++      free_interval_node(interval);        /* free the current interval */+    }++    free_state_node(state);                     /* free the current state */+  } /* end of while (1) */++  /* cleanup memory */+  free(env);+}+++PRIVATE void+scan_interval(vrna_fold_compound_t *vc,+              int i,+              int j,+              int array_flag,+              int threshold,+              STATE * state,+              subopt_env *env){++  /* real backtrack routine */++  /* array_flag = 0:  trace back in f5-array  */+  /* array_flag = 1:  trace back in fML-array */+  /* array_flag = 2:  trace back in repeat()  */+  /* array_flag = 3:  trace back in fM1-array */++  STATE           *new_state, *temp_state;+  INTERVAL        *new_interval;+  vrna_param_t    *P;+  vrna_md_t       *md;+  register int    k, fi, cij, ij;+  register int    type;+  register int    dangle_model;+  register int    noLP;+  int             element_energy, best_energy;+  int             *fc, *f5, *c, *fML, *fM1, *ggg;+  int             FcH, FcI, FcM, *fM2;+  int             length, *indx, *rtype, circular, with_gquad, turn, cp;+  char            *ptype;+  short           *S1;+  char            *hard_constraints, hc_decompose;+  vrna_hc_t       *hc;+  vrna_sc_t       *sc;++  length    = vc->length;+  cp        = vc->cutpoint;+  indx      = vc->jindx;+  ptype     = vc->ptype;+  S1        = vc->sequence_encoding;+  P         = vc->params;+  md        = &(P->model_details);+  rtype     = &(md->rtype[0]);++  dangle_model  = md->dangles;+  noLP          = md->noLP;+  circular      = md->circ;+  with_gquad    = md->gquad;+  turn          = md->min_loop_size;++  fc  = vc->matrices->fc;+  f5  = vc->matrices->f5;+  c   = vc->matrices->c;+  fML = vc->matrices->fML;+  fM1 = vc->matrices->fM1;+  ggg = vc->matrices->ggg;+  FcH = vc->matrices->FcH;+  FcI = vc->matrices->FcI;+  FcM = vc->matrices->FcM;+  fM2 = vc->matrices->fM2;++  hc                = vc->hc;+  hard_constraints  = hc->matrix;++  sc                = vc->sc;++  best_energy = best_attainable_energy(vc, state);  /* .. on remaining intervals */+  env->nopush = true;++  if ((i > 1) && (!array_flag))+    vrna_message_error ("Error while backtracking!");++  if (j < i + turn + 1 && ON_SAME_STRAND(i,j,cp)) { /* minimal structure element */+    if(array_flag == 0){+      /* do not forget to add f5[j], since it may contain pseudo energies from soft constraining */+      state->partial_energy += f5[j];+    }+    if (env->nopush){+      push_back(env->Stack, state);+      env->nopush = false;+    }+    return;+  }++  ij = indx[j] + i;++  /* 13131313131313131313131313131313131313131313131313131313131313131313131 */+  if (array_flag == 3 || array_flag == 1) {+    /* array_flag = 3: interval i,j was generated during */+    /*                 a multiloop decomposition using array fM1 in repeat() */+    /*                 or in this block */++    /* array_flag = 1: interval i,j was generated from a */+    /*                 stack, bulge, or internal loop in repeat() */+    /*                 or in this block */++    if(hc->up_ml[j]){+      if (array_flag == 3)+        fi = fM1[indx[j-1] + i] + P->MLbase;+      else+        fi = fML[indx[j-1] + i] + P->MLbase;++      if(sc){+        if(sc->energy_up)+          fi += sc->energy_up[j][1];+        if(sc->f)+          fi += sc->f(i, j, i, j - 1, VRNA_DECOMP_ML_ML, sc->data);+      }++      if ((fi + best_energy <= threshold)&&(ON_SAME_STRAND(j-1,j, cp))) {+        /* no basepair, nibbling of 3'-end */+        fork_state(i, j-1, state, P->MLbase, array_flag, env);+      }+    }++    hc_decompose  = hard_constraints[ij];++    if (hc_decompose & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC) { /* i,j may pair */+      cij = c[ij];++      type = ptype[ij];++      if(type == 0)+        type = 7;++      switch(dangle_model){+        case 0:   element_energy = E_MLstem(type, -1, -1, P);+                  break;+        default:  element_energy = E_MLstem(type,+                                  (((i > 1)&&(ON_SAME_STRAND(i-1,i,cp))) || circular)       ? S1[i-1] : -1,+                                  (((j < length)&&(ON_SAME_STRAND(j,j+1,cp))) || circular)  ? S1[j+1] : -1,+                                  P);+                  break;+      }++      if(sc){+/* should be unnecessary+        if(sc->energy_bp)+          element_energy += sc->energy_bp[ij];+*/+        if(sc->f)+          element_energy += sc->f(i, j, i, j, VRNA_DECOMP_ML_STEM, sc->data);+      }+      cij += element_energy;++      if (cij + best_energy <= threshold)+        repeat(vc, i, j, state, element_energy, 0, best_energy, threshold, env);+    } else if (with_gquad){+      element_energy = E_MLstem(0, -1, -1, P);+      cij = ggg[ij] + element_energy;+      if(cij + best_energy <= threshold)+        repeat_gquad(vc, i, j, state, element_energy, 0, best_energy, threshold, env);+    }+  }                                   /* array_flag == 3 || array_flag == 1 */++  /* 11111111111111111111111111111111111111111111111111111111111111111111111 */++  if (array_flag == 1) {+    /* array_flag = 1:                   interval i,j was generated from a */+    /*                          stack, bulge, or internal loop in repeat() */+    /*                          or in this block */++    int stopp, k1j;+    if ((ON_SAME_STRAND(i-1,i,cp))&&(ON_SAME_STRAND(j,j+1,cp))) { /*backtrack in FML only if multiloop is possible*/+      for ( k = i+turn+1 ; k <= j-1-turn ; k++) {+        /* Multiloop decomposition if i,j contains more than 1 stack */++        if(with_gquad){+          if(ON_SAME_STRAND(k, k+1, cp)){+            element_energy = E_MLstem(0, -1, -1, P);+            if(fML[indx[k]+i] + ggg[indx[j] + k + 1] + element_energy + best_energy <= threshold){+              +              temp_state = derive_new_state(i, k, state, 0, array_flag);+              env->nopush = false;+              repeat_gquad(vc, k+1, j, temp_state, element_energy, fML[indx[k]+i], best_energy, threshold, env);+              free_state_node(temp_state);+            }+          }+        }++        k1j = indx[j] + k + 1;++        if(hard_constraints[k1j] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+          short s5, s3;+          type = ptype[k1j];++          if(type == 0)+            type = 7;++          switch(dangle_model){+            case 0:   s5 = s3 = -1;+                      break;+            default:  s5 = (ON_SAME_STRAND(i-1,i,cp)) ? S1[k] : -1;+                      s3 = (ON_SAME_STRAND(j,j+1,cp)) ? S1[j+1] : -1;+                      break;+          }++          element_energy = E_MLstem(type, s5, s3, P);++          if(sc){+/* should be unnecessary+            if(sc->energy_bp)+              element_energy += sc->energy_bp[k1j];+*/+            if(sc->f)+              element_energy += sc->f(i, j, k, k + 1, VRNA_DECOMP_ML_ML_STEM, sc->data);+          }++          if(ON_SAME_STRAND(k, k+1, cp)){+            if(fML[indx[k]+i] + c[k1j] + element_energy + best_energy <= threshold){+              temp_state  = derive_new_state(i, k, state, 0, array_flag);+              env->nopush = false;+              repeat(vc, k+1, j, temp_state, element_energy, fML[indx[k]+i], best_energy, threshold, env);+              free_state_node(temp_state);+            }+          }+        }+      }+    }++    stopp=(cp>0)? (cp-2):(length); /*if cp -1: k on cut, => no ml*/+    stopp=MIN2(stopp, j-1-turn);+    if (i>cp) stopp=j-1-turn;+    else if (i==cp) stopp=0;   /*not a multi loop*/++    int up = 1;+    for(k = i; k <= stopp; k++, up++){++      if(hc->up_ml[i] >= up){+        k1j = indx[j] + k + 1;++        /* Multiloop decomposition if i,j contains only 1 stack */+        if(with_gquad){+          element_energy = E_MLstem(0, -1, -1, P) + P->MLbase * up;++          if(sc){+            if(sc->energy_up)+              element_energy += sc->energy_up[i][up];+          }++          if(ggg[k1j] + element_energy + best_energy <= threshold)+            repeat_gquad(vc, k+1, j, state, element_energy, 0, best_energy, threshold, env);+        }++        if(hard_constraints[k1j] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP_ENC){+          int s5, s3;+          type = ptype[k1j];++          if(type == 0)+            type = 7;++          switch(dangle_model){+            case 0:   s5 = s3 = -1;+                      break;+            default:  s5 = (ON_SAME_STRAND(k-1,k,cp)) ? S1[k] : -1;+                      s3 = (ON_SAME_STRAND(j,j+1,cp)) ? S1[j+1] : -1;+                      break;+          }++          element_energy = E_MLstem(type, s5, s3, P);++          element_energy += P->MLbase * up;++          if(sc){+            if(sc->energy_up)+              element_energy += sc->energy_up[i][up];++/* should be unnecessary+            if(sc->energy_bp)+              element_energy += sc->energy_bp[k1j];+*/+          }++          if (c[k1j] + element_energy + best_energy <= threshold)+            repeat(vc, k+1, j, state, element_energy, 0, best_energy, threshold, env);+        }+      }+    }+  } /* array_flag == 1 */++  /* 22222222222222222222222222222222222222222222222222 */+  /*                                                    */+  /* array_flag = 2:  interval i,j was generated from a */+  /* stack, bulge, or internal loop in repeat()         */+  /*                                                    */+  /* 22222222222222222222222222222222222222222222222222 */+  if(array_flag == 2){+    repeat(vc, i, j, state, 0, 0, best_energy, threshold, env);++    if (env->nopush){+      if (!noLP){+        vrna_message_warning("%d,%d\nOops, no solution in repeat!", i, j);+      }+    }+    return;+  }++  /* 00000000000000000000000000000000000000000000000000 */+  /*                                                    */+  /* array_flag = 0:  interval i,j was found while      */+  /* tracing back through f5-array and c-array          */+  /* or within this block                               */+  /*                                                    */+  /* 00000000000000000000000000000000000000000000000000 */+  if((array_flag == 0) && !circular){+    int s5, s3, kj, tmp_en;++    if(hc->up_ext[j]){+      tmp_en = 0;+      if(sc){+        if(sc->energy_up)+          tmp_en += sc->energy_up[j][1];+      }+      if (f5[j-1] + tmp_en + best_energy <= threshold) {+        /* no basepair, nibbling of 3'-end */+        fork_state(i, j-1, state, tmp_en, 0, env);+      }+    }++    for (k = j-turn-1; k > 1; k--) {+      kj = indx[j] + k;++      if(with_gquad){+        if(ON_SAME_STRAND(k,j,cp)){+          element_energy = 0;+          if(f5[k-1] + ggg[kj] + element_energy + best_energy <= threshold){+            temp_state = derive_new_state(1, k-1, state, 0, 0);+            env->nopush = false;+            /* backtrace the quadruplex */+            repeat_gquad(vc, k, j, temp_state, element_energy, f5[k-1], best_energy, threshold, env);+            free_state_node(temp_state);+          }+        }+      }++      if(hard_constraints[kj] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+        type = ptype[kj];++        if(type == 0)+          type = 7;++        /* k and j pair */+        switch(dangle_model){+          case 0:   s5 = s3 = -1;+                    break;+          default:  s5 = (ON_SAME_STRAND(k-1,k,cp)) ? S1[k-1] : -1;+                    s3 = ((j < length)&&(ON_SAME_STRAND(j,j+1,cp))) ? S1[j+1] : -1;+                    break;+        }+        +        element_energy = E_ExtLoop(type, s5, s3, P);++        if (!(ON_SAME_STRAND(k,j,cp)))/*&&(state->is_duplex==0))*/ {+          element_energy+=P->DuplexInit;+          /*state->is_duplex=1;*/+        }++        if (f5[k-1] + c[kj] + element_energy + best_energy <= threshold){+          temp_state = derive_new_state(1, k-1, state, 0, 0);+          env->nopush = false;+          repeat(vc, k, j, temp_state, element_energy, f5[k-1], best_energy, threshold, env);+          free_state_node(temp_state);+        }+      }+    }++    kj = indx[j] + 1;++    if(with_gquad){+      if(ON_SAME_STRAND(k,j,cp)){+        element_energy = 0;+        if(ggg[kj] + element_energy + best_energy <= threshold){+          /* backtrace the quadruplex */+          repeat_gquad(vc, 1, j, state, element_energy, 0, best_energy, threshold, env);+        }+      }+    }++    if(hard_constraints[kj] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+      type  = ptype[kj];+      s5    = -1;++      if(type == 0)+        type = 7;++      switch(dangle_model){+        case 0:   s3 = -1;+                  break;+        default:  s3 = (j < length) && (ON_SAME_STRAND(j,j+1,cp)) ? S1[j+1] : -1;+                  break;+      }++      element_energy = E_ExtLoop(type, s5, s3, P);++      if(!(ON_SAME_STRAND(1,j,cp)))+        element_energy += P->DuplexInit;+      if (c[kj] + element_energy + best_energy <= threshold)+        repeat(vc, 1, j, state, element_energy, 0, best_energy, threshold, env);+    }+  } /* end array_flag == 0 && !circular*/+  /* or do we subopt circular? */+  else if(array_flag == 0){+    int k, l, p, q, tmp_en;+    /* if we've done everything right, we will never reach this case more than once   */+    /* right after the initilization of the stack with ([1,n], empty, 0)              */+    /* lets check, if we can have an open chain without breaking the threshold        */+    /* this is an ugly work-arround cause in case of an open chain we do not have to  */+    /* backtrack anything further...                                                  */+    if(hc->up_ext[1] >= length){+      tmp_en = 0;++      if(sc){+        if(sc->energy_up)+          tmp_en += sc->energy_up[1][length];+      }++      if(tmp_en <= threshold){+        new_state = derive_new_state(1,2,state,0,0);+        new_state->partial_energy = 0;+        push(env->Stack, new_state);+        env->nopush = false;+      }+    }++    /* ok, lets check if we can do an exterior hairpin without breaking the threshold */+    /* best energy should be 0 if we are here                                         */+    if(FcH + best_energy <= threshold){+      /* lets search for all exterior hairpin cases, that fit into our threshold barrier  */+      /* we use index k,l to avoid confusion with i,j index of our state...               */+      /* if we reach here, i should be 1 and j should be n respectively                   */+      for(k=i; k<j; k++){+        if(hc->up_hp[1] < k)+          break;++        for (l=j; l >= k + turn + 1; l--){+          int kl, tmpE;++          kl    = indx[l] + k;+          tmpE  = vrna_E_hp_loop(vc, l, k);++          if(c[kl] + tmpE + best_energy <= threshold){+            /* what we really have to do is something like this, isn't it?  */+            /* we have to create a new state, with interval [k,l], then we  */+            /* add our loop energy as initial energy of this state and put  */+            /* the state onto the stack R... for further refinement...      */+            /* we also denote this new interval to be scanned in C          */+            fork_state(k, l, state, tmpE, 2, env);+          }+        }+      }+    }++    /* now lets see, if we can do an exterior interior loop without breaking the threshold */+    if(FcI + best_energy <= threshold){+      /* now we search for our exterior interior loop possibilities */+      for(k=i; k<j; k++){+        for (l=j; l >= k + turn + 1; l--){+          int kl, type, tmpE;++          kl    = indx[l]+k;        /* just confusing these indices ;-) */++          if(hard_constraints[kl] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+            type  = ptype[kl];+            type  = rtype[type];++            if(type == 0)+              type = 7;++            for (p = l+1; p < j ; p++){+              int u1, qmin;+              u1 = p-l-1;+              if (u1+k-1>MAXLOOP) break;+              if (hc->up_int[l+1] < u1) break;++              qmin = u1+k-1+j-MAXLOOP;+              if(qmin<p+turn+1) qmin = p+turn+1;++              for(q = j; q >= qmin; q--){+                int u2, type_2;++                if(hc->up_int[q+1] < (j - q + k - 1))+                  break;++                if(hard_constraints[indx[q]+p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+                  type_2 = rtype[ptype[indx[q]+p]];++                  if(type_2 == 0)+                    type_2 = 7;++                  u2 = k-1 + j-q;+                  if(u1+u2>MAXLOOP) continue;+                  tmpE = E_IntLoop(u1, u2, type, type_2, S1[l+1], S1[k-1], S1[p-1], S1[q+1], P);+                  +                  if(sc){+                    if(sc->energy_up)+                      tmpE += sc->energy_up[l+1][p-l-1]+                              + sc->energy_up[q+1][j-q]+                              + sc->energy_up[1][k-1];+                    +                    if(sc->energy_stack)+                      if(u1 + u2 == 0)+                        tmpE += sc->energy_stack[k]+                                + sc->energy_stack[l]+                                + sc->energy_stack[p]+                                + sc->energy_stack[q];+                  }++                  if(c[kl] + c[indx[q]+p] + tmpE + best_energy <= threshold){+                    /* ok, similar to the hairpin stuff, we add new states onto the stack R */+                    /* but in contrast to the hairpin decomposition, we have to add two new */+                    /* intervals, enclosed by k,l and p,q respectively and we also have to  */+                    /* add the partial energy, that comes from the exterior interior loop   */+                    fork_two_states(k, l, p, q, state, tmpE, 2, 2, env);+                  }+                }+              }+            }+          }+        }+      }+    }++    /* and last but not least, we have a look, if we can do an exterior multiloop within the energy threshold */+    if(FcM <= threshold){+      /* this decomposition will be somehow more complicated...so lets see what we do here...           */+      /* first we want to find out which split inidices we can use without exceeding the threshold */+      int tmpE2;+      for (k=turn+1; k<j-2*turn; k++){+        tmpE2 = fML[indx[k]+1]+fM2[k+1]+P->MLclosing;+        if(tmpE2 + best_energy <= threshold){+          /* grmpfh, we have found a possible split index k so we have to split fM2 and fML now */+          /* lets do it first in fM2 anyway */+          for(l=k+turn+2; l<j-turn-1; l++){+            tmpE2 = fM1[indx[l]+k+1] + fM1[indx[j]+l+1];+            if(tmpE2 + fML[indx[k]+1] + P->MLclosing <= threshold){+              /* we've (hopefully) found a valid decomposition of fM2 and therefor we have all */+              /* three intervals for our new state to be pushed on stack R */+              new_state = copy_state(state);++              /* first interval leads for search in fML array */+              new_interval = make_interval(1, k, 1);+              push(new_state->Intervals, new_interval);+              env->nopush = false;++              /* next, we have the first interval that has to be traced in fM1 */+              new_interval = make_interval(k+1, l, 3);+              push(new_state->Intervals, new_interval);+              env->nopush = false;++              /* and the last of our three intervals is also one to be traced within fM1 array... */+              new_interval = make_interval(l+1, j, 3);+              push(new_state->Intervals, new_interval);+              env->nopush = false;++              /* mmh, we add the energy for closing the multiloop now... */+              new_state->partial_energy += P->MLclosing;+              /* next we push our state onto the R stack */+              push(env->Stack, new_state);+              env->nopush = false;++            }+            /* else we search further... */+          }++          /* ok, we have to decompose fML now... */+        }+      }+    }+  }        /* thats all folks for the circular case... */++  /* 44444444444444444444444444444444444444444444444444 */+  /*                                                    */+  /* array_flag = 4:  interval i,j was found while      */+  /* tracing back through fc-array smaller than than cp */+  /* or within this block                               */+  /*                                                    */+  /* 44444444444444444444444444444444444444444444444444 */+  if (array_flag == 4) {+    int ik, s5, s3, tmp_en;++    if(hc->up_ext[i]){+      tmp_en = 0;++      if(sc){+        if(sc->energy_up)+          tmp_en += sc->energy_up[i][1];+      }++      if (fc[i+1] + tmp_en + best_energy <= threshold) {+        /* no basepair, nibbling of 5'-end */+        fork_state(i+1, j, state, tmp_en, 4, env);+      }+    }++    for (k = i+TURN+1; k < j; k++) {++      ik = indx[k] + i;++      if(with_gquad){+        if(fc[k+1] + ggg[ik] + best_energy <= threshold){+          temp_state = derive_new_state(k+1, j, state, 0, 4);+          env->nopush = false;+          repeat_gquad(vc, i, k, temp_state, 0, fc[k+1], best_energy, threshold, env);+          free_state_node(temp_state);+        }+      }++      if(hard_constraints[ik] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+        type = ptype[ik];++        if(type == 0)+          type = 7;++        switch(dangle_model){+          case 0:   s5 = s3 = -1;+                    break;+          default:  s5 = (i > 1) ? S1[i-1]: -1;+                    s3 = S1[k+1];+                    break;+        }++        element_energy = E_ExtLoop(type, s5, s3, P);++/* should be unnecessary+        if(sc){+          if(sc->energy_bp)+            element_energy += sc->energy_bp[ik];+        }+*/++        if (fc[k+1] + c[ik] + element_energy + best_energy <= threshold){+          temp_state = derive_new_state(k+1, j, state, 0, 4);+          env->nopush = false;+          repeat(vc, i, k, temp_state, element_energy, fc[k+1], best_energy, threshold, env);+          free_state_node(temp_state);+        }+      }+    }++    ik = indx[cp -1] + i; /* indx[j] + i; */++    if(with_gquad){+      if(ggg[ik] + best_energy <= threshold)+        repeat_gquad(vc, i, cp - 1, state, 0, 0, best_energy, threshold, env);+    }++    if(hard_constraints[ik] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+      type  = ptype[ik];+      s3    = -1;++      if(type == 0)+        type = 7;++      switch(dangle_model){+        case 0:   s5 = -1;+                  break;+        default:  s5 = (i>1) ? S1[i-1] : -1;+                  break;+      }++      element_energy = E_ExtLoop(type, s5, s3, P);++/* should be unnecessary+      if(sc){+        if(sc->energy_bp)+          element_energy += sc->energy_bp[ik];+      }+*/++      if(c[ik] + element_energy + best_energy <= threshold)+        repeat(vc, i, cp-1, state, element_energy, 0, best_energy, threshold, env);+    }+  } /* array_flag == 4 */++  /* 55555555555555555555555555555555555555555555555555 */+  /*                                                    */+  /* array_flag = 5:  interval cp=i,j was found while   */+  /* tracing back through fc-array greater than cp      */+  /* or within this block                               */+  /*                                                    */+  /* 55555555555555555555555555555555555555555555555555 */+  if (array_flag == 5) {+    int kj, s5, s3, tmp_en;++    if(hc->up_ext[j]){+      tmp_en = 0;++      if(sc){+        if(sc->energy_up)+          tmp_en += sc->energy_up[j][1];+      }++      if (fc[j-1] + tmp_en + best_energy <= threshold) {+        /* no basepair, nibbling of 3'-end */+        fork_state(i, j-1, state, tmp_en, 5, env);+      }+    }+++    for (k = j-TURN-1; k > i; k--) {+      kj = indx[j] + k;++      if(with_gquad){+        if(fc[k-1] + ggg[kj] + best_energy <= threshold){+          temp_state = derive_new_state(i, k-1, state, 0, 5);+          env->nopush = false;+          repeat_gquad(vc, k, j, temp_state, 0, fc[k-1], best_energy, threshold, env);+          free_state_node(temp_state);+        }+      }++      if(hard_constraints[kj] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+        type            = ptype[kj];+        element_energy  = 0;++        if(type == 0)+          type = 7;++        switch(dangle_model){+          case 0:   s3 = s5 = -1;+                    break;+          default:  s5 = S1[k-1];+                    s3 = (j < length) ? S1[j+1] : -1;+                    break;+        }++        element_energy = E_ExtLoop(type, s5, s3, P);++/*  should be unnecessary+        if(sc){+          if(sc->energy_bp)+            element_energy += sc->energy_bp[kj];+        }+*/++        if (fc[k-1] + c[kj] + element_energy + best_energy <= threshold) {+          temp_state = derive_new_state(i, k-1, state, 0, 5);+          env->nopush = false;+          repeat(vc, k, j, temp_state, element_energy, fc[k-1], best_energy, threshold, env);+          free_state_node(temp_state);+        }+      }+    }++    kj = indx[j] + cp; /* indx[j] + i; */++    if(with_gquad){+      if(ggg[kj] + best_energy <= threshold)+        repeat_gquad(vc, cp, j, state, 0, 0, best_energy, threshold, env);+    }++    if(hard_constraints[kj] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+      type  = ptype[kj];+      s5    = -1;++      if(type == 0)+        type = 7;++      switch(dangle_model){+        case 0:   s3 = -1;+                  break;+        default:  s3 = (j<length) ? S1[j+1] : -1;+                  break;+      }++      element_energy = E_ExtLoop(type, s5, s3, P);++      if (c[kj] + element_energy + best_energy <= threshold)+        repeat(vc, cp, j, state, element_energy, 0, best_energy, threshold, env);+    }+  } /* array_flag == 5 */++  if (array_flag == 6) { /* we have a gquad */+    repeat_gquad(vc, i, j, state, 0, 0, best_energy, threshold, env);+    if (env->nopush){+      vrna_message_warning("%d,%d\nOops, no solution in gquad-repeat!", i, j);+    }+    return;+  }++  if (env->nopush){+    push_back(env->Stack, state);+    env->nopush = false;+  }+  return;+}++/*---------------------------------------------------------------------------*/+PRIVATE void+repeat_gquad( vrna_fold_compound_t *vc,+              int i,+              int j,+              STATE *state,+              int part_energy,+              int temp_energy,+              int best_energy,+              int threshold,+              subopt_env *env){++  int           *ggg, *indx, element_energy, cp;+  short         *S1;+  vrna_param_t  *P;++  indx  = vc->jindx;+  cp    = vc->cutpoint;+  ggg   = vc->matrices->ggg;+  S1    = vc->sequence_encoding;+  P     = vc->params;+++  /* find all gquads that fit into the energy range and the interval [i,j] */+  STATE *new_state;+  best_energy += part_energy; /* energy of current structural element */+  best_energy += temp_energy; /* energy from unpushed interval */++  if(ON_SAME_STRAND(i,j,cp)){+    element_energy = ggg[indx[j] + i];+    if(element_energy + best_energy <= threshold){+      int cnt;+      int *L;+      int *l;+      /* find out how many gquads we might expect in the interval [i,j] */+      int num_gquads = get_gquad_count(S1, i, j);+      num_gquads++;+      L = (int *)vrna_alloc(sizeof(int) * num_gquads);+      l = (int *)vrna_alloc(sizeof(int) * num_gquads * 3);+      L[0] = -1;++      get_gquad_pattern_exhaustive(S1, i, j, P, L, l, threshold - best_energy);++      for(cnt = 0; L[cnt] != -1; cnt++){+        new_state = copy_state(state);++        make_gquad(i, L[cnt], &(l[3*cnt]), new_state);+        new_state->partial_energy += part_energy;+        new_state->partial_energy += element_energy;+        /* new_state->best_energy =+           hairpin[unpaired] + element_energy + best_energy; */+        push(env->Stack, new_state);+        env->nopush = false;+      }+      free(L);+      free(l);+    }+  }++  best_energy -= part_energy;+  best_energy -= temp_energy;+  return;+}++++PRIVATE void+repeat( vrna_fold_compound_t *vc,+        int i,+        int j,+        STATE * state,+        int part_energy,+        int temp_energy,+        int best_energy,+        int threshold,+        subopt_env *env){++  /* routine to find stacks, bulges, internal loops and  multiloops */+  /* within interval closed by basepair i,j */++  STATE           *new_state;+  vrna_param_t    *P;+  vrna_md_t       *md;++  register int  ij, k, p, q, energy, new;+  register int  mm;+  register int  no_close, type, type_2;+  char          *ptype;+  int           element_energy;+  int             *fc, *c, *fML, *fM1, *ggg;+  int           rt, *indx, *rtype, noGUclosure, noLP, with_gquad, dangle_model, turn, cp;+  short         *S1;+  vrna_hc_t     *hc;+  vrna_sc_t     *sc;++  S1        = vc->sequence_encoding;+  ptype     = vc->ptype;+  indx      = vc->jindx;+  cp        = vc->cutpoint;+  P         = vc->params;+  md        = &(P->model_details);+  rtype     = &(md->rtype[0]);++  noGUclosure   = md->noGUclosure;+  noLP          = md->noLP;+  with_gquad    = md->gquad;+  dangle_model  = md->dangles;+  turn          = md->min_loop_size;++  fc  = vc->matrices->fc;+  c   = vc->matrices->c;+  fML = vc->matrices->fML;+  fM1 = vc->matrices->fM1;+  ggg = vc->matrices->ggg;++  hc    = vc->hc;+  sc    = vc->sc;++  ij = indx[j]+i;++  type = ptype[ij];+/*+  if (type==0) fprintf(stderr, "repeat: Warning: %d %d can't pair\n", i,j);+*/++  if(type == 0)+    type = 7;++  no_close = (((type == 3) || (type == 4)) && noGUclosure);++  if(hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+    if (noLP) /* always consider the structure with additional stack */+      if(i + turn + 2 < j){+        if(hc->matrix[indx[j-1]+i+1] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC){+          type_2 = rtype[ptype[indx[j-1]+i+1]];++          if(type_2 == 0)+            type_2 = 7;++          energy = 0;++          if(ON_SAME_STRAND(i,i+1,cp) && ON_SAME_STRAND(j-1,j, cp)){+            energy = E_IntLoop(0, 0, type, type_2,S1[i+1],S1[j-1],S1[i+1],S1[j-1], P);++            if(sc){+              if(sc->energy_bp)+                energy += sc->energy_bp[ij];++              if(sc->energy_stack)+                energy += sc->energy_stack[i]+                          + sc->energy_stack[i+1]+                          + sc->energy_stack[j-1]+                          + sc->energy_stack[j];++              if(sc->f)+                energy += sc->f(i, j, i+1, j-1, VRNA_DECOMP_PAIR_IL, sc->data);+            }++            new_state = derive_new_state(i+1, j-1, state, part_energy + energy, 2);+            make_pair(i, j, new_state);+            make_pair(i+1, j-1, new_state);++            /* new_state->best_energy = new + best_energy; */+            push(env->Stack, new_state);+            env->nopush = false;+            if (i==1 || state->structure[i-2]!='('  || state->structure[j]!=')')+              /* adding a stack is the only possible structure */+              return;+          }+        }+      }+  }++  best_energy += part_energy; /* energy of current structural element */+  best_energy += temp_energy; /* energy from unpushed interval */++  if(hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP){+    for (p = i + 1; p <= MIN2 (j-2-turn,  i+MAXLOOP+1); p++) {+      int minq = j-i+p-MAXLOOP-2;+      if (minq<p+1+turn) minq = p+1+turn;++      if(hc->up_int[i+1] < (p - i - 1))+        break;++      for (q = j - 1; q >= minq; q--) {+        if(hc->up_int[q+1] < (j - q - 1))+          break;++        /* skip stack if noLP, since we've already processed it above */+        if((noLP) && (p==i+1) && (q==j-1))+          continue;++        if(!(hc->matrix[indx[q]+p] & VRNA_CONSTRAINT_CONTEXT_INT_LOOP_ENC))+          continue;++        type_2 = ptype[indx[q]+p];++        if(type_2 == 0)+          type_2 = 7;++        if (noGUclosure)+          if (no_close||(type_2==3)||(type_2==4))+            if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */++        if (ON_SAME_STRAND(i,p,cp) && ON_SAME_STRAND(q,j,cp)) {+          energy = E_IntLoop(p-i-1, j-q-1, type, rtype[type_2],+                              S1[i+1],S1[j-1],S1[p-1],S1[q+1], P);++          new = energy + c[indx[q]+p];++          if(sc){+            if(sc->energy_up)+              energy  +=  sc->energy_up[i+1][p-i-1]+                          + sc->energy_up[q+1][j-q-1];++            if(sc->energy_bp)+              energy  += sc->energy_bp[ij];++            if(sc->energy_stack)+              if((p == i+1) && (q == j-1))+                energy  +=  sc->energy_stack[i]+                            + sc->energy_stack[p]+                            + sc->energy_stack[q]+                            + sc->energy_stack[j];++            if(sc->f)+              energy  += sc->f(i, j, p, q, VRNA_DECOMP_PAIR_IL, sc->data);+          }++          new = energy + c[indx[q]+p];++          if (new + best_energy <= threshold) {+            /* stack, bulge, or interior loop */+            fork_int_state(i, j, p, q, state, part_energy + energy, env);+          }+        }/*end of if block */+      } /* end of q-loop */+    } /* end of p-loop */+  }++  if (!ON_SAME_STRAND(i,j,cp)) { /*look in fc*/+    if(hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_EXT_LOOP){+      rt = rtype[type];++      if(rt == 0)+        rt = 7;++      element_energy=0;+      switch(dangle_model){+        case 0:   element_energy = E_ExtLoop(rt, -1, -1, P);+                  break;+        default:  element_energy = E_ExtLoop(rt, (ON_SAME_STRAND(j-1,j,cp)) ? S1[j-1] : -1, (ON_SAME_STRAND(i,i+1,cp)) ? S1[i+1] : -1, P);+                  break;+      }++      if (fc[i+1] + fc[j-1] +element_energy + best_energy  <= threshold)+        {+          fork_two_states_pair(i, j, cp, state, part_energy + element_energy, 4, 5, env);+        }+    }+  }++  mm = P->MLclosing;+  rt = rtype[type];++  if((hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_MB_LOOP) && (i != cp-1) && (j != cp)){++    if(rt == 0)+      rt = 7;++    element_energy = mm;+    switch(dangle_model){+      case 0:   element_energy = E_MLstem(rt, -1, -1, P) + mm;+                break;+      default:  element_energy = E_MLstem(rt, S1[j-1], S1[i+1], P) + mm;+                break;+    }++    if(sc){+      if(sc->energy_bp)+        element_energy += sc->energy_bp[ij];+    }++    for (k = i + turn + 2; k <= j - turn - 2; k++)  {+      /* multiloop decomposition */+      if ((fML[indx[k-1] + i+1] + fM1[indx[j-1] + k] ++          element_energy + best_energy)  <= threshold)+        {+          fork_two_states_pair(i, j, k, state, part_energy + element_energy, 1, 3, env);+        }+    }+  }++  if (ON_SAME_STRAND(i,j,cp)) {+    if(hc->matrix[ij] & VRNA_CONSTRAINT_CONTEXT_HP_LOOP){++      if(no_close)+        element_energy = FORBIDDEN;+      else+          element_energy = vrna_E_hp_loop(vc, i, j);++      if (element_energy + best_energy <= threshold) {+        /* hairpin structure */+        fork_state_pair(i, j, state, part_energy + element_energy, env);+      }+    }++    if(with_gquad){+      /* now we have to find all loops where (i,j) encloses a gquad in an interior loops style */+      int cnt, *p, *q, *en, tmp_en;+      p = q = en = NULL;+      en = E_GQuad_IntLoop_exhaustive(i, j, &p, &q, type, S1, ggg, threshold - best_energy, indx, P);+      for(cnt = 0; p[cnt] != -1; cnt++){+        if((hc->up_int[i+1] >= p[cnt] - i - 1) && (hc->up_int[q[cnt]+1] >= j - q[cnt] - 1)){+          tmp_en = en[cnt];++          if(sc){+            if(sc->energy_bp)+              tmp_en += sc->energy_bp[ij];++            if(sc->energy_up)+              tmp_en += sc->energy_up[i+1][p[cnt] - i - 1]+                        + sc->energy_up[q[cnt]+1][j - q[cnt] - 1];+          }++          new_state = derive_new_state(p[cnt], q[cnt], state, tmp_en + part_energy, 6);++          make_pair(i, j, new_state);++          /* new_state->best_energy = new + best_energy; */+          push(env->Stack, new_state);+          env->nopush = false;+        }+      }+      free(en);+      free(p);+      free(q);+    }+  }++  best_energy -= part_energy;+  best_energy -= temp_energy;+  return;+}++PRIVATE void+old_subopt_print( const char *structure,+                  float energy,+                  void *data){++  struct old_subopt_dat *d = (struct old_subopt_dat *)data;++  if(structure && d->fp){+    char *e_string = vrna_strdup_printf(" %6.2f", energy);+    print_structure(d->fp, structure, e_string);+    free(e_string);+  }+}+++PRIVATE void+old_subopt_store( const char *structure,+                  float energy,+                  void *data){++  struct old_subopt_dat *d = (struct old_subopt_dat *)data;++  /* store solution */+  if(d->n_sol + 1 == d->max_sol){+    d->max_sol     *= 2;+    d->SolutionList = (SOLUTION *)vrna_realloc(d->SolutionList, d->max_sol*sizeof(SOLUTION));+  }++  if(structure){+    d->SolutionList[d->n_sol].energy      = energy;+    d->SolutionList[d->n_sol++].structure = strdup(structure);+  } else {+    d->SolutionList[d->n_sol].energy      = 0;+    d->SolutionList[d->n_sol++].structure = NULL;+  }+}++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/+#ifdef VRNA_BACKWARD_COMPAT++PUBLIC SOLUTION *+subopt( char *seq,+        char *structure,+        int delta,+        FILE *fp){++  return wrap_subopt(seq, structure, NULL, delta, fold_constrained, 0, fp);+}++PUBLIC SOLUTION *+subopt_circ(char *seq,+            char *structure,+            int delta,+            FILE *fp){++  return wrap_subopt(seq, structure, NULL, delta, fold_constrained, 1, fp);+}++PUBLIC SOLUTION *subopt_par(char *seq,+                            char *structure,+                            vrna_param_t *parameters,+                            int delta,+                            int is_constrained,+                            int is_circular,+                            FILE *fp){++  return wrap_subopt(seq, structure, parameters, delta, is_constrained, is_circular, fp);+}++PRIVATE SOLUTION *+wrap_subopt(char *string,+            char *structure,+            vrna_param_t *parameters,+            int delta,+            int is_constrained,+            int is_circular,+            FILE *fp){++  vrna_fold_compound_t  *vc;+  vrna_param_t        *P;+  char                *seq;++#ifdef _OPENMP+/* Explicitly turn off dynamic threads */+  omp_set_dynamic(0);+#endif++  /* we need the parameter structure for hard constraints */+  if(parameters){+    P = vrna_params_copy(parameters);+  } else {+    vrna_md_t md;+    set_model_details(&md);+    md.temperature = temperature;+    P = vrna_params(&md);+  }+  P->model_details.circ     = is_circular;+  P->model_details.uniq_ML  = uniq_ML = 1;++  /* what about cofold sequences here? Is it safe to call the below cut_point_insert() ? */+  /* dirty hack to reinsert the '&' according to the global variable 'cut_point' */+  seq = vrna_cut_point_insert(string, cut_point);++  vc = vrna_fold_compound(seq, &(P->model_details), ((is_circular == 0) ? VRNA_OPTION_HYBRID : VRNA_OPTION_DEFAULT));++  if(parameters){ /* replace params if necessary */+    free(vc->params);+    vc->params = P;+  } else {+    free(P);+  }++  /* handle hard constraints in pseudo dot-bracket format if passed via simple interface */+  if(is_constrained && structure){+    unsigned int constraint_options = 0;+    constraint_options |= VRNA_CONSTRAINT_DB+                          | VRNA_CONSTRAINT_DB_PIPE+                          | VRNA_CONSTRAINT_DB_DOT+                          | VRNA_CONSTRAINT_DB_X+                          | VRNA_CONSTRAINT_DB_ANG_BRACK+                          | VRNA_CONSTRAINT_DB_RND_BRACK+                          | VRNA_CONSTRAINT_DB_INTRAMOL+                          | VRNA_CONSTRAINT_DB_INTERMOL;++    vrna_constraints_add(vc, (const char *)structure, constraint_options);+  }++  if(backward_compat_compound && backward_compat)+    vrna_fold_compound_free(backward_compat_compound);++  backward_compat_compound  = vc;+  backward_compat           = 1;++  /* cleanup */+  free(seq);++  return vrna_subopt(vc, delta, subopt_sorted, fp);+}++#endif++/*---------------------------------------------------------------------------*/+/* Well, that is the end!----------------------------------------------------*/+/*---------------------------------------------------------------------------*/
+ C/ViennaRNA/subopt.h view
@@ -0,0 +1,280 @@+/* subopt.h */+#ifndef VIENNA_RNA_PACKAGE_SUBOPT_H+#define VIENNA_RNA_PACKAGE_SUBOPT_H++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file subopt.h+ *  @ingroup subopt_and_representatives+ *  @brief RNAsubopt and density of states declarations+ */++#define VRNA_BACKWARD_COMPAT++/**+ *  @brief Typename for the subopt solution list repesenting data structure #vrna_subopt_sol_s+ */+typedef struct vrna_subopt_sol_s   vrna_subopt_solution_t;++/**+ *  @brief  Callback for vrna_subopt_cb()+ *  @ingroup subopt_wuchty+ */+typedef void (vrna_subopt_callback)(const char *stucture, float energy, void *data);++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief  Backward compatibility typedef for #vrna_subopt_sol_s+ *  @deprecated Use #vrna_subopt_solution_t instead!+ */+typedef struct vrna_subopt_sol_s   SOLUTION;++#endif++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/params.h>+++/**+ *  @brief  Solution element from subopt.c+ */+struct vrna_subopt_sol_s {+  float energy;       /**< @brief Free Energy of structure in kcal/mol */+  char *structure;    /**< @brief Structure in dot-bracket notation */+};++/**+ *  @brief Maximum density of states discretization for subopt+ */+#define MAXDOS                1000++/**+ *  @addtogroup subopt_wuchty+ *  @{+ *+ *  @}+ */++/**+ *  @brief Returns list of subopt structures or writes to fp+ * + *  This function produces <b>all</b> suboptimal secondary structures within+ *  'delta' * 0.01 kcal/mol of the optimum, see @cite wuchty:1999. The results+ *  are either directly written to a 'fp' (if 'fp' is not NULL), or+ *  (fp==NULL) returned in a #vrna_subopt_solution_t * list terminated+ *  by an entry were the 'structure' member is NULL.+ *+ *  @ingroup subopt_wuchty+ *+ *  @note This function requires all multibranch loop DP matrices for unique+ *        multibranch loop backtracing. Therefore, the supplied #vrna_fold_compound_t+ *        @p vc (argument 1) must be initialized with #vrna_md_t.uniq_ML = 1, for+ *        instance like this:+ *        @code+  vrna_md_t md;+  vrna_md_set_default(&md);+  md.uniq_ML = 1;++  vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);+ *        @endcode+ *+ *  @see vrna_subopt_cb(), vrna_subopt_zuker()+ *  @param  vc+ *  @param  delta+ *  @param  sorted  Sort results by energy in ascending order+ *  @param  fp+ *  @return+ */+vrna_subopt_solution_t *+vrna_subopt(vrna_fold_compound_t *vc,+            int delta,+            int sorted,+            FILE *fp);++/**+ *  @brief  Generate suboptimal structures within an energy band arround the MFE+ *+ *  This is the most generic implementation of the suboptimal structure generator+ *  according to Wuchty et al. 1999 @cite wuchty:1999. Identical to vrna_subopt(), it computes all+ *  secondary structures within an energy band @p delta arround the MFE. However,+ *  this function does not print the resulting structures and their corresponding+ *  free energies to a file pointer, or returns them as a list. Instead, it calls+ *  a user-provided callback function which it passes the structure in dot-bracket+ *  format, the corresponding free energy in kcal/mol, and a user-provided data+ *  structure each time a structure was backtracked successfully. This function+ *  indicates the final output, i.e. the end of the backtracking procedure by+ *  passing NULL instead of an actual dot-bracket string to the callback.+ *+ *  @ingroup subopt_wuchty+ *+ *  @note This function requires all multibranch loop DP matrices for unique+ *        multibranch loop backtracing. Therefore, the supplied #vrna_fold_compound_t+ *        @p vc (argument 1) must be initialized with #vrna_md_t.uniq_ML = 1, for+ *        instance like this:+ *        @code+  vrna_md_t md;+  vrna_md_set_default(&md);+  md.uniq_ML = 1;++  vrna_fold_compound_t *vc=vrna_fold_compound("GGGGGGAAAAAACCCCCC", &md, VRNA_OPTION_DEFAULT);+ *        @endcode+ *+ *  @see vrna_subopt_callback, vrna_subopt(), vrna_subopt_zuker()+ *  @param  vc      fold compount with the sequence data+ *  @param  delta   Energy band arround the MFE in 10cal/mol, i.e. deka-calories+ *  @param  cb      Pointer to a callback function that handles the backtracked structure and its free energy in kcal/mol+ *  @param  data    Pointer to some data structure that is passed along to the callback+ */+void+vrna_subopt_cb( vrna_fold_compound_t *vc,+                int delta,+                vrna_subopt_callback *cb,+                void *data);++/**+ *  @brief Compute Zuker type suboptimal structures+ *+ *  Compute Suboptimal structures according to M. Zuker @cite zuker:1989 , i.e. for every+ *  possible base pair the minimum energy structure containing the resp. base pair.+ *  Returns a list of these structures and their energies.+ *+ *  @note This function internally uses the cofold implementation to compute+ *        the suboptimal structures. For that purpose, the function doubles+ *        the sequence and enlarges the DP matrices, which in fact will grow+ *        by a factor of 4 during the computation!+ *        At the end of the structure prediction, everything will be re-set+ *        to its original requriements, i.e. normal sequence, normal (empty)+ *        DP matrices.+ *+ *  @bug  Due to resizing, any pre-existing constraints will be lost!+ *+ *  @ingroup subopt_zuker+ *+ *  @see vrna_subopt(), zukersubopt(), zukersubopt_par()+ *+ *  @param  vc  fold compound+ *  @return     List of zuker suboptimal structures+ */+vrna_subopt_solution_t *+vrna_subopt_zuker(vrna_fold_compound_t *vc);++/**+ *  @brief printing threshold for use with logML+ * + *  @ingroup subopt_wuchty+ *+ */+extern  double  print_energy;++/**+ *  @brief Sort output by energy+ * + *  @ingroup subopt_wuchty+ *+ */+extern  int     subopt_sorted;++/**+ *  @addtogroup dos+ *  @{+ */++/**+ *  @brief The Density of States+ *+ *  This array contains the density of states for an RNA sequences after a call to subopt_par(),+ *  subopt() or subopt_circ().+ *+ *  @pre  Call one of the functions subopt_par(), subopt() or subopt_circ() prior accessing the contents+ *        of this array+ *  @see  subopt_par(), subopt(), subopt_circ()+ *+ */+extern  int     density_of_states[MAXDOS+1];++/** @} */ /* End of group dos */++#ifdef VRNA_BACKWARD_COMPAT++/**+ *  @brief Returns list of subopt structures or writes to fp+ * + *  This function produces <b>all</b> suboptimal secondary structures within+ *  'delta' * 0.01 kcal/mol of the optimum. The results are either+ *  directly written to a 'fp' (if 'fp' is not NULL), or+ *  (fp==NULL) returned in a #SOLUTION * list terminated+ *  by an entry were the 'structure' pointer is NULL.+ *+ *  @ingroup subopt_wuchty+ *+ *  @param  seq+ *  @param  structure+ *  @param  delta+ *  @param  fp+ *  @return+ */+DEPRECATED(SOLUTION *subopt (char *seq, char *structure, int delta, FILE *fp));++/**+ *  @brief Returns list of subopt structures or writes to fp+ * + *  @ingroup subopt_wuchty+ */+DEPRECATED(SOLUTION *subopt_par(char *seq, char *structure, vrna_param_t *parameters, int delta, int is_constrained, int is_circular, FILE *fp));++/**+ *  @brief Returns list of circular subopt structures or writes to fp+ * + *  This function is similar to subopt() but calculates secondary structures+ *  assuming the RNA sequence to be circular instead of linear+ * + *  @ingroup subopt_wuchty+ *+ *  @param  seq+ *  @param  sequence+ *  @param  delta+ *  @param  fp+ *  @return+ */+DEPRECATED(SOLUTION *subopt_circ(char *seq, char *sequence, int delta, FILE *fp));++/**+ *  @brief Compute Zuker type suboptimal structures+ *+ *  Compute Suboptimal structures according to M. Zuker, i.e. for every+ *  possible base pair the minimum energy structure containing the resp. base pair.+ *  Returns a list of these structures and their energies.+ *+ *  @ingroup subopt_zuker+ *+ *  @deprecated use vrna_zukersubopt() instead+ *+ *  @param  string  RNA sequence+ *  @return         List of zuker suboptimal structures+ */+DEPRECATED(SOLUTION  *zukersubopt(const char *string));++/**+ *  @brief Compute Zuker type suboptimal structures+ *+ *  @ingroup subopt_zuker+ *+ *  @deprecated use vrna_zukersubopt() instead+ *+ */+DEPRECATED(SOLUTION  *zukersubopt_par(const char *string, vrna_param_t *parameters));+++#endif++#endif
+ C/ViennaRNA/svm_utils.c view
@@ -0,0 +1,478 @@++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <math.h>+#include <ctype.h>+#include <string.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/fold_vars.h"+#include "ViennaRNA/pair_mat.h"+#include "svm_utils.h"++#include "ViennaRNA/model_avg.inc"  /* defines avg_model_string */+#include "ViennaRNA/model_sd.inc"   /* defines sd_model_string */++++PRIVATE struct svm_model *avg_model;+PRIVATE struct svm_model *sd_model;++PRIVATE void    freeFields(char** fields);+PRIVATE char**  splitFields(char* string);+PRIVATE char**  splitLines(char* string);++PUBLIC float get_z(char *sequence, double energy) {+  double average_free_energy;+  double sd_free_energy;+  float my_z = 0.;+  int info_avg;+  make_pair_matrix();+  short *S      = encode_sequence(sequence, 0);+  unsigned int   length  = strlen(sequence);+  int   *AUGC   = get_seq_composition(S, 1, length, length);+  avg_model     = svm_load_model_string(avg_model_string);+  sd_model      = svm_load_model_string(sd_model_string);+  average_free_energy = avg_regression(AUGC[0],AUGC[1],AUGC[2],AUGC[3],AUGC[4], avg_model, &info_avg);++  if(info_avg == 0){+    double difference = (energy/* /100*/) - average_free_energy;+    sd_free_energy    = sd_regression(AUGC[0], AUGC[1], AUGC[2], AUGC[3], AUGC[4], sd_model);+    my_z              = difference / sd_free_energy;+  }+  else{+    vrna_message_warning("sequence out of bounds");+#if 0+    my_z = shuffle_score(sequence, energy);+#endif+  }+  free(AUGC);+  free(S);+  svm_free_model_content(avg_model);+  svm_free_model_content(sd_model);+  return my_z;+}++PUBLIC int *get_seq_composition(short *S, unsigned int start, unsigned int stop, unsigned int length){+  unsigned int i;+  int *ret = (int *)vrna_alloc(sizeof(int) * 6);++  for (i=MAX2(start, 1); i <= MIN2(stop, length); i++){+    if(S[i] > 4)  ret[0]++;+    else          ret[S[i]]++;+  }+  ret[5] = -1; /* indicate last entry */+  return ret;+}++PUBLIC double sd_regression(int N, int A, int C, int G, int T,  struct svm_model *sd_model){+  double sd_free_energy = 0.0;+  int length = A + C + G + T + N;+  double GC_content  = (double) (G + C)/length;+  double AT_ratio    = (double) A/(A+T);+  double CG_ratio    = (double) C/(C+G);+  double norm_length = (double) (length-50)/350.0;+  struct svm_node node_mono[5];++  node_mono[0].index = 1; node_mono[0].value = GC_content;+  node_mono[1].index = 2; node_mono[1].value = AT_ratio;+  node_mono[2].index = 3; node_mono[2].value = CG_ratio;+  node_mono[3].index = 4; node_mono[3].value = norm_length;+  node_mono[4].index =-1;++  sd_free_energy = svm_predict(sd_model,node_mono);++  sd_free_energy = (double) sd_free_energy * sqrt(length);++  return sd_free_energy;+}++PUBLIC double avg_regression(int N, int A, int C, int G, int T, struct svm_model *avg_model, int *info ){+  double average_free_energy = 0.0;++  int length = A + C + G + T + N;+  double N_fraction = (double) N/length;+  double GC_content = (double) (G + C)/length;+  double AT_ratio   = (double) A/(A+T);+  double CG_ratio   = (double) C/(C+G);++  double norm_length = (double) (length-50)/350.0;++  struct svm_node node_mono[5];+  *info = 0;+  if ( length < 50 || length > 400 ) {+    *info = 1;+    return 0.0;+  }+  if ( N_fraction > 0.05 ) {+    *info = 2;+    return 0.0;+  }+  if ( GC_content < 0.20 || GC_content > 0.80 ) {+    *info = 3;+    return 0.0;+  }+  if ( AT_ratio < 0.20 || AT_ratio > 0.80 ) {+    *info = 4;+    return 0.0;+  }+  if ( CG_ratio < 0.20 || CG_ratio > 0.80 ) {+    *info = 5;+    return 0.0;+  }++  node_mono[0].index = 1; node_mono[0].value = GC_content;+  node_mono[1].index = 2; node_mono[1].value = AT_ratio;+  node_mono[2].index = 3; node_mono[2].value = CG_ratio;+  node_mono[3].index = 4; node_mono[3].value = norm_length;+  node_mono[4].index =-1;++  average_free_energy = svm_predict(avg_model,node_mono);++  average_free_energy = (double) average_free_energy * length;++  return average_free_energy;+}++PUBLIC double minimal_sd(int N, int A, int C, int G, int T ){+  int length = A + C + G + T + N;+  if ( length <  60 ) return 0.450324;+  if ( length <  70 ) return 0.749771;+  if ( length <  80 ) return 1.029421;+  if ( length <  90 ) return 1.027517;+  if ( length <  100 ) return 1.347283;+  if ( length <  120 ) return 1.112086;+  if ( length <  150 ) return 1.574339;+  if ( length <  170 ) return 1.779043;+  if ( length <  200 ) return 1.922908;+  if ( length <  250 ) return 2.226856;+  if ( length <  300 ) return 2.349300;+  if ( length <  350 ) return 2.589703;+  if ( length <  400 ) return 2.791215;++  return 0.450324;+}++PUBLIC struct svm_model  *svm_load_model_string(char *modelString){++  /* redefinition from svm.cpp */+  char *svm_type_table[]={"c_svc","nu_svc","one_class","epsilon_svr","nu_svr",NULL};+  char *kernel_type_table[]={"linear","polynomial","rbf","sigmoid",NULL};++  struct svm_model *model;+  char **lines, **fields;+  int i,j,k,l,m;+  char *key, *value, *field;+  char c;+  int dataStart, elements;+  int isColon;+  struct svm_node *x_space=NULL;++  model = (struct svm_model*)vrna_alloc(sizeof(struct svm_model));++  model->rho = NULL;+  model->probA = NULL;+  model->probB = NULL;+  model->label = NULL;+  model->nSV = NULL;+++  /* Read header until support vectors start */+  lines=splitLines(modelString);+  i=0;+  while (lines[i] && (strcmp(lines[i],"SV")!=0)){+        fields=splitFields(lines[i]);++        key=fields[0];++        if(strcmp(key,"svm_type")==0){+          value=fields[1];+          for(j=0;svm_type_table[j];j++){+                if(strcmp(svm_type_table[j],value)==0){+                  model->param.svm_type=j;+                  break;+                }+          }+          if(svm_type_table[i] == NULL){+                vrna_message_warning("unknown svm type.");+                free(model->rho);+                free(model->label);+                free(model->nSV);+                free(model);+                return NULL;+          }+        } else++        if(strcmp(key,"kernel_type")==0){+          value=fields[1];+          for(j=0;kernel_type_table[j];j++){+                if(strcmp(kernel_type_table[j],value)==0){+                  model->param.kernel_type=j;+                  break;+                }+          }+          if(kernel_type_table[i] == NULL){+                vrna_message_warning("unknown kernel type.");+                free(model->rho);+                free(model->label);+                free(model->nSV);+                free(model);+                return NULL;+          }+        } else++        if (strcmp(key,"gamma")==0){+          value=fields[1];+          sscanf(value,"%lf",&model->param.gamma);+        }++        if (strcmp(key,"degree")==0){+          value=fields[1];+          sscanf(value,"%d",&model->param.degree);+        } else++        if (strcmp(key,"coef0")==0){+          value=fields[1];+          sscanf(value,"%lf",&model->param.coef0);+        } else+        if (strcmp(key,"nr_class")==0){+          value=fields[1];+          sscanf(value,"%d",&model->nr_class);+        } else+        if (strcmp(key,"total_sv")==0){+          value=fields[1];+          sscanf(value,"%d",&model->l);+        } else++        if (strcmp(key,"rho")==0){+          int n = model->nr_class * (model->nr_class-1)/2;+          model->rho = (double*)vrna_alloc(sizeof(double)*n);+          for(j=0;j<n;j++){+                sscanf(fields[j+1],"%lf",&model->rho[j]);+          }+        } else++        if (strcmp(key,"nr_sv")==0){+          int n = model->nr_class;+          model->nSV = (int*)vrna_alloc(sizeof(int)*n);+          for(j=0;j<n;j++){+                sscanf(fields[j+1],"%d",&model->nSV[j]);+          }+        } else++        if (strcmp(key,"label")==0){+          int n = model->nr_class;+          model->label = (int*)vrna_alloc(sizeof(int)*n);+          for(j=0;j<n;j++){+                sscanf(fields[j+1],"%d",&model->label[j]);+          }+        } else++        if (strcmp(key,"probA")==0){+          int n = model->nr_class * (model->nr_class-1)/2;+          model->probA = (double*)vrna_alloc(sizeof(double)*n);+          for(j=0;j<n;j++){+                sscanf(fields[j+1],"%lf",&model->probA[j]);+          }+        } else++        if (strcmp(key,"probB")==0){+          int n = model->nr_class * (model->nr_class-1)/2;+          model->probB = (double*)vrna_alloc(sizeof(double)*n);+          for(j=0;j<n;j++){+                sscanf(fields[j+1],"%lf",&model->probB[j]);+          }+        }+        i++;+        freeFields(fields);+  }++  dataStart=i+1;+  elements=0;++  /* Count number of nodes (by counting colons) in advance to allocate+         memory in one block */+  while (lines[i]!=NULL){+        j=0;+        while ((c=lines[i][j])!='\0'){+          if (c==':'){+                elements++;+          }+          j++;+        }+        elements++;+        i++;+  }++  /* allocate memory for SVs and coefficients */+  m = model->nr_class - 1;+  l = model->l;+  model->sv_coef = (double**)vrna_alloc(sizeof(double*)*m);+  for(i=0;i<m;i++){+        model->sv_coef[i] = (double*)vrna_alloc(sizeof(double)*l);+  }+  model->SV = (struct svm_node**)vrna_alloc(sizeof(struct svm_node*)*l);++  if(l>0){+    x_space = (struct svm_node*)vrna_alloc(sizeof(struct svm_node)*(elements));+  }+++  /* parse support vector data */+  j=0;+  for(i=0;i<l;i++){+        fields=splitFields(lines[dataStart+i]);+        model->SV[i] = &x_space[j];+        k=0;+        while ((field=fields[k])!=NULL){+          if (k<m){+            sscanf(fields[k],"%lf",&model->sv_coef[k][i]);+          } else {+            sscanf(fields[k],"%d:%lf",&(x_space[j].index),&(x_space[j].value));+            j++;+          }+          k++;+        }+        x_space[j++].index = -1;+        freeFields(fields);+  }+  freeFields(lines);++  model->free_sv = 1;++  return(model);+}++PRIVATE char **splitFields(char* string){++  char c;+  char* currField;+  char** output=NULL;+  int* seps;+  int nSep;+  int nField=0;+  int i=0;++  if (strlen(string)==0 || string==NULL){+        return NULL;+  }++  /* First find all characters which are whitespaces and store the+         positions in the array seps */++  seps=(int *)vrna_alloc(sizeof(int));+  seps[0]=-1;+  nSep=1;++  while ((c=string[i])!='\0' && (c!='\n')){+        if (isspace(c)){+          seps=(int*)vrna_realloc(seps,sizeof(int)*(nSep+1));+          seps[nSep++]=i;+        }+        i++;+  }++  seps=(int*)vrna_realloc(seps,sizeof(int)*(nSep+1));+  seps[nSep]=strlen(string);+++  /* Then go through all intervals in between of two whitespaces (or+         end or start of string) and store the fields in the array+         "output"; if there are two adjacent whitespaces this is ignored+         resulting in a behaviour like "split /\s+/" in perl */++  for (i=0;i<nSep;i++){++        int start=seps[i];+        int stop=seps[i+1];+        int length=(stop-start);+        int notSpace,j;+++        currField=(char *)vrna_alloc(sizeof(char)*(length+1));+        strncpy(currField,string+start+1,length-1);+        currField[length]='\0';++        /* check if field is not only whitespace */+        notSpace=0;+        j=0;+        while ((c=currField[j])!='\0'){+          if (!isspace(c)){+                notSpace=1;+                break;+          }+        }++        if (notSpace){+          output=(char**)vrna_realloc(output,sizeof(char**)*(nField+1));+          output[nField++]=currField;+          currField=NULL;+        } else {+          free(currField);+          currField=NULL;+        }++        /* printf("%s|\n",output[nField-1]); */+  }++  if (nField==0){+        return NULL;+  }+++  output=(char**)vrna_realloc(output,sizeof(char**)*(nField+1));+  output[nField]=NULL;++  free(seps);+  return output;++}++PRIVATE char **splitLines(char* string){++  char c;+  char* currLine=NULL;+  char** output=NULL;+  int i=0;+  int currLength=0;+  int lineN=0;++  while ((c=string[i])!='\0'){++        if (c=='\n'){+          output=(char**)vrna_realloc(output,sizeof(char**)*(lineN+1));+          currLine=(char*)vrna_realloc(currLine,sizeof(char)*(currLength+1));+          currLine[currLength]='\0';+          output[lineN]=currLine;+          currLength=0;+          currLine=NULL;+          lineN++;+        } else {++          currLine=(char*)vrna_realloc(currLine,sizeof(char)*(currLength+1));+          currLine[currLength]=c;+          currLength++;+        }+        i++;+  }++  output=(char**)vrna_realloc(output,sizeof(char**)*(lineN+1));+  output[lineN]=NULL;++  return output;++}++/*  for both splitLines and splitFields */+void freeFields(char** fields){++  int i=0;+  while (fields[i]!=NULL){+        free(fields[i++]);+  }+  free(fields);+}
+ C/ViennaRNA/svm_utils.h view
@@ -0,0 +1,35 @@+#ifndef VIENNA_RNA_PACKAGE_SUBOPT_H+#define VIENNA_RNA_PACKAGE_SUBOPT_H++#include "svm.h"++extern  char *avg_model_string;+extern  char *sd_model_string;++float     get_z(char *sequence,+                double energy);+double    avg_regression (int N,+                          int A,+                          int C,+                          int G,+                          int T,+                          struct svm_model *avg_model,+                          int *info );+double    sd_regression  (int N,+                          int A,+                          int C,+                          int G,+                          int T,+                          struct svm_model  *sd_model);+double    minimal_sd     (int N,+                          int A,+                          int C,+                          int G,+                          int T);+struct svm_model *svm_load_model_string(char *modelString);+int       *get_seq_composition( short *S,+                                unsigned int start,+                                unsigned int stop,+                                unsigned int length);++#endif
+ C/ViennaRNA/treedist.c view
@@ -0,0 +1,660 @@+/*+		Tree edit distances for RNA secondary structures+		Walter Fontana, Ivo L Hofacker, Peter F Stadler+			     Vienna RNA Package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include "ViennaRNA/edit_cost.h"+#include "ViennaRNA/dist_vars.h"+#include "ViennaRNA/utils.h"++#define PRIVATE  static+#define PUBLIC++#define MNODES	  4000	  /* Maximal number of nodes for alignment    */++PUBLIC  Tree     *make_tree(char *struc);+PUBLIC  float     tree_edit_distance(Tree *T1, Tree *T2);+PUBLIC  void      print_tree(Tree *t);+PUBLIC  void      free_tree(Tree *t);+++PRIVATE void            tree_dist(int i, int j);+PRIVATE int             edit_cost(int i, int j);+PRIVATE int            *make_keyroots(Postorder_list *pl);+PRIVATE void            sort(int n, int *ra);+PRIVATE Postorder_list *make_postorder_list(char *struc);+PRIVATE int             decode(char *id);+PRIVATE int             number_of_nodes(char *struc);+PRIVATE void            encode(int type, char *label);+PRIVATE void            print_keyroots(int *keyroots);+PRIVATE void            print_postorder_list(Postorder_list *pl);+PRIVATE void            backtracking(void);+PRIVATE void            sprint_aligned_trees(void);+++PRIVATE  Tree  *tree1, *tree2;+PRIVATE  int  **tdist;       /* contains distances between subtrees */+PRIVATE  int  **fdist;       /* contains distances between forests */+PRIVATE  int  *alignment[2]; /* contains numeric information on the alignment:+				alignment[0][p], aligment[1][p] are aligned postions.+				INDELs have one 0.+				alignment[0][0] contains the length of the alignment. */++/*---------------------------------------------------------------------------*/++PUBLIC float tree_edit_distance(Tree *T1, Tree *T2)+{+   int i1,j1,i,j, dist;+   int n1, n2;++   if (cost_matrix==0) EditCost = &UsualCost;+   else EditCost = &ShapiroCost;++   n1 = T1->postorder_list[0].sons;+   n2 = T2->postorder_list[0].sons;++   tdist = (int **) vrna_alloc(sizeof(int *) * (n1+1));+   fdist = (int **) vrna_alloc(sizeof(int *) * (n1+1));+   for (i=0; i<=n1; i++) {+      tdist[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+      fdist[i] = (int *) vrna_alloc(sizeof(int) * (n2+1));+   }++   tree1 = T1;  tree2 = T2;++   for (i1 = 1; i1 <= T1->keyroots[0]; i1++) {+      i = T1->keyroots[i1];+      for (j1 = 1; j1 <= T2->keyroots[0]; j1++) {+	 j = T2->keyroots[j1];++	 tree_dist(i,j);+      }+   }++   if (edit_backtrack) {++      if ((n1>MNODES)||(n2>MNODES)) vrna_message_error("tree too large for alignment");++      alignment[0] = (int *) vrna_alloc((n1+1)*sizeof(int));+      alignment[1] = (int *) vrna_alloc((n2+1)*sizeof(int));++      backtracking();+      sprint_aligned_trees();+      free(alignment[0]);+      free(alignment[1]);+   }+   dist = tdist[n1][n2];+   for (i=0; i<=n1; i++) {+      free(tdist[i]);+      free(fdist[i]);+   }+   free(tdist);+   free(fdist);++   return (float) dist;+}++/*---------------------------------------------------------------------------*/++PRIVATE void tree_dist(int i, int j)+{+   int li,lj,i1,j1,i1_1,j1_1,li1_1,lj1_1,f1,f2,f3,f;+   int cost, lleaf_i1, lleaf_j1;++   fdist[0][0] = 0;++   li = tree1->postorder_list[i].leftmostleaf;+   lj = tree2->postorder_list[j].leftmostleaf;++   for (i1 = li; i1 <= i; i1++) {+      i1_1 = (li == i1 ? 0 : i1-1);+      fdist[i1][0] = fdist[i1_1][0] + edit_cost(i1, 0);+   }++   for (j1 = lj; j1 <= j; j1++) {+      j1_1 = (lj == j1 ? 0 : j1-1);+      fdist[0][j1] = fdist[0][j1_1] + edit_cost(0, j1);+   }++   for (i1 = li; i1 <= i; i1++) {++      lleaf_i1 = tree1->postorder_list[i1].leftmostleaf;+      li1_1 = (li > lleaf_i1-1 ? 0 : lleaf_i1-1);+      i1_1 = (i1 == li ? 0: i1-1);+      cost = edit_cost(i1, 0);++      for (j1 = lj; j1 <= j; j1++) {++	 lleaf_j1 = tree2->postorder_list[j1].leftmostleaf;+	 j1_1 = (j1 == lj ? 0: j1-1);++	 f1 = fdist[i1_1][j1] + cost;+	 f2 = fdist[i1][j1_1] + edit_cost(0, j1);++	 f = f1 < f2 ? f1 : f2;++	 if (lleaf_i1 == li && lleaf_j1 == lj)   {++	    f3 = fdist[i1_1][j1_1] + edit_cost(i1, j1);++	    fdist[i1][j1] = f3 < f ? f3 : f;++	    tdist[i1][j1] = fdist[i1][j1];   /* store in array permanently */+	 }+	 else {+	    lj1_1 = (lj > lleaf_j1-1 ? 0 : lleaf_j1-1);++	    f3 = fdist[li1_1][lj1_1] + tdist[i1][j1];++	    fdist[i1][j1] = f3 < f ? f3 : f;+	 }+      }+   }+}++/*---------------------------------------------------------------------------*/++PRIVATE int edit_cost(int i, int j)+{+   int  c, diff, cd, min, a, b;++   c = (*EditCost)[tree1->postorder_list[i].type][tree2->postorder_list[j].type];++   diff = abs((a=tree1->postorder_list[i].weight) - (b=tree2->postorder_list[j].weight));++   min = (a < b ? a: b);+   if (min == a) cd = (*EditCost)[0][tree2->postorder_list[j].type];+   else          cd = (*EditCost)[0][tree1->postorder_list[i].type];++   return (c * min + cd * diff);++}++/*---------------------------------------------------------------------------*/++PUBLIC Tree *make_tree(char *struc)+{+   Tree *tree;++   tree = (Tree *) vrna_alloc(sizeof(Tree));++   tree->postorder_list = make_postorder_list(struc);+   tree->keyroots       = make_keyroots(tree->postorder_list);++   return (tree);+}+++/*---------------------------------------------------------------------------*/++PRIVATE int  *make_keyroots(Postorder_list *pl)+{+   int   i, k, keys;+   int  *keyroots;++   keyroots = (int *) vrna_alloc(sizeof(int)*(pl[0].sons+1));+   keys      = 0;++   for (i = 1; i <= pl[0].sons; i++) {+      if (!pl[i].sons) {++	 /* leaf */++	 k = pl[0].sons;+	 while (pl[k].leftmostleaf != i) k--;+	 keyroots[++keys] = k;+      }+   }++   sort(keys, keyroots);+   keyroots[0] = keys;++   return (keyroots);+}++/*---------------------------------------------------------------------------*/++PRIVATE void sort(int n, int *ra)       /* heap sort,  indices are 1..n !!! */+{+   int l,j,ir,i;+   int rra;++   if (n == 1) return;++   l = (n >> 1)+1;+   ir = n;+   for (;;) {+      if (l > 1)+	 rra = ra[--l];+      else {+	 rra = ra[ir];+	 ra[ir] = ra[1];+	 if (--ir == 1) {+	    ra[1] = rra;+	    return;+	 }+      }+      i = l;+      j = l << 1;+      while (j <= ir) {+	 if (j < ir && ra[j] < ra[j+1]) ++j;+	 if (rra < ra[j]) {+	    ra[i] = ra[j];+	    j += (i = j);+	 }+	 else j = ir+1;+      }+      ra[i] = rra;+   }+}++/*---------------------------------------------------------------------------*/++PRIVATE Postorder_list *make_postorder_list(char *struc)++     /*+       Convention for structure representation "struc":+       Nodes are one pair of matching parentheses, with the type and possibly+       a weight of the node immediately preceding the closing parentheses.++       Types:++       U....unpaired+       P....paired+       H....hairpin loop+       B....bulge loop+       I....internal loop+       M....multiloop+       S....stack+       R....virtual root++       Example:++       .((..(((...)))..((..)))). in usual notation becomes:++       full tree:+       ((U)(((U)(U)((((U)(U)(U)P)P)P)(U)(U)(((U)(U)P)P)P)P)(U)R)+       HIT:+       ((U1)((U2)((U3)P3)(U2)((U2)P2)P2)(U1)R)+       Shapiro:+       (((((H)S)((H)S)M)S)R)++       */+{+   int  paren, i, l, order, local_order, w, sons, count;+   int  n_nodes, p;+   char id[100];+   Postorder_list *pl;+   int  match_pos[MNODES], match_order[MNODES];+++   n_nodes = number_of_nodes(struc);+   if (n_nodes>MNODES) vrna_message_error("structure too long in make_postorder_list");+   pl = (Postorder_list *) vrna_alloc(sizeof(Postorder_list)*(n_nodes+1));+   pl[0].sons = n_nodes;++   paren = 1;+   match_pos[paren]   = 0;+   match_order[paren] = 0;++   i     = 1;+   l     = 0;+   order = 0;++   while (paren) {+      switch (struc[i]) {+       case '(':+	 match_pos[++paren] = i;+	 match_order[paren] = order;+	 break;+       case ')':+	 order++;+	 id[l] = '\0';+	 l = 0;+	 while (isalpha((int) id[l])) l++;+	 if (id[l]) sscanf(id+l, "%d", &w);+	 else  w = 1;+	 id[l] = '\0';+	 pl[order].type         = decode(id);+	 pl[order].weight       = w;+	 pl[order].leftmostleaf = match_order[paren]+1;++	 sons = count = 0;+	 local_order  = match_order[paren];+	 for (p = match_pos[paren]+1; p < i; p++) {+	    if (struc[p] == '(') count++;+	    else if (struc[p] == ')') {+	       local_order++;+	       if (count == 1) {+		  sons++;+		  pl[local_order].father = order;+	       }+	       count--;+	    }+	 }++	 pl[order].sons         = sons;+	 paren--;+	 l = 0;+	 break;+       default:+	 id[l++] = struc[i];+	 break;+      }+      i++;+   }++   return (pl);+}++/*---------------------------------------------------------------------------*/++PRIVATE int decode(char *id)+{+   int   n, quit, i;+   char  label[100], *code;++   n = 0;++   quit = 0;+   code = coding;++   while (!quit) {+      for (i = 0; code[i] != sep; i++) {+	 if (code[i] == '\0') {+	    quit = 1;+	    break;+	 }+	 label[i] = code[i];+      }+      label[i] = '\0';+      if (strcmp(id, label) == 0) return (n);+      code += (i+1);+      n++;+   }++   vrna_message_error( "Syntax error: node identifier \"%s\" not found "+                              "in coding string \"%s\"\n"+                              "Exiting...",+                              id, coding);+   exit(0);+}++/*---------------------------------------------------------------------------*/++PRIVATE void encode(int type, char label[])+{+   int   i, l;++   l = 0;+   for (i = 0; i < type; i++) {+      while (coding[l] != sep && coding[l]) l++;+      l++;+   }++   for (i = 0; coding[l+i] != sep; i++) {+      if (coding[l+i] == '\0') break;+      label[i] = coding[l+i];+   }+   label[i] = '\0';+}++/*---------------------------------------------------------------------------*/++PRIVATE int number_of_nodes(char *struc)+{+   int  l, c, i;++   l = strlen(struc);+   for (c = 0, i = 0; i < l; i++) if (struc[i] == ')') c++;+   return (c);+}++/*---------------------------------------------------------------------------*/++PRIVATE void print_keyroots(int *keyroots)+{+   int i;++   printf("--->  key roots  <---\n\n");++   printf("entries: %d\n", keyroots[0]);+   printf("{");+   for (i = 1; i <= keyroots[0]; i++) printf(" %d", keyroots[i]);+   printf(" }\n\n");+}++/*---------------------------------------------------------------------------*/++PRIVATE void print_postorder_list(Postorder_list *pl)+{+   register int i;+   char     label[100];++   printf("--->  postorder list  <---\n\n");++   for (i = 1; i <= pl[0].sons; i++) {+      printf("    postorder: %3d\n", i);+      *label = '\0';+      encode(pl[i].type, label);+      printf("         type: %3d (%s)\n", pl[i].type, label);+      printf("       weight: %3d\n", pl[i].weight);+      printf("       father: %3d\n", pl[i].father);+      printf("         sons: %3d\n", pl[i].sons);+      printf("leftmost leaf: %3d\n", pl[i].leftmostleaf);+      printf("\n");+   }+}++/*---------------------------------------------------------------------------*/++PUBLIC void print_tree(Tree *t)+{+   print_postorder_list(t->postorder_list);+   print_keyroots(t->keyroots);+   fflush(stdout);+}++/*---------------------------------------------------------------------------*/++PUBLIC void free_tree(Tree *t)+{+   free(t->postorder_list);+   free(t->keyroots);+   free(t);+}++/*---------------------------------------------------------------------------*/+++PRIVATE void backtracking(void)+{+   int li,lj,i1,j1,i1_1,j1_1,li1_1,lj1_1,f;+   int cost, lleaf_i1, lleaf_j1, ss, i,j,k;+   struct {int i,j;} sector[MNODES/2];++   ss=0;++   i=i1=tree1->postorder_list[0].sons;+   j=j1=tree2->postorder_list[0].sons;++ start:+   li = tree1->postorder_list[i].leftmostleaf;+   lj = tree2->postorder_list[j].leftmostleaf;+++   while ((i1>=li)&&(j1>=lj)) {++      lleaf_i1 = tree1->postorder_list[i1].leftmostleaf;+      li1_1 = (li > lleaf_i1-1 ? 0 : lleaf_i1-1);+      i1_1 = (i1 == li ? 0: i1-1);+      lleaf_j1 = tree2->postorder_list[j1].leftmostleaf;+      lj1_1 = (lj > lleaf_j1-1 ? 0 : lleaf_j1-1);+      j1_1 = (j1 == lj ? 0: j1-1);++      f = fdist[i1][j1];++      cost = edit_cost(i1, 0);+      if (f == fdist[i1_1][j1] + cost) {+	 alignment[0][i1]=0;+	 i1=i1_1;+      }+      else {+	 if (f ==  fdist[i1][j1_1] + edit_cost(0, j1)) {+	    alignment[1][j1]=0;+	    j1=j1_1;+	 }+	 else if (lleaf_i1 == li && lleaf_j1 == lj) {+	    alignment[0][i1] = j1;+	    alignment[1][j1] = i1;+	    i1=i1_1; j1=j1_1;+	 } else  {+	    sector[ss].i=i1;+	    sector[ss++].j=j1;+	    i1=li1_1;+	    j1=lj1_1;+	 }+      }+   }+   for (; i1>=li; ) {+      alignment[0][i1]=0;+      i1 = (i1 == li ? 0: i1-1);+   }+   for (; j1>=lj; ) {+      alignment[1][j1]=0;+      j1 = (j1 == lj ? 0: j1-1);+   }+   while (ss>0) {+      i1=sector[--ss].i;+      j1=sector[ss].j;+      for (k=1; 1; k++) {+	 i = tree1->keyroots[k];+	 if (tree1->postorder_list[i].leftmostleaf ==+	     tree1->postorder_list[i1].leftmostleaf) break;+      }+      for (k=1; 1; k++) {+	 j = tree2->keyroots[k];+	 if (tree2->postorder_list[j].leftmostleaf ==+	     tree2->postorder_list[j1].leftmostleaf) break;+      }+      tree_dist(i,j);+      goto start;+   }+}++/*---------------------------------------------------------------------------*/++PRIVATE void sprint_aligned_trees(void)+{+   int i,j,n1,n2,k,l,p, ni, nj, weights;+   char t1[2*MNODES+1], t2[2*MNODES+1], a1[8*MNODES], a2[8*MNODES], ll[20], ll1[20];++   weights=0;+   n1=tree1->postorder_list[0].sons;+   n2=tree2->postorder_list[0].sons;+   for (i=1; i<=n1; i++) weights |= (tree1->postorder_list[i].weight!=1);+   for (i=1; i<=n2; i++) weights |= (tree2->postorder_list[i].weight!=1);++   for (i=n1, l=2*n1-1; i>0; i--) {+      if (alignment[0][i]!=0) t1[l--]=']';+      else t1[l--]=')';+      p=i;+      while(i==tree1->postorder_list[p].leftmostleaf) {+	 if (alignment[0][p]!=0) t1[l--]='[';+	 else t1[l--]='(';+	 p=tree1->postorder_list[p].father;+      }+   }+   t1[2*n1]='\0';+   for (j=n2, l=2*n2-1; j>0; j--) {+      if (alignment[1][j]!=0) t2[l--]=']';+      else t2[l--]=')';+      p=j;+      while(j==tree2->postorder_list[p].leftmostleaf) {+	 if (alignment[1][p]!=0) t2[l--]='[';+	 else t2[l--]='(';+	 p=tree2->postorder_list[p].father;+      }+   }+   t2[2*n2]='\0';++   ni=nj=l=i=j=0;+   while (t1[i]||t2[j]) {+      while ((t1[i]=='(')||(t1[i]==')')) {+	 if (t1[i]==')') {+	    ni++;+	    encode(tree1->postorder_list[ni].type, ll);+	    if (weights)+	       sprintf(ll+strlen(ll), "%d", tree1->postorder_list[ni].weight);+	    for (k=0; k< strlen(ll); k++) {+	       a1[l]=ll[k];+	       a2[l++]='_';+	    }+	    a1[l]=')'; a2[l++]='_';+	 } else {+	    a1[l] = t1[i];+	    a2[l++] ='_';+	 }+	 i++;+      }++      while ((t2[j]=='(')||(t2[j]==')')) {+	 if (t2[j]==')') {+	    nj++;+	    encode(tree2->postorder_list[nj].type, ll);+	    if (weights)+	       sprintf(ll+strlen(ll), "%d", tree2->postorder_list[nj].weight);+	    for (k=0; k< strlen(ll); k++) {+	       a2[l]=ll[k];+	       a1[l++]='_';+	    }+	    a2[l]=')'; a1[l++]='_';+	 } else {+	    a2[l] = t2[j];+	    a1[l++] ='_';+	 }+	 j++;+      }++      if (t2[j]==']') {+	 ni++; nj++;+	 encode(tree2->postorder_list[nj].type, ll);+	 if (weights)+	    sprintf(ll+strlen(ll), "%d", tree2->postorder_list[nj].weight);+	 encode(tree1->postorder_list[ni].type, ll1);+	 if (weights)+	    sprintf(ll1+strlen(ll1), "%d", tree1->postorder_list[ni].weight);+	 if (strlen(ll)>strlen(ll1))+	    for (k=0; k<strlen(ll)-strlen(ll1); k++) strcat(ll1,"_");+	 if (strlen(ll)<strlen(ll1))+	    for (k=0; k<strlen(ll1)-strlen(ll); k++) strcat(ll,"_");+	 for (k=0; k< strlen(ll); k++) a2[l+k]=ll[k];+	 for (k=0; k< strlen(ll); k++) a1[l+k]=ll1[k];+	 l+=k;+	 a1[l]=a2[l]=')'; l++;+	 i++; j++;+      } else if (t2[j]=='[') {+	 a1[l]=a2[l]='('; l++;+	 i++; j++;+      }+   }+   a1[l]=a2[l]='\0';+   if (l>8*MNODES) vrna_message_error("structure too long in sprint_aligned_trees");+   if (aligned_line[0]!= NULL)  free(aligned_line[0]);+   if (aligned_line[1]!= NULL)  free(aligned_line[1]);+   aligned_line[0] = (char *) vrna_alloc((l+1)*sizeof(char));+   aligned_line[1] = (char *) vrna_alloc((l+1)*sizeof(char));+   strcpy(aligned_line[0], a1);+   strcpy(aligned_line[1], a2);+}++/*---------------------------------------------------------------------------*/
+ C/ViennaRNA/treedist.h view
@@ -0,0 +1,42 @@+#ifndef VIENNA_RNA_PACKAGE_TREE_DIST_H+#define VIENNA_RNA_PACKAGE_TREE_DIST_H++/**+ *  \file treedist.h+ *  \brief Functions for Tree Edit Distances+ */++#include <ViennaRNA/dist_vars.h>++/**+ *  \brief Constructs a Tree ( essentially the postorder list ) of the+ *  structure 'struc', for use in tree_edit_distance().+ * + *  \param  struc may be any rooted structure representation.+ *  \return+ */+Tree   *make_tree(char *struc);++/**+ *  \brief Calculates the edit distance of the two trees.+ * + *  \param T1+ *  \param T2+ *  \return+ */+float   tree_edit_distance( Tree *T1,+                            Tree *T2);++/**+ *  \brief Print a tree (mainly for debugging)+ */+void    print_tree(Tree *t);++/**+ *  \brief Free the memory allocated for Tree t.+ * + *  \param t+ */+void    free_tree(Tree *t);++#endif
+ C/ViennaRNA/unstructured_domains.c view
@@ -0,0 +1,1503 @@+/** \file unstructured_domains.c **/++/*+                  Unstructured domains++                  This file contains everything necessary to+                  deal with the default implementation for unstructured+                  domains in secondary structures. This feature enables,+                  for instance, ligand binding to unpaired stretches of+                  an RNA secondary structure.++                  c 2016 Ronny Lorenz++                  ViennaRNA package+*/++#include <config.h>+#include <stdlib.h>+#include <string.h>+#include <ctype.h>+#include <float.h>+#include <math.h>++#include "ViennaRNA/utils.h"+#include "ViennaRNA/alphabet.h"+#include "ViennaRNA/unstructured_domains.h"++/*+#################################+# PRIVATE MACROS                #+#################################+*/++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/++/*+#################################+# PRIVATE VARIABLES/STRUCTS     #+#################################+*/++struct default_outside {+  int         motif_num;+  FLT_OR_DBL  exp_energy;+};++/*+ *  Default data structure for ligand binding to unpaired stretches+ */+struct ligands_up_data_default {++  /*+  **********************************+    pre-computed position-wise+    motif list+  **********************************+  */+  int           n;+  int           **motif_list_ext;+  int           **motif_list_hp;+  int           **motif_list_int;+  int           **motif_list_mb;++  int           *dG;+  FLT_OR_DBL    *exp_dG;+  int           *len;++  /*+  **********************************+    below are DP matrices to store+    the production rule results+  **********************************+  */+  int           *energies_ext;+  int           *energies_hp;+  int           *energies_int;+  int           *energies_mb;+  FLT_OR_DBL    *exp_energies_ext;+  FLT_OR_DBL    *exp_energies_hp;+  FLT_OR_DBL    *exp_energies_int;+  FLT_OR_DBL    *exp_energies_mb;++  /*+  **********************************+    below are lists to store the+    outside partition function for+    each motif starting at each+    position+  **********************************+  */+  unsigned int            *outside_ext_count;+  struct default_outside  **outside_ext;+  unsigned int            *outside_hp_count;+  struct default_outside  **outside_hp;+  unsigned int            *outside_int_count;+  struct default_outside  **outside_int;+  unsigned int            *outside_mb_count;+  struct default_outside  **outside_mb;++  FLT_OR_DBL  (*default_cb[32])(int, int, struct ligands_up_data_default *);+  FLT_OR_DBL  *exp_e_mx[32];+};++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/++PRIVATE void        remove_ligands_up(vrna_fold_compound_t *vc);+PRIVATE void        init_ligands_up(vrna_fold_compound_t *vc);++PRIVATE void        add_ligand_motif(vrna_fold_compound_t *vc, const char *motif, double motif_en, unsigned int loop_type);+PRIVATE void        remove_default_data(void *d);++/* default implementations for unstructured domains feature */+PRIVATE void        default_prod_rule(vrna_fold_compound_t *vc, void *d);+PRIVATE void        default_exp_prod_rule(vrna_fold_compound_t *vc, void *d);+PRIVATE int         default_energy(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *d);+PRIVATE FLT_OR_DBL  default_exp_energy( vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *d);+PRIVATE void        default_probs_add(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, FLT_OR_DBL exp_energy, void *data);+PRIVATE FLT_OR_DBL  default_probs_get(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, int motif, void *data);++/* helper functions for default implementatations of unstructured domains feature */+PRIVATE int         default_energy_ext_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE int         default_energy_hp_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE int         default_energy_int_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE int         default_energy_mb_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE FLT_OR_DBL  default_exp_energy_ext_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE FLT_OR_DBL  default_exp_energy_hp_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE FLT_OR_DBL  default_exp_energy_int_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE FLT_OR_DBL  default_exp_energy_mb_motif(int i, int j, struct ligands_up_data_default *data);+PRIVATE void        free_default_data_matrices(struct ligands_up_data_default *data);+PRIVATE void        free_default_data_exp_matrices(struct ligands_up_data_default *data);+PRIVATE void        prepare_matrices( vrna_fold_compound_t *vc, struct ligands_up_data_default *data);+PRIVATE void        prepare_exp_matrices( vrna_fold_compound_t *vc, struct ligands_up_data_default *data);+PRIVATE struct ligands_up_data_default *get_default_data(void);+PRIVATE void        prepare_default_data(vrna_fold_compound_t *vc, struct ligands_up_data_default *data);+PRIVATE void        free_default_data(struct ligands_up_data_default *data);+PRIVATE int         *get_motifs(vrna_fold_compound_t *vc, int i, unsigned int loop_type);+PRIVATE void        annotate_ud(vrna_fold_compound_t *vc, int start, int end, char l, vrna_ud_motif_t **list, int *list_size, int *list_pos);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/+PUBLIC void+vrna_ud_remove( vrna_fold_compound_t *vc){++  if(vc && vc->domains_up)+    remove_ligands_up(vc);+}++PUBLIC void+vrna_ud_set_data( vrna_fold_compound_t                *vc,+                          void                        *data,+                          vrna_callback_free_auxdata  *free_cb){++  if(vc){+    /* init if not already present */+    if(!vc->domains_up)+      init_ligands_up(vc);++    /* free previous data if 'free_data' function present */+    if(vc->domains_up->free_data)+      vc->domains_up->free_data(vc->domains_up->data);++    /* set new data and free callback */+    vc->domains_up->free_data = free_cb;+    vc->domains_up->data      = data;+  }+}++PUBLIC void+vrna_ud_set_prod_rule_cb( vrna_fold_compound_t        *vc,+                          vrna_callback_ud_production *pre_cb,+                          vrna_callback_ud_energy     *e_cb){++  if(vc){+    /* init if not already present */+    if(!vc->domains_up)+      init_ligands_up(vc);++    /* set new callback */+    vc->domains_up->prod_cb   = pre_cb;+    vc->domains_up->energy_cb = e_cb;+  }+}++PUBLIC void+vrna_ud_set_exp_prod_rule_cb( vrna_fold_compound_t            *vc,+                              vrna_callback_ud_exp_production *pre_cb,+                              vrna_callback_ud_exp_energy     *exp_e_cb){++  if(vc){+    /* init if not already present */+    if(!vc->domains_up)+      init_ligands_up(vc);++    /* set new callback */+    vc->domains_up->exp_prod_cb   = pre_cb;+    vc->domains_up->exp_energy_cb = exp_e_cb;+  }+}+++PUBLIC void+vrna_ud_set_prob_cb(vrna_fold_compound_t        *vc,+                    vrna_callback_ud_probs_add  *setter,+                    vrna_callback_ud_probs_get  *getter){++  if(vc){+    /* init if not already present */+    if(!vc->domains_up)+      init_ligands_up(vc);++    /* set new callback */+    vc->domains_up->probs_add = setter;+    vc->domains_up->probs_get = getter;+  }+}++PUBLIC void+vrna_ud_add_motif(vrna_fold_compound_t  *vc,+                  const char            *motif,+                  double                motif_en,+                  unsigned int          loop_type){++  if(vc){+    if(!vc->domains_up){+      /* set all default callbacks */+      vrna_ud_set_prod_rule_cb(vc, &default_prod_rule, &default_energy);+      vrna_ud_set_exp_prod_rule_cb(vc, &default_exp_prod_rule, &default_exp_energy);+      vrna_ud_set_data(vc, get_default_data(), &remove_default_data);+      vrna_ud_set_prob_cb(vc, &default_probs_add, &default_probs_get);+    }+    add_ligand_motif(vc, motif, motif_en, loop_type);+  }+}+++PUBLIC int *+vrna_ud_get_motif_size_at(vrna_fold_compound_t  *vc,+                          int                   i,+                          unsigned int          loop_type){++  if(vc && vc->domains_up){+    int k, l, cnt, *ret, *ptr;++    ret = NULL;+    if((i > 0) && (i <= vc->length)){+      ptr = get_motifs(vc, i, loop_type);+      if(ptr){+        for(k = 0; ptr[k] != -1; k++) /* replace motif number with its size */+          ptr[k] = vc->domains_up->motif_size[ptr[k]];+        /* make the list unique */+        ret     = (int *)vrna_alloc(sizeof(int) * (k + 1));+        ret[0]  = -1;+        cnt     = 0;+        for(k = 0; ptr[k] != -1; k++){+          for(l = 0; l < cnt; l++){+            if(ptr[k] == ret[l])+              break; /* we've already seen this size */+          }+          if(l == cnt){ /* we've not seen this size before */+            ret[cnt]      = ptr[k];+            ret[cnt + 1]  = -1;+            cnt++;+          }+        }+        /* resize ret array */+        ret = (int *)vrna_realloc(ret, sizeof(int) * (cnt + 1));+      }+      free(ptr);+    }+    return ret;+  }+  return NULL;+}++PUBLIC int *+vrna_ud_get_motifs_at(vrna_fold_compound_t  *vc,+                      int                   i,+                      unsigned int          loop_type){++  if(vc && vc->domains_up){+    if((i > 0) && (i <= vc->length)){+      return get_motifs(vc, i, loop_type);+    }+  }+  return NULL;+}++vrna_ud_motif_t *+vrna_ud_detect_motifs(vrna_fold_compound_t  *vc,+                      const char            *structure){++  int list_size, list_pos;+  vrna_ud_motif_t *motif_list;++  motif_list = NULL;++  if(structure && vc->domains_up){+    int   l, start, end;+    char  last, *loops;++    l           = 0;+    list_pos    = 0;+    list_size   = 15;+    motif_list  = (vrna_ud_motif_t *)vrna_alloc(sizeof(vrna_ud_motif_t) * list_size);+    loops       = vrna_db_to_element_string(structure);++    while(l < vc->length){+      /* skip uppercase encodings */+      while(l < vc->length){+        if(islower(loops[l]))+          break;+        l++;+      }++      if(l < vc->length){+        start = 1 + l;+        last  = loops[l];+        while(loops[l++] == last){+          if(l == vc->length)+            break;+        }+        end = l - 1;+        annotate_ud(vc, start, end, last, &motif_list, &list_size, &list_pos);+      }+    }++    motif_list = (vrna_ud_motif_t *)vrna_realloc(motif_list, sizeof(vrna_ud_motif_t) * (list_pos + 1));+    motif_list[list_pos].start = 0;+    motif_list[list_pos].number = -1;+    free(loops);+  }++  return motif_list;+}++/*+#####################################+# BEGIN OF STATIC HELPER FUNCTIONS  #+#####################################+*/+PRIVATE struct ligands_up_data_default *+get_default_data(void){++  struct ligands_up_data_default *data = vrna_alloc(sizeof(struct ligands_up_data_default));+  data->n                 = 0;+  data->motif_list_ext    = NULL;+  data->motif_list_hp     = NULL;+  data->motif_list_int    = NULL;+  data->motif_list_mb     = NULL;+  data->dG                = NULL;+  data->exp_dG            = NULL;+  data->energies_ext      = NULL;+  data->energies_hp       = NULL;+  data->energies_int      = NULL;+  data->energies_mb       = NULL;+  data->exp_energies_ext  = NULL;+  data->exp_energies_hp   = NULL;+  data->exp_energies_int  = NULL;+  data->exp_energies_mb   = NULL;+  data->outside_ext       = NULL;+  data->outside_hp        = NULL;+  data->outside_int       = NULL;+  data->outside_mb        = NULL;+  data->outside_ext_count = NULL;+  data->outside_hp_count  = NULL;+  data->outside_int_count = NULL;+  data->outside_mb_count  = NULL;+  return data;+}++PRIVATE void+remove_ligands_up(vrna_fold_compound_t *vc){++  int i;++  /* free auxiliary data */+  if(vc->domains_up->free_data)+    vc->domains_up->free_data(vc->domains_up->data);++  for( i = 0; i < vc->domains_up->motif_count; i++ ){+    free(vc->domains_up->motif[i]);+  }+  free(vc->domains_up->motif);+  free(vc->domains_up->motif_size);+  free(vc->domains_up->motif_en);+  free(vc->domains_up->motif_type);++  free(vc->domains_up->uniq_motif_size);++  free(vc->domains_up);++  vc->domains_up = NULL;+}++PRIVATE void+init_ligands_up(vrna_fold_compound_t *vc){++  vc->domains_up = (vrna_ud_t *)vrna_alloc(sizeof(vrna_ud_t));++  vc->domains_up->uniq_motif_count  = 0;+  vc->domains_up->uniq_motif_size   = NULL;+  vc->domains_up->motif_count       = 0;+  vc->domains_up->motif             = NULL;+  vc->domains_up->motif_size        = NULL;+  vc->domains_up->motif_en          = NULL;+  vc->domains_up->motif_type        = NULL;+  vc->domains_up->prod_cb           = NULL;+  vc->domains_up->exp_prod_cb       = NULL;+  vc->domains_up->energy_cb         = NULL;+  vc->domains_up->exp_energy_cb     = NULL;+  vc->domains_up->data              = NULL;+  vc->domains_up->free_data         = NULL;+  vc->domains_up->probs_add         = NULL;+  vc->domains_up->probs_get         = NULL;+}++/*+**********************************+  Default implementation for+  ligand binding to unpaired+  stretches follows below+**********************************+*/++PRIVATE void+add_ligand_motif( vrna_fold_compound_t *vc,+                  const char *motif,+                  double motif_en,+                  unsigned int loop_type){++  unsigned int  i, n, same_size;+  vrna_ud_t     *ud;++  n   = (unsigned int)strlen(motif);+  ud  = vc->domains_up;++  /* First, we update the list of unique motif lengths */+  for(same_size = i = 0; i < ud->uniq_motif_count; i++){+    if(ud->uniq_motif_size[i] == n){+      same_size = 1;+      break;+    }+  }++  if(!same_size){+    ud->uniq_motif_size = (unsigned int *)vrna_realloc(ud->uniq_motif_size, sizeof(unsigned int *) * (ud->uniq_motif_count + 1));+    ud->uniq_motif_size[ud->uniq_motif_count] = n;+    ud->uniq_motif_count++;+  }++  /* And finally, we store the motif */+  ud->motif                       = (char **)vrna_realloc(ud->motif, sizeof(char *) * (ud->motif_count + 1));+  ud->motif[ud->motif_count]      = strdup(motif);+  ud->motif_size                  = (unsigned int *)vrna_realloc(ud->motif_size, sizeof(unsigned int *) * (ud->motif_count + 1));+  ud->motif_size[ud->motif_count] = n;+  ud->motif_en                    = (double *)vrna_realloc(ud->motif_en, sizeof(double) * (ud->motif_count + 1));+  ud->motif_en[ud->motif_count]   = motif_en;+  ud->motif_type                  = (unsigned int *)vrna_realloc(ud->motif_type, sizeof(double) * (ud->motif_count + 1));+  ud->motif_type[ud->motif_count] = loop_type;+  ud->motif_count++;++}++PRIVATE void+remove_default_data(void *d){++  struct ligands_up_data_default  *data;++  data = (struct ligands_up_data_default *)d;++  free_default_data_matrices(data);+  free_default_data_exp_matrices(data);+  free_default_data(data);++  free(data->dG);+  free(data->exp_dG);+}++PRIVATE void+free_default_data(struct ligands_up_data_default *data){++  int i;+  if(data->motif_list_ext){+    for(i=0; i <= data->n; i++)+      free(data->motif_list_ext[i]);+    free(data->motif_list_ext);+  }+  if(data->motif_list_hp){+    for(i=0; i <= data->n; i++)+      free(data->motif_list_hp[i]);+    free(data->motif_list_hp);+  }+  if(data->motif_list_int){+    for(i=0; i <= data->n; i++)+      free(data->motif_list_int[i]);+    free(data->motif_list_int);+  }+  if(data->motif_list_mb){+    for(i=0; i <= data->n; i++)+      free(data->motif_list_mb[i]);+    free(data->motif_list_mb);+  }++  free(data->len);++}++PRIVATE void+free_default_data_matrices(struct ligands_up_data_default *data){++  /* the following four pointers may point to the same memory */+  if(data->energies_ext){+    /* check whether one of the other b* points to the same memory location */+    if(data->energies_ext == data->energies_hp)+      data->energies_hp = NULL;+    if(data->energies_ext == data->energies_int)+      data->energies_int = NULL;+    if(data->energies_ext == data->energies_mb)+      data->energies_mb = NULL;+    free(data->energies_ext);+    data->energies_ext = NULL;+  }+  if(data->energies_hp){+    /* check whether one of the other b* points to the same memory location */+    if(data->energies_hp == data->energies_int)+      data->energies_int = NULL;+    if(data->energies_hp == data->energies_mb)+      data->energies_mb = NULL;+    free(data->energies_hp);+    data->energies_hp = NULL;+  }+  if(data->energies_int){+    /* check whether one of the other b* points to the same memory location */+    if(data->energies_int == data->energies_mb)+      data->energies_mb = NULL;+    free(data->energies_int);+    data->energies_int = NULL;+  }+  free(data->energies_mb);+  data->energies_mb = NULL;+}++PRIVATE void+free_default_data_exp_matrices(struct ligands_up_data_default *data){++  int i;++  /* the following four pointers may point to the same memory */+  if(data->exp_energies_ext){+    /* check whether one of the other b* points to the same memory location */+    if(data->exp_energies_ext == data->exp_energies_hp)+      data->exp_energies_hp = NULL;+    if(data->exp_energies_ext == data->exp_energies_int)+      data->exp_energies_int = NULL;+    if(data->exp_energies_ext == data->exp_energies_mb)+      data->exp_energies_mb = NULL;+    free(data->exp_energies_ext);+    data->exp_energies_ext = NULL;+  }+  if(data->exp_energies_hp){+    /* check whether one of the other b* points to the same memory location */+    if(data->exp_energies_hp == data->exp_energies_int)+      data->exp_energies_int = NULL;+    if(data->exp_energies_hp == data->exp_energies_mb)+      data->exp_energies_mb = NULL;+    free(data->exp_energies_hp);+    data->exp_energies_hp = NULL;+  }+  if(data->exp_energies_int){+    /* check whether one of the other b* points to the same memory location */+    if(data->exp_energies_int == data->exp_energies_mb)+      data->exp_energies_mb = NULL;+    free(data->exp_energies_int);+    data->exp_energies_int = NULL;+  }+  free(data->exp_energies_mb);+  data->exp_energies_mb = NULL;++  if(data->outside_ext)+    for(i = 0; i <= data->n; i++)+      if(data->outside_ext[i])+        free(data->outside_ext[i]);+  free(data->outside_ext);+  free(data->outside_ext_count);++  if(data->outside_hp)+    for(i = 0; i <= data->n; i++)+      if(data->outside_hp[i])+        free(data->outside_hp[i]);+  free(data->outside_hp);+  free(data->outside_hp_count);++  if(data->outside_int)+    for(i = 0; i <= data->n; i++)+      if(data->outside_int[i])+        free(data->outside_int[i]);+  free(data->outside_int);+  free(data->outside_int_count);++  if(data->outside_mb)+    for(i = 0; i <= data->n; i++)+      if(data->outside_mb[i])+        free(data->outside_mb[i]);+  free(data->outside_mb);+  free(data->outside_mb_count);+}++PRIVATE int *+get_motifs(vrna_fold_compound_t *vc, int i, unsigned int loop_type){++  int               k, j, u, n, *motif_list, cnt, guess;+  char              *sequence;+  vrna_ud_t         *domains_up;++  sequence    = vc->sequence;+  n           = (int)vc->length;+  domains_up  = vc->domains_up;++  cnt         = 0;+  guess       = domains_up->motif_count;+  motif_list  = (int *)vrna_alloc(sizeof(int) * (guess + 1));++  /* collect list of motif numbers we find that start at position i */+  for(k = 0; k < domains_up->motif_count; k++){++    if(!(domains_up->motif_type[k] & loop_type))+      continue;++    j = i + domains_up->motif_size[k] - 1;+    if(j <= n){ /* only consider motif that does not exceed sequence length (does not work for circular RNAs!) */+      for(u = i; u <= j; u++){+        if(!vrna_nucleotide_IUPAC_identity(sequence[u-1], domains_up->motif[k][u-i]))+          break;+      }+      if(u > j) /* got a complete motif match */+        motif_list[cnt++] = k;+    }+  }++  if(cnt == 0){+    free(motif_list);+    return NULL;+  }+  +  motif_list = (int *)vrna_realloc(motif_list, sizeof(int) * (cnt + 1));+  motif_list[cnt] = -1; /* end of list marker */++  return motif_list;+}+++static void+annotate_ud(vrna_fold_compound_t *vc,+            int start,+            int end,+            char l,+            vrna_ud_motif_t **list,+            int *list_size,+            int *list_pos){++  int i,j;++  /* get motifs in segment [start,end] */+  for(i = start; i <= end; i++){+    unsigned int type = 0;+    switch(l){+      case 'e': type = VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP;+                break;+      case 'h': type = VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP;+                break;+      case 'i': type = VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP;+                break;+      case 'm': type = VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP;+                break;+    }++    int *m = vrna_ud_get_motifs_at(vc, i, type);+    if(m){+      for(j = 0; m[j] != -1; j++){+        int size = vc->domains_up->motif_size[m[j]];++        if(i + size - 1 <= end){+          if(*list_pos == *list_size){+            *list_size *= 1.2;+            *list = (vrna_ud_motif_t *)vrna_realloc(*list, sizeof(vrna_ud_motif_t) * (*list_size));+          }+          (*list)[*list_pos].start = i;+          (*list)[*list_pos].number = m[j];+          (*list_pos)++;+        }+      }+    }+    free(m);+  }+}+++PRIVATE void+prepare_matrices( vrna_fold_compound_t *vc,+                  struct ligands_up_data_default *data){++  int         i,j,k,n,size;+  vrna_ud_t   *domains_up;++  n             = (int)vc->length;+  size          = ((n+1)*(n+2))/2 + 1;+  domains_up    = vc->domains_up;++  free_default_data_matrices(data);++  /* here we save memory by re-using DP matrices */+  unsigned int lt[4] = {  VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP };+  int **m[4], *mx;+  m[0] = &data->energies_ext;+  m[1] = &data->energies_hp;+  m[2] = &data->energies_int;+  m[3] = &data->energies_mb;++  for(i=0; i<4; i++){+    unsigned int *col,*col2;+    if(*(m[i]))+      continue;++    mx      = (int *)vrna_alloc(sizeof(int) * size);+    col     = (unsigned int *)vrna_alloc(sizeof(unsigned int) * domains_up->motif_count);+    col2    = (unsigned int *)vrna_alloc(sizeof(unsigned int) * domains_up->motif_count);+    *(m[i]) = mx;++    for(k = 0; k < domains_up->motif_count; k++)+      col[k] = domains_up->motif_type[k] & lt[i];++    /* check if any of the remaining DP matrices can point to the same location */+    for(j=i+1;j<4;j++){+      for(k = 0; k < domains_up->motif_count; k++){+        col2[k] = domains_up->motif_type[k] & lt[j];+        if(col[k] != col2[k])+          break;+      }+      if(k == domains_up->motif_count){+        *(m[j]) = mx;+      }+    }++    free(col);+    free(col2);+  }+}++PRIVATE void+prepare_exp_matrices( vrna_fold_compound_t *vc,+                      struct ligands_up_data_default *data){++  int         i,j,k,n,size;+  vrna_ud_t   *domains_up;++  n             = (int)vc->length;+  size          = ((n+1)*(n+2))/2 + 1;+  domains_up    = vc->domains_up;++  free_default_data_exp_matrices(data);++  /* here we save memory by re-using DP matrices */+  unsigned int lt[4] = {  VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP,+                          VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP };+  FLT_OR_DBL **m[4], *mx;+  m[0] = &data->exp_energies_ext;+  m[1] = &data->exp_energies_hp;+  m[2] = &data->exp_energies_int;+  m[3] = &data->exp_energies_mb;++  for(i=0; i<4; i++){+    unsigned int *col,*col2;+    if(*(m[i]))+      continue;++    mx      = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * size);+    col     = (unsigned int *)vrna_alloc(sizeof(unsigned int) * domains_up->motif_count);+    col2    = (unsigned int *)vrna_alloc(sizeof(unsigned int) * domains_up->motif_count);+    *(m[i]) = mx;++    for(k = 0; k < domains_up->motif_count; k++)+      col[k] = domains_up->motif_type[k] & lt[i];++    /* check if any of the remaining DP matrices can point to the same location */+    for(j=i+1;j<4;j++){+      for(k = 0; k < domains_up->motif_count; k++){+        col2[k] = domains_up->motif_type[k] & lt[j];+        if(col[k] != col2[k])+          break;+      }+      if(k == domains_up->motif_count){+        *(m[j]) = mx;+      }+    }++    free(col);+    free(col2);+  }++  /* now prepate memory for outside partition function */+  data->outside_ext = (struct default_outside **)vrna_alloc(sizeof(struct default_outside *) * (n + 2));+  data->outside_hp  = (struct default_outside **)vrna_alloc(sizeof(struct default_outside *) * (n + 2));+  data->outside_int = (struct default_outside **)vrna_alloc(sizeof(struct default_outside *) * (n + 2));+  data->outside_mb  = (struct default_outside **)vrna_alloc(sizeof(struct default_outside *) * (n + 2));+  data->outside_ext_count = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (n + 2));+  data->outside_hp_count  = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (n + 2));+  data->outside_int_count = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (n + 2));+  data->outside_mb_count  = (unsigned int *)vrna_alloc(sizeof(unsigned int) * (n + 2));+}++PRIVATE void+prepare_default_data( vrna_fold_compound_t *vc,+                      struct ligands_up_data_default *data){++  int         i, n;+  vrna_ud_t   *domains_up;++  n           = (int)vc->length;+  domains_up  = vc->domains_up;++  data->n = n;+  free_default_data(data);++  /*+      create motif_list for associating a nucleotide position with all+      motifs that start there+  */+  data->motif_list_ext  = (int **)vrna_alloc(sizeof(int *) * (n+1));+  data->motif_list_hp   = (int **)vrna_alloc(sizeof(int *) * (n+1));+  data->motif_list_int  = (int **)vrna_alloc(sizeof(int *) * (n+1));+  data->motif_list_mb   = (int **)vrna_alloc(sizeof(int *) * (n+1));+  data->motif_list_ext[0] = NULL;+  data->motif_list_hp[0]  = NULL;+  data->motif_list_int[0] = NULL;+  data->motif_list_mb[0]  = NULL;+  for(i = 1; i <= n; i++){+    data->motif_list_ext[i] = get_motifs(vc, i, VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP);+    data->motif_list_hp[i]  = get_motifs(vc, i, VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP);+    data->motif_list_int[i] = get_motifs(vc, i, VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP);+    data->motif_list_mb[i]  = get_motifs(vc, i, VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP);+  }++  /*  store length of motifs in 'data' */+  data->len = (int *)vrna_alloc(sizeof(int) * domains_up->motif_count);+  for(i = 0; i < domains_up->motif_count; i++)+    data->len[i] = domains_up->motif_size[i];++}++PRIVATE void+default_prod_rule(vrna_fold_compound_t *vc,+                  void *d){++  int                             i,j,k,l,u,n,size,e_ext, e_hp, e_int, e_mb,en,en2,*idx;+  unsigned int                    loop_type;+  vrna_ud_t                       *domains_up;+  struct ligands_up_data_default  *data;++  int           *energies_ext;+  int           *energies_hp;+  int           *energies_int;+  int           *energies_mb;++  n             = (int)vc->length;+  size          = ((n+1)*(n+2))/2 + 1;+  idx           = vc->jindx;+  domains_up    = vc->domains_up;+  data          = (struct ligands_up_data_default *)d;++  prepare_default_data(vc, data);+  prepare_matrices(vc, data);++  energies_ext  = data->energies_ext;+  energies_hp   = data->energies_hp;+  energies_int  = data->energies_int;+  energies_mb   = data->energies_mb;++  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP] = default_exp_energy_ext_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP]  = default_exp_energy_hp_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP] = default_exp_energy_int_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP]  = default_exp_energy_mb_motif;++  /*  precompute energy contributions of the motifs */+  data->dG = (int *)vrna_alloc(sizeof(int) * domains_up->motif_count);+  for(i = 0; i < domains_up->motif_count; i++)+    data->dG[i] = (int)roundf(domains_up->motif_en[i] * 100.);++  /* now we can start to fill the DP matrices */+  for(i=n; i>0; i--){+    int *list_ext = data->motif_list_ext[i];+    int *list_hp  = data->motif_list_hp[i];+    int *list_int = data->motif_list_int[i];+    int *list_mb  = data->motif_list_mb[i];+    for(j=i;j<=n;j++){+      if(i < j){+        e_ext = energies_ext[idx[j]+i+1];+        e_hp  = energies_hp[idx[j]+i+1];+        e_int = energies_int[idx[j]+i+1];+        e_mb  = energies_mb[idx[j]+i+1];+      } else {+        e_ext = INF;+        e_hp  = INF;+        e_int = INF;+        e_mb  = INF;+      }+      if(list_ext){+        for(k = 0; -1 != (l = list_ext[k]); k++){+          u   = i + data->len[l] - 1;+          en  = data->dG[l];+          if(u <= j){+            e_ext = MIN2(e_ext, en);+            if(u < j){+              en2 = en + energies_ext[idx[j]+u+1];+              e_ext = MIN2(e_ext, en2);+            }+          }+        }+      }+      if(list_hp){+        for(k = 0; -1 != (l = list_hp[k]); k++){+          u   = i + data->len[l] - 1;+          en  = data->dG[l];+          if(u <= j){+            e_hp = MIN2(e_hp, en);+            if(u < j){+              en2 = en + energies_hp[idx[j]+u+1];+              e_hp = MIN2(e_hp, en2);+            }+          }+        }+      }+      if(list_int){+        for(k = 0; -1 != (l = list_int[k]); k++){+          u   = i + data->len[l] - 1;+          en  = data->dG[l];+          if(u <= j){+            e_int = MIN2(e_int, en);+            if(u < j){+              en2 = en + energies_int[idx[j]+u+1];+              e_int = MIN2(e_int, en2);+            }+          }+        }+      }+      if(list_mb){+        for(k = 0; -1 != (l = list_mb[k]); k++){+          u   = i + data->len[l] - 1;+          en  = data->dG[l];+          if(u <= j){+            e_mb = MIN2(e_mb, en);+            if( u < j){+              en2 = en + energies_mb[idx[j]+u+1];+              e_mb = MIN2(e_mb, en2);+            }+          }+        }+      }++      energies_ext[idx[j]+i]  = e_ext;+      energies_hp[idx[j]+i]   = e_hp;+      energies_int[idx[j]+i]  = e_int;+      energies_mb[idx[j]+i]   = e_mb;+    }+  }+}++PRIVATE void+default_exp_prod_rule(vrna_fold_compound_t *vc,+                      void *d){++  int                             i,j,k,l,u,n,size,*idx;+  unsigned int                    loop_type;+  FLT_OR_DBL                      q_ext, q_hp, q_int, q_mb, q, qq;+  vrna_ud_t                       *domains_up;+  struct ligands_up_data_default  *data;++  FLT_OR_DBL    *exp_energies_ext;+  FLT_OR_DBL    *exp_energies_hp;+  FLT_OR_DBL    *exp_energies_int;+  FLT_OR_DBL    *exp_energies_mb;+  double        kT;++  n             = (int)vc->length;+  size          = ((n+1)*(n+2))/2 + 1;+  idx           = vc->iindx;+  domains_up    = vc->domains_up;+  data          = (struct ligands_up_data_default *)d;+  kT            = vc->exp_params->kT;++  prepare_default_data(vc, data);+  prepare_exp_matrices(vc, data);++  exp_energies_ext  = data->exp_energies_ext;+  exp_energies_hp   = data->exp_energies_hp;+  exp_energies_int  = data->exp_energies_int;+  exp_energies_mb   = data->exp_energies_mb;++  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP] = default_exp_energy_ext_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP]  = default_exp_energy_hp_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP] = default_exp_energy_int_motif;+  data->default_cb[VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP]  = default_exp_energy_mb_motif;++  data->exp_e_mx[VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP] = data->exp_energies_ext;+  data->exp_e_mx[VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP]  = data->exp_energies_hp;+  data->exp_e_mx[VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP] = data->exp_energies_int;+  data->exp_e_mx[VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP]  = data->exp_energies_mb;++  /*  precompute energy contributions of the motifs */+  data->exp_dG = (FLT_OR_DBL *)vrna_alloc(sizeof(FLT_OR_DBL) * domains_up->motif_count);+  for(i = 0; i < domains_up->motif_count; i++){+    double GT = domains_up->motif_en[i] * 1000.; /* in cal/mol */+    data->exp_dG[i] = (FLT_OR_DBL)exp( -GT / kT);+  }++  /* now we can start to fill the DP matrices */+  for(i=n; i>0; i--){+    int *list_ext = data->motif_list_ext[i];+    int *list_hp  = data->motif_list_hp[i];+    int *list_int = data->motif_list_int[i];+    int *list_mb  = data->motif_list_mb[i];+    for(j = i; j <= n; j++){+      if(i < j){+        q_ext = exp_energies_ext[idx[i + 1] - j];+        q_hp  = exp_energies_hp[idx[i + 1] - j];+        q_int = exp_energies_int[idx[i + 1] - j];+        q_mb  = exp_energies_mb[idx[i + 1] - j];+      } else {+        q_ext = 0;+        q_hp  = 0;+        q_int = 0;+        q_mb  = 0;+      }+      if(list_ext){+        for(k = 0; -1 != (l = list_ext[k]); k++){+          u = i + data->len[l] - 1;+          q = data->exp_dG[l];+          if(u <= j){+            q_ext += q;+            if(u < j)+              q_ext += q * exp_energies_ext[idx[u + 1] - j];+          }+        }+      }+      if(list_hp){+        for(k = 0; -1 != (l = list_hp[k]); k++){+          u   = i + data->len[l] - 1;+          q  = data->exp_dG[l];+          if(u <= j){+            q_hp += q;+            if(u < j)+              q_hp += q * exp_energies_hp[idx[u + 1] - j];+          }+        }+      }+      if(list_int){+        for(k = 0; -1 != (l = list_int[k]); k++){+          u   = i + data->len[l] - 1;+          q  = data->exp_dG[l];+          if(u <= j){+            q_int += q;+            if(u < j)+              q_int += q * exp_energies_int[idx[u + 1] - j];+          }+        }+      }+      if(list_mb){+        for(k = 0; -1 != (l = list_mb[k]); k++){+          u   = i + data->len[l] - 1;+          q  = data->exp_dG[l];+          if(u <= j){+            q_mb += q;+            if(u < j)+              q_mb += q * exp_energies_mb[idx[u + 1] - j];+          }+        }+      }++      exp_energies_ext[idx[i] - j]  = q_ext;+      exp_energies_hp[idx[i] - j]   = q_hp;+      exp_energies_int[idx[i] - j]  = q_int;+      exp_energies_mb[idx[i] - j]   = q_mb;+    }+  }+}++PRIVATE int+default_energy( vrna_fold_compound_t *vc,+                int i,+                int j,+                unsigned int loop_type,+                void *d){++  int en, ij, *idx = vc->jindx;+  struct ligands_up_data_default *data = (struct ligands_up_data_default *)d;++  en = INF;+  ij = idx[j] + i;++  if(j < i)+    return INF;++  if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MOTIF){+    if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP)+      en = default_energy_ext_motif(i, j, data);+    else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP)+      en = default_energy_hp_motif(i, j, data);+    else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP)+      en = default_energy_int_motif(i, j, data);+    else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)+      en = default_energy_mb_motif(i, j, data);+  } else {+    if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP){+      if(data->energies_ext)+        en = data->energies_ext[ij];+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP){+      if(data->energies_hp)+        en = data->energies_hp[ij];+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP){+      if(data->energies_int)+        en = data->energies_int[ij];+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP){+      if(data->energies_mb)+        en = data->energies_mb[ij];+    }+  }++  return en;+}++PRIVATE FLT_OR_DBL+default_exp_energy( vrna_fold_compound_t *vc,+                    int i,+                    int j,+                    unsigned int loop_type,+                    void *d){++  FLT_OR_DBL                      q;+  int                             ij, *idx;+  struct ligands_up_data_default  *data;++  q     = 0;+  data  = (struct ligands_up_data_default *)d;++  if(j < i)+    return 0.;++  if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MOTIF){+    q = data->default_cb[loop_type & ~(VRNA_UNSTRUCTURED_DOMAIN_MOTIF)](i, j, data);+  } else {+    idx = vc->iindx;+    ij  = idx[i] - j;+    q   = data->exp_e_mx[loop_type][ij];+  }++  return q;+}++PRIVATE int+default_energy_ext_motif( int i,+                          int j,+                          struct ligands_up_data_default *data){++  int k, m;+  int e = INF;++  if(data->motif_list_ext[i]){+    k = 0;+    while(-1 != (m = data->motif_list_ext[i][k])){+      if((i + data->len[m] - 1) == j)+        e = MIN2(e, data->dG[m]);+      k++;+    }+  }+  return e;+}++PRIVATE int+default_energy_hp_motif(int i,+                        int j,+                        struct ligands_up_data_default *data){++  int k, m;+  int e = INF;++  if(data->motif_list_hp[i]){+    k = 0;+    while(-1 != (m = data->motif_list_hp[i][k])){+      if((i + data->len[m] - 1) == j)+        e = MIN2(e, data->dG[m]);+      k++;+    }+  }+  return e;+}++PRIVATE int+default_energy_int_motif( int i,+                          int j,+                          struct ligands_up_data_default *data){++  int k, m;+  int e = INF;++  if(data->motif_list_int[i]){+    k = 0;+    while(-1 != (m = data->motif_list_int[i][k])){+      if((i + data->len[m] - 1) == j)+        e = MIN2(e, data->dG[m]);+      k++;+    }+  }+  return e;+}++PRIVATE int+default_energy_mb_motif(int i,+                        int j,+                        struct ligands_up_data_default *data){++  int k, m;+  int e = INF;++  if(data->motif_list_mb[i]){+    k = 0;+    while(-1 != (m = data->motif_list_mb[i][k])){+      if((i + data->len[m] - 1) == j)+        e = MIN2(2, data->dG[m]);+      k++;+    }+  }+  return e;+}++PRIVATE FLT_OR_DBL+default_exp_energy_ext_motif( int i,+                              int j,+                              struct ligands_up_data_default *data){++  int         k, m;+  FLT_OR_DBL  q = 0;++  if(data->motif_list_ext[i]){+    k = 0;+    while(-1 != (m = data->motif_list_ext[i][k])){+      if((i + data->len[m] - 1) == j)+        q += data->exp_dG[m];+      k++;+    }+  }++  return q;+}++PRIVATE FLT_OR_DBL+default_exp_energy_hp_motif(int i,+                            int j,+                            struct ligands_up_data_default *data){++  int         k, m;+  FLT_OR_DBL  q = 0;++  if(data->motif_list_hp[i]){+    k = 0;+    while(-1 != (m = data->motif_list_hp[i][k])){+      if((i + data->len[m] - 1) == j)+        q += data->exp_dG[m];+      k++;+    }+  }++  return q;+}++PRIVATE FLT_OR_DBL+default_exp_energy_int_motif( int i,+                              int j,+                              struct ligands_up_data_default *data){++  int         k, m;+  FLT_OR_DBL  q = 0;++  if(data->motif_list_int[i]){+    k = 0;+    while(-1 != (m = data->motif_list_int[i][k])){+      if((i + data->len[m] - 1) == j)+        q += data->exp_dG[m];+      k++;+    }+  }++  return q;+}++PRIVATE FLT_OR_DBL+default_exp_energy_mb_motif(int i,+                            int j,+                            struct ligands_up_data_default *data){++  int         k, m;+  FLT_OR_DBL  q = 0;++  if(data->motif_list_mb[i]){+    k = 0;+    while(-1 != (m = data->motif_list_mb[i][k])){+      if((i + data->len[m] - 1) == j)+        q += data->exp_dG[m];+      k++;+    }+  }++  return q;+}++PRIVATE void+default_probs_add(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  unsigned int loop_type,+                  FLT_OR_DBL exp_energy,+                  void *data){++  int                             **motif_list, k, l, m;+  unsigned int                    *size, *cnt, o;+  struct ligands_up_data_default  *d;+  struct default_outside          **storage, **st;++  d = (struct ligands_up_data_default  *)data;++  if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MOTIF){+    if(j < i)+      return;++    if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP){+      motif_list  = d->motif_list_ext;+      storage     = &(d->outside_ext[i]);+      size        = &(d->outside_ext_count[i]);+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP) {+      motif_list = d->motif_list_hp;+      storage     = &(d->outside_hp[i]);+      size        = &(d->outside_hp_count[i]);+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP){+      motif_list = d->motif_list_int;+      storage     = &(d->outside_int[i]);+      size        = &(d->outside_int_count[i]);+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP){+      motif_list = d->motif_list_mb;+      storage     = &(d->outside_mb[i]);+      size        = &(d->outside_mb_count[i]);+    } else{+      vrna_message_warning("Unknown unstructured domain loop type");+      return;+    }++    k = 0;+    while(-1 != (m = motif_list[i][k])){+      if((i + d->len[m] - 1) == j){++        /* check for addition first */+        for(o = 0; o < *size; o++)+          if((*storage)[o].motif_num == m){ /* found previously added motif constribution */+            (*storage)[o].exp_energy += exp_energy;+            break;+          }++        /* if we haven't added yet, create new list entry */+        if(o == *size){+          *storage = (struct default_outside *)vrna_realloc(*storage, sizeof(struct default_outside) * (*size + 1));+          (*storage)[*size].motif_num   = m;+          (*storage)[*size].exp_energy  = exp_energy;+          (*size)++;+        }+      }+      k++;+    }++  } else {+    if(j < i)+      return;++    FLT_OR_DBL pf, exp_e;+    pf = default_exp_energy(vc, i, j, loop_type, data);++    if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP){+      motif_list  = d->motif_list_ext;+      storage     = d->outside_ext;+      size        = d->outside_ext_count;+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP) {+      motif_list = d->motif_list_hp;+      storage     = d->outside_hp;+      size        = d->outside_hp_count;+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP){+      motif_list = d->motif_list_int;+      storage     = d->outside_int;+      size        = d->outside_int_count;+    } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP){+      motif_list = d->motif_list_mb;+      storage     = d->outside_mb;+      size        = d->outside_mb_count;+    } else{+      vrna_message_warning("Unknown unstructured domain loop type");+      return;+    }++    /* check for each motif starting at any k with i <= k <= j */+    for(k = i; k <= j; k++){+      if(motif_list[k]){+        st  = &(storage[k]);+        cnt = &(size[k]);+        for(l = 0; motif_list[k][l] != -1; l++){+          m = motif_list[k][l];++          if(j < k + d->len[m] - 1) /* motifs must be sorted be length */+            continue;++          exp_e         = d->exp_dG[m];+          FLT_OR_DBL p  = exp_e / pf;++          /* add/insert contribution */++          /* check for addition first */+          for(o = 0; o < *cnt; o++)+            if((*st)[o].motif_num == m){ /* found previously added motif constribution */+              (*st)[o].exp_energy += p * exp_energy;+              break;+            }++          /* if we haven't added yet, create new list entry */+          if(o == *cnt){+            *st = (struct default_outside *)vrna_realloc(*st, sizeof(struct default_outside) * (*cnt + 1));+            (*st)[*cnt].motif_num   = m;+            (*st)[*cnt].exp_energy  = p * exp_energy;+            (*cnt)++;+          }+        }+      }+    }+  }++}++PRIVATE FLT_OR_DBL+default_probs_get(vrna_fold_compound_t *vc,+                  int i,+                  int j,+                  unsigned int loop_type,+                  int motif,+                  void *data){++  FLT_OR_DBL                      outside = 0.;+  unsigned int                    *size, k;+  struct ligands_up_data_default  *d;+  struct default_outside          **storage;++  d = (struct ligands_up_data_default  *)data;++  if(j < i)+    return 0.;++  if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP){+    storage     = &(d->outside_ext[i]);+    size        = &(d->outside_ext_count[i]);+  } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP) {+    storage     = &(d->outside_hp[i]);+    size        = &(d->outside_hp_count[i]);+  } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP){+    storage     = &(d->outside_int[i]);+    size        = &(d->outside_int_count[i]);+  } else if(loop_type & VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP){+    storage     = &(d->outside_mb[i]);+    size        = &(d->outside_mb_count[i]);+  } else{+    vrna_message_warning("Unknown unstructured domain loop type");+    return 0.;+  }++  for(k = 0; k < *size; k++){+    /* check for motif number match */+    if((*storage)[k].motif_num == motif)+      /* check for length match */+      if(i + d->len[motif] - 1 == j){+        outside += (*storage)[k].exp_energy;+      }+  }++  return outside;+}
+ C/ViennaRNA/unstructured_domains.h view
@@ -0,0 +1,343 @@+#ifndef VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H+#define VIENNA_RNA_PACKAGE_UNSTRUCTURED_DOMAIN_H++/**+ *  @file unstructured_domains.h+ *  @ingroup domains_up+ *  @brief    Functions to modify unstructured domains, e.g. to incorporate ligands binding to unpaired stretches+ */++/**+ *  @addtogroup domains_up+ *+ *  @brief  Add and modify unstructured domains to the RNA folding grammar+ *+ *  This module provides the tools to add and modify unstructured domains to the production rules of the RNA folding grammar.+ *  Usually this functionality is utilized for incorporating ligand binding to unpaired stretches of an RNA.+ *+ *  Unstructured domains appear in the production rules of the RNA folding grammar+ *  whereever new unpaired nucleotides are attached to a growing substructure (see also @cite lorenz:2016b):+ *  @image html   Crecursion.svg+ *  @image latex  Crecursion.eps+ *+ *  The white boxes represent the stretch of RNA bound to the ligand and represented by a more or less specific+ *  sequence motif. The motif itself is considered unable to form basepairs. The additional production rule @em U+ *  is used to precompute the contribution of unpaired stretches possibly bound by one or more ligands. The+ *  auxiliary DP matrix for this production rule is filled right before processing the other (regular) production+ *  rules of the RNA folding grammar.+ *+ *  In a context with @ref domains_struc the grammar is extended as follows:+ *+ *  @image html   GCrecursion.svg+ *  @image latex  GCrecursion.eps+ *+ *  @bug  Although the additional production rule(s) for unstructured domains in the descriptions of this feature+ *        are always treated as 'segments possibly bound to one or more ligands', the current implementation requires+ *        that at least one ligand is bound. The default implementation already takes care of the required changes,+ *        however, upon using callback functions other than the default ones, one has to take care of this fact.+ *        Please also note, that this behavior might change in one of the next releases, such that the decomposition+ *        schemes as shown above comply with the actual implementation.+ *+ *  A default implementation allows one to readily use this feature by simply adding sequence motifs and corresponding+ *  binding free energies with the function vrna_ud_add_motif() (see also @ref ligands_up).+ *+ *  The grammar extension is realized using a callback function that+ *  - evaluates the binding free energy of a ligand to its target sequence segment (white boxes in the figures above), or+ *  - returns the free energy of an unpaired stretch possibly bound by a ligand, stored in the additional @em U DP matrix.+ *+ *  The callback is passed the segment positions, the loop context, and which of the two above mentioned+ *  evaluations are required. A second callback implements the pre-processing step that+ *  prepares the @em U DP matrix by evaluating all possible cases of the additional production rule.+ *  Both callbacks have a default implementation in @em RNAlib, but may be over-written by a+ *  user-implementation, making it fully user-customizable.+ *+ *  For equilibrium probability computations, two additional callbacks exist. One to store/add and one to retrieve the+ *  probability of unstructured domains at particular positions. Our implementation already takes care of computing+ *  the probabilities, but users of the unstructured domain feature are required to provide a mechanism to efficiently+ *  store/add the corresponding values into some external data structure.+ */++/** @brief Typename for the ligand binding extension data structure #vrna_unstructured_domain_s+ *  @ingroup domains_up+ */+typedef struct vrna_unstructured_domain_s  vrna_ud_t;++typedef struct vrna_unstructured_domain_motif_s  vrna_ud_motif_t;++#include <ViennaRNA/data_structures.h>++/**+ *  @brief Callback to retrieve binding free energy of a ligand bound to an unpaired sequence segment+ *  @ingroup domains_up+ */+typedef int (vrna_callback_ud_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);++/**+ *  @brief Callback to retrieve Boltzmann factor of the binding free energy of a ligand bound to an unpaired sequence segment+ *  @ingroup domains_up+ */+typedef FLT_OR_DBL (vrna_callback_ud_exp_energy)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, void *data);++/**+ *  @brief Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature+ *  @ingroup domains_up+ */+typedef void (vrna_callback_ud_production)(vrna_fold_compound_t *vc, void *data);++/**+ *  @brief Callback for pre-processing the production rule of the ligand binding to unpaired stretches feature (partition function variant)+ *  @ingroup domains_up+ */+typedef void (vrna_callback_ud_exp_production)(vrna_fold_compound_t *vc, void *data);+++/**+ *  @brief Callback to store/add equilibrium probability for a ligand bound to an unpaired sequence segment+ *  @ingroup domains_up+ */+typedef void (vrna_callback_ud_probs_add)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, FLT_OR_DBL exp_energy, void *data);++/**+ *  @brief Callback to retrieve equilibrium probability for a ligand bound to an unpaired sequence segment+ *  @ingroup domains_up+ */+typedef FLT_OR_DBL (vrna_callback_ud_probs_get)(vrna_fold_compound_t *vc, int i, int j, unsigned int loop_type, int motif, void *data);+++/**+ *  @brief Flag to indicate ligand bound to unpiared stretch in the exterior loop+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP    1U++/**+ *  @brief Flag to indicate ligand bound to unpaired stretch in a hairpin loop+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP     2U++/**+ *  @brief Flag to indicate ligand bound to unpiared stretch in an interior loop+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP    4U++/**+ *  @brief Flag to indicate ligand bound to unpiared stretch in a multibranch loop+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP     8U++/**+ *  @brief Flag to indicate ligand binding without additional unbound nucleotides (motif-only)+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_MOTIF       16U++/**+ *  @brief Flag to indicate ligand bound to unpiared stretch in any loop (convenience macro)+ *  @ingroup domains_up+ */+#define VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS   (VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP | VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP | VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP)++/**+ *  @brief  Data structure to store all functionality for ligand binding+ *  @ingroup domains_up+ */+struct vrna_unstructured_domain_s {++  /*+  **********************************+    Keep track of all added motifs+  **********************************+  */+  int                             uniq_motif_count; /**<  @brief The unique number of motifs of different lengths */ +  unsigned int                    *uniq_motif_size; /**<  @brief An array storing a unique list of motif lengths */++  int                             motif_count;      /**<  @brief Total number of distinguished motifs */+  char                            **motif;          /**<  @brief Motif sequences */+  unsigned int                    *motif_size;      /**<  @brief Motif lengths */+  double                          *motif_en;        /**<  @brief Ligand binding free energy contribution */+  unsigned int                    *motif_type;      /**<  @brief Type of motif, i.e. loop type the ligand binds to */++  /*+  **********************************+    Grammar extension for ligand+    binding+  **********************************+  */+  vrna_callback_ud_production     *prod_cb;       /**<  @brief Callback to ligand binding production rule, i.e. create/fill DP free energy matrices+                                                   *    @details This callback will be executed right before the actual secondary structure decompositions,+                                                   *    and, therefore, any implementation must not interleave with the regular DP matrices.+                                                   */+  vrna_callback_ud_exp_production *exp_prod_cb;   /**<  @brief Callback to ligand binding production rule, i.e. create/fill DP partition function matrices */+  vrna_callback_ud_energy         *energy_cb;     /**<  @brief Callback to evaluate free energy of ligand binding to a particular unpaired stretch */+  vrna_callback_ud_exp_energy     *exp_energy_cb; /**<  @brief Callback to evaluate Boltzmann factor of ligand binding to a particular unpaired stretch */+  void                            *data;          /**<  @brief Auxiliary data structure passed to energy evaluation callbacks */+  vrna_callback_free_auxdata      *free_data;     /**<  @brief Callback to free auxiliary data structure */+  vrna_callback_ud_probs_add      *probs_add;     /**<  @brief Callback to store/add outside partition function */+  vrna_callback_ud_probs_get      *probs_get;     /**<  @brief Callback to retrieve outside partition function */+};+++struct vrna_unstructured_domain_motif_s {+  int start;+  int number;+};+++/**+ *  @brief  Add an unstructured domain motif, e.g. for ligand binding+ *+ *  This function adds a ligand binding motif and the associated binding free energy+ *  to the #vrna_ud_t attribute of a #vrna_fold_compound_t. The motif data+ *  will then be used in subsequent secondary structure predictions. Multiple calls+ *  to this function with different motifs append all additional data to a list of+ *  ligands, which all will be evaluated. Ligand motif data can be removed from the+ *  #vrna_fold_compound_t again using the vrna_ud_remove() function. The loop+ *  type parameter allows one to limit the ligand binding to particular loop type,+ *  such as the exterior loop, hairpin loops, interior loops, or multibranch loops.+ *+ *  @see  #VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP, #VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP,+ *  #VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP, #VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP, #VRNA_UNSTRUCTURED_DOMAIN_ALL_LOOPS,+ *  vrna_ud_remove()+ *+ *  @ingroup domains_up+ *+ *  @param  vc        The #vrna_fold_compound_t data structure the ligand motif should be bound to+ *  @param  motif     The sequence motif the ligand binds to+ *  @param  motif_en  The binding free energy of the ligand in kcal/mol+ *  @param  loop_type The loop type the ligand binds to+ *+ */+void  vrna_ud_add_motif(vrna_fold_compound_t *vc,+                        const char *motif,+                        double motif_en,+                        unsigned int loop_type);+++/**+ *  @brief  Get a list of unique motif sizes that start at a certain position within the sequence+ *+ */+int *vrna_ud_get_motif_size_at( vrna_fold_compound_t *vc,+                                int i,+                                unsigned int loop_type);+++int *+vrna_ud_get_motifs_at(vrna_fold_compound_t *vc,+                      int i,+                      unsigned int loop_type);+++vrna_ud_motif_t *+vrna_ud_detect_motifs(vrna_fold_compound_t *vc,+                      const char *structure);+++/**+ *  @brief Remove ligand binding to unpaired stretches+ *+ *  This function removes all ligand motifs that were bound to a #vrna_fold_compound_t using+ *  the vrna_ud_add_motif() function.+ *+ *  @ingroup domains_up+ *+ *  @param vc The #vrna_fold_compound_t data structure the ligand motif data should be removed from+ */+void  vrna_ud_remove(vrna_fold_compound_t *vc);++/**+ *  @brief  Attach an auxiliary data structure+ *+ *  This function binds an arbitrary, auxiliary data structure for user-implemented ligand binding.+ *  The optional callback @p free will be passed the bound data structure whenever the #vrna_fold_compound_t+ *  is removed from memory to avoid memory leaks.+ *+ *  @see vrna_ud_set_prod_rule_cb(), vrna_ud_set_exp_prod_rule_cb(),+ *  vrna_ud_remove()+ *+ *  @ingroup domains_up+ *+ *  @param  vc      The #vrna_fold_compound_t data structure the auxiliary data structure should be bound to+ *  @param  data    A pointer to the auxiliary data structure+ *  @param  free_cb A pointer to a callback function that free's memory occupied by @p data+ */+void  vrna_ud_set_data( vrna_fold_compound_t        *vc,+                        void                        *data,+                        vrna_callback_free_auxdata  *free_cb);++/**+ *  @brief Attach production rule callbacks for free energies computations+ *+ *  Use this function to bind a user-implemented grammar extension for unstructured+ *  domains.+ *+ *  The callback @p e_cb needs to evaluate the free energy contribution @f$f(i,j)@f$ of+ *  the unpaired segment @f$[i,j]@f$. It will be executed in each of the regular secondary+ *  structure production rules. Whenever the callback is passed the #VRNA_UNSTRUCTURED_DOMAIN_MOTIF+ *  flag via its @p loop_type parameter the contribution of any ligand that consecutively+ *  binds from position @f$i@f$ to @f$j@f$ (the white box) is requested. Otherwise, the callback+ *  usually performs a lookup in the precomputed @p B matrices. Which @p B matrix is+ *  addressed will be indicated by the flags #VRNA_UNSTRUCTURED_DOMAIN_EXT_LOOP, #VRNA_UNSTRUCTURED_DOMAIN_HP_LOOP+ *  #VRNA_UNSTRUCTURED_DOMAIN_INT_LOOP, and #VRNA_UNSTRUCTURED_DOMAIN_MB_LOOP. As their names already imply,+ *  they specify exterior loops (@p F production rule), hairpin loops and interior loops+ *  (@p C production rule), and multibranch loops (@p M and @p M1 production rule).+ *  + *  @image html   ligands_up_callback.svg+ *  @image latex  ligands_up_callback.eps+ *+ *  The @p pre_cb callback will be executed as a pre-processing step right before the+ *  regular secondary structure rules. Usually one would use this callback to fill the+ *  dynamic programming matrices @p U and preparations of the auxiliary data structure+ *  #vrna_unstructured_domain_s.data+ *+ *  @image html   B_prod_rule.svg+ *  @image latex  B_prod_rule.eps+ *+ *  @ingroup domains_up+ *+ *  @param  vc      The #vrna_fold_compound_t data structure the callback will be bound to+ *  @param  pre_cb  A pointer to a callback function for the @p B production rule+ *  @param  e_cb    A pointer to a callback function for free energy evaluation+ */+void vrna_ud_set_prod_rule_cb(vrna_fold_compound_t        *vc,+                              vrna_callback_ud_production *pre_cb,+                              vrna_callback_ud_energy     *e_cb);+++/**+ *  @brief Attach production rule for partition function+ *+ *  This function is the partition function companion of vrna_ud_set_prod_rule_cb().+ *+ *  Use it to bind callbacks to (i) fill the @p U production rule dynamic programming+ *  matrices and/or prepare the #vrna_unstructured_domain_s.data, and (ii) provide a callback+ *  to retrieve partition functions for subsegments @f$ [i,j] @f$.+ *+ *  @image html   B_prod_rule.svg+ *  @image latex  B_prod_rule.eps+ *+ *  @image html   ligands_up_callback.svg+ *  @image latex  ligands_up_callback.eps+ *+ *  @ingroup domains_up+ *+ *  @see vrna_ud_set_prod_rule_cb()+ *+ *  @param  vc        The #vrna_fold_compound_t data structure the callback will be bound to+ *  @param  pre_cb    A pointer to a callback function for the @p B production rule+ *  @param  exp_e_cb  A pointer to a callback function that retrieves the partition function+ *                    for a segment @f$[i,j]@f$ that may be bound by one or more ligands.+ */+void  vrna_ud_set_exp_prod_rule_cb( vrna_fold_compound_t            *vc,+                                    vrna_callback_ud_exp_production *pre_cb,+                                    vrna_callback_ud_exp_energy     *exp_e_cb);+++void  vrna_ud_set_prob_cb(vrna_fold_compound_t        *vc,+                          vrna_callback_ud_probs_add  *setter,+                          vrna_callback_ud_probs_get  *getter);++#endif
+ C/ViennaRNA/utils.c view
@@ -0,0 +1,524 @@+/*+                               utils.c++                 c  Ivo L Hofacker and Walter Fontana+                          Vienna RNA package+*/++#ifdef HAVE_CONFIG_H+#include "config.h"+#endif++#include <stdio.h>+#include <stdlib.h>+#include <ctype.h>+#include <time.h>+#include <string.h>+#include <sys/types.h>+#include <sys/stat.h>+#include <stdint.h>+#include <stdarg.h>+#include <errno.h>++/* for getpid() we need some distinction between UNIX and Win systems */+#ifdef _WIN32+#include <windows.h>+#define getpid() GetCurrentProcessId() /* rename windows specific getpid function */+#else+#include <unistd.h>+#endif++#include "ViennaRNA/utils.h"++#ifdef WITH_DMALLOC+#include "dmalloc.h"+#endif++#define PRIVATE  static+#define PUBLIC++#define EXIT_ON_ERROR++#include "ViennaRNA/color_output.inc"++/*+#################################+# GLOBAL VARIABLES              #+#################################+*/+/*@notnull@ @only@*/+PUBLIC unsigned short xsubi[3];+++/*+#################################+# PRIVATE VARIABLES             #+#################################+*/+PRIVATE char  scale1[] = "....,....1....,....2....,....3....,....4";+PRIVATE char  scale2[] = "....,....5....,....6....,....7....,....8";+PRIVATE char  *inbuf = NULL;+PRIVATE char  *inbuf2 = NULL;+PRIVATE unsigned int typebuf2 = 0;+++/*+#################################+# PRIVATE FUNCTION DECLARATIONS #+#################################+*/+PRIVATE uint32_t  rj_mix( uint32_t a, uint32_t b, uint32_t c);+++/*+#################################+# BEGIN OF FUNCTION DEFINITIONS #+#################################+*/++#ifndef WITH_DMALLOC+/* include the following two functions only if not including <dmalloc.h> */++PUBLIC void *+vrna_alloc(unsigned size){++  void *pointer;++  if ( (pointer = (void *) calloc(1, (size_t) size)) == NULL) {+#ifdef EINVAL+    if (errno==EINVAL) {+      fprintf(stderr,"vrna_alloc: requested size: %d\n", size);+      vrna_message_error("Memory allocation failure -> EINVAL");+    }+    if (errno==ENOMEM)+#endif+      vrna_message_error("Memory allocation failure -> no memory");+  }+  return  pointer;+}++PUBLIC void *+vrna_realloc(void *p, unsigned size){++  if (p == NULL)+    return vrna_alloc(size);+  p = (void *) realloc(p, size);+  if (p == NULL) {+#ifdef EINVAL+    if (errno==EINVAL) {+      fprintf(stderr,"vrna_realloc: requested size: %d\n", size);+      vrna_message_error("vrna_realloc allocation failure -> EINVAL");+    }+    if (errno==ENOMEM)+#endif+      vrna_message_error("vrna_realloc allocation failure -> no memory");+  }+  return p;+}++#endif++/*------------------------------------------------------------------------*/++PUBLIC void+vrna_message_error(const char *format, ...){++  va_list args;+  va_start(args, format);+  vrna_message_verror(format, args);+  va_end(args);+}+++PUBLIC void+vrna_message_verror(const char *format, va_list args){++#ifndef WITHOUT_TTY_COLORS+  if(isatty(fileno(stderr))){+    fprintf(stderr, ANSI_COLOR_RED_B "ERROR: " ANSI_COLOR_RESET ANSI_COLOR_BRIGHT);+    vfprintf(stderr, format, args);+    fprintf(stderr, ANSI_COLOR_RESET "\n");+  } else {+#endif+    fprintf(stderr, "ERROR: ");+    vfprintf(stderr, format, args);+    fprintf(stderr, "\n");+#ifndef WITHOUT_TTY_COLORS+  }+#endif++#ifdef EXIT_ON_ERROR+  exit(EXIT_FAILURE);+#endif+}+++PUBLIC void+vrna_message_warning(const char *format, ...){++  va_list args;+  va_start(args, format);+  vrna_message_vwarning(format, args);+  va_end(args);+}+++PUBLIC void+vrna_message_vwarning(const char *format, va_list args){++#ifndef WITHOUT_TTY_COLORS+  if(isatty(fileno(stderr))){+    fprintf(stderr, ANSI_COLOR_MAGENTA_B "WARNING: " ANSI_COLOR_RESET ANSI_COLOR_BRIGHT);+    vfprintf(stderr, format, args);+    fprintf(stderr, ANSI_COLOR_RESET "\n");+  } else {+#endif+    fprintf(stderr, "WARNING: ");+    vfprintf(stderr, format, args);+    fprintf(stderr, "\n");+#ifndef WITHOUT_TTY_COLORS+  }+#endif+}+++PUBLIC void+vrna_message_info(FILE *fp, const char *format, ...){++  va_list args;+  va_start(args, format);+  vrna_message_vinfo(fp, format, args);+  va_end(args);+}+++PUBLIC void+vrna_message_vinfo(FILE *fp, const char *format, va_list args){++  if(!fp)+    fp = stdout;++#ifndef WITHOUT_TTY_COLORS+  if(isatty(fileno(fp))){+    fprintf(fp, ANSI_COLOR_BLUE_B);+    vfprintf(fp, format, args);+    fprintf(fp, ANSI_COLOR_RESET "\n");+  } else {+#endif+    vfprintf(fp, format, args);+    fprintf(fp, "\n");+#ifndef WITHOUT_TTY_COLORS+  }+#endif+}+++/*------------------------------------------------------------------------*/+PUBLIC void+vrna_init_rand(void){++  uint32_t seed = rj_mix(clock(), time(NULL), getpid());++  xsubi[0] = xsubi[1] = xsubi[2] = (unsigned short) seed;  /* lower 16 bit */+  xsubi[1] += (unsigned short) ((unsigned)seed >> 6);+  xsubi[2] += (unsigned short) ((unsigned)seed >> 12);+#ifndef HAVE_ERAND48+  srand((unsigned int) seed);+#endif+}++/*------------------------------------------------------------------------*/++/* uniform random number generator; vrna_urn() is in [0,1] */+/* uses a linear congruential library routine */+/* 48 bit arithmetic */+PUBLIC double+vrna_urn(void){++#ifdef HAVE_ERAND48+  extern double erand48(unsigned short[]);+  return erand48(xsubi);+#else+  return ((double) rand())/RAND_MAX;+#endif+}++/*------------------------------------------------------------------------*/++PUBLIC int+vrna_int_urn(int from, int to){++  return ( ( (int) (vrna_urn()*(to-from+1)) ) + from );+}++/*------------------------------------------------------------------------*/++/*-----------------------------------------------------------------*/++PUBLIC char *+vrna_time_stamp(void){++  time_t  cal_time;++  cal_time = time(NULL);+  return ( ctime(&cal_time) );+}++/*-----------------------------------------------------------------*/++PUBLIC  unsigned int get_input_line(char **string, unsigned int option){+  char  *line;+  int   i, l, r;++  /*+  * read lines until informative data appears or+  * report an error if anything goes wrong+  */+  if((line = vrna_read_line(stdin))==NULL) return VRNA_INPUT_ERROR;++  if(!(option & VRNA_INPUT_NOSKIP_COMMENTS))+    while((*line=='*')||(*line=='\0')){+      free(line);+      if((line = vrna_read_line(stdin))==NULL) return VRNA_INPUT_ERROR;+    }++  l = (int) strlen(line);++  /* break on '@' sign if not disabled */+  if(*line == '@'){+    free(line);+    return VRNA_INPUT_QUIT;+  }+  /* print line read if not disabled */+  /* if(!(option & VRNA_INPUT_NOPRINT)) printf("%s\n", line); */++  /* eliminate whitespaces at the end of the line read */+  if(!(option & VRNA_INPUT_NO_TRUNCATION)){+    for(i = l-1; i >= 0; i--){+      if      (line[i] == ' ')  continue;+      else if (line[i] == '\t') continue;+      else                      break;+    }+    line[(i >= 0) ? (i+1) : 0] = '\0';+  }++  if(*line == '>'){+    /* fasta header */+    /* alloc memory for the string */+    *string = (char *) vrna_alloc(sizeof(char) * (strlen(line) + 1));+    r = VRNA_INPUT_FASTA_HEADER;+    i = sscanf(line, ">%s", *string);+    if(i > 0){+      i       = (int)     strlen(*string);+      *string = (char *)  vrna_realloc(*string, (i+1)*sizeof(char));+      free(line);+      return r;+    }+    else{+      free(line);+      free(*string);+      *string = NULL;+      return VRNA_INPUT_ERROR;+    }+  }+  else{+    *string = strdup(line);+    free(line);+  }+  return VRNA_INPUT_MISC;+}+++PUBLIC void+vrna_message_input_seq_simple(void){++  vrna_message_input_seq("Input string (upper or lower case)");+}++PUBLIC  void+vrna_message_input_seq(const char *s){+#ifndef WITHOUT_TTY_COLORS+  if(isatty(fileno(stdout))){+    printf("\n" ANSI_COLOR_CYAN "%s; @ to quit" ANSI_COLOR_RESET "\n", s);+    printf(ANSI_COLOR_BRIGHT "%s%s" ANSI_COLOR_RESET "\n", scale1, scale2);+  } else {+#endif+    printf("\n%s; @ to quit\n", s);+    printf("%s%s\n", scale1, scale2);+#ifndef WITHOUT_TTY_COLORS+  }+#endif+  (void) fflush(stdout);+}++PUBLIC int *+vrna_idx_row_wise(unsigned int length){++  int i;+  int *idx = (int *)vrna_alloc(sizeof(int) * (length+1));+  for (i=1; i <= length; i++)+    idx[i] = (((length + 1 - i) * (length - i)) / 2) + length + 1;+  return idx;+}++PUBLIC int *+vrna_idx_col_wise(unsigned int length){++  unsigned int i;+  int *idx = (int *)vrna_alloc(sizeof(int) * (length+1));+  for (i = 1; i <= length; i++)+    idx[i] = (i*(i-1)) / 2; +  return idx;+}+++/*+#################################+# STATIC helper functions below #+#################################+*/+PRIVATE uint32_t+rj_mix( uint32_t a,+        uint32_t b,+        uint32_t c){++/*+  This is Robert Jenkins' 96 bit Mix function++  we use it to produce a more diverse seed for our random number+  generators. E.g.:+  +  seed = rj_mix(clock(), time(NULL), getpid());++  original comments on that function can be found below+*/+++/*+--------------------------------------------------------------------+mix -- mix 3 32-bit values reversibly.+For every delta with one or two bits set, and the deltas of all three+  high bits or all three low bits, whether the original value of a,b,c+  is almost all zero or is uniformly distributed,+* If mix() is run forward or backward, at least 32 bits in a,b,c+  have at least 1/4 probability of changing.+* If mix() is run forward, every bit of c will change between 1/3 and+  2/3 of the time.  (Well, 22/100 and 78/100 for some 2-bit deltas.)+mix() was built out of 36 single-cycle latency instructions in a +  structure that could supported 2x parallelism, like so:+      a -= b; +      a -= c; x = (c>>13);+      b -= c; a ^= x;+      b -= a; x = (a<<8);+      c -= a; b ^= x;+      c -= b; x = (b>>13);+      ...+  Unfortunately, superscalar Pentiums and Sparcs can't take advantage +  of that parallelism.  They've also turned some of those single-cycle+  latency instructions into multi-cycle latency instructions.  Still,+  this is the fastest good hash I could find.  There were about 2^^68+  to choose from.  I only looked at a billion or so.+--------------------------------------------------------------------+*/++  a=a-b;  a=a-c;  a=a^(c >> 13);+  b=b-c;  b=b-a;  b=b^(a << 8); +  c=c-a;  c=c-b;  c=c^(b >> 13);+  a=a-b;  a=a-c;  a=a^(c >> 12);+  b=b-c;  b=b-a;  b=b^(a << 16);+  c=c-a;  c=c-b;  c=c^(b >> 5);+  a=a-b;  a=a-c;  a=a^(c >> 3);+  b=b-c;  b=b-a;  b=b^(a << 10);+  c=c-a;  c=c-b;  c=c^(b >> 15);+  return c;+}++#ifdef  VRNA_BACKWARD_COMPAT++/*###########################################*/+/*# deprecated functions below              #*/+/*###########################################*/++PUBLIC int *+get_iindx(unsigned int length){++  return vrna_idx_row_wise(length);+}++PUBLIC int *+get_indx(unsigned int length){++  return vrna_idx_col_wise(length);+}++PUBLIC void+print_tty_input_seq(void){++  vrna_message_input_seq_simple();+}++PUBLIC void+print_tty_input_seq_str(const char *s){++  vrna_message_input_seq(s);+}++PUBLIC void+warn_user(const char message[]){++  vrna_message_warning(message);+}++PUBLIC void+nrerror(const char message[]){++  vrna_message_error(message);+}++PUBLIC void *space(unsigned size) {++  return vrna_alloc(size);+}++#undef  xrealloc+/* dmalloc.h #define's vrna_realloc */+PUBLIC void *xrealloc(void *p, unsigned size){++  return vrna_realloc(p, size);+}++PUBLIC void+init_rand(void){++  vrna_init_rand();+}++PUBLIC double urn(void){++  return vrna_urn();+}++PUBLIC int+int_urn(int from, int to){++  return vrna_int_urn(from, to);+}++PUBLIC void+filecopy(FILE *from, FILE *to){++  vrna_file_copy(from, to);+}++PUBLIC char *+time_stamp(void){++  return vrna_time_stamp();+}++PUBLIC char *+get_line(FILE *fp){ /* reads lines of arbitrary length from fp */++  return vrna_read_line(fp);+}+#endif
+ C/ViennaRNA/utils.h view
@@ -0,0 +1,471 @@+#ifndef VIENNA_RNA_PACKAGE_UTILS_H+#define VIENNA_RNA_PACKAGE_UTILS_H++/* make this interface backward compatible with RNAlib < 2.2.0 */+#define VRNA_BACKWARD_COMPAT++#ifdef DEPRECATION_WARNINGS+# ifdef __GNUC__+#  define DEPRECATED(func) func __attribute__ ((deprecated))+# else+#  define DEPRECATED(func) func+# endif+#else+# define DEPRECATED(func) func+#endif++/**+ *  @file     utils.h+ *  @ingroup  utils+ *  @brief    General utility- and helper-functions used throughout the @em ViennaRNA @em Package+ */++/**+ *  @{+ *  @ingroup  utils+ */++#include <stdio.h>+#include <stdarg.h>++#include <ViennaRNA/data_structures.h>+#include <ViennaRNA/string_utils.h>+#include <ViennaRNA/structure_utils.h>+#include <ViennaRNA/file_utils.h>+#include <ViennaRNA/alphabet.h>++/* two helper macros to indicate whether a function should be exported in+the library or stays hidden */+#define PUBLIC+#define PRIVATE static++/**+ *  @brief Output flag of get_input_line():  @e "An ERROR has occured, maybe EOF"+ */+#define VRNA_INPUT_ERROR                  1U+/**+ *  @brief @brief Output flag of get_input_line():  @e "the user requested quitting the program"+ */+#define VRNA_INPUT_QUIT                   2U+/**+ *  @brief Output flag of get_input_line():  @e "something was read"+ */+#define VRNA_INPUT_MISC                   4U++/**+ *  @brief  Input/Output flag of get_input_line():\n+ *  if used as input option this tells get_input_line() that the data to be read should comply+ *  with the FASTA format+ * + *  the function will return this flag if a fasta header was read+ */+#define VRNA_INPUT_FASTA_HEADER           8U++/*+ *  @brief  Input flag for get_input_line():\n+ *  Tell get_input_line() that we assume to read a nucleotide sequence+ * + */+#define VRNA_INPUT_SEQUENCE               16U++/** @brief  Input flag for get_input_line():\n+ *  Tell get_input_line() that we assume to read a structure constraint+ * + */+#define VRNA_INPUT_CONSTRAINT             32U++/**+ *  @brief  Input switch for get_input_line():+ *  @e "do not trunkate the line by eliminating white spaces at end of line"+ */+#define VRNA_INPUT_NO_TRUNCATION          256U++/**+ *  @brief  Input switch for vrna_file_fasta_read_record():  @e "do fill rest array"+ */+#define VRNA_INPUT_NO_REST                512U++/**+ *  @brief  Input switch for vrna_file_fasta_read_record():  @e "never allow data to span more than one line"+ */+#define VRNA_INPUT_NO_SPAN                1024U++/**+ *  @brief  Input switch for vrna_file_fasta_read_record():  @e "do not skip empty lines"+ */+#define VRNA_INPUT_NOSKIP_BLANK_LINES     2048U++/**+ *  @brief  Output flag for vrna_file_fasta_read_record():  @e "read an empty line"+ */+#define VRNA_INPUT_BLANK_LINE             4096U++/**+ *  @brief Input switch for get_input_line():  @e "do not skip comment lines"+ */+#define VRNA_INPUT_NOSKIP_COMMENTS        128U++/**+ *  @brief  Output flag for vrna_file_fasta_read_record():  @e "read a comment"+ */+#define VRNA_INPUT_COMMENT                8192U++/**+ *  @brief Get the minimum of two comparable values+ */+#define MIN2(A, B)      ((A) < (B) ? (A) : (B))++/**+ *  @brief Get the maximum of two comparable values+ */+#define MAX2(A, B)      ((A) > (B) ? (A) : (B))++/**+ *  @brief Get the minimum of three comparable values+ */+#define MIN3(A, B, C)   (MIN2(  (MIN2((A),(B))) ,(C)))++/**+ *  @brief Get the maximum of three comparable values+ */+#define MAX3(A, B, C)   (MAX2(  (MAX2((A),(B))) ,(C)))+++#ifdef WITH_DMALLOC+/* use dmalloc library to check for memory management bugs */+#include "dmalloc.h"+#define vrna_alloc(S)       calloc(1,(S))+#define vrna_realloc(p, S)  xrealloc(p, S)+#else++/**+ *  @brief Allocate space safely+ *+ *  @param size The size of the memory to be allocated in bytes+ *  @return     A pointer to the allocated memory+ */+void  *vrna_alloc(unsigned size);++/**+ *  @brief Reallocate space safely+ *+ *  @param p    A pointer to the memory region to be reallocated+ *  @param size The size of the memory to be allocated in bytes+ *  @return     A pointer to the newly allocated memory+ */+void  *vrna_realloc(void *p, unsigned size);++#endif++/**+ *  @brief Print an error message and die+ *+ *  This function is a wrapper to @em fprintf(stderr, ...) that+ *  puts a capital <b>ERROR:</b> in front of the message and then exits+ *  the calling program.+ *+ *  @see vrna_message_verror(), vrna_message_warning(), vrna_message_info()+ *+ *  @param format The error message to be printed+ *  @param ...    Optional arguments for the formatted message string+ */+void vrna_message_error(const char *format, ...);+++/**+ *  @brief Print an error message and die+ *+ *  This function is a wrapper to @em vfprintf(stderr, ...) that+ *  puts a capital <b>ERROR:</b> in front of the message and then exits+ *  the calling program.+ *+ *  @see vrna_message_error(), vrna_message_warning(), vrna_message_info()+ *+ *  @param format The error message to be printed+ *  @param args   The argument list for the formatted message string+ */+void vrna_message_verror(const char *format, va_list args);+++/**+ *  @brief Print a warning message+ *+ *  This function is a wrapper to @em fprintf(stderr, ...) that+ *  puts a capital <b>WARNING:</b> in front of the message.+ *+ *  @see vrna_message_vwarning(), vrna_message_error(), vrna_message_info()+ *+ *  @param format The warning message to be printed+ *  @param ...    Optional arguments for the formatted message string+ */+void vrna_message_warning(const char *format, ...);+++/**+ *  @brief Print a warning message+ *+ *  This function is a wrapper to @em fprintf(stderr, ...) that+ *  puts a capital <b>WARNING:</b> in front of the message.+ *+ *  @see vrna_message_vwarning(), vrna_message_error(), vrna_message_info()+ *+ *  @param format The warning message to be printed+ *  @param args   The argument list for the formatted message string+ */+void vrna_message_vwarning(const char *format, va_list args);+++/**+ *  @brief Print an info message+ *+ *  This function is a wrapper to @em fprintf(...).+ *+ *  @see vrna_message_vinfo(), vrna_message_error(), vrna_message_warning()+ *+ *  @param fp     The file pointer where the message is printed to+ *  @param format The warning message to be printed+ *  @param ...    Optional arguments for the formatted message string+ */+void vrna_message_info(FILE *fp, const char *format, ...);+++/**+ *  @brief Print an info message+ *+ *  This function is a wrapper to @em fprintf(...).+ *+ *  @see vrna_message_vinfo(), vrna_message_error(), vrna_message_warning()+ *+ *  @param fp     The file pointer where the message is printed to+ *  @param format The info message to be printed+ *  @param args   The argument list for the formatted message string+ */+void vrna_message_vinfo(FILE *fp, const char *format, va_list args);+++/**+ *  @brief  Initialize seed for random number generator+ */+void vrna_init_rand(void);++/**+ * @brief Current 48 bit random number+ *+ *  This variable is used by vrna_urn(). These should be set to some+ *  random number seeds before the first call to vrna_urn().+ *+ *  @see vrna_urn()+ */+extern unsigned short xsubi[3];++/**+ *  @brief get a random number from [0..1]+ *+ *  @see  vrna_int_urn(), vrna_init_rand()+ *  @note Usually implemented by calling @e erand48().+ *  @return   A random number in range [0..1]+ */+double vrna_urn(void);++/**+ *  @brief Generates a pseudo random integer in a specified range+ *+ *  @see  vrna_urn(), vrna_init_rand()+ *  @param from   The first number in range+ *  @param to     The last number in range+ *  @return       A pseudo random number in range [from, to]+ */+int vrna_int_urn(int from, int to);++/**+ *  @brief Get a timestamp+ *+ *  Returns a string containing the current date in the format+ *  @verbatim Fri Mar 19 21:10:57 1993 @endverbatim+ *+ *  @return A string containing the timestamp+ */+char  *vrna_time_stamp(void);++/**+ *  Retrieve a line from 'stdin' savely while skipping comment characters and+ *  other features+ *  This function returns the type of input it has read if recognized.+ *  An option argument allows one to switch between different reading modes.\n+ *  Currently available options are:\n+ *  #VRNA_INPUT_NOPRINT_COMMENTS, #VRNA_INPUT_NOSKIP_COMMENTS, #VRNA_INPUT_NOELIM_WS_SUFFIX+ * + *  pass a collection of options as one value like this:+ *  @verbatim get_input_line(string, option_1 | option_2 | option_n) @endverbatim+ * + *  If the function recognizes the type of input, it will report it in the return+ *  value. It also reports if a user defined 'quit' command (@-sign on 'stdin')+ *  was given. Possible return values are:\n+ *  #VRNA_INPUT_FASTA_HEADER, #VRNA_INPUT_ERROR, #VRNA_INPUT_MISC, #VRNA_INPUT_QUIT+ * + *  @param string   A pointer to the character array that contains the line read+ *  @param options  A collection of options for switching the functions behavior+ *  @return         A flag with information about what has been read+ */+unsigned int get_input_line(char **string,+                            unsigned int options);+++/**+ *  @brief Print a line to @e stdout that asks for an input sequence+ *+ *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions+ */+void vrna_message_input_seq_simple(void);+++/**+ *  @brief Print a line with a user defined string and a ruler to stdout.+ *+ *  (usually this is used to ask for user input)+ *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions+ * + *  @param s A user defined string that will be printed to stdout+ */+void vrna_message_input_seq(const char *s);++/**+ *  @brief Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions.+ *+ *  Access of a position "(i,j)" is then accomplished by using @verbatim (i,j) ~ iindx[i]-j @endverbatim+ *  This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout+ *  the ViennaRNA Package+ * + *  Consult the implemented code to find out about the mapping formula ;)+ * + *  @see vrna_idx_col_wise()+ *  @param length The length of the RNA sequence+ *  @return       The mapper array+ */+int *vrna_idx_row_wise(unsigned int length);++/**+ *  @brief Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.+ *+ *  Access of a position "(i,j)" is then accomplished by using @verbatim (i,j) ~ indx[j]+i @endverbatim+ *  This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout+ *  the ViennaRNAPackage+ * + *  Consult the implemented code to find out about the mapping formula ;)+ * + *  @see vrna_idx_row_wise()+ *  @param length The length of the RNA sequence+ *  @return       The mapper array+ * + */+int *vrna_idx_col_wise(unsigned int length);++/**+ *  @}+ */++#ifdef  VRNA_BACKWARD_COMPAT++DEPRECATED(int   *get_indx(unsigned int length));++DEPRECATED(int   *get_iindx(unsigned int length));++/**+ *  @brief Read a line of arbitrary length from a stream+ *+ *  Returns a pointer to the resulting string. The necessary memory is+ *  allocated and should be released using @e free() when the string is+ *  no longer needed.+ *+ *	@deprecated	Use vrna_read_line() as a substitute!+ *+ *  @param  fp  A file pointer to the stream where the function should read from+ *  @return     A pointer to the resulting string+ */+DEPRECATED(char  *get_line(FILE *fp));++/**+ *  @brief Print a line to @e stdout that asks for an input sequence+ *+ *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions+ *  @deprecated Use vrna_message_input_seq_simple() instead!+ */+DEPRECATED(void print_tty_input_seq(void));++/**+ *  @brief Print a line with a user defined string and a ruler to stdout.+ *+ *  (usually this is used to ask for user input)+ *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions+ * + *  @deprecated Use vrna_message_input_seq() instead!+ */+DEPRECATED(void print_tty_input_seq_str(const char *s));++/**+ *  @brief Print a warning message+ *+ *  Print a warning message to @e stderr+ *+ *  @deprecated Use vrna_message_warning() instead!+ */+DEPRECATED(void warn_user(const char message[]));++/**+ *  @brief Die with an error message+ *+ *  @deprecated Use vrna_message_error() instead!+ */+DEPRECATED(void nrerror(const char message[]));++/**+ *  @brief Allocate space safely+ *+ *  @deprecated Use vrna_alloc() instead!+ */+DEPRECATED(void *space(unsigned size));++/**+ *  @brief Reallocate space safely+ *+ *  @deprecated Use vrna_realloc() instead!+ */+DEPRECATED(void *xrealloc(void *p, unsigned size));++/**+ *  @brief  Make random number seeds+ *  @deprecated Use vrna_init_rand() instead!+ */+DEPRECATED(void init_rand(void));++/**+ *  @brief get a random number from [0..1]+ *+ *  @deprecated Use vrna_urn() instead!+ */+DEPRECATED(double urn(void));++/**+ *  @brief Generates a pseudo random integer in a specified range+ *+ *  @deprecated Use vrna_int_urn() instead!+ */+DEPRECATED(int int_urn(int from, int to));++/**+ *  @brief  Inefficient `cp`+ *+ *  @deprecated Use vrna_file_copy() instead!+ */+DEPRECATED(void filecopy(FILE *from, FILE *to));++/**+ *  @brief Get a timestamp+ *+ *  @deprecated Use vrna_time_stamp() instead!+ */+DEPRECATED(char *time_stamp(void));++#endif++#endif
+ C/ffiwrap_centroid.c view
@@ -0,0 +1,42 @@++// functions wrapped in here need a C-wrapper because they do "more work"+// before they can be called from C.++#include <stdio.h>+#include <string.h>+#include <stdlib.h>++#include "ViennaRNA/part_func.h"+#include "ViennaRNA/part_func_co.h"+#include "ViennaRNA/duplex.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/alifold.h"+#include "ViennaRNA/fold.h"++double ffiwrap_centroid_temp (double temp, const char *sequence, char *structure)+{+  double                dist, e;+  char*                 cent;+  char*                 pf_struc;+  double                cent_en;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.noLP = 1;+  md.dangles = 2;+//  md.noGUclosure = 1;+  md.temperature = temp;+  vc  = vrna_fold_compound(sequence, &md, 0);+  e = vrna_pf(vc, pf_struc);+  cent = vrna_centroid(vc, &dist);+  cent_en = vrna_eval_structure(vc, (const char*) cent);+  strcpy (structure, cent);+  free (cent);+  free (pf_struc);++  vrna_fold_compound_free(vc);++  return cent_en;+}+
+ C/ffiwrap_fold.c view
@@ -0,0 +1,52 @@++// functions wrapped in here need a C-wrapper because they do "more work"+// before they can be called from C.++#include <stdio.h>++#include "ViennaRNA/part_func.h"+#include "ViennaRNA/part_func_co.h"+#include "ViennaRNA/duplex.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/alifold.h"+#include "ViennaRNA/fold.h"++float ffiwrap_fold_temp (float temp, const char *sequence, char *structure)+{+  float                 mfe;+  vrna_fold_compound_t  *vc;+  vrna_md_t             md;++  vrna_md_set_default(&md);+  md.noLP = 1;+  md.temperature = temp;+  vc  = vrna_fold_compound(sequence, &md, 0);+  mfe = vrna_mfe(vc, structure);++  vrna_fold_compound_free(vc);++  return mfe;+}++float+ffiwrap_eos_temp (float temp, const char *string, const char *structure)+{+  float e;++  vrna_md_t             md;+  vrna_md_set_default(&md);+  md.temperature = temp;++  /* create fold_compound with default parameters and without DP matrices */+  vrna_fold_compound_t *vc = vrna_fold_compound(string, &md, VRNA_OPTION_EVAL_ONLY);++  /* evaluate structure */+  e = vrna_eval_structure(vc, structure);++  /* free fold_compound */+  vrna_fold_compound_free(vc);++  return e;+}++
+ C/ffiwrap_part_func.c view
@@ -0,0 +1,50 @@++// functions wrapped in here need a C-wrapper because they do "more work"+// before they can be called from C.++#include <stdio.h>++#include "ViennaRNA/part_func.h"+#include "ViennaRNA/part_func_co.h"+#include "ViennaRNA/duplex.h"+#include "ViennaRNA/plex.h"+#include "ViennaRNA/alifold.h"++// wrap the RNAfold constrained partition function++float ffiwrap_pf_fold_constrained (const char *sequence, char *structure, int constrained)+{+  return pf_fold_par (sequence, structure, 0, 1, constrained, 0);+}++// wrap the RNAfold constrained partition function for circular RNAs++float ffiwrap_pf_circ_fold_constrained (const char *sequence, char *structure, int constrained)+{+  return pf_fold_par (sequence, structure, 0, 1, constrained, 1);+}++// wrap the RNAcofold constrained partition function.++void ffiwrap_co_pf_fold_constrained (cofoldF * x, char *sequence, char *structure, int constrained)+{+  *x = co_pf_fold_par (sequence, structure, 0, 1, constrained);+  return;+}++// wrap RNAcofold partition function++void ffiwrap_co_pf_fold (cofoldF * x, char * inp, char * str)+{+  *x = co_pf_fold (inp, str);+  return;+}++// wrap folding a duplex++void ffiwrap_duplexfold (duplexT * x, char * linp, char * rinp)+{+  *x = duplexfold (linp, rinp);+  return;+}+
+ README.md view
@@ -0,0 +1,16 @@+[![Build Status](https://travis-ci.org/choener/ViennaRNA-bindings.svg?branch=master)](https://travis-ci.org/choener/ViennaRNA-bindings)++# ViennaRNA Bindings++This package provides bindings to a subset of the functions provided by the+ViennaRNA package, v2. The relevant C functionality is provided directly.++++#### Contact++Christian Hoener zu Siederdissen  +Leipzig University, Leipzig, Germany  +choener@bioinf.uni-leipzig.de  +http://www.bioinf.uni-leipzig.de/~choener/  +
ViennaRNA-bindings.cabal view
@@ -1,96 +1,147 @@-name:                ViennaRNA-bindings-version:             0.1.2.2-synopsis:            ViennaRNA v2 bindings-homepage:            http://www.tbi.univie.ac.at/~choener/-license:             OtherLicense-license-file:        LICENSE-author:              Christian Hoener zu Siederdissen (bindings) 2013-4, The ViennaRNA Team (library) 1994-2014-maintainer:          choener@tbi.univie.ac.at-copyright:           The ViennaRNA Team 1994-2014-category:            Bioinformatics, FFI-build-type:          Simple-cabal-version:       >=1.8+name:           ViennaRNA-bindings+version:        0.233.1.1+maintainer:     choener@tbi.univie.ac.at+homepage:       https://github.com/choener/ViennaRNA-bindings+bug-reports:    https://github.com/choener/ViennaRNA-bindings/issues+license:        OtherLicense+license-file:   LICENSE+author:         Christian Hoener zu Siederdissen (bindings) 2013-2017, The ViennaRNA Team (library) 1994-2017+copyright:      The ViennaRNA Team 1994-2017+category:       Bioinformatics, Bindings, FFI+build-type:     Simple+cabal-version:  >=1.10+tested-with:    GHC == 7.8.4, GHC == 7.10.3, GHC == 8.0.1, GHC == 8.0.2+synopsis:       ViennaRNA v2 bindings+description:    Bindings to the ViennaRNA package, version 2.3.3.+                .+                Only a partial set of bindings is provided. If you need+                additional functions, please open an issue on github.+                .+                The ViennaRNA bindings package now directly provide all+                necessary functionality. Please note that this package uses the+                same license as the ViennaRNA package.+                .+                If you use this software, please cite:+                .+                @+                R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011)+                ViennaRNA Package 2.0+                Algorithms for Molecular Biology: 6:26+                @+                .+                <http://www.almob.org/content/6/1/26> -description:-  Bindings to the ViennaRNA package, version 2.x.y.-  .-  Only a partial set of bindings is provided. If you need additional functions,-  please open an issue on github.-  .-  The ViennaRNA bindings package now directly provide all necessary-  functionality. Please note that this package uses the same license as the-  ViennaRNA package.-  .-  If you use this software, please cite:-  .-  @-  R. Lorenz, S.H. Bernhart, C. Hoener zu Siederdissen, H. Tafer, C. Flamm, P.F. Stadler and I.L. Hofacker (2011)-  ViennaRNA Package 2.0-  Algorithms for Molecular Biology: 6:26-  @-  .-  <http://www.almob.org/content/6/1/26> + extra-source-files:-  cbits/circfold.inc-  include/1.8.4_epars.h-  include/1.8.4_intloops.h-  include/aln_util.h-  include/cofold.h-  include/config.h-  include/data_structures.h-  include/energy_const.h-  include/energy_par.h-  include/fold.h-  include/fold_vars.h-  include/gquad.h-  include/intl11dH.h-  include/intl11.h-  include/intl21dH.h-  include/intl21.h-  include/intl22dH.h-  include/intl22.h-  include/list.h-  include/loop_energies.h-  include/naview.h-  include/pair_mat.h-  include/params.h,-  include/part_func_co.h-  include/part_func.h-  include/plot_layouts.h-  include/PS_dot.h-  include/subopt.h-  include/utils.h-  changelog+  C/ViennaRNA/*.h+  C/ViennaRNA/*.c+  C/ViennaRNA/*.inc +  changelog.md+  README.md ++ library   exposed-modules:     -- public interfaces     BioInf.ViennaRNA.Bindings     -- the FFI+    BioInf.ViennaRNA.Bindings.FFI.Centroid     BioInf.ViennaRNA.Bindings.FFI.CoFold+    BioInf.ViennaRNA.Bindings.FFI.Duplex     BioInf.ViennaRNA.Bindings.FFI.Fold     BioInf.ViennaRNA.Bindings.FFI.PartFunc     BioInf.ViennaRNA.Bindings.FFI.Utils-  build-depends:-    base == 4.* ,-    array+  build-depends: base == 4.*+               , array   build-tools:     c2hs   extra-libraries:+  default-language:+    Haskell2010+  default-extensions: CPP+                    , ForeignFunctionInterface+                    , NondecreasingIndentation+                    , ScopedTypeVariables   c-sources:-    cbits/fold.c-    cbits/utils.c-    cbits/fold_vars.c-    cbits/energy_par.c-    cbits/gquad.c-    cbits/params.c-    cbits/part_func.c-    cbits/part_func_co.c-    cbits/cofold.c-    cbits/ffiwrap_part_func.c+    C/ffiwrap_part_func.c+    C/ffiwrap_fold.c+    C/ffiwrap_centroid.c+    -- remove all of these, then @stack build --test@ and include files that have the missing definitions+    C/ViennaRNA/aln_util.c+    C/ViennaRNA/alphabet.c+    C/ViennaRNA/boltzmann_sampling.c+    C/ViennaRNA/centroid.c+    C/ViennaRNA/cofold.c+    C/ViennaRNA/commands.c+    C/ViennaRNA/constraints.c+    C/ViennaRNA/constraints_hard.c+    C/ViennaRNA/constraints_SHAPE.c+    C/ViennaRNA/constraints_soft.c+    C/ViennaRNA/data_structures.c+    C/ViennaRNA/dp_matrices.c+    C/ViennaRNA/duplex.c+    C/ViennaRNA/energy_par.c+    C/ViennaRNA/equilibrium_probs.c+    C/ViennaRNA/eval.c+    C/ViennaRNA/exterior_loops.c+    C/ViennaRNA/file_formats.c+    C/ViennaRNA/file_formats_msa.c+    C/ViennaRNA/file_utils.c+    C/ViennaRNA/fold.c+    C/ViennaRNA/gquad.c+    C/ViennaRNA/hairpin_loops.c+    C/ViennaRNA/interior_loops.c+    C/ViennaRNA/list.c+    C/ViennaRNA/mfe.c+    C/ViennaRNA/mm.c+    C/ViennaRNA/model.c+    C/ViennaRNA/multibranch_loops.c+    C/ViennaRNA/params.c+    C/ViennaRNA/part_func.c+    C/ViennaRNA/part_func_co.c+    C/ViennaRNA/plex.c+    C/ViennaRNA/plex_functions.c+    C/ViennaRNA/ribo.c+    C/ViennaRNA/string_utils.c+    C/ViennaRNA/structure_utils.c+    C/ViennaRNA/subopt.c+    C/ViennaRNA/unstructured_domains.c+    C/ViennaRNA/utils.c   cc-options:-  include-dirs: include-  includes: config.h+    -fPIC -DHAVE_STRDUP+  include-dirs:+    C++++test-suite properties+  type:+    exitcode-stdio-1.0+  main-is:+    properties.hs+  ghc-options:+    -O2 -rtsopts+  hs-source-dirs:+    tests+  default-language:+    Haskell2010+  default-extensions: CPP+                    , TemplateHaskell+  build-depends: base+               , array+               , QuickCheck+               , tasty                >= 0.11+               , tasty-hunit          >= 0.9+               , tasty-silver         >= 3.1+               , tasty-th             >= 0.1+               , ViennaRNA-bindings++++source-repository head+  type: git+  location: git://github.com/choener/ViennaRNA-bindings
− cbits/circfold.inc 
@@ -1,211 +0,0 @@-/* -*-C-*- */-/* this file contains code for folding circular RNAs */-/* it's #include'd into fold.c */--PRIVATE void fill_arrays_circ(const char *string, int *bt){-  /* variant of fold() for circular RNAs */-  /* auxiliarry arrays:-     fM2 = multiloop region with exactly two stems, extending to 3' end-     for stupid dangles=1 case we also need:-     fM_d3 = multiloop region with >= 2 stems, starting at pos 2-             (a pair (k,n) will form 3' dangle with pos 1)-     fM_d5 = multiloop region with >= 2 stems, extending to pos n-1-             (a pair (1,k) will form a 5' dangle with pos n)-  */-  int Hi, Hj, Ii, Ij, Ip, Iq, Mi;-  int *fM_d3, *fM_d5, Md3i, Md5i, FcMd3, FcMd5;-  int i,j, p,q,length, energy;-  int dangle_model = P->model_details.dangles;--  length = (int) strlen(string);--  FcH = FcI= FcM = FcMd3= FcMd5= Fc = INF;-  for (i=1; i<length; i++)-    for (j=i+TURN+1; j <= length; j++) {-      int ij, bonus=0, type, u, new_c, no_close;-      u = length-j + i-1;-      if (u<TURN) continue;--      ij = indx[j]+i;-      type = ptype[ij];--      /* enforcing structure constraints */-      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;-      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;-      if ((BP[i]==-4)||(BP[j]==-4)) type=0;--      no_close = (((type==3)||(type==4))&&no_closingGU&&(bonus==0));--      /* if (j-i-1 > max_separation) type = 0; */  /* forces locality degree */--      type=rtype[type];-      if (!type) continue;-      if (no_close) new_c = FORBIDDEN;-      else {-        char loopseq[10];-        /*int si1, sj1;*/-        if (u<7) {-          strcpy(loopseq , string+j-1);-          strncat(loopseq, string, i);-        }-        new_c = E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, P)+bonus+c[ij];-      }-      if (new_c<FcH) {-        FcH = new_c; Hi=i; Hj=j;-      }--      for (p = j+1; p < length ; p++) {-        int u1, qmin;-        u1 = p-j-1;-        if (u1+i-1>MAXLOOP) break;-        qmin = u1+i-1+length-MAXLOOP;-        if (qmin<p+TURN+1) qmin = p+TURN+1;-        for (q = qmin; q <=length; q++) {-          int u2, type_2/*, si1, sq1*/;-          type_2 = rtype[ptype[indx[q]+p]];-          if (type_2==0) continue;-          u2 = i-1 + length-q;-          if (u1+u2>MAXLOOP) continue;-          energy = E_IntLoop(u1, u2, type, type_2, S1[j+1], S1[i-1], S1[p-1], S1[q+1], P);-          new_c = c[ij] + c[indx[q]+p] + energy;-          if (new_c<FcI) {-            FcI = new_c; Ii=i; Ij=j; Ip=p; Iq=q;-          }-        }-      }-    }-  Fc = MIN2(FcI, FcH);--  /* compute the fM2 array (multi loops with exactly 2 helices) */-  /* to get a unique ML decomposition, just use fM1 instead of fML-     below. However, that will not work with dangle_model==1  */-  for (i=1; i<length-TURN; i++) {-    int u;-    fM2[i] = INF;-    for (u=i+TURN; u<length-TURN; u++)-      fM2[i] = MIN2(fM2[i], fML[indx[u]+i] + fML[indx[length]+u+1]);-  }--  for (i=TURN+1; i<length-2*TURN; i++) {-    int fm;-    fm = fML[indx[i]+1]+fM2[i+1]+P->MLclosing;-    if (fm<FcM) {-      FcM=fm; Mi=i;-    }-  }-  Fc = MIN2(Fc, FcM);--  if (dangle_model==1) {-    int u;-    fM_d3 =  (int *) space(sizeof(int)*(length+2));-    fM_d5 =  (int *) space(sizeof(int)*(length+2));-    for (i=TURN+1; i<length-TURN; i++) {-      fM_d3[i] = INF;-      for (u=2+TURN; u<i-TURN; u++)-        fM_d3[i] = MIN2(fM_d3[i], fML[indx[u]+2] + fML[indx[i]+u+1]);-    }-    for (i=2*TURN+1; i<length-TURN; i++) {-      int fm, type;-      type = ptype[indx[length]+i+1];-      if (type==0) continue;-      fm = fM_d3[i]+c[indx[length]+i+1]+E_MLstem(type, -1, S1[1], P) + P->MLclosing;-      if (fm<FcMd3) {-        FcMd3=fm; Md3i=i;-      }-      fm = fM_d3[i-1]+c[indx[length]+i+1]+E_MLstem(type, S1[i], S1[1], P) + P->MLclosing;-      if (fm<FcMd3) {-        FcMd3=fm; Md3i=-i;-      }-    }--    for (i=TURN+1; i<length-TURN; i++) {-      fM_d5[i] = INF;-      for (u=i+TURN; u<length-TURN; u++)-        fM_d5[i] = MIN2(fM_d5[i], fML[indx[u]+i] + fML[indx[length-1]+u+1]);-    }-    for (i=TURN+1; i<length-2*TURN; i++) {-      int fm, type;-      type = ptype[indx[i]+1];-      if (type==0) continue;-      fm = E_MLstem(type, S1[length], -1, P) + c[indx[i]+1] + fM_d5[i+1] + P->MLclosing;-      if (fm<FcMd5) {-        FcMd5=fm; Md5i=i;-      }-      fm = E_MLstem(type, S1[length], S1[i+1], P) + c[indx[i]+1] + fM_d5[i+2] + P->MLclosing;-      if (fm<FcMd5) {-        FcMd5=fm; Md5i=-i;-      }-    }-    if (FcMd5<MIN2(Fc,FcMd3)) {-      /* looks like we have to do this ... */-      sector[++(*bt)].i = 1;-      sector[(*bt)].j = (Md5i>0)?Md5i:-Md5i;-      sector[(*bt)].ml = 2;-      i = (Md5i>0)?Md5i+1 : -Md5i+2; /* let's backtrack fm_d5[Md5i+1] */-      for (u=i+TURN; u<length-TURN; u++)-        if (fM_d5[i] == fML[indx[u]+i] + fML[indx[length-1]+u+1]) {-          sector[++(*bt)].i = i;-          sector[(*bt)].j = u;-          sector[(*bt)].ml = 1;-          sector[++(*bt)].i =u+1;-          sector[(*bt)].j = length-1;-          sector[(*bt)].ml = 1;-          break;-        }-      Fc = FcMd5;-    } else if (FcMd3<Fc) {-      /* here we go again... */-      sector[++(*bt)].i = (Md3i>0)?Md3i+1:-Md3i+1;-      sector[(*bt)].j = length;-      sector[(*bt)].ml = 2;-      i = (Md3i>0)? Md3i : -Md3i-1; /* let's backtrack fm_d3[Md3i] */-      for (u=2+TURN; u<i-TURN; u++)-        if (fM_d3[i] == fML[indx[u]+2] + fML[indx[i]+u+1]) {-          sector[++(*bt)].i = 2;-          sector[(*bt)].j = u;-          sector[(*bt)].ml = 1;-          sector[++(*bt)].i =u+1;-          sector[(*bt)].j = i;-          sector[(*bt)].ml = 1;-          break;-        }-      Fc = FcMd3;-    }-    free(fM_d3);-    free(fM_d5);-  }-  else if(Fc < INF){-    if (FcH==Fc) {-      sector[++(*bt)].i = Hi;-      sector[(*bt)].j = Hj;-      sector[(*bt)].ml = 2;-    }-    else if (FcI==Fc) {-      sector[++(*bt)].i = Ii;-      sector[(*bt)].j = Ij;-      sector[(*bt)].ml = 2;-      sector[++(*bt)].i = Ip;-      sector[(*bt)].j = Iq;-      sector[(*bt)].ml = 2;-    }-    else if (FcM==Fc) { /* grumpf we found a Multiloop */-      int fm, u;-      /* backtrack in fM2 */-      fm = fM2[Mi+1];-      for (u=Mi+TURN+1; u<length-TURN; u++)-        if (fm == fML[indx[u]+Mi+1] + fML[indx[length]+u+1]) {-                sector[++(*bt)].i=Mi+1;-                sector[(*bt)].j=u;-                sector[(*bt)].ml = 1;-                sector[++(*bt)].i=u+1;-                sector[(*bt)].j=length;-                sector[(*bt)].ml = 1;-                break;-        }-      sector[++(*bt)].i = 1;-      sector[(*bt)].j = Mi;-      sector[(*bt)].ml = 1;-    }-  }-}-
− cbits/cofold.c 
@@ -1,1502 +0,0 @@-/* Last changed Time-stamp: <2008-12-03 17:44:38 ivo> */-/*-                  minimum free energy-                  RNA secondary structure prediction--                  c Ivo Hofacker, Chrisoph Flamm-                  original implementation by-                  Walter Fontana--                  Vienna RNA package-*/--#include <config.h>-#include <stdio.h>-#include <stdlib.h>-#include <math.h>-#include <ctype.h>-#include <string.h>-#include <limits.h>--#include "utils.h"-#include "energy_par.h"-#include "fold_vars.h"-#include "pair_mat.h"-#include "params.h"-#include "subopt.h"-#include "fold.h"-#include "loop_energies.h"-#include "gquad.h"-#include "cofold.h"--#ifdef _OPENMP-#include <omp.h>-#endif--#define PAREN--#define STACK_BULGE1      1       /* stacking energies for bulges of size 1 */-#define NEW_NINIO         1       /* new asymetry penalty */-#define MAXSECTORS        500     /* dimension for a backtrack array */-#define LOCALITY          0.      /* locality parameter for base-pairs */-#undef TURN-#define TURN              0       /* reset minimal base pair span for intermolecular pairings */-#define TURN2             3       /* used by zukersubopt */-#define SAME_STRAND(I,J)  (((I)>=cut_point)||((J)<cut_point))--/*-#################################-# GLOBAL VARIABLES              #-#################################-*/---/*-#################################-# PRIVATE VARIABLES             #-#################################-*/--PRIVATE float   mfe1, mfe2;       /* minimum free energies of the monomers */-PRIVATE int     *indx   = NULL;   /* index for moving in the triangle matrices c[] and fMl[]*/-PRIVATE int     *c      = NULL;   /* energy array, given that i-j pair */-PRIVATE int     *cc     = NULL;   /* linear array for calculating canonical structures */-PRIVATE int     *cc1    = NULL;   /*   "     "        */-PRIVATE int     *f5     = NULL;   /* energy of 5' end */-PRIVATE int     *fc     = NULL;   /* energy from i to cutpoint (and vice versa if i>cut) */-PRIVATE int     *fML    = NULL;   /* multi-loop auxiliary energy array */-PRIVATE int     *fM1    = NULL;   /* second ML array, only for subopt */-PRIVATE int     *Fmi    = NULL;   /* holds row i of fML (avoids jumps in memory) */-PRIVATE int     *DMLi   = NULL;   /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */-PRIVATE int     *DMLi1  = NULL;   /*             MIN(fML[i+1,k]+fML[k+1,j])  */-PRIVATE int     *DMLi2  = NULL;   /*             MIN(fML[i+2,k]+fML[k+1,j])  */-PRIVATE char    *ptype  = NULL;   /* precomputed array of pair types */-PRIVATE short   *S = NULL, *S1 = NULL;-PRIVATE paramT  *P          = NULL;-PRIVATE int     init_length = -1;-PRIVATE int     zuker       = 0; /* Do Zuker style suboptimals? */-PRIVATE sect    sector[MAXSECTORS];   /* stack for backtracking */-PRIVATE int     length;-PRIVATE bondT   *base_pair2 = NULL;-PRIVATE int     *BP; /* contains the structure constrainsts: BP[i]-                        -1: | = base must be paired-                        -2: < = base must be paired with j<i-                        -3: > = base must be paired with j>i-                        -4: x = base must not pair-                        positive int: base is paired with int      */-PRIVATE int     struct_constrained  = 0;-PRIVATE int     with_gquad          = 0;--PRIVATE int     *ggg = NULL;    /* minimum free energies of the gquadruplexes */--#ifdef _OPENMP--#pragma omp threadprivate(mfe1, mfe2, indx, c, cc, cc1, f5, fc, fML, fM1, Fmi, DMLi, DMLi1, DMLi2,\-                          ptype, S, S1, P, zuker, sector, length, base_pair2, BP, struct_constrained,\-                          ggg, with_gquad)--#endif--/*-#################################-# PRIVATE FUNCTION DECLARATIONS #-#################################-*/--PRIVATE void  init_cofold(int length, paramT *parameters);-PRIVATE void  get_arrays(unsigned int size);-/* PRIVATE void  scale_parameters(void); */-PRIVATE void  make_ptypes(const short *S, const char *structure);-PRIVATE void  backtrack(const char *sequence);-PRIVATE int   fill_arrays(const char *sequence);-PRIVATE void  free_end(int *array, int i, int start);--/*-#################################-# BEGIN OF FUNCTION DEFINITIONS #-#################################-*/--/*--------------------------------------------------------------------------*/-PRIVATE void init_cofold(int length, paramT *parameters){--#ifdef _OPENMP-/* Explicitly turn off dynamic threads */-  omp_set_dynamic(0);-#endif--  if (length<1) nrerror("init_cofold: argument must be greater 0");-  free_co_arrays();-  get_arrays((unsigned) length);-  init_length=length;--  indx = get_indx((unsigned) length);--  update_cofold_params_par(parameters);-}--/*--------------------------------------------------------------------------*/--PRIVATE void get_arrays(unsigned int size){-  if(size >= (unsigned int)sqrt((double)INT_MAX))-    nrerror("get_arrays@cofold.c: sequence length exceeds addressable range");--  c     = (int *) space(sizeof(int)*((size*(size+1))/2+2));-  fML   = (int *) space(sizeof(int)*((size*(size+1))/2+2));-  if (uniq_ML)-    fM1    = (int *) space(sizeof(int)*((size*(size+1))/2+2));--  ptype = (char *) space(sizeof(char)*((size*(size+1))/2+2));-  f5    = (int *) space(sizeof(int)*(size+2));-  fc    = (int *) space(sizeof(int)*(size+2));-  cc    = (int *) space(sizeof(int)*(size+2));-  cc1   = (int *) space(sizeof(int)*(size+2));-  Fmi   = (int *) space(sizeof(int)*(size+1));-  DMLi  = (int *) space(sizeof(int)*(size+1));-  DMLi1 = (int *) space(sizeof(int)*(size+1));-  DMLi2 = (int *) space(sizeof(int)*(size+1));--  base_pair2 = (bondT *) space(sizeof(bondT)*(1+size/2));-}--/*--------------------------------------------------------------------------*/--PUBLIC void free_co_arrays(void){-  if(indx)        free(indx);-  if(c)           free(c);-  if(fML)         free(fML);-  if(f5)          free(f5);-  if(cc)          free(cc);-  if(cc1)         free(cc1);-  if(fc)          free(fc);-  if(ptype)       free(ptype);-  if(fM1)         free(fM1);-  if(base_pair2)  free(base_pair2);-  if(Fmi)         free(Fmi);-  if(DMLi)        free(DMLi);-  if(DMLi1)       free(DMLi1);-  if(DMLi2)       free(DMLi2);-  if(P)           free(P);-  if(ggg)         free(ggg);--  indx = c = fML = f5 = cc = cc1 = fc = fM1 = Fmi = DMLi = DMLi1 = DMLi2 = ggg = NULL;-  ptype       = NULL;-  base_pair2  = NULL;-  P           = NULL;-  init_length = 0;-}---/*--------------------------------------------------------------------------*/--PUBLIC void export_cofold_arrays_gq(  int **f5_p,-                                      int **c_p,-                                      int **fML_p,-                                      int **fM1_p,-                                      int **fc_p,-                                      int **ggg_p,-                                      int **indx_p,-                                      char **ptype_p){--  /* make the DP arrays available to routines such as subopt() */-  *f5_p = f5; *c_p = c;-  *fML_p = fML; *fM1_p = fM1;-  *ggg_p = ggg;-  *indx_p = indx; *ptype_p = ptype;-  *fc_p =fc;-}--PUBLIC void export_cofold_arrays( int **f5_p,-                                  int **c_p,-                                  int **fML_p,-                                  int **fM1_p,-                                  int **fc_p,-                                  int **indx_p,-                                  char **ptype_p){--  /* make the DP arrays available to routines such as subopt() */-  *f5_p = f5; *c_p = c;-  *fML_p = fML; *fM1_p = fM1;-  *indx_p = indx; *ptype_p = ptype;-  *fc_p =fc;-}--/*--------------------------------------------------------------------------*/--PUBLIC float cofold(const char *string, char *structure) {-  return cofold_par(string, structure, NULL, fold_constrained);-}--PUBLIC float cofold_par(const char *string,-                        char *structure,-                        paramT *parameters,-                        int is_constrained){--  int i, length, energy, bonus=0, bonus_cnt=0;--  zuker = 0;--  struct_constrained  = is_constrained;-  length              = (int) strlen(string);--#ifdef _OPENMP-  /* always init everything since all global static variables are uninitialized when entering a thread */-  init_cofold(length, parameters);-#else-  if(parameters) init_cofold(length, parameters);-  else if (length>init_length) init_cofold(length, parameters);-  else if (fabs(P->temperature - temperature)>1e-6) update_cofold_params_par(parameters);-#endif--  with_gquad  = P->model_details.gquad;-  S           = encode_sequence(string, 0);-  S1          = encode_sequence(string, 1);-  S1[0]       = S[0]; /* store length at pos. 0 */--  BP = (int *)space(sizeof(int)*(length+2));-  if(with_gquad){ /* add a guess of how many G's may be involved in a G quadruplex */-    if(base_pair2)-      free(base_pair2);-    base_pair2 = (bondT *) space(sizeof(bondT)*(4*(1+length/2)));-  }--  make_ptypes(S, structure);--  energy = fill_arrays(string);--  backtrack(string);--#ifdef PAREN-  parenthesis_structure(structure, base_pair2, length);-#else-  letter_structure(structure, base_pair2, length);-#endif--  /*-  *  Backward compatibility:-  *  This block may be removed if deprecated functions-  *  relying on the global variable "base_pair" vanish from within the package!-  */-  base_pair = base_pair2;-  /*-  {-    if(base_pair) free(base_pair);-    base_pair = (bondT *)space(sizeof(bondT) * (1+length/2));-    memcpy(base_pair, base_pair2, sizeof(bondT) * (1+length/2));-  }-  */--  /* check constraints */-  for(i=1;i<=length;i++) {-    if((BP[i]<0)&&(BP[i]>-4)) {-      bonus_cnt++;-      if((BP[i]==-3)&&(structure[i-1]==')')) bonus++;-      if((BP[i]==-2)&&(structure[i-1]=='(')) bonus++;-      if((BP[i]==-1)&&(structure[i-1]!='.')) bonus++;-    }--    if(BP[i]>i) {-      int l;-      bonus_cnt++;-      for(l=1; l<=base_pair2[0].i; l++)-        if(base_pair2[l].i != base_pair2[l].j)-          if((i==base_pair2[l].i)&&(BP[i]==base_pair2[l].j)) bonus++;-    }-  }--  if (bonus_cnt>bonus) fprintf(stderr,"\ncould not enforce all constraints\n");-  bonus*=BONUS;--  free(S); free(S1); free(BP);--  energy += bonus;      /*remove bonus energies from result */--  if (backtrack_type=='C')-    return (float) c[indx[length]+1]/100.;-  else if (backtrack_type=='M')-    return (float) fML[indx[length]+1]/100.;-  else-    return (float) energy/100.;-}--PRIVATE int fill_arrays(const char *string) {-  /* fill "c", "fML" and "f5" arrays and return  optimal energy */--  int   i, j, k, length, energy;-  int   decomp, new_fML, max_separation;-  int   no_close, type, type_2, tt, maxj;-  int   bonus=0;-  int   dangle_model  = P->model_details.dangles;-  int   noGUclosure   = P->model_details.noGUclosure;-  int   noLP          = P->model_details.noLP;--  length = (int) strlen(string);--  max_separation = (int) ((1.-LOCALITY)*(double)(length-2)); /* not in use */--  if(with_gquad)-    ggg = get_gquad_matrix(S, P);--  for (j=1; j<=length; j++) {-    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;-    fc[j]=0;-  }--  for (j = 1; j<=length; j++)-    for (i=1; i<=j; i++) {-      c[indx[j]+i] = fML[indx[j]+i] = INF;-      if (uniq_ML) fM1[indx[j]+i] = INF;-    }--  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */--    maxj=(zuker)? (MIN2(i+cut_point-1,length)):length;-    for (j = i+TURN+1; j <= maxj; j++) {-      int p, q, ij;-      ij = indx[j]+i;-      bonus = 0;-      type = ptype[ij];--      /* enforcing structure constraints */-      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;-      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;-      if ((BP[i]==-4)||(BP[j]==-4)) type=0;--      no_close = (((type==3)||(type==4))&&noGUclosure&&(bonus==0));--      if (j-i-1 > max_separation) type = 0;  /* forces locality degree */--      if (type) {   /* we have a pair */-        int new_c=0, stackEnergy=INF;-        short si, sj;-        si  = SAME_STRAND(i, i+1) ? S1[i+1] : -1;-        sj  = SAME_STRAND(j-1, j) ? S1[j-1] : -1;-        /* hairpin ----------------------------------------------*/--        if (SAME_STRAND(i,j)) {-          if (no_close) new_c = FORBIDDEN;-          else-            new_c = E_Hairpin(j-i-1, type, si, sj, string+i-1, P);-        }-        else {-          if (dangle_model)-            new_c += E_ExtLoop(rtype[type], sj, si, P);-          else-            new_c += E_ExtLoop(rtype[type], -1, -1, P);-        }-        /*---------------------------------------------------------          check for elementary structures involving more than one-          closing pair.-          --------------------------------------------------------*/--        for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {-          int minq = j-i+p-MAXLOOP-2;-          if (minq<p+1+TURN) minq = p+1+TURN;-          for (q = minq; q < j; q++) {-            type_2 = ptype[indx[q]+p];--            if (type_2==0) continue;-            type_2 = rtype[type_2];--            if (noGUclosure)-              if (no_close||(type_2==3)||(type_2==4))-                if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */--            if (SAME_STRAND(i,p) && SAME_STRAND(q,j))-              energy = E_IntLoop(p-i-1, j-q-1, type, type_2, si, sj, S1[p-1], S1[q+1], P);-            else-              energy = E_IntLoop_Co(rtype[type], rtype[type_2],-                                    i, j, p, q,-                                    cut_point,-                                    si, sj,-                                    S1[p-1], S1[q+1],-                                    dangle_model,-                                    P);--            new_c = MIN2(energy+c[indx[q]+p], new_c);-            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */--          } /* end q-loop */-        } /* end p-loop */--        /* multi-loop decomposition ------------------------*/---        if (!no_close) {-          int MLenergy;--          if((si >= 0) && (sj >= 0)){-            decomp = DMLi1[j-1];-            tt = rtype[type];-            MLenergy = P->MLclosing;-            switch(dangle_model){-              case 0:   MLenergy += decomp + E_MLstem(tt, -1, -1, P);-                        break;-              case 2:   MLenergy += decomp + E_MLstem(tt, sj, si, P);-                        break;-              default:  decomp += E_MLstem(tt, -1, -1, P);-                        decomp = MIN2(decomp, DMLi1[j-2] + E_MLstem(tt, sj, -1, P) + P->MLbase);-                        decomp = MIN2(decomp, DMLi2[j-1] + E_MLstem(tt, -1, si, P) + P->MLbase);-                        decomp = MIN2(decomp, DMLi2[j-2] + E_MLstem(tt, sj, si, P) + 2*P->MLbase);-                        MLenergy += decomp;-                        break;-            }-            new_c = MIN2(new_c, MLenergy);-          }--          if (!SAME_STRAND(i,j)) { /* cut is somewhere in the multiloop*/-            decomp = fc[i+1] + fc[j-1];-            tt = rtype[type];-            switch(dangle_model){-              case 0:   decomp += E_ExtLoop(tt, -1, -1, P);-                        break;-              case 2:   decomp += E_ExtLoop(tt, sj, si, P);-                        break;-              default:  decomp += E_ExtLoop(tt, -1, -1, P);-                        decomp = MIN2(decomp, fc[i+2] + fc[j-2] + E_ExtLoop(tt, sj, si, P));-                        decomp = MIN2(decomp, fc[i+2] + fc[j-1] + E_ExtLoop(tt, -1, si, P));-                        decomp = MIN2(decomp, fc[i+1] + fc[j-2] + E_ExtLoop(tt, sj, -1, P));-                        break;-            }-            new_c = MIN2(new_c, decomp);-          }-        } /* end >> if (!no_close) << */--        /* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */--        if (dangle_model==3) {-          decomp = INF;-          for (k = i+2+TURN; k < j-2-TURN; k++) {-            type_2 = ptype[indx[k]+i+1]; type_2 = rtype[type_2];-            if (type_2)-              decomp = MIN2(decomp, c[indx[k]+i+1]+P->stack[type][type_2]+-                            fML[indx[j-1]+k+1]);-            type_2 = ptype[indx[j-1]+k+1]; type_2 = rtype[type_2];-            if (type_2)-              decomp = MIN2(decomp, c[indx[j-1]+k+1]+P->stack[type][type_2]+-                            fML[indx[k]+i+1]);-          }-          /* no TermAU penalty if coax stack */-          decomp += 2*P->MLintern[1] + P->MLclosing;-          new_c = MIN2(new_c, decomp);-        }--        if(with_gquad){-          /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */-          if (!no_close && SAME_STRAND(i,j)) {-            tt = rtype[type];-            energy = E_GQuad_IntLoop(i, j, type, S1, ggg, indx, P);-            new_c = MIN2(new_c, energy);-          }-        }--        new_c = MIN2(new_c, cc1[j-1]+stackEnergy);-        cc[j] = new_c + bonus;-        if (noLP){-          if (SAME_STRAND(i,i+1) && SAME_STRAND(j-1,j))-            c[ij] = cc1[j-1]+stackEnergy+bonus;-          else /* currently we don't allow stacking over the cut point */-            c[ij] = FORBIDDEN;-        }-        else-          c[ij] = cc[j];--      } /* end >> if (pair) << */--      else c[ij] = INF;---      /* done with c[i,j], now compute fML[i,j] */-      /* free ends ? -----------------------------------------*/-      new_fML=INF;-      if (SAME_STRAND(i-1,i)) {-        if (SAME_STRAND(i,i+1)) new_fML = fML[ij+1]+P->MLbase;-        if (SAME_STRAND(j-1,j)) new_fML = MIN2(fML[indx[j-1]+i]+P->MLbase, new_fML);-        if (SAME_STRAND(j,j+1)) {-          energy = c[ij];-          if(dangle_model == 2)-            energy += E_MLstem(type,(i>1) ? S1[i-1] : -1, (j<length) ? S1[j+1] : -1, P);-          else-            energy += E_MLstem(type, -1, -1, P);--          new_fML = MIN2(new_fML, energy);--          if(with_gquad){-            int gggg = ggg[ij] + E_MLstem(0, -1, -1, P);-            energy = MIN2(energy, gggg);-            new_fML = MIN2(new_fML, energy);-          }--          if(uniq_ML){-            fM1[ij] = energy;-            if(SAME_STRAND(j-1,j))-              fM1[ij] = MIN2(energy, fM1[indx[j-1]+i] + P->MLbase);-          }-        }-        if (dangle_model%2==1) {  /* normal dangles */-          if (SAME_STRAND(i,i+1)) {-            tt = ptype[ij+1]; /* i+1,j */-            new_fML = MIN2(new_fML, c[ij+1] + P->MLbase + E_MLstem(tt, S1[i], -1, P));-          }-          if (SAME_STRAND(j-1,j)) {-            tt = ptype[indx[j-1]+i]; /* i,j-1 */-            new_fML = MIN2(new_fML, c[indx[j-1]+i] + P->MLbase + E_MLstem(tt, -1, S1[j], P));-          }-          if ((SAME_STRAND(j-1,j))&&(SAME_STRAND(i,i+1))) {-            tt = ptype[indx[j-1]+i+1]; /* i+1,j-1 */-            new_fML = MIN2(new_fML, c[indx[j-1]+i+1] + 2*P->MLbase + E_MLstem(tt, S1[i], S1[j], P));-          }-        }-      }--      if(with_gquad){-        if(SAME_STRAND(i, j))-          new_fML = MIN2(new_fML, ggg[indx[j] + i] + E_MLstem(0, -1, -1, P));-      }--      /* modular decomposition -------------------------------*/--      {-        int stopp;     /*loop 1 up to cut, then loop 2*/-        stopp=(cut_point>0)? (cut_point):(j-2-TURN);-        for (decomp=INF, k = i+1+TURN; k<stopp; k++)-          decomp = MIN2(decomp, Fmi[k]+fML[indx[j]+k+1]);-        k++;-        for (;k <= j-2-TURN;k++)-          decomp = MIN2(decomp, Fmi[k]+fML[indx[j]+k+1]);-      }-      DMLi[j] = decomp;               /* store for use in ML decompositon */-      new_fML = MIN2(new_fML,decomp);--      /* coaxial stacking */-      if (dangle_model==3) {-        int stopp;-        stopp=(cut_point>0)? (cut_point):(j-2-TURN);-        /* additional ML decomposition as two coaxially stacked helices */-        for (decomp = INF, k = i+1+TURN; k<stopp; k++) {-          type = ptype[indx[k]+i]; type = rtype[type];-          type_2 = ptype[indx[j]+k+1]; type_2 = rtype[type_2];-          if (type && type_2)-            decomp = MIN2(decomp,-                          c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]);-        }-        k++;-        for (;k <= j-2-TURN; k++) {-          type = ptype[indx[k]+i]; type = rtype[type];-          type_2 = ptype[indx[j]+k+1]; type_2 = rtype[type_2];-          if (type && type_2)-            decomp = MIN2(decomp,-                          c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]);-        }--        decomp += 2*P->MLintern[1];--#if 0-        /* This is needed for Y shaped ML loops with coax stacking of-           interior pairs, but backtracking will fail if activated */-        DMLi[j] = MIN2(DMLi[j], decomp);-        if (SAME_STRAND(j-1,j)) DMLi[j] = MIN2(DMLi[j], DMLi[j-1]+P->MLbase);-        if (SAME_STRAND(i,i+1)) DMLi[j] = MIN2(DMLi[j], DMLi1[j]+P->MLbase);-        new_fML = MIN2(new_fML, DMLi[j]);-#endif-        new_fML = MIN2(new_fML, decomp);-      }--      fML[ij] = Fmi[j] = new_fML;     /* substring energy */--    }--    if (i==cut_point)-      for (j=i; j<=maxj; j++)-        free_end(fc, j, cut_point);-    if (i<cut_point)-      free_end(fc,i,cut_point-1);---    {-      int *FF; /* rotate the auxilliary arrays */-      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;-      FF = cc1; cc1=cc; cc=FF;-      for (j=1; j<=maxj; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }-    }-  }--  /* calculate energies of 5' and 3' fragments */--  for (i=1; i<=length; i++)-    free_end(f5, i, 1);--  if (cut_point>0) {-    mfe1=f5[cut_point-1];-    mfe2=fc[length];-    /* add DuplexInit, check whether duplex*/-    for (i=cut_point; i<=length; i++) {-      f5[i]=MIN2(f5[i]+P->DuplexInit, fc[i]+fc[1]);-    }-  }--  energy = f5[length];-  if (cut_point<1) mfe1=mfe2=energy;-  return energy;-}--PRIVATE void backtrack_co(const char *string, int s, int b /* b=0: start new structure, b \ne 0: add to existing structure */) {--  /*-------------------------------------------------------------------    trace back through the "c", "fc", "f5" and "fML" arrays to get the-    base pairing list. No search for equivalent structures is done.-    This is fast, since only few structure elements are recalculated.-    ------------------------------------------------------------------*/--  int   i, j, k, length, energy, new;-  int   no_close, type, type_2, tt;-  int   bonus;-  int   dangle_model  = P->model_details.dangles;-  int   noGUclosure   = P->model_details.noGUclosure;-  int   noLP          = P->model_details.noLP;--  /* int   b=0;*/--  length = strlen(string);-  if (s==0) {-    sector[++s].i = 1;-    sector[s].j   = length;-    sector[s].ml  = (backtrack_type=='M') ? 1 : ((backtrack_type=='C')?2:0);-  }-  while (s>0) {-    int ml, fij, fi, cij, traced, i1, j1, mm, p, q, jj=0, gq=0;-    int canonical = 1;     /* (i,j) closes a canonical structure */-    i  = sector[s].i;-    j  = sector[s].j;-    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to-                              occur in the fML- (1) or in the f-array (0) */-    if (ml==2) {-      base_pair2[++b].i = i;-      base_pair2[b].j   = j;-      goto repeat1;-    }--    if (j < i+TURN+1) continue; /* no more pairs in this interval */---    if (ml==0) {fij = f5[j]; fi = f5[j-1];}-    else if (ml==1) {fij = fML[indx[j]+i]; fi = fML[indx[j-1]+i]+P->MLbase;}-    else /* 3 or 4 */ {-      fij = fc[j];-      fi = (ml==3) ? INF : fc[j-1];-    }-    if (fij == fi) {  /* 3' end is unpaired */-      sector[++s].i = i;-      sector[s].j   = j-1;-      sector[s].ml  = ml;-      continue;-    }--    if (ml==0 || ml==4) { /* backtrack in f5 or fc[i=cut,j>cut] */-      int *ff;-      ff = (ml==4) ? fc : f5;-      switch(dangle_model){-        case 0:   /* j or j-1 is paired. Find pairing partner */-                  for (k=j-TURN-1,traced=0; k>=i; k--) {-                    int cc;--                    if(with_gquad){-                      if(fij == ff[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j]+k];-                    if(type){-                      cc = c[indx[j]+k];-                      if(!SAME_STRAND(k,j)) cc += P->DuplexInit;-                      if(fij == ff[k-1] + cc + E_ExtLoop(type, -1, -1, P)){-                        traced = j; jj = k-1;-                      }-                    }-                    if(traced) break;-                  }--                  break;--        case 2:   /* j or j-1 is paired. Find pairing partner */-                  for (k=j-TURN-1,traced=0; k>=i; k--) {-                    int cc;--                    if(with_gquad){-                      if(fij == ff[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j]+k];-                    if(type){-                      cc = c[indx[j]+k];-                      if(!SAME_STRAND(k,j)) cc += P->DuplexInit;-                      if(fij == ff[k-1] + cc + E_ExtLoop(type, (k>1) && SAME_STRAND(k-1,k) ? S1[k-1] : -1, (j<length) && SAME_STRAND(j,j+1) ? S1[j+1] : -1, P)){-                        traced = j; jj = k-1;-                      }-                    }-                    if(traced) break;-                  }-                  break;--        default:  for(k=j-TURN-1,traced=0; k>=i; k--){-                    int cc;-                    type = ptype[indx[j]+k];--                    if(with_gquad){-                      if(fij == ff[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    if(type){-                      cc = c[indx[j]+k];-                      if(!SAME_STRAND(k,j)) cc += P->DuplexInit;-                      if(fij == ff[k-1] + cc + E_ExtLoop(type, -1, -1, P)){-                        traced = j; jj = k-1; break;-                      }-                      if((k>1) && SAME_STRAND(k-1,k))-                        if(fij == ff[k-2] + cc + E_ExtLoop(type, S1[k-1], -1, P)){-                              traced=j; jj=k-2; break;-                        }-                    }--                    type = ptype[indx[j-1]+k];-                    if(type && SAME_STRAND(j-1,j)){-                      cc = c[indx[j-1]+k];-                      if (!SAME_STRAND(k,j-1)) cc += P->DuplexInit; /*???*/-                      if (fij == cc + ff[k-1] + E_ExtLoop(type, -1, S1[j], P)){-                            traced=j-1; jj = k-1; break;-                      }-                      if(k>i){-                        if (fij == ff[k-2] + cc + E_ExtLoop(type, SAME_STRAND(k-1,k) ? S1[k-1] : -1, S1[j], P)){-                          traced=j-1; jj=k-2; break;-                        }-                      }-                    }-                  }--                  break;-      }-      if (!traced) nrerror("backtrack failed in f5 (or fc)");-      sector[++s].i = i;-      sector[s].j   = jj;-      sector[s].ml  = ml;--      i=k; j=traced;--      if(with_gquad && gq){-        /* goto backtrace of gquadruplex */-        goto repeat_gquad;-      }--      base_pair2[++b].i = i;-      base_pair2[b].j   = j;-      goto repeat1;-    }-    else if (ml==3) { /* backtrack in fc[i<cut,j=cut-1] */-      if (fc[i] == fc[i+1]) { /* 5' end is unpaired */-        sector[++s].i = i+1;-        sector[s].j   = j;-        sector[s].ml  = ml;-        continue;-      }-      /* i or i+1 is paired. Find pairing partner */-      switch(dangle_model){-        case 0:   for (k=i+TURN+1, traced=0; k<=j; k++){-                    jj=k+1;-                    type = ptype[indx[k]+i];-                    if (type) {-                      if(fc[i] == fc[k+1] + c[indx[k]+i] + E_ExtLoop(type, -1, -1, P)){-                        traced = i;-                      }-                    } else if (with_gquad){-                      if(fc[i] == fc[k+1] + ggg[indx[k]+i]){-                        traced = i; gq = 1;-                        break;-                      }-                    }--                    if (traced) break;-                  }-                  break;-        case 2:   for (k=i+TURN+1, traced=0; k<=j; k++){-                    jj=k+1;-                    type = ptype[indx[k]+i];-                    if(type){-                      if(fc[i] == fc[k+1] + c[indx[k]+i] + E_ExtLoop(type,(i>1 && SAME_STRAND(i-1,i)) ? S1[i-1] : -1,  SAME_STRAND(k,k+1) ? S1[k+1] : -1, P)){-                        traced = i;-                      }-                    } else if (with_gquad){-                      if(fc[i] == fc[k+1] + ggg[indx[k]+i]){-                        traced = i; gq = 1;-                        break;-                      }-                    }-                    if (traced) break;-                  }-                  break;-        default:  for(k=i+TURN+1, traced=0; k<=j; k++){-                    jj=k+1;-                    type = ptype[indx[k]+i];-                    if(type){-                      if(fc[i] == fc[k+1] + c[indx[k]+i] + E_ExtLoop(type, -1, -1, P)){-                        traced = i; break;-                      }-                      else if(fc[i] == fc[k+2] + c[indx[k]+i] + E_ExtLoop(type, -1, SAME_STRAND(k,k+1) ? S1[k+1] : -1, P)){-                        traced = i; jj=k+2; break;-                      }-                    } else if (with_gquad){-                      if(fc[i] == fc[k+1] + ggg[indx[k]+i]){-                        traced = i; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[k]+i+1];-                    if(type){-                      if(fc[i] == fc[k+1] + c[indx[k]+i+1] + E_ExtLoop(type, SAME_STRAND(i, i+1) ? S1[i] : -1, -1, P)){-                        traced = i+1; break;-                      }-                      if(k<j){-                        if(fc[i] == fc[k+2] + c[indx[k]+i+1] + E_ExtLoop(type, SAME_STRAND(i, i+1) ? S1[i] : -1, SAME_STRAND(k, k+1) ? S1[k+1] : -1, P)){-                          traced = i+1; jj=k+2; break;-                        }-                      }-                    }-                  }-                  break;-      }--      if (!traced) nrerror("backtrack failed in fc[] 5' of cut");--      sector[++s].i = jj;-      sector[s].j   = j;-      sector[s].ml  = ml;--      j=k; i=traced;-      if(with_gquad && gq){-        /* goto backtrace of gquadruplex */-        goto repeat_gquad;-      }---      base_pair2[++b].i = i;-      base_pair2[b].j   = j;-      goto repeat1;-    }--    else { /* true multi-loop backtrack in fML */-      if (fML[indx[j]+i+1]+P->MLbase == fij) { /* 5' end is unpaired */-        sector[++s].i = i+1;-        sector[s].j   = j;-        sector[s].ml  = ml;-        continue;-      }--      if(with_gquad){-        if(fij == ggg[indx[j]+i] + E_MLstem(0, -1, -1, P)){-          /* go to backtracing of quadruplex */-          goto repeat_gquad;-        }-      }--      tt  = ptype[indx[j]+i];-      cij = c[indx[j]+i];-      switch(dangle_model){-        case 0:   if(fij == cij + E_MLstem(tt, -1, -1, P)){-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  break;-        case 2:   if(fij == cij + E_MLstem(tt, (i>1) ? S1[i-1] : -1, (j<length) ? S1[j+1] : -1, P)){-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  break;-        default:  if(fij == cij + E_MLstem(tt, -1, -1, P)){-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  tt = ptype[indx[j]+i+1];-                  if(fij == c[indx[j]+i+1] + P->MLbase + E_MLstem(tt, S1[i], -1, P)){-                    i++;-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  tt = ptype[indx[j-1]+i];-                  if(fij == c[indx[j-1]+i] + P->MLbase + E_MLstem(tt, -1, S1[j], P)){-                    j--;-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  tt = ptype[indx[j-1]+i+1];-                  if(fij == c[indx[j-1]+i+1] + 2*P->MLbase + E_MLstem(tt, S1[i], S1[j], P)){-                    i++; j--;-                    base_pair2[++b].i  = i;-                    base_pair2[b].j    = j;-                    goto repeat1;-                  }-                  break;-      }--      /* find next component of multiloop */-      for (k = i+1+TURN; k <= j-2-TURN; k++)-        if (fij == (fML[indx[k]+i]+fML[indx[j]+k+1]))-          break;--      if ((dangle_model==3)&&(k>j-2-TURN)) { /* must be coax stack */-        ml = 2;-        for (k = i+1+TURN; k <= j-2-TURN; k++) {-          type = ptype[indx[k]+i];  type= rtype[type];-          type_2 = ptype[indx[j]+k+1]; type_2= rtype[type_2];-          if (type && type_2)-            if (fij == c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]+-                2*P->MLintern[1])-              break;-        }-      }--      sector[++s].i = i;-      sector[s].j   = k;-      sector[s].ml  = ml;-      sector[++s].i = k+1;-      sector[s].j   = j;-      sector[s].ml  = ml;--      if (k>j-2-TURN) nrerror("backtrack failed in fML");-      continue;-    }--  repeat1:--    /*----- begin of "repeat:" -----*/-    if (canonical)  cij = c[indx[j]+i];-    type = ptype[indx[j]+i];--    bonus = 0;--    if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;-    if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;--    if (noLP)-      if (cij == c[indx[j]+i]) {-        /* (i.j) closes canonical structures, thus-           (i+1.j-1) must be a pair                */-        type_2 = ptype[indx[j-1]+i+1]; type_2 = rtype[type_2];-        cij -= P->stack[type][type_2] + bonus;-        base_pair2[++b].i = i+1;-        base_pair2[b].j   = j-1;-        i++; j--;-        canonical=0;-        goto repeat1;-      }-    canonical = 1;---    no_close = (((type==3)||(type==4))&&noGUclosure&&(bonus==0));-    if (SAME_STRAND(i,j)) {-      if (no_close) {-        if (cij == FORBIDDEN) continue;-      } else-        if (cij == E_Hairpin(j-i-1, type, S1[i+1], S1[j-1],string+i-1, P)+bonus)-          continue;-    }-    else {-      if(dangle_model){-        if(cij == E_ExtLoop(rtype[type], SAME_STRAND(j-1,j) ? S1[j-1] : -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P)) continue;-      }-      else if(cij == E_ExtLoop(rtype[type], -1, -1, P)) continue;-    }--    for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1); p++) {-      int minq;-      minq = j-i+p-MAXLOOP-2;-      if (minq<p+1+TURN) minq = p+1+TURN;-      for (q = j-1; q >= minq; q--) {--        type_2 = ptype[indx[q]+p];-        if (type_2==0) continue;-        type_2 = rtype[type_2];-        if (noGUclosure)-          if (no_close||(type_2==3)||(type_2==4))-            if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */--        /* energy = oldLoopEnergy(i, j, p, q, type, type_2); */-        if (SAME_STRAND(i,p) && SAME_STRAND(q,j))-          energy = E_IntLoop(p-i-1, j-q-1, type, type_2,-                              S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);-        else {-          energy = E_IntLoop_Co(rtype[type], rtype[type_2], i, j, p, q, cut_point, S1[i+1], S1[j-1], S1[p-1], S1[q+1], dangle_model, P);-        }--        new = energy+c[indx[q]+p]+bonus;-        traced = (cij == new);-        if (traced) {-          base_pair2[++b].i = p;-          base_pair2[b].j   = q;-          i = p, j = q;-          goto repeat1;-        }-      }-    }--    /* end of repeat: --------------------------------------------------*/--    /* (i.j) must close a fake or true multi-loop */-    tt = rtype[type];-    i1 = i+1;-    j1 = j-1;--    if(with_gquad){-      /*-        The case that is handled here actually resembles something like-        an interior loop where the enclosing base pair is of regular-        kind and the enclosed pair is not a canonical one but a g-quadruplex-        that should then be decomposed further...-      */-      if(SAME_STRAND(i,j)){-        if(backtrack_GQuad_IntLoop(cij - bonus, i, j, type, S, ggg, indx, &p, &q, P)){-          i = p; j = q;-          goto repeat_gquad;-        }-      }-    }--    /* fake multi-loop */-    if(!SAME_STRAND(i,j)){-      int ii, jj, decomp;-      ii = jj = 0;-      decomp = fc[i1] + fc[j1];-      switch(dangle_model){-        case 0:   if(cij == decomp + E_ExtLoop(tt, -1, -1, P)){-                    ii=i1, jj=j1;-                  }-                  break;-        case 2:   if(cij == decomp + E_ExtLoop(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P)){-                    ii=i1, jj=j1;-                  }--                  break;-        default:  if(cij == decomp + E_ExtLoop(tt, -1, -1, P)){-                    ii=i1, jj=j1;-                  }-                  else if(cij == fc[i+2] + fc[j-1] + E_ExtLoop(tt, -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P)){-                    ii = i+2; jj = j1;-                  }-                  else if(cij == fc[i+1] + fc[j-2] + E_ExtLoop(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, -1, P)){-                    ii = i1; jj = j-2;-                  }-                  else if(cij == fc[i+2] + fc[j-2] + E_ExtLoop(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P)){-                    ii = i+2; jj = j-2;-                  }-                  break;-      }-      if(ii){-        sector[++s].i = ii;-        sector[s].j   = cut_point-1;-        sector[s].ml  = 3;-        sector[++s].i = cut_point;-        sector[s].j   = jj;-        sector[s].ml  = 4;-        continue;-      }-    }--    /* true multi-loop */-    mm = bonus + P->MLclosing;-    sector[s+1].ml  = sector[s+2].ml = 1;-    int ml0   = E_MLstem(tt, -1, -1, P);-    int ml5   = E_MLstem(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, -1, P);-    int ml3   = E_MLstem(tt, -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P);-    int ml53  = E_MLstem(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, P);-    for (traced = 0, k = i+2+TURN; k < j-2-TURN; k++) {-      switch(dangle_model){-        case 0:   /* no dangles */-                  if(cij == mm + fML[indx[k]+i+1] + fML[indx[j-1]+k+1] + ml0)-                    traced = i+1;-                  break;-        case 2:   /*double dangles */-                  if(cij == mm + fML[indx[k]+i+1] + fML[indx[j-1]+k+1] + ml53)-                    traced = i+1;-                  break;-        default:  /* normal dangles */-                  if(cij == mm + fML[indx[k]+i+1] + fML[indx[j-1]+k+1] + ml0){-                    traced = i+1;-                    break;-                  }-                  else if (cij == fML[indx[k]+i+2] + fML[indx[j-1]+k+1] + ml3 + mm + P->MLbase){-                    traced = i1 = i+2;-                    break;-                  }-                  else if (cij == fML[indx[k]+i+1] + fML[indx[j-2]+k+1] + ml5 + mm + P->MLbase){-                    traced = i1 = i+1; j1 = j-2;-                    break;-                  }-                  else if (cij == fML[indx[k]+i+2] + fML[indx[j-2]+k+1] + ml53 + mm + 2*P->MLbase){-                    traced = i1 = i+2; j1 = j-2;-                    break;-                  }-                  break;-      }-      if(traced) break;-      /* coaxial stacking of (i.j) with (i+1.k) or (k.j-1) */-      /* use MLintern[1] since coax stacked pairs don't get TerminalAU */-      if (dangle_model==3) {-        int en;-        type_2 = ptype[indx[k]+i+1]; type_2 = rtype[type_2];-        if (type_2) {-          en = c[indx[k]+i+1]+P->stack[type][type_2]+fML[indx[j-1]+k+1];-          if (cij == en+2*P->MLintern[1]+P->MLclosing) {-            ml = 2;-            sector[s+1].ml  = 2;-            break;-          }-        }-        type_2 = ptype[indx[j-1]+k+1]; type_2 = rtype[type_2];-        if (type_2) {-          en = c[indx[j-1]+k+1]+P->stack[type][type_2]+fML[indx[k]+i+1];-          if (cij == en+2*P->MLintern[1]+P->MLclosing) {-            sector[s+2].ml = 2;-            break;-          }-        }-      }-    }-    if (k<=j-3-TURN) { /* found the decomposition */-      sector[++s].i = i1;-      sector[s].j   = k;-      sector[++s].i = k+1;-      sector[s].j   = j1;-    } else {-#if 0-      /* Y shaped ML loops don't work yet */-      if (dangle_model==3) {-        /* (i,j) must close a Y shaped ML loop with coax stacking */-        if (cij == fML[indx[j-2]+i+2] + mm + d3 + d5 + P->MLbase + P->MLbase) {-          i1 = i+2;-          j1 = j-2;-        } else if (cij ==  fML[indx[j-2]+i+1] + mm + d5 + P->MLbase)-          j1 = j-2;-        else if (cij ==  fML[indx[j-1]+i+2] + mm + d3 + P->MLbase)-          i1 = i+2;-        else /* last chance */-          if (cij != fML[indx[j-1]+i+1] + mm + P->MLbase)-            fprintf(stderr,  "backtracking failed in repeat");-        /* if we arrive here we can express cij via fML[i1,j1]+dangles */-        sector[++s].i = i1;-        sector[s].j   = j1;-      }-      else-#endif-        nrerror("backtracking failed in repeat");-    }--    continue; /* this is a workarround to not accidentally proceed in the following block */--  repeat_gquad:-    /*-      now we do some fancy stuff to backtrace the stacksize and linker lengths-      of the g-quadruplex that should reside within position i,j-    */-    {-      int l[3], L, a;-      L = -1;-      -      get_gquad_pattern_mfe(S, i, j, P, &L, l);-      if(L != -1){-        /* fill the G's of the quadruplex into base_pair2 */-        for(a=0;a<L;a++){-          base_pair2[++b].i = i+a;-          base_pair2[b].j   = i+a;-          base_pair2[++b].i = i+L+l[0]+a;-          base_pair2[b].j   = i+L+l[0]+a;-          base_pair2[++b].i = i+L+l[0]+L+l[1]+a;-          base_pair2[b].j   = i+L+l[0]+L+l[1]+a;-          base_pair2[++b].i = i+L+l[0]+L+l[1]+L+l[2]+a;-          base_pair2[b].j   = i+L+l[0]+L+l[1]+L+l[2]+a;-        }-        goto repeat_gquad_exit;-      }-      nrerror("backtracking failed in repeat_gquad");-    }-  repeat_gquad_exit:-    asm("nop");--  } /* end >> while (s>0) << */--  base_pair2[0].i = b;    /* save the total number of base pairs */-}--PRIVATE void free_end(int *array, int i, int start) {-  int inc, type, energy, length, j, left, right;-  int dangle_model = P->model_details.dangles;--  inc = (i>start)? 1:-1;-  length = S[0];--  if (i==start) array[i]=0;-  else array[i] = array[i-inc];-  if (inc>0) {-    left = start; right=i;-  } else {-    left = i; right = start;-  }--  for (j=start; inc*(i-j)>TURN; j+=inc) {-    int ii, jj;-    short si, sj;-    if (i>j) { ii = j; jj = i;} /* inc>0 */-    else     { ii = i; jj = j;} /* inc<0 */-    type = ptype[indx[jj]+ii];-    if (type) {  /* i is paired with j */-      si = (ii>1)       && SAME_STRAND(ii-1,ii) ? S1[ii-1] : -1;-      sj = (jj<length)  && SAME_STRAND(jj,jj+1) ? S1[jj+1] : -1;-      energy = c[indx[jj]+ii];-      switch(dangle_model){-        case 0:   -                  array[i] = MIN2(array[i], array[j-inc] + energy + E_ExtLoop(type, -1, -1, P));-                  break;-        case 2:   -                  array[i] = MIN2(array[i], array[j-inc] + energy + E_ExtLoop(type, si, sj, P));-                  break;-        default:     -                  array[i] = MIN2(array[i], array[j-inc] + energy + E_ExtLoop(type, -1, -1, P));-                  if(inc > 0){-                    if(j > left)-                    array[i] = MIN2(array[i], array[j-2] + energy + E_ExtLoop(type, si, -1, P));-                  }-                  else if(j < right)-                    array[i] = MIN2(array[i], array[j+2] + energy + E_ExtLoop(type, -1, sj, P));-                  break;-      }-    }--    if(with_gquad){-      if(SAME_STRAND(ii, jj))-        array[i] = MIN2(array[i], array[j-inc] + ggg[indx[jj]+ii]);-    }--    if (dangle_model%2==1) {-      /* interval ends in a dangle (i.e. i-inc is paired) */-      if (i>j) { ii = j; jj = i-1;} /* inc>0 */-      else     { ii = i+1; jj = j;} /* inc<0 */-      type = ptype[indx[jj]+ii];-      if (!type) continue;--      si = (ii > left)  && SAME_STRAND(ii-1,ii) ? S1[ii-1] : -1;-      sj = (jj < right) && SAME_STRAND(jj,jj+1) ? S1[jj+1] : -1;-      energy = c[indx[jj]+ii];-      if(inc>0)-        array[i] = MIN2(array[i], array[j - inc] + energy + E_ExtLoop(type, -1, sj, P));-      else-        array[i] = MIN2(array[i], array[j - inc] + energy + E_ExtLoop(type, si, -1, P));-      if(j!= start){ /* dangle_model on both sides */-        array[i] = MIN2(array[i], array[j-2*inc] + energy + E_ExtLoop(type, si, sj, P));-      }-    }-  }-}--PUBLIC void update_cofold_params(void){-  update_cofold_params_par(NULL);-}--PUBLIC void update_cofold_params_par(paramT *parameters){-  if(P) free(P);--  if(parameters){-    P = get_parameter_copy(parameters);-  } else {-    model_detailsT md;-    set_model_details(&md);-    P = get_scaled_parameters(temperature, md);-  }-  make_pair_matrix();-  if (init_length < 0) init_length=0;-}--/*---------------------------------------------------------------------------*/--PRIVATE void make_ptypes(const short *S, const char *structure) {-  int n,i,j,k,l;-  int noLP = P->model_details.noLP;--  n=S[0];-  for (k=1; k<n-TURN; k++)-    for (l=1; l<=2; l++) {-      int type,ntype=0,otype=0;-      i=k; j = i+TURN+l; if (j>n) continue;-      type = pair[S[i]][S[j]];-      while ((i>=1)&&(j<=n)) {-        if ((i>1)&&(j<n)) ntype = pair[S[i-1]][S[j+1]];-        if (noLP && (!otype) && (!ntype))-          type = 0; /* i.j can only form isolated pairs */-        ptype[indx[j]+i] = (char) type;-        otype =  type;-        type  = ntype;-        i--; j++;-      }-    }--  if (struct_constrained && (structure != NULL))-    constrain_ptypes(structure, (unsigned int)n, ptype, BP, TURN, 0);-}--PUBLIC void get_monomere_mfes(float *e1, float *e2) {-  /*exports monomere free energies*/-  *e1 = mfe1;-  *e2 = mfe2;-}--PRIVATE void backtrack(const char *sequence) {-  /*routine to call backtrack_co from 1 to n, backtrack type??*/-  backtrack_co(sequence, 0,0);-}--PRIVATE int comp_pair(const void *A, const void *B) {-  bondT *x,*y;-  int ex, ey;-  x = (bondT *) A;-  y = (bondT *) B;-  ex = c[indx[x->j]+x->i]+c[indx[x->i+length]+x->j];-  ey = c[indx[y->j]+y->i]+c[indx[y->i+length]+y->j];-  if (ex>ey) return 1;-  if (ex<ey) return -1;-  return (indx[x->j]+x->i - indx[y->j]+y->i);-}--PUBLIC SOLUTION *zukersubopt(const char *string) {-  return zukersubopt_par(string, NULL);-}--PUBLIC SOLUTION *zukersubopt_par(const char *string, paramT *parameters){--/* Compute zuker suboptimal. Here, we're abusing the cofold() code-   "double" sequence, compute dimerarray entries, track back every base pair.-   This is slightly wasteful compared to the normal solution */--  char      *doubleseq, *structure, *mfestructure, **todo;-  int       i, j, counter, num_pairs, psize, p;-  float     energy;-  SOLUTION  *zukresults;-  bondT     *pairlist;--  num_pairs       = counter = 0;-  zuker           = 1;-  length          = (int)strlen(string);-  doubleseq       = (char *)space((2*length+1)*sizeof(char));-  mfestructure    = (char *) space((unsigned) 2*length+1);-  structure       = (char *) space((unsigned) 2*length+1);-  zukresults      = (SOLUTION *)space(((length*(length-1))/2)*sizeof(SOLUTION));-  mfestructure[0] = '\0';-  BP              = (int *)space(sizeof(int)*(2*length+2));--  /* double the sequence */-  strcpy(doubleseq,string);-  strcat(doubleseq,string);-  cut_point = length + 1;--  /* get mfe and do forward recursion */-#ifdef _OPENMP-  /* always init everything since all global static variables are uninitialized when entering a thread */-  init_cofold(2 * length, parameters);-#else-  if(parameters) init_cofold(2 * length, parameters);-  else if ((2 * length) > init_length) init_cofold(2 * length, parameters);-  else if (fabs(P->temperature - temperature)>1e-6) update_cofold_params_par(parameters);-#endif---  S     = encode_sequence(doubleseq, 0);-  S1    = encode_sequence(doubleseq, 1);-  S1[0] = S[0]; /* store length at pos. 0 */-  make_ptypes(S, NULL); /* no constraint folding possible (yet?) with zukersubopt */--  (void)fill_arrays(doubleseq);--  psize     = length;-  pairlist  = (bondT *) space(sizeof(bondT)*(psize+1));-  todo      = (char **) space(sizeof(char *)*(length+1));-  for (i=1; i<length; i++) {-    todo[i] = (char *) space(sizeof(char)*(length+1));-  }--  /* Make a list of all base pairs */-  for (i=1; i<length; i++) {-    for (j=i+TURN2+1/*??*/; j<=length; j++) {-      if (ptype[indx[j]+i]==0) continue;-      if (num_pairs>=psize) {-        psize = 1.2*psize + 32;-        pairlist = xrealloc(pairlist, sizeof(bondT)*(psize+1));-      }-      pairlist[num_pairs].i   = i;-      pairlist[num_pairs++].j = j;-      todo[i][j]=1;-    }-  }-  qsort(pairlist, num_pairs, sizeof(bondT), comp_pair);--  for (p=0; p<num_pairs; p++) {-    i=pairlist[p].i;-    j=pairlist[p].j;-    if (todo[i][j]) {-      int k;-      sector[1].i   = i;-      sector[1].j   = j;-      sector[1].ml  = 2;-      backtrack_co(doubleseq, 1,0);-      sector[1].i   = j;-      sector[1].j   = i + length;-      sector[1].ml  = 2;-      backtrack_co(doubleseq, 1,base_pair2[0].i);-      energy = c[indx[j]+i]+c[indx[i+length]+j];-      parenthesis_zuker(structure, base_pair2, length);-      zukresults[counter].energy      = energy;-      zukresults[counter++].structure = strdup(structure);-      for (k = 1; k <= base_pair2[0].i; k++) { /* mark all pairs in structure as done */-        int x,y;-        x=base_pair2[k].i;-        y=base_pair2[k].j;-        if (x>length) x-=length;-        if (y>length) y-=length;-        if (x>y) {-          int temp;-          temp=x; x=y; y=temp;-        }-        todo[x][y] = 0;-      }-    }-  }-  /*free zeugs*/-  free(pairlist);-  for (i=1; i<length; i++)-    free(todo[i]);-  free(todo);-  free(structure);-  free(mfestructure);-  free(doubleseq);-  zuker=0;-  free(S); free(S1); free(BP);-  return zukresults;-}---/*###########################################*/-/*# deprecated functions below              #*/-/*###########################################*/--PUBLIC void initialize_cofold(int length){ /* DO NOTHING */ }
− cbits/energy_par.c 
@@ -1,791 +0,0 @@---/*-    Automatically generated using the TurnerParser-    TurnerParser (c) 2008,2009,2010-      Christian Hoener zu Siederdissen, TBI Vienna-      choener (at) tbi.univie.ac.at--    The library enabling this can be found at:-    http://hackage.haskell.org/package/BiobaseVienna-    the program can be found at:-    (sorry, not yet)-    install using cabal: cabal install (sorry, not yet)-*/--/*-     Current free energy parameters are summarized in:--     D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner-     "Expanded sequence dependence of thermodynamic parameters improves-     prediction of RNA secondary structure"-     JMB, 288, pp 911-940, 1999--     Enthalpies taken from:--     A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker-     "Coaxial stacking of helices enhances binding of oligoribonucleotides.."-     PNAS, 91, pp 9218-9222, 1994--     D.H. Turner, N. Sugimoto, and S.M. Freier.-     "RNA Structure Prediction",-     Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.--     John A.Jaeger, Douglas H.Turner, and Michael Zuker.-     "Improved predictions of secondary structures for RNA",-     PNAS, 86, 7706-7710, October 1989.--     L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner-     "Nearest-Neighbor Parameters for GU Mismatches...."-     Biochemistry 1991, 30 11124-11132--     A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner-     "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."-     Biochemistry 1991, 30, 6428--6435-*/----#include "energy_const.h"-/*@unused@*/-static char rcsid[] = "$Id: energy_par.c,v 1.6 2004/08/12 12:11:57 ivo Exp $";--#define NST 0     /* Energy for nonstandard stacked pairs */-#define DEF -50   /* Default terminal mismatch, used for I */-                  /* and any non_pairing bases */-#define NSM 0     /* terminal mismatch for non standard pairs */--#define PUBLIC--PUBLIC double Tmeasure = 37+K0;  /* temperature of param measurements */---/* PUBLIC double lxc37=107.9; */-PUBLIC double lxc37=107.856;-PUBLIC int ML_intern37=-90;-PUBLIC int ML_interndH=-220;-PUBLIC int ML_closing37=930;-PUBLIC int ML_closingdH=3000;-PUBLIC int ML_BASE37=0;-PUBLIC int ML_BASEdH=0;-PUBLIC int MAX_NINIO=300;-PUBLIC int ninio37=60;-PUBLIC int niniodH=320;-PUBLIC int TerminalAU37=50;-PUBLIC int TerminalAUdH=370;-PUBLIC int DuplexInit37=410;-PUBLIC int DuplexInitdH=360;-PUBLIC int TripleC37=100;-PUBLIC int TripleCdH=1860;-PUBLIC int MultipleCA37=30;-PUBLIC int MultipleCAdH=340;-PUBLIC int MultipleCB37=160;-PUBLIC int MultipleCBdH=760;--PUBLIC int GQuadAlpha37 = -1800;-PUBLIC int GQuadAlphadH = -11934;-PUBLIC int GQuadBeta37 = 1200;-PUBLIC int GQuadBetadH = 0;--PUBLIC int stack37[NBPAIRS+1][NBPAIRS+1] =-{{   INF,   INF,   INF,   INF,   INF,   INF,   INF,   INF}-,{   INF,  -240,  -330,  -210,  -140,  -210,  -210,  -140}-,{   INF,  -330,  -340,  -250,  -150,  -220,  -240,  -150}-,{   INF,  -210,  -250,   130,   -50,  -140,  -130,   130}-,{   INF,  -140,  -150,   -50,    30,   -60,  -100,    30}-,{   INF,  -210,  -220,  -140,   -60,  -110,   -90,   -60}-,{   INF,  -210,  -240,  -130,  -100,   -90,  -130,   -90}-,{   INF,  -140,  -150,   130,    30,   -60,   -90,   130}};-PUBLIC int stackdH[NBPAIRS+1][NBPAIRS+1] =-{{   INF,   INF,   INF,   INF,   INF,   INF,   INF,   INF}-,{   INF, -1060, -1340, -1210,  -560, -1050, -1040,  -560}-,{   INF, -1340, -1490, -1260,  -830, -1140, -1240,  -830}-,{   INF, -1210, -1260, -1460, -1350,  -880, -1280,  -880}-,{   INF,  -560,  -830, -1350,  -930,  -320,  -700,  -320}-,{   INF, -1050, -1140,  -880,  -320,  -940,  -680,  -320}-,{   INF, -1040, -1240, -1280,  -700,  -680,  -770,  -680}-,{   INF,  -560,  -830,  -880,  -320,  -320,  -680,  -320}};--PUBLIC int hairpin37[31] = {   INF,   INF,   INF,   540,   560,   570,   540,   600,   550,   640,   650,   660,   670,   680,   690,   690,   700,   710,   710,   720,   720,   730,   730,   740,   740,   750,   750,   750,   760,   760,   770};-PUBLIC int hairpindH[31] = {   INF,   INF,   INF,   130,   480,   360,  -290,   130,  -290,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500,   500};-PUBLIC int bulge37[31] = {   INF,   380,   280,   320,   360,   400,   440,   460,   470,   480,   490,   500,   510,   520,   530,   540,   540,   550,   550,   560,   570,   570,   580,   580,   580,   590,   590,   600,   600,   600,   610};-PUBLIC int bulgedH[31] = {   INF,  1060,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710,   710};-PUBLIC int internal_loop37[31] = {   INF,   INF,   100,   100,   110,   200,   200,   210,   230,   240,   250,   260,   270,   280,   290,   290,   300,   310,   310,   320,   330,   330,   340,   340,   350,   350,   350,   360,   360,   370,   370};-PUBLIC int internal_loopdH[31] = {   INF,   INF,   -720,   -720,  -720,  -680,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130,  -130};--PUBLIC int mismatchI37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,   -80,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,  -100,     0,  -100,     0}- ,{     0,     0,     0,     0,   -60}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,   -80,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,  -100,     0,  -100,     0}- ,{     0,     0,     0,     0,   -60}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,   -10,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -30,    70,   -30,    70}- ,{    70,    70,    70,    70,    10}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,   -10,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -30,    70,   -30,    70}- ,{    70,    70,    70,    70,    10}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,   -10,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -30,    70,   -30,    70}- ,{    70,    70,    70,    70,    10}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,   -10,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -30,    70,   -30,    70}- ,{    70,    70,    70,    70,    10}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,   -10,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -30,    70,   -30,    70}- ,{    70,    70,    70,    70,    10}- }};-PUBLIC int mismatchIdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{   280,     0,     0,   280,     0}- ,{     0,     0,     0,  -340,     0}- ,{     0,     0,     0,     0,     0}- ,{   280,  -760,     0,   280,     0}- ,{     0,     0,     0,     0,  -580}- }-,{{   280,     0,     0,   280,     0}- ,{     0,     0,     0,  -340,     0}- ,{     0,     0,     0,     0,     0}- ,{   280,  -760,     0,   280,     0}- ,{     0,     0,     0,     0,  -580}- }-,{{   790,   500,   500,   790,   500}- ,{   500,   500,   500,   170,   500}- ,{   500,   500,   500,   500,   500}- ,{   790,  -260,   500,   790,   500}- ,{   500,   500,   500,   500,   -80}- }-,{{   790,   500,   500,   790,   500}- ,{   500,   500,   500,   170,   500}- ,{   500,   500,   500,   500,   500}- ,{   790,  -260,   500,   790,   500}- ,{   500,   500,   500,   500,   -80}- }-,{{   790,   500,   500,   790,   500}- ,{   500,   500,   500,   170,   500}- ,{   500,   500,   500,   500,   500}- ,{   790,  -260,   500,   790,   500}- ,{   500,   500,   500,   500,   -80}- }-,{{   790,   500,   500,   790,   500}- ,{   500,   500,   500,   170,   500}- ,{   500,   500,   500,   500,   500}- ,{   790,  -260,   500,   790,   500}- ,{   500,   500,   500,   500,   -80}- }-,{{   790,   500,   500,   790,   500}- ,{   500,   500,   500,   170,   500}- ,{   500,   500,   500,   500,   500}- ,{   790,  -260,   500,   790,   500}- ,{   500,   500,   500,   500,   -80}- }};--PUBLIC int mismatchH37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{   -80,  -100,  -110,  -100,   -80}- ,{  -140,  -150,  -150,  -140,  -150}- ,{   -80,  -100,  -110,  -100,   -80}- ,{  -150,  -230,  -150,  -240,  -150}- ,{  -100,  -100,  -140,  -100,  -210}- }-,{{   -50,  -110,   -70,  -110,   -50}- ,{  -110,  -110,  -150,  -130,  -150}- ,{   -50,  -110,   -70,  -110,   -50}- ,{  -150,  -250,  -150,  -220,  -150}- ,{  -100,  -110,  -100,  -110,  -160}- }-,{{    20,    20,   -20,   -10,   -20}- ,{    20,    20,   -50,   -30,   -50}- ,{   -10,   -10,   -20,   -10,   -20}- ,{   -50,  -100,   -50,  -110,   -50}- ,{   -10,   -10,   -30,   -10,  -100}- }-,{{     0,   -20,   -10,   -20,     0}- ,{   -30,   -50,   -30,   -60,   -30}- ,{     0,   -20,   -10,   -20,     0}- ,{   -30,   -90,   -30,  -110,   -30}- ,{   -10,   -20,   -10,   -20,   -90}- }-,{{   -10,   -10,   -20,   -10,   -20}- ,{   -30,   -30,   -50,   -30,   -50}- ,{   -10,   -10,   -20,   -10,   -20}- ,{   -50,  -120,   -50,  -110,   -50}- ,{   -10,   -10,   -30,   -10,  -120}- }-,{{     0,   -20,   -10,   -20,     0}- ,{   -30,   -50,   -30,   -50,   -30}- ,{     0,   -20,   -10,   -20,     0}- ,{   -30,  -150,   -30,  -150,   -30}- ,{   -10,   -20,   -10,   -20,   -90}- }-,{{    20,    20,   -10,   -10,     0}- ,{    20,    20,   -30,   -30,   -30}- ,{     0,   -10,   -10,   -10,     0}- ,{   -30,   -90,   -30,  -110,   -30}- ,{   -10,   -10,   -10,   -10,   -90}- }};-PUBLIC int mismatchHdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{   560,  -570,   560,  -560,  -270}- ,{  -560,  -910,  -560,  -560,  -560}- ,{  -270,  -570,  -340,  -570,  -270}- ,{   560, -1400,   560,  -920,  -560}- ,{  -530,  -570,  -530,  -570, -1440}- }-,{{    50,  -520,    50,  -560,  -400}- ,{  -400,  -520,  -400,  -560,  -400}- ,{    50,  -720,    50,  -720,  -420}- ,{  -400, -1290,  -400,  -620,  -400}- ,{   -30,  -720,   -30,  -720, -1080}- }-,{{   970,   140,   970,   140,   570}- ,{   570,    30,   570,    20,   570}- ,{   970,   140,   970,   140,   340}- ,{   570,  -270,   570,    20,   570}- ,{   830,   140,   830,   140,   -50}- }-,{{   230,   100,   230,   220,   190}- ,{  -110,  -110,  -260,  -520,  -260}- ,{   190,   -60,  -140,   -60,   190}- ,{   220,   100,  -260,   220,  -260}- ,{   230,   -60,   230,   -60,   -70}- }-,{{   970,   140,   970,   140,   570}- ,{   570,   -20,   570,    20,   570}- ,{   970,   140,   970,   140,   340}- ,{   570,  -520,   570,    20,   570}- ,{   830,   140,   830,   140,  -380}- }-,{{   230,   -30,   230,   -60,   190}- ,{   -30,   -30,  -260,  -520,  -260}- ,{   190,   -60,  -140,   -60,   190}- ,{  -260,  -590,  -260,  -520,  -260}- ,{   230,   -60,   230,   -60,   -70}- }-,{{   970,   140,   970,   220,   570}- ,{   570,    30,   570,    20,   570}- ,{   970,   140,   970,   140,   340}- ,{   570,   100,   570,   220,   570}- ,{   830,   140,   830,   140,   -50}- }};--PUBLIC int mismatchM37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{   -80,  -100,  -110,  -100,   -80}- ,{  -140,  -150,  -150,  -140,  -150}- ,{   -80,  -100,  -110,  -100,   -80}- ,{  -140,  -140,  -150,  -160,  -150}- ,{  -100,  -100,  -140,  -100,  -120}- }-,{{   -50,  -110,   -70,  -110,   -50}- ,{  -110,  -110,  -150,  -130,  -150}- ,{   -50,  -110,   -70,  -110,   -50}- ,{  -140,  -160,  -150,  -140,  -150}- ,{   -70,  -110,  -100,  -110,   -70}- }-,{{   -30,   -30,   -70,   -60,   -60}- ,{   -30,   -30,  -100,   -80,  -100}- ,{   -60,   -60,   -70,   -60,   -70}- ,{   -60,   -60,  -100,   -80,  -100}- ,{   -60,   -60,   -80,   -60,   -60}- }-,{{   -50,   -50,   -60,   -70,   -50}- ,{   -80,  -100,   -80,  -110,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- ,{   -50,   -50,   -80,   -80,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- }-,{{   -60,   -60,   -70,   -60,   -70}- ,{   -80,   -80,  -100,   -80,  -100}- ,{   -60,   -60,   -70,   -60,   -70}- ,{   -80,   -80,  -100,   -80,  -100}- ,{   -60,   -60,   -80,   -60,   -80}- }-,{{   -50,   -70,   -60,   -70,   -50}- ,{   -80,  -100,   -80,  -110,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- ,{   -80,  -110,   -80,  -120,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- }-,{{   -30,   -30,   -60,   -60,   -50}- ,{   -30,   -30,   -80,   -80,   -80}- ,{   -50,   -60,   -60,   -60,   -50}- ,{   -50,   -50,   -80,   -80,   -80}- ,{   -50,   -60,   -60,   -60,   -50}- }};-PUBLIC int mismatchMdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{  -270,  -570,  -340,  -560,  -270}- ,{  -560,  -910,  -560,  -560,  -560}- ,{  -270,  -570,  -340,  -570,  -270}- ,{  -560,  -820,  -560,  -920,  -560}- ,{  -530,  -570,  -530,  -570,  -860}- }-,{{    50,  -520,    50,  -560,  -400}- ,{  -400,  -520,  -400,  -560,  -400}- ,{    50,  -720,    50,  -720,  -420}- ,{  -400,  -710,  -400,  -620,  -400}- ,{   -30,  -720,   -30,  -720,  -500}- }-,{{   600,   -60,   600,  -230,   200}- ,{   200,  -340,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   200,   -60,   200,  -350,   200}- ,{   460,  -230,   460,  -230,   160}- }-,{{   310,   310,  -140,  -150,   140}- ,{  -480,  -480,  -630,  -890,  -630}- ,{  -180,  -430,  -510,  -430,  -180}- ,{   310,   310,  -630,  -150,  -630}- ,{   140,  -430,  -140,  -430,   140}- }-,{{   600,  -230,   600,  -230,   200}- ,{   200,  -390,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   200,  -310,   200,  -350,   200}- ,{   460,  -230,   460,  -230,  -170}- }-,{{   140,  -380,  -140,  -430,   140}- ,{  -400,  -400,  -630,  -890,  -630}- ,{  -180,  -430,  -510,  -430,  -180}- ,{  -380,  -380,  -630,  -890,  -630}- ,{   140,  -430,  -140,  -430,   140}- }-,{{   600,   310,   600,  -150,   200}- ,{   200,  -340,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   310,   310,   200,  -150,   200}- ,{   460,  -230,   460,  -230,   160}- }};--PUBLIC int mismatch1nI37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- }};-PUBLIC int mismatch1nIdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- }};--PUBLIC int mismatch23I37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,   -50,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,  -110,     0,   -70,     0}- ,{     0,     0,     0,     0,   -30}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,  -120,     0,   -70,     0}- ,{     0,     0,     0,     0,   -30}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -40,    70,     0,    70}- ,{    70,    70,    70,    70,    40}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    20,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -40,    70,     0,    70}- ,{    70,    70,    70,    70,    40}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -40,    70,     0,    70}- ,{    70,    70,    70,    70,    40}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    20,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -40,    70,     0,    70}- ,{    70,    70,    70,    70,    40}- }-,{{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,    70,    70,    70,    70}- ,{    70,   -40,    70,     0,    70}- ,{    70,    70,    70,    70,    40}- }};-PUBLIC int mismatch23IdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,  -570,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,  -860,     0,  -900,     0}- ,{     0,     0,     0,     0,  -640}- }-,{{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0,     0,     0,     0,     0}- ,{     0, -1090,     0,  -900,     0}- ,{     0,     0,     0,     0,  -640}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,  -580,   500,  -400,   500}- ,{   500,   500,   500,   500,  -140}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   -60,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,  -360,   500,  -400,   500}- ,{   500,   500,   500,   500,  -140}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,  -580,   500,  -400,   500}- ,{   500,   500,   500,   500,  -140}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   -60,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,  -360,   500,  -400,   500}- ,{   500,   500,   500,   500,  -140}- }-,{{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,   500,   500,   500,   500}- ,{   500,  -360,   500,  -400,   500}- ,{   500,   500,   500,   500,  -140}- }};--PUBLIC int mismatchExt37[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{   -80,  -100,  -110,  -100,   -80}- ,{  -140,  -150,  -150,  -140,  -150}- ,{   -80,  -100,  -110,  -100,   -80}- ,{  -140,  -140,  -150,  -160,  -150}- ,{  -100,  -100,  -140,  -100,  -120}- }-,{{   -50,  -110,   -70,  -110,   -50}- ,{  -110,  -110,  -150,  -130,  -150}- ,{   -50,  -110,   -70,  -110,   -50}- ,{  -140,  -160,  -150,  -140,  -150}- ,{   -70,  -110,  -100,  -110,   -70}- }-,{{   -30,   -30,   -70,   -60,   -60}- ,{   -30,   -30,  -100,   -80,  -100}- ,{   -60,   -60,   -70,   -60,   -70}- ,{   -60,   -60,  -100,   -80,  -100}- ,{   -60,   -60,   -80,   -60,   -60}- }-,{{   -50,   -50,   -60,   -70,   -50}- ,{   -80,  -100,   -80,  -110,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- ,{   -50,   -50,   -80,   -80,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- }-,{{   -60,   -60,   -70,   -60,   -70}- ,{   -80,   -80,  -100,   -80,  -100}- ,{   -60,   -60,   -70,   -60,   -70}- ,{   -80,   -80,  -100,   -80,  -100}- ,{   -60,   -60,   -80,   -60,   -80}- }-,{{   -50,   -70,   -60,   -70,   -50}- ,{   -80,  -100,   -80,  -110,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- ,{   -80,  -110,   -80,  -120,   -80}- ,{   -50,   -70,   -60,   -70,   -50}- }-,{{   -30,   -30,   -60,   -60,   -50}- ,{   -30,   -30,   -80,   -80,   -80}- ,{   -50,   -60,   -60,   -60,   -50}- ,{   -50,   -50,   -80,   -80,   -80}- ,{   -50,   -60,   -60,   -60,   -50}- }};-PUBLIC int mismatchExtdH[NBPAIRS+1][5][5] =-{{{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- ,{   INF,   INF,   INF,   INF,   INF}- }-,{{  -270,  -570,  -340,  -560,  -270}- ,{  -560,  -910,  -560,  -560,  -560}- ,{  -270,  -570,  -340,  -570,  -270}- ,{  -560,  -820,  -560,  -920,  -560}- ,{  -530,  -570,  -530,  -570,  -860}- }-,{{    50,  -520,    50,  -560,  -400}- ,{  -400,  -520,  -400,  -560,  -400}- ,{    50,  -720,    50,  -720,  -420}- ,{  -400,  -710,  -400,  -620,  -400}- ,{   -30,  -720,   -30,  -720,  -500}- }-,{{   600,   -60,   600,  -230,   200}- ,{   200,  -340,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   200,   -60,   200,  -350,   200}- ,{   460,  -230,   460,  -230,   160}- }-,{{   310,   310,  -140,  -150,   140}- ,{  -480,  -480,  -630,  -890,  -630}- ,{  -180,  -430,  -510,  -430,  -180}- ,{   310,   310,  -630,  -150,  -630}- ,{   140,  -430,  -140,  -430,   140}- }-,{{   600,  -230,   600,  -230,   200}- ,{   200,  -390,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   200,  -310,   200,  -350,   200}- ,{   460,  -230,   460,  -230,  -170}- }-,{{   140,  -380,  -140,  -430,   140}- ,{  -400,  -400,  -630,  -890,  -630}- ,{  -180,  -430,  -510,  -430,  -180}- ,{  -380,  -380,  -630,  -890,  -630}- ,{   140,  -430,  -140,  -430,   140}- }-,{{   600,   310,   600,  -150,   200}- ,{   200,  -340,   200,  -350,   200}- ,{   600,  -230,   600,  -230,   -30}- ,{   310,   310,   200,  -150,   200}- ,{   460,  -230,   460,  -230,   160}- }};---PUBLIC int dangle3_37[NBPAIRS+1][5] =-{{   INF,   INF,   INF,   INF,   INF}-,{   -80,  -170,   -80,  -170,  -120}-,{   -40,  -110,   -40,  -130,   -60}-,{   -50,   -80,   -50,   -80,   -60}-,{   -10,   -70,   -10,   -70,   -10}-,{   -50,   -80,   -50,   -80,   -60}-,{   -10,   -70,   -10,   -70,   -10}-,{   -10,   -70,   -10,   -70,   -10}};-PUBLIC int dangle3_dH[NBPAIRS+1][5] =-{{   INF,   INF,   INF,   INF,   INF}-,{  -410,  -900,  -410,  -860,  -750}-,{  -280,  -740,  -280,  -640,  -360}-,{   -90,  -490,   -90,  -550,  -230}-,{   -70,  -570,   -70,  -580,  -220}-,{   -90,  -490,   -90,  -550,  -230}-,{   -70,  -570,   -70,  -580,  -220}-,{   -70,  -490,   -70,  -550,  -220}};-PUBLIC int dangle5_37[NBPAIRS+1][5] =-{{   INF,   INF,   INF,   INF,   INF}-,{     0,   -20,   -30,     0,     0}-,{   -10,   -50,   -30,   -20,   -10}-,{   -10,   -30,   -10,   -20,   -20}-,{   -20,   -30,   -30,   -40,   -20}-,{   -10,   -30,   -10,   -20,   -20}-,{   -20,   -30,   -30,   -40,   -20}-,{     0,   -20,   -10,     0,     0}};-PUBLIC int dangle5_dH[NBPAIRS+1][5] =-{{   INF,   INF,   INF,   INF,   INF}-,{    70,  -160,    70,  -460,   -40}-,{   330,  -240,   330,    80,  -140}-,{   690,   -50,   690,    60,    60}-,{   310,   160,   220,    70,   310}-,{   690,   -50,   690,    60,    60}-,{   310,   160,   220,    70,   310}-,{   690,   160,   690,    80,   310}};--PUBLIC char Triloops[241] =-  "CAACG "-  "GUUAC "-;-PUBLIC int Triloop37[40] = {   680,   690};-PUBLIC int TriloopdH[40] = {  2370,  1080};--PUBLIC char Tetraloops[281] =-  "CAACGG "-  "CCAAGG "-  "CCACGG "-  "CCCAGG "-  "CCGAGG "-  "CCGCGG "-  "CCUAGG "-  "CCUCGG "-  "CUAAGG "-  "CUACGG "-  "CUCAGG "-  "CUCCGG "-  "CUGCGG "-  "CUUAGG "-  "CUUCGG "-  "CUUUGG "-;-PUBLIC int Tetraloop37[40] = {   550,   330,   370,   340,   350,   360,   370,   250,   360,   280,   370,   270,   280,   350,   370,   370};-PUBLIC int TetraloopdH[40] = {   690, -1030,  -330,  -890,  -660,  -750,  -350, -1390,  -760, -1070,  -660, -1290, -1070,  -620, -1530,  -680};--PUBLIC char Hexaloops[361] =-  "ACAGUACU "-  "ACAGUGAU "-  "ACAGUGCU "-  "ACAGUGUU "-;-PUBLIC int Hexaloop37[40] = {   280,   360,   290,   180};-PUBLIC int HexaloopdH[40] = { -1680, -1140, -1280, -1540};--#include "intl11.h"-#include "intl11dH.h"-#include "intl21.h"-#include "intl21dH.h"-#include "intl22.h"-#include "intl22dH.h"-
− cbits/ffiwrap_part_func.c 
@@ -1,32 +0,0 @@--// functions wrapped in here need a C-wrapper because they do "more work"-// before they can be called from C.--#include <stdio.h>--#include "part_func.h"-#include "part_func_co.h"--// wrap the RNAfold constrained partition function--float ffiwrap_pf_fold_constrained (const char *sequence, char *structure, int constrained)-{-  return pf_fold_par (sequence, structure, 0, 1, constrained, 0);-}--// wrap the RNAcofold constrained partition function.--void ffiwrap_co_pf_fold_constrained (cofoldF * x, char *sequence, char *structure, int constrained)-{-  *x = co_pf_fold_par (sequence, structure, 0, 1, constrained);-  return;-}--// wrap RNAcofold partition function--void ffiwrap_co_pf_fold (cofoldF * x, char * inp, char * str)-{-  *x = co_pf_fold (inp, str);-  return;-}-
− cbits/fold.c 
@@ -1,2765 +0,0 @@-/** \file **/--/*-                  minimum free energy-                  RNA secondary structure prediction--                  c Ivo Hofacker, Chrisoph Flamm-                  original implementation by-                  Walter Fontana-                  g-quadruplex support and threadsafety-                  by Ronny Lorenz--                  Vienna RNA package-*/--#include <config.h>-#include <stdio.h>-#include <stdlib.h>-#include <math.h>-#include <ctype.h>-#include <string.h>-#include <limits.h>--#include "utils.h"-#include "energy_par.h"-#include "fold_vars.h"-#include "pair_mat.h"-#include "params.h"-#include "loop_energies.h"-#include "data_structures.h"-#include "gquad.h"-#include "fold.h"--#ifdef _OPENMP-#include <omp.h>-#endif---#define PAREN-#define STACK_BULGE1      1       /* stacking energies for bulges of size 1 */-#define NEW_NINIO         1       /* new asymetry penalty */-#define MAXSECTORS        500     /* dimension for a backtrack array */-#define LOCALITY          0.      /* locality parameter for base-pairs */--#define SAME_STRAND(I,J)  (((I)>=cut_point)||((J)<cut_point))--/*-#################################-# GLOBAL VARIABLES              #-#################################-*/-PUBLIC  int logML     = 0;  /* if nonzero use logarithmic ML energy in energy_of_struct */-PUBLIC  int uniq_ML   = 0;  /* do ML decomposition uniquely (for subopt) */-PUBLIC  int cut_point = -1; /* set to first pos of second seq for cofolding */-PUBLIC  int eos_debug = 0;  /* verbose info from energy_of_struct */--/*-#################################-# PRIVATE VARIABLES             #-#################################-*/-PRIVATE int     *indx     = NULL; /* index for moving in the triangle matrices c[] and fMl[]*/-PRIVATE int     *c        = NULL; /* energy array, given that i-j pair */-PRIVATE int     *cc       = NULL; /* linear array for calculating canonical structures */-PRIVATE int     *cc1      = NULL; /*   "     "        */-PRIVATE int     *f5       = NULL; /* energy of 5' end */-PRIVATE int     *f53      = NULL; /* energy of 5' end with 3' nucleotide not available for mismatches */-PRIVATE int     *fML      = NULL; /* multi-loop auxiliary energy array */-PRIVATE int     *fM1      = NULL; /* second ML array, only for subopt */-PRIVATE int     *fM2      = NULL; /* fM2 = multiloop region with exactly two stems, extending to 3' end        */-PRIVATE int     *Fmi      = NULL; /* holds row i of fML (avoids jumps in memory) */-PRIVATE int     *DMLi     = NULL; /* DMLi[j] holds MIN(fML[i,k]+fML[k+1,j])  */-PRIVATE int     *DMLi1    = NULL; /*             MIN(fML[i+1,k]+fML[k+1,j])  */-PRIVATE int     *DMLi2    = NULL; /*             MIN(fML[i+2,k]+fML[k+1,j])  */-PRIVATE int     *DMLi_a   = NULL; /* DMLi_a[j] holds min energy for at least two multiloop stems in [i,j], where j is available for dangling onto a surrounding stem */-PRIVATE int     *DMLi_o   = NULL; /* DMLi_o[j] holds min energy for at least two multiloop stems in [i,j], where j is unavailable for dangling onto a surrounding stem */-PRIVATE int     *DMLi1_a  = NULL;-PRIVATE int     *DMLi1_o  = NULL;-PRIVATE int     *DMLi2_a  = NULL;-PRIVATE int     *DMLi2_o  = NULL;-PRIVATE int     Fc, FcH, FcI, FcM;  /* parts of the exterior loop energies */-PRIVATE sect    sector[MAXSECTORS]; /* stack of partial structures for backtracking */-PRIVATE char    *ptype = NULL;      /* precomputed array of pair types */-PRIVATE short   *S = NULL, *S1 = NULL;-PRIVATE paramT  *P          = NULL;-PRIVATE int     init_length = -1;-PRIVATE int     *BP = NULL; /* contains the structure constrainsts: BP[i]-                        -1: | = base must be paired-                        -2: < = base must be paired with j<i-                        -3: > = base must be paired with j>i-                        -4: x = base must not pair-                        positive int: base is paired with int      */-PRIVATE short   *pair_table         = NULL; /* needed by energy of struct */-PRIVATE bondT   *base_pair2         = NULL; /* this replaces base_pair from fold_vars.c */-PRIVATE int     circular            = 0;-PRIVATE int     struct_constrained  = 0;-PRIVATE int     with_gquad          = 0;--PRIVATE int     *ggg = NULL;    /* minimum free energies of the gquadruplexes */--#ifdef _OPENMP--#pragma omp threadprivate(indx, c, cc, cc1, f5, f53, fML, fM1, fM2, Fmi,\-                          DMLi, DMLi1, DMLi2, DMLi_a, DMLi_o, DMLi1_a, DMLi1_o, DMLi2_a, DMLi2_o,\-                          Fc, FcH, FcI, FcM,\-                          sector, ptype, S, S1, P, init_length, BP, pair_table, base_pair2, circular, struct_constrained,\-                          ggg, with_gquad)--#endif--/*-#################################-# PRIVATE FUNCTION DECLARATIONS #-#################################-*/-PRIVATE void  get_arrays(unsigned int size);-PRIVATE int   stack_energy(int i, const char *string, int verbostiy_level);-PRIVATE int   energy_of_extLoop_pt(int i, short *pair_table);-PRIVATE int   energy_of_ml_pt(int i, short *pt);-PRIVATE int   ML_Energy(int i, int is_extloop);-PRIVATE void  make_ptypes(const short *S, const char *structure);-PRIVATE void  backtrack(const char *sequence, int s);-PRIVATE int   fill_arrays(const char *sequence);-PRIVATE void  fill_arrays_circ(const char *string, int *bt);-PRIVATE void  init_fold(int length, paramT *parameters);-/* needed by cofold/eval */-PRIVATE int   cut_in_loop(int i);--/* deprecated functions */-/*@unused@*/-int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2);-int LoopEnergy(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1);-int HairpinE(int size, int type, int si1, int sj1, const char *string);---/*-#################################-# BEGIN OF FUNCTION DEFINITIONS #-#################################-*/--/* allocate memory for folding process */-PRIVATE void init_fold(int length, paramT *parameters){--#ifdef _OPENMP-/* Explicitly turn off dynamic threads */-  omp_set_dynamic(0);-#endif--  if (length<1) nrerror("initialize_fold: argument must be greater 0");-  free_arrays();-  get_arrays((unsigned) length);-  init_length=length;--  indx = get_indx((unsigned)length);--  update_fold_params_par(parameters);-}--/*--------------------------------------------------------------------------*/--PRIVATE void get_arrays(unsigned int size){-  if(size >= (unsigned int)sqrt((double)INT_MAX))-    nrerror("get_arrays@fold.c: sequence length exceeds addressable range");--  c     = (int *) space(sizeof(int)*((size*(size+1))/2+2));-  fML   = (int *) space(sizeof(int)*((size*(size+1))/2+2));-  if (uniq_ML)-    fM1 = (int *) space(sizeof(int)*((size*(size+1))/2+2));--  ptype = (char *)space(sizeof(char)*((size*(size+1))/2+2));-  f5    = (int *) space(sizeof(int)*(size+2));-  f53   = (int *) space(sizeof(int)*(size+2));-  cc    = (int *) space(sizeof(int)*(size+2));-  cc1   = (int *) space(sizeof(int)*(size+2));-  Fmi   = (int *) space(sizeof(int)*(size+1));-  DMLi  = (int *) space(sizeof(int)*(size+1));-  DMLi1 = (int *) space(sizeof(int)*(size+1));-  DMLi2 = (int *) space(sizeof(int)*(size+1));--  DMLi_a  = (int *) space(sizeof(int)*(size+1));-  DMLi_o  = (int *) space(sizeof(int)*(size+1));-  DMLi1_a = (int *) space(sizeof(int)*(size+1));-  DMLi1_o = (int *) space(sizeof(int)*(size+1));-  DMLi2_a = (int *) space(sizeof(int)*(size+1));-  DMLi2_o = (int *) space(sizeof(int)*(size+1));--  base_pair2 = (bondT *) space(sizeof(bondT)*(1+size/2));--  /* extra array(s) for circfold() */-  if(circular) fM2 =  (int *) space(sizeof(int)*(size+2));-}--/*--------------------------------------------------------------------------*/--PUBLIC void free_arrays(void){-  if(indx)      free(indx);-  if(c)         free(c);-  if(fML)       free(fML);-  if(f5)        free(f5);-  if(f53)       free(f53);-  if(cc)        free(cc);-  if(cc1)       free(cc1);-  if(ptype)     free(ptype);-  if(fM1)       free(fM1);-  if(fM2)       free(fM2);-  if(base_pair2) free(base_pair2);-  if(Fmi)       free(Fmi);-  if(DMLi)      free(DMLi);-  if(DMLi1)     free(DMLi1);-  if(DMLi2)     free(DMLi2);-  if(DMLi_a)    free(DMLi_a);-  if(DMLi_o)    free(DMLi_o);-  if(DMLi1_a)   free(DMLi1_a);-  if(DMLi1_o)   free(DMLi1_o);-  if(DMLi2_a)   free(DMLi2_a);-  if(DMLi2_o)   free(DMLi2_o);-  if(P)         free(P);-  if(ggg)       free(ggg);--  indx = c = fML = f5 = f53 = cc = cc1 = fM1 = fM2 = Fmi = DMLi = DMLi1 = DMLi2 = ggg = NULL;-  DMLi_a = DMLi_o = DMLi1_a = DMLi1_o = DMLi2_a = DMLi2_o = NULL;-  ptype       = NULL;-  base_pair   = NULL;-  base_pair2  = NULL;-  P           = NULL;-  init_length = 0;-}--/*--------------------------------------------------------------------------*/--PUBLIC void export_fold_arrays( int **f5_p,-                                int **c_p,-                                int **fML_p,-                                int **fM1_p,-                                int **indx_p,-                                char **ptype_p){-  /* make the DP arrays available to routines such as subopt() */-  *f5_p     = f5;-  *c_p      = c;-  *fML_p    = fML;-  *fM1_p    = fM1;-  *indx_p   = indx;-  *ptype_p  = ptype;-}--PUBLIC void export_fold_arrays_par( int **f5_p,-                                    int **c_p,-                                    int **fML_p,-                                    int **fM1_p,-                                    int **indx_p,-                                    char **ptype_p,-                                    paramT **P_p){-  export_fold_arrays(f5_p, c_p, fML_p, fM1_p, indx_p,ptype_p);-  *P_p = P;-}--PUBLIC void export_circfold_arrays( int *Fc_p,-                                    int *FcH_p,-                                    int *FcI_p,-                                    int *FcM_p,-                                    int **fM2_p,-                                    int **f5_p,-                                    int **c_p,-                                    int **fML_p,-                                    int **fM1_p,-                                    int **indx_p,-                                    char **ptype_p){-  /* make the DP arrays available to routines such as subopt() */-  *f5_p     = f5;-  *c_p      = c;-  *fML_p    = fML;-  *fM1_p    = fM1;-  *fM2_p    = fM2;-  *Fc_p     = Fc;-  *FcH_p    = FcH;-  *FcI_p    = FcI;-  *FcM_p    = FcM;-  *indx_p   = indx;-  *ptype_p  = ptype;-}--PUBLIC void export_circfold_arrays_par( int *Fc_p,-                                    int *FcH_p,-                                    int *FcI_p,-                                    int *FcM_p,-                                    int **fM2_p,-                                    int **f5_p,-                                    int **c_p,-                                    int **fML_p,-                                    int **fM1_p,-                                    int **indx_p,-                                    char **ptype_p,-                                    paramT **P_p){-  export_circfold_arrays(Fc_p, FcH_p, FcI_p, FcM_p, fM2_p, f5_p, c_p, fML_p, fM1_p, indx_p, ptype_p);-  *P_p = P;-}-/*--------------------------------------------------------------------------*/---PUBLIC float fold(const char *string, char *structure){-  return fold_par(string, structure, NULL, fold_constrained, 0);-}--PUBLIC float circfold(const char *string, char *structure){-  return fold_par(string, structure, NULL, fold_constrained, 1);-}--PUBLIC float fold_par(const char *string,-                      char *structure,-                      paramT *parameters,-                      int is_constrained,-                      int is_circular){--  int i, length, energy, bonus, bonus_cnt, s;--  bonus               = 0;-  bonus_cnt           = 0;-  s                   = 0;-  circular            = is_circular;-  struct_constrained  = is_constrained;-  length              = (int) strlen(string);--#ifdef _OPENMP-  init_fold(length, parameters);-#else-  if (parameters) init_fold(length, parameters);-  else if (length>init_length) init_fold(length, parameters);-  else if (fabs(P->temperature - temperature)>1e-6) update_fold_params();-#endif--  with_gquad  = P->model_details.gquad;-  S           = encode_sequence(string, 0);-  S1          = encode_sequence(string, 1);-  BP          = (int *)space(sizeof(int)*(length+2));-  if(with_gquad){ /* add a guess of how many G's may be involved in a G quadruplex */-    if(base_pair2)-      free(base_pair2);-    base_pair2 = (bondT *) space(sizeof(bondT)*(4*(1+length/2)));-  }--  make_ptypes(S, structure);--  energy = fill_arrays(string);--  if(circular){-    fill_arrays_circ(string, &s);-    energy = Fc;-  }-  backtrack(string, s);--#ifdef PAREN-  parenthesis_structure(structure, base_pair2, length);-#else-  letter_structure(structure, base_pair2, length);-#endif--  /*-  *  Backward compatibility:-  *  This block may be removed if deprecated functions-  *  relying on the global variable "base_pair" vanishs from within the package!-  */-  base_pair = base_pair2;-  /*-  {-    if(base_pair) free(base_pair);-    base_pair = (bondT *)space(sizeof(bondT) * (1+length/2));-    memcpy(base_pair, base_pair2, sizeof(bondT) * (1+length/2));-  }-  */--  /* check constraints */-  for(i=1;i<=length;i++) {-    if((BP[i]<0)&&(BP[i]>-4)) {-      bonus_cnt++;-      if((BP[i]==-3)&&(structure[i-1]==')')) bonus++;-      if((BP[i]==-2)&&(structure[i-1]=='(')) bonus++;-      if((BP[i]==-1)&&(structure[i-1]!='.')) bonus++;-    }--    if(BP[i]>i) {-      int l;-      bonus_cnt++;-      for(l=1; l<=base_pair2[0].i; l++)-        if(base_pair2[l].i != base_pair2[l].j)-          if((i==base_pair2[l].i)&&(BP[i]==base_pair2[l].j)) bonus++;-    }-  }--  if (bonus_cnt>bonus) fprintf(stderr,"\ncould not enforce all constraints\n");-  bonus*=BONUS;--  free(S); free(S1); free(BP);--  energy += bonus;      /*remove bonus energies from result */--  if (backtrack_type=='C')-    return (float) c[indx[length]+1]/100.;-  else if (backtrack_type=='M')-    return (float) fML[indx[length]+1]/100.;-  else-    return (float) energy/100.;-}--/**-*** fill "c", "fML" and "f5" arrays and return  optimal energy-**/-PRIVATE int fill_arrays(const char *string) {--  int   i, j, k, length, energy, en, mm5, mm3;-  int   decomp, new_fML, max_separation;-  int   no_close, type, type_2, tt;-  int   bonus=0;-  -  int   dangle_model, noGUclosure, with_gquads;--  dangle_model  = P->model_details.dangles;-  noGUclosure   = P->model_details.noGUclosure;--  length = (int) strlen(string);--  max_separation = (int) ((1.-LOCALITY)*(double)(length-2)); /* not in use */--  if(with_gquad)-    ggg = get_gquad_matrix(S, P);---  for (j=1; j<=length; j++) {-    Fmi[j]=DMLi[j]=DMLi1[j]=DMLi2[j]=INF;-  }--  for (j = 1; j<=length; j++)-    for (i=(j>TURN?(j-TURN):1); i<j; i++) {-      c[indx[j]+i] = fML[indx[j]+i] = INF;-      if (uniq_ML) fM1[indx[j]+i] = INF;-    }--  if (length <= TURN) return 0;--  for (i = length-TURN-1; i >= 1; i--) { /* i,j in [1..length] */--    for (j = i+TURN+1; j <= length; j++) {-      int p, q, ij, jj, ee;-      int minq, maxq, l1, up, c0, c1, c2, c3;-      int MLenergy;-      ij = indx[j]+i;-      bonus = 0;-      type = ptype[ij];-      energy = INF;-      /* enforcing structure constraints */-      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;-      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;-      if ((BP[i]==-4)||(BP[j]==-4)) type=0;--      no_close = (((type==3)||(type==4))&&noGUclosure&&(bonus==0));--      if (j-i-1 > max_separation) type = 0;  /* forces locality degree */--      if (type) {   /* we have a pair */-        int new_c=0, stackEnergy=INF;-        /* hairpin ----------------------------------------------*/--        new_c = (no_close) ? FORBIDDEN : E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], string+i-1, P);--        /*---------------------------------------------------------          check for elementary structures involving more than one-          closing pair.-          --------------------------------------------------------*/--        for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1) ; p++) {-          minq = j-i+p-MAXLOOP-2;-          if (minq<p+1+TURN) minq = p+1+TURN;-          for (q = minq; q < j; q++) {-            type_2 = ptype[indx[q]+p];--            if (type_2==0) continue;-            type_2 = rtype[type_2];--            if (noGUclosure)-              if (no_close||(type_2==3)||(type_2==4))-                if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */--            energy = E_IntLoop(p-i-1, j-q-1, type, type_2,-                                S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);--            ee = energy+c[indx[q]+p];-            new_c = MIN2(new_c, ee);-            if ((p==i+1)&&(j==q+1)) stackEnergy = energy; /* remember stack energy */--          } /* end q-loop */-        } /* end p-loop */-        /* multi-loop decomposition ------------------------*/---        if (!no_close) {-          decomp = DMLi1[j-1];-          tt = rtype[type];-          switch(dangle_model){-            /* no dangles */-            case 0:   decomp += E_MLstem(tt, -1, -1, P);-                      break;--            /* double dangles */-            case 2:   decomp += E_MLstem(tt, S1[j-1], S1[i+1], P);-                      break;--            /* normal dangles, aka dangles = 1 || 3 */-            default:  decomp += E_MLstem(tt, -1, -1, P);-                      decomp = MIN2(decomp, DMLi2[j-1] + E_MLstem(tt, -1, S1[i+1], P) + P->MLbase);-                      decomp = MIN2(decomp, DMLi2[j-2] + E_MLstem(tt, S1[j-1], S1[i+1], P) + 2*P->MLbase);-                      decomp = MIN2(decomp, DMLi1[j-2] + E_MLstem(tt, S1[j-1], -1, P) + P->MLbase);-                      break;-          }-          MLenergy = decomp + P->MLclosing;-          new_c = MIN2(new_c, MLenergy);-        }--        /* coaxial stacking of (i.j) with (i+1.k) or (k+1.j-1) */--        if (dangle_model==3) {-          decomp = INF;-          for (k = i+2+TURN; k < j-2-TURN; k++) {-            type_2 = rtype[ptype[indx[k]+i+1]];-            if (type_2)-              decomp = MIN2(decomp, c[indx[k]+i+1]+P->stack[type][type_2]+fML[indx[j-1]+k+1]);-            type_2 = rtype[ptype[indx[j-1]+k+1]];-            if (type_2)-              decomp = MIN2(decomp, c[indx[j-1]+k+1]+P->stack[type][type_2]+fML[indx[k]+i+1]);-          }-          /* no TermAU penalty if coax stack */-          decomp += 2*P->MLintern[1] + P->MLclosing;-          new_c = MIN2(new_c, decomp);-        }--        if(with_gquad){-          /* include all cases where a g-quadruplex may be enclosed by base pair (i,j) */-          if (!no_close) {-            tt = rtype[type];-            energy = E_GQuad_IntLoop(i, j, type, S1, ggg, indx, P);-            new_c = MIN2(new_c, energy);-          }-        }--        new_c = MIN2(new_c, cc1[j-1]+stackEnergy);-        cc[j] = new_c + bonus;-        if (noLonelyPairs)-          c[ij] = cc1[j-1]+stackEnergy+bonus;-        else-          c[ij] = cc[j];--      } /* end >> if (pair) << */--      else c[ij] = INF;--      /* done with c[i,j], now compute fML[i,j] and fM1[i,j] */--      /* (i,j) + MLstem ? */-      new_fML = INF;-      if(type){-        new_fML = c[ij];-        switch(dangle_model){-          case 2:   new_fML += E_MLstem(type, (i==1) ? S1[length] : S1[i-1], S1[j+1], P);-                    break;-          default:  new_fML += E_MLstem(type, -1, -1, P);-                    break;-        }-      }--      if(with_gquad){-        new_fML = MIN2(new_fML, ggg[indx[j] + i] + E_MLstem(0, -1, -1, P));-      }--      if (uniq_ML){-        fM1[ij] = MIN2(fM1[indx[j-1]+i] + P->MLbase, new_fML);-      }--      /* free ends ? -----------------------------------------*/-      /*  we must not just extend 3'/5' end by unpaired nucleotides if-      *   dangle_model == 1, this could lead to d5+d3 contributions were-      *   mismatch must be taken!-      */-      switch(dangle_model){-        /* no dangles */-        case 0:   new_fML = MIN2(new_fML, fML[ij+1]+P->MLbase);-                  new_fML = MIN2(fML[indx[j-1]+i]+P->MLbase, new_fML);-                  break;--        /* double dangles */-        case 2:   new_fML = MIN2(new_fML, fML[ij+1]+P->MLbase);-                  new_fML = MIN2(fML[indx[j-1]+i]+P->MLbase, new_fML);-                  break;--        /* normal dangles, aka dangle_model = 1 || 3 */-        default:  mm5 = ((i>1) || circular) ? S1[i] : -1;-                  mm3 = ((j<length) || circular) ? S1[j] : -1;-                  new_fML = MIN2(new_fML, fML[ij+1] + P->MLbase);-                  new_fML = MIN2(new_fML, fML[indx[j-1]+i] + P->MLbase);-                  tt = ptype[ij+1];-                  if(tt) new_fML = MIN2(new_fML, c[ij+1] + E_MLstem(tt, mm5, -1, P) + P->MLbase);-                  tt = ptype[indx[j-1]+i];-                  if(tt) new_fML = MIN2(new_fML, c[indx[j-1]+i] + E_MLstem(tt, -1, mm3, P) + P->MLbase);-                  tt = ptype[indx[j-1]+i+1];-                  if(tt) new_fML = MIN2(new_fML, c[indx[j-1]+i+1] + E_MLstem(tt, mm5, mm3, P) + 2*P->MLbase);-                  break;-      }--      /* modular decomposition -------------------------------*/-      for (decomp = INF, k = i + 1 + TURN; k <= j - 2 - TURN; k++)-        decomp = MIN2(decomp, Fmi[k]+fML[indx[j]+k+1]);-      DMLi[j] = decomp;               /* store for use in ML decompositon */-      new_fML = MIN2(new_fML,decomp);--      /* coaxial stacking */-      if (dangle_model==3) {-        /* additional ML decomposition as two coaxially stacked helices */-        for (decomp = INF, k = i+1+TURN; k <= j-2-TURN; k++) {-          type = ptype[indx[k]+i]; type = rtype[type];-          type_2 = ptype[indx[j]+k+1]; type_2 = rtype[type_2];-          if (type && type_2)-            decomp = MIN2(decomp,-                          c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]);-        }--        decomp += 2*P->MLintern[1];        /* no TermAU penalty if coax stack */-#if 0-        /* This is needed for Y shaped ML loops with coax stacking of-           interior pairts, but backtracking will fail if activated */-        DMLi[j] = MIN2(DMLi[j], decomp);-        DMLi[j] = MIN2(DMLi[j], DMLi[j-1]+P->MLbase);-        DMLi[j] = MIN2(DMLi[j], DMLi1[j]+P->MLbase);-        new_fML = MIN2(new_fML, DMLi[j]);-#endif-        new_fML = MIN2(new_fML, decomp);-      }-      fML[ij] = Fmi[j] = new_fML;     /* substring energy */--    }--    {-      int *FF; /* rotate the auxilliary arrays */-      FF = DMLi2; DMLi2 = DMLi1; DMLi1 = DMLi; DMLi = FF;-      FF = cc1; cc1=cc; cc=FF;-      for (j=1; j<=length; j++) {cc[j]=Fmi[j]=DMLi[j]=INF; }-    }-  }--  /* calculate energies of 5' and 3' fragments */--  f5[TURN+1]= 0;-  /* duplicated code may be faster than conditions inside loop ;) */-  switch(dangle_model){-    /* dont use dangling end and mismatch contributions at all */-    case 0:   for(j=TURN+2; j<=length; j++){-                f5[j] = f5[j-1];-                for (i=j-TURN-1; i>1; i--){--                  if(with_gquad){-                    f5[j] = MIN2(f5[j], f5[i-1] + ggg[indx[j]+i]);-                  }--                  type = ptype[indx[j]+i];-                  if(!type) continue;-                  en = c[indx[j]+i];-                  f5[j] = MIN2(f5[j], f5[i-1] + en + E_ExtLoop(type, -1, -1, P));-                }--                if(with_gquad){-                  f5[j] = MIN2(f5[j], ggg[indx[j]+1]);-                }--                type=ptype[indx[j]+1];-                if(!type) continue;-                en = c[indx[j]+1];-                f5[j] = MIN2(f5[j], en + E_ExtLoop(type, -1, -1, P));-              }-              break;--    /* always use dangles on both sides */-    case 2:   for(j=TURN+2; j<length; j++){-                f5[j] = f5[j-1];-                for (i=j-TURN-1; i>1; i--){--                  if(with_gquad){-                    f5[j] = MIN2(f5[j], f5[i-1] + ggg[indx[j]+i]);-                  }--                  type = ptype[indx[j]+i];-                  if(!type) continue;-                  en = c[indx[j]+i];-                  f5[j] = MIN2(f5[j], f5[i-1] + en + E_ExtLoop(type, S1[i-1], S1[j+1], P));-                }--                if(with_gquad){-                  f5[j] = MIN2(f5[j], ggg[indx[j]+1]);-                }--                type=ptype[indx[j]+1];-                if(!type) continue;-                en = c[indx[j]+1];-                f5[j] = MIN2(f5[j], en + E_ExtLoop(type, -1, S1[j+1], P));-              }-              f5[length] = f5[length-1];-              for (i=length-TURN-1; i>1; i--){--                if(with_gquad){-                  f5[length] = MIN2(f5[length], f5[i-1] + ggg[indx[length]+i]);-                }--                type = ptype[indx[length]+i];-                if(!type) continue;-                en = c[indx[length]+i];-                f5[length] = MIN2(f5[length], f5[i-1] + en + E_ExtLoop(type, S1[i-1], -1, P));-              }--              if(with_gquad){-                f5[length] = MIN2(f5[length], ggg[indx[length]+1]);-              }--              type=ptype[indx[length]+1];-              if(!type) break;-              en = c[indx[length]+1];-              f5[length] = MIN2(f5[length], en + E_ExtLoop(type, -1, -1, P));---              break;--    /* normal dangles, aka dangle_model = 1 || 3 */-    default:  for(j=TURN+2; j<=length; j++){-                f5[j] = f5[j-1];-                for (i=j-TURN-1; i>1; i--){--                  if(with_gquad){-                    f5[j] = MIN2(f5[j], f5[i-1] + ggg[indx[j]+i]);-                  }--                  type = ptype[indx[j]+i];-                  if(type){-                    en = c[indx[j]+i];-                    f5[j] = MIN2(f5[j], f5[i-1] + en + E_ExtLoop(type, -1, -1, P));-                    f5[j] = MIN2(f5[j], f5[i-2] + en + E_ExtLoop(type, S1[i-1], -1, P));-                  }-                  type = ptype[indx[j-1]+i];-                  if(type){-                    en = c[indx[j-1]+i];-                    f5[j] = MIN2(f5[j], f5[i-1] + en + E_ExtLoop(type, -1, S1[j], P));-                    f5[j] = MIN2(f5[j], f5[i-2] + en + E_ExtLoop(type, S1[i-1], S1[j], P));-                  }-                }--                if(with_gquad){-                  f5[j] = MIN2(f5[j], ggg[indx[j]+1]);-                }--                type = ptype[indx[j]+1];-                if(type) f5[j] = MIN2(f5[j], c[indx[j]+1] + E_ExtLoop(type, -1, -1, P));-                type = ptype[indx[j-1]+1];-                if(type) f5[j] = MIN2(f5[j], c[indx[j-1]+1] + E_ExtLoop(type, -1, S1[j], P));-              }-  }-  return f5[length];-}--#include "circfold.inc"--/**-*** trace back through the "c", "f5" and "fML" arrays to get the-*** base pairing list. No search for equivalent structures is done.-*** This is fast, since only few structure elements are recalculated.-***-*** normally s=0.-*** If s>0 then s items have been already pushed onto the sector stack-**/-PRIVATE void backtrack(const char *string, int s) {-  int   i, j, ij, k, l1, mm5, mm3, length, energy, en, new;-  int   no_close, type, type_2, tt, minq, maxq, c0, c1, c2, c3;-  int   bonus;-  int   b=0;-  int   dangle_model = P->model_details.dangles;--  length = strlen(string);-  if (s==0) {-    sector[++s].i = 1;-    sector[s].j = length;-    sector[s].ml = (backtrack_type=='M') ? 1 : ((backtrack_type=='C')? 2: 0);-  }-  while (s>0) {-    int ml, fij, fi, cij, traced, i1, j1, p, q, jj=0, gq=0;-    int canonical = 1;     /* (i,j) closes a canonical structure */-    i  = sector[s].i;-    j  = sector[s].j;-    ml = sector[s--].ml;   /* ml is a flag indicating if backtracking is to-                              occur in the fML- (1) or in the f-array (0) */-    if (ml==2) {-      base_pair2[++b].i = i;-      base_pair2[b].j   = j;-      goto repeat1;-    }--    else if(ml==7) { /* indicates that i,j are enclosing a gquadruplex */-      /* actually, do something here */-    }--    if (j < i+TURN+1) continue; /* no more pairs in this interval */--    fij = (ml == 1)? fML[indx[j]+i] : f5[j];-    fi  = (ml == 1)?(fML[indx[j-1]+i]+P->MLbase): f5[j-1];--    if (fij == fi) {  /* 3' end is unpaired */-      sector[++s].i = i;-      sector[s].j   = j-1;-      sector[s].ml  = ml;-      continue;-    }--    if (ml == 0) { /* backtrack in f5 */-      switch(dangle_model){-        case 0:   /* j is paired. Find pairing partner */-                  for(k=j-TURN-1,traced=0; k>=1; k--){--                    if(with_gquad){-                      if(fij == f5[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j]+k];-                    if(type)-                      if(fij == E_ExtLoop(type, -1, -1, P) + c[indx[j]+k] + f5[k-1]){-                        traced=j; jj = k-1;-                        break;-                      }-                  }-                  break;--        case 2:   mm3 = (j<length) ? S1[j+1] : -1;-                  for(k=j-TURN-1,traced=0; k>=1; k--){--                    if(with_gquad){-                      if(fij == f5[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j]+k];-                    if(type)-                      if(fij == E_ExtLoop(type, (k>1) ? S1[k-1] : -1, mm3, P) + c[indx[j]+k] + f5[k-1]){-                        traced=j; jj = k-1;-                        break;-                      }-                  }-                  break;--        default:  for(traced = 0, k=j-TURN-1; k>1; k--){--                    if(with_gquad){-                      if(fij == f5[k-1] + ggg[indx[j]+k]){-                        /* found the decomposition */-                        traced = j; jj = k - 1; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j] + k];-                    if(type){-                      en = c[indx[j] + k];-                      if(fij == f5[k-1] + en + E_ExtLoop(type, -1, -1, P)){-                        traced = j;-                        jj = k-1;-                        break;-                      }-                      if(fij == f5[k-2] + en + E_ExtLoop(type, S1[k-1], -1, P)){-                        traced = j;-                        jj = k-2;-                        break;-                      }-                    }-                    type = ptype[indx[j-1] + k];-                    if(type){-                      en = c[indx[j-1] + k];-                      if(fij == f5[k-1] + en + E_ExtLoop(type, -1, S1[j], P)){-                        traced = j-1;-                        jj = k-1;-                        break;-                      }-                      if(fij == f5[k-2] + en + E_ExtLoop(type, S1[k-1], S1[j], P)){-                        traced = j-1;-                        jj = k-2;-                        break;-                      }-                    }-                  }-                  if(!traced){--                    if(with_gquad){-                      if(fij == ggg[indx[j]+1]){-                        /* found the decomposition */-                        traced = j; jj = 0; gq = 1;-                        break;-                      }-                    }--                    type = ptype[indx[j]+1];-                    if(type){-                      if(fij == c[indx[j]+1] + E_ExtLoop(type, -1, -1, P)){-                        traced = j;-                        jj = 0;-                        break;-                      }-                    }-                    type = ptype[indx[j-1]+1];-                    if(type){-                      if(fij == c[indx[j-1]+1] + E_ExtLoop(type, -1, S1[j], P)){-                        traced = j-1;-                        jj = 0;-                        break;-                      }-                    }-                  }-                  break;-      }--      if (!traced){-        fprintf(stderr, "%s\n", string);-        nrerror("backtrack failed in f5");-      }-      /* push back the remaining f5 portion */-      sector[++s].i = 1;-      sector[s].j   = jj;-      sector[s].ml  = ml;--      /* trace back the base pair found */-      i=k; j=traced;--      if(with_gquad && gq){-        /* goto backtrace of gquadruplex */-        goto repeat_gquad;-      }--      base_pair2[++b].i = i;-      base_pair2[b].j   = j;-      goto repeat1;-    }-    else { /* trace back in fML array */-      if (fML[indx[j]+i+1]+P->MLbase == fij) { /* 5' end is unpaired */-        sector[++s].i = i+1;-        sector[s].j   = j;-        sector[s].ml  = ml;-        continue;-      }--      ij  = indx[j]+i;--      if(with_gquad){-        if(fij == ggg[ij] + E_MLstem(0, -1, -1, P)){-          /* go to backtracing of quadruplex */-          goto repeat_gquad;-        }-      }--      tt  = ptype[ij];-      en  = c[ij];-      switch(dangle_model){-        case 0:   if(fij == en + E_MLstem(tt, -1, -1, P)){-                    base_pair2[++b].i = i;-                    base_pair2[b].j   = j;-                    goto repeat1;-                  }-                  break;--        case 2:   if(fij == en + E_MLstem(tt, S1[i-1], S1[j+1], P)){-                    base_pair2[++b].i = i;-                    base_pair2[b].j   = j;-                    goto repeat1;-                  }-                  break;--        default:  if(fij == en + E_MLstem(tt, -1, -1, P)){-                    base_pair2[++b].i = i;-                    base_pair2[b].j   = j;-                    goto repeat1;-                  }-                  tt = ptype[ij+1];-                  if(fij == c[ij+1] + E_MLstem(tt, S1[i], -1, P) + P->MLbase){-                    base_pair2[++b].i = ++i;-                    base_pair2[b].j   = j;-                    goto repeat1;-                  }-                  tt = ptype[indx[j-1]+i];-                  if(fij == c[indx[j-1]+i] + E_MLstem(tt, -1, S1[j], P) + P->MLbase){-                    base_pair2[++b].i = i;-                    base_pair2[b].j   = --j;-                    goto repeat1;-                  }-                  tt = ptype[indx[j-1]+i+1];-                  if(fij == c[indx[j-1]+i+1] + E_MLstem(tt, S1[i], S1[j], P) + 2*P->MLbase){-                    base_pair2[++b].i = ++i;-                    base_pair2[b].j   = --j;-                    goto repeat1;-                  }-                  break;-      }--      for(k = i + 1 + TURN; k <= j - 2 - TURN; k++)-        if(fij == (fML[indx[k]+i]+fML[indx[j]+k+1]))-          break;--      if ((dangle_model==3)&&(k > j - 2 - TURN)) { /* must be coax stack */-        ml = 2;-        for (k = i+1+TURN; k <= j - 2 - TURN; k++) {-          type    = rtype[ptype[indx[k]+i]];-          type_2  = rtype[ptype[indx[j]+k+1]];-          if (type && type_2)-            if (fij == c[indx[k]+i]+c[indx[j]+k+1]+P->stack[type][type_2]+-                       2*P->MLintern[1])-              break;-        }-      }-      sector[++s].i = i;-      sector[s].j   = k;-      sector[s].ml  = ml;-      sector[++s].i = k+1;-      sector[s].j   = j;-      sector[s].ml  = ml;--      if (k>j-2-TURN) nrerror("backtrack failed in fML");-      continue;-    }--  repeat1:--    /*----- begin of "repeat:" -----*/-    ij = indx[j]+i;-    if (canonical)  cij = c[ij];--    type = ptype[ij];--    bonus = 0;-    if (struct_constrained) {-      if ((BP[i]==j)||(BP[i]==-1)||(BP[i]==-2)) bonus -= BONUS;-      if ((BP[j]==-1)||(BP[j]==-3)) bonus -= BONUS;-    }-    if (noLonelyPairs)-      if (cij == c[ij]){-        /* (i.j) closes canonical structures, thus-           (i+1.j-1) must be a pair                */-        type_2 = ptype[indx[j-1]+i+1]; type_2 = rtype[type_2];-        cij -= P->stack[type][type_2] + bonus;-        base_pair2[++b].i = i+1;-        base_pair2[b].j   = j-1;-        i++; j--;-        canonical=0;-        goto repeat1;-      }-    canonical = 1;---    no_close = (((type==3)||(type==4))&&no_closingGU&&(bonus==0));-    if (no_close) {-      if (cij == FORBIDDEN) continue;-    } else-      if (cij == E_Hairpin(j-i-1, type, S1[i+1], S1[j-1],string+i-1, P)+bonus)-        continue;--    for (p = i+1; p <= MIN2(j-2-TURN,i+MAXLOOP+1); p++) {-      minq = j-i+p-MAXLOOP-2;-      if (minq<p+1+TURN) minq = p+1+TURN;-      for (q = j-1; q >= minq; q--) {--        type_2 = ptype[indx[q]+p];-        if (type_2==0) continue;-        type_2 = rtype[type_2];-        if (no_closingGU)-          if (no_close||(type_2==3)||(type_2==4))-            if ((p>i+1)||(q<j-1)) continue;  /* continue unless stack */--        /* energy = oldLoopEnergy(i, j, p, q, type, type_2); */-        energy = E_IntLoop(p-i-1, j-q-1, type, type_2,-                            S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);--        new = energy+c[indx[q]+p]+bonus;-        traced = (cij == new);-        if (traced) {-          base_pair2[++b].i = p;-          base_pair2[b].j   = q;-          i = p, j = q;-          goto repeat1;-        }-      }-    }--    /* end of repeat: --------------------------------------------------*/--    /* (i.j) must close a multi-loop */-    tt = rtype[type];-    i1 = i+1; j1 = j-1;--    if(with_gquad){-      /*-        The case that is handled here actually resembles something like-        an interior loop where the enclosing base pair is of regular-        kind and the enclosed pair is not a canonical one but a g-quadruplex-        that should then be decomposed further...-      */-      if(backtrack_GQuad_IntLoop(cij - bonus, i, j, type, S, ggg, indx, &p, &q, P)){-        i = p; j = q;-        goto repeat_gquad;-      }-    }--    sector[s+1].ml  = sector[s+2].ml = 1;--    switch(dangle_model){-      case 0:   en = cij - E_MLstem(tt, -1, -1, P) - P->MLclosing - bonus;-                for(k = i+2+TURN; k < j-2-TURN; k++){-                  if(en == fML[indx[k]+i+1] + fML[indx[j-1]+k+1])-                    break;-                }-                break;--      case 2:   en = cij - E_MLstem(tt, S1[j-1], S1[i+1], P) - P->MLclosing - bonus;-                for(k = i+2+TURN; k < j-2-TURN; k++){-                    if(en == fML[indx[k]+i+1] + fML[indx[j-1]+k+1])-                      break;-                }-                break;--      default:  for(k = i+2+TURN; k < j-2-TURN; k++){-                  en = cij - P->MLclosing - bonus;-                  if(en == fML[indx[k]+i+1] + fML[indx[j-1]+k+1] + E_MLstem(tt, -1, -1, P)){-                    break;-                  }-                  else if(en == fML[indx[k]+i+2] + fML[indx[j-1]+k+1] + E_MLstem(tt, -1, S1[i+1], P) + P->MLbase){-                    i1 = i+2;-                    break;-                  }-                  else if(en == fML[indx[k]+i+1] + fML[indx[j-2]+k+1] + E_MLstem(tt, S1[j-1], -1, P) + P->MLbase){-                    j1 = j-2;-                    break;-                  }-                  else if(en == fML[indx[k]+i+2] + fML[indx[j-2]+k+1] + E_MLstem(tt, S1[j-1], S1[i+1], P) + 2*P->MLbase){-                    i1 = i+2;-                    j1 = j-2;-                    break;-                  }-                  /* coaxial stacking of (i.j) with (i+1.k) or (k.j-1) */-                  /* use MLintern[1] since coax stacked pairs don't get TerminalAU */-                  if(dangle_model == 3){-                    type_2 = rtype[ptype[indx[k]+i+1]];-                    if (type_2) {-                      en = c[indx[k]+i+1]+P->stack[type][type_2]+fML[indx[j-1]+k+1];-                      if (cij == en+2*P->MLintern[1]+P->MLclosing) {-                        ml = 2;-                        sector[s+1].ml  = 2;-                        traced = 1;-                        break;-                      }-                    }-                    type_2 = rtype[ptype[indx[j-1]+k+1]];-                    if (type_2) {-                      en = c[indx[j-1]+k+1]+P->stack[type][type_2]+fML[indx[k]+i+1];-                      if (cij == en+2*P->MLintern[1]+P->MLclosing) {-                        sector[s+2].ml = 2;-                        traced = 1;-                        break;-                      }-                    }-                  }-                }-                break;-    }--    if (k<=j-3-TURN) { /* found the decomposition */-      sector[++s].i = i1;-      sector[s].j   = k;-      sector[++s].i = k+1;-      sector[s].j   = j1;-    } else {-#if 0-      /* Y shaped ML loops fon't work yet */-      if (dangle_model==3) {-        d5 = P->dangle5[tt][S1[j-1]];-        d3 = P->dangle3[tt][S1[i+1]];-        /* (i,j) must close a Y shaped ML loop with coax stacking */-        if (cij ==  fML[indx[j-2]+i+2] + mm + d3 + d5 + P->MLbase + P->MLbase) {-          i1 = i+2;-          j1 = j-2;-        } else if (cij ==  fML[indx[j-2]+i+1] + mm + d5 + P->MLbase)-          j1 = j-2;-        else if (cij ==  fML[indx[j-1]+i+2] + mm + d3 + P->MLbase)-          i1 = i+2;-        else /* last chance */-          if (cij != fML[indx[j-1]+i+1] + mm + P->MLbase)-            fprintf(stderr,  "backtracking failed in repeat");-        /* if we arrive here we can express cij via fML[i1,j1]+dangles */-        sector[++s].i = i1;-        sector[s].j   = j1;-      }-      else-#endif-        nrerror("backtracking failed in repeat");-    }--    continue; /* this is a workarround to not accidentally proceed in the following block */--  repeat_gquad:-    /*-      now we do some fancy stuff to backtrace the stacksize and linker lengths-      of the g-quadruplex that should reside within position i,j-    */-    {-      int l[3], L, a;-      L = -1;-      -      get_gquad_pattern_mfe(S, i, j, P, &L, l);-      if(L != -1){-        /* fill the G's of the quadruplex into base_pair2 */-        for(a=0;a<L;a++){-          base_pair2[++b].i = i+a;-          base_pair2[b].j   = i+a;-          base_pair2[++b].i = i+L+l[0]+a;-          base_pair2[b].j   = i+L+l[0]+a;-          base_pair2[++b].i = i+L+l[0]+L+l[1]+a;-          base_pair2[b].j   = i+L+l[0]+L+l[1]+a;-          base_pair2[++b].i = i+L+l[0]+L+l[1]+L+l[2]+a;-          base_pair2[b].j   = i+L+l[0]+L+l[1]+L+l[2]+a;-        }-        goto repeat_gquad_exit;-      }-      nrerror("backtracking failed in repeat_gquad");-    }-  repeat_gquad_exit:-    asm("nop");--  } /* end of infinite while loop */--  base_pair2[0].i = b;    /* save the total number of base pairs */-}--PUBLIC char *backtrack_fold_from_pair(char *sequence, int i, int j) {-  char *structure;-  sector[1].i  = i;-  sector[1].j  = j;-  sector[1].ml = 2;-  base_pair2[0].i=0;-  S   = encode_sequence(sequence, 0);-  S1  = encode_sequence(sequence, 1);-  backtrack(sequence, 1);-  structure = (char *) space((strlen(sequence)+1)*sizeof(char));-  parenthesis_structure(structure, base_pair2, strlen(sequence));-  free(S);free(S1);-  return structure;-}--/*---------------------------------------------------------------------------*/--PUBLIC void letter_structure(char *structure, bondT *bp, int length){-  int   n, k, x, y;-  char  alpha[] = "ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz";--  for (n = 0; n < length; structure[n++] = ' ');-  structure[length] = '\0';--  for (n = 0, k = 1; k <= bp[0].i; k++) {-    y = bp[k].j;-    x = bp[k].i;-    if (x-1 > 0 && y+1 <= length) {-      if (structure[x-2] != ' ' && structure[y] == structure[x-2]) {-        structure[x-1] = structure[x-2];-        structure[y-1] = structure[x-1];-        continue;-      }-    }-    if (structure[x] != ' ' && structure[y-2] == structure[x]) {-      structure[x-1] = structure[x];-      structure[y-1] = structure[x-1];-      continue;-    }-    n++;-    structure[x-1] = alpha[n-1];-    structure[y-1] = alpha[n-1];-  }-}--/*---------------------------------------------------------------------------*/--PUBLIC void parenthesis_structure(char *structure, bondT *bp, int length){-  int n, k;--  for (n = 0; n < length; structure[n++] = '.');-  structure[length] = '\0';--  for (k = 1; k <= bp[0].i; k++){--    if(bp[k].i == bp[k].j){ /* Gquad bonds are marked as bp[i].i == bp[i].j */-      structure[bp[k].i-1] = '+';-    } else { /* the following ones are regular base pairs */-      structure[bp[k].i-1] = '(';-      structure[bp[k].j-1] = ')';-    }-  }-}--PUBLIC void parenthesis_zuker(char *structure, bondT *bp, int length){-  int k, i, j, temp;--  for (k = 0; k < length; structure[k++] = '.');-  structure[length] = '\0';--  for (k = 1; k <= bp[0].i; k++) {-    i=bp[k].i;-    j=bp[k].j;-    if (i>length) i-=length;-    if (j>length) j-=length;-    if (i>j) {-      temp=i; i=j; j=temp;-    }-    if(i == j){ /* Gquad bonds are marked as bp[i].i == bp[i].j */-      structure[i-1] = '+';-    } else { /* the following ones are regular base pairs */-      structure[i-1] = '(';-      structure[j-1] = ')';-    }-  }-}---/*---------------------------------------------------------------------------*/--PUBLIC void update_fold_params(void){-  update_fold_params_par(NULL);-}--PUBLIC void update_fold_params_par(paramT *parameters){-  if(P) free(P);-  if(parameters){-    P = get_parameter_copy(parameters);-  } else {-    model_detailsT md;-    set_model_details(&md);-    P = get_scaled_parameters(temperature, md);-  }-  make_pair_matrix();-  if (init_length < 0) init_length=0;-}--/*---------------------------------------------------------------------------*/-PUBLIC float energy_of_structure(const char *string, const char *structure, int verbosity_level){-  return energy_of_struct_par(string, structure, NULL, verbosity_level);-}--PUBLIC float energy_of_struct_par(const char *string,-                                  const char *structure,-                                  paramT *parameters,-                                  int verbosity_level){-  int   energy;-  short *ss, *ss1;--  update_fold_params_par(parameters);--  if (strlen(structure)!=strlen(string))-    nrerror("energy_of_struct: string and structure have unequal length");--  /* save the S and S1 pointers in case they were already in use */-  ss = S; ss1 = S1;-  S   = encode_sequence(string, 0);-  S1  = encode_sequence(string, 1);--  pair_table = make_pair_table(structure);--  energy = energy_of_structure_pt(string, pair_table, S, S1, verbosity_level);--  free(pair_table);-  free(S); free(S1);-  S=ss; S1=ss1;-  return  (float) energy/100.;-}--/*  returns a correction term that may be added to the energy retrieved-    from energy_of_struct_par() to correct misinterpreted loops. This-    correction is necessary since energy_of_struct_par() will forget -    about the existance of gquadruplexes and just treat them as unpaired-    regions.--    recursive variant-*/-PRIVATE int en_corr_of_loop_gquad(int i,-                                  int j,-                                  const char *string,-                                  const char *structure,-                                  short *pt,-                                  int *loop_idx,-                                  const short *s1){--  int pos, energy, p, q, r, s, u, type, type2;-  int L, l[3];--  energy = 0;-  q = i;-  while((pos = parse_gquad(structure + q-1, &L, l)) > 0){-    q += pos-1;-    p = q - 4*L - l[0] - l[1] - l[2] + 1;-    if(q > j) break;-    /* we've found the first g-quadruplex at position [p,q] */-    energy += E_gquad(L, l, P);-    /* check if it's enclosed in a base pair */-    if(loop_idx[p] == 0){ q++; continue; /* g-quad in exterior loop */}-    else{-      energy += E_MLstem(0, -1, -1, P); /*  do not forget to remove this energy if-                                            the gquad is the only one surrounded by-                                            the enclosing pair-                                        */--      /*  find its enclosing pair */-      int num_elem, num_g, elem_i, elem_j, up_mis;-      num_elem  = 0;-      num_g     = 1;-      r         = p - 1;-      up_mis    = q - p + 1;--      /* seek for first pairing base located 5' of the g-quad */-      for(r = p - 1; !pt[r] && (r >= i); r--);-      if(r < i) nrerror("this should not happen");--      if(r < pt[r]){ /* found the enclosing pair */-        s = pt[r];-      } else {-        num_elem++;-        elem_i = pt[r];-        elem_j = r;-        r = pt[r]-1 ;-        /* seek for next pairing base 5' of r */-        for(; !pt[r] && (r >= i); r--);-        if(r < i) nrerror("so nich");-        if(r < pt[r]){ /* found the enclosing pair */-          s = pt[r];-        } else {-          /* hop over stems and unpaired nucleotides */-          while((r > pt[r]) && (r >= i)){-            if(pt[r]){ r = pt[r]; num_elem++;}-            r--;-          }-          if(r < i) nrerror("so nich");-          s = pt[r]; /* found the enclosing pair */-        }-      }-      /* now we have the enclosing pair (r,s) */--      u = q+1;-      /* we know everything about the 5' part of this loop so check the 3' part */-      while(u<s){-        if(structure[u-1] == '.') u++;-        else if (structure[u-1] == '+'){ /* found another gquad */-          pos = parse_gquad(structure + u - 1, &L, l);-          if(pos > 0){-            energy += E_gquad(L, l, P) + E_MLstem(0, -1, -1, P);-            up_mis += pos;-            u += pos;-            num_g++;-          }-        } else { /* we must have found a stem */-          if(!(u < pt[u])) nrerror("wtf!");-          num_elem++; elem_i = u; elem_j = pt[u];-          energy += en_corr_of_loop_gquad(u, pt[u], string, structure, pt, loop_idx, s1);-          u = pt[u] + 1;-        }-      }-      if(u!=s) nrerror("what the hell");-      else{ /* we are done since we've found no other 3' structure element */-        switch(num_elem){-          /* g-quad was misinterpreted as hairpin closed by (r,s) */-          case 0:   /* if(num_g == 1)-                      if((p-r-1 == 0) || (s-q-1 == 0))-                        nrerror("too few unpaired bases");-                    */-                    type = pair[s1[r]][s1[s]];-                    if(dangles == 2)-                      energy += P->mismatchI[type][s1[r+1]][s1[s-1]];-                    if(type > 2)-                      energy += P->TerminalAU;-                    energy += P->internal_loop[s - r - 1 - up_mis];-                    energy -= E_MLstem(0, -1, -1, P);-                    energy -= E_Hairpin(s - r - 1,-                                        type,-                                        s1[r + 1],-                                        s1[s - 1],-                                        string + r - 1,-                                        P);-                    break;-          /* g-quad was misinterpreted as interior loop closed by (r,s) with enclosed pair (elem_i, elem_j) */-          case 1:   type = pair[s1[r]][s1[s]];-                    type2 = pair[s1[elem_i]][s1[elem_j]];-                    energy += P->MLclosing-                              + E_MLstem(rtype[type], s1[s-1], s1[r+1], P)-                              + (elem_i - r - 1 + s - elem_j - 1 - up_mis) * P->MLbase-                              + E_MLstem(type2, s1[elem_i-1], s1[elem_j+1], P);-                    energy -= E_IntLoop(elem_i - r - 1,-                                        s - elem_j - 1,-                                        type,-                                        rtype[type2],-                                        s1[r + 1],-                                        s1[s - 1],-                                        s1[elem_i - 1],-                                        s1[elem_j + 1],-                                        P);-                    break;-          /* gquad was misinterpreted as unpaired nucleotides in a multiloop */-          default:  energy -= (up_mis) * P->MLbase;-                    break;-        }-      }-      q = s+1;-    }-  }-  return energy;-}--PUBLIC float-energy_of_gquad_structure(const char *string,-                          const char *structure,-                          int verbosity_level){--  return energy_of_gquad_struct_par(string, structure, NULL, verbosity_level);-}--PUBLIC float-energy_of_gquad_struct_par( const char *string,-                            const char *structure,-                            paramT *parameters,-                            int verbosity_level){--  int   energy, gge, *loop_idx;-  short *ss, *ss1;--  update_fold_params_par(parameters);--  if (strlen(structure)!=strlen(string))-    nrerror("energy_of_struct: string and structure have unequal length");--  /* save the S and S1 pointers in case they were already in use */-  ss = S; ss1 = S1;-  S   = encode_sequence(string, 0);-  S1  = encode_sequence(string, 1);--  /* the pair_table looses every information about the gquad position-     thus we have to find add the energy contributions for each loop-     that contains a gquad by ourself, substract all miscalculated-     contributions, i.e. loops that actually contain a gquad, from-     energy_of_structure_pt()-  */-  pair_table  = make_pair_table(structure);-  energy      = energy_of_structure_pt(string, pair_table, S, S1, verbosity_level);--  loop_idx    = make_loop_index_pt(pair_table);-  gge         = en_corr_of_loop_gquad(1, S[0], string, structure, pair_table, loop_idx, S1);-  energy     += gge;--  free(pair_table);-  free(loop_idx);-  free(S); free(S1);-  S=ss; S1=ss1;-  return  (float) energy/100.;-}--PUBLIC int energy_of_structure_pt(const char *string,-                                  short *ptable,-                                  short *s,-                                  short *s1,-                                  int verbosity_level){-  return energy_of_struct_pt_par(string, ptable, s, s1, NULL, verbosity_level);-}--PUBLIC int energy_of_struct_pt_par( const char *string,-                                    short *ptable,-                                    short *s,-                                    short *s1,-                                    paramT *parameters,-                                    int verbosity_level){-  /* auxiliary function for kinfold,-     for most purposes call energy_of_struct instead */--  int   i, length, energy;-  short *ss, *ss1;--  update_fold_params_par(parameters);--  pair_table = ptable;-  ss  = S;-  ss1 = S1;-  S = s;-  S1 = s1;--  length = S[0];-/*   energy =  backtrack_type=='M' ? ML_Energy(0, 0) : ML_Energy(0, 1); */-    energy =  backtrack_type=='M' ? energy_of_ml_pt(0, ptable) : energy_of_extLoop_pt(0, ptable);-  if (verbosity_level>0)-    printf("External loop                           : %5d\n", energy);-  for (i=1; i<=length; i++) {-    if (pair_table[i]==0) continue;-    energy += stack_energy(i, string, verbosity_level);-    i=pair_table[i];-  }-  for (i=1; !SAME_STRAND(i,length); i++) {-    if (!SAME_STRAND(i,pair_table[i])) {-      energy+=P->DuplexInit;-      break;-    }-  }-  S   = ss;-  S1  = ss1;-  return energy;-}--PUBLIC float energy_of_circ_structure(const char *string,-                                      const char *structure,-                                      int verbosity_level){-  return energy_of_circ_struct_par(string, structure, NULL, verbosity_level);-}--PUBLIC float energy_of_circ_struct_par( const char *string,-                                        const char *structure,-                                        paramT *parameters,-                                        int verbosity_level){--  int   i, j, length, energy=0, en0, degree=0, type;-  short *ss, *ss1;--  update_fold_params_par(parameters);--  int dangle_model = P->model_details.dangles;--  if (strlen(structure)!=strlen(string))-    nrerror("energy_of_struct: string and structure have unequal length");--  /* save the S and S1 pointers in case they were already in use */-  ss = S; ss1 = S1;-  S   = encode_sequence(string, 0);-  S1  = encode_sequence(string, 1);--  pair_table = make_pair_table(structure);--  length = S[0];--  for (i=1; i<=length; i++) {-    if (pair_table[i]==0) continue;-    degree++;-    energy += stack_energy(i, string, verbosity_level);-    i=pair_table[i];-  }--  if (degree==0) return 0.;-  for (i=1; pair_table[i]==0; i++);-  j = pair_table[i];-  type=pair[S[j]][S[i]];-  if (type==0) type=7;-  if (degree==1) {-    char loopseq[10];-    int u, si1, sj1;-    for (i=1; pair_table[i]==0; i++);-    u = length-j + i-1;-    if (u<7) {-      strcpy(loopseq , string+j-1);-      strncat(loopseq, string, i);-    }-    si1 = (i==1)?S1[length] : S1[i-1];-    sj1 = (j==length)?S1[1] : S1[j+1];-    en0 = E_Hairpin(u, type, sj1, si1, loopseq, P);-  } else-    if (degree==2) {-      int p,q, u1,u2, si1, sq1, type_2;-      for (p=j+1; pair_table[p]==0; p++);-      q=pair_table[p];-      u1 = p-j-1;-      u2 = i-1 + length-q;-      type_2 = pair[S[q]][S[p]];-      if (type_2==0) type_2=7;-      si1 = (i==1)? S1[length] : S1[i-1];-      sq1 = (q==length)? S1[1] : S1[q+1];-      en0 = E_IntLoop(u1, u2, type, type_2,-                       S1[j+1], si1, S1[p-1], sq1,P);-    } else { /* degree > 2 */-      en0 = ML_Energy(0, 0) - P->MLintern[0];-      if (dangle_model) {-        int d5, d3;-        if (pair_table[1]) {-          j = pair_table[1];-          type = pair[S[1]][S[j]];-          if (dangle_model==2)-            en0 += P->dangle5[type][S1[length]];-          else { /* dangle_model==1 */-            if (pair_table[length]==0) {-              d5 = P->dangle5[type][S1[length]];-              if (pair_table[length-1]!=0) {-                int tt;-                tt = pair[S[pair_table[length-1]]][S[length-1]];-                d3 = P->dangle3[tt][S1[length]];-                if (d3<d5) d5 = 0;-                else d5 -= d3;-              }-              en0 += d5;-            }-          }-        }-        if (pair_table[length]) {-          i = pair_table[length];-          type = pair[S[i]][S[length]];-          if (dangle_model==2)-            en0 += P->dangle3[type][S1[1]];-          else { /* dangle_model==1 */-            if (pair_table[1]==0) {-              d3 = P->dangle3[type][S1[1]];-              if (pair_table[2]) {-                int tt;-                tt = pair[S[2]][S[pair_table[2]]];-                d5 = P->dangle5[tt][1];-                if (d5<d3) d3=0;-                else d3 -= d5;-              }-              en0 += d3;-            }-          }-        }-      }-    }--  if (verbosity_level>0)-    printf("External loop                           : %5d\n", en0);-  energy += en0;-  /* fprintf(stderr, "ext loop degree %d tot %d\n", degree, energy); */-  free(S); free(S1);-  S=ss; S1=ss1;-  return  (float) energy/100.0;-}--/*---------------------------------------------------------------------------*/-PRIVATE int stack_energy(int i, const char *string, int verbosity_level)-{-  /* calculate energy of substructure enclosed by (i,j) */-  int ee, energy = 0;-  int j, p, q, type;--  j=pair_table[i];-  type = pair[S[i]][S[j]];-  if (type==0) {-    type=7;-    if (verbosity_level>=0)-      fprintf(stderr,"WARNING: bases %d and %d (%c%c) can't pair!\n", i, j,-              string[i-1],string[j-1]);-  }--  p=i; q=j;-  while (p<q) { /* process all stacks and interior loops */-    int type_2;-    while (pair_table[++p]==0);-    while (pair_table[--q]==0);-    if ((pair_table[q]!=(short)p)||(p>q)) break;-    type_2 = pair[S[q]][S[p]];-    if (type_2==0) {-      type_2=7;-      if (verbosity_level>=0)-        fprintf(stderr,"WARNING: bases %d and %d (%c%c) can't pair!\n", p, q,-                string[p-1],string[q-1]);-    }-    /* energy += LoopEnergy(i, j, p, q, type, type_2); */-    if ( SAME_STRAND(i,p) && SAME_STRAND(q,j) )-      ee = E_IntLoop(p-i-1, j-q-1, type, type_2, S1[i+1], S1[j-1], S1[p-1], S1[q+1],P);-    else-      ee = energy_of_extLoop_pt(cut_in_loop(i), pair_table);-    if (verbosity_level>0)-      printf("Interior loop (%3d,%3d) %c%c; (%3d,%3d) %c%c: %5d\n",-             i,j,string[i-1],string[j-1],p,q,string[p-1],string[q-1], ee);-    energy += ee;-    i=p; j=q; type = rtype[type_2];-  } /* end while */--  /* p,q don't pair must have found hairpin or multiloop */--  if (p>q) {                       /* hair pin */-    if (SAME_STRAND(i,j))-      ee = E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], string+i-1, P);-    else-      ee = energy_of_extLoop_pt(cut_in_loop(i), pair_table);-    energy += ee;-    if (verbosity_level>0)-      printf("Hairpin  loop (%3d,%3d) %c%c              : %5d\n",-             i, j, string[i-1],string[j-1], ee);--    return energy;-  }--  /* (i,j) is exterior pair of multiloop */-  while (p<j) {-    /* add up the contributions of the substructures of the ML */-    energy += stack_energy(p, string, verbosity_level);-    p = pair_table[p];-    /* search for next base pair in multiloop */-    while (pair_table[++p]==0);-  }-  {-    int ii;-    ii = cut_in_loop(i);-    ee = (ii==0) ? energy_of_ml_pt(i, pair_table) : energy_of_extLoop_pt(ii, pair_table);-  }-  energy += ee;-  if (verbosity_level>0)-    printf("Multi    loop (%3d,%3d) %c%c              : %5d\n",-           i,j,string[i-1],string[j-1],ee);--  return energy;-}--/*---------------------------------------------------------------------------*/----/**-*** Calculate the energy contribution of-*** stabilizing dangling-ends/mismatches-*** for all stems branching off the exterior-*** loop-**/-PRIVATE int energy_of_extLoop_pt(int i, short *pair_table) {-  int energy, mm5, mm3;-  int p, q, q_prev;-  int length = (int)pair_table[0];--  /* helper variables for dangles == 1 case */-  int E3_available;  /* energy of 5' part where 5' mismatch is available for current stem */-  int E3_occupied;   /* energy of 5' part where 5' mismatch is unavailable for current stem */--  int dangle_model = P->model_details.dangles;--  /* initialize vars */-  energy      = 0;-  p           = (i==0) ? 1 : i;-  q_prev      = -1;--  if(dangle_model%2 == 1){-    E3_available = INF;-    E3_occupied  = 0;-  }--  /* seek to opening base of first stem */-  while(p <= length && !pair_table[p]) p++;--  while(p < length){-    int tt;-    /* p must have a pairing partner */-    q  = (int)pair_table[p];-    /* get type of base pair (p,q) */-    tt = pair[S[p]][S[q]];-    if(tt==0) tt=7;--    switch(dangle_model){-      /* no dangles */-      case 0:   energy += E_ExtLoop(tt, -1, -1, P);-                break;-      /* the beloved double dangles */-      case 2:   mm5 = ((SAME_STRAND(p-1,p)) && (p>1))       ? S1[p-1] : -1;-                mm3 = ((SAME_STRAND(q,q+1)) && (q<length))  ? S1[q+1] : -1;-                energy += E_ExtLoop(tt, mm5, mm3, P);-                break;--      default:  {-                  int tmp;-                  if(q_prev + 2 < p){-                    E3_available = MIN2(E3_available, E3_occupied);-                    E3_occupied  = E3_available;-                  }-                  mm5 = ((SAME_STRAND(p-1,p)) && (p>1) && !pair_table[p-1])       ? S1[p-1] : -1;-                  mm3 = ((SAME_STRAND(q,q+1)) && (q<length) && !pair_table[q+1])  ? S1[q+1] : -1;-                  tmp = MIN2(-                                                E3_occupied  + E_ExtLoop(tt, -1, mm3, P),-                                                E3_available + E_ExtLoop(tt, mm5, mm3, P)-                                              );-                  E3_available =       MIN2(-                                                E3_occupied  + E_ExtLoop(tt, -1, -1, P),-                                                E3_available + E_ExtLoop(tt, mm5, -1, P)-                                              );-                  E3_occupied = tmp;-                }-                break;--    } /* end switch dangle_model */-    /* seek to the next stem */-    p = q + 1;-    q_prev = q;-    while (p <= length && !pair_table[p]) p++;-    if(p==i) break; /* cut was in loop */-  }--  if(dangle_model%2 == 1)-    energy = MIN2(E3_occupied, E3_available);--  return energy;-}--/**-*** i is the 5'-base of the closing pair-***-*** since each helix can coaxially stack with at most one of its-*** neighbors we need an auxiliarry variable  cx_energy-*** which contains the best energy given that the last two pairs stack.-*** energy  holds the best energy given the previous two pairs do not-*** stack (i.e. the two current helices may stack)-*** We don't allow the last helix to stack with the first, thus we have to-*** walk around the Loop twice with two starting points and take the minimum-***/-PRIVATE int energy_of_ml_pt(int i, short *pt){--  int energy, cx_energy, tmp, tmp2, best_energy=INF;-  int i1, j, p, q, q_prev, q_prev2, u, x, type, count, mm5, mm3, tt, ld5, new_cx, dang5, dang3, dang;-  int mlintern[NBPAIRS+1];--  /* helper variables for dangles == 1|5 case */-  int E_mm5_available;  /* energy of 5' part where 5' mismatch of current stem is available */-  int E_mm5_occupied;   /* energy of 5' part where 5' mismatch of current stem is unavailable */-  int E2_mm5_available; /* energy of 5' part where 5' mismatch of current stem is available with possible 3' dangle for enclosing pair (i,j) */-  int E2_mm5_occupied;  /* energy of 5' part where 5' mismatch of current stem is unavailable with possible 3' dangle for enclosing pair (i,j) */-  int dangle_model = P->model_details.dangles;--  if(i >= pt[i])-    nrerror("energy_of_ml_pt: i is not 5' base of a closing pair!");--  j = (int)pt[i];--  /* init the variables */-  energy      = 0;-  p           = i+1;-  q_prev      = i-1;-  q_prev2     = i;--  for (x = 0; x <= NBPAIRS; x++) mlintern[x] = P->MLintern[x];--  /* seek to opening base of first stem */-  while(p <= j && !pair_table[p]) p++;-  u = p - i - 1;--  switch(dangle_model){-    case 0:   while(p < j){-                /* p must have a pairing partner */-                q  = (int)pair_table[p];-                /* get type of base pair (p,q) */-                tt = pair[S[p]][S[q]];-                if(tt==0) tt=7;-                energy += E_MLstem(tt, -1, -1, P);-                /* seek to the next stem */-                p = q + 1;-                q_prev = q_prev2 = q;-                while (p <= j && !pair_table[p]) p++;-                u += p - q - 1; /* add unpaired nucleotides */-              }-              /* now lets get the energy of the enclosing stem */-              type = pair[S[j]][S[i]]; if (type==0) type=7;-              energy += E_MLstem(type, -1, -1, P);-              break;--    case 2:   while(p < j){-                /* p must have a pairing partner */-                q  = (int)pair_table[p];-                /* get type of base pair (p,q) */-                tt = pair[S[p]][S[q]];-                if(tt==0) tt=7;-                mm5 = (SAME_STRAND(p-1,p))  ? S1[p-1] : -1;-                mm3 = (SAME_STRAND(q,q+1))  ? S1[q+1] : -1;-                energy += E_MLstem(tt, mm5, mm3, P);-                /* seek to the next stem */-                p = q + 1;-                q_prev = q_prev2 = q;-                while (p <= j && !pair_table[p]) p++;-                u += p - q - 1; /* add unpaired nucleotides */-              }-              type = pair[S[j]][S[i]]; if (type==0) type=7;-              mm5 = ((SAME_STRAND(j-1,j)) && !pair_table[j-1])  ? S1[j-1] : -1;-              mm3 = ((SAME_STRAND(i,i+1)) && !pair_table[i+1])  ? S1[i+1] : -1;-              energy += E_MLstem(type, S1[j-1], S1[i+1], P);-              break;--    case 3:   /* we treat helix stacking different */-              for (count=0; count<2; count++) { /* do it twice */-                ld5 = 0; /* 5' dangle energy on prev pair (type) */-                if ( i==0 ) {-                  j = (unsigned int)pair_table[0]+1;-                  type = 0;  /* no pair */-                }-                else {-                  j = (unsigned int)pair_table[i];-                  type = pair[S[j]][S[i]]; if (type==0) type=7;-                  /* prime the ld5 variable */-                  if (SAME_STRAND(j-1,j)) {-                    ld5 = P->dangle5[type][S1[j-1]];-                    if ((p=(unsigned int)pair_table[j-2]) && SAME_STRAND(j-2, j-1))-                    if (P->dangle3[pair[S[p]][S[j-2]]][S1[j-1]]<ld5) ld5 = 0;-                  }-                }-                i1=i; p = i+1; u=0;-                energy = 0; cx_energy=INF;-                do { /* walk around the multi-loop */-                  new_cx = INF;--                  /* hop over unpaired positions */-                  while (p <= (unsigned int)pair_table[0] && pair_table[p]==0) p++;--                  /* memorize number of unpaired positions */-                  u += p-i1-1;-                  /* get position of pairing partner */-                  if ( p == (unsigned int)pair_table[0]+1 ){-                    q = 0;tt = 0; /* virtual root pair */-                  } else {-                    q  = (unsigned int)pair_table[p];-                    /* get type of base pair P->q */-                    tt = pair[S[p]][S[q]]; if (tt==0) tt=7;-                  }--                  energy += mlintern[tt];-                  cx_energy += mlintern[tt];--                  dang5=dang3=0;-                  if ((SAME_STRAND(p-1,p))&&(p>1))-                    dang5=P->dangle5[tt][S1[p-1]];      /* 5'dangle of pq pair */-                  if ((SAME_STRAND(i1,i1+1))&&(i1<(unsigned int)S[0]))-                    dang3 = P->dangle3[type][S1[i1+1]]; /* 3'dangle of previous pair */--                  switch (p-i1-1) {-                    case 0:   /* adjacent helices */-                              if (i1!=0){-                                if (SAME_STRAND(i1,p)) {-                                  new_cx = energy + P->stack[rtype[type]][rtype[tt]];-                                  /* subtract 5'dangle and TerminalAU penalty */-                                  new_cx += -ld5 - mlintern[tt]-mlintern[type]+2*mlintern[1];-                                }-                                ld5=0;-                                energy = MIN2(energy, cx_energy);-                              }-                              break;-                    case 1:   /* 1 unpaired base between helices */-                              dang = MIN2(dang3, dang5);-                              energy = energy +dang; ld5 = dang - dang3;-                              /* may be problem here: Suppose-                                cx_energy>energy, cx_energy+dang5<energy-                                and the following helices are also stacked (i.e.-                                we'll subtract the dang5 again */-                              if (cx_energy+dang5 < energy) {-                                energy = cx_energy+dang5;-                                ld5 = dang5;-                              }-                              new_cx = INF;  /* no coax stacking with mismatch for now */-                              break;-                    default:  /* many unpaired base between helices */-                              energy += dang5 +dang3;-                              energy = MIN2(energy, cx_energy + dang5);-                              new_cx = INF;  /* no coax stacking possible */-                              ld5 = dang5;-                              break;-                  }-                  type = tt;-                  cx_energy = new_cx;-                  i1 = q; p=q+1;-                } while (q!=i);-                best_energy = MIN2(energy, best_energy); /* don't use cx_energy here */-                /* fprintf(stderr, "%6.2d\t", energy); */-                /* skip a helix and start again */-                while (pair_table[p]==0) p++;-                if (i == (unsigned int)pair_table[p]) break;-                i = (unsigned int)pair_table[p];-              } /* end doing it twice */-              energy = best_energy;-              break;--    default:  E_mm5_available = E2_mm5_available  = INF;-              E_mm5_occupied  = E2_mm5_occupied   = 0;-              while(p < j){-                /* p must have a pairing partner */-                q  = (int)pair_table[p];-                /* get type of base pair (p,q) */-                tt = pair[S[p]][S[q]];-                if(tt==0) tt=7;-                if(q_prev + 2 < p){-                  E_mm5_available = MIN2(E_mm5_available, E_mm5_occupied);-                  E_mm5_occupied  = E_mm5_available;-                }-                if(q_prev2 + 2 < p){-                  E2_mm5_available  = MIN2(E2_mm5_available, E2_mm5_occupied);-                  E2_mm5_occupied   = E2_mm5_available;-                }-                mm5 = ((SAME_STRAND(p-1,p)) && !pair_table[p-1])  ? S1[p-1] : -1;-                mm3 = ((SAME_STRAND(q,q+1)) && !pair_table[q+1])  ? S1[q+1] : -1;-                tmp =                   MIN2(-                                              E_mm5_occupied  + E_MLstem(tt, -1, mm3, P),-                                              E_mm5_available + E_MLstem(tt, mm5, mm3, P)-                                            );-                tmp   =                 MIN2(tmp, E_mm5_available + E_MLstem(tt, -1, mm3, P));-                tmp2  =                 MIN2(-                                              E_mm5_occupied  + E_MLstem(tt, -1, -1, P),-                                              E_mm5_available + E_MLstem(tt, mm5, -1, P)-                                            );-                E_mm5_available =       MIN2(tmp2, E_mm5_available  + E_MLstem(tt, -1, -1, P));-                E_mm5_occupied  = tmp;--                tmp =                  MIN2(-                                              E2_mm5_occupied  + E_MLstem(tt, -1, mm3, P),-                                              E2_mm5_available + E_MLstem(tt, mm5, mm3, P)-                                            );-                tmp =                   MIN2(tmp, E2_mm5_available + E_MLstem(tt, -1, mm3, P));-                tmp2 =                  MIN2(-                                              E2_mm5_occupied  + E_MLstem(tt, -1, -1, P),-                                              E2_mm5_available + E_MLstem(tt, mm5, -1, P)-                                            );-                E2_mm5_available =      MIN2(tmp2, E2_mm5_available + E_MLstem(tt, -1, -1, P));-                E2_mm5_occupied = tmp;-                /* printf("(%d,%d): \n E_o = %d, E_a = %d, E2_o = %d, E2_a = %d\n", p, q, E_mm5_occupied,E_mm5_available,E2_mm5_occupied,E2_mm5_available); */-                /* seek to the next stem */-                p = q + 1;-                q_prev = q_prev2 = q;-                while (p <= j && !pair_table[p]) p++;-                u += p - q - 1; /* add unpaired nucleotides */-              }-              /* now lets see how we get the minimum including the enclosing stem */-              type = pair[S[j]][S[i]]; if (type==0) type=7;-              mm5 = ((SAME_STRAND(j-1,j)) && !pair_table[j-1])  ? S1[j-1] : -1;-              mm3 = ((SAME_STRAND(i,i+1)) && !pair_table[i+1])  ? S1[i+1] : -1;-              if(q_prev + 2 < p){-                E_mm5_available = MIN2(E_mm5_available, E_mm5_occupied);-                E_mm5_occupied  = E_mm5_available;-              }-              if(q_prev2 + 2 < p){-                E2_mm5_available  = MIN2(E2_mm5_available, E2_mm5_occupied);-                E2_mm5_occupied   = E2_mm5_available;-              }-              energy = MIN2(E_mm5_occupied  + E_MLstem(type, -1, -1, P),-                            E_mm5_available + E_MLstem(type, mm5, -1, P)-                          );-              energy = MIN2(energy, E_mm5_available   + E_MLstem(type, -1, -1, P));-              energy = MIN2(energy, E2_mm5_occupied   + E_MLstem(type, -1, mm3, P));-              energy = MIN2(energy, E2_mm5_occupied   + E_MLstem(type, -1, -1, P));-              energy = MIN2(energy, E2_mm5_available  + E_MLstem(type, mm5, mm3, P));-              energy = MIN2(energy, E2_mm5_available  + E_MLstem(type, -1, mm3, P));-              energy = MIN2(energy, E2_mm5_available  + E_MLstem(type, mm5, -1, P));-              energy = MIN2(energy, E2_mm5_available  + E_MLstem(type, -1, -1, P));-              break;-  }/* end switch dangle_model */--  energy += P->MLclosing;-  /* logarithmic ML loop energy if logML */-  if(logML && (u>6))-    energy += 6*P->MLbase+(int)(P->lxc*log((double)u/6.));-  else-    energy += (u*P->MLbase);--  return energy;-}--/*---------------------------------------------------------------------------*/--PUBLIC int loop_energy(short * ptable, short *s, short *s1, int i) {-  /* compute energy of a single loop closed by base pair (i,j) */-  int j, type, p,q, energy;-  short *Sold, *S1old, *ptold;--  ptold=pair_table;   Sold = S;   S1old = S1;-  pair_table = ptable;   S = s;   S1 = s1;--  if (i==0) { /* evaluate exterior loop */-    energy = energy_of_extLoop_pt(0,pair_table);-    pair_table=ptold; S=Sold; S1=S1old;-    return energy;-  }-  j = pair_table[i];-  if (j<i) nrerror("i is unpaired in loop_energy()");-  type = pair[S[i]][S[j]];-  if (type==0) {-    type=7;-    if (eos_debug>=0)-      fprintf(stderr,"WARNING: bases %d and %d (%c%c) can't pair!\n", i, j,-              Law_and_Order[S[i]],Law_and_Order[S[j]]);-  }-  p=i; q=j;---  while (pair_table[++p]==0);-  while (pair_table[--q]==0);-  if (p>q) { /* Hairpin */-    char loopseq[8] = "";-    if (SAME_STRAND(i,j)) {-      if (j-i-1<7) {-        int u;-        for (u=0; i+u<=j; u++) loopseq[u] = Law_and_Order[S[i+u]];-        loopseq[u] = '\0';-      }-      energy = E_Hairpin(j-i-1, type, S1[i+1], S1[j-1], loopseq, P);-    } else {-      energy = energy_of_extLoop_pt(cut_in_loop(i), pair_table);-    }-  }-  else if (pair_table[q]!=(short)p) { /* multi-loop */-    int ii;-    ii = cut_in_loop(i);-    energy = (ii==0) ? energy_of_ml_pt(i, pair_table) : energy_of_extLoop_pt(ii, pair_table);-  }-  else { /* found interior loop */-    int type_2;-    type_2 = pair[S[q]][S[p]];-    if (type_2==0) {-      type_2=7;-      if (eos_debug>=0)-        fprintf(stderr,"WARNING: bases %d and %d (%c%c) can't pair!\n", p, q,-                Law_and_Order[S[p]],Law_and_Order[S[q]]);-    }-    /* energy += LoopEnergy(i, j, p, q, type, type_2); */-    if ( SAME_STRAND(i,p) && SAME_STRAND(q,j) )-      energy = E_IntLoop(p-i-1, j-q-1, type, type_2,-                          S1[i+1], S1[j-1], S1[p-1], S1[q+1], P);-    else-      energy = energy_of_extLoop_pt(cut_in_loop(i), pair_table);-  }--  pair_table=ptold; S=Sold; S1=S1old;-  return energy;-}--/*---------------------------------------------------------------------------*/---PUBLIC float energy_of_move(const char *string, const char *structure, int m1, int m2) {-  int   energy;-  short *ss, *ss1;--#ifdef _OPENMP-  if(P == NULL) update_fold_params();-#else-  if((init_length<0)||(P==NULL)) update_fold_params();-#endif--  if (fabs(P->temperature - temperature)>1e-6) update_fold_params();--  if (strlen(structure)!=strlen(string))-    nrerror("energy_of_struct: string and structure have unequal length");--  /* save the S and S1 pointers in case they were already in use */-  ss = S; ss1 = S1;-  S   = encode_sequence(string, 0);-  S1  = encode_sequence(string, 1);--  pair_table = make_pair_table(structure);--  energy = energy_of_move_pt(pair_table, S, S1, m1, m2);--  free(pair_table);-  free(S); free(S1);-  S=ss; S1=ss1;-  return  (float) energy/100.;-}--/*---------------------------------------------------------------------------*/--PUBLIC int energy_of_move_pt(short *pt, short *s, short *s1, int m1, int m2) {-  /*compute change in energy given by move (m1,m2)*/-  int en_post, en_pre, i,j,k,l, len;--  len = pt[0];-  k = (m1>0)?m1:-m1;-  l = (m2>0)?m2:-m2;-  /* first find the enclosing pair i<k<l<j */-  for (j=l+1; j<=len; j++) {-    if (pt[j]<=0) continue; /* unpaired */-    if (pt[j]<k) break;   /* found it */-    if (pt[j]>j) j=pt[j]; /* skip substructure */-    else {-      fprintf(stderr, "%d %d %d %d ", m1, m2, j, pt[j]);-      nrerror("illegal move or broken pair table in energy_of_move()");-    }-  }-  i = (j<=len) ? pt[j] : 0;-  en_pre = loop_energy(pt, s, s1, i);-  en_post = 0;-  if (m1<0) { /*it's a delete move */-    en_pre += loop_energy(pt, s, s1, k);-    pt[k]=0;-    pt[l]=0;-  } else { /* insert move */-    pt[k]=l;-    pt[l]=k;-    en_post += loop_energy(pt, s, s1, k);-  }-  en_post += loop_energy(pt, s, s1, i);-  /*  restore pair table */-  if (m1<0) {-    pt[k]=l;-    pt[l]=k;-  } else {-    pt[k]=0;-    pt[l]=0;-  }-  return (en_post - en_pre);-}----PRIVATE int cut_in_loop(int i) {-  /* walk around the loop;  return j pos of pair after cut if-     cut_point in loop else 0 */-  int  p, j;-  p = j = pair_table[i];-  do {-    i  = pair_table[p];  p = i+1;-    while ( pair_table[p]==0 ) p++;-  } while (p!=j && SAME_STRAND(i,p));-  return SAME_STRAND(i,p) ? 0 : j;-}--/*---------------------------------------------------------------------------*/--PRIVATE void make_ptypes(const short *S, const char *structure) {-  int n,i,j,k,l;--  n=S[0];-  for (k=1; k<n-TURN; k++)-    for (l=1; l<=2; l++) {-      int type,ntype=0,otype=0;-      i=k; j = i+TURN+l; if (j>n) continue;-      type = pair[S[i]][S[j]];-      while ((i>=1)&&(j<=n)) {-        if ((i>1)&&(j<n)) ntype = pair[S[i-1]][S[j+1]];-        if (noLonelyPairs && (!otype) && (!ntype))-          type = 0; /* i.j can only form isolated pairs */-        ptype[indx[j]+i] = (char) type;-        otype =  type;-        type  = ntype;-        i--; j++;-      }-    }--  if (struct_constrained && (structure != NULL))-    constrain_ptypes(structure, (unsigned int)n, ptype, BP, TURN, 0);-}--PUBLIC void assign_plist_from_db(plist **pl, const char *struc, float pr){-  /* convert bracket string to plist */-  short *pt;-  int i, k = 0, size, n;-  plist *gpl, *ptr;--  size  = strlen(struc);-  n     = 2;--  pt  = make_pair_table(struc);-  *pl = (plist *)space(n*size*sizeof(plist));-  for(i = 1; i < size; i++){-    if(pt[i]>i){-      (*pl)[k].i      = i;-      (*pl)[k].j      = pt[i];-      (*pl)[k].p      = pr;-      (*pl)[k++].type = 0;-    }-  }--  gpl = get_plist_gquad_from_db(struc, pr);-  for(ptr = gpl; ptr->i != 0; ptr++){-    if (k == n * size - 1){-      n *= 2;-      *pl = (plist *)xrealloc(*pl, n * size * sizeof(plist));-    }-    (*pl)[k].i      = ptr->i;-    (*pl)[k].j      = ptr->j;-    (*pl)[k].p       = ptr->p;-    (*pl)[k++].type = ptr->type;-  }-  free(gpl);--  (*pl)[k].i      = 0;-  (*pl)[k].j      = 0;-  (*pl)[k].p      = 0.;-  (*pl)[k++].type = 0.;-  free(pt);-  *pl = (plist *)xrealloc(*pl, k * sizeof(plist));-}---/*###########################################*/-/*# deprecated functions below              #*/-/*###########################################*/--PUBLIC int HairpinE(int size, int type, int si1, int sj1, const char *string) {-  int energy;--  energy = (size <= 30) ? P->hairpin[size] :-    P->hairpin[30]+(int)(P->lxc*log((size)/30.));--  if (tetra_loop){-    if (size == 4) { /* check for tetraloop bonus */-      char tl[7]={0}, *ts;-      strncpy(tl, string, 6);-      if ((ts=strstr(P->Tetraloops, tl)))-        return (P->Tetraloop_E[(ts - P->Tetraloops)/7]);-    }-    if (size == 6) {-      char tl[9]={0}, *ts;-      strncpy(tl, string, 8);-      if ((ts=strstr(P->Hexaloops, tl)))-        return (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);-    }-    if (size == 3) {-      char tl[6]={0,0,0,0,0,0}, *ts;-      strncpy(tl, string, 5);-      if ((ts=strstr(P->Triloops, tl))) {-        return (P->Triloop_E[(ts - P->Triloops)/6]);-      }-      if (type>2)  /* neither CG nor GC */-        energy += P->TerminalAU; /* penalty for closing AU GU pair IVOO??-                                    sind dass jetzt beaunuesse oder mahlnuesse (vorzeichen?)*/-      return energy;-    }-   }-   energy += P->mismatchH[type][si1][sj1];--  return energy;-}--/*---------------------------------------------------------------------------*/--PUBLIC int oldLoopEnergy(int i, int j, int p, int q, int type, int type_2) {-  /* compute energy of degree 2 loop (stack bulge or interior) */-  int n1, n2, m, energy;-  n1 = p-i-1;-  n2 = j-q-1;--  if (n1>n2) { m=n1; n1=n2; n2=m; } /* so that n2>=n1 */--  if (n2 == 0)-    energy = P->stack[type][type_2];   /* stack */--  else if (n1==0) {                  /* bulge */-    energy = (n2<=MAXLOOP)?P->bulge[n2]:-      (P->bulge[30]+(int)(P->lxc*log(n2/30.)));--#if STACK_BULGE1-    if (n2==1) energy+=P->stack[type][type_2];-#endif-  } else {                           /* interior loop */--    if ((n1+n2==2)&&(james_rule))-      /* special case for loop size 2 */-      energy = P->int11[type][type_2][S1[i+1]][S1[j-1]];-    else {-      energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]):-        (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));--#if NEW_NINIO-      energy += MIN2(MAX_NINIO, (n2-n1)*P->ninio[2]);-#else-      m       = MIN2(4, n1);-      energy += MIN2(MAX_NINIO,((n2-n1)*P->ninio[m]));-#endif-      energy += P->mismatchI[type][S1[i+1]][S1[j-1]]+-        P->mismatchI[type_2][S1[q+1]][S1[p-1]];-    }-  }-  return energy;-}--/*--------------------------------------------------------------------------*/--PUBLIC int LoopEnergy(int n1, int n2, int type, int type_2,-                      int si1, int sj1, int sp1, int sq1) {-  /* compute energy of degree 2 loop (stack bulge or interior) */-  int nl, ns, energy;--  if (n1>n2) { nl=n1; ns=n2;}-  else {nl=n2; ns=n1;}--  if (nl == 0)-    return P->stack[type][type_2];    /* stack */--  if (ns==0) {                       /* bulge */-    energy = (nl<=MAXLOOP)?P->bulge[nl]:-      (P->bulge[30]+(int)(P->lxc*log(nl/30.)));-    if (nl==1) energy += P->stack[type][type_2];-    else {-      if (type>2) energy += P->TerminalAU;-      if (type_2>2) energy += P->TerminalAU;-    }-    return energy;-  }-  else {                             /* interior loop */-    if (ns==1) {-      if (nl==1)                     /* 1x1 loop */-        return P->int11[type][type_2][si1][sj1];-      if (nl==2) {                   /* 2x1 loop */-        if (n1==1)-          energy = P->int21[type][type_2][si1][sq1][sj1];-        else-          energy = P->int21[type_2][type][sq1][si1][sp1];-        return energy;-      }-        else {  /* 1xn loop */-        energy = (nl+1<=MAXLOOP)?(P->internal_loop[nl+1]):-        (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));-        energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);-        energy += P->mismatch1nI[type][si1][sj1]+-        P->mismatch1nI[type_2][sq1][sp1];-        return energy;-        }-    }-    else if (ns==2) {-      if(nl==2)      {   /* 2x2 loop */-        return P->int22[type][type_2][si1][sp1][sq1][sj1];}-      else if (nl==3)  { /* 2x3 loop */-        energy = P->internal_loop[5]+P->ninio[2];-        energy += P->mismatch23I[type][si1][sj1]+-          P->mismatch23I[type_2][sq1][sp1];-        return energy;-      }--    }-    { /* generic interior loop (no else here!)*/-      energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]):-        (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));--      energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);--      energy += P->mismatchI[type][si1][sj1]+-        P->mismatchI[type_2][sq1][sp1];-    }-  }-  return energy;-}--PRIVATE int ML_Energy(int i, int is_extloop) {-  /* i is the 5'-base of the closing pair (or 0 for exterior loop)-     loop is scored as ML if extloop==0 else as exterior loop--     since each helix can coaxially stack with at most one of its-     neighbors we need an auxiliarry variable  cx_energy-     which contains the best energy given that the last two pairs stack.-     energy  holds the best energy given the previous two pairs do not-     stack (i.e. the two current helices may stack)-     We don't allow the last helix to stack with the first, thus we have to-     walk around the Loop twice with two starting points and take the minimum-  */--  int energy, cx_energy, best_energy=INF;-  int i1, j, p, q, u, x, type, count;-  int mlintern[NBPAIRS+1], mlclosing, mlbase;-  int dangle_model = P->model_details.dangles;--  if (is_extloop) {-    for (x = 0; x <= NBPAIRS; x++)-      mlintern[x] = P->MLintern[x]-P->MLintern[1]; /* 0 or TerminalAU */-    mlclosing = mlbase = 0;-  } else {-    for (x = 0; x <= NBPAIRS; x++) mlintern[x] = P->MLintern[x];-    mlclosing = P->MLclosing; mlbase = P->MLbase;-  }--  /*  as we do not only have dangling end but also mismatch contributions,-  **  we do this a bit different to previous implementations-  */-  if(is_extloop){-    energy = 0;-    i1  = i;-    p   = i+1;--    int E_mm5_available, E_mm5_occupied;-    /* find out if we may have 5' mismatch for the next stem */-    while (p <= (int)pair_table[0] && pair_table[p]==0) p++;-    /* get position of pairing partner */-    if(p < (int)pair_table[0]){-        E_mm5_occupied  = (p - i - 1 > 0) ? INF : 0;-        E_mm5_available = (p - i - 1 > 0) ? 0 : INF;-    }--    if(p < (int)pair_table[0])-      do{-        int tt;-        /* p must have a pairing partner */-        q  = (int)pair_table[p];-        /* get type of base pair (p,q) */-        tt = pair[S[p]][S[q]];-        if(tt==0) tt=7;--        int mm5 = ((SAME_STRAND(p-1,p)) && (p>1)) ? S1[p-1]: -1;-        int mm3 = ((SAME_STRAND(q,q+1)) && (q<(unsigned int)pair_table[0])) ? S1[q+1]: -1;--        switch(dangle_model){-          /* dangle_model == 0 */-          case 0: energy += E_ExtLoop(tt, -1, -1, P);-                  break;-          /* dangle_model == 1 */-          case 1: {-                    /* check for unpaired nucleotide 3' to the current stem */-                    int u3 = ((q < pair_table[0]) && (pair_table[q+1] == 0)) ? 1 : 0;-                    if(pair_table[p-1] != 0) mm5 = -1;--                    if(!u3){-                      mm3 = -1;-                      E_mm5_occupied  = MIN2(-                                              E_mm5_occupied  + E_ExtLoop(tt, -1, -1, P),-                                              E_mm5_available + E_ExtLoop(tt, mm5, -1, P)-                                            );-                      E_mm5_available = E_mm5_occupied;-                    }-                    else{-                      E_mm5_occupied  = MIN2(-                                              E_mm5_occupied  + E_ExtLoop(tt, -1, mm3, P),-                                              E_mm5_available + E_ExtLoop(tt, mm5, mm3, P)-                                            );-                      E_mm5_available = MIN2(-                                              E_mm5_occupied  + E_ExtLoop(tt, -1, -1, P),-                                              E_mm5_available + E_ExtLoop(tt, mm5, -1, P)-                                            );-                    }-                  }-                  break;--          /* the beloved case dangle_model == 2 */-          case 2: energy += E_ExtLoop(tt, mm5, mm3, P);-                  break;--          /* dangle_model == 3 a.k.a. helix stacking */-          case 3: break;--        } /* end switch dangle_model */--        /* seek to the next stem */-        p = q + 1;-        while (p <= (int)pair_table[0] && pair_table[p]==0) p++;-        if(p == (int)pair_table[0] + 1){-          if(dangle_model == 1)-            energy = (p > q + 1) ? E_mm5_occupied : E_mm5_available;-          q = 0;-          break;-        }-      } while(q != i);-  }-  /* not exterior loop */-  else{-    for (count=0; count<2; count++) { /* do it twice */-      int ld5 = 0; /* 5' dangle energy on prev pair (type) */-      if ( i==0 ) {-        j = (unsigned int)pair_table[0]+1;-        type = 0;  /* no pair */-      }-      else {-        j = (unsigned int)pair_table[i];-        type = pair[S[j]][S[i]]; if (type==0) type=7;--        if (dangle_model==3) { /* prime the ld5 variable */-          if (SAME_STRAND(j-1,j)) {-            ld5 = P->dangle5[type][S1[j-1]];-            if ((p=(unsigned int)pair_table[j-2]) && SAME_STRAND(j-2, j-1))-                if (P->dangle3[pair[S[p]][S[j-2]]][S1[j-1]]<ld5) ld5 = 0;-          }-        }-      }-      i1=i; p = i+1; u=0;-      energy = 0; cx_energy=INF;-      do { /* walk around the multi-loop */-        int tt, new_cx = INF;--        /* hop over unpaired positions */-        while (p <= (unsigned int)pair_table[0] && pair_table[p]==0) p++;--        /* memorize number of unpaired positions */-        u += p-i1-1;-        /* get position of pairing partner */-        if ( p == (unsigned int)pair_table[0]+1 ){-          q = 0;tt = 0; /* virtual root pair */-        } else {-        q  = (unsigned int)pair_table[p];-          /* get type of base pair P->q */-        tt = pair[S[p]][S[q]]; if (tt==0) tt=7;-        }--        energy += mlintern[tt];-        cx_energy += mlintern[tt];--        if (dangle_model) {-          int dang5=0, dang3=0, dang;-          if ((SAME_STRAND(p-1,p))&&(p>1))-            dang5=P->dangle5[tt][S1[p-1]];      /* 5'dangle of pq pair */-          if ((SAME_STRAND(i1,i1+1))&&(i1<(unsigned int)S[0]))-            dang3 = P->dangle3[type][S1[i1+1]]; /* 3'dangle of previous pair */--          switch (p-i1-1) {-          case 0: /* adjacent helices */-            if (dangle_model==2)-              energy += dang3+dang5;-            else if (dangle_model==3 && i1!=0) {-              if (SAME_STRAND(i1,p)) {-                new_cx = energy + P->stack[rtype[type]][rtype[tt]];-                /* subtract 5'dangle and TerminalAU penalty */-                new_cx += -ld5 - mlintern[tt]-mlintern[type]+2*mlintern[1];-              }-              ld5=0;-              energy = MIN2(energy, cx_energy);-            }-            break;-          case 1: /* 1 unpaired base between helices */-            dang = (dangle_model==2)?(dang3+dang5):MIN2(dang3, dang5);-            if (dangle_model==3) {-              energy = energy +dang; ld5 = dang - dang3;-              /* may be problem here: Suppose-                 cx_energy>energy, cx_energy+dang5<energy-                 and the following helices are also stacked (i.e.-                 we'll subtract the dang5 again */-              if (cx_energy+dang5 < energy) {-                energy = cx_energy+dang5;-                ld5 = dang5;-              }-              new_cx = INF;  /* no coax stacking with mismatch for now */-            } else-              energy += dang;-            break;-          default: /* many unpaired base between helices */-            energy += dang5 +dang3;-            if (dangle_model==3) {-              energy = MIN2(energy, cx_energy + dang5);-              new_cx = INF;  /* no coax stacking possible */-              ld5 = dang5;-            }-          }-          type = tt;-        }-        if (dangle_model==3) cx_energy = new_cx;-        i1 = q; p=q+1;-      } while (q!=i);-      best_energy = MIN2(energy, best_energy); /* don't use cx_energy here */-      /* fprintf(stderr, "%6.2d\t", energy); */-      if (dangle_model!=3 || is_extloop) break;  /* may break cofold with co-ax */-      /* skip a helix and start again */-      while (pair_table[p]==0) p++;-      if (i == (unsigned int)pair_table[p]) break;-      i = (unsigned int)pair_table[p];-    }-    energy = best_energy;-    energy += mlclosing;-    /* logarithmic ML loop energy if logML */-    if ( (!is_extloop) && logML && (u>6) )-      energy += 6*mlbase+(int)(P->lxc*log((double)u/6.));-    else-      energy += mlbase*u;-    /* fprintf(stderr, "\n"); */-  }-  return energy;-}--PUBLIC void initialize_fold(int length){-  /* DO NOTHING */-}--PUBLIC float energy_of_struct(const char *string, const char *structure){-  return energy_of_structure(string, structure, eos_debug);-}--PUBLIC int energy_of_struct_pt(const char *string, short * ptable, short *s, short *s1){-  return energy_of_structure_pt(string, ptable, s, s1, eos_debug);-}--PUBLIC float energy_of_circ_struct(const char *string, const char *structure){-  return energy_of_circ_structure(string, structure, eos_debug);-}-
− cbits/fold_vars.c 
@@ -1,88 +0,0 @@-/* Last changed Time-stamp: <2008-06-27 17:21:42 ivo> */--/**-*** \file fold_vars.c-*** global variables to change behaviour of folding routines<BR>-*** Also there are some functions that make the live easier when-*** using functions of the Vienna RNA package-**/-#include <string.h>-#include <stdio.h>-#include "fold_vars.h"--int         circ = 0;--int         noGU = 0;             /* GU not allowed at all */--int         no_closingGU = 0;     /* GU allowed only inside stacks */--int         tetra_loop = 1;       /* Fold with specially stable 4-loops */--int         energy_set = 0;       /* 0 = BP; 1=any with GC; 2=any with AU parameters */--int         dangles = 2;          /* use dangling end energies */--char        *nonstandards = (char *)0;  /* contains allowed non standard bases */--double      temperature = 37.0;--int         james_rule = 1;       /* interior loops of size 2 get energy 0.8Kcal and-                                    no mismatches (no longer used) */--int         oldAliEn = 0;         /* use old alifold-energies (without removing gaps) */--int         ribo = 0;             /* use ribosum instead of classic covariance term */--char        *RibosumFile = NULL;  /* TODO: compile ribosums into program-                                    Warning: this variable will vanish */--int         csv = 0;              /*generate comma seperated output*/--bondT       *base_pair = NULL;--FLT_OR_DBL  *pr = NULL;           /* base pairing prob. matrix */--int         *iindx = NULL;        /* pr[i,j] -> pr[iindx[i]-j] */--double      pf_scale = -1;        /* scaling factor to avoid floating point overflows */--int         fold_constrained = 0; /* fold with constraints */--int         do_backtrack = 1;     /* calculate pair prob matrix in part_func() */--int         noLonelyPairs = 0;    /* avoid helices of length 1 */--char        backtrack_type = 'F'; /* 'C' require (1,N) to be bonded;-                                    'M' seq is part of s multi loop */--int         *cut_points;--int         *strand;--int         gquad = 0;            /* consider g-qudruplexes in the calculations */--PUBLIC char * option_string(void){-  static char options[100];-  *options = '\0';-  if (noGU) strcat(options, "-noGU ");-  if (no_closingGU) strcat(options, "-noCloseGU ");-  if (!tetra_loop) strcat(options, "-4 ");-  if (noLonelyPairs) strcat(options, "-noLP ");-  if (fold_constrained) strcat(options, "-C ");-  if (dangles!=1) sprintf(options+strlen(options), "-d%d ", dangles);-  if (temperature!=37.0)-    sprintf(options+strlen(options), "-T %f ", temperature);-  return options;-}--PUBLIC void set_model_details(model_detailsT *md){-  if(md){-    md->dangles     = dangles;-    md->special_hp  = tetra_loop;-    md->noLP        = noLonelyPairs;-    md->noGU        = noGU;-    md->noGUclosure = no_closingGU;-    md->logML       = logML;-    md->gquad       = gquad;-  }-}
− cbits/gquad.c 
@@ -1,1043 +0,0 @@-/*-  gquad.c--  Ronny Lorenz 2012--  Vienna RNA package-*/--#include <stdio.h>-#include <stdlib.h>-#include <math.h>-#include <string.h>--#include "config.h" // chzs-#include "fold_vars.h"-#include "data_structures.h"-#include "energy_const.h"-#include "utils.h"-#include "aln_util.h"-#include "gquad.h"--#ifndef INLINE-#ifdef __GNUC__-# define INLINE inline-#else-# define INLINE-#endif-#endif--/**- *  Use this macro to loop over each G-quadruplex- *  delimited by a and b within the subsequence [c,d]- */-#define FOR_EACH_GQUAD(a, b, c, d)  \-          for((a) = (d) - VRNA_GQUAD_MIN_BOX_SIZE + 1; (a) >= (c); (a)--)\-            for((b) = (a) + VRNA_GQUAD_MIN_BOX_SIZE - 1;\-                (b) <= MIN2((d), (a) + VRNA_GQUAD_MAX_BOX_SIZE - 1);\-                (b)++)--/**- *  This macro does almost the same as FOR_EACH_GQUAD() but keeps- *  the 5' delimiter fixed. 'b' is the 3' delimiter of the gquad,- *  for gquads within subsequence [a,c] that have 5' delimiter 'a'- */-#define FOR_EACH_GQUAD_AT(a, b, c)  \-          for((b) = (a) + VRNA_GQUAD_MIN_BOX_SIZE - 1;\-              (b) <= MIN2((c), (a) + VRNA_GQUAD_MAX_BOX_SIZE - 1);\-              (b)++)---/*-#################################-# PRIVATE FUNCTION DECLARATIONS #-#################################-*/--PRIVATE INLINE-int *-get_g_islands(short *S);--PRIVATE INLINE-int *-get_g_islands_sub(short *S, int i, int j);--/**- *  IMPORTANT:- *  If you don't know how to use this function, DONT'T USE IT!- *- *  The function pointer this function takes as argument is- *  used for individual calculations with each g-quadruplex- *  delimited by [i,j].- *  The function it points to always receives as first 3 arguments- *  position i, the stack size L and an array l[3] containing the- *  individual linker sizes.- *  The remaining 4 (void *) pointers of the callback function receive- *  the parameters 'data', 'P', 'aux1' and 'aux2' and thus may be- *  used to pass whatever data you like to.- *  As the names of those parameters suggest the convention is that- *  'data' should be used as a pointer where data is stored into,- *  e.g the MFE or PF and the 'P' parameter should actually be a- *  'paramT *' or 'pf_paramT *' type.- *  However, what you actually pass obviously depends on the- *  function the pointer is pointing to.- *- *  Although all of this may look like an overkill, it is found- *  to be almost as fast as implementing g-quadruplex enumeration- *  in each individual scenario, i.e. code duplication.- *  Using this function, however, ensures that all g-quadruplex- *  enumerations are absolutely identical.- */-PRIVATE-void-process_gquad_enumeration(int *gg,-                          int i,-                          int j,-                          void (*f)(int, int, int *,-                                    void *, void *, void *, void *),-                          void *data,-                          void *P,-                          void *aux1,-                          void *aux2);--/**- *  MFE callback for process_gquad_enumeration()- */-PRIVATE-void-gquad_mfe(int i,-          int L,-          int *l,-          void *data,-          void *P,-          void *NA,-          void *NA2);--PRIVATE-void-gquad_mfe_pos(int i,-              int L,-              int *l,-              void *data,-              void *P,-              void *Lmfe,-              void *lmfe);--PRIVATE-void-gquad_pos_exhaustive( int i,-                      int L,-                      int *l,-                      void *data,-                      void *P,-                      void *Lex,-                      void *lex);--/**- * Partition function callback for process_gquad_enumeration()- */-PRIVATE-void-gquad_pf( int i,-          int L,-          int *l,-          void *data,-          void *P,-          void *NA,-          void *NA2);--/**- * Partition function callback for process_gquad_enumeration()- * in contrast to gquad_pf() it stores the stack size L and- * the linker lengths l[3] of the g-quadruplex that dominates- * the interval [i,j]- * (FLT_OR_DBL *)data must be 0. on entry- */-PRIVATE-void-gquad_pf_pos( int i,-              int L,-              int *l,-              void *data,-              void *pf,-              void *Lmax,-              void *lmax);--/**- * MFE (alifold) callback for process_gquad_enumeration()- */-PRIVATE-void-gquad_mfe_ali(int i,-              int L,-              int *l,-              void *data,-              void *P,-              void *S,-              void *n_seq);--/**- * MFE (alifold) callback for process_gquad_enumeration()- * with seperation of free energy and penalty contribution- */-PRIVATE-void-gquad_mfe_ali_en( int i,-                  int L,-                  int *l,-                  void *data,-                  void *P,-                  void *S,-                  void *n_seq);--PRIVATE-void-gquad_interact( int i,-                int L,-                int *l,-                void *data,-                void *pf,-                void *index,-                void *NA2);--PRIVATE-void-gquad_count(int i,-            int L,-            int *l,-            void *data,-            void *NA,-            void *NA2,-            void *NA3);--PRIVATE-void-gquad_count_layers( int i,-                    int L,-                    int *l,-                    void *data,-                    void *NA,-                    void *NA2,-                    void *NA3);--/* other useful static functions */--PRIVATE-int-gquad_ali_penalty(int i,-                  int L,-                  int l[3],-                  const short **S,-                  paramT *P);--/*-#########################################-# BEGIN OF PUBLIC FUNCTION DEFINITIONS  #-#      (all available in RNAlib)        #-#########################################-*/--/********************************-  Here are the G-quadruplex energy-  contribution functions-*********************************/--PUBLIC int E_gquad( int L,-                    int l[3],-                    paramT *P){--  int i, c = INF;--  for(i=0;i<3;i++){-    if(l[i] > VRNA_GQUAD_MAX_LINKER_LENGTH) return c;-    if(l[i] < VRNA_GQUAD_MIN_LINKER_LENGTH) return c;-  }-  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return c;-  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return c;-  -  gquad_mfe(0, L, l,-            (void *)(&c),-            (void *)P,-            NULL,-            NULL);-  return c;-}--PUBLIC FLT_OR_DBL exp_E_gquad(int L,-                              int l[3],-                              pf_paramT *pf){--  int i;-  FLT_OR_DBL q = 0.;--  for(i=0;i<3;i++){-    if(l[i] > VRNA_GQUAD_MAX_LINKER_LENGTH) return q;-    if(l[i] < VRNA_GQUAD_MIN_LINKER_LENGTH) return q;-  }-  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return q;-  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return q;--  gquad_pf( 0, L, l,-            (void *)(&q),-            (void *)pf,-            NULL,-            NULL);-  return q;-}--PUBLIC int E_gquad_ali( int i,-                        int L,-                        int l[3],-                        const short **S,-                        int n_seq,-                        paramT *P){--  int en[2];-  E_gquad_ali_en(i, L, l, S, n_seq, en, P);-  return en[0] + en[1];-}---PUBLIC void E_gquad_ali_en( int i,-                            int L,-                            int l[3],-                            const short **S,-                            int n_seq,-                            int en[2],-                            paramT *P){--  int j;-  en[0] = en[1] = INF;--  for(j=0;j<3;j++){-    if(l[j] > VRNA_GQUAD_MAX_LINKER_LENGTH) return;-    if(l[j] < VRNA_GQUAD_MIN_LINKER_LENGTH) return;-  }-  if(L > VRNA_GQUAD_MAX_STACK_SIZE) return;-  if(L < VRNA_GQUAD_MIN_STACK_SIZE) return;--  gquad_mfe_ali_en( i, L, l,-                    (void *)(&(en[0])),-                    (void *)P,-                    (void *)S,-                    (void *)(&n_seq));-}--/********************************-  Now, the triangular matrix-  generators for the G-quadruplex-  contributions are following-*********************************/--PUBLIC int *get_gquad_matrix(short *S, paramT *P){--  int n, size, i, j, *gg, *my_index, *data;--  n         = S[0];-  my_index  = get_indx(n);-  gg        = get_g_islands(S);-  size      = (n * (n+1))/2 + 2;-  data      = (int *)space(sizeof(int) * size);--  /* prefill the upper triangular matrix with INF */-  for(i = 0; i < size; i++) data[i] = INF;--  FOR_EACH_GQUAD(i, j, 1, n){-    process_gquad_enumeration(gg, i, j,-                              &gquad_mfe,-                              (void *)(&(data[my_index[j]+i])),-                              (void *)P,-                              NULL,-                              NULL);-  }--  free(my_index);-  free(gg);-  return data;-}--PUBLIC FLT_OR_DBL *get_gquad_pf_matrix( short *S,-                                        FLT_OR_DBL *scale,-                                        pf_paramT *pf){--  int n, size, *gg, i, j, *my_index;-  FLT_OR_DBL *data;---  n         = S[0];-  size      = (n * (n+1))/2 + 2;-  data      = (FLT_OR_DBL *)space(sizeof(FLT_OR_DBL) * size);-  gg        = get_g_islands(S);-  my_index  = get_iindx(n);--  FOR_EACH_GQUAD(i, j, 1, n){-    process_gquad_enumeration(gg, i, j,-                              &gquad_pf,-                              (void *)(&(data[my_index[i]-j])),-                              (void *)pf,-                              NULL,-                              NULL);-    data[my_index[i]-j] *= scale[j-i+1];-  }--  free(my_index);-  free(gg);-  return data;-}--PUBLIC int *get_gquad_ali_matrix( short *S_cons,-                                  short **S,-                                  int n_seq,-                                  paramT *P){--  int n, size, *data, *gg;-  int i, j, *my_index;---  n         = S[0][0];-  size      = (n * (n+1))/2 + 2;-  data      = (int *)space(sizeof(int) * size);-  gg        = get_g_islands(S_cons);-  my_index  = get_indx(n);--  /* prefill the upper triangular matrix with INF */-  for(i=0;i<size;i++) data[i] = INF;--  FOR_EACH_GQUAD(i, j, 1, n){-    process_gquad_enumeration(gg, i, j,-                              &gquad_mfe_ali,-                              (void *)(&(data[my_index[j]+i])),-                              (void *)P,-                              (void *)S,-                              (void *)(&n_seq));-  }--  free(my_index);-  free(gg);-  return data;-}--PUBLIC int **get_gquad_L_matrix(short *S,-                                int start,-                                int maxdist,-                                int **g,-                                paramT *P){--  int **data;-  int n, i, j, k, l, *gg;-  -  n   = S[0];-  gg  = get_g_islands_sub(S, start, MIN2(n, start + maxdist + 4));--  if(g){ /* we just update the gquadruplex contribution for the current-            start and rotate the rest */-    data = g;-    /* we re-use the memory allocated previously */-    data[start] = data[start + maxdist + 5];-    data[start + maxdist + 5] = NULL;--    /* prefill with INF */-    for(i = 0; i < maxdist + 5; i++)-      data[start][i] = INF;--    /*  now we compute contributions for all gquads with 5' delimiter at-        position 'start'-    */-    FOR_EACH_GQUAD_AT(start, j, start + maxdist + 4){-      process_gquad_enumeration(gg, start, j,-                                &gquad_mfe,-                                (void *)(&(data[start][j-start])),-                                (void *)P,-                                NULL,-                                NULL);-    }--  } else { /* create a new matrix from scratch since this is the first-              call to this function */--    /* allocate memory and prefill with INF */-    data = (int **) space(sizeof(int *) * (n+1));-    for(k = n; (k>n-maxdist-5) && (k>=0); k--){-      data[k] = (int *) space(sizeof(int)*(maxdist+5));-      for(i = 0; i < maxdist+5; i++) data[k][i] = INF;-    }-    -    /* compute all contributions for the gquads in this interval */-    FOR_EACH_GQUAD(i, j, n - maxdist - 4, n){-      process_gquad_enumeration(gg, i, j,-                                &gquad_mfe,-                                (void *)(&(data[i][j-i])),-                                (void *)P,-                                NULL,-                                NULL);-    }-  }--  gg += start - 1;-  free(gg);-  return data;-}--PUBLIC plist *get_plist_gquad_from_db(const char *structure, float pr){-  int x, size, actual_size, L, n, ge, ee, gb, l[3];-  plist *pl;--  actual_size = 0;-  ge          = 0;-  n           = 2;-  size        = strlen(structure);-  pl          = (plist *)space(n*size*sizeof(plist));--  while((ee = parse_gquad(structure + ge, &L, l)) > 0){-    ge += ee;-    gb = ge - L*4 - l[0] - l[1] - l[2] + 1;-    /* add pseudo-base pair encloding gquad */-    for(x = 0; x < L; x++){-      if (actual_size >= n * size - 5){-        n *= 2;-        pl = (plist *)xrealloc(pl, n * size * sizeof(plist));-      }-      pl[actual_size].i = gb + x;-      pl[actual_size].j = ge + x - L + 1;-      pl[actual_size].p = pr;-      pl[actual_size++].type = 0;--      pl[actual_size].i = gb + x;-      pl[actual_size].j = gb + x + l[0] + L;-      pl[actual_size].p = pr;-      pl[actual_size++].type = 0;--      pl[actual_size].i = gb + x + l[0] + L;-      pl[actual_size].j = ge + x - 2*L - l[2] + 1;-      pl[actual_size].p = pr;-      pl[actual_size++].type = 0;--      pl[actual_size].i = ge + x - 2*L - l[2] + 1;-      pl[actual_size].j = ge + x - L + 1;-      pl[actual_size].p = pr;-      pl[actual_size++].type = 0;-    }-  } --  pl[actual_size].i = pl[actual_size].j = 0;-  pl[actual_size++].p = 0;-  pl = (plist *)xrealloc(pl, actual_size * sizeof(plist));-  return pl;-}--PUBLIC void get_gquad_pattern_mfe(short *S,-                                  int i,-                                  int j,-                                  paramT *P,-                                  int *L,-                                  int l[3]){--  int *gg = get_g_islands_sub(S, i, j);-  int c = INF;--  process_gquad_enumeration(gg, i, j,-                            &gquad_mfe_pos,-                            (void *)(&c),-                            (void *)P,-                            (void *)L,-                            (void *)l);--  gg += i - 1;-  free(gg);-}--PUBLIC void-get_gquad_pattern_exhaustive( short *S,-                              int i,-                              int j,-                              paramT *P,-                              int *L,-                              int *l,-                              int threshold){--  int *gg = get_g_islands_sub(S, i, j);--  process_gquad_enumeration(gg, i, j,-                            &gquad_pos_exhaustive,-                            (void *)(&threshold),-                            (void *)P,-                            (void *)L,-                            (void *)l);--  gg += i - 1;-  free(gg);-}--PUBLIC void get_gquad_pattern_pf( short *S,-                                  int i,-                                  int j,-                                  pf_paramT *pf,-                                  int *L,-                                  int l[3]){--  int *gg = get_g_islands_sub(S, i, j);-  FLT_OR_DBL q = 0.;--  process_gquad_enumeration(gg, i, j,-                            &gquad_pf_pos,-                            (void *)(&q),-                            (void *)pf,-                            (void *)L,-                            (void *)l);--  gg += i - 1;-  free(gg);-}--PUBLIC plist *get_plist_gquad_from_pr(short *S,-                                      int gi,-                                      int gj,-                                      FLT_OR_DBL *G,-                                      FLT_OR_DBL *probs,-                                      FLT_OR_DBL *scale,-                                      pf_paramT *pf){--  int L, l[3];-  return  get_plist_gquad_from_pr_max(S, gi, gj, G, probs, scale, &L, l, pf);-}---PUBLIC plist *get_plist_gquad_from_pr_max(short *S,-                                      int gi,-                                      int gj,-                                      FLT_OR_DBL *G,-                                      FLT_OR_DBL *probs,-                                      FLT_OR_DBL *scale,-                                      int *Lmax,-                                      int lmax[3],-                                      pf_paramT *pf){ --  int n, size, *gg, counter, i, j, *my_index;-  FLT_OR_DBL pp, *tempprobs;-  plist *pl;-  -  n         = S[0];-  size      = (n * (n + 1))/2 + 2;-  tempprobs = (FLT_OR_DBL *)space(sizeof(FLT_OR_DBL) * size);-  pl        = (plist *)space((S[0]*S[0])*sizeof(plist));-  gg        = get_g_islands_sub(S, gi, gj);-  counter   = 0;-  my_index  = get_iindx(n);--  process_gquad_enumeration(gg, gi, gj,-                            &gquad_interact,-                            (void *)tempprobs,-                            (void *)pf,-                            (void *)my_index,-                            NULL);--  pp = 0.;-  process_gquad_enumeration(gg, gi, gj,-                            &gquad_pf_pos,-                            (void *)(&pp),-                            (void *)pf,-                            (void *)Lmax,-                            (void *)lmax);--  pp = probs[my_index[gi]-gj] * scale[gj-gi+1] / G[my_index[gi]-gj];-  for (i=gi;i<gj; i++) {-    for (j=i; j<=gj; j++) {-      if (tempprobs[my_index[i]-j]>0.) {-        pl[counter].i=i;-        pl[counter].j=j;-        pl[counter++].p = pp * tempprobs[my_index[i]-j];-      }-    }-  }-  pl[counter].i = pl[counter].j = 0;-  pl[counter++].p = 0.;-  /* shrink memory to actual size needed */-  pl = (plist *) xrealloc(pl, counter * sizeof(plist));--  gg += gi - 1; free(gg);-  free(my_index);-  free (tempprobs);-  return pl;-}--PUBLIC int-get_gquad_count(short *S,-                int i,-                int j){--  int *gg     = get_g_islands_sub(S, i, j);-  int p,q,counter = 0;--  FOR_EACH_GQUAD(p, q, i, j)-    process_gquad_enumeration(gg, p, q,-                              &gquad_count,-                              (void *)(&counter),-                              NULL,-                              NULL,-                              NULL);--  gg += i - 1;-  free(gg);-  return counter;-}--PUBLIC int-get_gquad_layer_count(short *S,-                      int i,-                      int j){--  int *gg     = get_g_islands_sub(S, i, j);-  int p,q,counter = 0;--  FOR_EACH_GQUAD(p, q, i, j)-    process_gquad_enumeration(gg, p, q,-                              &gquad_count_layers,-                              (void *)(&counter),-                              NULL,-                              NULL,-                              NULL);--  gg += i - 1;-  free(gg);-  return counter;-}--PUBLIC int parse_gquad(const char *struc, int *L, int l[3]) {-  int i, il, start, end, len;--  for (i=0; struc[i] && struc[i]!='+'; i++);-  if (struc[i] == '+') { /* start of gquad */-    for (il=0; il<=3; il++) {-      start=i; /* pos of first '+' */-      while (struc[++i] == '+'){-        if((il) && (i-start == *L))-          break;-      }-      end=i; len=end-start; -      if (il==0) *L=len;-      else if (len!=*L)-        nrerror("unequal stack lengths in gquad");-      if (il==3) break;-      while (struc[++i] == '.'); /* linker */-      l[il] = i-end;-      if (struc[i] != '+')-        nrerror("illegal character in gquad linker region");-    }-  }-  else return 0;-  /* printf("gquad at %d %d %d %d %d\n", end, *L, l[0], l[1], l[2]); */-  return end;-}----/*-#########################################-# BEGIN OF PRIVATE FUNCTION DEFINITIONS #-#          (internal use only)          #-#########################################-*/--PRIVATE int gquad_ali_penalty(int i,-                              int L,-                              int l[3],-                              const short **S,-                              paramT *P){--  int s, cnt;-  int penalty     = 0;-  int gg_mismatch = 0;--  /* check for compatibility in the alignment */-  for(s = 0; S[s]; s++){-    unsigned int  ld  = 0; /* !=0 if layer destruction was detected */-    int           pen = 0;--    /* check bottom layer */-    if(S[s][i] != 3)                            ld |= 1U;-    if(S[s][i + L + l[0]] != 3)                 ld |= 2U;-    if(S[s][i + 2*L + l[0] + l[1]] != 3)        ld |= 4U;-    if(S[s][i + 3*L + l[0] + l[1] + l[2]] != 3) ld |= 8U;-     /* add 1x penalty for missing bottom layer */-    if(ld) pen += VRNA_GQUAD_MISMATCH_PENALTY;--    /* check top layer */-    ld = 0;-    if(S[s][i + L - 1] != 3)                        ld |= 1U;-    if(S[s][i + 2*L + l[0] - 1] != 3)               ld |= 2U;-    if(S[s][i + 3*L + l[0] + l[1] - 1] != 3)        ld |= 4U;-    if(S[s][i + 4*L + l[0] + l[1] + l[2] - 1] != 3) ld |= 8U;-     /* add 1x penalty for missing top layer */-    if(ld) pen += VRNA_GQUAD_MISMATCH_PENALTY;--    /* check inner layers */-    for(cnt=1;cnt<L-1;cnt++){-      if(S[s][i + cnt] != 3)                            ld |= 1U;-      if(S[s][i + L + l[0] + cnt] != 3)                 ld |= 2U;-      if(S[s][i + 2*L + l[0] + l[1] + cnt] != 3)        ld |= 4U;-      if(S[s][i + 3*L + l[0] + l[1] + l[2] + cnt] != 3) ld |= 8U;-      /* add 2x penalty for missing inner layer */-      if(ld) pen += 2*VRNA_GQUAD_MISMATCH_PENALTY;-    }--    /* if all layers are missing, we have a complete gg mismatch */-    if(pen >= (2*VRNA_GQUAD_MISMATCH_PENALTY * (L-1)))-      gg_mismatch++;--    /* add the penalty to the score */-    penalty += pen;-  }-  /* if gg_mismatch exceeds maximum allowed, this g-quadruplex is forbidden */-  if(gg_mismatch > VRNA_GQUAD_MISMATCH_NUM_ALI) return INF;-  else return penalty;-}---PRIVATE void gquad_mfe( int i,-                        int L,-                        int *l,-                        void *data,-                        void *P,-                        void *NA,-                        void *NA2){--  int cc = ((paramT *)P)->gquad[L][l[0] + l[1] + l[2]];-  if(cc < *((int *)data))-    *((int *)data) = cc;-}--PRIVATE void gquad_mfe_pos( int i,-                            int L,-                            int *l,-                            void *data,-                            void *P,-                            void *Lmfe,-                            void *lmfe){--  int cc = ((paramT *)P)->gquad[L][l[0] + l[1] + l[2]];-  if(cc < *((int *)data)){-    *((int *)data)        = cc;-    *((int *)Lmfe)        = L;-    *((int *)lmfe)        = l[0];-    *(((int *)lmfe) + 1)  = l[1];-    *(((int *)lmfe) + 2)  = l[2];-  }-}--PRIVATE-void-gquad_pos_exhaustive( int i,-                      int L,-                      int *l,-                      void *data,-                      void *P,-                      void *Lex,-                      void *lex){--  int cnt;-  int cc = ((paramT *)P)->gquad[L][l[0] + l[1] + l[2]];-  if(cc <= *((int *)data)){-    /*  since Lex is an array of L values and lex an-        array of l triples we need to find out where-        the current gquad position is to be stored...-		the below implementation might be slow but we-		still use it for now-    */-    for(cnt = 0; ((int *)Lex)[cnt] != -1; cnt++);--    *((int *)Lex + cnt)           = L;-    *((int *)Lex + cnt + 1)       = -1;-    *(((int *)lex) + (3*cnt) + 0) = l[0];-    *(((int *)lex) + (3*cnt) + 1) = l[1];-    *(((int *)lex) + (3*cnt) + 2) = l[2];-  }-}--PRIVATE-void-gquad_count(int i,-            int L,-            int *l,-            void *data,-            void *NA,-            void *NA2,-            void *NA3){--  *((int *)data) += 1;-}--PRIVATE-void-gquad_count_layers( int i,-                    int L,-                    int *l,-                    void *data,-                    void *NA,-                    void *NA2,-                    void *NA3){--  *((int *)data) += L;-}---PRIVATE void gquad_pf(int i,-                      int L,-                      int *l,-                      void *data,-                      void *pf,-                      void *NA,-                      void *NA2){--  *((FLT_OR_DBL *)data) += ((pf_paramT *)pf)->expgquad[L][l[0] + l[1] + l[2]];-}--PRIVATE void gquad_pf_pos(int i,-                          int L,-                          int *l,-                          void *data,-                          void *pf,-                          void *Lmax,-                          void *lmax){--  FLT_OR_DBL gq = ((pf_paramT *)pf)->expgquad[L][l[0] + l[1] + l[2]];-  if(gq > *((FLT_OR_DBL *)data)){-    *((FLT_OR_DBL *)data) = gq;-    *((int *)Lmax)        = L;-    *((int *)lmax)        = l[0];-    *(((int *)lmax) + 1)  = l[1];-    *(((int *)lmax) + 2)  = l[2];-  }-}--PRIVATE void gquad_mfe_ali( int i,-                            int L,-                            int *l,-                            void *data,-                            void *P,-                            void *S,-                            void *n_seq){--  int en[2], cc;-  en[0] = en[1] = INF;-  gquad_mfe_ali_en(i, L, l, (void *)(&(en[0])), P, S, n_seq);-  if(en[1] != INF){-    cc  = en[0] + en[1];-    if(cc < *((int *)data)) *((int *)data) = cc;-  }-}--PRIVATE void gquad_mfe_ali_en(int i,-                              int L,-                              int *l,-                              void *data,-                              void *P,-                              void *S,-                              void *n_seq){--  int en[2], cc, dd;-  en[0] = ((paramT *)P)->gquad[L][l[0] + l[1] + l[2]] * (*(int *)n_seq);-  en[1] = gquad_ali_penalty(i, L, l, (const short **)S, (paramT *)P);-  if(en[1] != INF){-    cc = en[0] + en[1];-    dd = ((int *)data)[0] + ((int *)data)[1];-    if(cc < dd){-      ((int *)data)[0] = en[0];-      ((int *)data)[1] = en[1];-    }-  }-}--PRIVATE void gquad_interact(int i,-                      int L,-                      int *l,-                      void *data,-                      void *pf,-                      void *index,-                      void *NA2){--  int x, *idx;-  FLT_OR_DBL gq, *pp;--  idx = (int *)index;-  pp  = (FLT_OR_DBL *)data;-  gq  = exp_E_gquad(L, l, (pf_paramT *)pf);--  for(x = 0; x < L; x++){-    pp[idx[i + x] - (i + x + 3*L + l[0] + l[1] + l[2])] += gq;-    pp[idx[i + x] - (i + x + L + l[0])] += gq;-    pp[idx[i + x + L + l[0]] - (i + x + 2*L + l[0] + l[1])] += gq;-    pp[idx[i + x + 2*L + l[0] + l[1]] - (i + x + 3*L + l[0] + l[1] + l[2])] += gq;-  }-  -}--PRIVATE INLINE int *get_g_islands(short *S){-  return get_g_islands_sub(S, 1, S[0]);-}--PRIVATE INLINE int *get_g_islands_sub(short *S, int i, int j){-  int x, *gg;--  gg = (int *)space(sizeof(int)*(j-i+2));-  gg -= i - 1;--  if(S[j]==3) gg[j] = 1;-  for(x = j - 1; x >= i; x--)-    if(S[x] == 3)-      gg[x] = gg[x+1]+1;--  return gg;-}--/**- *  We could've also created a macro that loops over all G-quadruplexes- *  delimited by i and j. However, for the fun of it we use this function- *  that receives a pointer to a callback function which in turn does the- *  actual computation for each quadruplex found.- */-PRIVATE-void-process_gquad_enumeration(int *gg,-                          int i,-                          int j,-                          void (*f)(int, int, int *,-                                    void *, void *, void *, void *),-                          void *data,-                          void *P,-                          void *aux1,-                          void *aux2){--  int L, l[3], n, max_linker, maxl0, maxl1;--  n = j - i + 1;--  if((n >= VRNA_GQUAD_MIN_BOX_SIZE) && (n <= VRNA_GQUAD_MAX_BOX_SIZE))-    for(L = MIN2(gg[i], VRNA_GQUAD_MAX_STACK_SIZE);-        L >= VRNA_GQUAD_MIN_STACK_SIZE;-        L--)-      if(gg[j-L+1] >= L){-        max_linker = n-4*L;-        if(     (max_linker >= 3*VRNA_GQUAD_MIN_LINKER_LENGTH)-            &&  (max_linker <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH)){-          maxl0 = MIN2( VRNA_GQUAD_MAX_LINKER_LENGTH,-                        max_linker - 2*VRNA_GQUAD_MIN_LINKER_LENGTH-                      );-          for(l[0] = VRNA_GQUAD_MIN_LINKER_LENGTH;-              l[0] <= maxl0;-              l[0]++)-            if(gg[i+L+l[0]] >= L){-              maxl1 = MIN2( VRNA_GQUAD_MAX_LINKER_LENGTH,-                            max_linker - l[0] - VRNA_GQUAD_MIN_LINKER_LENGTH-                          );-              for(l[1] = VRNA_GQUAD_MIN_LINKER_LENGTH;-                  l[1] <= maxl1;-                  l[1]++)-                if(gg[i + 2*L + l[0] + l[1]] >= L){-                  l[2] = max_linker - l[0] - l[1];-                  f(i, L, &(l[0]), data, P, aux1, aux2);-                }-            }-        }-      }-}-
− cbits/params.c 
@@ -1,751 +0,0 @@-/*--                  c Ivo Hofacker--                  Vienna RNA package-*/-#include <config.h>-#include <stdio.h>-#include <stdlib.h>-#include <math.h>-#include <string.h>-#include "energy_par.h"-#include "fold_vars.h"-#include "utils.h"-#include "params.h"-/**-*** \file params.c-*** <P>-*** This file provides functions that return temperature scaled energy parameters and-*** Boltzmann weights packed in datastructures-*** </P>-***/--/*@unused@*/-static char rcsid[] UNUSED = "$Id: params.c,v 1.9 2008/07/04 14:29:14 ivo Exp $";--PRIVATE paramT p;-PRIVATE int id=-1;-/* variables for partition function */-PRIVATE pf_paramT pf;-PRIVATE int pf_id=-1;--#ifdef _OPENMP-#pragma omp threadprivate(id, pf_id)-#endif--PUBLIC paramT *scale_parameters(void){-  model_detailsT  md;-  set_model_details(&md);-  return get_scaled_parameters(temperature, md);-}--PUBLIC paramT *get_scaled_parameters( double temp,-                                      model_detailsT md){--  unsigned int i,j,k,l;-  double tempf;-  paramT *params;--  params  = (paramT *)space(sizeof(paramT));--  /* store the model details */-  params->model_details = md;-  params->temperature   = temp;-  tempf                 = ((params->temperature+K0)/Tmeasure);--  for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)-    for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){-      double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * tempf;-      double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * tempf;-      params->gquad[i][j] = (int)GQuadAlpha_T*(i-1) + (int)(((double)GQuadBeta_T)*log(j - 2));-    }--  for (i=0; i<31; i++)-    params->hairpin[i]  = hairpindH[i] - (hairpindH[i] - hairpin37[i])*tempf;-  for (i=0; i<=MIN2(30,MAXLOOP); i++) {-    params->bulge[i]          = bulgedH[i] - (bulgedH[i] - bulge37[i]) * tempf;-    params->internal_loop[i]  = internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i]) * tempf;-  }-  params->lxc = lxc37*tempf;-  for (; i<=MAXLOOP; i++) {-    params->bulge[i] = params->bulge[30]+(int)(params->lxc*log((double)(i)/30.));-    params->internal_loop[i] = params->internal_loop[30]+(int)(params->lxc*log((double)(i)/30.));-  }--  params->ninio[2] = niniodH - (niniodH - ninio37) * tempf;--  params->TripleC = TripleCdH - (TripleCdH - TripleC37) * tempf;-  params->MultipleCA = MultipleCAdH - (MultipleCAdH - MultipleCA37) * tempf;-  params->MultipleCB = MultipleCBdH - (MultipleCBdH - MultipleCB37) * tempf;--  for (i=0; (i*7)<strlen(Tetraloops); i++)-    params->Tetraloop_E[i] = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*tempf;-  for (i=0; (i*5)<strlen(Triloops); i++)-    params->Triloop_E[i] =  TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*tempf;-  for (i=0; (i*9)<strlen(Hexaloops); i++)-    params->Hexaloop_E[i] =  HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*tempf;--  params->TerminalAU = TerminalAUdH - (TerminalAUdH - TerminalAU37) * tempf;--  params->DuplexInit = DuplexInitdH - (DuplexInitdH - DuplexInit37) *tempf;--  params->MLbase = ML_BASEdH - (ML_BASEdH - ML_BASE37) * tempf;--  for (i=0; i<=NBPAIRS; i++)-    params->MLintern[i] = ML_interndH - (ML_interndH - ML_intern37) * tempf;--  params->MLclosing = ML_closingdH - (ML_closingdH - ML_closing37) * tempf;---  /* stacks    G(T) = H - [H - G(T0)]*T/T0 */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      params->stack[i][j] = stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*tempf;--  /* mismatches */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<5; j++)-      for (k=0; k<5; k++) {-        int mm;-        params->mismatchI[i][j][k]    = mismatchIdH[i][j][k] - (mismatchIdH[i][j][k] - mismatchI37[i][j][k])*tempf;-        params->mismatchH[i][j][k]    = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*tempf;-        params->mismatch1nI[i][j][k]  = mismatch1nIdH[i][j][k]-(mismatch1nIdH[i][j][k]-mismatch1nI37[i][j][k])*tempf;/* interior nx1 loops */-        params->mismatch23I[i][j][k]  = mismatch23IdH[i][j][k]-(mismatch23IdH[i][j][k]-mismatch23I37[i][j][k])*tempf;/* interior 2x3 loops */-        if(md.dangles){-          mm                      = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*tempf;-          params->mismatchM[i][j][k]    = (mm > 0) ? 0 : mm;-          mm                      = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*tempf;-          params->mismatchExt[i][j][k]  = (mm > 0) ? 0 : mm;-        }-        else{-          params->mismatchM[i][j][k] = params->mismatchExt[i][j][k] = 0;-        }-      }--  /* dangles */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<5; j++) {-      int dd;-      dd = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*tempf;-      params->dangle5[i][j] = (dd>0) ? 0 : dd;  /* must be <= 0 */-      dd = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*tempf;-      params->dangle3[i][j] = (dd>0) ? 0 : dd;  /* must be <= 0 */-    }-  /* interior 1x1 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++)-          params->int11[i][j][k][l] = int11_dH[i][j][k][l] - (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*tempf;--  /* interior 2x1 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m;-          for (m=0; m<5; m++)-            params->int21[i][j][k][l][m] = int21_dH[i][j][k][l][m] - (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*tempf;-        }-  /* interior 2x2 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m,n;-          for (m=0; m<5; m++)-            for (n=0; n<5; n++)-              params->int22[i][j][k][l][m][n] = int22_dH[i][j][k][l][m][n] - (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*tempf;-        }--  strncpy(params->Tetraloops, Tetraloops, 281);-  strncpy(params->Triloops, Triloops, 241);-  strncpy(params->Hexaloops, Hexaloops, 361);--  params->id = ++id;-  return params;-}---/*------------------------------------------------------------------------*/-#define SCALE 10-/**-*** dangling ends should never be destabilizing, i.e. expdangle>=1<BR>-*** specific heat needs smooth function (2nd derivative)<BR>-*** we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2,-*** in the interval b<x<sqrt(3)/2-*/-#define SMOOTH(X) ((X)/SCALE<-1.2283697)?0:(((X)/SCALE>0.8660254)?(X):\-          SCALE*0.38490018*(sin((X)/SCALE-0.34242663)+1)*(sin((X)/SCALE-0.34242663)+1))--/* #define SMOOTH(X) ((X)<0 ? 0 : (X)) */---PUBLIC pf_paramT *get_scaled_pf_parameters(void){-  model_detailsT  md;-  set_model_details(&md);-  return get_boltzmann_factors(temperature, 1.0, md, pf_scale);-}--PUBLIC pf_paramT *get_boltzmann_factors(double temp,-                                        double betaScale,-                                        model_detailsT md,-                                        double pf_scale){--  unsigned  int i, j, k, l;-  double        kT, TT;-  double        GT;-  pf_paramT     *pf;--  pf                = (pf_paramT *)space(sizeof(pf_paramT));-  pf->model_details = md;-  pf->temperature   = temp;-  pf->alpha         = betaScale;-  pf->kT = kT       = betaScale*(temp+K0)*GASCONST;   /* kT in cal/mol  */-  pf->pf_scale      = pf_scale;-  TT                = (temp+K0)/(Tmeasure);--  for(i = VRNA_GQUAD_MIN_STACK_SIZE; i <= VRNA_GQUAD_MAX_STACK_SIZE; i++)-    for(j = 3*VRNA_GQUAD_MIN_LINKER_LENGTH; j <= 3*VRNA_GQUAD_MAX_LINKER_LENGTH; j++){-      double GQuadAlpha_T = (double)GQuadAlphadH - (double)(GQuadAlphadH - GQuadAlpha37) * TT;-      double GQuadBeta_T = (double)GQuadBetadH - (double)(GQuadBetadH - GQuadBeta37) * TT;-      GT = ((double)GQuadAlpha_T)*((double)(i-1)) + ((double)GQuadBeta_T)*log(((double)j) - 2.);-      pf->expgquad[i][j] = exp( -GT*10./kT);-    }--  /* loop energies: hairpins, bulges, interior, mulit-loops */-  for (i=0; i<31; i++){-    GT  = hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;-    pf->exphairpin[i] = exp( -GT*10./kT);-  }--  for (i=0; i<=MIN2(30, MAXLOOP); i++) {-    GT =  bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;-    pf->expbulge[i] = exp( -GT*10./kT);-    GT =  internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;-    pf->expinternal[i] = exp( -GT*10./kT);-  }-  /* special case of size 2 interior loops (single mismatch) */-  if (james_rule) pf->expinternal[2] = exp ( -80*10./kT);--  pf->lxc = lxc37*TT;--  GT =  DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;-  pf->expDuplexInit = exp( -GT*10./kT);--  for (i=31; i<=MAXLOOP; i++) {-    GT = bulge37[30]*TT + (pf->lxc*log( i/30.));-    pf->expbulge[i] = exp( -GT*10./kT);-    GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));-    pf->expinternal[i] = exp( -GT*10./kT);-  }--  GT = niniodH - (niniodH - ninio37)*TT;-  for (j=0; j<=MAXLOOP; j++)-      pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kT);--  for (i=0; (i*7)<strlen(Tetraloops); i++) {-    GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;-    pf->exptetra[i] = exp( -GT*10./kT);-  }-  for (i=0; (i*5)<strlen(Triloops); i++) {-    GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;-    pf->exptri[i] = exp( -GT*10./kT);-  }-  for (i=0; (i*9)<strlen(Hexaloops); i++) {-    GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;-    pf->exphex[i] = exp( -GT*10./kT);-  }-  GT =  ML_closingdH - (ML_closingdH - ML_closing37)*TT;-  pf->expMLclosing = exp( -GT*10./kT);--  for (i=0; i<=NBPAIRS; i++) {-    GT =  ML_interndH - (ML_interndH - ML_intern37)*TT;-    /* if (i>2) GT += TerminalAU; */-    pf->expMLintern[i] = exp( -GT*10./kT);-  }-  GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;-  pf->expTermAU = exp(-GT*10./kT);--  GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;--  pf->expMLbase=exp(-10.*GT/kT);---  /* if dangles==0 just set their energy to 0,-     don't let dangle energies become > 0 (at large temps),-     but make sure go smoothly to 0                        */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=4; j++) {-      if (md.dangles) {-        GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;-        pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kT);-        GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;-        pf->expdangle3[i][j] =  exp(SMOOTH(-GT)*10./kT);-      } else-        pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;-    }--  /* stacking energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++) {-      GT =  stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;-      pf->expstack[i][j] = exp( -GT*10./kT);-    }--  /* mismatch energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<5; j++)-      for (k=0; k<5; k++) {-        GT =  mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;-        pf->expmismatchI[i][j][k] = exp(-GT*10.0/kT);-        GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;-        pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kT);-        GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;-        pf->expmismatchH[i][j][k] = exp(-GT*10.0/kT);-        if (md.dangles) {-          GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;-          pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);-          GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;-          pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kT);-        }-        else{-          pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;-        }-        GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;-        pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kT);-      }--  /* interior lops of length 2 */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          GT = int11_dH[i][j][k][l] --            (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;-          pf->expint11[i][j][k][l] = exp(-GT*10./kT);-        }-  /* interior 2x1 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m;-          for (m=0; m<5; m++) {-            GT = int21_dH[i][j][k][l][m] --              (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;-            pf->expint21[i][j][k][l][m] = exp(-GT*10./kT);-          }-        }--  /* interior 2x2 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m,n;-          for (m=0; m<5; m++)-            for (n=0; n<5; n++) {-              GT = int22_dH[i][j][k][l][m][n] --                (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;-              pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kT);-            }-        }--  strncpy(pf->Tetraloops, Tetraloops, 281);-  strncpy(pf->Triloops, Triloops, 241);-  strncpy(pf->Hexaloops, Hexaloops, 361);--  return pf;-}--PUBLIC pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq){-  model_detailsT  md;-  set_model_details(&md);-  return get_boltzmann_factors_ali(n_seq, temperature, 1.0, md, pf_scale);-}--PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,-                                            double temperature,-                                            double betaScale,-                                            model_detailsT md,-                                            double pf_scale){--  /* scale energy parameters and pre-calculate Boltzmann weights */-  unsigned int  i, j, k, l;-  double        kTn, TT;-  double        GT;-  pf_paramT     *pf;--  pf                = (pf_paramT *)space(sizeof(pf_paramT));-  pf->model_details = md;-  pf->alpha         = betaScale;-  pf->temperature   = temperature;-  pf->pf_scale      = pf_scale;-  pf->kT = kTn      = ((double)n_seq)*betaScale*(temperature+K0)*GASCONST;   /* kT in cal/mol  */-  TT                = (temperature+K0)/(Tmeasure);---   /* loop energies: hairpins, bulges, interior, mulit-loops */-  for (i=0; i<31; i++) {-    GT =  hairpindH[i] - (hairpindH[i] - hairpin37[i])*TT;-    pf->exphairpin[i] = exp( -GT*10./kTn);-  }-  /*add penalty for too short hairpins*/-  for (i=0; i<3; i++) {-    GT= 600/*Penalty*/*TT;-    pf->exphairpin[i] = exp( -GT*10./kTn);-  }--  for (i=0; i<=MIN2(30, MAXLOOP); i++) {-    GT =  bulgedH[i]- (bulgedH[i] - bulge37[i])*TT;-    pf->expbulge[i] = exp( -GT*10./kTn);-    GT =  internal_loopdH[i] - (internal_loopdH[i] - internal_loop37[i])*TT;-    pf->expinternal[i] = exp( -GT*10./kTn);-  }-  /* special case of size 2 interior loops (single mismatch) */-  if (james_rule) pf->expinternal[2] = exp ( -80*10./kTn);--  pf->lxc = lxc37*TT;--  GT =  DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;-  pf->expDuplexInit = exp( -GT*10./kTn);--  for (i=31; i<=MAXLOOP; i++) {-    GT = bulge37[30]*TT + (pf->lxc*log( i/30.));-    pf->expbulge[i] = exp( -GT*10./kTn);-    GT = internal_loop37[30]*TT + (pf->lxc*log( i/30.));-    pf->expinternal[i] = exp( -GT*10./kTn);-  }--  GT = niniodH - (niniodH - ninio37)*TT;-  for (j=0; j<=MAXLOOP; j++)-    pf->expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kTn);--  for (i=0; (i*7)<strlen(Tetraloops); i++) {-    GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;-    pf->exptetra[i] = exp( -GT*10./kTn);-  }-  for (i=0; (i*5)<strlen(Triloops); i++) {-    GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;-    pf->exptri[i] = exp( -GT*10./kTn);-  }-  for (i=0; (i*9)<strlen(Hexaloops); i++) {-    GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;-    pf->exphex[i] = exp( -GT*10./kTn);-  }-  GT =  ML_closingdH - (ML_closingdH - ML_closing37)*TT;-  pf->expMLclosing = exp( -GT*10./kTn);--  for (i=0; i<=NBPAIRS; i++) { /* includes AU penalty */-    GT =  ML_interndH - (ML_interndH - ML_intern37)*TT;-    /* if (i>2) GT += TerminalAU; */-    pf->expMLintern[i] = exp( -GT*10./kTn);-  }-  GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;-  pf->expTermAU = exp(-GT*10./kTn);--  GT = ML_BASEdH - (ML_BASEdH - ML_BASE37)*TT;-  pf->expMLbase=exp(-10.*GT/(kTn/n_seq));---  /* if dangle_model==0 just set their energy to 0,-     don't let dangle energies become > 0 (at large temps),-     but make sure go smoothly to 0                        */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=4; j++) {-      if (md.dangles) {-        GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;-        pf->expdangle5[i][j] = exp(SMOOTH(-GT)*10./kTn);-        GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;-        pf->expdangle3[i][j] =  exp(SMOOTH(-GT)*10./kTn);-      } else-        pf->expdangle3[i][j] = pf->expdangle5[i][j] = 1;-    }--  /* stacking energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++) {-      GT =  stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;-      pf->expstack[i][j] = exp( -GT*10./kTn);-    }--  /* mismatch energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<5; j++)-      for (k=0; k<5; k++) {-        GT =  mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;-        pf->expmismatchI[i][j][k] = exp(-GT*10.0/kTn);-        GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;-        pf->expmismatch1nI[i][j][k] = exp(-GT*10.0/kTn);-        GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;-        pf->expmismatchH[i][j][k] = exp(-GT*10.0/kTn);-        if (md.dangles) {-          GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;-          pf->expmismatchM[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);-          GT = mismatchExtdH[i][j][k] - (mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;-          pf->expmismatchExt[i][j][k] = exp(SMOOTH(-GT)*10.0/kTn);-        }-        else{-          pf->expmismatchM[i][j][k] = pf->expmismatchExt[i][j][k] = 1.;-        }-        GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;-        pf->expmismatch23I[i][j][k] = exp(-GT*10.0/kTn);-      }---  /* interior lops of length 2 */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          GT = int11_dH[i][j][k][l] --            (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;-          pf->expint11[i][j][k][l] = exp(-GT*10./kTn);-        }-  /* interior 2x1 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m;-          for (m=0; m<5; m++) {-            GT = int21_dH[i][j][k][l][m] --              (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;-            pf->expint21[i][j][k][l][m] = exp(-GT*10./kTn);-          }-        }--  /* interior 2x2 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m,n;-          for (m=0; m<5; m++)-            for (n=0; n<5; n++) {-              GT = int22_dH[i][j][k][l][m][n] --                (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;-              pf->expint22[i][j][k][l][m][n] = exp(-GT*10./kTn);-            }-        }--  strncpy(pf->Tetraloops, Tetraloops, 281);-  strncpy(pf->Triloops, Triloops, 241);-  strncpy(pf->Hexaloops, Hexaloops, 361);--  return pf;-}--PUBLIC pf_paramT *get_boltzmann_factor_copy(pf_paramT *par){-  pf_paramT *copy = NULL;-  if(par){-    copy = (pf_paramT *) space(sizeof(pf_paramT));-    memcpy(copy, par, sizeof(pf_paramT));-  }-  return copy;-}--PUBLIC paramT *get_parameter_copy(paramT *par){-  paramT *copy = NULL;-  if(par){-    copy = (paramT *) space(sizeof(paramT));-    memcpy(copy, par, sizeof(paramT));-  }-  return copy;-}--/*###########################################*/-/*# deprecated functions below              #*/-/*###########################################*/--PUBLIC paramT *copy_parameters(void){-  paramT *copy;-  if (p.id != id) scale_parameters();-  copy = (paramT *) space(sizeof(paramT));-  memcpy(copy, &p, sizeof(paramT));-  return copy;-}--PUBLIC paramT *set_parameters(paramT *dest){-  memcpy(&p, dest, sizeof(paramT));-  return &p;-}--PUBLIC pf_paramT *copy_pf_param(void){-  pf_paramT *copy;-  if (pf.id != pf_id) scale_pf_parameters();-  copy = (pf_paramT *) space(sizeof(pf_paramT));-  memcpy(copy, &pf, sizeof(pf_paramT));-  return copy;-}--PUBLIC pf_paramT *set_pf_param(paramT *dest){-  memcpy(&pf, dest, sizeof(pf_paramT));-  return &pf;-}--PUBLIC pf_paramT *scale_pf_parameters(void){-  return get_scaled_pf_parameters();-#if 0-  /* scale energy parameters and pre-calculate Boltzmann weights */-  unsigned int i, j, k, l;-  double  kT, TT;-  double  GT;--  /* scale pf_params() in partfunc.c is only a wrapper, that calls-     this functions !! */--  pf.temperature = temperature;-  kT = (pf.temperature+K0)*GASCONST;   /* kT in cal/mol  */-  TT = (pf.temperature+K0)/(Tmeasure);--   /* loop energies: hairpins, bulges, interior, mulit-loops */-  for (i=0; i<31; i++) {-    GT =  hairpin37[i]*TT;-    pf.exphairpin[i] = exp( -GT*10./kT);-  }-  for (i=0; i<=MIN2(30, MAXLOOP); i++) {-    GT =  bulge37[i]*TT;-    pf.expbulge[i] = exp( -GT*10./kT);-    GT =  internal_loop37[i]*TT;-    pf.expinternal[i] = exp( -GT*10./kT);-  }-  /* special case of size 2 interior loops (single mismatch) */-  if (james_rule) pf.expinternal[2] = exp ( -80*10./kT);--  pf.lxc = lxc37*TT;--  GT =  DuplexInitdH - (DuplexInitdH - DuplexInit37)*TT;-  pf.expDuplexInit = exp( -GT*10./kT);--  for (i=31; i<=MAXLOOP; i++) {-    GT = bulge37[30]*TT + (pf.lxc*log( i/30.));-    pf.expbulge[i] = exp( -GT*10./kT);-    GT = internal_loop37[30]*TT + (pf.lxc*log( i/30.));-    pf.expinternal[i] = exp( -GT*10./kT);-  }--  GT = niniodH - (niniodH - ninio37)*TT;-  for (j=0; j<=MAXLOOP; j++)-      pf.expninio[2][j]=exp(-MIN2(MAX_NINIO,j*GT)*10./kT);--  for (i=0; (i*7)<strlen(Tetraloops); i++) {-    GT = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*TT;-    pf.exptetra[i] = exp( -GT*10./kT);-  }-  for (i=0; (i*5)<strlen(Triloops); i++) {-    GT = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*TT;-    pf.exptri[i] = exp( -GT*10./kT);-  }-  for (i=0; (i*9)<strlen(Hexaloops); i++) {-    GT = HexaloopdH[i] - (HexaloopdH[i]-Hexaloop37[i])*TT;-    pf.exphex[i] = exp( -GT*10./kT);-  }-  GT =  ML_closing37*TT;-  pf.expMLclosing = exp( -GT*10./kT);--  for (i=0; i<=NBPAIRS; i++) { /* includes AU penalty */-    GT =  ML_intern37*TT;-    /* if (i>2) GT += TerminalAU; */-    pf.expMLintern[i] = exp( -GT*10./kT);-  }-  GT = TerminalAUdH - (TerminalAUdH - TerminalAU37)*TT;-  pf.expTermAU = exp(-GT*10./kT);--  GT = ML_BASE37*TT;-  pf.expMLbase=exp(-10.*GT/kT);---  /* if dangle_model==0 just set their energy to 0,-     don't let dangle energies become > 0 (at large temps),-     but make sure go smoothly to 0                        */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=4; j++) {-      if (dangles) {-        GT = dangle5_dH[i][j] - (dangle5_dH[i][j] - dangle5_37[i][j])*TT;-        pf.expdangle5[i][j] = exp(SMOOTH(-GT)*10./kT);-        GT = dangle3_dH[i][j] - (dangle3_dH[i][j] - dangle3_37[i][j])*TT;-        pf.expdangle3[i][j] =  exp(SMOOTH(-GT)*10./kT);-      } else-        pf.expdangle3[i][j] = pf.expdangle5[i][j] = 1;-      if (i>2) /* add TermAU penalty into dangle3 */-        pf.expdangle3[i][j] *= pf.expTermAU;-    }--  /* stacking energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++) {-      GT =  stackdH[i][j] - (stackdH[i][j] - stack37[i][j])*TT;-      pf.expstack[i][j] = exp( -GT*10./kT);-    }--  /* mismatch energies */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<5; j++)-      for (k=0; k<5; k++) {-        GT =  mismatchIdH[i][j][k] - ( mismatchIdH[i][j][k] - mismatchI37[i][j][k])*TT;-        pf.expmismatchI[i][j][k] = exp(-GT*10./kT);-        GT = mismatch1nIdH[i][j][k] - (mismatch1nIdH[i][j][k] - mismatch1nI37[i][j][k])*TT;-        pf.expmismatch1nI[i][j][k] = exp(-GT*10./kT);-        GT = mismatchHdH[i][j][k] - (mismatchHdH[i][j][k] - mismatchH37[i][j][k])*TT;-        pf.expmismatchH[i][j][k] = exp(-GT*10./kT);-        GT = mismatch23IdH[i][j][k] - (mismatch23IdH[i][j][k] - mismatch23I37[i][j][k])*TT;-        pf.expmismatch23I[i][j][k] = exp(-GT*10./kT);-        if (dangles) {-          GT = mismatchMdH[i][j][k] - (mismatchMdH[i][j][k] - mismatchM37[i][j][k])*TT;-          pf.expmismatchM[i][j][k] = exp(-GT*10./kT);-          GT =  mismatchExtdH[i][j][k] - ( mismatchExtdH[i][j][k] - mismatchExt37[i][j][k])*TT;-          pf.expmismatchExt[i][j][k] = exp(-GT*10./kT);-        }-        else{-          pf.expmismatchM[i][j][k] = pf.expmismatchExt[i][j][k] = 1.;-        }-      }---  /* interior lops of length 2 */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          GT = int11_dH[i][j][k][l] --            (int11_dH[i][j][k][l] - int11_37[i][j][k][l])*TT;-          pf.expint11[i][j][k][l] = exp(-GT*10./kT);-        }-  /* interior 2x1 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m;-          for (m=0; m<5; m++) {-            GT = int21_dH[i][j][k][l][m] --              (int21_dH[i][j][k][l][m] - int21_37[i][j][k][l][m])*TT;-            pf.expint21[i][j][k][l][m] = exp(-GT*10./kT);-          }-        }--  /* interior 2x2 loops */-  for (i=0; i<=NBPAIRS; i++)-    for (j=0; j<=NBPAIRS; j++)-      for (k=0; k<5; k++)-        for (l=0; l<5; l++) {-          int m,n;-          for (m=0; m<5; m++)-            for (n=0; n<5; n++) {-              GT = int22_dH[i][j][k][l][m][n] --                (int22_dH[i][j][k][l][m][n]-int22_37[i][j][k][l][m][n])*TT;-              pf.expint22[i][j][k][l][m][n] = exp(-GT*10./kT);-            }-        }--  strncpy(pf.Tetraloops, Tetraloops, 281);-  strncpy(pf.Triloops, Triloops, 241);-  strncpy(pf.Hexaloops, Hexaloops, 361);--  pf.id = ++pf_id;-  return &pf;-#endif-}
− cbits/part_func.c 
@@ -1,1714 +0,0 @@-/*-                  partiton function for RNA secondary structures--                  Ivo L Hofacker-                  Vienna RNA package-*/-/*-  $Log: part_func.c,v $-  Revision 1.29  2008/02/23 10:10:49  ivo-  list returned from StackProb was sometimes not terminated correctly--  Revision 1.28  2008/01/08 15:08:10  ivo-  circular fold would fail for open chain--  Revision 1.27  2007/12/05 13:04:04  ivo-  add various circfold variants from Ronny--  Revision 1.26  2007/09/19 12:41:56  ivo-  add computation of centroid() structure for RNAfold -p--  Revision 1.25  2007/04/30 15:12:00  ivo-  merge RNAup into package--  Revision 1.24  2007/03/03 17:57:44  ivo-  make sure entries in scale[] decrease to 0--  Revision 1.23  2006/12/01 12:40:23  ivo-  undo Ulli's accidental commit--  Revision 1.21  2006/08/04 15:39:06  ivo-  new function stackProb returns probability for stacks-  p[(i,j)(i+1,j-1)]--  Revision 1.20  2004/08/12 12:14:46  ivo-  update--  Revision 1.19  2004/05/14 16:28:05  ivo-  fix the bug in make_ptype here too (fixed in 1.27 of fold.c)--  Revision 1.18  2004/02/17 10:46:52  ivo-  make sure init_pf_fold is called before scale_parameters--  Revision 1.17  2004/02/09 18:37:59  ivo-  new mean_bp_dist() function to compute ensemble diversity--  Revision 1.16  2003/08/04 09:14:09  ivo-  finish up stochastic backtracking--  Revision 1.15  2002/03/19 16:51:12  ivo-  more on stochastic backtracking (still incomplete)--  Revision 1.14  2002/02/08 17:37:23  ivo-  set freed S,S1 pointers to NULL--  Revision 1.13  2001/11/16 17:30:04  ivo-  add stochastic backtracking (still incomplete)-*/-#include <config.h>-#include <stdio.h>-#include <stdlib.h>-#include <string.h>-#include <math.h>-#include <float.h>    /* #defines FLT_MAX ... */-#include <limits.h>--#include "utils.h"-#include "energy_par.h"-#include "fold_vars.h"-#include "pair_mat.h"-#include "params.h"-#include "loop_energies.h"-#include "gquad.h"-#include "part_func.h"--#ifdef _OPENMP-#include <omp.h>-#endif--#define ISOLATED  256.0--/*-#################################-# GLOBAL VARIABLES              #-#################################-*/-PUBLIC  int         st_back = 0;--/*-#################################-# PRIVATE VARIABLES             #-#################################-*/-PRIVATE FLT_OR_DBL  *q = NULL, *qb=NULL, *qm = NULL, *qm1 = NULL, *qqm = NULL, *qqm1 = NULL, *qq = NULL, *qq1 = NULL;-PRIVATE FLT_OR_DBL  *probs=NULL, *prml=NULL, *prm_l=NULL, *prm_l1=NULL, *q1k=NULL, *qln=NULL;-PRIVATE FLT_OR_DBL  *scale=NULL;-PRIVATE FLT_OR_DBL  *expMLbase=NULL;-PRIVATE FLT_OR_DBL  qo=0., qho=0., qio=0., qmo=0., *qm2=NULL;-PRIVATE int         *jindx=NULL;-PRIVATE int         *my_iindx=NULL;-PRIVATE int         init_length = -1;   /* length in last call to init_pf_fold() */-PRIVATE int         circular=0;-PRIVATE int         do_bppm = 1;             /* do backtracking per default */-PRIVATE int         struct_constrained = 0;-PRIVATE char        *pstruc=NULL;-PRIVATE char        *sequence=NULL;-PRIVATE char        *ptype=NULL;        /* precomputed array of pair types */-PRIVATE pf_paramT   *pf_params=NULL;    /* the precomputed Boltzmann weights */-PRIVATE short       *S=NULL, *S1=NULL;-PRIVATE int         with_gquad = 0;--PRIVATE FLT_OR_DBL  *G = NULL, *Gj = NULL, *Gj1 = NULL;--#ifdef _OPENMP--#pragma omp threadprivate(q, qb, qm, qm1, qqm, qqm1, qq, qq1, prml, prm_l, prm_l1, q1k, qln,\-                          probs, scale, expMLbase, qo, qho, qio, qmo, qm2, jindx, my_iindx, init_length,\-                          circular, pstruc, sequence, ptype, pf_params, S, S1, do_bppm, struct_constrained,\-                          G, Gj, Gj1, with_gquad)--#endif--/*-#################################-# PRIVATE FUNCTION DECLARATIONS #-#################################-*/-PRIVATE void  init_partfunc(int length, pf_paramT *parameters);-PRIVATE void  scale_pf_params(unsigned int length, pf_paramT *parameters);-PRIVATE void  get_arrays(unsigned int length);-PRIVATE void  make_ptypes(const short *S, const char *structure);-PRIVATE void  pf_circ(const char *sequence, char *structure);-PRIVATE void  pf_linear(const char *sequence, char *structure);-PRIVATE void  pf_create_bppm(const char *sequence, char *structure);-PRIVATE void  backtrack(int i, int j);-PRIVATE void  backtrack_qm(int i, int j);-PRIVATE void  backtrack_qm1(int i,int j);-PRIVATE void  backtrack_qm2(int u, int n);--/*-#################################-# BEGIN OF FUNCTION DEFINITIONS #-#################################-*/--PRIVATE void init_partfunc(int length, pf_paramT *parameters){-  if (length<1) nrerror("init_pf_fold: length must be greater 0");--#ifdef _OPENMP-/* Explicitly turn off dynamic threads */-  omp_set_dynamic(0);-  free_pf_arrays(); /* free previous allocation */-#else-  if (init_length>0) free_pf_arrays(); /* free previous allocation */-#endif--#ifdef SUN4-  nonstandard_arithmetic();-#else-#ifdef HP9-  fpsetfastmode(1);-#endif-#endif-  make_pair_matrix();-  get_arrays((unsigned) length);-  scale_pf_params((unsigned) length, parameters);--  init_length = length;-}--PRIVATE void get_arrays(unsigned int length){-  unsigned int size;--  if((length +1) >= (unsigned int)sqrt((double)INT_MAX))-    nrerror("get_arrays@part_func.c: sequence length exceeds addressable range");--  size  = sizeof(FLT_OR_DBL) * ((length+1)*(length+2)/2);--  q     = (FLT_OR_DBL *) space(size);-  qb    = (FLT_OR_DBL *) space(size);-  qm    = (FLT_OR_DBL *) space(size);-  qm1   = (st_back || circular) ? (FLT_OR_DBL *) space(size) : NULL;-  qm2   = (circular) ? (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2)) : NULL;-  probs = (do_bppm) ? (FLT_OR_DBL *) space(size) : NULL;--  ptype     = (char *) space(sizeof(char)*((length+1)*(length+2)/2));-  q1k       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));-  qln       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qq        = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qq1       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qqm       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qqm1      = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prm_l     = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prm_l1    = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prml      = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  expMLbase = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));-  scale     = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));--  Gj        = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  Gj1       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));--  my_iindx  = get_iindx(length);-  iindx     = get_iindx(length); /* for backward compatibility and Perl wrapper */-  jindx     = get_indx(length);-}--/**-*** Allocate memory for all matrices and other stuff-**/-PUBLIC void free_pf_arrays(void){-  if(q)         free(q);-  if(qb)        free(qb);-  if(qm)        free(qm);-  if(qm1)       free(qm1);-  if(qm2)       free(qm2);-  if(ptype)     free(ptype);-  if(qq)        free(qq);-  if(qq1)       free(qq1);-  if(qqm)       free(qqm);-  if(qqm1)      free(qqm1);-  if(q1k)       free(q1k);-  if(qln)       free(qln);-  if(probs)     free(probs);-  if(prm_l)     free(prm_l);-  if(prm_l1)    free(prm_l1);-  if(prml)      free(prml);-  if(expMLbase) free(expMLbase);-  if(scale)     free(scale);-  if(my_iindx)  free(my_iindx);-  if(iindx)     free(iindx); /* for backward compatibility and Perl wrapper */-  if(jindx)     free(jindx);-  if(S)         free(S);-  if(S1)        free(S1);-  if(G)         free(G);-  if(Gj)        free(Gj);-  if(Gj1)       free(Gj1);--  S = S1 = NULL;-  q = pr = probs = qb = qm = qm1 = qm2 = qq = qq1 = qqm = qqm1 = q1k = qln = prm_l = prm_l1 = prml = expMLbase = scale = G = Gj = Gj1 = NULL;-  my_iindx = jindx = iindx = NULL;--  ptype = NULL;--#ifdef SUN4-  standard_arithmetic();-#else-#ifdef HP9-  fpsetfastmode(0);-#endif-#endif--  init_length = 0;-}--/*-----------------------------------------------------------------*/-PUBLIC float pf_fold(const char *sequence, char *structure){-  return pf_fold_par(sequence, structure, NULL, do_backtrack, fold_constrained, 0);-}--PUBLIC float pf_circ_fold(const char *sequence, char *structure){-  return pf_fold_par(sequence, structure, NULL, do_backtrack, fold_constrained, 1);-}--PUBLIC float pf_fold_par( const char *sequence,-                          char *structure,-                          pf_paramT *parameters,-                          int calculate_bppm,-                          int is_constrained,-                          int is_circular){--  FLT_OR_DBL  Q;-  double      free_energy;-  int         n = (int) strlen(sequence);--  circular            = is_circular;-  do_bppm             = calculate_bppm;-  struct_constrained  = is_constrained;--#ifdef _OPENMP-  init_partfunc(n, parameters);-#else-  if(parameters) init_partfunc(n, parameters);-  else if (n > init_length) init_partfunc(n, parameters);-  else if (fabs(pf_params->temperature - temperature)>1e-6) update_pf_params_par(n, parameters);-#endif--  with_gquad  = pf_params->model_details.gquad;-  S           = encode_sequence(sequence, 0);-  S1          = encode_sequence(sequence, 1);--  make_ptypes(S, structure);--  /* do the linear pf fold and fill all matrices  */-  pf_linear(sequence, structure);--  if(circular)-    pf_circ(sequence, structure); /* do post processing step for circular RNAs */--  if (backtrack_type=='C')      Q = qb[my_iindx[1]-n];-  else if (backtrack_type=='M') Q = qm[my_iindx[1]-n];-  else Q = (circular) ? qo : q[my_iindx[1]-n];--  /* ensemble free energy in Kcal/mol              */-  if (Q<=FLT_MIN) fprintf(stderr, "pf_scale too large\n");-  free_energy = (-log(Q)-n*log(pf_params->pf_scale))*pf_params->kT/1000.0;-  /* in case we abort because of floating point errors */-  if (n>1600) fprintf(stderr, "free energy = %8.2f\n", free_energy);--  /* calculate base pairing probability matrix (bppm)  */-  if(do_bppm){-    pf_create_bppm(sequence, structure);-    /*-    *  Backward compatibility:-    *  This block may be removed if deprecated functions-    *  relying on the global variable "pr" vanish from within the package!-    */-    pr = probs;-    /*-     {-      if(pr) free(pr);-      pr = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));-      memcpy(pr, probs, sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));-    }-    */-  }-  return free_energy;-}--PRIVATE void pf_linear(const char *sequence, char *structure){--  int n, i,j,k,l, ij, u,u1,d,ii, type, type_2, tt, minl, maxl;--  int noGUclosure;-  FLT_OR_DBL expMLstem = 0.;--  FLT_OR_DBL temp, Qmax=0;-  FLT_OR_DBL qbt1, *tmp;--  FLT_OR_DBL  expMLclosing = pf_params->expMLclosing;-  double      max_real;--  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;--  n = (int) strlen(sequence);---  noGUclosure = pf_params->model_details.noGUclosure;--  /*array initialization ; qb,qm,q-    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */--  if(with_gquad){-    expMLstem = exp_E_MLstem(0, -1, -1, pf_params);-    G         = get_gquad_pf_matrix(S, scale, pf_params);-  }--  for (d=0; d<=TURN; d++)-    for (i=1; i<=n-d; i++) {-      j=i+d;-      ij = my_iindx[i]-j;-      q[ij]=1.0*scale[d+1];-      qb[ij]=qm[ij]=0.0;-    }- -  for (i=1; i<=n; i++)-    qq[i]=qq1[i]=qqm[i]=qqm1[i]=0;--  for (j=TURN+2;j<=n; j++) {-    for (i=j-TURN-1; i>=1; i--) {-      /* construction of partition function of segment i,j*/-      /*firstly that given i binds j : qb(i,j) */-      u = j-i-1; ij = my_iindx[i]-j;-      type = ptype[ij];-      if (type!=0) {-        /*hairpin contribution*/-        if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;-        else-          qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params) * scale[u+2];-        /* interior loops with interior pair k,l */-        for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {-          u1 = k-i-1;-          for (l=MAX2(k+TURN+1,j-1-MAXLOOP+u1); l<j; l++) {-            type_2 = ptype[my_iindx[k]-l];-            if (type_2) {-              type_2 = rtype[type_2];-              qbt1 += qb[my_iindx[k]-l] * (scale[u1+j-l+1] *-                                        exp_E_IntLoop(u1, j-l-1, type, type_2,-                                        S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params));-            }-          }-        }-        /*multiple stem loop contribution*/-        ii = my_iindx[i+1]; /* ii-k=[i+1,k-1] */-        temp = 0.0;-        for (k=i+2; k<=j-1; k++) temp += qm[ii-(k-1)]*qqm1[k];-        tt = rtype[type];-        qbt1 += temp * expMLclosing * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params) * scale[2];--        if(with_gquad){-          qbt1 += exp_E_GQuad_IntLoop(i, j, type, S1, G, my_iindx, pf_params) * scale[2];-        }--        qb[ij] = qbt1;-      }-      /* end if (type!=0) */-      else-        qb[ij] = 0.0;--      /* construction of qqm matrix containing final stem-         contributions to multiple loop partition function-         from segment i,j */-      qqm[i] = qqm1[i]*expMLbase[1];-      if (type) {-        qbt1 = qb[ij] * exp_E_MLstem(type, ((i>1) || circular) ? S1[i-1] : -1, ((j<n) || circular) ? S1[j+1] : -1, pf_params);-        qqm[i] += qbt1;-      }--      if(with_gquad){-        /*include gquads into qqm*/-        qqm[i] += G[my_iindx[i]-j] * expMLstem;-      }--      if (qm1) qm1[jindx[j]+i] = qqm[i]; /* for stochastic backtracking and circfold */--      /*construction of qm matrix containing multiple loop-        partition function contributions from segment i,j */-      temp = 0.0;-      ii = my_iindx[i];  /* ii-k=[i,k-1] */-      for (k=j; k>i; k--) temp += (qm[ii-(k-1)] + expMLbase[k-i])*qqm[k];-      qm[ij] = (temp + qqm[i]);--      /*auxiliary matrix qq for cubic order q calculation below */-      qbt1=0.0;-      if (type){-        qbt1 += qb[ij];-        qbt1 *= exp_E_ExtLoop(type, ((i>1) || circular) ? S1[i-1] : -1, ((j<n) || circular) ? S1[j+1] : -1, pf_params);-      }--      if(with_gquad){-        qbt1 += G[ij];-      }--      qq[i] = qq1[i]*scale[1] + qbt1;--      /*construction of partition function for segment i,j */-      temp = 1.0*scale[1+j-i] + qq[i];-      for (k=i; k<=j-1; k++) temp += q[ii-k]*qq[k+1];-      q[ij] = temp;-      if (temp>Qmax) {-        Qmax = temp;-        if (Qmax>max_real/10.)-          fprintf(stderr, "Q close to overflow: %d %d %g\n", i,j,temp);-      }-      if (temp>=max_real) {-        PRIVATE char msg[128];-        sprintf(msg, "overflow in pf_fold while calculating q[%d,%d]\n"-                     "use larger pf_scale", i,j);-        nrerror(msg);-      }-    }-    tmp = qq1;  qq1 =qq;  qq =tmp;-    tmp = qqm1; qqm1=qqm; qqm=tmp;--    if(with_gquad){ /* rotate the auxilary g-quadruplex matrices */-      tmp = Gj1; Gj1=Gj; Gj=tmp;-    }-  }-}--/* calculate partition function for circular case */-/* NOTE: this is the postprocessing step ONLY     */-/* You have to call pf_linear first to calculate  */-/* complete circular case!!!                      */-PRIVATE void pf_circ(const char *sequence, char *structure){--  int u, p, q, k, l;-  int noGUclosure;-  int n = (int) strlen(sequence);--  FLT_OR_DBL  qot;-  FLT_OR_DBL  expMLclosing  = pf_params->expMLclosing;--  noGUclosure = pf_params->model_details.noGUclosure;-  qo = qho = qio = qmo = 0.;--  /* construct qm2 matrix from qm1 entries  */-  for(k=1; k<n-TURN-1; k++){-    qot = 0.;-    for (u=k+TURN+1; u<n-TURN-1; u++)-      qot += qm1[jindx[u]+k]*qm1[jindx[n]+(u+1)];-    qm2[k] = qot;-   }--  for(p = 1; p < n; p++){-    for(q = p + TURN + 1; q <= n; q++){-      int type;-      /* 1. get exterior hairpin contribution  */-      u = n-q + p-1;-      if (u<TURN) continue;-      type = ptype[my_iindx[p]-q];-      if (!type) continue;-       /* cause we want to calc the exterior loops, we need the reversed pair type from now on  */-      type=rtype[type];--      char loopseq[10];-      if (u<7){-        strcpy(loopseq , sequence+q-1);-        strncat(loopseq, sequence, p);-      }-      qho += (((type==3)||(type==4))&&noGUclosure) ? 0. : qb[my_iindx[p]-q] * exp_E_Hairpin(u, type, S1[q+1], S1[p-1],  loopseq, pf_params) * scale[u];--      /* 2. exterior interior loops, i "define" the (k,l) pair as "outer pair"  */-      /* so "outer type" is rtype[type[k,l]] and inner type is type[p,q]        */-      qot = 0.;-      for(k=q+1; k < n; k++){-        int ln1, lstart;-        ln1 = k - q - 1;-        if(ln1+p-1>MAXLOOP) break;-        lstart = ln1+p-1+n-MAXLOOP;-        if(lstart<k+TURN+1) lstart = k + TURN + 1;-        for(l=lstart;l <= n; l++){-          int ln2, type2;-          ln2 = (p - 1) + (n - l);--          if((ln1+ln2) > MAXLOOP) continue;--          type2 = ptype[my_iindx[k]-l];-          if(!type2) continue;-          qio += qb[my_iindx[p]-q] * qb[my_iindx[k]-l] * exp_E_IntLoop(ln2, ln1, rtype[type2], type, S1[l+1], S1[k-1], S1[p-1], S1[q+1], pf_params) * scale[ln1+ln2];-        }-      } /* end of kl double loop */-    }-  } /* end of pq double loop */--  /* 3. Multiloops  */-  for(k=TURN+2; k<n-2*TURN-3; k++)-    qmo += qm[my_iindx[1]-k] * qm2[k+1] * expMLclosing;--  /* add an additional pf of 1.0 to take the open chain into account too           */-  qo = qho + qio + qmo + 1.0*scale[n];-}--/* calculate base pairing probs */-PUBLIC void pf_create_bppm(const char *sequence, char *structure){-  int n, i,j,k,l, ij, kl, ii, i1, ll, type, type_2, tt, u1, ov=0;-  FLT_OR_DBL  temp, Qmax=0, prm_MLb;-  FLT_OR_DBL  prmt,prmt1;-  FLT_OR_DBL  *tmp;-  FLT_OR_DBL  tmp2;-  FLT_OR_DBL  expMLclosing = pf_params->expMLclosing;-  double      max_real;--  FLT_OR_DBL  expMLstem = (with_gquad) ? exp_E_MLstem(0, -1, -1, pf_params) : 0;--  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;--  if((S != NULL) && (S1 != NULL)){-    n = S[0];-    Qmax=0;--    for (k=1; k<=n; k++) {-      q1k[k] = q[my_iindx[1] - k];-      qln[k] = q[my_iindx[k] -n];-    }-    q1k[0] = 1.0;-    qln[n+1] = 1.0;--/*  pr = q; */     /* recycling */---    /* 1. exterior pair i,j and initialization of pr array */-    if(circular){-      for (i=1; i<=n; i++) {-        for (j=i; j<=MIN2(i+TURN,n); j++)-          probs[my_iindx[i]-j] = 0;-        for (j=i+TURN+1; j<=n; j++) {-          ij = my_iindx[i]-j;-          type = ptype[ij];-          if (type&&(qb[ij]>0.)) {-            probs[ij] = 1./qo;-            int rt = rtype[type];--            /* 1.1. Exterior Hairpin Contribution */-            int u = i + n - j -1;-            /* get the loop sequence */-            char loopseq[10];-            if (u<7){-              strcpy(loopseq , sequence+j-1);-              strncat(loopseq, sequence, i);-            }-            tmp2 = exp_E_Hairpin(u, rt, S1[j+1], S1[i-1], loopseq, pf_params) * scale[u];--            /* 1.2. Exterior Interior Loop Contribution                    */-            /* 1.2.1. i,j  delimtis the "left" part of the interior loop    */-            /* (j,i) is "outer pair"                                                */-            for(k=1; k < i-TURN-1; k++){-              int ln1, lstart;-              ln1 = k + n - j - 1;-              if(ln1>MAXLOOP) break;-              lstart = ln1+i-1-MAXLOOP;-              if(lstart<k+TURN+1) lstart = k + TURN + 1;-              for(l=lstart; l < i; l++){-                int ln2, type_2;-                type_2 = ptype[my_iindx[k]-l];-                if (type_2==0) continue;-                ln2 = i - l - 1;-                if(ln1+ln2>MAXLOOP) continue;-                tmp2 += qb[my_iindx[k] - l]-                        * exp_E_IntLoop(ln1,-                                        ln2,-                                        rt,-                                        rtype[type_2],-                                        S1[j+1],-                                        S1[i-1],-                                        S1[k-1],-                                        S1[l+1],-                                        pf_params)-                        * scale[ln1 + ln2];-              }-            }-            /* 1.2.2. i,j  delimtis the "right" part of the interior loop  */-            for(k=j+1; k < n-TURN; k++){-              int ln1, lstart;-              ln1 = k - j - 1;-              if((ln1 + i - 1)>MAXLOOP) break;-              lstart = ln1+i-1+n-MAXLOOP;-              if(lstart<k+TURN+1) lstart = k + TURN + 1;-              for(l=lstart; l <= n; l++){-                int ln2, type_2;-                type_2 = ptype[my_iindx[k]-l];-                if (type_2==0) continue;-                ln2 = i - 1 + n - l;-                if(ln1+ln2>MAXLOOP) continue;-                tmp2 += qb[my_iindx[k] - l]-                        * exp_E_IntLoop(ln2,-                                        ln1,-                                        rtype[type_2],-                                        rt,-                                        S1[l+1],-                                        S1[k-1],-                                        S1[i-1],-                                        S1[j+1],-                                        pf_params)-                        * scale[ln1 + ln2];-              }-            }-            /* 1.3 Exterior multiloop decomposition */-            /* 1.3.1 Middle part                    */-            if((i>TURN+2) && (j<n-TURN-1))-              tmp2 += qm[my_iindx[1]-i+1]-                      * qm[my_iindx[j+1]-n]-                      * expMLclosing-                      * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);--            /* 1.3.2 Left part                      */-            for(k=TURN+2; k < i-TURN-2; k++)-              tmp2 += qm[my_iindx[1]-k]-                      * qm1[jindx[i-1]+k+1]-                      * expMLbase[n-j]-                      * expMLclosing-                      * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);--            /* 1.3.3 Right part                      */-            for(k=j+TURN+2; k < n-TURN-1;k++)-              tmp2 += qm[my_iindx[j+1]-k]-                      * qm1[jindx[n]+k+1]-                      * expMLbase[i-1]-                      * expMLclosing-                      * exp_E_MLstem(type, S1[i-1], S1[j+1], pf_params);--            /* all exterior loop decompositions for pair i,j done  */-            probs[ij] *= tmp2;--          }-          else probs[ij] = 0;-        }-      }-    } /* end if(circular)  */-    else {-      for (i=1; i<=n; i++) {-        for (j=i; j<=MIN2(i+TURN,n); j++) probs[my_iindx[i]-j] = 0;-        for (j=i+TURN+1; j<=n; j++) {-          ij = my_iindx[i]-j;-          type = ptype[ij];-          if (type&&(qb[ij]>0.)) {-            probs[ij] = q1k[i-1]*qln[j+1]/q1k[n];-            probs[ij] *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);-          }-          else-            probs[ij] = 0.;-        }-      }-    } /* end if(!circular)  */--    for (l=n; l>TURN+1; l--) {--      /* 2. bonding k,l as substem of 2:loop enclosed by i,j */-      for (k=1; k<l-TURN; k++) {-        kl = my_iindx[k]-l;-        type_2 = ptype[kl]; -        if (type_2==0) continue;-        type_2 = rtype[type_2];-        if (qb[kl]==0.) continue;--        tmp2 = 0.;-        for (i=MAX2(1,k-MAXLOOP-1); i<=k-1; i++)-          for (j=l+1; j<=MIN2(l+ MAXLOOP -k+i+2,n); j++) {-            ij = my_iindx[i] - j;-            type = ptype[ij];-            if (type && (probs[ij]>0.)) {-              /* add *scale[u1+u2+2] */-              tmp2 +=  probs[ij]-                       * (scale[k-i+j-l]-                       * exp_E_IntLoop(k - i - 1,-                                       j - l - 1,-                                       type,-                                       type_2,-                                       S1[i + 1],-                                       S1[j - 1],-                                       S1[k - 1],-                                       S1[l + 1],-                                       pf_params));-            }-          }-        probs[kl] += tmp2;-      }--      if(with_gquad){-        /* 2.5. bonding k,l as gquad enclosed by i,j */-        FLT_OR_DBL *expintern = &(pf_params->expinternal[0]);-        FLT_OR_DBL qe;--        if(l < n - 3){-          for(k = 2; k <= l - VRNA_GQUAD_MIN_BOX_SIZE; k++){-            kl = my_iindx[k]-l;-            if (G[kl]==0.) continue;-            tmp2 = 0.;-            i = k - 1;-            for(j = MIN2(l + MAXLOOP + 1, n); j > l + 3; j--){-              ij = my_iindx[i] - j;-              type = ptype[ij];-              if(!type) continue;-              qe = (type > 2) ? pf_params->expTermAU : 1.;-              tmp2 += probs[ij] * qe * expintern[j-l-1] * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]] * scale[2];-            }-            probs[kl] += tmp2 * G[kl];-          }-        }--        if (l < n - 1){-          for (k=3; k<=l-VRNA_GQUAD_MIN_BOX_SIZE; k++) {-            kl = my_iindx[k]-l;-            if (G[kl]==0.) continue;-            tmp2 = 0.;-            for (i=MAX2(1,k-MAXLOOP-1); i<=k-2; i++){-              u1 = k - i - 1;-              for (j=l+2; j<=MIN2(l + MAXLOOP - u1 + 1,n); j++) {-                ij = my_iindx[i] - j;-                type = ptype[ij];-                if(!type) continue;-                qe = (type > 2) ? pf_params->expTermAU : 1.;-                tmp2 += probs[ij] * qe * expintern[u1+j-l-1] * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]] * scale[2];-              }-            }-            probs[kl] += tmp2 * G[kl];-          }-        }--        if(l < n){-          for(k = 4; k <= l - VRNA_GQUAD_MIN_BOX_SIZE; k++){-            kl = my_iindx[k]-l;-            if (G[kl]==0.) continue;-            tmp2 = 0.;-            j = l + 1;-            for (i=MAX2(1,k-MAXLOOP-1); i < k - 3; i++){-              ij = my_iindx[i] - j;-              type = ptype[ij];-              if(!type) continue;-              qe = (type > 2) ? pf_params->expTermAU : 1.;-              tmp2 += probs[ij] * qe * expintern[k - i - 1] * pf_params->expmismatchI[type][S1[i+1]][S1[j-1]] * scale[2];-            }-            probs[kl] += tmp2 * G[kl];-          }-        }-      }--      /* 3. bonding k,l as substem of multi-loop enclosed by i,j */-      prm_MLb = 0.;-      if (l<n) for (k=2; k<l-TURN; k++) {-        i = k-1;-        prmt = prmt1 = 0.0;--        ii = my_iindx[i];     /* ii-j=[i,j]     */-        ll = my_iindx[l+1];   /* ll-j=[l+1,j-1] */-        tt = ptype[ii-(l+1)]; tt=rtype[tt];-        /* (i, l+1) closes the ML with substem (k,l) */-        if(tt)-          prmt1 = probs[ii-(l+1)] * expMLclosing * exp_E_MLstem(tt, S1[l], S1[i+1], pf_params);--        /* (i,j) with j>l+1 closes the ML with substem (k,l) */-        for (j=l+2; j<=n; j++) {-          tt = ptype[ii-j]; tt = rtype[tt];-          if(tt)-            prmt += probs[ii-j] * exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params) * qm[ll-(j-1)];-        }-        kl = my_iindx[k]-l;-        tt = ptype[kl];-        prmt *= expMLclosing;-        prml[ i] = prmt;-        prm_l[i] = prm_l1[i]*expMLbase[1]+prmt1;--        prm_MLb = prm_MLb*expMLbase[1] + prml[i];-        /* same as:    prm_MLb = 0;-           for (i=1; i<=k-1; i++) prm_MLb += prml[i]*expMLbase[k-i-1]; */--        prml[i] = prml[ i] + prm_l[i];--        if(with_gquad){-          if ((!tt) && (G[kl] == 0.)) continue;-        } else {-          if (qb[kl] == 0.) continue;-        }--        temp = prm_MLb;--        for (i=1;i<=k-2; i++)-          temp += prml[i]*qm[my_iindx[i+1] - (k-1)];--        if(with_gquad){-          if(tt)-            temp    *= exp_E_MLstem(tt, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params) * scale[2];-          else-            temp    *= G[kl] * expMLstem * scale[2];-        } else {-          temp    *= exp_E_MLstem(tt, (k>1) ? S1[k-1] : -1, (l<n) ? S1[l+1] : -1, pf_params) * scale[2];-        }--        probs[kl]  += temp;--        if (probs[kl]>Qmax) {-          Qmax = probs[kl];-          if (Qmax>max_real/10.)-            fprintf(stderr, "P close to overflow: %d %d %g %g\n",-              i, j, probs[kl], qb[kl]);-        }-        if (probs[kl]>=max_real) {-          ov++;-          probs[kl]=FLT_MAX;-        }--      } /* end for (k=..) */-      tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;--    }  /* end for (l=..)   */--    for (i=1; i<=n; i++)-      for (j=i+TURN+1; j<=n; j++) {-        ij = my_iindx[i]-j;--        if(with_gquad){-          if (qb[ij] > 0.)-            probs[ij] *= qb[ij];-          if (G[ij] > 0.){-            probs[ij] += q1k[i-1] * G[ij] * qln[j+1]/q1k[n];-          }-        } else {-          if (qb[ij] > 0.)-            probs[ij] *= qb[ij];-        }-      }--    if (structure!=NULL)-      bppm_to_structure(structure, probs, n);-    if (ov>0) fprintf(stderr, "%d overflows occurred while backtracking;\n"-        "you might try a smaller pf_scale than %g\n",-        ov, pf_params->pf_scale);-  } /* end if((S != NULL) && (S1 != NULL))  */-  else-    nrerror("bppm calculations have to be done after calling forward recursion\n");-  return;-}--PRIVATE void scale_pf_params(unsigned int length, pf_paramT *parameters){-  unsigned int  i;-  double        scaling_factor;--  if(pf_params) free(pf_params);--  if(parameters){-    pf_params = get_boltzmann_factor_copy(parameters);-  } else {-    model_detailsT md;-    set_model_details(&md);-    pf_params = get_boltzmann_factors(temperature, 1.0, md, pf_scale);-  }--  scaling_factor = pf_params->pf_scale;--  /* scaling factors (to avoid overflows) */-  if (scaling_factor == -1) { /* mean energy for random sequences: 184.3*length cal */-    scaling_factor = exp(-(-185+(pf_params->temperature-37.)*7.27)/pf_params->kT);-    if (scaling_factor<1) scaling_factor=1;-    pf_params->pf_scale = scaling_factor;-    pf_scale = pf_params->pf_scale; /* compatibility with RNAup, may be removed sometime */-  }-  scale[0] = 1.;-  scale[1] = 1./scaling_factor;-  expMLbase[0] = 1;-  expMLbase[1] = pf_params->expMLbase/scaling_factor;-  for (i=2; i<=length; i++) {-    scale[i] = scale[i/2]*scale[i-(i/2)];-    expMLbase[i] = pow(pf_params->expMLbase, (double)i) * scale[i];-  }-}--/*---------------------------------------------------------------------------*/--PUBLIC void update_pf_params(int length){-  update_pf_params_par(length, NULL);-}--PUBLIC void update_pf_params_par(int length, pf_paramT *parameters){-#ifdef _OPENMP-  make_pair_matrix(); /* is this really necessary? */-  scale_pf_params((unsigned) length, parameters);-#else-  if(parameters) init_partfunc(length, parameters);-  else if (length>init_length) init_partfunc(length, parameters);  /* init not update */-  else {-    make_pair_matrix();-    scale_pf_params((unsigned) length, parameters);-  }-#endif-}--/*---------------------------------------------------------------------------*/--PUBLIC char bppm_symbol(const float *x){-/*  if( ((x[1]-x[2])*(x[1]-x[2]))<0.1&&x[0]<=0.677) return '|'; */-  if( x[0] > 0.667 )  return '.';-  if( x[1] > 0.667 )  return '(';-  if( x[2] > 0.667 )  return ')';-  if( (x[1]+x[2]) > x[0] ) {-    if( (x[1]/(x[1]+x[2])) > 0.667) return '{';-    if( (x[2]/(x[1]+x[2])) > 0.667) return '}';-    else return '|';-  }-  if( x[0] > (x[1]+x[2]) ) return ',';-  return ':';-}--PUBLIC void bppm_to_structure(char *structure, FLT_OR_DBL *p, unsigned int length){-  int    i, j;-  int   *index = get_iindx(length);-  float  P[3];   /* P[][0] unpaired, P[][1] upstream p, P[][2] downstream p */--  for( j=1; j<=length; j++ ) {-    P[0] = 1.0;-    P[1] = P[2] = 0.0;-    for( i=1; i<j; i++) {-      P[2] += p[index[i]-j];    /* j is paired downstream */-      P[0] -= p[index[i]-j];    /* j is unpaired */-    }-    for( i=j+1; i<=length; i++ ) {-      P[1] += p[index[j]-i];    /* j is paired upstream */-      P[0] -= p[index[j]-i];    /* j is unpaired */-    }-    structure[j-1] = bppm_symbol(P);-  }-  structure[length] = '\0';-  free(index);-}---/*---------------------------------------------------------------------------*/-PRIVATE void make_ptypes(const short *S, const char *structure){-  int n,i,j,k,l, noLP;--  noLP = pf_params->model_details.noLP;--  n=S[0];-  for (k=1; k<n-TURN; k++)-    for (l=1; l<=2; l++) {-      int type,ntype=0,otype=0;-      i=k; j = i+TURN+l; if (j>n) continue;-      type = pair[S[i]][S[j]];-      while ((i>=1)&&(j<=n)) {-        if ((i>1)&&(j<n)) ntype = pair[S[i-1]][S[j+1]];-        if (noLP && (!otype) && (!ntype))-          type = 0; /* i.j can only form isolated pairs */-        qb[my_iindx[i]-j] = 0.;-        ptype[my_iindx[i]-j] = (char) type;-        otype =  type;-        type  = ntype;-        i--; j++;-      }-    }--  if (struct_constrained && (structure != NULL))-    constrain_ptypes(structure, (unsigned int)n, ptype, NULL, TURN, 1);-}--/*-  stochastic backtracking in pf_fold arrays-  returns random structure S with Boltzman probabilty-  p(S) = exp(-E(S)/kT)/Z-*/-char *pbacktrack(char *seq){-  double r, qt;-  int i,j,n, start;-  sequence = seq;-  n = strlen(sequence);--  if (init_length<1)-    nrerror("can't backtrack without pf arrays.\n"-            "Call pf_fold() before pbacktrack()");-  pstruc = space((n+1)*sizeof(char));--  for (i=0; i<n; i++) pstruc[i] = '.';--  start = 1;-  while (start<n) {-  /* find i position of first pair */-    for (i=start; i<n; i++) {-      r = urn() * qln[i];-      if (r > qln[i+1]*scale[1])  break; /* i is paired */-    }-    if (i>=n) break; /* no more pairs */-    /* now find the pairing partner j */-    r = urn() * (qln[i] - qln[i+1]*scale[1]);-    for (qt=0, j=i+1; j<=n; j++) {-      int type;-      type = ptype[my_iindx[i]-j];-      if (type) {-        double qkl;-        qkl = qb[my_iindx[i]-j];-        if (j<n) qkl *= qln[j+1];-        qkl *=  exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);-        qt += qkl;-        if (qt > r) break; /* j is paired */-      }-    }-    if (j==n+1) nrerror("backtracking failed in ext loop");-    start = j+1;-    backtrack(i,j);-  }--  return pstruc;-}-char *pbacktrack_circ(char *seq){-  double r, qt;-  int i, j, k, l, n;-  FLT_OR_DBL  expMLclosing      = pf_params->expMLclosing;--  sequence = seq;-  n = strlen(sequence);--  if (init_length<1)-    nrerror("can't backtrack without pf arrays.\n"-      "Call pf_circ_fold() before pbacktrack_circ()");-  pstruc = space((n+1)*sizeof(char));--  /* initialize pstruct with single bases  */-  for (i=0; i<n; i++) pstruc[i] = '.';--  qt = 1.0*scale[n];-  r = urn() * qo;--  /* open chain? */-  if(qt > r) return pstruc;--  for(i=1; (i < n); i++){-    for(j=i+TURN+1;(j<=n); j++){--      int type, u;-      /* 1. first check, wether we can do a hairpin loop  */-      u = n-j + i-1;-      if (u<TURN) continue;--      type = ptype[my_iindx[i]-j];-      if (!type) continue;--      type=rtype[type];--      char loopseq[10];-      if (u<7){-        strcpy(loopseq , sequence+j-1);-        strncat(loopseq, sequence, i);-      }--      qt += qb[my_iindx[i]-j] * exp_E_Hairpin(u, type, S1[j+1], S1[i-1],  loopseq, pf_params) * scale[u];-      /* found a hairpin? so backtrack in the enclosed part and we're done  */-      if(qt>r){ backtrack(i,j); return pstruc;}--      /* 2. search for (k,l) with which we can close an interior loop  */-      for(k=j+1; (k < n); k++){-        int ln1, lstart;-        ln1 = k - j - 1;-        if(ln1+i-1>MAXLOOP) break;--        lstart = ln1+i-1+n-MAXLOOP;-        if(lstart<k+TURN+1) lstart = k + TURN + 1;-        for(l=lstart; (l <= n); l++){-            int ln2, type2;-            ln2 = (i - 1) + (n - l);-            if((ln1+ln2) > MAXLOOP) continue;--            type2 = ptype[my_iindx[k]-l];-            if(!type) continue;-            type2 = rtype[type2];-            qt += qb[my_iindx[i]-j] * qb[my_iindx[k]-l] * exp_E_IntLoop(ln2, ln1, type2, type, S1[l+1], S1[k-1], S1[i-1], S1[j+1], pf_params) * scale[ln1 + ln2];-            /* found an exterior interior loop? also this time, we can go straight  */-            /* forward and backtracking the both enclosed parts and we're done      */-            if(qt>r){ backtrack(i,j); backtrack(k,l); return pstruc;}-        }-      } /* end of kl double loop */-    }-  } /* end of ij double loop  */-  {-    /* as we reach this part, we have to search for our barrier between qm and qm2  */-    qt = 0.;-    r = urn()*qmo;-    for(k=TURN+2; k<n-2*TURN-3; k++){-      qt += qm[my_iindx[1]-k] * qm2[k+1] * expMLclosing;-      /* backtrack in qm and qm2 if we've found a valid barrier k  */-      if(qt>r){ backtrack_qm(1,k); backtrack_qm2(k+1,n); return pstruc;}-    }-  }-  /* if we reach the actual end of this function, an error has occured  */-  /* cause we HAVE TO find an exterior loop or an open chain!!!         */-  nrerror("backtracking failed in exterior loop");-  return pstruc;-}--PRIVATE void backtrack_qm(int i, int j){-  /* divide multiloop into qm and qm1  */-  double qmt, r;-  int k;-  while(j>i){-    /* now backtrack  [i ... j] in qm[] */-    r = urn() * qm[my_iindx[i] - j];-    qmt = qm1[jindx[j]+i]; k=i;-    if(qmt<r)-      for(k=i+1; k<=j; k++){-        qmt += (qm[my_iindx[i]-(k-1)]+expMLbase[k-i])*qm1[jindx[j]+k];-        if(qmt >= r) break;-      }-    if(k>j) nrerror("backtrack failed in qm");--    backtrack_qm1(k,j);--    if(k<i+TURN) break; /* no more pairs */-    r = urn() * (qm[my_iindx[i]-(k-1)] + expMLbase[k-i]);-    if(expMLbase[k-i] >= r) break; /* no more pairs */-    j = k-1;-  }-}--PRIVATE void backtrack_qm1(int i,int j){-  /* i is paired to l, i<l<j; backtrack in qm1 to find l */-  int ii, l, type;-  double qt, r;-  r = urn() * qm1[jindx[j]+i];-  ii = my_iindx[i];-  for (qt=0., l=i+TURN+1; l<=j; l++) {-    type = ptype[ii-l];-    if (type)-      qt +=  qb[ii-l] * exp_E_MLstem(type, S1[i-1], S1[l+1], pf_params) * expMLbase[j-l];-    if (qt>=r) break;-  }-  if (l>j) nrerror("backtrack failed in qm1");-  backtrack(i,l);-}--PRIVATE void backtrack_qm2(int k, int n){-  double qom2t, r;-  int u;-  r= urn()*qm2[k];-  /* we have to search for our barrier u between qm1 and qm1  */-  for (qom2t = 0.,u=k+TURN+1; u<n-TURN-1; u++){-    qom2t += qm1[jindx[u]+k]*qm1[jindx[n]+(u+1)];-    if(qom2t > r) break;-  }-  if(u==n-TURN) nrerror("backtrack failed in qm2");-  backtrack_qm1(k,u);-  backtrack_qm1(u+1,n);-}--PRIVATE void backtrack(int i, int j){-  int noGUclosure = pf_params->model_details.noGUclosure;--  do {-    double r, qbt1;-    int k, l, type, u, u1;--    pstruc[i-1] = '('; pstruc[j-1] = ')';--    r = urn() * qb[my_iindx[i]-j];-    type = ptype[my_iindx[i]-j];-    u = j-i-1;-    /*hairpin contribution*/-    if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;-    else-      qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params)*-        scale[u+2]; /* add scale[u+2] */--    if (qbt1>=r) return; /* found the hairpin we're done */--    for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {-      u1 = k-i-1;-      for (l=MAX2(k+TURN+1,j-1-MAXLOOP+u1); l<j; l++) {-        int type_2;-        type_2 = ptype[my_iindx[k]-l];-        if (type_2) {-          type_2 = rtype[type_2];-          /* add *scale[u1+u2+2] */-          qbt1 += qb[my_iindx[k]-l] * (scale[u1+j-l+1] *-            exp_E_IntLoop(u1, j-l-1, type, type_2,-                          S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params));-        }-        if (qbt1 > r) break;-      }-      if (qbt1 > r) break;-    }-    if (l<j) {-      i=k; j=l;-    }-    else break;-  } while (1);--  /* backtrack in multi-loop */-  {-    double r, qt;-    int k, ii, jj;--    i++; j--;-    /* find the first split index */-    ii = my_iindx[i]; /* ii-j=[i,j] */-    jj = jindx[j]; /* jj+i=[j,i] */-    for (qt=0., k=i+1; k<j; k++) qt += qm[ii-(k-1)]*qm1[jj+k];-    r = urn() * qt;-    for (qt=0., k=i+1; k<j; k++) {-      qt += qm[ii-(k-1)]*qm1[jj+k];-      if (qt>=r) break;-    }-    if (k>=j) nrerror("backtrack failed, can't find split index ");--    backtrack_qm1(k, j);--    j = k-1;-    backtrack_qm(i,j);-  }-}--PUBLIC void assign_plist_from_pr(plist **pl, FLT_OR_DBL *probs, int length, double cut_off){-  int i, j, n, count, *index;-  count = 0;-  n     = 2;--  index = get_iindx(length);--  /* first guess of the size needed for pl */-  *pl = (plist *)space(n*length*sizeof(plist));--  for (i=1; i<length; i++) {-    for (j=i+1; j<=length; j++) {-      /* skip all entries below the cutoff */-      if (probs[index[i]-j] < cut_off) continue;-      /* do we need to allocate more memory? */-      if (count == n * length - 1){-        n *= 2;-        *pl = (plist *)xrealloc(*pl, n * length * sizeof(plist));-      }-      (*pl)[count].i    = i;-      (*pl)[count].j    = j;-      (*pl)[count].p  = probs[index[i] - j];-      (*pl)[count++].type = 0;-    }-  }-  /* mark the end of pl */-  (*pl)[count].i   = 0;-  (*pl)[count].j   = 0;-  (*pl)[count].p = 0.;-  (*pl)[count++].type = 0;-  /* shrink memory to actual size needed */-  *pl = (plist *)xrealloc(*pl, count * sizeof(plist));--  free(index);-}--/* this doesn't work if free_pf_arrays() is called before */-PUBLIC void assign_plist_gquad_from_pr( plist **pl,-                                        int length,-                                        double cut_off){--  int i, j, k, n, count, *index;-  count = 0;-  n     = 2;--  if(!probs){ *pl = NULL; return;}--  index = get_iindx(length);--  /* first guess of the size needed for pl */-  *pl = (plist *)space(n*length*sizeof(plist));--  for (i=1; i<length; i++) {-    for (j=i+1; j<=length; j++) {-      /* skip all entries below the cutoff */-      if (probs[index[i]-j] < cut_off) continue;--      /* do we need to allocate more memory? */-      if (count == n * length - 1){-        n *= 2;-        *pl = (plist *)xrealloc(*pl, n * length * sizeof(plist));-      }--      /* check for presence of gquadruplex */-      if((S[i] == 3) && (S[j] == 3)){-          /* add probability of a gquadruplex at position (i,j)-             for dot_plot-          */-          (*pl)[count].i      = i;-          (*pl)[count].j      = j;-          (*pl)[count].p      = probs[index[i] - j];-          (*pl)[count++].type = 1;-          /* now add the probabilies of it's actual pairing patterns */-          plist *inner, *ptr;-          inner = get_plist_gquad_from_pr(S, i, j, G, probs, scale, pf_params);-          for(ptr=inner; ptr->i != 0; ptr++){-              if (count == n * length - 1){-                n *= 2;-                *pl = (plist *)xrealloc(*pl, n * length * sizeof(plist));-              }-              /* check if we've already seen this pair */-              for(k = 0; k < count; k++)-                if(((*pl)[k].i == ptr->i) && ((*pl)[k].j == ptr->j))-                  break;-              (*pl)[k].i      = ptr->i;-              (*pl)[k].j      = ptr->j;-              (*pl)[k].type = 0;-              if(k == count){-                (*pl)[k].p  = ptr->p;-                count++;-              } else-                (*pl)[k].p  += ptr->p;-          }-      } else {-          (*pl)[count].i      = i;-          (*pl)[count].j      = j;-          (*pl)[count].p      = probs[index[i] - j];-          (*pl)[count++].type = 0;-      }-    }-  }-  /* mark the end of pl */-  (*pl)[count].i   = 0;-  (*pl)[count].j   = 0;-  (*pl)[count++].p = 0.;-  /* shrink memory to actual size needed */-  *pl = (plist *)xrealloc(*pl, count * sizeof(plist));-  free(index);-}--/* this doesn't work if free_pf_arrays() is called before */-PUBLIC char *get_centroid_struct_gquad_pr( int length,-                                          double *dist){--  /* compute the centroid structure of the ensemble, i.e. the strutcure-     with the minimal average distance to all other structures-     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}-     Thus, the centroid is simply the structure containing all pairs with-     p_ij>0.5 */-  int i,j, k;-  double p;-  char  *centroid;-  int   *my_iindx = get_iindx(length);--  if (probs == NULL)-    nrerror("get_centroid_struct_pr: probs==NULL!");--  *dist = 0.;-  centroid = (char *) space((length+1)*sizeof(char));-  for (i=0; i<length; i++) centroid[i]='.';-  for (i=1; i<=length; i++)-    for (j=i+TURN+1; j<=length; j++) {-      if ((p=probs[my_iindx[i]-j])>0.5) {-        /* check for presence of gquadruplex */-        if((S[i] == 3) && (S[j] == 3)){-          int L, l[3];-          get_gquad_pattern_pf(S, i, j, pf_params, &L, l);-          for(k=0;k<L;k++){-            centroid[i+k-1]\-            = centroid[i+k+L+l[0]-1]\-            = centroid[i+k+2*L+l[0]+l[1]-1]\-            = centroid[i+k+3*L+l[0]+l[1]+l[2]-1]\-            = '+';-          }-          /* skip everything within the gquad */-          i = j; j = j+TURN+1;-          *dist += (1-p); /* right? */-          break;-        } else {-            centroid[i-1] = '(';-            centroid[j-1] = ')';-        }-        *dist += (1-p);-      } else-        *dist += p;-    }-  free(my_iindx);-  centroid[length] = '\0';-  return centroid;-}--/* this function is a threadsafe replacement for centroid() */-PUBLIC char *get_centroid_struct_pl(int length, double *dist, plist *pl){-  /* compute the centroid structure of the ensemble, i.e. the strutcure-     with the minimal average distance to all other structures-     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}-     Thus, the centroid is simply the structure containing all pairs with-     p_ij>0.5 */-  int i;-  char *centroid;--  if (pl==NULL)-    nrerror("get_centroid_struct: pl==NULL!");--  *dist = 0.;-  centroid = (char *) space((length+1)*sizeof(char));-  for (i=0; i<length; i++) centroid[i]='.';-  for (i=0; pl[i].i>0; i++){-    if ((pl[i].p)>0.5) {-      centroid[pl[i].i-1] = '(';-      centroid[pl[i].j-1] = ')';-      *dist += (1-pl[i].p);-    } else-      *dist += pl[i].p;-  }-  centroid[length] = '\0';-  return centroid;-}--/* this function is a threadsafe replacement for centroid() */-PUBLIC char *get_centroid_struct_pr(int length, double *dist, FLT_OR_DBL *probs){-  /* compute the centroid structure of the ensemble, i.e. the strutcure-     with the minimal average distance to all other structures-     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}-     Thus, the centroid is simply the structure containing all pairs with-     p_ij>0.5 */-  int i,j;-  double p;-  char  *centroid;-  int   *index = get_iindx(length);--  if (probs == NULL)-    nrerror("get_centroid_struct_pr: probs==NULL!");--  *dist = 0.;-  centroid = (char *) space((length+1)*sizeof(char));-  for (i=0; i<length; i++) centroid[i]='.';-  for (i=1; i<=length; i++)-    for (j=i+TURN+1; j<=length; j++) {-      if ((p=probs[index[i]-j])>0.5) {-        centroid[i-1] = '(';-        centroid[j-1] = ')';-        *dist += (1-p);-      } else-        *dist += p;-    }-  free(index);-  centroid[length] = '\0';-  return centroid;-}--PUBLIC plist *stackProb(double cutoff){-  plist *pl;-  int i,j,plsize=256;-  int num = 0;--  if (probs==NULL)-    nrerror("probs==NULL. You need to call pf_fold() before stackProb()");--  int length  = S[0];-  int *index  = get_iindx(length);--  pl = (plist *) space(plsize*sizeof(plist));--  for (i=1; i<length; i++)-    for (j=i+TURN+3; j<=length; j++) {-      double p;-      if((p=probs[index[i]-j]) < cutoff) continue;-      if (qb[index[i+1]-(j-1)]<FLT_MIN) continue;-      p *= qb[index[i+1]-(j-1)]/qb[index[i]-j];-      p *= exp_E_IntLoop(0,0,ptype[index[i]-j],rtype[ptype[index[i+1]-(j-1)]],-                         0,0,0,0, pf_params)*scale[2];/* add *scale[u1+u2+2] */-      if (p>cutoff) {-        pl[num].i = i;-        pl[num].j = j;-        pl[num++].p = p;-        if (num>=plsize) {-          plsize *= 2;-          pl = xrealloc(pl, plsize*sizeof(plist));-        }-      }-    }-  pl[num].i=0;-  free(index);-  return pl;-}--/*-------------------------------------------------------------------------*/-/* make arrays used for pf_fold available to other routines */-PUBLIC int get_pf_arrays( short **S_p,-                          short **S1_p,-                          char **ptype_p,-                          FLT_OR_DBL **qb_p,-                          FLT_OR_DBL **qm_p,-                          FLT_OR_DBL **q1k_p,-                          FLT_OR_DBL **qln_p){--  if(qb == NULL) return(0); /* check if pf_fold() has been called */-  *S_p = S; *S1_p = S1; *ptype_p = ptype;-  *qb_p = qb; *qm_p = qm;-  *q1k_p = q1k; *qln_p = qln;-  return(1); /* success */-}--/* get the free energy of a subsequence from the q[] array */-PUBLIC double get_subseq_F(int i, int j){-  if (!q)-    nrerror("call pf_fold() to fill q[] array before calling get_subseq_F()");-  return ((-log(q[my_iindx[i]-j])-(j-i+1)*log(pf_params->pf_scale))*pf_params->kT/1000.0);-}---PUBLIC double mean_bp_distance(int length){-  return mean_bp_distance_pr(length, probs);-}--PUBLIC double mean_bp_distance_pr(int length, FLT_OR_DBL *p){-  /* compute the mean base pair distance in the thermodynamic ensemble */-  /* <d> = \sum_{a,b} p_a p_b d(S_a,S_b)-     this can be computed from the pair probs p_ij as-     <d> = \sum_{ij} p_{ij}(1-p_{ij}) */-  int i,j;-  double d=0;-  int *index = get_iindx((unsigned int) length);--  if (p==NULL)-    nrerror("p==NULL. You need to supply a valid probability matrix for mean_bp_distance_pr()");--  for (i=1; i<=length; i++)-    for (j=i+TURN+1; j<=length; j++)-      d += p[index[i]-j] * (1-p[index[i]-j]);--  free(index);-  return 2*d;-}--PUBLIC FLT_OR_DBL *export_bppm(void){-  return probs;-}--/*###########################################*/-/*# deprecated functions below              #*/-/*###########################################*/--/* this function is deprecated since it is not threadsafe */-PUBLIC char *centroid(int length, double *dist) {-  /* compute the centroid structure of the ensemble, i.e. the strutcure-     with the minimal average distance to all other structures-     <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij}-     Thus, the centroid is simply the structure containing all pairs with-     p_ij>0.5 */-  int i,j;-  double p;-  char *centroid;--  if (pr==NULL)-    nrerror("pr==NULL. You need to call pf_fold() before centroid()");--  *dist = 0.;-  centroid = (char *) space((length+1)*sizeof(char));-  for (i=0; i<length; i++) centroid[i]='.';-  for (i=1; i<=length; i++)-    for (j=i+TURN+1; j<=length; j++) {-      if ((p=pr[my_iindx[i]-j])>0.5) {-        centroid[i-1] = '(';-        centroid[j-1] = ')';-        *dist += (1-p);-      } else-        *dist += p;-    }-  return centroid;-}---/* This function is deprecated since it uses the global array pr for calculations */-PUBLIC double mean_bp_dist(int length) {-  /* compute the mean base pair distance in the thermodynamic ensemble */-  /* <d> = \sum_{a,b} p_a p_b d(S_a,S_b)-     this can be computed from the pair probs p_ij as-     <d> = \sum_{ij} p_{ij}(1-p_{ij}) */-  int i,j;-  double d=0;--  if (pr==NULL)-    nrerror("pr==NULL. You need to call pf_fold() before mean_bp_dist()");--  for (i=1; i<=length; i++)-    for (j=i+TURN+1; j<=length; j++)-      d += pr[my_iindx[i]-j] * (1-pr[my_iindx[i]-j]);-  return 2*d;-}--/*----------------------------------------------------------------------*/-PUBLIC double expHairpinEnergy(int u, int type, short si1, short sj1,-                                const char *string) {-/* compute Boltzmann weight of a hairpin loop, multiply by scale[u+2] */-  double q, kT;-  kT = pf_params->kT;   /* kT in cal/mol  */-  if(u <= 30)-    q = pf_params->exphairpin[u];-  else-    q = pf_params->exphairpin[30] * exp( -(pf_params->lxc*log( u/30.))*10./kT);-  if ((tetra_loop)&&(u==4)) {-    char tl[7]={0}, *ts;-    strncpy(tl, string, 6);-    if ((ts=strstr(pf_params->Tetraloops, tl)))-      return (pf_params->exptetra[(ts-pf_params->Tetraloops)/7]);-  }-  if ((tetra_loop)&&(u==6)) {-    char tl[9]={0}, *ts;-    strncpy(tl, string, 6);-    if ((ts=strstr(pf_params->Hexaloops, tl)))-      return  (pf_params->exphex[(ts-pf_params->Hexaloops)/9]);-  }-  if (u==3) {-    char tl[6]={0}, *ts;-    strncpy(tl, string, 5);-    if ((ts=strstr(pf_params->Triloops, tl)))-      return (pf_params->exptri[(ts-pf_params->Triloops)/6]);-    if (type>2)-      q *= pf_params->expTermAU;-  }-  else /* no mismatches for tri-loops */-    q *= pf_params->expmismatchH[type][si1][sj1];--  return q;-}-PUBLIC double expLoopEnergy(int u1, int u2, int type, int type2,-                             short si1, short sj1, short sp1, short sq1) {-/* compute Boltzmann weight of interior loop,-   multiply by scale[u1+u2+2] for scaling */-  double z=0;-  int no_close = 0;--  if ((no_closingGU) && ((type2==3)||(type2==4)||(type==2)||(type==4)))-    no_close = 1;--  if ((u1==0) && (u2==0)) /* stack */-    z = pf_params->expstack[type][type2];-  else if (no_close==0) {-    if ((u1==0)||(u2==0)) { /* bulge */-      int u;-      u = (u1==0)?u2:u1;-      z = pf_params->expbulge[u];-      if (u2+u1==1) z *= pf_params->expstack[type][type2];-      else {-        if (type>2) z *= pf_params->expTermAU;-        if (type2>2) z *= pf_params->expTermAU;-      }-    }-    else {     /* interior loop */-      if (u1+u2==2) /* size 2 is special */-        z = pf_params->expint11[type][type2][si1][sj1];-      else if ((u1==1) && (u2==2))-        z = pf_params->expint21[type][type2][si1][sq1][sj1];-      else if ((u1==2) && (u2==1))-        z = pf_params->expint21[type2][type][sq1][si1][sp1];-      else if ((u1==2) && (u2==2))-        z = pf_params->expint22[type][type2][si1][sp1][sq1][sj1];-      else if (((u1==2)&&(u2==3))||((u1==3)&&(u2==2))){ /*2-3 is special*/-        z = pf_params->expinternal[5]*-          pf_params->expmismatch23I[type][si1][sj1]*-          pf_params->expmismatch23I[type2][sq1][sp1];-        z *= pf_params->expninio[2][1];-      }-      else if ((u1==1)||(u2==1)) {  /*1-n is special*/-        z = pf_params->expinternal[u1+u2]*-          pf_params->expmismatch1nI[type][si1][sj1]*-          pf_params->expmismatch1nI[type2][sq1][sp1];-        z *= pf_params->expninio[2][abs(u1-u2)];-      }-      else {-        z = pf_params->expinternal[u1+u2]*-          pf_params->expmismatchI[type][si1][sj1]*-          pf_params->expmismatchI[type2][sq1][sp1];-        z *= pf_params->expninio[2][abs(u1-u2)];-      }-    }-  }-  return z;-}--PUBLIC void init_pf_circ_fold(int length){-/* DO NOTHING */-}--PUBLIC void init_pf_fold(int length){-/* DO NOTHING */-}--
− cbits/part_func_co.c 
@@ -1,1046 +0,0 @@-/* Last changed Time-stamp: <2007-05-09 16:11:21 ivo> */-/*-                  partiton function for RNA secondary structures--                  Ivo L Hofacker-                  Stephan Bernhart-                  Vienna RNA package-*/-/*-  $Log: part_func_co.c,v $-  Revision 1.10  2007/05/10 17:27:01  ivo-  make sure the relative error eps is positive in newton iteration--  Revision 1.9  2006/05/10 15:12:11  ivo-  some compiler choked on  double semicolon after declaration--  Revision 1.8  2006/04/05 12:52:31  ivo-  Fix performance bug (O(n^4) loop)--  Revision 1.7  2006/01/19 11:30:04  ivo-  compute_probabilities should only look at one dimer at a time--  Revision 1.6  2006/01/18 12:55:40  ivo-  major cleanup of berni code-  fix bugs related to confusing which free energy is returned by co_pf_fold()--  Revision 1.5  2006/01/16 11:32:25  ivo-  small bug in multiloop pair probs--  Revision 1.4  2006/01/05 18:13:40  ivo-  update--  Revision 1.3  2006/01/04 15:14:29  ivo-  fix bug in concentration calculations--  Revision 1.2  2004/12/23 12:14:41  berni-  *** empty log message ***--  Revision 1.1  2004/12/22 10:46:17  berni--  Partition function Cofolding 0.9, Computation of concentrations.--  Revision 1.16  2003/08/04 09:14:09  ivo-  finish up stochastic backtracking--  Revision 1.15  2002/03/19 16:51:12  ivo-  more on stochastic backtracking (still incomplete)--  Revision 1.13  2001/11/16 17:30:04  ivo-  add stochastic backtracking (still incomplete)-*/--#include <config.h>-#include <stdio.h>-#include <stdlib.h>-#include <string.h>-#include <math.h>-#include <float.h>    /* #defines FLT_MAX ... */-#include <limits.h>--#include "utils.h"-#include "energy_par.h"-#include "fold_vars.h"-#include "pair_mat.h"-#include "PS_dot.h"-#include "params.h"-#include "loop_energies.h"-#include "part_func.h"-#include "part_func_co.h"--#ifdef _OPENMP-#include <omp.h>-#endif---/*@unused@*/-PRIVATE char rcsid[] UNUSED = "$Id: part_func_co.c,v 1.10 2007/05/10 17:27:01 ivo Exp $";--#define ISOLATED  256.0-#undef TURN-#define TURN 0-#define SAME_STRAND(I,J) (((I)>=cut_point)||((J)<cut_point))--/* #define SAME_STRAND(I,J) (((J)<cut_point)||((I)>=cut_point2)||(((I)>=cut_point)&&((J)<cut_point2)))- */--/*-#################################-# GLOBAL VARIABLES              #-#################################-*/-int     mirnatog      = 0;-double  F_monomer[2]  = {0,0}; /* free energies of the two monomers */--/*-#################################-# PRIVATE VARIABLES             #-#################################-*/-PRIVATE FLT_OR_DBL  *expMLbase=NULL;-PRIVATE FLT_OR_DBL  *q=NULL, *qb=NULL, *qm=NULL, *qm1=NULL, *qqm=NULL, *qqm1=NULL, *qq=NULL, *qq1=NULL;-PRIVATE FLT_OR_DBL  *prml=NULL, *prm_l=NULL, *prm_l1=NULL, *q1k=NULL, *qln=NULL, *probs=NULL;-PRIVATE FLT_OR_DBL  *scale=NULL;-PRIVATE pf_paramT   *pf_params = NULL;-PRIVATE char        *ptype=NULL; /* precomputed array of pair types */-PRIVATE int         *jindx=NULL;-PRIVATE int         *my_iindx=NULL;-PRIVATE int         init_length; /* length in last call to init_pf_fold() */-PRIVATE int         do_bppm = 1;             /* do backtracking per default */-PRIVATE short       *S=NULL, *S1=NULL;-PRIVATE char        *pstruc=NULL;-PRIVATE char        *sequence=NULL;-PRIVATE double      alpha = 1.0;-PRIVATE int         struct_constrained = 0;--#ifdef _OPENMP--/* NOTE: all variables are assumed to be uninitialized if they are declared as threadprivate-*/-#pragma omp threadprivate(expMLbase, q, qb, qm, qm1, qqm, qqm1, qq, qq1, prml, prm_l, prm_l1, q1k, qln,\-                          scale, pf_params, ptype, jindx, my_iindx, init_length, S, S1, pstruc, sequence, probs, do_bppm, alpha, struct_constrained)--#endif---/*-#################################-# PRIVATE FUNCTION DECLARATIONS #-#################################-*/-PRIVATE void    init_partfunc_co(int length, pf_paramT *parameters);-PRIVATE void    pf_co(const char *sequence);-PRIVATE void    pf_co_bppm(const char *sequence, char *structure);-PRIVATE double  *Newton_Conc(double ZAB, double ZAA, double ZBB, double concA, double concB,double* ConcVec);-PRIVATE void    scale_pf_params(unsigned int length, pf_paramT *parameters);-PRIVATE void    get_arrays(unsigned int length);-PRIVATE void    make_ptypes(const short *S, const char *structure);-PRIVATE void    backtrack(int i, int j);---/*-#################################-# BEGIN OF FUNCTION DEFINITIONS #-#################################-*/--PRIVATE void init_partfunc_co(int length, pf_paramT *parameters){-  if (length<1) nrerror("init_pf_fold: length must be greater 0");--#ifdef _OPENMP-/* Explicitly turn off dynamic threads */-  omp_set_dynamic(0);-  free_co_pf_arrays(); /* free previous allocation */-#else-  if (init_length>0) free_co_pf_arrays(); /* free previous allocation */-#endif--#ifdef SUN4-  nonstandard_arithmetic();-#else-#ifdef HP9-  fpsetfastmode(1);-#endif-#endif-  make_pair_matrix();-  get_arrays((unsigned) length);-  scale_pf_params((unsigned) length, parameters);-  init_length = length;-}--PRIVATE void get_arrays(unsigned int length){-  unsigned int size;--  if((length +1) >= (unsigned int)sqrt((double)INT_MAX))-    nrerror("get_arrays@part_func_co.c: sequence length exceeds addressable range");--  size      = sizeof(FLT_OR_DBL) * ((length+1)*(length+2)/2);-  q         = (FLT_OR_DBL *) space(size);-  qb        = (FLT_OR_DBL *) space(size);-  qm        = (FLT_OR_DBL *) space(size);-  probs     = (FLT_OR_DBL *) space(size);-  qm1       = (FLT_OR_DBL *) space(size);-  q1k       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));-  qln       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qq        = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qq1       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qqm       = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  qqm1      = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prm_l     = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prm_l1    = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  prml      = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+2));-  expMLbase = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));-  scale     = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL)*(length+1));-  ptype     = (char *) space(sizeof(char)*((length+1)*(length+2)/2));-  my_iindx  = get_iindx(length);-  iindx     = get_iindx(length); /* for backward compatibility and Perl wrapper */-  jindx     = get_indx(length);-}--PUBLIC void free_co_pf_arrays(void){-  if(q)         free(q);-  if(qb)        free(qb);-  if(qm)        free(qm);-  if(qm1)       free(qm1);-  if(ptype)     free(ptype);-  if(qq)        free(qq);-  if(qq1)       free(qq1);-  if(qqm)       free(qqm);-  if(qqm1)      free(qqm1);-  if(q1k)       free(q1k);-  if(qln)       free(qln);-  if(prm_l)     free(prm_l);-  if(prm_l1)    free(prm_l1);-  if(prml)      free(prml);-  if(probs)     free(probs);-  if(expMLbase) free(expMLbase);-  if(scale)     free(scale);-  if(my_iindx)  free(my_iindx);-  if(iindx)     free(iindx); /* for backward compatibility and Perl wrapper */-  if(jindx)     free(jindx);-  if(S)         free(S);-  if(S1)        free(S1);--  init_length=0;-  q = qb = qm = qm1 = qq = qq1 = qqm = qqm1 = q1k = qln = prm_l = prm_l1 = prml = expMLbase = scale = probs = NULL;-  ptype = NULL;-  S = S1 = NULL;-  my_iindx = jindx = iindx = NULL;--#ifdef SUN4-  standard_arithmetic();-#else-#ifdef HP9-  fpsetfastmode(0);-#endif-#endif-}--/*-----------------------------------------------------------------*/-PUBLIC cofoldF co_pf_fold(char *sequence, char *structure){-  return co_pf_fold_par(sequence, structure, NULL, do_backtrack, fold_constrained);-}--PUBLIC cofoldF co_pf_fold_par(char *sequence,-                              char *structure,-                              pf_paramT *parameters,-                              int calculate_bppm,-                              int is_constrained){--  int         n;-  FLT_OR_DBL  Q;-  cofoldF     X;-  double      free_energy;--  n                   = (int) strlen(sequence);-  do_bppm             = calculate_bppm;-  struct_constrained  = is_constrained;--#ifdef _OPENMP-  /* always init everything since all global static variables are uninitialized when entering a thread */-  init_partfunc_co(n, parameters);-#else-  if(parameters) init_partfunc_co(n, parameters);-  else if (n > init_length) init_partfunc_co(n, parameters);-  else if (fabs(pf_params->temperature - temperature)>1e-6) update_co_pf_params_par(n, parameters);-#endif-- /* printf("mirnatog=%d\n",mirnatog); */--  if(S) free(S);-  S   = encode_sequence(sequence, 0);-  if(S1) free(S1);-  S1  = encode_sequence(sequence, 1);--  make_ptypes(S, structure);--  pf_co(sequence);--  if (backtrack_type=='C')      Q = qb[my_iindx[1]-n];-  else if (backtrack_type=='M') Q = qm[my_iindx[1]-n];-  else Q = q[my_iindx[1]-n];-  /* ensemble free energy in Kcal/mol */-  if (Q<=FLT_MIN) fprintf(stderr, "pf_scale too large\n");-  free_energy = (-log(Q)-n*log(pf_params->pf_scale))*pf_params->kT/1000.0;-  /* in case we abort because of floating point errors */-  if (n>1600) fprintf(stderr, "free energy = %8.2f\n", free_energy);-  /*probability of molecules being bound together*/---  /*Computation of "real" Partition function*/-  /*Need that for concentrations*/-  if (cut_point>0){-    double kT, pbound, QAB, QToT, Qzero;--    kT = pf_params->kT/1000.0;-    Qzero=q[my_iindx[1]-n];-    QAB=(q[my_iindx[1]-n]-q[my_iindx[1]-(cut_point-1)]*q[my_iindx[cut_point]-n])*pf_params->expDuplexInit;-    /*correction for symmetry*/-    if((n-(cut_point-1)*2)==0) {-      if ((strncmp(sequence, sequence+cut_point-1, cut_point-1))==0) {-        QAB/=2;-      }}--    QToT=q[my_iindx[1]-(cut_point-1)]*q[my_iindx[cut_point]-n]+QAB;-    pbound=1-(q[my_iindx[1]-(cut_point-1)]*q[my_iindx[cut_point]-n]/QToT);-     X.FAB  = -kT*(log(QToT)+n*log(pf_params->pf_scale));-    X.F0AB = -kT*(log(Qzero)+n*log(pf_params->pf_scale));-    X.FcAB = (QAB>1e-17) ? -kT*(log(QAB)+n*log(pf_params->pf_scale)) : 999;-    X.FA = -kT*(log(q[my_iindx[1]-(cut_point-1)]) + (cut_point-1)*log(pf_params->pf_scale));-    X.FB = -kT*(log(q[my_iindx[cut_point]-n]) + (n-cut_point+1)*log(pf_params->pf_scale));--    /* printf("QAB=%.9f\tQtot=%.9f\n",QAB/scale[n],QToT/scale[n]);*/-  }-  else {-    X.FA = X.FB = X.FAB = X.F0AB = free_energy;-    X.FcAB = 0;-  }--  /* backtracking to construct binding probabilities of pairs*/-  if(do_bppm){-    pf_co_bppm(sequence, structure);-    /*-    *  Backward compatibility:-    *  This block may be removed if deprecated functions-    *  relying on the global variable "pr" vanish from within the package!-    */-    pr = probs;-    /*-    {-      if(pr) free(pr);-      pr = (FLT_OR_DBL *) space(sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));-      memcpy(pr, probs, sizeof(FLT_OR_DBL) * ((n+1)*(n+2)/2));-    }-    */-  }-  return X;-}--/* forward recursion of pf cofolding */-PRIVATE void pf_co(const char *sequence){-  int         n, i,j,k,l, ij, u,u1,ii, type, type_2, tt;-  FLT_OR_DBL  temp, Qmax=0;-  FLT_OR_DBL  qbt1, *tmp;-  FLT_OR_DBL  expMLclosing;-  double      max_real;-  int         noGUclosure = pf_params->model_details.noGUclosure;--  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;-  n = (int) strlen(sequence);--  expMLclosing = pf_params->expMLclosing;---  /*array initialization ; qb,qm,q-    qb,qm,q (i,j) are stored as ((n+1-i)*(n-i) div 2 + n+1-j */--  /* for (d=0; d<=TURN; d++) */-  for (i=1; i<=n/*-d*/; i++) {-      ij = my_iindx[i]-i;-      q[ij]=scale[1];-      qb[ij]=qm[ij]=0.0;-    }--  for (i=0; i<=n; i++)-    qq[i]=qq1[i]=qqm[i]=qqm1[i]=prm_l[i]=prm_l1[i]=prml[i]=0;--  for (j=TURN+2;j<=n; j++) {-    for (i=j-TURN-1; i>=1; i--) {-      /* construction of partition function of segment i,j*/-       /*firstly that given i bound to j : qb(i,j) */-      u = j-i-1; ij = my_iindx[i]-j;-      type = ptype[ij];-      qbt1=0;-      if (type!=0) {-        /*hairpin contribution*/-        if SAME_STRAND(i,j){-          if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;-          else-            qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params)*scale[u+2];--        }--        /* interior loops with interior pair k,l */-        for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {-          u1 = k-i-1;-          for (l=MAX2(k+TURN+1,j-1-MAXLOOP+u1); l<j; l++) {-            if ((SAME_STRAND(i,k))&&(SAME_STRAND(l,j))){-              type_2 = ptype[my_iindx[k]-l];-              if (type_2) {-                type_2 = rtype[type_2];-                qbt1 += qb[my_iindx[k]-l] *-                  exp_E_IntLoop(u1, j-l-1, type, type_2,-                                S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params)*scale[u1+j-l+1];-              }-            }-          }-        }-        /*multiple stem loop contribution*/-        ii = my_iindx[i+1]; /* ii-k=[i+1,k-1] */-        temp = 0.0;-        if (SAME_STRAND(i,i+1) && SAME_STRAND(j-1,j)) {-          for (k=i+2; k<=j-1; k++) {-            if (SAME_STRAND(k-1,k))-              temp += qm[ii-(k-1)]*qqm1[k];-          }-          tt = rtype[type];-          temp*=exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params)*scale[2];-          temp*=expMLclosing;-          qbt1 += temp;-        }-        /*qc contribution*/-        temp=0.0;-        if (!SAME_STRAND(i,j)){-          tt = rtype[type];-          temp=q[my_iindx[i+1]-(cut_point-1)]*q[my_iindx[cut_point]-(j-1)];-          if ((j==cut_point)&&(i==cut_point-1)) temp=scale[2];-          else if (i==cut_point-1) temp=q[my_iindx[cut_point]-(j-1)]*scale[1];-          else if (j==cut_point) temp=q[my_iindx[i+1]-(cut_point-1)]*scale[1];-          if (j>cut_point) temp*=scale[1];-          if (i<cut_point-1) temp*=scale[1];-          temp *= exp_E_ExtLoop(tt, SAME_STRAND(j-1,j) ? S1[j-1] : -1, SAME_STRAND(i,i+1) ? S1[i+1] : -1, pf_params);-          qbt1+=temp;-        }-        qb[ij] = qbt1;-      } /* end if (type!=0) */-      else qb[ij] = 0.0;-      /* construction of qqm matrix containing final stem-         contributions to multiple loop partition function-         from segment i,j */-      if (SAME_STRAND(j-1,j)) {-        qqm[i] = qqm1[i]*expMLbase[1];-      }-      else qqm[i]=0;-      if (type&&SAME_STRAND(i-1,i)&&SAME_STRAND(j,j+1)) {-        qbt1 = qb[ij];-        qbt1 *= exp_E_MLstem(type, (i>1) ? S1[i-1] : -1, (j<n) ? S1[j+1] : -1, pf_params);-        qqm[i] += qbt1;-      }--      if (qm1) qm1[jindx[j]+i] = qqm[i]; /* for stochastic backtracking */---      /*construction of qm matrix containing multiple loop-        partition function contributions from segment i,j */-      temp = 0.0;-      ii = my_iindx[i];  /* ii-k=[i,k] */--      for (k=i+1; k<=j; k++) {-        if (SAME_STRAND(k-1,k)) temp += (qm[ii-(k-1)])*qqm[k];-        if (SAME_STRAND(i,k))   temp += expMLbase[k-i]*qqm[k];--      }--      qm[ij] = (temp + qqm[i]);--      /*auxiliary matrix qq for cubic order q calculation below */-      qbt1 = qb[ij];-      if (type) {-        qbt1 *= exp_E_ExtLoop(type, ((i>1)&&(SAME_STRAND(i-1,i))) ? S1[i-1] : -1, ((j<n)&&(SAME_STRAND(j,j+1))) ? S1[j+1] : -1, pf_params);-      }-      qq[i] = qq1[i]*scale[1] + qbt1;-       /*construction of partition function for segment i,j */-      temp = 1.0*scale[1+j-i] + qq[i];-      for (k=i; k<=j-1; k++) temp += q[ii-k]*qq[k+1];-      q[ij] = temp;--      if (temp>Qmax) {-        Qmax = temp;-        if (Qmax>max_real/10.)-          fprintf(stderr, "Q close to overflow: %d %d %g\n", i,j,temp);-      }-      if (temp>=max_real) {-        PRIVATE char msg[128];-        snprintf(msg, 127, "overflow in co_pf_fold while calculating q[%d,%d]\n"-                "use larger pf_scale", i,j);-        nrerror(msg);-      }-    }-    tmp = qq1;  qq1 =qq;  qq =tmp;-    tmp = qqm1; qqm1=qqm; qqm=tmp;-  }-}--/* backward recursion of pf cofolding */-PRIVATE void pf_co_bppm(const char *sequence, char *structure){-  int         n, i,j,k,l, ij, kl, ii, ll, type, type_2, tt, ov=0;-  FLT_OR_DBL  temp, Qmax=0, prm_MLb;-  FLT_OR_DBL  prmt,prmt1;-  FLT_OR_DBL  *tmp;-  FLT_OR_DBL  expMLclosing;-  double      max_real;--  max_real = (sizeof(FLT_OR_DBL) == sizeof(float)) ? FLT_MAX : DBL_MAX;-  n = (int) strlen(sequence);--  expMLclosing = pf_params->expMLclosing;--  /* backtracking to construct binding probabilities of pairs*/-  if ((S != NULL) && (S1 != NULL)) {-    FLT_OR_DBL   *Qlout, *Qrout;-    Qmax=0;-    Qrout=(FLT_OR_DBL *)space(sizeof(FLT_OR_DBL) * (n+2));-    Qlout=(FLT_OR_DBL *)space(sizeof(FLT_OR_DBL) * (cut_point+2));--    for (k=1; k<=n; k++) {-      q1k[k] = q[my_iindx[1] - k];-      qln[k] = q[my_iindx[k] -n];-    }-    q1k[0] = 1.0;-    qln[n+1] = 1.0;--    /*    pr = q;     /  * recycling */--    /* 1. exterior pair i,j and initialization of pr array */-    for (i=1; i<=n; i++) {-      for (j=i; j<=MIN2(i+TURN,n); j++) probs[my_iindx[i]-j] = 0;-      for (j=i+TURN+1; j<=n; j++) {-        ij = my_iindx[i]-j;-        type = ptype[ij];-        if (type&&(qb[ij]>0.)) {-          probs[ij] = q1k[i-1]*qln[j+1]/q1k[n];-          probs[ij] *= exp_E_ExtLoop(type, ((i>1)&&(SAME_STRAND(i-1,i))) ? S1[i-1] : -1, ((j<n)&&(SAME_STRAND(j,j+1))) ? S1[j+1] : -1, pf_params);-        } else-          probs[ij] = 0;-      }-    }--    for (l=n; l>TURN+1; l--) {--      /* 2. bonding k,l as substem of 2:loop enclosed by i,j */-      for (k=1; k<l-TURN; k++) {-        kl = my_iindx[k]-l;-        type_2 = ptype[kl]; type_2 = rtype[type_2];-        if (qb[kl]==0) continue;--        for (i=MAX2(1,k-MAXLOOP-1); i<=k-1; i++)-          for (j=l+1; j<=MIN2(l+ MAXLOOP -k+i+2,n); j++) {-            if ((SAME_STRAND(i,k))&&(SAME_STRAND(l,j))){-              ij = my_iindx[i] - j;-              type = ptype[ij];-              if ((probs[ij]>0)) {-                probs[kl] += probs[ij]*exp_E_IntLoop(k-i-1, j-l-1, type, type_2,-                                               S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params)*scale[k-i+j-l];-              }-            }-          }-      }-      /* 3. bonding k,l as substem of multi-loop enclosed by i,j */-      prm_MLb = 0.;-      if ((l<n)&&(SAME_STRAND(l,l+1)))-        for (k=2; k<l-TURN; k++) {-          i = k-1;-          prmt = prmt1 = 0.0;--          ii = my_iindx[i];     /* ii-j=[i,j]     */-          ll = my_iindx[l+1];   /* ll-j=[l+1,j] */-          tt = ptype[ii-(l+1)]; tt=rtype[tt];-          if (SAME_STRAND(i,k)){-            prmt1 = probs[ii-(l+1)]*expMLclosing;-            prmt1 *= exp_E_MLstem(tt, S1[l], S1[i+1], pf_params);-            for (j=l+2; j<=n; j++) {-              if (SAME_STRAND(j-1,j)){ /*??*/-                tt = ptype[ii-j]; tt = rtype[tt];-                prmt += probs[ii-j]*exp_E_MLstem(tt, S1[j-1], S1[i+1], pf_params)*qm[ll-(j-1)];-              }-            }-          }-          kl = my_iindx[k]-l;-          tt = ptype[kl];-          prmt *= expMLclosing;-          prml[ i] = prmt;-          prm_l[i] = prm_l1[i]*expMLbase[1]+prmt1;--          prm_MLb = prm_MLb*expMLbase[1] + prml[i];-          /* same as:    prm_MLb = 0;-             for (i=1; i<=k-1; i++) prm_MLb += prml[i]*expMLbase[k-i-1]; */--          prml[i] = prml[ i] + prm_l[i];--          if (qb[kl] == 0.) continue;--          temp = prm_MLb;--          for (i=1;i<=k-2; i++) {-            if ((SAME_STRAND(i,i+1))&&(SAME_STRAND(k-1,k))){-              temp += prml[i]*qm[my_iindx[i+1] - (k-1)];-            }-          }-          temp *= exp_E_MLstem( tt,-                                ((k>1)&&SAME_STRAND(k-1,k)) ? S1[k-1] : -1,-                                ((l<n)&&SAME_STRAND(l,l+1)) ? S1[l+1] : -1,-                                pf_params) * scale[2];-          probs[kl] += temp;--          if (probs[kl]>Qmax) {-            Qmax = probs[kl];-            if (Qmax>max_real/10.)-              fprintf(stderr, "P close to overflow: %d %d %g %g\n",-                      i, j, probs[kl], qb[kl]);-          }-          if (probs[kl]>=max_real) {-            ov++;-            probs[kl]=FLT_MAX;-          }--        } /* end for (k=..) multloop*/-      else  /* set prm_l to 0 to get prm_l1 to be 0 */-        for (i=0; i<=n; i++) prm_l[i]=0;--      tmp = prm_l1; prm_l1=prm_l; prm_l=tmp;-      /*computation of .(..(...)..&..). type features?*/-      if (cut_point<=0) continue;  /* no .(..(...)..&..). type features*/-      if ((l==n)||(l<=2)) continue; /* no .(..(...)..&..). type features*/-      /*new version with O(n^3)??*/-      if (l>cut_point) {-        if (l<n) {-          int t,kt;-          for (t=n; t>l; t--) {-            for (k=1; k<cut_point; k++) {-              kt=my_iindx[k]-t;-              type=rtype[ptype[kt]];-              temp = probs[kt] * exp_E_ExtLoop(type, S1[t-1], (SAME_STRAND(k,k+1)) ? S1[k+1] : -1, pf_params) * scale[2];-              if (l+1<t)               temp*=q[my_iindx[l+1]-(t-1)];-              if (SAME_STRAND(k,k+1))  temp*=q[my_iindx[k+1]-(cut_point-1)];-              Qrout[l]+=temp;-            }-          }-        }-        for (k=l-1; k>=cut_point; k--) {-          if (qb[my_iindx[k]-l]) {-            kl=my_iindx[k]-l;-            type=ptype[kl];-            temp = Qrout[l];-            temp *= exp_E_ExtLoop(type, (k>cut_point) ? S1[k-1] : -1, (l < n) ? S1[l+1] : -1, pf_params);-            if (k>cut_point) temp*=q[my_iindx[cut_point]-(k-1)];-            probs[kl]+=temp;-          }-        }-      }-      else if (l==cut_point ) {-        int t, sk,s;-        for (t=2; t<cut_point;t++) {-          for (s=1; s<t; s++) {-            for (k=cut_point; k<=n; k++) {-              sk=my_iindx[s]-k;-              if (qb[sk]) {-                type=rtype[ptype[sk]];-                temp=probs[sk]*exp_E_ExtLoop(type, (SAME_STRAND(k-1,k)) ? S1[k-1] : -1, S1[s+1], pf_params)*scale[2];-                if (s+1<t)               temp*=q[my_iindx[s+1]-(t-1)];-                if (SAME_STRAND(k-1,k))  temp*=q[my_iindx[cut_point]-(k-1)];-                Qlout[t]+=temp;-              }-            }-          }-        }-      }-      else if (l<cut_point) {-        for (k=1; k<l; k++) {-          if (qb[my_iindx[k]-l]) {-            type=ptype[my_iindx[k]-l];-            temp=Qlout[k];-            temp *= exp_E_ExtLoop(type, (k>1) ? S1[k-1] : -1, (l<(cut_point-1)) ? S1[l+1] : -1, pf_params);-            if (l+1<cut_point) temp*=q[my_iindx[l+1]-(cut_point-1)];-            probs[my_iindx[k]-l]+=temp;-          }-        }-      }-    }  /* end for (l=..)   */-    free(Qlout);-    free(Qrout);-    for (i=1; i<=n; i++)-      for (j=i+TURN+1; j<=n; j++) {-        ij = my_iindx[i]-j;-        probs[ij] *= qb[ij];-      }--    if (structure!=NULL)-      bppm_to_structure(structure, probs, n);-  }   /* end if (do_backtrack)*/--  if (ov>0) fprintf(stderr, "%d overflows occurred while backtracking;\n"-                    "you might try a smaller pf_scale than %g\n",-                    ov, pf_params->pf_scale);-}---PRIVATE void scale_pf_params(unsigned int length, pf_paramT *parameters){-  unsigned int  i;-  double        kT, scaling_factor;--  if(pf_params) free(pf_params);--  if(parameters){-    pf_params = get_boltzmann_factor_copy(parameters);-  } else {-    model_detailsT md;-    set_model_details(&md);-    pf_params = get_boltzmann_factors(temperature, alpha, md, pf_scale);-  }--  scaling_factor  = pf_params->pf_scale;-  kT              = pf_params->kT;        /* kT in cal/mol  */--   /* scaling factors (to avoid overflows) */-  if (scaling_factor == -1) { /* mean energy for random sequences: 184.3*length cal */-    scaling_factor = exp(-(-185+(pf_params->temperature-37.)*7.27)/kT);-    if (scaling_factor<1) scaling_factor=1;-    pf_params->pf_scale = scaling_factor;-  }-  scale[0] = 1.;-  scale[1] = 1./scaling_factor;-  expMLbase[0] = 1;-  expMLbase[1] = pf_params->expMLbase/scaling_factor;-  for (i=2; i<=length; i++) {-    scale[i] = scale[i/2]*scale[i-(i/2)];-    expMLbase[i] = pow(pf_params->expMLbase, (double)i) * scale[i];-  }-}--/*----------------------------------------------------------------------*/--/*----------------------------------------------------------------------*/--/*---------------------------------------------------------------------------*/--PUBLIC void update_co_pf_params(int length){-  update_co_pf_params_par(length, NULL);-}--PUBLIC void update_co_pf_params_par(int length, pf_paramT *parameters){-  make_pair_matrix();-  scale_pf_params((unsigned) length, parameters);-}--/*---------------------------------------------------------------------------*/-PRIVATE void make_ptypes(const short *S, const char *structure) {-  int n,i,j,k,l;-  int noLP = pf_params->model_details.noLP;--  n=S[0];-  for (k=1; k<=n-TURN-1; k++)-    for (l=1; l<=2; l++) {-      int type,ntype=0,otype=0;-      i=k; j = i+TURN+l;-      if (j>n) continue;-      type = pair[S[i]][S[j]];-      while ((i>=1)&&(j<=n)) {-        if ((i>1)&&(j<n)) ntype = pair[S[i-1]][S[j+1]];-        if (noLP && (!otype) && (!ntype))-          type = 0; /* i.j can only form isolated pairs */-        qb[my_iindx[i]-j] = 0.;-        ptype[my_iindx[i]-j] = (char) type;-        otype =  type;-        type  = ntype;-        i--; j++;-      }--    }--  if (struct_constrained&&(structure!=NULL)) {-    constrain_ptypes(structure, (unsigned int)n, ptype, NULL, TURN, 1);-    for(j=1; j<=n; j++) {-      switch (structure[j-1]) {-        case 'l': /*only intramolecular basepairing*/-                  if (j<cut_point) for (l=cut_point; l<=n; l++) ptype[my_iindx[j]-l] = 0;-                  else for (l=1; l<cut_point; l++) ptype[my_iindx[l]-j] =0;-                  break;-        case 'e': /*only intermolecular bp*/-                  if (j<cut_point) {-                    for (l=1; l<j; l++) ptype[my_iindx[l]-j] =0;-                    for (l=j+1; l<cut_point; l++) ptype[my_iindx[j]-l] = 0;-                  }-                  else {-                    for (l=cut_point; l<j; l++) ptype[my_iindx[l]-j] =0;-                    for (l=j+1; l<=n; l++) ptype[my_iindx[j]-l] = 0;-                  }-                  break;-      }-    }-  }-  if (mirnatog==1) {   /*microRNA toggle: no intramolec. bp in 2. molec*/-    for (j=cut_point; j<n; j++) {-      for (l=j+1; l<=n; l++) {-        ptype[my_iindx[j]-l] = 0;-      }-    }-  }-}--/*-  stochastic backtracking in pf_fold arrays-  returns random structure S with Boltzman probabilty-  p(S) = exp(-E(S)/kT)/Z-*/-PRIVATE void backtrack_qm1(int i,int j) {-  /* i is paired to l, i<l<j; backtrack in qm1 to find l */-  int ii, l, type;-  double qt, r;-  r = urn() * qm1[jindx[j]+i];-  ii = my_iindx[i];-  for (qt=0., l=i+TURN+1; l<=j; l++) {-    type = ptype[ii-l];-    if (type)-      qt +=  qb[ii-l]*exp_E_MLstem(type, S1[i-1], S1[l+1], pf_params) * expMLbase[j-l];-    if (qt>=r) break;-  }-  if (l>j) nrerror("backtrack failed in qm1");-  backtrack(i,l);-}--PRIVATE void backtrack(int i, int j) {-  int noGUclosure = pf_params->model_details.noGUclosure;--  do {-    double r, qbt1;-    int k, l, type, u, u1;--    pstruc[i-1] = '('; pstruc[j-1] = ')';--    r = urn() * qb[my_iindx[i]-j];-    type = ptype[my_iindx[i]-j];-    u = j-i-1;-    /*hairpin contribution*/-    if (((type==3)||(type==4))&&noGUclosure) qbt1 = 0;-    else-      qbt1 = exp_E_Hairpin(u, type, S1[i+1], S1[j-1], sequence+i-1, pf_params)*scale[u+2];--    if (qbt1>r) return; /* found the hairpin we're done */--    for (k=i+1; k<=MIN2(i+MAXLOOP+1,j-TURN-2); k++) {-      u1 = k-i-1;-      for (l=MAX2(k+TURN+1,j-1-MAXLOOP+u1); l<j; l++) {-        int type_2;-        type_2 = ptype[my_iindx[k]-l];-        if (type_2) {-          type_2 = rtype[type_2];-          qbt1 += qb[my_iindx[k]-l] *-            exp_E_IntLoop(u1, j-l-1, type, type_2,-                          S1[i+1], S1[j-1], S1[k-1], S1[l+1], pf_params)*scale[u1+j-l+1];-        }-        if (qbt1 > r) break;-      }-      if (qbt1 > r) break;-    }-    if (l<j) {-      i=k; j=l;-    }-    else break;-  } while (1);--  /* backtrack in multi-loop */-  {-    double r, qt;-    int k, ii, jj;--    i++; j--;-    /* find the first split index */-    ii = my_iindx[i]; /* ii-j=[i,j] */-    jj = jindx[j]; /* jj+i=[j,i] */-    for (qt=0., k=i+1; k<j; k++) qt += qm[ii-(k-1)]*qm1[jj+k];-    r = urn() * qt;-    for (qt=0., k=i+1; k<j; k++) {-      qt += qm[ii-(k-1)]*qm1[jj+k];-      if (qt>=r) break;-    }-    if (k>=j) nrerror("backtrack failed, can't find split index ");--    backtrack_qm1(k, j);--    j = k-1;-    while (j>i) {-      /* now backtrack  [i ... j] in qm[] */-      jj = jindx[j];-      ii = my_iindx[i];-      r = urn() * qm[ii - j];-      qt = qm1[jj+i]; k=i;-      if (qt<r)-        for (k=i+1; k<=j; k++) {-          qt += (qm[ii-(k-1)]+expMLbase[k-i])*qm1[jj+k];-          if (qt >= r) break;-        }-      if (k>j) nrerror("backtrack failed in qm");--      backtrack_qm1(k,j);--      if (k<i+TURN) break; /* no more pairs */-      r = urn() * (qm[ii-(k-1)] + expMLbase[k-i]);-      if (expMLbase[k-i] >= r) break; /* no more pairs */-      j = k-1;-    }-  }-}--PUBLIC void compute_probabilities(double FAB, double FA,double FB,-                                  struct plist *prAB,-                                  struct plist *prA, struct plist *prB,-                                  int Alength) {-  /*computes binding probabilities and dimer free energies*/-  int i, j;-  double pAB;-  double mykT;-  struct plist  *lp1, *lp2;-  int offset;--  mykT=pf_params->kT/1000.;--  /* pair probabilities in pr are relative to the null model (without DuplexInit) */--  /*Compute probabilities pAB, pAA, pBB*/--  pAB=1.-exp((1/mykT)*(FAB-FA-FB));--  /* compute pair probabilities given that it is a dimer */-  /* AB dimer */-  offset=0;-  lp2=prA;-  if (pAB>0)-    for (lp1=prAB; lp1->j>0; lp1++) {-      float pp=0;-      i=lp1->i; j=lp1->j;-      while (offset+lp2->i < i && lp2->i>0) lp2++;-      if (offset+lp2->i == i)-        while ((offset+lp2->j) < j  && (lp2->j>0)) lp2++;-      if (lp2->j == 0) {lp2=prB; offset=Alength;}/* jump to next list */-      if ((offset+lp2->i==i) && (offset+lp2->j ==j)) {-        pp = lp2->p;-        lp2++;-      }-      lp1->p=(lp1->p-(1-pAB)*pp)/pAB;-      if(lp1->p < 0.){-        warn_user("part_func_co: numeric instability detected, probability below zero!");-        lp1->p = 0.;-      }-    }-  return;-}--PRIVATE double *Newton_Conc(double KAB, double KAA, double KBB, double concA, double concB,double* ConcVec) {-  double TOL, EPS, xn, yn, det, cA, cB;-  int i=0;-  /*Newton iteration for computing concentrations*/-  cA=concA;-  cB=concB;-  TOL=1e-6; /*Tolerance for convergence*/-  ConcVec=(double*)space(5*sizeof(double)); /* holds concentrations */-  do {-    /* det = (4.0 * KAA * cA + KAB *cB + 1.0) * (4.0 * KBB * cB + KAB *cA + 1.0) - (KAB *cB) * (KAB *cA); */-    det = 1 + 16. *KAA*KBB*cA*cB + KAB*(cA+cB) + 4.*KAA*cA + 4.*KBB*cB + 4.*KAB*(KBB*cB*cB + KAA*cA*cA);-    /* xn  = ( (2.0 * KBB * cB*cB + KAB *cA *cB + cB - concB) * (KAB *cA) --       (2.0 * KAA * cA*cA + KAB *cA *cB + cA - concA) * (4.0 * KBB * cB + KAB *cA + 1.0) ) /det; */-    xn  = ( (2.0 * KBB * cB*cB + cB - concB) * (KAB *cA) - KAB*cA*cB*(4. * KBB*cB + 1.) --	    (2.0 * KAA * cA*cA + cA - concA) * (4.0 * KBB * cB + KAB *cA + 1.0) ) /det;-    /* yn  = ( (2.0 * KAA * cA*cA + KAB *cA *cB + cA - concA) * (KAB *cB) --       (2.0 * KBB * cB*cB + KAB *cA *cB + cB - concB) * (4.0 * KAA * cA + KAB *cB + 1.0) ) /det; */-    yn  = ( (2.0 * KAA * cA*cA + cA - concA) * (KAB *cB) - KAB*cA*cB*(4. * KAA*cA + 1.) --            (2.0 * KBB * cB*cB + cB - concB) * (4.0 * KAA * cA + KAB *cB + 1.0) ) /det;-    EPS = fabs(xn/cA) + fabs(yn/cB);-    cA += xn;-    cB += yn;-    i++;-    if (i>10000) {-      fprintf(stderr, "Newton did not converge after %d steps!!\n",i);-      break;-    }-  } while(EPS>TOL);--  ConcVec[0]= cA*cB*KAB ;/*AB concentration*/-  ConcVec[1]= cA*cA*KAA ;/*AA concentration*/-  ConcVec[2]= cB*cB*KBB ;/*BB concentration*/-  ConcVec[3]= cA;        /* A concentration*/-  ConcVec[4]= cB;        /* B concentration*/--  return ConcVec;-}--PUBLIC struct ConcEnt *get_concentrations(double FcAB, double FcAA, double FcBB, double FEA, double FEB, double *startconc)-{-  /*takes an array of start concentrations, computes equilibrium concentrations of dimers, monomers, returns array of concentrations in strucutre ConcEnt*/-  double *ConcVec;-  int i;-  struct ConcEnt *Concentration;-  double KAA, KAB, KBB, kT;--  kT=pf_params->kT/1000.;-  Concentration=(struct ConcEnt *)space(20*sizeof(struct ConcEnt));- /* Compute equilibrium constants */-  /* again note the input free energies are not from the null model (without DuplexInit) */--  KAA = exp(( 2.0 * FEA - FcAA)/kT);-  KBB = exp(( 2.0 * FEB - FcBB)/kT);-  KAB = exp(( FEA + FEB - FcAB)/kT);-  /* printf("Kaa..%g %g %g\n", KAA, KBB, KAB); */-  for (i=0; ((startconc[i]!=0)||(startconc[i+1]!=0));i+=2) {-    ConcVec=Newton_Conc(KAB, KAA, KBB, startconc[i], startconc[i+1], ConcVec);-    Concentration[i/2].A0=startconc[i];-    Concentration[i/2].B0=startconc[i+1];-    Concentration[i/2].ABc=ConcVec[0];-    Concentration[i/2].AAc=ConcVec[1];-    Concentration[i/2].BBc=ConcVec[2];-    Concentration[i/2].Ac=ConcVec[3];-    Concentration[i/2].Bc=ConcVec[4];--   if (!(((i+2)/2)%20))  {-     Concentration=(struct ConcEnt *)xrealloc(Concentration,((i+2)/2+20)*sizeof(struct ConcEnt));-     }-    free(ConcVec);-  }--  return Concentration;-}--PUBLIC FLT_OR_DBL *export_co_bppm(void){-  return probs;-}--/*###########################################*/-/*# deprecated functions below              #*/-/*###########################################*/---PUBLIC struct plist *get_plist(struct plist *pl, int length, double cut_off) {-  int i, j,n, count;-  /*get pair probibilities out of pr array*/-  count=0;-  n=2;-  for (i=1; i<length; i++) {-    for (j=i+1; j<=length; j++) {-      if (pr[my_iindx[i]-j]<cut_off) continue;-      if (count==n*length-1) {-        n*=2;-        pl=(struct plist *)xrealloc(pl,n*length*sizeof(struct plist));-      }-      pl[count].i=i;-      pl[count].j=j;-      pl[count++].p=pr[my_iindx[i]-j];-      /*      printf("gpl: %2d %2d %.9f\n",i,j,pr[my_iindx[i]-j]);*/-    }-  }-  pl[count].i=0;-  pl[count].j=0; /*->??*/-  pl[count++].p=0.;-  pl=(struct plist *)xrealloc(pl,(count)*sizeof(struct plist));-  return pl;-}--PUBLIC void init_co_pf_fold(int length){ /* DO NOTHING */ }
− cbits/utils.c 
@@ -1,1154 +0,0 @@-/*-                               utils.c--                 c  Ivo L Hofacker and Walter Fontana-                          Vienna RNA package-*/-/* Last changed Time-stamp: <2008-11-25 16:34:36 ivo> */--#include <stdio.h>-#include <stdlib.h>-#include <ctype.h>-#include <errno.h>-#include <time.h>-#include <string.h>-#include "config.h" // chzs-#include "utils.h"--#ifdef WITH_DMALLOC-#include "dmalloc.h"-#endif--#define PRIVATE  static-#define PUBLIC--/*@notnull@ @only@*/-PUBLIC unsigned short xsubi[3];--PRIVATE char  scale1[] = "....,....1....,....2....,....3....,....4";-PRIVATE char  scale2[] = "....,....5....,....6....,....7....,....8";-PRIVATE char  *inbuf = NULL;--PRIVATE char  *inbuf2 = NULL;-PRIVATE unsigned int typebuf2 = 0;--/*-------------------------------------------------------------------------*/--PUBLIC void *space(unsigned size) {-  void *pointer;--  if ( (pointer = (void *) calloc(1, (size_t) size)) == NULL) {-#ifdef EINVAL-    if (errno==EINVAL) {-      fprintf(stderr,"SPACE: requested size: %d\n", size);-      nrerror("SPACE allocation failure -> EINVAL");-    }-    if (errno==ENOMEM)-#endif-      nrerror("SPACE allocation failure -> no memory");-  }-  return  pointer;-}--#ifdef WITH_DMALLOC-#define space(S) calloc(1,(S))-#endif--#undef xrealloc-/* dmalloc.h #define's xrealloc */-void *xrealloc (void *p, unsigned size) {-  if (p == 0)-    return space(size);-  p = (void *) realloc(p, size);-  if (p == NULL) {-#ifdef EINVAL-    if (errno==EINVAL) {-      fprintf(stderr,"xrealloc: requested size: %d\n", size);-      nrerror("xrealloc allocation failure -> EINVAL");-    }-    if (errno==ENOMEM)-#endif-      nrerror("xrealloc allocation failure -> no memory");-  }-  return p;-}--/*------------------------------------------------------------------------*/--PUBLIC void nrerror(const char message[])       /* output message upon error */-{-  fprintf(stderr, "ERROR: %s\n", message);-  exit(EXIT_FAILURE);-}--PUBLIC void warn_user(const char message[]){-  fprintf(stderr, "WARNING: %s\n", message);-}--/*------------------------------------------------------------------------*/-PUBLIC void init_rand(void)-{-  time_t t;-  (void) time(&t);-  xsubi[0] = xsubi[1] = xsubi[2] = (unsigned short) t;  /* lower 16 bit */-  xsubi[1] += (unsigned short) ((unsigned)t >> 6);-  xsubi[2] += (unsigned short) ((unsigned)t >> 12);-#ifndef HAVE_ERAND48-  srand((unsigned int) t);-#endif-}--/*------------------------------------------------------------------------*/--PUBLIC double urn(void)-     /* uniform random number generator; urn() is in [0,1] */-     /* uses a linear congruential library routine */-     /* 48 bit arithmetic */-{-#ifdef HAVE_ERAND48-  extern double erand48(unsigned short[]);-  return erand48(xsubi);-#else-  return ((double) rand())/RAND_MAX;-#endif-}--/*------------------------------------------------------------------------*/--PUBLIC int int_urn(int from, int to)-{-  return ( ( (int) (urn()*(to-from+1)) ) + from );-}--/*------------------------------------------------------------------------*/--PUBLIC void filecopy(FILE *from, FILE *to)-{-  int c;--  while ((c = getc(from)) != EOF) (void)putc(c, to);-}--/*-----------------------------------------------------------------*/--PUBLIC char *time_stamp(void)-{-  time_t  cal_time;--  cal_time = time(NULL);-  return ( ctime(&cal_time) );-}--/*-----------------------------------------------------------------*/--PUBLIC char *random_string(int l, const char symbols[])-{-  char *r;-  int   i, rn, base;--  base = (int) strlen(symbols);-  r = (char *) space(sizeof(char)*(l+1));--  for (i = 0; i < l; i++) {-    rn = (int) (urn()*base);  /* [0, base-1] */-    r[i] = symbols[rn];-  }-  r[l] = '\0';-  return r;-}--/*-----------------------------------------------------------------*/--PUBLIC int   hamming(const char *s1, const char *s2)-{-  int h=0;--  for (; *s1 && *s2; s1++, s2++)-    if (*s1 != *s2) h++;-  return h;-}--PUBLIC int   hamming_bound(const char *s1, const char *s2, int boundary)-{-  int h=0;--  for (; *s1 && *s2 && boundary; s1++, s2++, boundary--)-    if (*s1 != *s2) h++;-  return h;-}-/*-----------------------------------------------------------------*/--PUBLIC char *get_line(FILE *fp) /* reads lines of arbitrary length from fp */-{-  char s[512], *line, *cp;-  int len=0, size=0, l;-  line=NULL;-  do {-    if (fgets(s, 512, fp)==NULL) break;-    cp = strchr(s, '\n');-    if (cp != NULL) *cp = '\0';-    l = len + (int)strlen(s);-    if (l+1>size) {-      size = (int)((l+1)*1.2);-      line = (char *) xrealloc(line, size*sizeof(char));-    }-    strcat(line+len, s);-    len=l;-  } while(cp==NULL);--  return line;-}--PUBLIC int  skip_comment_lines(char **line){-  if((*line = get_line(stdin))==NULL) return -1;--  while((**line=='*')||(**line=='\0')){-    free(*line);-    if((*line = get_line(stdin))==NULL) return -1;-  }-  return 0;-}--PUBLIC  unsigned int get_input_line(char **string, unsigned int option){-  char  *line;-  int   i, l, r;--  /*-  * read lines until informative data appears or-  * report an error if anything goes wrong-  */-  if((line = get_line(stdin))==NULL) return VRNA_INPUT_ERROR;--  if(!(option & VRNA_INPUT_NOSKIP_COMMENTS))-    while((*line=='*')||(*line=='\0')){-      free(line);-      if((line = get_line(stdin))==NULL) return VRNA_INPUT_ERROR;-    }--  l = (int) strlen(line);--  /* break on '@' sign if not disabled */-  if(*line == '@'){-    free(line);-    return VRNA_INPUT_QUIT;-  }-  /* print line read if not disabled */-  /* if(!(option & VRNA_INPUT_NOPRINT)) printf("%s\n", line); */--  /* eliminate whitespaces at the end of the line read */-  if(!(option & VRNA_INPUT_NO_TRUNCATION)){-    for(i = l-1; i >= 0; i--){-      if      (line[i] == ' ')  continue;-      else if (line[i] == '\t') continue;-      else                      break;-    }-    line[(i >= 0) ? (i+1) : 0] = '\0';-  }--  if(*line == '>'){-    /* fasta header */-    /* alloc memory for the string */-    *string = (char *) space(sizeof(char) * (strlen(line) + 1));-    r = VRNA_INPUT_FASTA_HEADER;-    i = sscanf(line, ">%s", *string);-    if(i > 0){-      i       = (int)     strlen(*string);-      *string = (char *)  xrealloc(*string, (i+1)*sizeof(char));-      free(line);-      return r;-    }-    else{-      free(line);-      free(*string);-      *string = NULL;-      return VRNA_INPUT_ERROR;-    }-  }-  else{-    *string = strdup(line);-    free(line);-  }-  return VRNA_INPUT_MISC;-}--PUBLIC  unsigned int get_multi_input_line(char **string, unsigned int option){-  char  *line;-  int   i, l;-  int   state = 0;-  int   str_length = 0;--  line = (inbuf) ? inbuf : get_line(stdin);-  inbuf = NULL;-  do{--    /*-    * read lines until informative data appears or-    * report an error if anything goes wrong-    */-    if(!line) return VRNA_INPUT_ERROR;--    l = (int)strlen(line);--    /* eliminate whitespaces at the end of the line read */-    if(!(option & VRNA_INPUT_NO_TRUNCATION)){-      for(i = l-1; i >= 0; i--){-        if      (line[i] == ' ')  continue;-        else if (line[i] == '\t') continue;-        else                      break;-      }-      line[(i >= 0) ? (i+1) : 0] = '\0';-    }--    l           = (int)strlen(line);-    str_length  = (*string) ? (int) strlen(*string) : 0;--    switch(*line){-      case  '@':    /* user abort */-                    if(state) inbuf = line;-                    else      free(line);-                    return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_QUIT;--      case  '\0':   /* empty line */-                    if(option & VRNA_INPUT_NOSKIP_BLANK_LINES){-                      if(state) inbuf = line;-                      else      free(line);-                      return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_BLANK_LINE;-                    }-                    break;--      case  '#': case  '%': case  ';': case  '/': case  '*': case ' ':-                    /* comments */-                    if(option & VRNA_INPUT_NOSKIP_COMMENTS){-                      if(state) inbuf   = line;-                      else      *string = line;-                      return (state == 2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_COMMENT;-                    }-                    break;--      case  '>':    /* fasta header */-                    if(state) inbuf   = line;-                    else      *string = line;-                    return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_FASTA_HEADER;--      case  'x': case 'e': case 'l': case '&':   /* seems to be a constraint or line starting with second sequence for dimer calculations */-                    i = 1;-                    /* lets see if this assumption holds for the complete line */-                    while((line[i] == 'x') || (line[i] == 'e') || (line[i] == 'l')) i++;-                    /* lines solely consisting of 'x's, 'e's or 'l's will be considered as structure constraint */-                    -                    if(-                            ((line[i]>64) && (line[i]<91))  /* A-Z */-                        ||  ((line[i]>96) && (line[i]<123)) /* a-z */-                      ){-                      if(option & VRNA_INPUT_FASTA_HEADER){-                        /* are we in structure mode? Then we remember this line for the next round */-                        if(state == 2){ inbuf = line; return VRNA_INPUT_CONSTRAINT;}-                        else{-                          *string = (char *)xrealloc(*string, sizeof(char) * (str_length + l + 1));-                          strcpy(*string + str_length, line);-                          state = 1;-                        }-                        break;-                      }-                      /* otherwise return line read */-                      else{ *string = line; return VRNA_INPUT_SEQUENCE;}-                    }-                    /* mmmh? it really seems to be a constraint */-                    /* fallthrough */-      case  '<': case  '.': case  '|': case  '(': case ')': case '[': case ']': case '{': case '}': case ',': case '+':-                    /* seems to be a structure or a constraint */-                    /* either we concatenate this line to one that we read previously */-                    if(option & VRNA_INPUT_FASTA_HEADER){-                      if(state == 1){-                        inbuf = line;-                        return VRNA_INPUT_SEQUENCE;-                      }-                      else{-                        *string = (char *)xrealloc(*string, sizeof(char) * (str_length + l + 1));-                        strcpy(*string + str_length, line);-                        state = 2;-                      }-                    }-                    /* or we return it as it is */-                    else{-                      *string = line;-                      return VRNA_INPUT_CONSTRAINT;-                    }-                    break;-      default:      if(option & VRNA_INPUT_FASTA_HEADER){-                      /* are we already in sequence mode? */-                      if(state == 2){-                        inbuf = line;-                        return VRNA_INPUT_CONSTRAINT;-                      }-                      else{-                        *string = (char *)xrealloc(*string, sizeof(char) * (str_length + l + 1));-                        strcpy(*string + str_length, line);-                        state = 1;-                      }-                    }-                    /* otherwise return line read */-                    else{-                      *string = line;-                      return VRNA_INPUT_SEQUENCE;-                    }-    }-    free(line);-    line = get_line(stdin);-  }while(line);--  return (state==2) ? VRNA_INPUT_CONSTRAINT : (state==1) ? VRNA_INPUT_SEQUENCE : VRNA_INPUT_ERROR;-}--PUBLIC  unsigned int read_record(char **header, char **sequence, char ***rest, unsigned int options){-  unsigned int  input_type, return_type, tmp_type;-  int           rest_count;-  char          *input_string;--  rest_count    = 0;-  return_type   = tmp_type = 0;-  input_string  = *header = *sequence = NULL;-  *rest         = (char **)space(sizeof(char *));--  /* remove unnecessary option flags from options variable... */-  options &= ~VRNA_INPUT_FASTA_HEADER;--  /* read first input or last buffered input */-  if(typebuf2){-    input_type    = typebuf2;-    input_string  = inbuf2;-    typebuf2      = 0;-    inbuf2        = NULL;-  }-  else input_type  = get_multi_input_line(&input_string, options);--  if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;--  /* skip everything until we read either a fasta header or a sequence */-  while(input_type & (VRNA_INPUT_MISC | VRNA_INPUT_CONSTRAINT | VRNA_INPUT_BLANK_LINE)){-    free(input_string); input_string = NULL;-    input_type    = get_multi_input_line(&input_string, options);-    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;-  }--  if(input_type & VRNA_INPUT_FASTA_HEADER){-    return_type  |= VRNA_INPUT_FASTA_HEADER; /* remember that we've read a fasta header */-    *header       = input_string;-    input_string  = NULL;-    /* get next data-block with fasta support if not explicitely forbidden by VRNA_INPUT_NO_SPAN */-    input_type  = get_multi_input_line(-                    &input_string,-                    ((options & VRNA_INPUT_NO_SPAN) ? 0 : VRNA_INPUT_FASTA_HEADER) | options-                  );-    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return (return_type | input_type);-  }--  if(input_type & VRNA_INPUT_SEQUENCE){-    return_type  |= VRNA_INPUT_SEQUENCE; /* remember that we've read a sequence */-    *sequence     = input_string;-    input_string  = NULL;-  } else nrerror("sequence input missing");--  /* read the rest until we find user abort, EOF, new sequence or new fasta header */-  if(!(options & VRNA_INPUT_NO_REST)){-    options |= VRNA_INPUT_NOSKIP_COMMENTS; /* allow commetns to appear in rest output */-    tmp_type = VRNA_INPUT_QUIT | VRNA_INPUT_ERROR | VRNA_INPUT_SEQUENCE | VRNA_INPUT_FASTA_HEADER;-    if(options & VRNA_INPUT_NOSKIP_BLANK_LINES) tmp_type |= VRNA_INPUT_BLANK_LINE;-    while(!((input_type = get_multi_input_line(&input_string, options)) & tmp_type)){-      *rest = xrealloc(*rest, sizeof(char **)*(++rest_count + 1));-      (*rest)[rest_count-1] = input_string;-      input_string = NULL;-    }-    /*-    if(input_type & (VRNA_INPUT_QUIT | VRNA_INPUT_ERROR)) return input_type;-    */--    /*  finished reading everything...-    *   we now put the last line into the buffer if necessary-    *   since it should belong to the next record-    */-    inbuf2 = input_string;-    typebuf2 = input_type;-  }-  (*rest)[rest_count] = NULL;-  return (return_type);-}---/*-----------------------------------------------------------------*/--PUBLIC char *pack_structure(const char *struc) {-  /* 5:1 compression using base 3 encoding */-  int i,j,l,pi;-  unsigned char *packed;--  l = (int) strlen(struc);-  packed = (unsigned char *) space(((l+4)/5+1)*sizeof(unsigned char));--  j=i=pi=0;-  while (i<l) {-    register int p;-    for (p=pi=0; pi<5; pi++) {-      p *= 3;-      switch (struc[i]) {-      case '(':-      case '\0':-        break;-      case '.':-        p++;-        break;-      case ')':-        p += 2;-        break;-      default: nrerror("pack_structure: illegal charcter in structure");-      }-      if (i<l) i++;-    }-    packed[j++] = (unsigned char) (p+1); /* never use 0, so we can use-                                            strcmp()  etc. */-  }-  packed[j] = '\0';      /* for str*() functions */-  return (char *) packed;-}--PUBLIC char *unpack_structure(const char *packed) {-  /* 5:1 compression using base 3 encoding */-  int i,j,l;-  char *struc;-  unsigned const char *pp;-  char code[3] = {'(', '.', ')'};--  l = (int) strlen(packed);-  pp = (const unsigned char *) packed;-  struc = (char *) space((l*5+1)*sizeof(char));   /* up to 4 byte extra */--  for (i=j=0; i<l; i++) {-    register int p, c, k;--    p = (int) pp[i] - 1;-    for (k=4; k>=0; k--) {-      c = p % 3;-      p /= 3;-      struc[j+k] = code[c];-    }-    j += 5;-  }-  struc[j--] = '\0';-  while (struc[j] == '(') /* strip trailing ( */-    struc[j--] = '\0';--  return struc;-}--/*--------------------------------------------------------------------------*/--PUBLIC short *make_pair_table(const char *structure)-{-    /* returns array representation of structure.-       table[i] is 0 if unpaired or j if (i.j) pair.  */-   short i,j,hx;-   short length;-   short *stack;-   short *table;--   length = (short) strlen(structure);-   stack = (short *) space(sizeof(short)*(length+1));-   table = (short *) space(sizeof(short)*(length+2));-   table[0] = length;--   for (hx=0, i=1; i<=length; i++) {-      switch (structure[i-1]) {-       case '(':-         stack[hx++]=i;-         break;-       case ')':-         j = stack[--hx];-         if (hx<0) {-            fprintf(stderr, "%s\n", structure);-            nrerror("unbalanced brackets in make_pair_table");-         }-         table[i]=j;-         table[j]=i;-         break;-       default:   /* unpaired base, usually '.' */-         table[i]= 0;-         break;-      }-   }-   if (hx!=0) {-      fprintf(stderr, "%s\n", structure);-      nrerror("unbalanced brackets in make_pair_table");-   }-   free(stack);-   return(table);-}--PUBLIC short *make_pair_table_pk(const char *structure){-   short i,j,hx, hx2;-   short length;-   short *stack;-   short *stack2;-   short *table;--   length = (short) strlen(structure);-   stack  = (short *) space(sizeof(short)*(length+1));-   stack2 = (short *) space(sizeof(short)*(length+1));-   table  = (short *) space(sizeof(short)*(length+2));-   table[0] = length;--   for (hx=0, hx2=0, i=1; i<=length; i++) {-      switch (structure[i-1]) {-       case '(':-         stack[hx++]=i;-         break;-       case ')':-         j = stack[--hx];-         if (hx<0) {-            fprintf(stderr, "%s\n", structure);-            nrerror("unbalanced '()' brackets in make_pair_table_pk");-         }-         table[i]=j;-         table[j]=i;-         break;-       case '[':-         stack2[hx2++]=i;-         break;-       case ']':-         j = stack2[--hx2];-         if (hx2<0) {-            fprintf(stderr, "%s\n", structure);-            nrerror("unbalanced '[]' brackets in make_pair_table_pk");-         }-         table[i]=j;-         table[j]=i;-         break;-       default:   /* unpaired base, usually '.' */-         table[i]= 0;-         break;-      }-   }-   if (hx!=0) {-      fprintf(stderr, "%s\n", structure);-      nrerror("unbalanced '()' brackets in make_pair_table_pk");-   } else if (hx2!=0) {-      fprintf(stderr, "%s\n", structure);-      nrerror("unbalanced '[]' brackets in make_pair_table_pk");-   }-   free(stack);-   free(stack2);-   return(table);-}--PUBLIC short *make_pair_table_snoop(const char *structure)-{-    /* returns array representation of structure.-       table[i] is 0 if unpaired or j if (i.j) pair.  */-   short i,j,hx;-   short length;-   short *stack;-   short *table;--   length = (short) strlen(structure);-   stack = (short *) space(sizeof(short)*(length+1));-   table = (short *) space(sizeof(short)*(length+2));-   table[0] = length;--   for (hx=0, i=1; i<=length; i++) {-     switch (structure[i-1]) {-     case '<':-       stack[hx++]=i;-       break;-     case '>':-       j = stack[--hx];-       if (hx<0) {-	 fprintf(stderr, "%s\n", structure);-	 nrerror("unbalanced brackets in make_pair_table");-       }-       table[i]=j;-       table[j]=i;-       break;-     default:   /* unpaired base, usually '.' */-       table[i]= table[i];-       break;-     }-   }-   if (hx!=0) {-     fprintf(stderr, "%s\n", structure);-     nrerror("unbalanced brackets in make_pair_table");-   }-   free(stack);-   return table ;-}---PUBLIC short *alimake_pair_table(const char *structure)-{-    /* returns array representation of structure.-       table[i] is 0 if unpaired or j if (i.j) pair.  */-   short i,j,hx;-   short length;-   short *stack;-   short *table;--   length = (short) strlen(structure);-   stack = (short *) space(sizeof(short)*(length+1));-   table = (short *) space(sizeof(short)*(length+2));-   table[0] = length;--   for (hx=0, i=1; i<=length; i++) {-      switch (structure[i-1]) {-       case '(':-	 stack[hx++]=i;-	 break;-       case ')':-	 j = stack[--hx];-	 if (hx<0) {-	    fprintf(stderr, "%s\n", structure);-	    nrerror("unbalanced brackets in make_pair_table");-	 }-	 table[i]=j;-	 table[j]=i;-	 break;-       default:   /* unpaired base, usually '.' */-	 table[i]= 0;-	 break;-      }-   }-   for (hx=0, i=1; i<=length; i++) {-      switch (structure[i-1]) {-       case '<':-	 stack[hx++]=i;-	 break;-       case '>':-	 j = stack[--hx];-	 if (hx<0) {-	    fprintf(stderr, "%s\n", structure);-	    nrerror("unbalanced brackets in make_pair_table");-	 }-	 table[i]=j;-	 table[j]=i;-	 break;-       default:   /* unpaired base, usually '.' */-	 table[i]= table[i];-	 break;-      }-   }-   for (hx=0, i=1; i<=length; i++) {-     switch (structure[i-1]) {-     case '[':-       stack[hx++]=i;-       break;-     case ']':-       j = stack[--hx];-       if (hx<0) {-	 fprintf(stderr, "%s\n", structure);-	 nrerror("unbalanced brackets in make_pair_table");-       }-       table[i]=j;-       table[j]=i;-       break;-     default:   /* unpaired base, usually '.' */-       break;-     }-   }-   if (hx!=0) {-      fprintf(stderr, "%s\n", structure);-      nrerror("unbalanced brackets in make_pair_table");-   }-   free(stack);-   return(table);-}--PUBLIC short *copy_pair_table(const short *pt){-  short *table = (short *)space(sizeof(short) * (pt[0]+2));-  memcpy(table, pt, sizeof(short)*(pt[0]+2));-  return table;-}---PUBLIC int *make_loop_index_pt(short *pt){--  /* number each position by which loop it belongs to (positions start-     at 1) */-  int i,hx,l,nl;-  int length;-  int *stack = NULL;-  int *loop = NULL;--  length = pt[0];-  stack  = (int *) space(sizeof(int)*(length+1));-  loop   = (int *) space(sizeof(int)*(length+2));-  hx=l=nl=0;--  for (i=1; i<=length; i++) {-    if ((pt[i] != 0) && (i < pt[i])) { /* ( */-      nl++; l=nl;-      stack[hx++]=i;-    }-    loop[i]=l;--    if ((pt[i] != 0) && (i > pt[i])) { /* ) */-      --hx;-      if (hx>0)-        l = loop[stack[hx-1]];  /* index of enclosing loop   */-      else l=0;                 /* external loop has index 0 */-      if (hx<0) {-        nrerror("unbalanced brackets in make_pair_table");-      }-    }-  }-  loop[0] = nl;-  free(stack);-  return (loop);-}--/*---------------------------------------------------------------------------*/--PUBLIC int bp_distance(const char *str1, const char *str2)-{-  /* dist = {number of base pairs in one structure but not in the other} */-  /* same as edit distance with pair_open pair_close as move set */-   int dist;-   short i,l;-   short *t1, *t2;--   dist = 0;-   t1 = make_pair_table(str1);-   t2 = make_pair_table(str2);--   l = (t1[0]<t2[0])?t1[0]:t2[0];    /* minimum of the two lengths */--   for (i=1; i<=l; i++)-     if (t1[i]!=t2[i]) {-       if (t1[i]>i) dist++;-       if (t2[i]>i) dist++;-     }-   free(t1); free(t2);-   return dist;-}--#ifndef HAVE_STRDUP-char *strdup(const char *s) {-  char *dup;--  dup = space(strlen(s)+1);-  strcpy(dup, s);-  return(dup);-}-#endif--PUBLIC  void  print_tty_input_seq(void){-  print_tty_input_seq_str("Input string (upper or lower case)");-}--PUBLIC  void  print_tty_input_seq_str(const char *s){-  printf("\n%s; @ to quit\n", s);-  printf("%s%s\n", scale1, scale2);-  (void) fflush(stdout);-}--PUBLIC  void  print_tty_constraint_full(void){-  print_tty_constraint(VRNA_CONSTRAINT_PIPE | VRNA_CONSTRAINT_DOT | VRNA_CONSTRAINT_X | VRNA_CONSTRAINT_ANG_BRACK | VRNA_CONSTRAINT_RND_BRACK);-}--PUBLIC  void  print_tty_constraint(unsigned int option){-  if(!(option & VRNA_CONSTRAINT_NO_HEADER)) printf("Input structure constraints using the following notation:\n");-  if(option & VRNA_CONSTRAINT_PIPE)       printf("| : paired with another base\n");-  if(option & VRNA_CONSTRAINT_DOT)        printf(". : no constraint at all\n");-  if(option & VRNA_CONSTRAINT_X)          printf("x : base must not pair\n");-  if(option & VRNA_CONSTRAINT_ANG_BRACK)  printf("< : base i is paired with a base j<i\n> : base i is paired with a base j>i\n");-  if(option & VRNA_CONSTRAINT_RND_BRACK)  printf("matching brackets ( ): base i pairs base j\n");-}--PUBLIC  void  str_DNA2RNA(char *sequence){-  unsigned int l, i;-  if(sequence != NULL){-    l = strlen(sequence);-    for(i = 0; i < l; i++){-      if(sequence[i] == 'T') sequence[i] = 'U';-      if(sequence[i] == 't') sequence[i] = 'u';-    }-  }-}--PUBLIC void str_uppercase(char *sequence){-  unsigned int l, i;-  if(sequence){-    l = strlen(sequence);-    for(i=0;i<l;i++)-      sequence[i] = toupper(sequence[i]);-  }-}--PUBLIC int *get_iindx(unsigned int length){-  int i;-  int *idx = (int *)space(sizeof(int) * (length+1));-  for (i=1; i <= length; i++)-    idx[i] = (((length + 1 - i) * (length - i))>>1) + length + 1;-  return idx;-}--PUBLIC int *get_indx(unsigned int length){-  unsigned int i;-  int *idx = (int *)space(sizeof(int) * (length+1));-  for (i = 1; i <= length; i++)-    idx[i] = (i*(i-1)) >> 1;        /* i(i-1)/2 */-  return idx;-}--PUBLIC void getConstraint(char **cstruc, const char **lines, unsigned int option){-  int r, i, l, cl, stop;-  char *c, *ptr;-  if(lines){-    if(option & VRNA_CONSTRAINT_ALL)-      option |= VRNA_CONSTRAINT_PIPE | VRNA_CONSTRAINT_ANG_BRACK | VRNA_CONSTRAINT_RND_BRACK | VRNA_CONSTRAINT_X | VRNA_CONSTRAINT_G;--    for(r=i=stop=0;lines[i];i++){-      l   = (int)strlen(lines[i]);-      c   = (char *) space(sizeof(char) * (l+1));-      (void) sscanf(lines[i], "%s", c);-      cl  = (int)strlen(c);-      /* line commented out ? */-      if((*c == '#') || (*c == '%') || (*c == ';') || (*c == '/') || (*c == '*' || (*c == '\0'))){-        /* skip leading comments only, i.e. do not allow comments inside the constraint */-        if(!r)  continue;-        else    break;-      }--      /* check current line for actual constraining structure */-      for(ptr = c;*c;c++){-        switch(*c){-          case '|':   if(!(option & VRNA_CONSTRAINT_PIPE)){-                        warn_user("constraints of type '|' not allowed");-                        *c = '.';-                      }-                      break;-          case '<':   -          case '>':   if(!(option & VRNA_CONSTRAINT_ANG_BRACK)){-                        warn_user("constraints of type '<' or '>' not allowed");-                        *c = '.';-                      }-                      break;-          case '(':-          case ')':   if(!(option & VRNA_CONSTRAINT_RND_BRACK)){-                        warn_user("constraints of type '(' or ')' not allowed");-                        *c = '.';-                      }-                      break;-          case 'x':   if(!(option & VRNA_CONSTRAINT_X)){-                        warn_user("constraints of type 'x' not allowed");-                        *c = '.';-                      }-                      break;-          case '+':   if(!(option & VRNA_CONSTRAINT_G)){-                        warn_user("character '+' ignored in structure");-                        *c = '.';-                      }-          case '.':   break;-          case '&':   break; /* ignore concatenation char */-          default:    warn_user("unrecognized character in constraint structure");-                      break;-        }-      }--      r += cl+1;-      *cstruc = (char *)xrealloc(*cstruc, r*sizeof(char));-      strcat(*cstruc, ptr);-      free(ptr);-      /* stop if not in fasta mode or multiple words on line */-      if(!(option & VRNA_CONSTRAINT_MULTILINE) || (cl != l)) break;-    }-  }-}--PUBLIC char *extract_record_rest_structure( const char **lines,-                                            unsigned int length,-                                            unsigned int option){--  char *structure = NULL;-  int r, i, l, cl, stop;-  char *c;--  if(lines){-    for(r = i = stop = 0; lines[i]; i++){-      l   = (int)strlen(lines[i]);-      c   = (char *) space(sizeof(char) * (l+1));-      (void) sscanf(lines[i], "%s", c);-      cl  = (int)strlen(c);--      /* line commented out ? */-      if((*c == '#') || (*c == '%') || (*c == ';') || (*c == '/') || (*c == '*' || (*c == '\0'))){-        /* skip leading comments only, i.e. do not allow comments inside the constraint */-        if(!r)  continue;-        else    break;-      }--      /* append the structure part to the output */-      r += cl+1;-      structure = (char *)xrealloc(structure, r*sizeof(char));-      strcat(structure, c);-      free(c);-      /* stop if the assumed structure length has been reached */-      if((length > 0) && (r-1 == length)) break;-      /* stop if not allowed to read from multiple lines */-      if(!(option & VRNA_OPTION_MULTILINE)) break;-    }-  }-  return structure;-}----PUBLIC void constrain_ptypes(const char *constraint, unsigned int length, char *ptype, int *BP, int min_loop_size, unsigned int idx_type){-  int n,i,j,k,l;-  int hx, *stack;-  char type;-  int *index;--  if(constraint == NULL) return;--  n = (int)strlen(constraint);--  stack = (int *) space(sizeof(int)*(n+1));--  if(!idx_type){ /* index allows access in energy matrices at pos (i,j) via index[j]+i */-    index = get_indx(length);--    for(hx=0, j=1; j<=n; j++){-      switch(constraint[j-1]){-        case '|':   if(BP) BP[j] = -1;-                    break;-        case 'x':   /* can't pair */-                    for (l=1; l<j-min_loop_size; l++) ptype[index[j]+l] = 0;-                    for (l=j+min_loop_size+1; l<=(int)length; l++) ptype[index[l]+j] = 0;-                    break;-        case '(':   stack[hx++]=j;-                    /* fallthrough */-        case '<':   /* pairs upstream */-                    for (l=1; l<j-min_loop_size; l++) ptype[index[j]+l] = 0;-                    break;-        case ')':   if (hx<=0) {-                      fprintf(stderr, "%s\n", constraint);-                      nrerror("unbalanced brackets in constraint");-                    }-                    i = stack[--hx];-                    type = ptype[index[j]+i];-                    for (k=i+1; k<=(int)length; k++) ptype[index[k]+i] = 0;-                    /* don't allow pairs i<k<j<l */-                    for (l=j; l<=(int)length; l++)-                      for (k=i+1; k<=j; k++) ptype[index[l]+k] = 0;-                    /* don't allow pairs k<i<l<j */-                    for (l=i; l<=j; l++)-                      for (k=1; k<=i; k++) ptype[index[l]+k] = 0;-                    for (k=1; k<j; k++) ptype[index[j]+k] = 0;-                    ptype[index[j]+i] = (type==0) ? 7 : type;-                    /* fallthrough */-        case '>':   /* pairs downstream */-                    for (l=j+min_loop_size+1; l<=(int)length; l++) ptype[index[l]+j] = 0;-                    break;-      }-    }-  }-  else{ /* index allows access in energy matrices at pos (i,j) via index[i]-j */-    index = get_iindx(length);--    for(hx=0, j=1; j<=n; j++) {-      switch (constraint[j-1]) {-        case 'x':   /* can't pair */-                    for (l=1; l<j-min_loop_size; l++) ptype[index[l]-j] = 0;-                    for (l=j+min_loop_size+1; l<=(int)length; l++) ptype[index[j]-l] = 0;-                    break;-        case '(':   stack[hx++]=j;-                    /* fallthrough */-        case '<':   /* pairs upstream */-                    for (l=1; l<j-min_loop_size; l++) ptype[index[l]-j] = 0;-                    break;-        case ')':   if (hx<=0) {-                      fprintf(stderr, "%s\n", constraint);-                      nrerror("unbalanced brackets in constraints");-                    }-                    i = stack[--hx];-                    type = ptype[index[i]-j];-                    /* don't allow pairs i<k<j<l */-                    for (k=i; k<=j; k++)-                      for (l=j; l<=(int)length; l++) ptype[index[k]-l] = 0;-                    /* don't allow pairs k<i<l<j */-                    for (k=1; k<=i; k++)-                      for (l=i; l<=j; l++) ptype[index[k]-l] = 0;-                    ptype[index[i]-j] = (type==0) ? 7 : type;-                    /* fallthrough */-        case '>':   /* pairs downstream */-                    for (l=j+min_loop_size+1; l<=(int)length; l++) ptype[index[j]-l] = 0;-                    break;-      }-    }-  }-  if (hx!=0) {-    fprintf(stderr, "%s\n", constraint);-    nrerror("unbalanced brackets in constraint string");-  }-  free(index);-  free(stack);-}--/* get a matrix containing the number of basepairs of a reference structure for each interval [i,j] with i<j-*  access it via iindx!!!-*/-PUBLIC unsigned int *make_referenceBP_array(short *reference_pt, unsigned int turn){-  unsigned int i,j,k,ij,length;-  int *iindx;-  unsigned int *array;-  unsigned int size;-  length = (unsigned int)reference_pt[0];-  size  = ((length+1)*(length+2))/2;-  iindx = get_iindx(length);-  array = (unsigned int *) space(sizeof(unsigned int)*size);    /* matrix containing number of basepairs of reference structure1 in interval [i,j] */;-  for (k=0; k<=turn; k++)-    for (i=1; i<=length-k; i++) {-      j=i+k;-      ij = iindx[i]-j;-      array[ij] = 0;-    }--  for (i = length-turn-1; i >= 1; i--)-    for (j = i+turn+1; j <= length; j++){-      int bps;-      ij = iindx[i]-j;-      bps = array[ij+1];-      if((i<=(unsigned int)reference_pt[j]) && ((unsigned int)reference_pt[j] < j))-        bps++;-      array[ij] = bps;-    }-  free(iindx);-  return array;-}--PUBLIC unsigned int *compute_BPdifferences(short *pt1, short *pt2, unsigned int turn){-  unsigned int *array;-  unsigned int n, size, i, j, ij, d;-  n = (unsigned int)pt1[0];-  size = ((n+1)*(n+2))/2;-  array = (unsigned int *)space(sizeof(unsigned int) * size);-  int *iindx = get_iindx(n);-  for(i = n - turn - 1; i>=1; i--){-    d = 0;-    for(j = i+turn+1; j <= n; j++){-      ij = iindx[i]-j;-      d = array[ij+1];-      if(pt1[j] != pt2[j]){-        if(i <= (unsigned int)pt1[j] && (unsigned int)pt1[j] < j){-          /* we got an additional base pair in reference structure 1 */-          d++;-        }-        if(i <= (unsigned int)pt2[j] && (unsigned int)pt2[j] < j){-          /* we got another base pair in reference structure 2 */-          d++;-        }-      }-      array[ij] = d;--    }-  }-  free(iindx);-  return array;-}
− changelog 
@@ -1,23 +0,0 @@-0.1.2.1--- removed debug statements--0.1.2.0--- constrained cofold partition function added--0.1.1.1--- export everything in the bindings--0.1.1.0----------- breaking changes to PartFunc.chs-- constrained partition function folding-- includes should now all be local (that one was bad)--0.1.0.0----------- relevant cbits are now provided as part of the cabal package
+ changelog.md view
@@ -0,0 +1,57 @@+0.233.1.1+---------++- track ViennaRNA version numbers in 2nd component+- bump to v 2.3.3++0.1.6.0+-------++- partial bindings to ViennaRNA 2.2.5+- tests/properties.hs++0.1.5.0+-------++- added stack.yaml file++0.1.4.0+-------++- added circular folding and partition function calculations+- NOTE due to circular dependencies in fold / fold_vars we currently can not+  cabal repl on ghc 7.8.{1,2,3}++0.1.3.0+-------++- added duplexfold+- added a bunch of c/h files due to duplexfold dependencies++0.1.2.1+-------++- removed debug statements++0.1.2.0+-------++- constrained cofold partition function added++0.1.1.1+-------++- export everything in the bindings++0.1.1.0+-------++- breaking changes to PartFunc.chs+- constrained partition function folding+- includes should now all be local (that one was bad)++0.1.0.0+-------++- relevant cbits are now provided as part of the cabal package+
− include/1.8.4_epars.h 
@@ -1,366 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_OLD_EPARS__-#define __VIENNA_RNA_PACKAGE_OLD_EPARS__-/**-    \file 1.8.4_epars.h-    \brief Free energy parameters for parameter file conversion--    This file contains the free energy parameters used in ViennaRNAPackage 1.8.4.-    They are summarized in:--    D.H.Mathews, J. Sabina, M. ZUker, D.H. Turner-    "Expanded sequence dependence of thermodynamic parameters improves-    prediction of RNA secondary structure"-    JMB, 288, pp 911-940, 1999--    Enthalpies taken from:--    A. Walter, D Turner, J Kim, M Lyttle, P M"uller, D Mathews, M Zuker-    "Coaxial stckaing of helices enhances binding of oligoribonucleotides.."-    PNAS, 91, pp 9218-9222, 1994--    D.H. Turner, N. Sugimoto, and S.M. Freier.-    "RNA Structure Prediction",-    Ann. Rev. Biophys. Biophys. Chem. 17, 167-192, 1988.--    John A.Jaeger, Douglas H.Turner, and Michael Zuker.-    "Improved predictions of secondary structures for RNA",-    PNAS, 86, 7706-7710, October 1989.--    L. He, R. Kierzek, J. SantaLucia, A.E. Walter, D.H. Turner-    "Nearest-Neughbor Parameters for GU Mismatches...."-    Biochemistry 1991, 30 11124-11132--    A.E. Peritz, R. Kierzek, N, Sugimoto, D.H. Turner-    "Thermodynamic Study of Internal Loops in Oligoribonucleotides..."-    Biochemistry 1991, 30, 6428--6435-*/--#define K0        273.15-#ifdef INF-#undef INF-#endif-#define INF       1000000-#define NBPAIRS   7-#define NST       0     /* Energy for nonstandard stacked pairs */-#define DEF       -50   /* Default terminal mismatch, used for I */-                        /* and any non_pairing bases */-#define NSM       0     /* terminal mismatch for non standard pairs */--PRIVATE double Tmeasure_184 = 37 + K0;  /* temperature of param measurements */-PRIVATE double lxc37_184    = 107.856;  /* parameter for logarithmic loop-                                           energy extrapolation */--PRIVATE int stack37_184[NBPAIRS+1][NBPAIRS+1] =-/*          CG     GC     GU     UG     AU     UA  */-{ {  INF,   INF,   INF,   INF,   INF,   INF,   INF, INF},-  {  INF,  -240,  -330,  -210,  -140,  -210,  -210, NST},-  {  INF,  -330,  -340,  -250,  -150,  -220,  -240, NST},-  {  INF,  -210,  -250,   130,   -50,  -140,  -130, NST},-  {  INF,  -140,  -150,   -50,    30,   -60,  -100, NST},-  {  INF,  -210,  -220,  -140,   -60,  -110,   -90, NST},-  {  INF,  -210,  -240,  -130,  -100,   -90,  -130, NST},-  {  INF,   NST,   NST,   NST,   NST,   NST,   NST, NST}};--/* enthalpies (0.01*kcal/mol at 37 C) for stacked pairs */-/* different from mfold-2.3, which uses values from mfold-2.2 */-PRIVATE int enthalpies_184[NBPAIRS+1][NBPAIRS+1] =-/*          CG     GC     GU     UG     AU     UA  */-{ {  INF,   INF,   INF,   INF,   INF,   INF,   INF, INF},-  {  INF, -1060, -1340, -1210,  -560, -1050, -1040, NST},-  {  INF, -1340, -1490, -1260,  -830, -1140, -1240, NST},-  {  INF, -1210, -1260, -1460, -1350,  -880, -1280, NST},-  {  INF,  -560,  -830, -1350,  -930,  -320,  -700, NST},-  {  INF, -1050, -1140,  -880,  -320,  -940,  -680, NST},-  {  INF, -1040, -1240, -1280,  -700,  -680,  -770, NST},-  {  INF,   NST,   NST,   NST,   NST,   NST,   NST, NST}};---/* old values are here just for comparison */-PRIVATE int oldhairpin37_184[31] = { /* from ViennaRNA 1.3 */-  INF, INF, INF, 410, 490, 440, 470, 500, 510, 520, 531,-       542, 551, 560, 568, 575, 582, 589, 595, 601, 606,-       611, 616, 621, 626, 630, 634, 638, 642, 646, 650};--PRIVATE int hairpin37_184[31] = {-  INF, INF, INF, 570, 560, 560, 540, 590, 560, 640, 650,-       660, 670, 678, 686, 694, 701, 707, 713, 719, 725,-       730, 735, 740, 744, 749, 753, 757, 761, 765, 769};--PRIVATE int oldbulge37_184[31] = {-  INF, 390, 310, 350, 420, 480, 500, 516, 531, 543, 555,-       565, 574, 583, 591, 598, 605, 612, 618, 624, 630,-       635, 640, 645, 649, 654, 658, 662, 666, 670, 673};--PRIVATE int bulge37_184[31] = {-  INF, 380, 280, 320, 360, 400, 440, 459, 470, 480, 490,-       500, 510, 519, 527, 534, 541, 548, 554, 560, 565,-  571, 576, 580, 585, 589, 594, 598, 602, 605, 609};--PRIVATE int oldinternal_loop37_184[31] = {-  INF, INF, 410, 510, 490, 530, 570, 587, 601, 614, 625,-       635, 645, 653, 661, 669, 676, 682, 688, 694, 700,-       705, 710, 715, 720, 724, 728, 732, 736, 740, 744};--PRIVATE int internal_loop37_184[31] = {-  INF, INF, 410, 510, 170, 180, 200, 220, 230, 240, 250,-       260, 270, 278, 286, 294, 301, 307, 313, 319, 325,-       330, 335, 340, 345, 349, 353, 357, 361, 365, 369};--/* terminal mismatches */-/* mismatch free energies for interior loops at 37C */-PRIVATE int mismatchI37_184[NBPAIRS+1][5][5] =-{ /* @@ */-  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},-  { /* CG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,    0,    0, -110,    0}, /* A@  AA  AC  AG  AU */-   {   0,    0,    0,    0,    0}, /* C@  CA  CC  CG  CU */-   {   0, -110,    0,    0,    0}, /* G@  GA  GC  GG  GU */-   {   0,    0,    0,    0,  -70}},/* U@  UA  UC  UG  UU */-  { /* GC */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,    0,    0, -110,    0}, /* A@  AA  AC  AG  AU */-   {   0,    0,    0,    0,    0}, /* C@  CA  CC  CG  CU */-   {   0, -110,    0,    0,    0}, /* G@  GA  GC  GG  GU */-   {   0,    0,    0,    0,  -70}},/* U@  UA  UC  UG  UU */-  { /* GU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */-   {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */-   {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */-   {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */-  { /* UG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */-   {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */-   {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */-   {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */-  { /* AU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */-   {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */-   {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */-   {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */-  { /* UA */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,   70,   70,  -40,   70}, /* A@  AA  AC  AG  AU */-   {   0,   70,   70,   70,   70}, /* C@  CA  CC  CG  CU */-   {   0,  -40,   70,   70,   70}, /* G@  GA  GC  GG  GU */-   {   0,   70,   70,   70,    0}},/* U@  UA  UC  UG  UU */-  { /* @@ */-   { 90, 90, 90, 90, 90},{ 90, 90, 90, 90,-20},{ 90, 90, 90, 90, 90},-   { 90,-20, 90, 90, 90},{ 90, 90, 90, 90, 20}}-};--/* mismatch free energies for hairpins at 37C */-PRIVATE int mismatchH37_184[NBPAIRS+1][5][5] =-{ /* @@ */-  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},-  { /* CG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { -90, -150, -150, -140, -180}, /* A@  AA  AC  AG  AU */-   { -90, -100,  -90, -290,  -80}, /* C@  CA  CC  CG  CU */-   { -90, -220, -200, -160, -110}, /* G@  GA  GC  GG  GU */-   { -90, -170, -140, -180, -200}},/* U@  UA  UC  UG  UU */-  { /* GC */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { -70, -110, -150, -130, -210}, /* A@  AA  AC  AG  AU */-   { -70, -110,  -70, -240,  -50}, /* C@  CA  CC  CG  CU */-   { -70, -240, -290, -140, -120}, /* G@  GA  GC  GG  GU */-   { -70, -190, -100, -220, -150}},/* U@  UA  UC  UG  UU */-  { /* GU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,   20,  -50,  -30,  -30}, /* A@  AA  AC  AG  AU */-   {   0,  -10,  -20, -150,  -20}, /* C@  CA  CC  CG  CU */-   {   0,  -90, -110,  -30,    0}, /* G@  GA  GC  GG  GU */-   {   0,  -30,  -30,  -40, -110}},/* U@  UA  UC  UG  UU */-  { /* UG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,  -50,  -30,  -60,  -50}, /* A@  AA  AC  AG  AU */-   {   0,  -20,  -10, -170,    0}, /* C@  CA  CC  CG  CU */-   {   0,  -80, -120,  -30,  -70}, /* G@  GA  GC  GG  GU */-   {   0,  -60,  -10,  -60,  -80}},/* U@  UA  UC  UG  UU */-  { /* AU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,  -30,  -50,  -30,  -30}, /* A@  AA  AC  AG  AU */-   {   0,  -10,  -20, -150,  -20}, /* C@  CA  CC  CG  CU */-   {   0, -110, -120,  -20,   20}, /* G@  GA  GC  GG  GU */-   {   0,  -30,  -30,  -60, -110}},/* U@  UA  UC  UG  UU */-  { /* UA */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   {   0,  -50,  -30,  -60,  -50}, /* A@  AA  AC  AG  AU */-   {   0,  -20,  -10, -120,   -0}, /* C@  CA  CC  CG  CU */-   {   0, -140, -120,  -70,  -20}, /* G@  GA  GC  GG  GU */-   {   0,  -30,  -10,  -50,  -80}},/* U@  UA  UC  UG  UU */-  { /* @@ */-   {  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0},-   {  0,  0,  0,  0,  0},{  0,  0,  0,  0,  0}}-};--/* mismatch energies in multiloops */-PRIVATE int mismatchM37_184[NBPAIRS+1][5][5];--/* these are probably junk */-/* mismatch enthalpies for temperature scaling */-PRIVATE int mism_H_184[NBPAIRS+1][5][5] =-{ /* no pair */-  {{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0},{0,0,0,0,0}},-  { /* CG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF,-1030, -950,-1030,-1030}, /* A@  AA  AC  AG  AU */-   { DEF, -520, -450, -520, -670}, /* C@  CA  CC  CG  CU */-   { DEF, -940, -940, -940, -940}, /* G@  GA  GC  GG  GU */-   { DEF, -810, -740, -810, -860}},/* U@  UA  UC  UG  UU */-  { /* GC */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF, -520, -880, -560, -880}, /* A@  AA  AC  AG  AU */-   { DEF, -720, -310, -310, -390}, /* C@  CA  CC  CG  CU */-   { DEF, -710, -740, -620, -740}, /* G@  GA  GC  GG  GU */-   { DEF, -500, -500, -500, -570}},/* U@  UA  UC  UG  UU */-  { /* GU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF, -430, -600, -600, -600}, /* A@  AA  AC  AG  AU */-   { DEF, -260, -240, -240, -240}, /* C@  CA  CC  CG  CU */-   { DEF, -340, -690, -690, -690}, /* G@  GA  GC  GG  GU */-   { DEF, -330, -330, -330, -330}},/* U@  UA  UC  UG  UU */-  { /* UG */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF, -720, -790, -960, -810}, /* A@  AA  AC  AG  AU */-   { DEF, -480, -480, -360, -480}, /* C@  CA  CC  CG  CU */-   { DEF, -660, -810, -920, -810}, /* G@  GA  GC  GG  GU */-   { DEF, -550, -440, -550, -360}},/* U@  UA  UC  UG  UU */-  { /* AU */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF, -430, -600, -600, -600}, /* A@  AA  AC  AG  AU */-   { DEF, -260, -240, -240, -240}, /* C@  CA  CC  CG  CU */-   { DEF, -340, -690, -690, -690}, /* G@  GA  GC  GG  GU */-   { DEF, -330, -330, -330, -330}},/* U@  UA  UC  UG  UU */-  { /* UA */-   {   0,    0,    0,    0,    0}, /* @@  @A  @C  @G  @U */-   { DEF, -400, -630, -890, -590}, /* A@  AA  AC  AG  AU */-   { DEF, -430, -510, -200, -180}, /* C@  CA  CC  CG  CU */-   { DEF, -380, -680, -890, -680}, /* G@  GA  GC  GG  GU */-   { DEF, -280, -140, -280, -140}},/* U@  UA  UC  UG  UU */-  { /* nonstandard pair */-   {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF},-   {DEF,DEF,DEF,DEF,DEF},{DEF,DEF,DEF,DEF,DEF}}-};--/* 5' dangling ends (unpaird base stacks on first paired base) */-PRIVATE int dangle5_37_184[NBPAIRS+1][5]=-{/*   @     A     C     G     U   */-   { INF,  INF,  INF,  INF,  INF}, /* no pair */-   { INF,  -50,  -30,  -20,  -10}, /* CG  (stacks on C) */-   { INF,  -20,  -30,   -0,   -0}, /* GC  (stacks on G) */-   { INF,  -30,  -30,  -40,  -20}, /* GU */-   { INF,  -30,  -10,  -20,  -20}, /* UG */-   { INF,  -30,  -30,  -40,  -20}, /* AU */-   { INF,  -30,  -10,  -20,  -20}, /* UA */-   {   0,    0,     0,    0,   0}  /*  @ */-};--/* 3' dangling ends (unpaired base stacks on second paired base */-PRIVATE int dangle3_37_184[NBPAIRS+1][5]=-{/*   @     A     C     G     U   */-   { INF,  INF,  INF,  INF,  INF},  /* no pair */-   { INF, -110,  -40, -130,  -60},  /* CG  (stacks on G) */-   { INF, -170,  -80, -170, -120},  /* GC */-   { INF,  -70,  -10,  -70,  -10},  /* GU */-   { INF,  -80,  -50,  -80,  -60},  /* UG */-   { INF,  -70,  -10,  -70,  -10},  /* AU */-   { INF,  -80,  -50,  -80,  -60},  /* UA */-   {   0,    0,     0,    0,   0}   /*  @ */-};--/* enthalpies for temperature scaling */-PRIVATE int dangle3_H_184[NBPAIRS+1][5] =-{/*   @     A     C     G     U   */-   { INF,  INF,  INF,  INF,  INF},  /* no pair */-   {   0, -740, -280, -640, -360},-   {   0, -900, -410, -860, -750},-   {   0, -740, -240, -720, -490},-   {   0, -490,  -90, -550, -230},-   {   0, -570,  -70, -580, -220},-   {   0, -490,  -90, -550, -230},-   {   0,    0,    0,    0,   0}-};--PRIVATE int dangle5_H_184[NBPAIRS+1][5] =-{/*   @     A     C     G     U   */-   { INF,  INF,  INF,  INF,  INF},  /* no pair */-   {   0, -240,  330,   80, -140},-   {   0, -160,   70, -460,  -40},-   {   0,  160,  220,   70,  310},-   {   0, -150,  510,   10,  100},-   {   0,  160,  220,   70,  310},-   {   0,  -50,  690,  -60,  -60},-   {   0,    0,    0,    0,   0}-};---/* constants for linearly destabilizing contributions for multi-loops-   F = ML_closing + ML_intern*k + ML_BASE*u  */-/* old versions erroneously used ML_intern*(k-1) */-PRIVATE int ML_BASE37_184 = 0;-PRIVATE int ML_closing37_184 = 340;-PRIVATE int ML_intern37_184 =  40;--/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */-/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */-PRIVATE int MAX_NINIO_184 = 300;                   /* maximum correction */-PRIVATE int F_ninio37_184[5] = { 0, 40, 50, 20, 10 };      /* only F[2] used */--/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */--PRIVATE char Tetraloops_184[1400] =  /* place for up to 200 tetra loops */-  "GGGGAC "-  "GGUGAC "-  "CGAAAG "-  "GGAGAC "-  "CGCAAG "-  "GGAAAC "-  "CGGAAG "-  "CUUCGG "-  "CGUGAG "-  "CGAAGG "-  "CUACGG "-  "GGCAAC "-  "CGCGAG "-  "UGAGAG "-  "CGAGAG "-  "AGAAAU "-  "CGUAAG "-  "CUAACG "-  "UGAAAG "-  "GGAAGC "-  "GGGAAC "-  "UGAAAA "-  "AGCAAU "-  "AGUAAU "-  "CGGGAG "-  "AGUGAU "-  "GGCGAC "-  "GGGAGC "-  "GUGAAC "-  "UGGAAA "-;--PRIVATE int   TETRA_ENERGY37_184[200] = {-  -300, -300, -300, -300, -300, -300, -300, -300, -300, -250, -250, -250,-  -250, -250, -200, -200, -200, -200, -200, -150, -150, -150, -150, -150,-  -150, -150, -150, -150, -150, -150};--PRIVATE int   TETRA_ENTH37_184   = -400;--PRIVATE char Triloops_184[241] = "";--PRIVATE int Triloop_E37_184[40];--/* penalty for AU (or GU) terminating helix) */-/* mismatches already contain these */-PRIVATE int TerminalAU_184 = 50;--/* penalty for forming a bi-molecular duplex */-PRIVATE int DuplexInit_184 = 410;--#endif
− include/1.8.4_intloops.h 
@@ -1,11073 +0,0 @@-/**-*** \file 1.8.4_intloops.h-*** \brief Free energy parameters for interior loop contributions needed by the parameter file conversion functions-**/-PRIVATE int int11_37_184[NBPAIRS+1][NBPAIRS+1][5][5] =-{ /* noPair */ {{{0}}},-{ /* noPair */ {{0}},-/* CG..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110,  40,  40,  40},-{ 110,  40,  40,  40,  40},-{ 110,  40,  40, -140,  40},-{ 110,  40,  40,  40,  40}-},-/* CG..GC */-{{ 110, 110, 110, 110, 110},-{ 110,  40, -40,  40,  40},-{ 110,  30,  50,  40,  50},-{ 110, -10,  40, -170,  40},-{ 110,  40,   0,  40, -30}-},-/* CG..GU */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* CG..UG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* CG..AU */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* CG..UA */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* CG..?? */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110}-}-},-{ /* noPair */ {{0}},-/* GC..CG */-{{ 110, 110, 110, 110, 110},-{ 110,  40,  30, -10,  40},-{ 110, -40,  50,  40,   0},-{ 110,  40,  40, -170,  40},-{ 110,  40,  50,  40, -30}-},-/* GC..GC */-{{ 110, 110, 110, 110, 110},-{ 110,  80,  40,  40,  40},-{ 110,  40,  40,  40,  40},-{ 110,  40,  40, -210,  40},-{ 110,  40,  40,  40, -70}-},-/* GC..GU */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* GC..UG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* GC..AU */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 100}-},-/* GC..UA */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* GC..?? */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110}-}-},-{ /* noPair */ {{0}},-/* GU..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* GU..GC */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* GU..GU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* GU..UG */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* GU..AU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* GU..UA */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* GU..?? */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-}-},-{ /* noPair */ {{0}},-/* UG..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* UG..GC */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* UG..GU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UG..UG */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UG..AU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UG..UA */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UG..?? */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-}-},-{ /* noPair */ {{0}},-/* AU..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* AU..GC */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 100}-},-/* AU..GU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* AU..UG */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* AU..AU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 120}-},-/* AU..UA */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 150}-},-/* AU..?? */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-}-},-{ /* noPair */ {{0}},-/* UA..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* UA..GC */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, -100, 110},-{ 110, 110, 110, 110, 110}-},-/* UA..GU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UA..UG */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 170}-},-/* UA..AU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 150}-},-/* UA..UA */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, -40, 170},-{ 170, 170, 170, 170, 180}-},-/* UA..?? */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-}-},-{ /* noPair */ {{0}},-/* ??..CG */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110}-},-/* ??..GC */-{{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110},-{ 110, 110, 110, 110, 110}-},-/* ??..GU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-},-/* ??..UG */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-},-/* ??..AU */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-},-/* ??..UA */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-},-/* ??..?? */-{{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170},-{ 170, 170, 170, 170, 170}-}-}-};--PRIVATE int int11_H_184[NBPAIRS+1][NBPAIRS+1][5][5] =- /* GC..GC */-{ /* noPair */ {{{0}}},-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GC.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /* CG..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* CG.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /* GU..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* GU.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /* UG..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UG.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /* AU..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* AU.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /* UA..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /* UA.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}},- /*  @..GC */-{ /* noPair */ {{0}},-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @..CG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @..GU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @..UG */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @..AU */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @..UA */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}},- /*  @.. @ */-{ {  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0},-{  0, 0, 0, 0, 0}}}};--PRIVATE int int21_37_184[NBPAIRS+1][NBPAIRS+1][5][5][5] =-{ /* noPair */ {{{{0}}}},-{ /* noPair */ {{{0}}},-{-/* CG.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 240, 220, 160, 400},{ 550, 210, 170, 160, 400},{ 550, 100,  60,  40, 400},{ 550, 400, 400, 400, 400}},-/* CG.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},-/* CG.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 170, 400,  80, 400},{ 550, 400, 400, 400, 400},{ 550,  80, 400, 220, 400},{ 550, 400, 400, 400, 400}},-/* CG.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 130},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}-},-{-/* CG.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 110, 400},{ 550, 210, 170, 160, 400},{ 550,  80,  60,  40, 400},{ 550, 400, 400, 400, 400}},-/* CG.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},-/* CG.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 170, 400,  80, 400},{ 550, 400, 400, 400, 400},{ 550,  80, 400, 220, 400},{ 550, 400, 400, 400, 400}},-/* CG.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 150},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}-},-{-/* CG.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* CG.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* CG.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* CG.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* CG.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* CG.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* CG.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* CG.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* CG.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* CG.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* CG.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* CG.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* CG.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* CG.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* CG.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* CG.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* CG.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* CG.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* GC.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 250, 220, 210, 400},{ 550, 210, 170, 160, 400},{ 550, 120,  60,  40, 400},{ 550, 400, 400, 400, 400}},-/* GC.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},-/* GC.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 170, 400,  80, 400},{ 550, 400, 400, 400, 400},{ 550,  80, 400, 220, 400},{ 550, 400, 400, 400, 400}},-/* GC.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 120},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}-},-{-/* GC.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 240, 220, 160, 400},{ 550, 210, 170, 160, 400},{ 550, 100,  60,  40, 400},{ 550, 400, 400, 400, 400}},-/* GC.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 230, 220, 400, 220},{ 550, 220, 250, 400, 220},{ 550, 400, 400, 400, 400},{ 550, 250, 190, 400, 220}},-/* GC.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 170, 400,  80, 400},{ 550, 400, 400, 400, 400},{ 550,  80, 400, 220, 400},{ 550, 400, 400, 400, 400}},-/* GC.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 400, 400, 400, 400},{ 550, 400, 220, 400, 130},{ 550, 400, 400, 400, 400},{ 550, 400, 170, 400, 120}}-},-{-/* GC.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GC.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GC.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GC.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GC.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GC.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GC.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GC.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GC.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GC.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GC.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GC.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GC.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GC.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GC.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GC.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GC.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GC.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* GU.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GU.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GU.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GU.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GU.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* GU.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* GU.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* GU.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* GU.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* GU.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* GU.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* GU.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* GU.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* GU.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* GU.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* GU.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* GU.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* GU.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* GU.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* GU.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* GU.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* GU.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* GU.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* GU.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* GU.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* GU.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* UG.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* UG.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* UG.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* UG.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* UG.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* UG.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* UG.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* UG.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* UG.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UG.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UG.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UG.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UG.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UG.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UG.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UG.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UG.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UG.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UG.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UG.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UG.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UG.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UG.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UG.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UG.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UG.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* AU.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* AU.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* AU.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* AU.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* AU.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* AU.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* AU.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* AU.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* AU.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* AU.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* AU.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* AU.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* AU.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* AU.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* AU.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* AU.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* AU.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* AU.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* AU.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* AU.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* AU.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* AU.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* AU.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* AU.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* AU.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* AU.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* UA.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* UA.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* UA.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* UA.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* UA.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 300, 240, 480},{ 550, 290, 250, 240, 480},{ 550, 180, 140, 120, 480},{ 550, 480, 480, 480, 480}},-/* UA.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 310, 300, 480, 300},{ 550, 300, 330, 480, 300},{ 550, 480, 480, 480, 480},{ 550, 330, 270, 480, 300}},-/* UA.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 250, 480, 160, 480},{ 550, 480, 480, 480, 480},{ 550, 160, 480, 300, 480},{ 550, 480, 480, 480, 480}},-/* UA.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 480, 480, 480, 480},{ 550, 480, 300, 480, 210},{ 550, 480, 480, 480, 480},{ 550, 480, 250, 480, 200}}-},-{-/* UA.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UA.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UA.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UA.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UA.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UA.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UA.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UA.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UA.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UA.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UA.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UA.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UA.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 390, 370, 310, 550},{ 550, 360, 320, 310, 550},{ 550, 250, 210, 190, 550},{ 550, 550, 550, 550, 550}},-/* UA.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 380, 370, 550, 370},{ 550, 370, 400, 550, 370},{ 550, 550, 550, 550, 550},{ 550, 400, 340, 550, 370}},-/* UA.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 320, 550, 230, 550},{ 550, 550, 550, 550, 550},{ 550, 230, 550, 370, 550},{ 550, 550, 550, 550, 550}},-/* UA.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 370, 550, 280},{ 550, 550, 550, 550, 550},{ 550, 550, 320, 550, 270}}-},-{-/* UA.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* UA.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-},-{ /* noPair */ {{{0}}},-{-/* ??.@..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..GC */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..CG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..UG */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..GU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..UA */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..AU */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-},-{-/* ??.@..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.A..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.C..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.G..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}},-/* ??.U..?? */-{{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550},{ 550, 550, 550, 550, 550}}-}-}-};--PRIVATE int int21_H_184[NBPAIRS+1][NBPAIRS+1][5][5][5] =-{ /* noPair */ {{{{0}}}},-{ /* noPair */ {{{0}}},-{-/* CG.@..CG */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..CG */-{{  DEF,-1029, -949,-1029,-1029},{-1079,-2058,-1978,-2058,-2058},{ -569,-1548,-1468,-1548,-1548},{ -989,-1968,-1888,-1968,-1968},{ -859,-1838,-1758,-1838,-1838}},-/* CG.C..CG */-{{  DEF, -519, -449, -519, -669},{ -999,-1468,-1398,-1468,-1618},{ -499, -968, -898, -968,-1118},{ -989,-1458,-1388,-1458,-1608},{ -789,-1258,-1188,-1258,-1408}},-/* CG.G..CG */-{{  DEF, -939, -939, -939, -939},{-1079,-1968,-1968,-1968,-1968},{ -569,-1458,-1458,-1458,-1458},{ -989,-1878,-1878,-1878,-1878},{ -859,-1748,-1748,-1748,-1748}},-/* CG.U..CG */-{{  DEF, -809, -739, -809, -859},{-1079,-1838,-1768,-1838,-1888},{ -719,-1478,-1408,-1478,-1528},{ -989,-1748,-1678,-1748,-1798},{ -909,-1668,-1598,-1668,-1718}}-},-{-/* CG.@..GC */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..GC */-{{  DEF,-1029, -949,-1029,-1029},{ -569,-1548,-1468,-1548,-1548},{ -769,-1748,-1668,-1748,-1748},{ -759,-1738,-1658,-1738,-1738},{ -549,-1528,-1448,-1528,-1528}},-/* CG.C..GC */-{{  DEF, -519, -449, -519, -669},{ -929,-1398,-1328,-1398,-1548},{ -359, -828, -758, -828, -978},{ -789,-1258,-1188,-1258,-1408},{ -549,-1018, -948,-1018,-1168}},-/* CG.G..GC */-{{  DEF, -939, -939, -939, -939},{ -609,-1498,-1498,-1498,-1498},{ -359,-1248,-1248,-1248,-1248},{ -669,-1558,-1558,-1558,-1558},{ -549,-1438,-1438,-1438,-1438}},-/* CG.U..GC */-{{  DEF, -809, -739, -809, -859},{ -929,-1688,-1618,-1688,-1738},{ -439,-1198,-1128,-1198,-1248},{ -789,-1548,-1478,-1548,-1598},{ -619,-1378,-1308,-1378,-1428}}-},-{-/* CG.@..GU */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..GU */-{{  DEF,-1029, -949,-1029,-1029},{ -479,-1458,-1378,-1458,-1458},{ -309,-1288,-1208,-1288,-1288},{ -389,-1368,-1288,-1368,-1368},{ -379,-1358,-1278,-1358,-1358}},-/* CG.C..GU */-{{  DEF, -519, -449, -519, -669},{ -649,-1118,-1048,-1118,-1268},{ -289, -758, -688, -758, -908},{ -739,-1208,-1138,-1208,-1358},{ -379, -848, -778, -848, -998}},-/* CG.G..GU */-{{  DEF, -939, -939, -939, -939},{ -649,-1538,-1538,-1538,-1538},{ -289,-1178,-1178,-1178,-1178},{ -739,-1628,-1628,-1628,-1628},{ -379,-1268,-1268,-1268,-1268}},-/* CG.U..GU */-{{  DEF, -809, -739, -809, -859},{ -649,-1408,-1338,-1408,-1458},{ -289,-1048, -978,-1048,-1098},{ -739,-1498,-1428,-1498,-1548},{ -379,-1138,-1068,-1138,-1188}}-},-{-/* CG.@..UG */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..UG */-{{  DEF,-1029, -949,-1029,-1029},{ -769,-1748,-1668,-1748,-1748},{ -529,-1508,-1428,-1508,-1508},{ -709,-1688,-1608,-1688,-1688},{ -599,-1578,-1498,-1578,-1578}},-/* CG.C..UG */-{{  DEF, -519, -449, -519, -669},{ -839,-1308,-1238,-1308,-1458},{ -529, -998, -928, -998,-1148},{ -859,-1328,-1258,-1328,-1478},{ -489, -958, -888, -958,-1108}},-/* CG.G..UG */-{{  DEF, -939, -939, -939, -939},{-1009,-1898,-1898,-1898,-1898},{ -409,-1298,-1298,-1298,-1298},{ -969,-1858,-1858,-1858,-1858},{ -599,-1488,-1488,-1488,-1488}},-/* CG.U..UG */-{{  DEF, -809, -739, -809, -859},{ -859,-1618,-1548,-1618,-1668},{ -529,-1288,-1218,-1288,-1338},{ -859,-1618,-1548,-1618,-1668},{ -409,-1168,-1098,-1168,-1218}}-},-{-/* CG.@..AU */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..AU */-{{  DEF,-1029, -949,-1029,-1029},{ -479,-1458,-1378,-1458,-1458},{ -309,-1288,-1208,-1288,-1288},{ -389,-1368,-1288,-1368,-1368},{ -379,-1358,-1278,-1358,-1358}},-/* CG.C..AU */-{{  DEF, -519, -449, -519, -669},{ -649,-1118,-1048,-1118,-1268},{ -289, -758, -688, -758, -908},{ -739,-1208,-1138,-1208,-1358},{ -379, -848, -778, -848, -998}},-/* CG.G..AU */-{{  DEF, -939, -939, -939, -939},{ -649,-1538,-1538,-1538,-1538},{ -289,-1178,-1178,-1178,-1178},{ -739,-1628,-1628,-1628,-1628},{ -379,-1268,-1268,-1268,-1268}},-/* CG.U..AU */-{{  DEF, -809, -739, -809, -859},{ -649,-1408,-1338,-1408,-1458},{ -289,-1048, -978,-1048,-1098},{ -739,-1498,-1428,-1498,-1548},{ -379,-1138,-1068,-1138,-1188}}-},-{-/* CG.@..UA */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A..UA */-{{  DEF,-1029, -949,-1029,-1029},{ -449,-1428,-1348,-1428,-1428},{ -479,-1458,-1378,-1458,-1458},{ -429,-1408,-1328,-1408,-1408},{ -329,-1308,-1228,-1308,-1308}},-/* CG.C..UA */-{{  DEF, -519, -449, -519, -669},{ -679,-1148,-1078,-1148,-1298},{ -559,-1028, -958,-1028,-1178},{ -729,-1198,-1128,-1198,-1348},{ -189, -658, -588, -658, -808}},-/* CG.G..UA */-{{  DEF, -939, -939, -939, -939},{ -939,-1828,-1828,-1828,-1828},{ -249,-1138,-1138,-1138,-1138},{ -939,-1828,-1828,-1828,-1828},{ -329,-1218,-1218,-1218,-1218}},-/* CG.U..UA */-{{  DEF, -809, -739, -809, -859},{ -639,-1398,-1328,-1398,-1448},{ -229, -988, -918, -988,-1038},{ -729,-1488,-1418,-1488,-1538},{ -190, -949, -879, -949, -999}}-},-{-/* CG.@.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.A.. @ */-{{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079},{ -100,-1079, -999,-1079,-1079}},-/* CG.C.. @ */-{{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719},{ -100, -569, -499, -569, -719}},-/* CG.G.. @ */-{{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989},{ -100, -989, -989, -989, -989}},-/* CG.U.. @ */-{{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909},{ -100, -859, -789, -859, -909}}-}-},-{ /* noPair */ {{{0}}},-{-/* GC.@..CG */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..CG */-{{  DEF, -519, -879, -559, -879},{-1079,-1548,-1908,-1588,-1908},{ -569,-1038,-1398,-1078,-1398},{ -989,-1458,-1818,-1498,-1818},{ -859,-1328,-1688,-1368,-1688}},-/* GC.C..CG */-{{  DEF, -719, -309, -309, -389},{ -999,-1668,-1258,-1258,-1338},{ -499,-1168, -758, -758, -838},{ -989,-1658,-1248,-1248,-1328},{ -789,-1458,-1048,-1048,-1128}},-/* GC.G..CG */-{{  DEF, -709, -739, -619, -739},{-1079,-1738,-1768,-1648,-1768},{ -569,-1228,-1258,-1138,-1258},{ -989,-1648,-1678,-1558,-1678},{ -859,-1518,-1548,-1428,-1548}},-/* GC.U..CG */-{{  DEF, -499, -499, -499, -569},{-1079,-1528,-1528,-1528,-1598},{ -719,-1168,-1168,-1168,-1238},{ -989,-1438,-1438,-1438,-1508},{ -909,-1358,-1358,-1358,-1428}}-},-{-/* GC.@..GC */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..GC */-{{  DEF, -519, -879, -559, -879},{ -569,-1038,-1398,-1078,-1398},{ -769,-1238,-1598,-1278,-1598},{ -759,-1228,-1588,-1268,-1588},{ -549,-1018,-1378,-1058,-1378}},-/* GC.C..GC */-{{  DEF, -719, -309, -309, -389},{ -929,-1598,-1188,-1188,-1268},{ -359,-1028, -618, -618, -698},{ -789,-1458,-1048,-1048,-1128},{ -549,-1218, -808, -808, -888}},-/* GC.G..GC */-{{  DEF, -709, -739, -619, -739},{ -609,-1268,-1298,-1178,-1298},{ -359,-1018,-1048, -928,-1048},{ -669,-1328,-1358,-1238,-1358},{ -549,-1208,-1238,-1118,-1238}},-/* GC.U..GC */-{{  DEF, -499, -499, -499, -569},{ -929,-1378,-1378,-1378,-1448},{ -439, -888, -888, -888, -958},{ -789,-1238,-1238,-1238,-1308},{ -619,-1068,-1068,-1068,-1138}}-},-{-/* GC.@..GU */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..GU */-{{  DEF, -519, -879, -559, -879},{ -479, -948,-1308, -988,-1308},{ -309, -778,-1138, -818,-1138},{ -389, -858,-1218, -898,-1218},{ -379, -848,-1208, -888,-1208}},-/* GC.C..GU */-{{  DEF, -719, -309, -309, -389},{ -649,-1318, -908, -908, -988},{ -289, -958, -548, -548, -628},{ -739,-1408, -998, -998,-1078},{ -379,-1048, -638, -638, -718}},-/* GC.G..GU */-{{  DEF, -709, -739, -619, -739},{ -649,-1308,-1338,-1218,-1338},{ -289, -948, -978, -858, -978},{ -739,-1398,-1428,-1308,-1428},{ -379,-1038,-1068, -948,-1068}},-/* GC.U..GU */-{{  DEF, -499, -499, -499, -569},{ -649,-1098,-1098,-1098,-1168},{ -289, -738, -738, -738, -808},{ -739,-1188,-1188,-1188,-1258},{ -379, -828, -828, -828, -898}}-},-{-/* GC.@..UG */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..UG */-{{  DEF, -519, -879, -559, -879},{ -769,-1238,-1598,-1278,-1598},{ -529, -998,-1358,-1038,-1358},{ -709,-1178,-1538,-1218,-1538},{ -599,-1068,-1428,-1108,-1428}},-/* GC.C..UG */-{{  DEF, -719, -309, -309, -389},{ -839,-1508,-1098,-1098,-1178},{ -529,-1198, -788, -788, -868},{ -859,-1528,-1118,-1118,-1198},{ -489,-1158, -748, -748, -828}},-/* GC.G..UG */-{{  DEF, -709, -739, -619, -739},{-1009,-1668,-1698,-1578,-1698},{ -409,-1068,-1098, -978,-1098},{ -969,-1628,-1658,-1538,-1658},{ -599,-1258,-1288,-1168,-1288}},-/* GC.U..UG */-{{  DEF, -499, -499, -499, -569},{ -859,-1308,-1308,-1308,-1378},{ -529, -978, -978, -978,-1048},{ -859,-1308,-1308,-1308,-1378},{ -409, -858, -858, -858, -928}}-},-{-/* GC.@..AU */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..AU */-{{  DEF, -519, -879, -559, -879},{ -479, -948,-1308, -988,-1308},{ -309, -778,-1138, -818,-1138},{ -389, -858,-1218, -898,-1218},{ -379, -848,-1208, -888,-1208}},-/* GC.C..AU */-{{  DEF, -719, -309, -309, -389},{ -649,-1318, -908, -908, -988},{ -289, -958, -548, -548, -628},{ -739,-1408, -998, -998,-1078},{ -379,-1048, -638, -638, -718}},-/* GC.G..AU */-{{  DEF, -709, -739, -619, -739},{ -649,-1308,-1338,-1218,-1338},{ -289, -948, -978, -858, -978},{ -739,-1398,-1428,-1308,-1428},{ -379,-1038,-1068, -948,-1068}},-/* GC.U..AU */-{{  DEF, -499, -499, -499, -569},{ -649,-1098,-1098,-1098,-1168},{ -289, -738, -738, -738, -808},{ -739,-1188,-1188,-1188,-1258},{ -379, -828, -828, -828, -898}}-},-{-/* GC.@..UA */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.A..UA */-{{  DEF, -519, -879, -559, -879},{ -449, -918,-1278, 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DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.A..CG */-{{  DEF, -719, -789, -959, -809},{-1079,-1748,-1818,-1988,-1838},{ -569,-1238,-1308,-1478,-1328},{ -989,-1658,-1728,-1898,-1748},{ -859,-1528,-1598,-1768,-1618}},-/* UG.C..CG */-{{  DEF, -479, -479, -359, -479},{ -999,-1428,-1428,-1308,-1428},{ -499, -928, -928, -808, -928},{ -989,-1418,-1418,-1298,-1418},{ -789,-1218,-1218,-1098,-1218}},-/* UG.G..CG */-{{  DEF, -659, -809, -919, -809},{-1079,-1688,-1838,-1948,-1838},{ -569,-1178,-1328,-1438,-1328},{ -989,-1598,-1748,-1858,-1748},{ -859,-1468,-1618,-1728,-1618}},-/* UG.U..CG */-{{  DEF, -549, -439, -549, -359},{-1079,-1578,-1468,-1578,-1388},{ -719,-1218,-1108,-1218,-1028},{ -989,-1488,-1378,-1488,-1298},{ -909,-1408,-1298,-1408,-1218}}-},-{-/* UG.@..GC */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.A..GC */-{{  DEF, -719, -789, -959, -809},{ -569,-1238,-1308,-1478,-1328},{ -769,-1438,-1508,-1678,-1528},{ -759,-1428,-1498,-1668,-1518},{ -549,-1218,-1288,-1458,-1308}},-/* UG.C..GC */-{{  DEF, -479, -479, -359, -479},{ -929,-1358,-1358,-1238,-1358},{ -359, -788, -788, -668, -788},{ -789,-1218,-1218,-1098,-1218},{ -549, -978, -978, -858, -978}},-/* UG.G..GC */-{{  DEF, -659, -809, -919, -809},{ -609,-1218,-1368,-1478,-1368},{ -359, -968,-1118,-1228,-1118},{ -669,-1278,-1428,-1538,-1428},{ -549,-1158,-1308,-1418,-1308}},-/* UG.U..GC */-{{  DEF, -549, -439, -549, -359},{ -929,-1428,-1318,-1428,-1238},{ -439, -938, -828, -938, -748},{ -789,-1288,-1178,-1288,-1098},{ -619,-1118,-1008,-1118, -928}}-},-{-/* UG.@..GU */-{{    0,    0,    0,    0,    0},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.A..GU */-{{  DEF, -719, -789, -959, -809},{ -479,-1148,-1218,-1388,-1238},{ -309, 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DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF},{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.A.. @ */-{{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639},{ -100, -449, -679, -939, -639}},-/* UA.C.. @ */-{{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229},{ -100, -479, -559, -249, -229}},-/* UA.G.. @ */-{{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729},{ -100, -429, -729, -939, -729}},-/* UA.U.. @ */-{{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190},{ -100, -329, -189, -329, -190}}-}-},-{ /* noPair */ {{{0}}},-{-/*  @.@..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{-1079,-1079,-1079,-1079,-1079},{ -569, -569, -569, -569, -569},{ -989, -989, -989, -989, -989},{ -859, -859, -859, -859, -859}},-/*  @.C..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -999, -999, -999, -999, -999},{ -499, -499, -499, -499, -499},{ -989, -989, -989, -989, -989},{ -789, -789, -789, -789, -789}},-/*  @.G..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{-1079,-1079,-1079,-1079,-1079},{ -569, -569, -569, -569, -569},{ -989, -989, -989, -989, -989},{ -859, -859, -859, -859, -859}},-/*  @.U..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{-1079,-1079,-1079,-1079,-1079},{ -719, -719, -719, -719, -719},{ -989, -989, -989, -989, -989},{ -909, -909, -909, -909, -909}}-},-{-/*  @.@..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -569, -569, -569, -569, -569},{ -769, -769, -769, -769, -769},{ -759, -759, -759, -759, -759},{ -549, -549, -549, -549, -549}},-/*  @.C..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -929, -929, -929, -929, -929},{ -359, -359, -359, -359, -359},{ -789, -789, -789, -789, -789},{ -549, -549, -549, -549, -549}},-/*  @.G..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -609, -609, -609, -609, -609},{ -359, -359, -359, -359, -359},{ -669, -669, -669, -669, -669},{ -549, -549, -549, -549, -549}},-/*  @.U..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -929, -929, -929, -929, -929},{ -439, -439, -439, -439, -439},{ -789, -789, -789, -789, -789},{ -619, -619, -619, -619, -619}}-},-{-/*  @.@..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -479, -479, -479, -479, -479},{ -309, -309, -309, -309, -309},{ -389, -389, -389, -389, -389},{ -379, -379, -379, -379, -379}},-/*  @.C..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},-/*  @.G..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},-/*  @.U..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}}-},-{-/*  @.@..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -769, -769, -769, -769, -769},{ -529, -529, -529, -529, -529},{ -709, -709, -709, -709, -709},{ -599, -599, -599, -599, -599}},-/*  @.C..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -839, -839, -839, -839, -839},{ -529, -529, -529, -529, -529},{ -859, -859, -859, -859, -859},{ -489, -489, -489, -489, -489}},-/*  @.G..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{-1009,-1009,-1009,-1009,-1009},{ -409, -409, -409, -409, -409},{ -969, -969, -969, -969, -969},{ -599, -599, -599, -599, -599}},-/*  @.U..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -859, -859, -859, -859, -859},{ -529, -529, -529, -529, -529},{ -859, -859, -859, -859, -859},{ -409, -409, -409, -409, -409}}-},-{-/*  @.@..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -479, -479, -479, -479, -479},{ -309, -309, -309, -309, -309},{ -389, -389, -389, -389, -389},{ -379, -379, -379, -379, -379}},-/*  @.C..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},-/*  @.G..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}},-/*  @.U..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -649, -649, -649, -649, -649},{ -289, -289, -289, -289, -289},{ -739, -739, -739, -739, -739},{ -379, -379, -379, -379, -379}}-},-{-/*  @.@..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -449, -449, -449, -449, -449},{ -479, -479, -479, -479, -479},{ -429, -429, -429, -429, -429},{ -329, -329, -329, -329, -329}},-/*  @.C..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -679, -679, -679, -679, -679},{ -559, -559, -559, -559, -559},{ -729, -729, -729, -729, -729},{ -189, -189, -189, -189, -189}},-/*  @.G..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -939, -939, -939, -939, -939},{ -249, -249, -249, -249, -249},{ -939, -939, -939, -939, -939},{ -329, -329, -329, -329, -329}},-/*  @.U..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},{ -639, -639, -639, -639, -639},{ -229, -229, -229, -229, -229},{ -729, -729, -729, -729, -729},{ -190, -190, -190, -190, -190}}-},-{-/*  @.@.. @ */-{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.A.. @ */-{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.C.. @ */-{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.G.. @ */-{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}},-/*  @.U.. @ */-{{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100},{ -100, -100, -100, -100, -100}}-}-}-};--PRIVATE int int22_37_184[NBPAIRS+1][NBPAIRS+1][5][5][5][5] = {-/* noPair */ {{{{{0}}}}},-{ /* noPair */ {{{{0}}}},-/* CG....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 160,  30, 200},{ 340, 120, 150,  20, 200},{ 340,  30,  60, -70, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 200,  60, 200},{ 340, 210, 180, 150, 200},{ 340, 200, 200, 200, 200},{ 340, 190, 170, 130, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  30,  60, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 100, 140,   0, 200},{ 340, -40, -110, -60, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 170, 130, 200},{ 340, 110,  40,  90, 200},{ 340, 140,  80, 130, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 120, 210, 200, 190},{ 340, 110, 140, 200, 120},{ 340,  20, 150, 200, 130},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 180, 200, 170},{ 340, 140, 170, 200, 150},{ 340, 200, 200, 200, 200},{ 340, 120, 150, 200, 140}},-{{ 340, 340, 340, 340, 340},{ 340,  20, 150, 200, 130},{ 340, 200, 200, 200, 200},{ 340,  90, 180, 200, 170},{ 340, -150, -20, 200, -40}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 150, 200, 140},{ 340,   0, 130, 200, 110},{ 340,  30,  60, 200,  50}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 200, 100, 110},{ 340,  20, 200,  90,   0},{ 340, -70, 200,   0,  90},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 200, 140,  40},{ 340, 150, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340, 130, 200, 170, 110}},-{{ 340, 340, 340, 340, 340},{ 340, -70, 200,   0,  90},{ 340, 200, 200, 200, 200},{ 340,   0, 200,  80,  90},{ 340, -60, 200, -70, -260}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 130, 200, 170, 110},{ 340,  90, 200,  90, -110},{ 340, 130, 200, 120, 110}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -40, 140},{ 340, 200, 120, -150,  30},{ 340, 200, 130, -60, 130},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -110,  80},{ 340, 200, 150, -20,  60},{ 340, 200, 200, 200, 200},{ 340, 200, 140, -40,  50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 130, -60, 130},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70, 120},{ 340, 200, -40, -420, -50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 140, -40,  50},{ 340, 200, 110, -260, 110},{ 340, 200,  50, -50, -40}}-}-},-/* CG....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  50,  60,   0, 200},{ 340, 110, 150, -70, 200},{ 340, -30,  10, -160, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 110, -100, 200},{ 340, 170, 150, -60, 200},{ 340, 200, 200, 200, 200},{ 340,  70,  50,  20, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  40,  50, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 100, 140,   0, 200},{ 340,  10, -70, -80, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 150, 120, 200},{ 340, -50, -60, -60, 200},{ 340, 150,   0,  90, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 200},{ 340, 100, 130, 200, 120},{ 340, -70,  70, 200,  40},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 190, 200, 110},{ 340, 100, 130, 200, 120},{ 340, 200, 200, 200, 200},{ 340,   0,  30, 200, 170}},-{{ 340, 340, 340, 340, 340},{ 340,  70,  70, 200, 100},{ 340, 200, 200, 200, 200},{ 340,  90, 180, 200, 170},{ 340, -190, -30, 200, -70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 110, 140, 200, 120},{ 340, -150, -20, 200, -30},{ 340, -20, -10, 200,  20}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, -20, 200, 110,  90},{ 340, -40, 200,  90,   0},{ 340, -170, 200, -90,  30},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200,  80, -10},{ 340, 110, 200, 150, 100},{ 340, 200, 200, 200, 200},{ 340,  20, 200,  50,   0}},-{{ 340, 340, 340, 340, 340},{ 340, -50, 200, -20,  60},{ 340, 200, 200, 200, 200},{ 340,   0, 200,  80,  90},{ 340, -90, 200, -100, -300}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 200, 150, 100},{ 340, -130, 200, -60, -240},{ 340,  90, 200, 110,  60}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, -10, 140},{ 340, 200, 120, -160,  30},{ 340, 200,  40, -160,  50},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 110, -160,  30},{ 340, 200, 120, -60,  30},{ 340, 200, 200, 200, 200},{ 340, 200,  20, -160,  10}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  50, -60, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70, 120},{ 340, 200, -70, -440, -100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 120, -50,  30},{ 340, 200, -10, -410,  10},{ 340, 200,  40, -100,  60}}-}-},-/* CG....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 180, 210,  80, 200},{ 340,  80, 110, -20, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 220,  90, 200},{ 340, 230, 210, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 110, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 170,  30, 200},{ 340,  60,   0,  40, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 160,  90, 140, 200},{ 340, 190, 130, 180, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 170, 200, 200, 180},{ 340,  70, 200, 200, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 210, 200, 190},{ 340, 160, 190, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 120, 210, 200, 200},{ 340, -50,  80, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340,  50, 180, 200, 160},{ 340,  80, 110, 200, 100}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340,  80, 200, 150,  60},{ 340, -20, 200,  50, 140},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 200, 160,  70},{ 340, 170, 200, 210, 150},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150}},-{{ 340, 340, 340, 340, 340},{ 340, -20, 200,  50, 140},{ 340, 200, 200, 200, 200},{ 340,  30, 200, 110, 110},{ 340,  40, 200,  40, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 140, 200, 130, -60},{ 340, 180, 200, 170, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 220},{ 340, 200, 180, -90,  90},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -80, 100},{ 340, 200, 180,   0,  90},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -40, 150},{ 340, 200,  70, -310,  60}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90},{ 340, 200, 160, -210, 160},{ 340, 200, 100,   0,  10}}-}-},-/* CG....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 160, 190,  60, 200},{ 340, 100, 130,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 260, 240, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 260, 240, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 130,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 170,  40, 200},{ 340,  20, -40,   0, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 150,  80, 130, 200},{ 340, 220, 150, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 150, 180, 200, 160},{ 340,  90, 220, 200, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 200, 210},{ 340, 190, 220, 200, 210},{ 340, 200, 200, 200, 200},{ 340, 190, 220, 200, 210}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 220, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 220, 200, 200},{ 340, -90,  40, 200,  30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340,  40, 170, 200, 150},{ 340, 110, 140, 200, 120}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340,  60, 200, 130,  40},{ 340,   0, 200,  70, 160},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180,  80},{ 340, 200, 200, 240, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 240, 180}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200,  70, 160},{ 340, 200, 200, 200, 200},{ 340,  40, 200, 110, 120},{ 340,   0, 200,   0, -200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 130, 200, 120, -70},{ 340, 200, 200, 190, 180}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 220},{ 340, 200, 160, -110,  70},{ 340, 200, 200,  10, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 210, -70, 120},{ 340, 200, 210,  30, 120},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200,  10, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -30, 150},{ 340, 200,  30, -350,  20}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90},{ 340, 200, 150, -220, 150},{ 340, 200, 120,  30,  30}}-}-},-/* CG....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 180, 210,  80, 200},{ 340,  80, 110, -20, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 220,  90, 200},{ 340, 230, 210, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 110, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 170,  30, 200},{ 340,  60,   0,  40, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 160,  90, 140, 200},{ 340, 190, 130, 180, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 170, 200, 200, 180},{ 340,  70, 200, 200, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 210, 200, 190},{ 340, 160, 190, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 200, 180},{ 340, 200, 200, 200, 200},{ 340, 120, 210, 200, 200},{ 340, -50,  80, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340,  50, 180, 200, 160},{ 340,  80, 110, 200, 100}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340,  80, 200, 150,  60},{ 340, -20, 200,  50, 140},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 200, 160,  70},{ 340, 170, 200, 210, 150},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150}},-{{ 340, 340, 340, 340, 340},{ 340, -20, 200,  50, 140},{ 340, 200, 200, 200, 200},{ 340,  30, 200, 110, 110},{ 340,  40, 200,  40, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 140, 200, 130, -60},{ 340, 180, 200, 170, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 220},{ 340, 200, 180, -90,  90},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 190, -80, 100},{ 340, 200, 180,   0,  90},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -10, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -40, 150},{ 340, 200,  70, -310,  60}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90},{ 340, 200, 160, -210, 160},{ 340, 200, 100,   0,  10}}-}-},-/* CG....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 160, 190,  60, 200},{ 340, 100, 130,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 100, 200},{ 340, 260, 240, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 260, 240, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 130,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 170,  40, 200},{ 340,  20, -40,   0, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 230, 210, 170, 200},{ 340, 150,  80, 130, 200},{ 340, 220, 150, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 280, 200, 270},{ 340, 150, 180, 200, 160},{ 340,  90, 220, 200, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 220, 200, 210},{ 340, 190, 220, 200, 210},{ 340, 200, 200, 200, 200},{ 340, 190, 220, 200, 210}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 220, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 130, 220, 200, 200},{ 340, -90,  40, 200,  30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 190, 200, 180},{ 340,  40, 170, 200, 150},{ 340, 110, 140, 200, 120}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180, 180},{ 340,  60, 200, 130,  40},{ 340,   0, 200,  70, 160},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 180,  80},{ 340, 200, 200, 240, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 240, 180}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200,  70, 160},{ 340, 200, 200, 200, 200},{ 340,  40, 200, 110, 120},{ 340,   0, 200,   0, -200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 210, 150},{ 340, 130, 200, 120, -70},{ 340, 200, 200, 190, 180}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 220},{ 340, 200, 160, -110,  70},{ 340, 200, 200,  10, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 210, -70, 120},{ 340, 200, 210,  30, 120},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200,  10, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 200, -30, 150},{ 340, 200,  30, -350,  20}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,   0,  90},{ 340, 200, 150, -220, 150},{ 340, 200, 120,  30,  30}}-}-},-/* CG....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-},-{ /* noPair */ {{{{0}}}},-/* GC....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 110,  40, 200},{ 340, 130, 100,  70, 200},{ 340, -20,  70, -50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 110,  50, 200},{ 340, 220, 190,  70, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 110,  50, 200}},-{{ 340, 340, 340, 340, 340},{ 340,   0, -100, -70, 200},{ 340, 200, 200, 200, 200},{ 340, 110,  80, -20, 200},{ 340, -10, -160, -60, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 110, 100, 200},{ 340,  90, -10,  60, 200},{ 340, 140,  30, 140, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 170, 200, 180},{ 340, 100, 100, 200, 110},{ 340, -40, 110, 200, 120},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 150, 200, 150},{ 340, 130, 130, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 120, 120, 200, 120}},-{{ 340, 340, 340, 340, 340},{ 340, -70, -60, 200, 120},{ 340, 200, 200, 200, 200},{ 340,  90, 150, 200, 150},{ 340, -160, -60, 200, -50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 120, 120, 200, 120},{ 340,   0, 100, 200, 100},{ 340,  30,  30, 200,  30}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, -30, 200, 100, -50},{ 340, -70, 200,  90, -150},{ 340, -170, 200,   0, -130},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 140, -60},{ 340,  70, 200, 180, -20},{ 340, 200, 200, 200, 200},{ 340,  40, 200, 170, -10}},-{{ 340, 340, 340, 340, 340},{ 340, -160, 200,   0, -60},{ 340, 200, 200, 200, 200},{ 340, -90, 200,  80, -60},{ 340, -160, 200, -70, -410}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  40, 200, 170, -30},{ 340,  30, 200,  90, -240},{ 340,  50, 200, 120,  10}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  70,  10, 150},{ 340, 200,   0, -190, -20},{ 340, 200,  20, -90,  90},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  50, -70,   0},{ 340, 200,  30, -30, -10},{ 340, 200, 200, 200, 200},{ 340, 200,  20, -70,  40}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  20, -80,  90},{ 340, 200, 200, 200, 200},{ 340, 200,  50, -100, 110},{ 340, 200, -160, -440, -100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 170, -70,  20},{ 340, 200,   0, -300,  60},{ 340, 200,  10, -100,  60}}-}-},-/* GC....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 120,  10, 200},{ 340, 120,  90, -10, 200},{ 340, -50, -80, -190, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 120,  90, -20, 200},{ 340, 180,  90,  90, 200},{ 340, 200, 200, 200, 200},{ 340,  80,   0, -10, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  10, -20, -130, 200},{ 340, 200, 200, 200, 200},{ 340, 110,  80, -20, 200},{ 340, -70, -200, -130, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 100,  90, 200},{ 340, -30, -160, -90, 200},{ 340, 150,  20,  90, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 120, 180, 200, 190},{ 340, 100, 100, 200, 100},{ 340, -80,  20, 200,  30},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  90,  90, 200, 100},{ 340, 100, 100, 200, 100},{ 340, 200, 200, 200, 200},{ 340,   0,   0, 200,   0}},-{{ 340, 340, 340, 340, 340},{ 340, -10,  90, 200,  90},{ 340, 200, 200, 200, 200},{ 340,  90, 150, 200, 150},{ 340, -190, -90, 200, -90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 100, 100, 200, 110},{ 340, -150, -50, 200, -50},{ 340,  20,  20, 200,  30}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, -50, 200, 110, -30},{ 340, -80, 200,  90, -150},{ 340, -260, 200, -90, -150},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, -80, 200,  80, -160},{ 340,  20, 200, 150, -50},{ 340, 200, 200, 200, 200},{ 340, -80, 200,  50, -150}},-{{ 340, 340, 340, 340, 340},{ 340, -190, 200, -20, -90},{ 340, 200, 200, 200, 200},{ 340, -90, 200,  80, -60},{ 340, -190, 200, -100, -450}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  30, 200, 150, -50},{ 340, -150, 200, -60, -410},{ 340,  30, 200, 110, -50}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  80, -70, 150},{ 340, 200,   0, -190,  20},{ 340, 200, -80, -190,  30},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,   0, -200,  20},{ 340, 200,   0, -90,  20},{ 340, 200, 200, 200, 200},{ 340, 200, -100, -190, -70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, -10, -130,  90},{ 340, 200, 200, 200, 200},{ 340, 200,  50, -100, 110},{ 340, 200, -190, -490, -90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200,   0, -90,  30},{ 340, 200, -150, -450, -50},{ 340, 200, -70, -90, -50}}-}-},-/* GC....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 190, 160,  50, 200},{ 340,  90,  60, -50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170,  60, 200},{ 340, 240, 150, 140, 200},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  90,  60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 110,   0, 200},{ 340,  70, -60,  10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 170,  40, 110, 200},{ 340, 200,  70, 150, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 160, 160, 200, 170},{ 340,  60, 160, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 200, 180},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 160, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 180},{ 340, -50,  50, 200,  50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340,  40, 140, 200, 150},{ 340,  80,  80, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180,  40},{ 340, -10, 200, 150, -90},{ 340, -110, 200,  50, -10},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200, 160, -80},{ 340,  80, 200, 210,  10},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10}},-{{ 340, 340, 340, 340, 340},{ 340, -110, 200,  50, -10},{ 340, 200, 200, 200, 200},{ 340, -60, 200, 110, -30},{ 340, -50, 200,  40, -310}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10},{ 340,  50, 200, 130, -210},{ 340,  80, 200, 170,  10}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150,   0, 210},{ 340, 200,  60, -130,  90},{ 340, 200,  70, -50, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  70, -120, 100},{ 340, 200,  60, -30,  80},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  70, -50, 170},{ 340, 200, 200, 200, 200},{ 340, 200,  80, -70, 140},{ 340, 200, -50, -350,  50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80},{ 340, 200,  50, -250, 150},{ 340, 200, -20, -30,   0}}-}-},-/* GC....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 170, 140,  30, 200},{ 340, 110,  80, -30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 270, 180, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 180, 170, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 110,  80, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 120,  10, 200},{ 340,  30, -100, -30, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 160,  30, 100, 200},{ 340, 230, 100, 170, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 140, 140, 200, 150},{ 340,  80, 180, 200, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 190, 200, 190},{ 340, 190, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 190, 190, 200, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 180, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 190},{ 340, -90,  10, 200,  10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340,  30, 130, 200, 140},{ 340, 100, 100, 200, 110}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180,  40},{ 340, -30, 200, 130, -110},{ 340, -90, 200,  70,  10},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180, -60},{ 340, 110, 200, 240,  40},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 240,  40}},-{{ 340, 340, 340, 340, 340},{ 340, -90, 200,  70,  10},{ 340, 200, 200, 200, 200},{ 340, -50, 200, 110, -30},{ 340, -90, 200,   0, -350}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10},{ 340,  40, 200, 120, -220},{ 340, 110, 200, 190,  30}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150,   0, 210},{ 340, 200,  40, -150,  70},{ 340, 200,  90, -30, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  90, -100, 110},{ 340, 200,  90,   0, 110},{ 340, 200, 200, 200, 200},{ 340, 200,  90,   0, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  90, -30, 190},{ 340, 200, 200, 200, 200},{ 340, 200,  80, -70, 150},{ 340, 200, -90, -390,  10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80},{ 340, 200,  40, -260, 140},{ 340, 200,   0, -10,  30}}-}-},-/* GC....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 190, 160,  50, 200},{ 340,  90,  60, -50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170,  60, 200},{ 340, 240, 150, 140, 200},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  90,  60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 140, 110,   0, 200},{ 340,  70, -60,  10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 170,  40, 110, 200},{ 340, 200,  70, 150, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 160, 160, 200, 170},{ 340,  60, 160, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170, 200, 180},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 160, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 180},{ 340, -50,  50, 200,  50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340,  40, 140, 200, 150},{ 340,  80,  80, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180,  40},{ 340, -10, 200, 150, -90},{ 340, -110, 200,  50, -10},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200, 160, -80},{ 340,  80, 200, 210,  10},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10}},-{{ 340, 340, 340, 340, 340},{ 340, -110, 200,  50, -10},{ 340, 200, 200, 200, 200},{ 340, -60, 200, 110, -30},{ 340, -50, 200,  40, -310}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10},{ 340,  50, 200, 130, -210},{ 340,  80, 200, 170,  10}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150,   0, 210},{ 340, 200,  60, -130,  90},{ 340, 200,  70, -50, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  70, -120, 100},{ 340, 200,  60, -30,  80},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  70, -50, 170},{ 340, 200, 200, 200, 200},{ 340, 200,  80, -70, 140},{ 340, 200, -50, -350,  50}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80},{ 340, 200,  50, -250, 150},{ 340, 200, -20, -30,   0}}-}-},-/* GC....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 170, 140,  30, 200},{ 340, 110,  80, -30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 180,  70, 200},{ 340, 270, 180, 170, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 180, 170, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 110,  80, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 150, 120,  10, 200},{ 340,  30, -100, -30, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 150, 140, 200},{ 340, 160,  30, 100, 200},{ 340, 230, 100, 170, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 250, 200, 250},{ 340, 140, 140, 200, 150},{ 340,  80, 180, 200, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 190, 200, 190},{ 340, 190, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 190, 190, 200, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 180, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 120, 180, 200, 190},{ 340, -90,  10, 200,  10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 160, 200, 160},{ 340,  30, 130, 200, 140},{ 340, 100, 100, 200, 110}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180,  40},{ 340, -30, 200, 130, -110},{ 340, -90, 200,  70,  10},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  10, 200, 180, -60},{ 340, 110, 200, 240,  40},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 240,  40}},-{{ 340, 340, 340, 340, 340},{ 340, -90, 200,  70,  10},{ 340, 200, 200, 200, 200},{ 340, -50, 200, 110, -30},{ 340, -90, 200,   0, -350}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 210,  10},{ 340,  40, 200, 120, -220},{ 340, 110, 200, 190,  30}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150,   0, 210},{ 340, 200,  40, -150,  70},{ 340, 200,  90, -30, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  90, -100, 110},{ 340, 200,  90,   0, 110},{ 340, 200, 200, 200, 200},{ 340, 200,  90,   0, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200,  90, -30, 190},{ 340, 200, 200, 200, 200},{ 340, 200,  80, -70, 150},{ 340, 200, -90, -390,  10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -30,  80},{ 340, 200,  40, -260, 140},{ 340, 200,   0, -10,  30}}-}-},-/* GC....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-},-{ /* noPair */ {{{{0}}}},-/* GU....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 190,  80, 200},{ 340, 190, 180,  70, 200},{ 340, 100,  90, -20, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 220, 110, 200},{ 340, 280, 210, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100,  90, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160,  50, 200},{ 340,  30, -80, -10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200},{ 340, 180,  70, 140, 200},{ 340, 220, 100, 180, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 230, 200, 230},{ 340, 170, 160, 200, 160},{ 340,  80, 170, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 200, 210},{ 340, 200, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 170, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -90,   0, 200,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180},{ 340,  60, 150, 200, 150},{ 340,  90,  90, 200,  90}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 200, 130, 160},{ 340,  70, 200, 120,  50},{ 340, -20, 200,  30, 140},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 170,  90},{ 340, 200, 200, 210, 180},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160}},-{{ 340, 340, 340, 340, 340},{ 340, -20, 200,  30, 140},{ 340, 200, 200, 200, 200},{ 340,  50, 200, 110, 130},{ 340, -10, 200, -40, -210}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160},{ 340, 140, 200, 110, -60},{ 340, 180, 200, 150, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  60, 190},{ 340, 200, 160, -50,  80},{ 340, 200, 170,  40, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 210,   0, 130},{ 340, 200, 190,  80, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 180,  70, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170,  40, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  40, 170},{ 340, 200,   0, -310,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,  70, 100},{ 340, 200, 150, -160, 160},{ 340, 200,  90,  60,  10}}-}-},-/* GU....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 200,  90, 200},{ 340, 190, 170,  60, 200},{ 340,  10,   0, -110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 170,  60, 200},{ 340, 250, 170, 160, 200},{ 340, 200, 200, 200, 200},{ 340, 150,  70,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  70,  60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160,  50, 200},{ 340,   0, -120, -50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 180, 170, 200},{ 340,  40, -80, -10, 200},{ 340, 210, 100, 170, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 240},{ 340, 160, 160, 200, 160},{ 340, -10,  80, 200,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 150, 200, 150},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340,  60,  60, 200,  60}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 140, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -130, -30, 200, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 160, 200, 160},{ 340, -90,  10, 200,  10},{ 340,  90,  80, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 200, 140, 170},{ 340,  60, 200, 120,  40},{ 340, -110, 200, -60,  50},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 200, 110,  40},{ 340, 160, 200, 180, 140},{ 340, 200, 200, 200, 200},{ 340,  70, 200,  80,  50}},-{{ 340, 340, 340, 340, 340},{ 340, -50, 200,   0, 110},{ 340, 200, 200, 200, 200},{ 340,  50, 200, 110, 130},{ 340, -50, 200, -70, -250}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 180, 150},{ 340, -10, 200, -30, -210},{ 340, 170, 200, 140, 150}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240,  70, 200},{ 340, 200, 160, -50,  80},{ 340, 200,  80, -50,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150, -60,  70},{ 340, 200, 160,  50,  80},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -50, -20}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 140,  10, 150},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  40, 170},{ 340, 200, -30, -350, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 160,  50,  80},{ 340, 200,  10, -310,  10},{ 340, 200,  80,  50,   0}}-}-},-/* GU....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190,  80, 200},{ 340, 130,  20,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340,  10, 100, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 140, 160},{ 340,  90, 200,  70, -110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220,  10, 140},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200, 100, -210, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110,  60}}-}-},-/* GU....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200,  90, 200},{ 340, 100, -20,  50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30,  70, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160,  90},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340,  90, 200, 140, 170},{ 340,  50, 200,  30, -150}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200,  70, -250,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130,  80}}-}-},-/* GU....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190,  80, 200},{ 340, 130,  20,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340,  10, 100, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 140, 160},{ 340,  90, 200,  70, -110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220,  10, 140},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200, 100, -210, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110,  60}}-}-},-/* GU....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200,  90, 200},{ 340, 100, -20,  50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30,  70, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160,  90},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340,  90, 200, 140, 170},{ 340,  50, 200,  30, -150}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200,  70, -250,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130,  80}}-}-},-/* GU....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-},-{ /* noPair */ {{{{0}}}},-/* UG....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 100, 200},{ 340, 190, 190,  90, 200},{ 340, 100, 100,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 240, 130, 200},{ 340, 280, 220, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 100,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180,  70, 200},{ 340,  30, -70,  10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200},{ 340, 180,  80, 160, 200},{ 340, 220, 120, 190, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 260, 200, 230},{ 340, 150, 190, 200, 160},{ 340,  60, 200, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 210},{ 340, 180, 220, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 200, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -110,  30, 200,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180},{ 340,  40, 180, 200, 150},{ 340,  70, 120, 200,  90}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 140, 150},{ 340,  90, 200, 130,  40},{ 340,   0, 200,  40, 130},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 200, 170,  80},{ 340, 220, 200, 220, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200,  40, 130},{ 340, 200, 200, 200, 200},{ 340,  70, 200, 110, 120},{ 340,  10, 200, -30, -220}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150},{ 340, 160, 200, 120, -70},{ 340, 190, 200, 150, 150}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260,  20, 220},{ 340, 200, 190, -90, 110},{ 340, 200, 200,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, -40, 150},{ 340, 200, 220,  40, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 240,   0, 190},{ 340, 200,  30, -350,  30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120},{ 340, 200, 180, -200, 180},{ 340, 200, 120,  20,  30}}-}-},-/* UG....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 110, 200},{ 340, 190, 190,  80, 200},{ 340,  10,  10, -90, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 180,  80, 200},{ 340, 250, 190, 180, 200},{ 340, 200, 200, 200, 200},{ 340, 150,  90,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  70,  70, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180,  70, 200},{ 340,   0, -100, -30, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 190, 190, 200},{ 340,  40, -60,  10, 200},{ 340, 210, 110, 190, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 270, 200, 240},{ 340, 140, 190, 200, 160},{ 340, -30, 110, 200,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 180, 200, 150},{ 340, 140, 190, 200, 160},{ 340, 200, 200, 200, 200},{ 340,  40,  90, 200,  60}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 170, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -150,   0, 200, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 150, 190, 200, 160},{ 340, -110,  40, 200,  10},{ 340,  70, 110, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 150, 160},{ 340,  80, 200, 120,  30},{ 340, -90, 200, -50,  40},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 200, 120,  30},{ 340, 180, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340,  90, 200,  80,  40}},-{{ 340, 340, 340, 340, 340},{ 340, -30, 200,  10, 100},{ 340, 200, 200, 200, 200},{ 340,  70, 200, 110, 120},{ 340, -30, 200, -70, -260}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 200, 190, 140},{ 340,  10, 200, -30, -220},{ 340, 190, 200, 150, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 230},{ 340, 200, 190, -90, 100},{ 340, 200, 110, -90, 110},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -100, 100},{ 340, 200, 190,  10, 100},{ 340, 200, 200, 200, 200},{ 340, 200,  90, -90,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -30, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 240,   0, 190},{ 340, 200,   0, -390, -10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 190,  10, 110},{ 340, 200,  40, -350,  30},{ 340, 200, 110,  10,  30}}-}-},-/* UG....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130,  30, 110, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  90, 230, 200, 200},{ 340, 120, 170, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200,  70, -120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250,  70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 220},{ 340, 200, 130, -250, 130}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170,  70,  80}}-}-},-/* UG....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100,   0,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  80, 220, 200, 190},{ 340, 150, 190, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170,  80},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340,  70, 200,  30, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 280,   0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 230},{ 340, 200, 100, -290,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190,  90, 110}}-}-},-/* UG....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130,  30, 110, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  90, 230, 200, 200},{ 340, 120, 170, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200,  70, -120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250,  70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 220},{ 340, 200, 130, -250, 130}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170,  70,  80}}-}-},-/* UG....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100,   0,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  80, 220, 200, 190},{ 340, 150, 190, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170,  80},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340,  70, 200,  30, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 280,   0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 230},{ 340, 200, 100, -290,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190,  90, 110}}-}-},-/* UG....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-},-{ /* noPair */ {{{{0}}}},-/* AU....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 190,  80, 200},{ 340, 190, 180,  70, 200},{ 340, 100,  90, -20, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 220, 110, 200},{ 340, 280, 210, 200, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100,  90, -20, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160,  50, 200},{ 340,  30, -80, -10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 190, 180, 200},{ 340, 180,  70, 140, 200},{ 340, 220, 100, 180, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 230, 200, 230},{ 340, 170, 160, 200, 160},{ 340,  80, 170, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 200, 210},{ 340, 200, 190, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 170, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -90,   0, 200,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 180, 200, 180},{ 340,  60, 150, 200, 150},{ 340,  90,  90, 200,  90}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 200, 130, 160},{ 340,  70, 200, 120,  50},{ 340, -20, 200,  30, 140},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 170,  90},{ 340, 200, 200, 210, 180},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160}},-{{ 340, 340, 340, 340, 340},{ 340, -20, 200,  30, 140},{ 340, 200, 200, 200, 200},{ 340,  50, 200, 110, 130},{ 340, -10, 200, -40, -210}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 180, 200, 200, 160},{ 340, 140, 200, 110, -60},{ 340, 180, 200, 150, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  60, 190},{ 340, 200, 160, -50,  80},{ 340, 200, 170,  40, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 210,   0, 130},{ 340, 200, 190,  80, 110},{ 340, 200, 200, 200, 200},{ 340, 200, 180,  70, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170,  40, 180},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  40, 170},{ 340, 200,   0, -310,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 180,  70, 100},{ 340, 200, 150, -160, 160},{ 340, 200,  90,  60,  10}}-}-},-/* AU....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 200,  90, 200},{ 340, 190, 170,  60, 200},{ 340,  10,   0, -110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 170,  60, 200},{ 340, 250, 170, 160, 200},{ 340, 200, 200, 200, 200},{ 340, 150,  70,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  70,  60, -50, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 160,  50, 200},{ 340,   0, -120, -50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 180, 170, 200},{ 340,  40, -80, -10, 200},{ 340, 210, 100, 170, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 240},{ 340, 160, 160, 200, 160},{ 340, -10,  80, 200,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 150, 200, 150},{ 340, 160, 160, 200, 160},{ 340, 200, 200, 200, 200},{ 340,  60,  60, 200,  60}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 140, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 150, 210, 200, 210},{ 340, -130, -30, 200, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 160, 200, 160},{ 340, -90,  10, 200,  10},{ 340,  90,  80, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340,  90, 200, 140, 170},{ 340,  60, 200, 120,  40},{ 340, -110, 200, -60,  50},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 200, 110,  40},{ 340, 160, 200, 180, 140},{ 340, 200, 200, 200, 200},{ 340,  70, 200,  80,  50}},-{{ 340, 340, 340, 340, 340},{ 340, -50, 200,   0, 110},{ 340, 200, 200, 200, 200},{ 340,  50, 200, 110, 130},{ 340, -50, 200, -70, -250}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 170, 200, 180, 150},{ 340, -10, 200, -30, -210},{ 340, 170, 200, 140, 150}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240,  70, 200},{ 340, 200, 160, -50,  80},{ 340, 200,  80, -50,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 150, -60,  70},{ 340, 200, 160,  50,  80},{ 340, 200, 200, 200, 200},{ 340, 200,  60, -50, -20}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 140,  10, 150},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  40, 170},{ 340, 200, -30, -350, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 160,  50,  80},{ 340, 200,  10, -310,  10},{ 340, 200,  80,  50,   0}}-}-},-/* AU....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190,  80, 200},{ 340, 130,  20,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340,  10, 100, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 140, 160},{ 340,  90, 200,  70, -110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220,  10, 140},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200, 100, -210, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110,  60}}-}-},-/* AU....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200,  90, 200},{ 340, 100, -20,  50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30,  70, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160,  90},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340,  90, 200, 140, 170},{ 340,  50, 200,  30, -150}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200,  70, -250,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130,  80}}-}-},-/* AU....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 250, 240, 130, 200},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 250, 140, 200},{ 340, 310, 230, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 140,  30, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 190,  80, 200},{ 340, 130,  20,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 230, 120, 190, 200},{ 340, 270, 150, 220, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 230, 220, 200, 220},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 230, 200, 230},{ 340, 220, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 220, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 180, 240, 200, 240},{ 340,  10, 100, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 110, 200, 200, 200},{ 340, 140, 140, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 130, 200, 180, 110},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 200, 190, 120},{ 340, 220, 200, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 200,  80, 190},{ 340, 200, 200, 200, 200},{ 340,  80, 200, 140, 160},{ 340,  90, 200,  70, -110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 190, 200, 160, -10},{ 340, 220, 200, 200, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 220,  10, 140},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 230,  20, 150},{ 340, 200, 220, 100, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 220,  90, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200, 100, -210, 110}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 200, -110, 200},{ 340, 200, 140, 110,  60}}-}-},-/* AU....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 230, 220, 110, 200},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 260, 150, 200},{ 340, 340, 260, 250, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 260, 250, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 160,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 200,  90, 200},{ 340, 100, -20,  50, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 230, 220, 200},{ 340, 220, 110, 180, 200},{ 340, 290, 180, 250, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 310, 200, 310},{ 340, 210, 200, 200, 200},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 250, 250, 200, 250},{ 340, 250, 250, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 250, 250, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 240, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 190, 240, 200, 240},{ 340, -30,  70, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 220, 200, 220},{ 340, 100, 190, 200, 190},{ 340, 170, 160, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 230},{ 340, 110, 200, 160,  90},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 200, 210, 130},{ 340, 250, 200, 270, 230},{ 340, 200, 200, 200, 200},{ 340, 250, 200, 270, 230}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200, 100, 210},{ 340, 200, 200, 200, 200},{ 340,  90, 200, 140, 170},{ 340,  50, 200,  30, -150}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 220, 200, 240, 200},{ 340, 180, 200, 150, -20},{ 340, 250, 200, 220, 230}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 310, 130, 270},{ 340, 200, 200, -10, 120},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  30, 170},{ 340, 200, 250, 130, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 130, 170}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, 110, 240},{ 340, 200, 200, 200, 200},{ 340, 200, 240,  70, 200},{ 340, 200,  70, -250,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 220, 100, 140},{ 340, 200, 190, -120, 190},{ 340, 200, 160, 130,  80}}-}-},-/* AU....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-},-{ /* noPair */ {{{{0}}}},-/* UA....CG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 100, 200},{ 340, 190, 190,  90, 200},{ 340, 100, 100,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 240, 240, 130, 200},{ 340, 280, 220, 220, 200},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 100,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180,  70, 200},{ 340,  30, -70,  10, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 270, 210, 200, 200},{ 340, 180,  80, 160, 200},{ 340, 220, 120, 190, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 260, 200, 230},{ 340, 150, 190, 200, 160},{ 340,  60, 200, 200, 170},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 190, 240, 200, 210},{ 340, 180, 220, 200, 190},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180}},-{{ 340, 340, 340, 340, 340},{ 340,  60, 200, 200, 170},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -110,  30, 200,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 160, 210, 200, 180},{ 340,  40, 180, 200, 150},{ 340,  70, 120, 200,  90}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 100, 200, 140, 150},{ 340,  90, 200, 130,  40},{ 340,   0, 200,  40, 130},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 200, 170,  80},{ 340, 220, 200, 220, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150}},-{{ 340, 340, 340, 340, 340},{ 340,   0, 200,  40, 130},{ 340, 200, 200, 200, 200},{ 340,  70, 200, 110, 120},{ 340,  10, 200, -30, -220}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 200, 200, 150},{ 340, 160, 200, 120, -70},{ 340, 190, 200, 150, 150}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260,  20, 220},{ 340, 200, 190, -90, 110},{ 340, 200, 200,   0, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 240, -40, 150},{ 340, 200, 220,  40, 140},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200,   0, 200},{ 340, 200, 200, 200, 200},{ 340, 200, 240,   0, 190},{ 340, 200,  30, -350,  30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 210,  30, 120},{ 340, 200, 180, -200, 180},{ 340, 200, 120,  20,  30}}-}-},-/* UA....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 210, 210, 110, 200},{ 340, 190, 190,  80, 200},{ 340,  10,  10, -90, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 180, 180,  80, 200},{ 340, 250, 190, 180, 200},{ 340, 200, 200, 200, 200},{ 340, 150,  90,  90, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  70,  70, -30, 200},{ 340, 200, 200, 200, 200},{ 340, 180, 180,  70, 200},{ 340,   0, -100, -30, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 250, 190, 190, 200},{ 340,  40, -60,  10, 200},{ 340, 210, 110, 190, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 270, 200, 240},{ 340, 140, 190, 200, 160},{ 340, -30, 110, 200,  80},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 140, 180, 200, 150},{ 340, 140, 190, 200, 160},{ 340, 200, 200, 200, 200},{ 340,  40,  90, 200,  60}},-{{ 340, 340, 340, 340, 340},{ 340,  30, 170, 200, 140},{ 340, 200, 200, 200, 200},{ 340, 130, 240, 200, 210},{ 340, -150,   0, 200, -30}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 150, 190, 200, 160},{ 340, -110,  40, 200,  10},{ 340,  70, 110, 200,  80}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 200, 150, 160},{ 340,  80, 200, 120,  30},{ 340, -90, 200, -50,  40},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340,  80, 200, 120,  30},{ 340, 180, 200, 180, 130},{ 340, 200, 200, 200, 200},{ 340,  90, 200,  80,  40}},-{{ 340, 340, 340, 340, 340},{ 340, -30, 200,  10, 100},{ 340, 200, 200, 200, 200},{ 340,  70, 200, 110, 120},{ 340, -30, 200, -70, -260}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 190, 200, 190, 140},{ 340,  10, 200, -30, -220},{ 340, 190, 200, 150, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  30, 230},{ 340, 200, 190, -90, 100},{ 340, 200, 110, -90, 110},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 180, -100, 100},{ 340, 200, 190,  10, 100},{ 340, 200, 200, 200, 200},{ 340, 200,  90, -90,   0}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 170, -30, 170},{ 340, 200, 200, 200, 200},{ 340, 200, 240,   0, 190},{ 340, 200,   0, -390, -10}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 190,  10, 110},{ 340, 200,  40, -350,  30},{ 340, 200, 110,  10,  30}}-}-},-/* UA....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130,  30, 110, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  90, 230, 200, 200},{ 340, 120, 170, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200,  70, -120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250,  70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 220},{ 340, 200, 130, -250, 130}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170,  70,  80}}-}-},-/* UA....UG */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100,   0,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  80, 220, 200, 190},{ 340, 150, 190, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170,  80},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340,  70, 200,  30, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 280,   0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 230},{ 340, 200, 100, -290,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190,  90, 110}}-}-},-/* UA....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 250, 250, 150, 200},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 260, 260, 160, 200},{ 340, 310, 250, 240, 200},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 150, 150,  50, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 100, 200},{ 340, 130,  30, 110, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 230, 130, 210, 200},{ 340, 270, 170, 240, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 210, 250, 200, 220},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 220, 260, 200, 230},{ 340, 200, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220}},-{{ 340, 340, 340, 340, 340},{ 340, 110, 250, 200, 220},{ 340, 200, 200, 200, 200},{ 340, 160, 270, 200, 240},{ 340, -10, 130, 200, 100}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  90, 230, 200, 200},{ 340, 120, 170, 200, 140}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 150, 200, 190, 100},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 160, 200, 200, 110},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190}},-{{ 340, 340, 340, 340, 340},{ 340,  50, 200,  90, 180},{ 340, 200, 200, 200, 200},{ 340, 100, 200, 140, 150},{ 340, 110, 200,  70, -120}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 210, 200, 170, -20},{ 340, 240, 200, 200, 190}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 250, -30, 170},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 260, -20, 180},{ 340, 200, 250,  70, 160},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 250,  50, 250},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 220},{ 340, 200, 130, -250, 130}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 230, -150, 230},{ 340, 200, 170,  70,  80}}-}-},-/* UA....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 230, 230, 130, 200},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 280, 280, 170, 200},{ 340, 340, 280, 270, 200},{ 340, 200, 200, 200, 200},{ 340, 340, 280, 270, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 170,  70, 200},{ 340, 200, 200, 200, 200},{ 340, 210, 210, 110, 200},{ 340, 100,   0,  70, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 310, 250, 240, 200},{ 340, 220, 120, 200, 200},{ 340, 290, 190, 270, 200}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 340, 200, 310},{ 340, 190, 230, 200, 200},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 230, 280, 200, 250},{ 340, 230, 280, 200, 250},{ 340, 200, 200, 200, 200},{ 340, 230, 280, 200, 250}},-{{ 340, 340, 340, 340, 340},{ 340, 130, 270, 200, 240},{ 340, 200, 200, 200, 200},{ 340, 170, 270, 200, 240},{ 340, -50, 100, 200,  70}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250, 200, 220},{ 340,  80, 220, 200, 190},{ 340, 150, 190, 200, 160}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 220},{ 340, 130, 200, 170,  80},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 170, 200, 210, 120},{ 340, 270, 200, 270, 220},{ 340, 200, 200, 200, 200},{ 340, 270, 200, 270, 220}},-{{ 340, 340, 340, 340, 340},{ 340,  70, 200, 110, 200},{ 340, 200, 200, 200, 200},{ 340, 110, 200, 150, 160},{ 340,  70, 200,  30, -160}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 240, 200, 240, 190},{ 340, 200, 200, 160, -30},{ 340, 270, 200, 230, 220}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 340, 100, 290},{ 340, 200, 230, -50, 150},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 280,   0, 190},{ 340, 200, 280, 100, 190},{ 340, 200, 200, 200, 200},{ 340, 200, 280, 100, 190}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 270,  70, 270},{ 340, 200, 200, 200, 200},{ 340, 200, 270,  30, 230},{ 340, 200, 100, -290,  90}},-{{ 340, 340, 340, 340, 340},{ 340, 200, 200, 200, 200},{ 340, 200, 250,  70, 160},{ 340, 200, 220, -160, 220},{ 340, 200, 190,  90, 110}}-}-},-/* UA....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 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340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 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340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 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340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-},-/* ??....GC */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 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340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-},-/* ??....GU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 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340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-},-/* ??....AU */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-},-/* ??....UA */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-},-/* ??....?? */-{{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-},-{-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}},-{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}-}-}-}-};--PRIVATE int int22_H_184[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =-{ /* noPair */ {{{{{0}}}}},-{ /* noPair */ {{{{0}}}},-/* CG.@@..CG */-{ { { {  0, 0, 0, 0, 0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..CG */-{ {  0, 0, 0, 0, 0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* CG.@C..CG */-{ {  0, 0, 0, 0, 0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* CG.@G..CG */-{ {  0, 0, 0, 0, 0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* CG.@U..CG */-{ {  0, 0, 0, 0, 0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* CG.A@..CG */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..CG */-{{  DEF,-1029, -949,-1029,-1029},-{-1079,-2058,-1978,-2058,-2058},-{ -569,-1548,-1468,-1548,-1548},-{ -989,-1968,-1888,-1968,-1968},-{ -859,-1838,-1758,-1838,-1838}},-/* CG.AC..CG */-{{  DEF,-1029, -949,-1029,-1029},-{ -999,-1978,-1898,-1978,-1978},-{ -499,-1478,-1398,-1478,-1478},-{ -989,-1968,-1888,-1968,-1968},-{ -789,-1768,-1688,-1768,-1768}},-/* CG.AG..CG */-{{  DEF,-1029, -949,-1029,-1029},-{-1079,-2058,-1978,-2058,-2058},-{ -569,-1548,-1468,-1548,-1548},-{ -989,-1968,-1888,-1968,-1968},-{ -859,-1838,-1758,-1838,-1838}},-/* CG.AU..CG */-{{  DEF,-1029, -949,-1029,-1029},-{-1079,-2058,-1978,-2058,-2058},-{ -719,-1698,-1618,-1698,-1698},-{ -989,-1968,-1888,-1968,-1968},-{ -909,-1888,-1808,-1888,-1888}}},-/* CG.C@..CG */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..CG */-{{  DEF, -519, -449, -519, -669},-{-1079,-1548,-1478,-1548,-1698},-{ -569,-1038, -968,-1038,-1188},-{ -989,-1458,-1388,-1458,-1608},-{ -859,-1328,-1258,-1328,-1478}},-/* CG.CC..CG */-{{  DEF, -519, -449, -519, -669},-{ -999,-1468,-1398,-1468,-1618},-{ -499, -968, -898, -968,-1118},-{ -989,-1458,-1388,-1458,-1608},-{ -789,-1258,-1188,-1258,-1408}},-/* CG.CG..CG */-{{  DEF, -519, -449, -519, -669},-{-1079,-1548,-1478,-1548,-1698},-{ -569,-1038, -968,-1038,-1188},-{ -989,-1458,-1388,-1458,-1608},-{ -859,-1328,-1258,-1328,-1478}},-/* CG.CU..CG */-{{  DEF, -519, -449, -519, -669},-{-1079,-1548,-1478,-1548,-1698},-{ -719,-1188,-1118,-1188,-1338},-{ -989,-1458,-1388,-1458,-1608},-{ -909,-1378,-1308,-1378,-1528}}},-/* CG.G@..CG */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..CG */-{{  DEF, -939, -939, -939, -939},-{-1079,-1968,-1968,-1968,-1968},-{ -569,-1458,-1458,-1458,-1458},-{ -989,-1878,-1878,-1878,-1878},-{ -859,-1748,-1748,-1748,-1748}},-/* CG.GC..CG */-{{  DEF, -939, -939, -939, -939},-{ -999,-1888,-1888,-1888,-1888},-{ -499,-1388,-1388,-1388,-1388},-{ -989,-1878,-1878,-1878,-1878},-{ -789,-1678,-1678,-1678,-1678}},-/* CG.GG..CG */-{{  DEF, -939, -939, -939, -939},-{-1079,-1968,-1968,-1968,-1968},-{ -569,-1458,-1458,-1458,-1458},-{ -989,-1878,-1878,-1878,-1878},-{ -859,-1748,-1748,-1748,-1748}},-/* CG.GU..CG */-{{  DEF, -939, -939, -939, -939},-{-1079,-1968,-1968,-1968,-1968},-{ -719,-1608,-1608,-1608,-1608},-{ -989,-1878,-1878,-1878,-1878},-{ -909,-1798,-1798,-1798,-1798}}},-/* CG.U@..CG */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..CG */-{{  DEF, -809, -739, -809, -859},-{-1079,-1838,-1768,-1838,-1888},-{ -569,-1328,-1258,-1328,-1378},-{ -989,-1748,-1678,-1748,-1798},-{ -859,-1618,-1548,-1618,-1668}},-/* CG.UC..CG */-{{  DEF, -809, -739, -809, -859},-{ -999,-1758,-1688,-1758,-1808},-{ -499,-1258,-1188,-1258,-1308},-{ -989,-1748,-1678,-1748,-1798},-{ -789,-1548,-1478,-1548,-1598}},-/* CG.UG..CG */-{{  DEF, -809, -739, -809, -859},-{-1079,-1838,-1768,-1838,-1888},-{ -569,-1328,-1258,-1328,-1378},-{ -989,-1748,-1678,-1748,-1798},-{ -859,-1618,-1548,-1618,-1668}},-/* CG.UU..CG */-{{  DEF, -809, -739, -809, -859},-{-1079,-1838,-1768,-1838,-1888},-{ -719,-1478,-1408,-1478,-1528},-{ -989,-1748,-1678,-1748,-1798},-{ -909,-1668,-1598,-1668,-1718}}}},-/* CG.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* CG.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* CG.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* CG.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* CG.A@..GC */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..GC */-{{  DEF,-1029, -949,-1029,-1029},-{ -569,-1548,-1468,-1548,-1548},-{ -769,-1748,-1668,-1748,-1748},-{ -759,-1738,-1658,-1738,-1738},-{ -549,-1528,-1448,-1528,-1528}},-/* CG.AC..GC */-{{  DEF,-1029, -949,-1029,-1029},-{ -929,-1908,-1828,-1908,-1908},-{ -359,-1338,-1258,-1338,-1338},-{ -789,-1768,-1688,-1768,-1768},-{ -549,-1528,-1448,-1528,-1528}},-/* CG.AG..GC */-{{  DEF,-1029, -949,-1029,-1029},-{ -609,-1588,-1508,-1588,-1588},-{ -359,-1338,-1258,-1338,-1338},-{ -669,-1648,-1568,-1648,-1648},-{ -549,-1528,-1448,-1528,-1528}},-/* CG.AU..GC */-{{  DEF,-1029, -949,-1029,-1029},-{ -929,-1908,-1828,-1908,-1908},-{ -439,-1418,-1338,-1418,-1418},-{ -789,-1768,-1688,-1768,-1768},-{ -619,-1598,-1518,-1598,-1598}}},-/* CG.C@..GC */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..GC */-{{  DEF, -519, -449, -519, -669},-{ -569,-1038, -968,-1038,-1188},-{ -769,-1238,-1168,-1238,-1388},-{ -759,-1228,-1158,-1228,-1378},-{ -549,-1018, -948,-1018,-1168}},-/* CG.CC..GC */-{{  DEF, -519, -449, -519, -669},-{ -929,-1398,-1328,-1398,-1548},-{ -359, -828, -758, -828, -978},-{ -789,-1258,-1188,-1258,-1408},-{ -549,-1018, -948,-1018,-1168}},-/* CG.CG..GC */-{{  DEF, -519, -449, -519, -669},-{ -609,-1078,-1008,-1078,-1228},-{ -359, -828, -758, -828, -978},-{ -669,-1138,-1068,-1138,-1288},-{ -549,-1018, -948,-1018,-1168}},-/* CG.CU..GC */-{{  DEF, -519, -449, -519, -669},-{ -929,-1398,-1328,-1398,-1548},-{ -439, -908, -838, -908,-1058},-{ -789,-1258,-1188,-1258,-1408},-{ -619,-1088,-1018,-1088,-1238}}},-/* CG.G@..GC */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..GC */-{{  DEF, -939, -939, -939, -939},-{ -569,-1458,-1458,-1458,-1458},-{ -769,-1658,-1658,-1658,-1658},-{ -759,-1648,-1648,-1648,-1648},-{ -549,-1438,-1438,-1438,-1438}},-/* CG.GC..GC */-{{  DEF, -939, -939, -939, -939},-{ -929,-1818,-1818,-1818,-1818},-{ -359,-1248,-1248,-1248,-1248},-{ -789,-1678,-1678,-1678,-1678},-{ -549,-1438,-1438,-1438,-1438}},-/* CG.GG..GC */-{{  DEF, -939, -939, -939, -939},-{ -609,-1498,-1498,-1498,-1498},-{ -359,-1248,-1248,-1248,-1248},-{ -669,-1558,-1558,-1558,-1558},-{ -549,-1438,-1438,-1438,-1438}},-/* CG.GU..GC */-{{  DEF, -939, -939, -939, -939},-{ -929,-1818,-1818,-1818,-1818},-{ -439,-1328,-1328,-1328,-1328},-{ -789,-1678,-1678,-1678,-3080},-{ -619,-1508,-1508,-1508,-1508}}},-/* CG.U@..GC */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..GC */-{{  DEF, -809, -739, -809, -859},-{ -569,-1328,-1258,-1328,-1378},-{ -769,-1528,-1458,-1528,-1578},-{ -759,-1518,-1448,-1518,-1568},-{ -549,-1308,-1238,-1308,-1358}},-/* CG.UC..GC */-{{  DEF, -809, -739, -809, -859},-{ -929,-1688,-1618,-1688,-1738},-{ -359,-1118,-1048,-1118,-1168},-{ -789,-1548,-1478,-1548,-1598},-{ -549,-1308,-1238,-1308,-1358}},-/* CG.UG..GC */-{{  DEF, -809, -739, -809, -859},-{ -609,-1368,-1298,-1368,-1418},-{ -359,-1118,-1048,-1118,-1168},-{ -669,-1428,-1358,-1428,-1478},-{ -549,-1308,-1238,-1308,-1358}},-/* CG.UU..GC */-{{  DEF, -809, -739, -809, -859},-{ -929,-1688,-1618,-1688,-1738},-{ -439,-1198,-1128,-1198,-1248},-{ -789,-1548,-1478,-1548,-1598},-{ -619,-1378,-1308,-1378,-1428}}}},-/* CG.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* CG.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* CG.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* CG.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* CG.A@..GU */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..GU */-{{  DEF,-1029, -949,-1029,-1029},-{ -479,-1458,-1378,-1458,-1458},-{ -309,-1288,-1208,-1288,-1288},-{ -389,-1368,-1288,-1368,-1368},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AC..GU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AG..GU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AU..GU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}}},-/* CG.C@..GU */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..GU */-{{  DEF, -519, -449, -519, -669},-{ -479, -948, -878, -948,-1098},-{ -309, -778, -708, -778, -928},-{ -389, -858, -788, -858,-1008},-{ -379, -848, -778, -848, -998}},-/* CG.CC..GU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}},-/* CG.CG..GU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}},-/* CG.CU..GU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}}},-/* CG.G@..GU */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..GU */-{{  DEF, -939, -939, -939, -939},-{ -479,-1368,-1368,-1368,-1368},-{ -309,-1198,-1198,-1198,-1198},-{ -389,-1278,-1278,-1278,-1278},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GC..GU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GG..GU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GU..GU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}}},-/* CG.U@..GU */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..GU */-{{  DEF, -809, -739, -809, -859},-{ -479,-1238,-1168,-1238,-1288},-{ -309,-1068, -998,-1068,-1118},-{ -389,-1148,-1078,-1148,-1198},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UC..GU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UG..GU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UU..GU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}}}},-/* CG.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* CG.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* CG.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* CG.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* CG.A@..UG */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..UG */-{{  DEF,-1029, -949,-1029,-1029},-{ -769,-1748,-1668,-1748,-1748},-{ -529,-1508,-1428,-1508,-1508},-{ -709,-1688,-1608,-1688,-1688},-{ -599,-1578,-1498,-1578,-1578}},-/* CG.AC..UG */-{{  DEF,-1029, -949,-1029,-1029},-{ -839,-1818,-1738,-1818,-1818},-{ -529,-1508,-1428,-1508,-1508},-{ -859,-1838,-1758,-1838,-1838},-{ -489,-1468,-1388,-1468,-1468}},-/* CG.AG..UG */-{{  DEF,-1029, -949,-1029,-1029},-{-1009,-1988,-1908,-1988,-1988},-{ -409,-1388,-1308,-1388,-1388},-{ -969,-1948,-1868,-1948,-1948},-{ -599,-1578,-1498,-1578,-1578}},-/* CG.AU..UG */-{{  DEF,-1029, -949,-1029,-1029},-{ -859,-1838,-1758,-1838,-1838},-{ -529,-1508,-1428,-1508,-1508},-{ -859,-1838,-1758,-1838,-1838},-{ -409,-1388,-1308,-1388,-1388}}},-/* CG.C@..UG */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..UG */-{{  DEF, -519, -449, -519, -669},-{ -769,-1238,-1168,-1238,-1388},-{ -529, -998, -928, -998,-1148},-{ -709,-1178,-1108,-1178,-1328},-{ -599,-1068, -998,-1068,-1218}},-/* CG.CC..UG */-{{  DEF, -519, -449, -519, -669},-{ -839,-1308,-1238,-1308,-1458},-{ -529, -998, -928, -998,-1148},-{ -859,-1328,-1258,-1328,-1478},-{ -489, -958, -888, -958,-1108}},-/* CG.CG..UG */-{{  DEF, -519, -449, -519, -669},-{-1009,-1478,-1408,-1478,-1628},-{ -409, -878, -808, -878,-1028},-{ -969,-1438,-1368,-1438,-1588},-{ -599,-1068, -998,-1068,-1218}},-/* CG.CU..UG */-{{  DEF, -519, -449, -519, -669},-{ -859,-1328,-1258,-1328,-1478},-{ -529, -998, -928, -998,-1148},-{ -859,-1328,-1258,-1328,-1478},-{ -409, -878, -808, -878,-1028}}},-/* CG.G@..UG */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..UG */-{{  DEF, -939, -939, -939, -939},-{ -769,-1658,-1658,-1658,-1658},-{ -529,-1418,-1418,-1418,-1418},-{ -709,-1598,-1598,-1598,-1598},-{ -599,-1488,-1488,-1488,-1488}},-/* CG.GC..UG */-{{  DEF, -939, -939, -939, -939},-{ -839,-1728,-1728,-1728,-1728},-{ -529,-1418,-1418,-1418,-1418},-{ -859,-1748,-1748,-1748,-1748},-{ -489,-1378,-1378,-1378,-1378}},-/* CG.GG..UG */-{{  DEF, -939, -939, -939, -939},-{-1009,-1898,-1898,-1898,-1898},-{ -409,-1298,-1298,-1298,-1298},-{ -969,-1858,-1858,-1858,-1858},-{ -599,-1488,-1488,-1488,-1488}},-/* CG.GU..UG */-{{  DEF, -939, -939, -939, -939},-{ -859,-1748,-1748,-1748,-1748},-{ -529,-1418,-1418,-1418,-1418},-{ -859,-1748,-1748,-1748,-1748},-{ -409,-1298,-1298,-1298,-1298}}},-/* CG.U@..UG */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..UG */-{{  DEF, -809, -739, -809, -859},-{ -769,-1528,-1458,-1528,-1578},-{ -529,-1288,-1218,-1288,-1338},-{ -709,-1468,-1398,-1468,-1518},-{ -599,-1358,-1288,-1358,-1408}},-/* CG.UC..UG */-{{  DEF, -809, -739, -809, -859},-{ -839,-1598,-1528,-1598,-1648},-{ -529,-1288,-1218,-1288,-1338},-{ -859,-1618,-1548,-1618,-1668},-{ -489,-1248,-1178,-1248,-1298}},-/* CG.UG..UG */-{{  DEF, -809, -739, -809, -859},-{-1009,-1768,-1698,-1768,-1818},-{ -409,-1168,-1098,-1168,-1218},-{ -969,-1728,-1658,-1728,-1778},-{ -599,-1358,-1288,-1358,-1408}},-/* CG.UU..UG */-{{  DEF, -809, -739, -809, -859},-{ -859,-1618,-1548,-1618,-1668},-{ -529,-1288,-1218,-1288,-1338},-{ -859,-1618,-1548,-1618,-1668},-{ -409,-1168,-1098,-1168,-1218}}}},-/* CG.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* CG.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* CG.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* CG.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* CG.A@..AU */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..AU */-{{  DEF,-1029, -949,-1029,-1029},-{ -479,-1458,-1378,-1458,-1458},-{ -309,-1288,-1208,-1288,-1288},-{ -389,-1368,-1288,-1368,-1368},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AC..AU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AG..AU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}},-/* CG.AU..AU */-{{  DEF,-1029, -949,-1029,-1029},-{ -649,-1628,-1548,-1628,-1628},-{ -289,-1268,-1188,-1268,-1268},-{ -739,-1718,-1638,-1718,-1718},-{ -379,-1358,-1278,-1358,-1358}}},-/* CG.C@..AU */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..AU */-{{  DEF, -519, -449, -519, -669},-{ -479, -948, -878, -948,-1098},-{ -309, -778, -708, -778, -928},-{ -389, -858, -788, -858,-1008},-{ -379, -848, -778, -848, -998}},-/* CG.CC..AU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}},-/* CG.CG..AU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}},-/* CG.CU..AU */-{{  DEF, -519, -449, -519, -669},-{ -649,-1118,-1048,-1118,-1268},-{ -289, -758, -688, -758, -908},-{ -739,-1208,-1138,-1208,-1358},-{ -379, -848, -778, -848, -998}}},-/* CG.G@..AU */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..AU */-{{  DEF, -939, -939, -939, -939},-{ -479,-1368,-1368,-1368,-1368},-{ -309,-1198,-1198,-1198,-1198},-{ -389,-1278,-1278,-1278,-1278},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GC..AU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GG..AU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}},-/* CG.GU..AU */-{{  DEF, -939, -939, -939, -939},-{ -649,-1538,-1538,-1538,-1538},-{ -289,-1178,-1178,-1178,-1178},-{ -739,-1628,-1628,-1628,-1628},-{ -379,-1268,-1268,-1268,-1268}}},-/* CG.U@..AU */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..AU */-{{  DEF, -809, -739, -809, -859},-{ -479,-1238,-1168,-1238,-1288},-{ -309,-1068, -998,-1068,-1118},-{ -389,-1148,-1078,-1148,-1198},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UC..AU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UG..AU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}},-/* CG.UU..AU */-{{  DEF, -809, -739, -809, -859},-{ -649,-1408,-1338,-1408,-1458},-{ -289,-1048, -978,-1048,-1098},-{ -739,-1498,-1428,-1498,-1548},-{ -379,-1138,-1068,-1138,-1188}}}},-/* CG.@@..UA */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* CG.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* CG.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* CG.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* CG.A@..UA */-{{{  DEF,-1029, -949,-1029,-1029},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA..UA */-{{  DEF,-1029, -949,-1029,-1029},-{ -449,-1428,-1348,-1428,-1428},-{ -479,-1458,-1378,-1458,-1458},-{ -429,-1408,-1328,-1408,-1408},-{ -329,-1308,-1228,-1308,-1308}},-/* CG.AC..UA */-{{  DEF,-1029, -949,-1029,-1029},-{ -679,-1658,-1578,-1658,-1658},-{ -559,-1538,-1458,-1538,-1538},-{ -729,-1708,-1628,-1708,-1708},-{ -189,-1168,-1088,-1168,-1168}},-/* CG.AG..UA */-{{  DEF,-1029, -949,-1029,-1029},-{ -939,-1918,-1838,-1918,-1918},-{ -249,-1228,-1148,-1228,-1228},-{ -939,-1918,-1838,-1918,-1918},-{ -329,-1308,-1228,-1308,-1308}},-/* CG.AU..UA */-{{  DEF,-1029, -949,-1029,-1029},-{ -639,-1618,-1538,-1618,-1618},-{ -229,-1208,-1128,-1208,-1208},-{ -729,-1708,-1628,-1708,-1708},-{ -190,-1169,-1089,-1169,-1169}}},-/* CG.C@..UA */-{{{  DEF, -519, -449, -519, -669},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA..UA */-{{  DEF, -519, -449, -519, -669},-{ -449, -918, -848, -918,-1068},-{ -479, -948, -878, -948,-1098},-{ -429, -898, -828, -898,-1048},-{ -329, -798, -728, -798, -948}},-/* CG.CC..UA */-{{  DEF, -519, -449, -519, -669},-{ -679,-1148,-1078,-1148,-1298},-{ -559,-1028, -958,-1028,-1178},-{ -729,-1198,-1128,-1198,-1348},-{ -189, -658, -588, -658, -808}},-/* CG.CG..UA */-{{  DEF, -519, -449, -519, -669},-{ -939,-1408,-1338,-1408,-1558},-{ -249, -718, -648, -718, -868},-{ -939,-1408,-1338,-1408,-1558},-{ -329, -798, -728, -798, -948}},-/* CG.CU..UA */-{{  DEF, -519, -449, -519, -669},-{ -639,-1108,-1038,-1108,-1258},-{ -229, -698, -628, -698, -848},-{ -729,-1198,-1128,-1198,-1348},-{ -190, -659, -589, -659, -809}}},-/* CG.G@..UA */-{{{  DEF, -939, -939, -939, -939},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA..UA */-{{  DEF, -939, -939, -939, -939},-{ -449,-1338,-1338,-1338,-1338},-{ -479,-1368,-1368,-1368,-1368},-{ -429,-1318,-1318,-1318,-1318},-{ -329,-1218,-1218,-1218,-1218}},-/* CG.GC..UA */-{{  DEF, -939, -939, -939, -939},-{ -679,-1568,-1568,-1568,-1568},-{ -559,-1448,-1448,-1448,-1448},-{ -729,-1618,-1618,-1618,-1618},-{ -189,-1078,-1078,-1078,-1078}},-/* CG.GG..UA */-{{  DEF, -939, -939, -939, -939},-{ -939,-1828,-1828,-1828,-1828},-{ -249,-1138,-1138,-1138,-1138},-{ -939,-1828,-1828,-1828,-1828},-{ -329,-1218,-1218,-1218,-1218}},-/* CG.GU..UA */-{{  DEF, -939, -939, -939, -939},-{ -639,-1528,-1528,-1528,-1528},-{ -229,-1118,-1118,-1118,-1118},-{ -729,-1618,-1618,-1618,-1618},-{ -190,-1079,-1079,-1079,-1079}}},-/* CG.U@..UA */-{{{  DEF, -809, -739, -809, -859},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA..UA */-{{  DEF, -809, -739, -809, -859},-{ -449,-1208,-1138,-1208,-1258},-{ -479,-1238,-1168,-1238,-1288},-{ -429,-1188,-1118,-1188,-1238},-{ -329,-1088,-1018,-1088,-1138}},-/* CG.UC..UA */-{{  DEF, -809, -739, -809, -859},-{ -679,-1438,-1368,-1438,-1488},-{ -559,-1318,-1248,-1318,-1368},-{ -729,-1488,-1418,-1488,-1538},-{ -189, -948, -878, -948, -998}},-/* CG.UG..UA */-{{  DEF, -809, -739, -809, -859},-{ -939,-1698,-1628,-1698,-1748},-{ -249,-1008, -938,-1008,-1058},-{ -939,-1698,-1628,-1698,-1748},-{ -329,-1088,-1018,-1088,-1138}},-/* CG.UU..UA */-{{  DEF, -809, -739, -809, -859},-{ -639,-1398,-1328,-1398,-1448},-{ -229, -988, -918, -988,-1038},-{ -729,-1488,-1418,-1488,-1538},-{ -190, -949, -879, -949, -999}}}},-/* CG.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* CG.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* CG.A@.. @ */-{{{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AA.. @ */-{{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AC.. @ */-{{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AG.. @ */-{{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}},-/* CG.AU.. @ */-{{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079},-{ -100,-1079, -999,-1079,-1079}}},-/* CG.C@.. @ */-{{{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CA.. @ */-{{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CC.. @ */-{{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CG.. @ */-{{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}},-/* CG.CU.. @ */-{{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719},-{ -100, -569, -499, -569, -719}}},-/* CG.G@.. @ */-{{{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GA.. @ */-{{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GC.. @ */-{{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GG.. @ */-{{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}},-/* CG.GU.. @ */-{{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989},-{ -100, -989, -989, -989, -989}}},-/* CG.U@.. @ */-{{{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UA.. @ */-{{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UC.. @ */-{{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UG.. @ */-{{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}},-/* CG.UU.. @ */-{{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909},-{ -100, -859, -789, -859, -909}}}}},-{ /* noPair */ {{{{0}}}},-/* GC.@@..CG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* GC.@C..CG */-{{    0,    0,    0,    0,    0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* GC.@G..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* GC.@U..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* GC.A@..CG */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..CG */-{{  DEF, -519, -879, -559, -879},-{-1079,-1548,-1908,-1588,-1908},-{ -569,-1038,-1398,-1078,-1398},-{ -989,-1458,-1818,-1498,-1818},-{ -859,-1328,-1688,-1368,-1688}},-/* GC.AC..CG */-{{  DEF, -519, -879, -559, -879},-{ -999,-1468,-1828,-1508,-1828},-{ -499, -968,-1328,-1008,-1328},-{ -989,-1458,-1818,-1498,-1818},-{ -789,-1258,-1618,-1298,-1618}},-/* GC.AG..CG */-{{  DEF, -519, -879, -559, -879},-{-1079,-1548,-1908,-1588,-1908},-{ -569,-1038,-1398,-1078,-1398},-{ -989,-1458,-1818,-1498,-1818},-{ -859,-1328,-1688,-1368,-1688}},-/* GC.AU..CG */-{{  DEF, -519, -879, -559, -879},-{-1079,-1548,-1908,-1588,-1908},-{ -719,-1188,-1548,-1228,-1548},-{ -989,-1458,-1818,-1498,-1818},-{ -909,-1378,-1738,-1418,-1738}}},-/* GC.C@..CG */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..CG */-{{  DEF, -719, -309, -309, -389},-{-1079,-1748,-1338,-1338,-1418},-{ -569,-1238, -828, -828, -908},-{ -989,-1658,-1248,-1248,-1328},-{ -859,-1528,-1118,-1118,-1198}},-/* GC.CC..CG */-{{  DEF, -719, -309, -309, -389},-{ -999,-1668,-1258,-1258,-1338},-{ -499,-1168, -758, -758, -838},-{ -989,-1658,-1248,-1248,-1328},-{ -789,-1458,-1048,-1048,-1128}},-/* GC.CG..CG */-{{  DEF, -719, -309, -309, -389},-{-1079,-1748,-1338,-1338,-1418},-{ -569,-1238, -828, -828, -908},-{ -989,-1658,-1248,-1248,-1328},-{ -859,-1528,-1118,-1118,-1198}},-/* GC.CU..CG */-{{  DEF, -719, -309, -309, -389},-{-1079,-1748,-1338,-1338,-1418},-{ -719,-1388, -978, -978,-1058},-{ -989,-1658,-1248,-1248,-1328},-{ -909,-1578,-1168,-1168,-1248}}},-/* GC.G@..CG */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..CG */-{{  DEF, -709, -739, -619, -739},-{-1079,-1738,-1768,-1648,-1768},-{ -569,-1228,-1258,-1138,-1258},-{ -989,-1648,-1678,-1558,-1678},-{ -859,-1518,-1548,-1428,-1548}},-/* GC.GC..CG */-{{  DEF, -709, -739, -619, -739},-{ -999,-1658,-1688,-1568,-1688},-{ -499,-1158,-1188,-1068,-1188},-{ -989,-1648,-1678,-1558,-1678},-{ -789,-1448,-1478,-1358,-1478}},-/* GC.GG..CG */-{{  DEF, -709, -739, -619, -739},-{-1079,-1738,-1768,-1648,-1768},-{ -569,-1228,-1258,-1138,-1258},-{ -989,-1648,-1678,-1558,-1678},-{ -859,-1518,-1548,-1428,-1548}},-/* GC.GU..CG */-{{  DEF, -709, -739, -619, -739},-{-1079,-1738,-1768,-1648,-1768},-{ -719,-1378,-1408,-1288,-1408},-{ -989,-1648,-1678,-1558,-3080},-{ -909,-1568,-1598,-1478,-1598}}},-/* GC.U@..CG */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..CG */-{{  DEF, -499, -499, -499, -569},-{-1079,-1528,-1528,-1528,-1598},-{ -569,-1018,-1018,-1018,-1088},-{ -989,-1438,-1438,-1438,-1508},-{ -859,-1308,-1308,-1308,-1378}},-/* GC.UC..CG */-{{  DEF, -499, -499, -499, -569},-{ -999,-1448,-1448,-1448,-1518},-{ -499, -948, -948, -948,-1018},-{ -989,-1438,-1438,-1438,-1508},-{ -789,-1238,-1238,-1238,-1308}},-/* GC.UG..CG */-{{  DEF, -499, -499, -499, -569},-{-1079,-1528,-1528,-1528,-1598},-{ -569,-1018,-1018,-1018,-1088},-{ -989,-1438,-1438,-1438,-1508},-{ -859,-1308,-1308,-1308,-1378}},-/* GC.UU..CG */-{{  DEF, -499, -499, -499, -569},-{-1079,-1528,-1528,-1528,-1598},-{ -719,-1168,-1168,-1168,-1238},-{ -989,-1438,-1438,-1438,-1508},-{ -909,-1358,-1358,-1358,-1428}}}},-/* GC.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* GC.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* GC.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* GC.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* GC.A@..GC */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..GC */-{{  DEF, -519, -879, -559, -879},-{ -569,-1038,-1398,-1078,-1398},-{ -769,-1238,-1598,-1278,-1598},-{ -759,-1228,-1588,-1268,-1588},-{ -549,-1018,-1378,-1058,-1378}},-/* GC.AC..GC */-{{  DEF, -519, -879, -559, -879},-{ -929,-1398,-1758,-1438,-1758},-{ -359, -828,-1188, -868,-1188},-{ -789,-1258,-1618,-1298,-1618},-{ -549,-1018,-1378,-1058,-1378}},-/* GC.AG..GC */-{{  DEF, -519, -879, -559, -879},-{ -609,-1078,-1438,-1118,-1438},-{ -359, -828,-1188, -868,-1188},-{ -669,-1138,-1498,-1178,-1498},-{ -549,-1018,-1378,-1058,-1378}},-/* GC.AU..GC */-{{  DEF, -519, -879, -559, -879},-{ -929,-1398,-1758,-1438,-1758},-{ -439, -908,-1268, -948,-1268},-{ -789,-1258,-1618,-1298,-1618},-{ -619,-1088,-1448,-1128,-1448}}},-/* GC.C@..GC */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..GC */-{{  DEF, -719, -309, -309, -389},-{ -569,-1238, -828, -828, -908},-{ -769,-1438,-1028,-1028,-1108},-{ -759,-1428,-1018,-1018,-1098},-{ -549,-1218, -808, -808, -888}},-/* GC.CC..GC */-{{  DEF, -719, -309, -309, -389},-{ -929,-1598,-1188,-1188,-1268},-{ -359,-1028, -618, -618, -698},-{ -789,-1458,-1048,-1048,-1128},-{ -549,-1218, -808, -808, -888}},-/* GC.CG..GC */-{{  DEF, -719, -309, -309, -389},-{ -609,-1278, -868, -868, -948},-{ -359,-1028, -618, -618, -698},-{ -669,-1338, -928, -928,-1008},-{ -549,-1218, -808, -808, -888}},-/* GC.CU..GC */-{{  DEF, -719, -309, -309, -389},-{ -929,-1598,-1188,-1188,-1268},-{ -439,-1108, -698, -698, -778},-{ -789,-1458,-1048,-1048,-1128},-{ -619,-1288, -878, -878, -958}}},-/* GC.G@..GC */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..GC */-{{  DEF, -709, -739, -619, -739},-{ -569,-1228,-1258,-1138,-1258},-{ -769,-1428,-1458,-1338,-1458},-{ -759,-1418,-1448,-1328,-1448},-{ -549,-1208,-1238,-1118,-1238}},-/* GC.GC..GC */-{{  DEF, -709, -739, -619, -739},-{ -929,-1588,-1618,-1498,-1618},-{ -359,-1018,-1048, -928,-1048},-{ -789,-1448,-1478,-1358,-1478},-{ -549,-1208,-1238,-1118,-1238}},-/* GC.GG..GC */-{{  DEF, -709, -739, -619, -739},-{ -609,-1268,-1298,-1178,-1298},-{ -359,-1018,-1048, -928,-1048},-{ -669,-1328,-1358,-1238,-1358},-{ -549,-1208,-1238,-1118,-1238}},-/* GC.GU..GC */-{{  DEF, -709, -739, -619, -739},-{ -929,-1588,-1618,-1498,-1618},-{ -439,-1098,-1128,-1008,-1128},-{ -789,-1448,-1478,-1358,-3080},-{ -619,-1278,-1308,-1188,-1308}}},-/* GC.U@..GC */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..GC */-{{  DEF, -499, -499, -499, -569},-{ -569,-1018,-1018,-1018,-1088},-{ -769,-1218,-1218,-1218,-1288},-{ -759,-1208,-1208,-1208,-1278},-{ -549, -998, -998, -998,-1068}},-/* GC.UC..GC */-{{  DEF, -499, -499, -499, -569},-{ -929,-1378,-1378,-1378,-1448},-{ -359, -808, -808, -808, -878},-{ -789,-1238,-1238,-1238,-1308},-{ -549, -998, -998, -998,-1068}},-/* GC.UG..GC */-{{  DEF, -499, -499, -499, -569},-{ -609,-1058,-1058,-1058,-1128},-{ -359, -808, -808, -808, -878},-{ -669,-1118,-1118,-1118,-1188},-{ -549, -998, -998, -998,-1068}},-/* GC.UU..GC */-{{  DEF, -499, -499, -499, -569},-{ -929,-1378,-1378,-1378,-1448},-{ -439, -888, -888, -888, -958},-{ -789,-1238,-1238,-1238,-1308},-{ -619,-1068,-1068,-1068,-1138}}}},-/* GC.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* GC.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GC.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GC.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* GC.A@..GU */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..GU */-{{  DEF, -519, -879, -559, -879},-{ -479, -948,-1308, -988,-1308},-{ -309, -778,-1138, -818,-1138},-{ -389, -858,-1218, -898,-1218},-{ -379, -848,-1208, -888,-1208}},-/* GC.AC..GU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}},-/* GC.AG..GU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}},-/* GC.AU..GU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}}},-/* GC.C@..GU */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..GU */-{{  DEF, -719, -309, -309, -389},-{ -479,-1148, -738, -738, -818},-{ -309, -978, -568, -568, -648},-{ -389,-1058, -648, -648, -728},-{ -379,-1048, -638, -638, -718}},-/* GC.CC..GU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}},-/* GC.CG..GU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}},-/* GC.CU..GU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}}},-/* GC.G@..GU */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..GU */-{{  DEF, -709, -739, -619, -739},-{ -479,-1138,-1168,-1048,-1168},-{ -309, -968, -998, -878, -998},-{ -389,-1048,-1078, -958,-1078},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GC..GU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GG..GU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GU..GU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}}},-/* GC.U@..GU */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..GU */-{{  DEF, -499, -499, -499, -569},-{ -479, -928, -928, -928, -998},-{ -309, -758, -758, -758, -828},-{ -389, -838, -838, -838, -908},-{ -379, -828, -828, -828, -898}},-/* GC.UC..GU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}},-/* GC.UG..GU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}},-/* GC.UU..GU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}}}},-/* GC.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* GC.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* GC.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* GC.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* GC.A@..UG */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..UG */-{{  DEF, -519, -879, -559, -879},-{ -769,-1238,-1598,-1278,-1598},-{ -529, -998,-1358,-1038,-1358},-{ -709,-1178,-1538,-1218,-1538},-{ -599,-1068,-1428,-1108,-1428}},-/* GC.AC..UG */-{{  DEF, -519, -879, -559, -879},-{ -839,-1308,-1668,-1348,-1668},-{ -529, -998,-1358,-1038,-1358},-{ -859,-1328,-1688,-1368,-1688},-{ -489, -958,-1318, -998,-1318}},-/* GC.AG..UG */-{{  DEF, -519, -879, -559, -879},-{-1009,-1478,-1838,-1518,-1838},-{ -409, -878,-1238, -918,-1238},-{ -969,-1438,-1798,-1478,-1798},-{ -599,-1068,-1428,-1108,-1428}},-/* GC.AU..UG */-{{  DEF, -519, -879, -559, -879},-{ -859,-1328,-1688,-1368,-1688},-{ -529, -998,-1358,-1038,-1358},-{ -859,-1328,-1688,-1368,-1688},-{ -409, -878,-1238, -918,-1238}}},-/* GC.C@..UG */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..UG */-{{  DEF, -719, -309, -309, -389},-{ -769,-1438,-1028,-1028,-1108},-{ -529,-1198, -788, -788, -868},-{ -709,-1378, -968, -968,-1048},-{ -599,-1268, -858, -858, -938}},-/* GC.CC..UG */-{{  DEF, -719, -309, -309, -389},-{ -839,-1508,-1098,-1098,-1178},-{ -529,-1198, -788, -788, -868},-{ -859,-1528,-1118,-1118,-1198},-{ -489,-1158, -748, -748, -828}},-/* GC.CG..UG */-{{  DEF, -719, -309, -309, -389},-{-1009,-1678,-1268,-1268,-1348},-{ -409,-1078, -668, -668, -748},-{ -969,-1638,-1228,-1228,-1308},-{ -599,-1268, -858, -858, -938}},-/* GC.CU..UG */-{{  DEF, -719, -309, -309, -389},-{ -859,-1528,-1118,-1118,-1198},-{ -529,-1198, -788, -788, -868},-{ -859,-1528,-1118,-1118,-1198},-{ -409,-1078, -668, -668, -748}}},-/* GC.G@..UG */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..UG */-{{  DEF, -709, -739, -619, -739},-{ -769,-1428,-1458,-1338,-1458},-{ -529,-1188,-1218,-1098,-1218},-{ -709,-1368,-1398,-1278,-1398},-{ -599,-1258,-1288,-1168,-1288}},-/* GC.GC..UG */-{{  DEF, -709, -739, -619, -739},-{ -839,-1498,-1528,-1408,-1528},-{ -529,-1188,-1218,-1098,-1218},-{ -859,-1518,-1548,-1428,-1548},-{ -489,-1148,-1178,-1058,-1178}},-/* GC.GG..UG */-{{  DEF, -709, -739, -619, -739},-{-1009,-1668,-1698,-1578,-1698},-{ -409,-1068,-1098, -978,-1098},-{ -969,-1628,-1658,-1538,-1658},-{ -599,-1258,-1288,-1168,-1288}},-/* GC.GU..UG */-{{  DEF, -709, -739, -619, -739},-{ -859,-1518,-1548,-1428,-1548},-{ -529,-1188,-1218,-1098,-1218},-{ -859,-1518,-1548,-1428,-1548},-{ -409,-1068,-1098, -978,-1098}}},-/* GC.U@..UG */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..UG */-{{  DEF, -499, -499, -499, -569},-{ -769,-1218,-1218,-1218,-1288},-{ -529, -978, -978, -978,-1048},-{ -709,-1158,-1158,-1158,-1228},-{ -599,-1048,-1048,-1048,-1118}},-/* GC.UC..UG */-{{  DEF, -499, -499, -499, -569},-{ -839,-1288,-1288,-1288,-1358},-{ -529, -978, -978, -978,-1048},-{ -859,-1308,-1308,-1308,-1378},-{ -489, -938, -938, -938,-1008}},-/* GC.UG..UG */-{{  DEF, -499, -499, -499, -569},-{-1009,-1458,-1458,-1458,-1528},-{ -409, -858, -858, -858, -928},-{ -969,-1418,-1418,-1418,-1488},-{ -599,-1048,-1048,-1048,-1118}},-/* GC.UU..UG */-{{  DEF, -499, -499, -499, -569},-{ -859,-1308,-1308,-1308,-1378},-{ -529, -978, -978, -978,-1048},-{ -859,-1308,-1308,-1308,-1378},-{ -409, -858, -858, -858, -928}}}},-/* GC.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* GC.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GC.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GC.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* GC.A@..AU */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..AU */-{{  DEF, -519, -879, -559, -879},-{ -479, -948,-1308, -988,-1308},-{ -309, -778,-1138, -818,-1138},-{ -389, -858,-1218, -898,-1218},-{ -379, -848,-1208, -888,-1208}},-/* GC.AC..AU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}},-/* GC.AG..AU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}},-/* GC.AU..AU */-{{  DEF, -519, -879, -559, -879},-{ -649,-1118,-1478,-1158,-1478},-{ -289, -758,-1118, -798,-1118},-{ -739,-1208,-1568,-1248,-1568},-{ -379, -848,-1208, -888,-1208}}},-/* GC.C@..AU */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..AU */-{{  DEF, -719, -309, -309, -389},-{ -479,-1148, -738, -738, -818},-{ -309, -978, -568, -568, -648},-{ -389,-1058, -648, -648, -728},-{ -379,-1048, -638, -638, -718}},-/* GC.CC..AU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}},-/* GC.CG..AU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}},-/* GC.CU..AU */-{{  DEF, -719, -309, -309, -389},-{ -649,-1318, -908, -908, -988},-{ -289, -958, -548, -548, -628},-{ -739,-1408, -998, -998,-1078},-{ -379,-1048, -638, -638, -718}}},-/* GC.G@..AU */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..AU */-{{  DEF, -709, -739, -619, -739},-{ -479,-1138,-1168,-1048,-1168},-{ -309, -968, -998, -878, -998},-{ -389,-1048,-1078, -958,-1078},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GC..AU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GG..AU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}},-/* GC.GU..AU */-{{  DEF, -709, -739, -619, -739},-{ -649,-1308,-1338,-1218,-1338},-{ -289, -948, -978, -858, -978},-{ -739,-1398,-1428,-1308,-1428},-{ -379,-1038,-1068, -948,-1068}}},-/* GC.U@..AU */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..AU */-{{  DEF, -499, -499, -499, -569},-{ -479, -928, -928, -928, -998},-{ -309, -758, -758, -758, -828},-{ -389, -838, -838, -838, -908},-{ -379, -828, -828, -828, -898}},-/* GC.UC..AU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}},-/* GC.UG..AU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}},-/* GC.UU..AU */-{{  DEF, -499, -499, -499, -569},-{ -649,-1098,-1098,-1098,-1168},-{ -289, -738, -738, -738, -808},-{ -739,-1188,-1188,-1188,-1258},-{ -379, -828, -828, -828, -898}}}},-/* GC.@@..UA */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* GC.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* GC.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* GC.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* GC.A@..UA */-{{{  DEF, -519, -879, -559, -879},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA..UA */-{{  DEF, -519, -879, -559, -879},-{ -449, -918,-1278, -958,-1278},-{ -479, -948,-1308, -988,-1308},-{ -429, -898,-1258, -938,-1258},-{ -329, -798,-1158, -838,-1158}},-/* GC.AC..UA */-{{  DEF, -519, -879, -559, -879},-{ -679,-1148,-1508,-1188,-1508},-{ -559,-1028,-1388,-1068,-1388},-{ -729,-1198,-1558,-1238,-1558},-{ -189, -658,-1018, -698,-1018}},-/* GC.AG..UA */-{{  DEF, -519, -879, -559, -879},-{ -939,-1408,-1768,-1448,-1768},-{ -249, -718,-1078, -758,-1078},-{ -939,-1408,-1768,-1448,-1768},-{ -329, -798,-1158, -838,-1158}},-/* GC.AU..UA */-{{  DEF, -519, -879, -559, -879},-{ -639,-1108,-1468,-1148,-1468},-{ -229, -698,-1058, -738,-1058},-{ -729,-1198,-1558,-1238,-1558},-{ -190, -659,-1019, -699,-1019}}},-/* GC.C@..UA */-{{{  DEF, -719, -309, -309, -389},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA..UA */-{{  DEF, -719, -309, -309, -389},-{ -449,-1118, -708, -708, -788},-{ -479,-1148, -738, -738, -818},-{ -429,-1098, -688, -688, -768},-{ -329, -998, -588, -588, -668}},-/* GC.CC..UA */-{{  DEF, -719, -309, -309, -389},-{ -679,-1348, -938, -938,-1018},-{ -559,-1228, -818, -818, -898},-{ -729,-1398, -988, -988,-1068},-{ -189, -858, -448, -448, -528}},-/* GC.CG..UA */-{{  DEF, -719, -309, -309, -389},-{ -939,-1608,-1198,-1198,-1278},-{ -249, -918, -508, -508, -588},-{ -939,-1608,-1198,-1198,-1278},-{ -329, -998, -588, -588, -668}},-/* GC.CU..UA */-{{  DEF, -719, -309, -309, -389},-{ -639,-1308, -898, -898, -978},-{ -229, -898, -488, -488, -568},-{ -729,-1398, -988, -988,-1068},-{ -190, -859, -449, -449, -529}}},-/* GC.G@..UA */-{{{  DEF, -709, -739, -619, -739},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA..UA */-{{  DEF, -709, -739, -619, -739},-{ -449,-1108,-1138,-1018,-1138},-{ -479,-1138,-1168,-1048,-1168},-{ -429,-1088,-1118, -998,-1118},-{ -329, -988,-1018, -898,-1018}},-/* GC.GC..UA */-{{  DEF, -709, -739, -619, -739},-{ -679,-1338,-1368,-1248,-1368},-{ -559,-1218,-1248,-1128,-1248},-{ -729,-1388,-1418,-1298,-1418},-{ -189, -848, -878, -758, -878}},-/* GC.GG..UA */-{{  DEF, -709, -739, -619, -739},-{ -939,-1598,-1628,-1508,-1628},-{ -249, -908, -938, -818, -938},-{ -939,-1598,-1628,-1508,-1628},-{ -329, -988,-1018, -898,-1018}},-/* GC.GU..UA */-{{  DEF, -709, -739, -619, -739},-{ -639,-1298,-1328,-1208,-1328},-{ -229, -888, -918, -798, -918},-{ -729,-1388,-1418,-1298,-1418},-{ -190, -849, -879, -759, -879}}},-/* GC.U@..UA */-{{{  DEF, -499, -499, -499, -569},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA..UA */-{{  DEF, -499, -499, -499, -569},-{ -449, -898, -898, -898, -968},-{ -479, -928, -928, -928, -998},-{ -429, -878, -878, -878, -948},-{ -329, -778, -778, -778, -848}},-/* GC.UC..UA */-{{  DEF, -499, -499, -499, -569},-{ -679,-1128,-1128,-1128,-1198},-{ -559,-1008,-1008,-1008,-1078},-{ -729,-1178,-1178,-1178,-1248},-{ -189, -638, -638, -638, -708}},-/* GC.UG..UA */-{{  DEF, -499, -499, -499, -569},-{ -939,-1388,-1388,-1388,-1458},-{ -249, -698, -698, -698, -768},-{ -939,-1388,-1388,-1388,-1458},-{ -329, -778, -778, -778, -848}},-/* GC.UU..UA */-{{  DEF, -499, -499, -499, -569},-{ -639,-1088,-1088,-1088,-1158},-{ -229, -678, -678, -678, -748},-{ -729,-1178,-1178,-1178,-1248},-{ -190, -639, -639, -639, -709}}}},-/* GC.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GC.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* GC.A@.. @ */-{{{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AA.. @ */-{{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AC.. @ */-{{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AG.. @ */-{{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}},-/* GC.AU.. @ */-{{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929},-{ -100, -569, -929, -609, -929}}},-/* GC.C@.. @ */-{{{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CA.. @ */-{{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CC.. @ */-{{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CG.. @ */-{{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}},-/* GC.CU.. @ */-{{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439},-{ -100, -769, -359, -359, -439}}},-/* GC.G@.. @ */-{{{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GA.. @ */-{{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GC.. @ */-{{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GG.. @ */-{{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}},-/* GC.GU.. @ */-{{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789},-{ -100, -759, -789, -669, -789}}},-/* GC.U@.. @ */-{{{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UA.. @ */-{{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UC.. @ */-{{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UG.. @ */-{{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}},-/* GC.UU.. @ */-{{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619},-{ -100, -549, -549, -549, -619}}}}},-{ /* noPair */ {{{{0}}}},-/* GU.@@..CG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* GU.@C..CG */-{{    0,    0,    0,    0,    0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* GU.@G..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* GU.@U..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* GU.A@..CG */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -569, -948,-1118,-1118,-1118},-{ -989,-1368,-1538,-1538,-1538},-{ -859,-1238,-1408,-1408,-1408}},-/* GU.AC..CG */-{{  DEF, -429, -599, -599, -599},-{ -999,-1378,-1548,-1548,-1548},-{ -499, -878,-1048,-1048,-1048},-{ -989,-1368,-1538,-1538,-1538},-{ -789,-1168,-1338,-1338,-1338}},-/* GU.AG..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -569, -948,-1118,-1118,-1118},-{ -989,-1368,-1538,-1538,-1538},-{ -859,-1238,-1408,-1408,-1408}},-/* GU.AU..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -719,-1098,-1268,-1268,-1268},-{ -989,-1368,-1538,-1538,-1538},-{ -909,-1288,-1458,-1458,-1458}}},-/* GU.C@..CG */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -569, -778, -758, -758, -758},-{ -989,-1198,-1178,-1178,-1178},-{ -859,-1068,-1048,-1048,-1048}},-/* GU.CC..CG */-{{  DEF, -259, -239, -239, -239},-{ -999,-1208,-1188,-1188,-1188},-{ -499, -708, -688, -688, -688},-{ -989,-1198,-1178,-1178,-1178},-{ -789, -998, -978, -978, -978}},-/* GU.CG..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -569, -778, -758, -758, -758},-{ -989,-1198,-1178,-1178,-1178},-{ -859,-1068,-1048,-1048,-1048}},-/* GU.CU..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -719, -928, -908, -908, -908},-{ -989,-1198,-1178,-1178,-1178},-{ -909,-1118,-1098,-1098,-1098}}},-/* GU.G@..CG */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -569, -858,-1208,-1208,-1208},-{ -989,-1278,-1628,-1628,-1628},-{ -859,-1148,-1498,-1498,-1498}},-/* GU.GC..CG */-{{  DEF, -339, -689, -689, -689},-{ -999,-1288,-1638,-1638,-1638},-{ -499, -788,-1138,-1138,-1138},-{ -989,-1278,-1628,-1628,-1628},-{ -789,-1078,-1428,-1428,-1428}},-/* GU.GG..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -569, -858,-1208,-1208,-1208},-{ -989,-1278,-1628,-1628,-1628},-{ -859,-1148,-1498,-1498,-1498}},-/* GU.GU..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -719,-1008,-1358,-1358,-1358},-{ -989,-1278,-1628,-1628,-1628},-{ -909,-1198,-1548,-1548,-1548}}},-/* GU.U@..CG */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -569, -848, -848, -848, -848},-{ -989,-1268,-1268,-1268,-1268},-{ -859,-1138,-1138,-1138,-1138}},-/* GU.UC..CG */-{{  DEF, -329, -329, -329, -329},-{ -999,-1278,-1278,-1278,-1278},-{ -499, -778, -778, -778, -778},-{ -989,-1268,-1268,-1268,-1268},-{ -789,-1068,-1068,-1068,-1068}},-/* GU.UG..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -569, -848, -848, -848, -848},-{ -989,-1268,-1268,-1268,-1268},-{ -859,-1138,-1138,-1138,-1138}},-/* GU.UU..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -719, -998, -998, -998, -998},-{ -989,-1268,-1268,-1268,-1268},-{ -909,-1188,-1188,-1188,-1188}}}},-/* GU.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* GU.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* GU.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* GU.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* GU.A@..GC */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..GC */-{{  DEF, -429, -599, -599, -599},-{ -569, -948,-1118,-1118,-1118},-{ -769,-1148,-1318,-1318,-1318},-{ -759,-1138,-1308,-1308,-1308},-{ -549, -928,-1098,-1098,-1098}},-/* GU.AC..GC */-{{  DEF, -429, -599, -599, -599},-{ -929,-1308,-1478,-1478,-1478},-{ -359, -738, -908, -908, -908},-{ -789,-1168,-1338,-1338,-1338},-{ -549, -928,-1098,-1098,-1098}},-/* GU.AG..GC */-{{  DEF, -429, -599, -599, -599},-{ -609, -988,-1158,-1158,-1158},-{ -359, -738, -908, -908, -908},-{ -669,-1048,-1218,-1218,-1218},-{ -549, -928,-1098,-1098,-1098}},-/* GU.AU..GC */-{{  DEF, -429, -599, -599, -599},-{ -929,-1308,-1478,-1478,-1478},-{ -439, -818, -988, -988, -988},-{ -789,-1168,-1338,-1338,-1338},-{ -619, -998,-1168,-1168,-1168}}},-/* GU.C@..GC */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..GC */-{{  DEF, -259, -239, -239, -239},-{ -569, -778, -758, -758, -758},-{ -769, -978, -958, -958, -958},-{ -759, -968, -948, -948, -948},-{ -549, -758, -738, -738, -738}},-/* GU.CC..GC */-{{  DEF, -259, -239, -239, -239},-{ -929,-1138,-1118,-1118,-1118},-{ -359, -568, -548, -548, -548},-{ -789, -998, -978, -978, -978},-{ -549, -758, -738, -738, -738}},-/* GU.CG..GC */-{{  DEF, -259, -239, -239, -239},-{ -609, -818, -798, -798, -798},-{ -359, -568, -548, -548, -548},-{ -669, -878, -858, -858, -858},-{ -549, -758, -738, -738, -738}},-/* GU.CU..GC */-{{  DEF, -259, -239, -239, -239},-{ -929,-1138,-1118,-1118,-1118},-{ -439, -648, -628, -628, -628},-{ -789, -998, -978, -978, -978},-{ -619, -828, -808, -808, -808}}},-/* GU.G@..GC */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA..GC */-{{  DEF, -339, -689, -689, -689},-{ -569, -858,-1208,-1208,-1208},-{ -769,-1058,-1408,-1408,-1408},-{ -759,-1048,-1398,-1398,-1398},-{ -549, -838,-1188,-1188,-1188}},-/* GU.GC..GC */-{{  DEF, -339, -689, -689, -689},-{ -929,-1218,-1568,-1568,-1568},-{ -359, -648, -998, -998, -998},-{ -789,-1078,-1428,-1428,-1428},-{ -549, -838,-1188,-1188,-1188}},-/* GU.GG..GC */-{{  DEF, -339, -689, -689, -689},-{ -609, -898,-1248,-1248,-1248},-{ -359, -648, -998, -998, -998},-{ -669, -958,-1308,-1308,-1308},-{ -549, -838,-1188,-1188,-1188}},-/* GU.GU..GC */-{{  DEF, -339, -689, -689, -689},-{ -929,-1218,-1568,-1568,-1568},-{ -439, -728,-1078,-1078,-1078},-{ -789,-1078,-1428,-1428,-1428},-{ -619, -908,-1258,-1258,-1258}}},-/* GU.U@..GC */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..GC */-{{  DEF, -329, -329, -329, -329},-{ -569, -848, -848, -848, -848},-{ -769,-1048,-1048,-1048,-1048},-{ -759,-1038,-1038,-1038,-1038},-{ -549, -828, -828, -828, -828}},-/* GU.UC..GC */-{{  DEF, -329, -329, -329, -329},-{ -929,-1208,-1208,-1208,-1208},-{ -359, -638, -638, -638, -638},-{ -789,-1068,-1068,-1068,-1068},-{ -549, -828, -828, -828, -828}},-/* GU.UG..GC */-{{  DEF, -329, -329, -329, -329},-{ -609, -888, -888, -888, -888},-{ -359, -638, -638, -638, -638},-{ -669, -948, -948, -948, -948},-{ -549, -828, -828, -828, -828}},-/* GU.UU..GC */-{{  DEF, -329, -329, -329, -329},-{ -929,-1208,-1208,-1208,-1208},-{ -439, -718, -718, -718, -718},-{ -789,-1068,-1068,-1068,-1068},-{ -619, -898, -898, -898, -898}}}},-/* GU.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* GU.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GU.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GU.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* GU.A@..GU */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..GU */-{{  DEF, -429, -599, -599, -599},-{ -479, -858,-1028,-1028,-1028},-{ -309, -688, -858, -858, -858},-{ -389, -768, -938, -938, -938},-{ -379, -758, -928, -928, -928}},-/* GU.AC..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* GU.AG..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* GU.AU..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}}},-/* GU.C@..GU */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..GU */-{{  DEF, -259, -239, -239, -239},-{ -479, -688, -668, -668, -668},-{ -309, -518, -498, -498, -498},-{ -389, -598, -578, -578, -578},-{ -379, -588, -568, -568, -568}},-/* GU.CC..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* GU.CG..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* GU.CU..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}}},-/* GU.G@..GU */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA..GU */-{{  DEF, -339, -689, -689, -689},-{ -479, -768,-1118,-1118,-1118},-{ -309, -598, -948, -948, -948},-{ -389, -678,-1028,-1028,-1028},-{ -379, -668,-1018,-1018,-1018}},-/* GU.GC..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* GU.GG..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* GU.GU..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}}},-/* GU.U@..GU */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..GU */-{{  DEF, -329, -329, -329, -329},-{ -479, -758, -758, -758, -758},-{ -309, -588, -588, -588, -588},-{ -389, -668, -668, -668, -668},-{ -379, -658, -658, -658, -658}},-/* GU.UC..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* GU.UG..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* GU.UU..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}}}},-/* GU.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* GU.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* GU.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* GU.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* GU.A@..UG */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..UG */-{{  DEF, -429, -599, -599, -599},-{ -769,-1148,-1318,-1318,-1318},-{ -529, -908,-1078,-1078,-1078},-{ -709,-1088,-1258,-1258,-1258},-{ -599, -978,-1148,-1148,-1148}},-/* GU.AC..UG */-{{  DEF, -429, -599, -599, -599},-{ -839,-1218,-1388,-1388,-1388},-{ -529, -908,-1078,-1078,-1078},-{ -859,-1238,-1408,-1408,-1408},-{ -489, -868,-1038,-1038,-1038}},-/* GU.AG..UG */-{{  DEF, -429, -599, -599, -599},-{-1009,-1388,-1558,-1558,-1558},-{ -409, -788, -958, -958, -958},-{ -969,-1348,-1518,-1518,-1518},-{ -599, -978,-1148,-1148,-1148}},-/* GU.AU..UG */-{{  DEF, -429, -599, -599, -599},-{ -859,-1238,-1408,-1408,-1408},-{ -529, -908,-1078,-1078,-1078},-{ -859,-1238,-1408,-1408,-1408},-{ -409, -788, -958, -958, -958}}},-/* GU.C@..UG */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..UG */-{{  DEF, -259, -239, -239, -239},-{ -769, -978, -958, -958, -958},-{ -529, -738, -718, -718, -718},-{ -709, -918, -898, -898, -898},-{ -599, -808, -788, -788, -788}},-/* GU.CC..UG */-{{  DEF, -259, -239, -239, -239},-{ -839,-1048,-1028,-1028,-1028},-{ -529, -738, -718, -718, -718},-{ -859,-1068,-1048,-1048,-1048},-{ -489, -698, -678, -678, -678}},-/* GU.CG..UG */-{{  DEF, -259, -239, -239, -239},-{-1009,-1218,-1198,-1198,-1198},-{ -409, -618, -598, -598, -598},-{ -969,-1178,-1158,-1158,-1158},-{ -599, -808, -788, -788, -788}},-/* GU.CU..UG */-{{  DEF, -259, -239, -239, -239},-{ -859,-1068,-1048,-1048,-1048},-{ -529, -738, -718, -718, -718},-{ -859,-1068,-1048,-1048,-1048},-{ -409, -618, -598, -598, -598}}},-/* GU.G@..UG */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA..UG */-{{  DEF, -339, -689, -689, -689},-{ -769,-1058,-1408,-1408,-1408},-{ -529, -818,-1168,-1168,-1168},-{ -709, -998,-1348,-1348,-1348},-{ -599, -888,-1238,-1238,-1238}},-/* GU.GC..UG */-{{  DEF, -339, -689, -689, -689},-{ -839,-1128,-1478,-1478,-1478},-{ -529, -818,-1168,-1168,-1168},-{ -859,-1148,-1498,-1498,-1498},-{ -489, -778,-1128,-1128,-1128}},-/* GU.GG..UG */-{{  DEF, -339, -689, -689, -689},-{-1009,-1298,-1648,-1648,-1648},-{ -409, -698,-1048,-1048,-1048},-{ -969,-1258,-1608,-1608,-1608},-{ -599, -888,-1238,-1238,-1238}},-/* GU.GU..UG */-{{  DEF, -339, -689, -689, -689},-{ -859,-1148,-1498,-1498,-1498},-{ -529, -818,-1168,-1168,-1168},-{ -859,-1148,-1498,-1498,-1498},-{ -409, -698,-1048,-1048,-1048}}},-/* GU.U@..UG */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..UG */-{{  DEF, -329, -329, -329, -329},-{ -769,-1048,-1048,-1048,-1048},-{ -529, -808, -808, -808, -808},-{ -709, -988, -988, -988, -988},-{ -599, -878, -878, -878, -878}},-/* GU.UC..UG */-{{  DEF, -329, -329, -329, -329},-{ -839,-1118,-1118,-1118,-1118},-{ -529, -808, -808, -808, -808},-{ -859,-1138,-1138,-1138,-1138},-{ -489, -768, -768, -768, -768}},-/* GU.UG..UG */-{{  DEF, -329, -329, -329, -329},-{-1009,-1288,-1288,-1288,-1288},-{ -409, -688, -688, -688, -688},-{ -969,-1248,-1248,-1248,-1248},-{ -599, -878, -878, -878, -878}},-/* GU.UU..UG */-{{  DEF, -329, -329, -329, -329},-{ -859,-1138,-1138,-1138,-1138},-{ -529, -808, -808, -808, -808},-{ -859,-1138,-1138,-1138,-1138},-{ -409, -688, -688, -688, -688}}}},-/* GU.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* GU.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GU.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* GU.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* GU.A@..AU */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..AU */-{{  DEF, -429, -599, -599, -599},-{ -479, -858,-1028,-1028,-1028},-{ -309, -688, -858, -858, -858},-{ -389, -768, -938, -938, -938},-{ -379, -758, -928, -928, -928}},-/* GU.AC..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* GU.AG..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* GU.AU..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}}},-/* GU.C@..AU */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..AU */-{{  DEF, -259, -239, -239, -239},-{ -479, -688, -668, -668, 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-668,-1018,-1018,-1018}},-/* GU.GC..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* GU.GG..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* GU.GU..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}}},-/* GU.U@..AU */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..AU */-{{  DEF, -329, -329, -329, -329},-{ -479, -758, -758, -758, -758},-{ -309, -588, -588, -588, -588},-{ -389, -668, -668, -668, -668},-{ -379, -658, -658, -658, -658}},-/* GU.UC..AU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* GU.UG..AU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* GU.UU..AU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}}}},-/* GU.@@..UA */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* GU.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* GU.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* GU.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* GU.A@..UA */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA..UA */-{{  DEF, -429, -599, -599, -599},-{ -449, -828, -998, -998, -998},-{ -479, -858,-1028,-1028,-1028},-{ -429, -808, -978, -978, -978},-{ -329, -708, -878, -878, -878}},-/* GU.AC..UA */-{{  DEF, -429, -599, -599, -599},-{ -679,-1058,-1228,-1228,-1228},-{ -559, -938,-1108,-1108,-1108},-{ -729,-1108,-1278,-1278,-1278},-{ -189, -568, -738, -738, -738}},-/* GU.AG..UA */-{{  DEF, -429, -599, -599, -599},-{ -939,-1318,-1488,-1488,-1488},-{ -249, -628, -798, -798, -798},-{ -939,-1318,-1488,-1488,-1488},-{ -329, -708, -878, -878, -878}},-/* GU.AU..UA */-{{  DEF, -429, -599, -599, -599},-{ -639,-1018,-1188,-1188,-1188},-{ -229, -608, -778, -778, -778},-{ -729,-1108,-1278,-1278,-1278},-{ -190, -569, -739, -739, -739}}},-/* GU.C@..UA */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA..UA */-{{  DEF, -259, -239, -239, -239},-{ -449, -658, -638, -638, -638},-{ -479, -688, -668, -668, -668},-{ -429, -638, -618, -618, -618},-{ -329, -538, -518, -518, -518}},-/* GU.CC..UA */-{{  DEF, -259, -239, -239, -239},-{ -679, -888, -868, -868, -868},-{ -559, -768, -748, -748, -748},-{ -729, -938, -918, -918, -918},-{ -189, -398, -378, -378, -378}},-/* GU.CG..UA */-{{  DEF, -259, -239, -239, -239},-{ -939,-1148,-1128,-1128,-1128},-{ -249, -458, -438, -438, -438},-{ -939,-1148,-1128,-1128,-1128},-{ -329, -538, -518, -518, -518}},-/* GU.CU..UA */-{{  DEF, -259, -239, -239, -239},-{ -639, -848, -828, -828, -828},-{ -229, -438, -418, -418, -418},-{ -729, -938, -918, -918, -918},-{ -190, -399, -379, -379, -379}}},-/* GU.G@..UA */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA..UA */-{{  DEF, -339, -689, -689, -689},-{ -449, -738,-1088,-1088,-1088},-{ -479, -768,-1118,-1118,-1118},-{ -429, -718,-1068,-1068,-1068},-{ -329, -618, -968, -968, -968}},-/* GU.GC..UA */-{{  DEF, -339, -689, -689, -689},-{ -679, -968,-1318,-1318,-1318},-{ -559, -848,-1198,-1198,-1198},-{ -729,-1018,-1368,-1368,-1368},-{ -189, -478, -828, -828, -828}},-/* GU.GG..UA */-{{  DEF, -339, -689, -689, -689},-{ -939,-1228,-1578,-1578,-1578},-{ -249, -538, -888, -888, -888},-{ -939,-1228,-1578,-1578,-1578},-{ -329, -618, -968, -968, -968}},-/* GU.GU..UA */-{{  DEF, -339, -689, -689, -689},-{ -639, -928,-1278,-1278,-1278},-{ -229, -518, -868, -868, -868},-{ -729,-1018,-1368,-1368,-1368},-{ -190, -479, -829, -829, -829}}},-/* GU.U@..UA */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA..UA */-{{  DEF, -329, -329, -329, -329},-{ -449, -728, -728, -728, -728},-{ -479, -758, -758, -758, -758},-{ -429, -708, -708, -708, -708},-{ -329, -608, -608, -608, -608}},-/* GU.UC..UA */-{{  DEF, -329, -329, -329, -329},-{ -679, -958, -958, -958, -958},-{ -559, -838, -838, -838, -838},-{ -729,-1008,-1008,-1008,-1008},-{ -189, -468, -468, -468, -468}},-/* GU.UG..UA */-{{  DEF, -329, -329, -329, -329},-{ -939,-1218,-1218,-1218,-1218},-{ -249, -528, -528, -528, -528},-{ -939,-1218,-1218,-1218,-1218},-{ -329, -608, -608, -608, -608}},-/* GU.UU..UA */-{{  DEF, -329, -329, -329, -329},-{ -639, -918, -918, -918, -918},-{ -229, -508, -508, -508, -508},-{ -729,-1008,-1008,-1008,-1008},-{ -190, -469, -469, -469, -469}}}},-/* GU.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* GU.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* GU.A@.. @ */-{{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AA.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AC.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AG.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* GU.AU.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}}},-/* GU.C@.. @ */-{{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CA.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CC.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CG.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* GU.CU.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}}},-/* GU.G@.. @ */-{{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GA.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GC.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GG.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* GU.GU.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}}},-/* GU.U@.. @ */-{{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UA.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UC.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UG.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* GU.UU.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}}}}},-{ /* noPair */ {{{{0}}}},-/* UG.@@..CG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* UG.@C..CG */-{{    0,    0,    0,    0,    0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* UG.@G..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* UG.@U..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* UG.A@..CG */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..CG */-{{  DEF, -719, -789, -959, -809},-{-1079,-1748,-1818,-1988,-1838},-{ -569,-1238,-1308,-1478,-1328},-{ -989,-1658,-1728,-1898,-1748},-{ -859,-1528,-1598,-1768,-1618}},-/* UG.AC..CG */-{{  DEF, -719, -789, -959, -809},-{ -999,-1668,-1738,-1908,-1758},-{ -499,-1168,-1238,-1408,-1258},-{ -989,-1658,-1728,-1898,-1748},-{ -789,-1458,-1528,-1698,-1548}},-/* UG.AG..CG */-{{  DEF, -719, -789, -959, -809},-{-1079,-1748,-1818,-1988,-1838},-{ -569,-1238,-1308,-1478,-1328},-{ -989,-1658,-1728,-1898,-1748},-{ -859,-1528,-1598,-1768,-1618}},-/* UG.AU..CG */-{{  DEF, -719, -789, -959, -809},-{-1079,-1748,-1818,-1988,-1838},-{ -719,-1388,-1458,-1628,-1478},-{ -989,-1658,-1728,-1898,-1748},-{ -909,-1578,-1648,-1818,-1668}}},-/* UG.C@..CG */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..CG */-{{  DEF, -479, -479, -359, -479},-{-1079,-1508,-1508,-1388,-1508},-{ -569, -998, -998, -878, -998},-{ -989,-1418,-1418,-1298,-1418},-{ -859,-1288,-1288,-1168,-1288}},-/* UG.CC..CG */-{{  DEF, -479, -479, -359, -479},-{ -999,-1428,-1428,-1308,-1428},-{ -499, -928, -928, -808, -928},-{ -989,-1418,-1418,-1298,-1418},-{ -789,-1218,-1218,-1098,-1218}},-/* UG.CG..CG */-{{  DEF, -479, -479, -359, -479},-{-1079,-1508,-1508,-1388,-1508},-{ -569, -998, -998, -878, -998},-{ -989,-1418,-1418,-1298,-1418},-{ -859,-1288,-1288,-1168,-1288}},-/* UG.CU..CG */-{{  DEF, -479, -479, -359, -479},-{-1079,-1508,-1508,-1388,-1508},-{ -719,-1148,-1148,-1028,-1148},-{ -989,-1418,-1418,-1298,-1418},-{ -909,-1338,-1338,-1218,-1338}}},-/* UG.G@..CG */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..CG */-{{  DEF, -659, -809, -919, -809},-{-1079,-1688,-1838,-1948,-1838},-{ -569,-1178,-1328,-1438,-1328},-{ -989,-1598,-1748,-1858,-1748},-{ -859,-1468,-1618,-1728,-1618}},-/* UG.GC..CG */-{{  DEF, -659, -809, -919, -809},-{ -999,-1608,-1758,-1868,-1758},-{ -499,-1108,-1258,-1368,-1258},-{ -989,-1598,-1748,-1858,-1748},-{ -789,-1398,-1548,-1658,-1548}},-/* UG.GG..CG */-{{  DEF, -659, -809, -919, -809},-{-1079,-1688,-1838,-1948,-1838},-{ -569,-1178,-1328,-1438,-1328},-{ -989,-1598,-1748,-1858,-1748},-{ -859,-1468,-1618,-1728,-1618}},-/* UG.GU..CG */-{{  DEF, -659, -809, -919, -809},-{-1079,-1688,-1838,-1948,-1838},-{ -719,-1328,-1478,-1588,-1478},-{ -989,-1598,-1748,-1858,-1748},-{ -909,-1518,-1668,-1778,-1668}}},-/* UG.U@..CG */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..CG */-{{  DEF, -549, -439, -549, -359},-{-1079,-1578,-1468,-1578,-1388},-{ -569,-1068, -958,-1068, -878},-{ -989,-1488,-1378,-1488,-1298},-{ -859,-1358,-1248,-1358,-1168}},-/* UG.UC..CG */-{{  DEF, -549, -439, -549, -359},-{ -999,-1498,-1388,-1498,-1308},-{ -499, -998, -888, -998, -808},-{ -989,-1488,-1378,-1488,-1298},-{ -789,-1288,-1178,-1288,-1098}},-/* UG.UG..CG */-{{  DEF, -549, -439, -549, -359},-{-1079,-1578,-1468,-1578,-1388},-{ -569,-1068, -958,-1068, -878},-{ -989,-1488,-1378,-1488,-1298},-{ -859,-1358,-1248,-1358,-1168}},-/* UG.UU..CG */-{{  DEF, -549, -439, -549, -359},-{-1079,-1578,-1468,-1578,-1388},-{ -719,-1218,-1108,-1218,-1028},-{ -989,-1488,-1378,-1488,-1298},-{ -909,-1408,-1298,-1408,-1218}}}},-/* UG.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* UG.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* UG.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* UG.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* UG.A@..GC */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..GC */-{{  DEF, -719, -789, -959, -809},-{ -569,-1238,-1308,-1478,-1328},-{ -769,-1438,-1508,-1678,-1528},-{ -759,-1428,-1498,-1668,-1518},-{ -549,-1218,-1288,-1458,-1308}},-/* UG.AC..GC */-{{  DEF, -719, -789, -959, -809},-{ -929,-1598,-1668,-1838,-1688},-{ -359,-1028,-1098,-1268,-1118},-{ -789,-1458,-1528,-1698,-1548},-{ -549,-1218,-1288,-1458,-1308}},-/* UG.AG..GC */-{{  DEF, -719, -789, -959, -809},-{ -609,-1278,-1348,-1518,-1368},-{ -359,-1028,-1098,-1268,-1118},-{ -669,-1338,-1408,-1578,-1428},-{ -549,-1218,-1288,-1458,-1308}},-/* UG.AU..GC */-{{  DEF, -719, -789, -959, -809},-{ -929,-1598,-1668,-1838,-1688},-{ -439,-1108,-1178,-1348,-1198},-{ -789,-1458,-1528,-1698,-1548},-{ -619,-1288,-1358,-1528,-1378}}},-/* UG.C@..GC */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..GC */-{{  DEF, -479, -479, -359, -479},-{ -569, -998, -998, -878, -998},-{ -769,-1198,-1198,-1078,-1198},-{ -759,-1188,-1188,-1068,-1188},-{ -549, -978, -978, -858, -978}},-/* UG.CC..GC */-{{  DEF, -479, -479, -359, -479},-{ -929,-1358,-1358,-1238,-1358},-{ -359, -788, -788, -668, -788},-{ -789,-1218,-1218,-1098,-1218},-{ -549, -978, -978, -858, -978}},-/* UG.CG..GC */-{{  DEF, -479, -479, -359, -479},-{ -609,-1038,-1038, -918,-1038},-{ -359, -788, -788, -668, -788},-{ -669,-1098,-1098, -978,-1098},-{ -549, -978, -978, -858, -978}},-/* UG.CU..GC */-{{  DEF, -479, -479, -359, -479},-{ -929,-1358,-1358,-1238,-1358},-{ -439, -868, -868, -748, -868},-{ -789,-1218,-1218,-1098,-1218},-{ -619,-1048,-1048, -928,-1048}}},-/* UG.G@..GC */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..GC */-{{  DEF, -659, -809, -919, -809},-{ -569,-1178,-1328,-1438,-1328},-{ -769,-1378,-1528,-1638,-1528},-{ -759,-1368,-1518,-1628,-1518},-{ -549,-1158,-1308,-1418,-1308}},-/* UG.GC..GC */-{{  DEF, -659, -809, -919, -809},-{ -929,-1538,-1688,-1798,-1688},-{ -359, -968,-1118,-1228,-1118},-{ -789,-1398,-1548,-1658,-1548},-{ -549,-1158,-1308,-1418,-1308}},-/* UG.GG..GC */-{{  DEF, -659, -809, -919, -809},-{ -609,-1218,-1368,-1478,-1368},-{ -359, -968,-1118,-1228,-1118},-{ -669,-1278,-1428,-1538,-1428},-{ -549,-1158,-1308,-1418,-1308}},-/* UG.GU..GC */-{{  DEF, -659, -809, -919, -809},-{ -929,-1538,-1688,-1798,-1688},-{ -439,-1048,-1198,-1308,-1198},-{ -789,-1398,-1548,-1658,-1548},-{ -619,-1228,-1378,-1488,-1378}}},-/* UG.U@..GC */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..GC */-{{  DEF, -549, -439, -549, -359},-{ -569,-1068, -958,-1068, -878},-{ -769,-1268,-1158,-1268,-1078},-{ -759,-1258,-1148,-1258,-1068},-{ -549,-1048, -938,-1048, -858}},-/* UG.UC..GC */-{{  DEF, -549, -439, -549, -359},-{ -929,-1428,-1318,-1428,-1238},-{ -359, -858, -748, -858, -668},-{ -789,-1288,-1178,-1288,-1098},-{ -549,-1048, -938,-1048, -858}},-/* UG.UG..GC */-{{  DEF, -549, -439, -549, -359},-{ -609,-1108, -998,-1108, -918},-{ -359, -858, -748, -858, -668},-{ -669,-1168,-1058,-1168, -978},-{ -549,-1048, -938,-1048, -858}},-/* UG.UU..GC */-{{  DEF, -549, -439, -549, -359},-{ -929,-1428,-1318,-1428,-1238},-{ -439, -938, -828, -938, -748},-{ -789,-1288,-1178,-1288,-1098},-{ -619,-1118,-1008,-1118, -928}}}},-/* UG.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* UG.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UG.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UG.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* UG.A@..GU */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..GU */-{{  DEF, -719, -789, -959, -809},-{ -479,-1148,-1218,-1388,-1238},-{ -309, -978,-1048,-1218,-1068},-{ -389,-1058,-1128,-1298,-1148},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AC..GU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AG..GU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AU..GU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}}},-/* UG.C@..GU */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..GU */-{{  DEF, -479, -479, -359, -479},-{ -479, -908, -908, -788, -908},-{ -309, -738, -738, -618, -738},-{ -389, -818, -818, -698, -818},-{ -379, -808, -808, -688, -808}},-/* UG.CC..GU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}},-/* UG.CG..GU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}},-/* UG.CU..GU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}}},-/* UG.G@..GU */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..GU */-{{  DEF, -659, -809, -919, -809},-{ -479,-1088,-1238,-1348,-1238},-{ -309, -918,-1068,-1178,-1068},-{ -389, -998,-1148,-1258,-1148},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GC..GU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GG..GU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GU..GU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}}},-/* UG.U@..GU */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..GU */-{{  DEF, -549, -439, -549, -359},-{ -479, -978, -868, -978, -788},-{ -309, -808, -698, -808, -618},-{ -389, -888, -778, -888, -698},-{ -379, -878, -768, -878, -688}},-/* UG.UC..GU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}},-/* UG.UG..GU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}},-/* UG.UU..GU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}}}},-/* UG.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* UG.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* UG.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* UG.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* UG.A@..UG */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..UG */-{{  DEF, -719, -789, -959, -809},-{ -769,-1438,-1508,-1678,-1528},-{ -529,-1198,-1268,-1438,-1288},-{ -709,-1378,-1448,-1618,-1468},-{ -599,-1268,-1338,-1508,-1358}},-/* UG.AC..UG */-{{  DEF, -719, -789, -959, -809},-{ -839,-1508,-1578,-1748,-1598},-{ -529,-1198,-1268,-1438,-1288},-{ -859,-1528,-1598,-1768,-1618},-{ -489,-1158,-1228,-1398,-1248}},-/* UG.AG..UG */-{{  DEF, -719, -789, -959, -809},-{-1009,-1678,-1748,-1918,-1768},-{ -409,-1078,-1148,-1318,-1168},-{ -969,-1638,-1708,-1878,-1728},-{ -599,-1268,-1338,-1508,-1358}},-/* UG.AU..UG */-{{  DEF, -719, -789, -959, -809},-{ -859,-1528,-1598,-1768,-1618},-{ -529,-1198,-1268,-1438,-1288},-{ -859,-1528,-1598,-1768,-1618},-{ -409,-1078,-1148,-1318,-1168}}},-/* UG.C@..UG */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..UG */-{{  DEF, -479, -479, -359, -479},-{ -769,-1198,-1198,-1078,-1198},-{ -529, -958, -958, -838, -958},-{ -709,-1138,-1138,-1018,-1138},-{ -599,-1028,-1028, -908,-1028}},-/* UG.CC..UG */-{{  DEF, -479, -479, -359, -479},-{ -839,-1268,-1268,-1148,-1268},-{ -529, -958, -958, -838, -958},-{ -859,-1288,-1288,-1168,-1288},-{ -489, -918, -918, -798, -918}},-/* UG.CG..UG */-{{  DEF, -479, -479, -359, -479},-{-1009,-1438,-1438,-1318,-1438},-{ -409, -838, -838, -718, -838},-{ -969,-1398,-1398,-1278,-1398},-{ -599,-1028,-1028, -908,-1028}},-/* UG.CU..UG */-{{  DEF, -479, -479, -359, -479},-{ -859,-1288,-1288,-1168,-1288},-{ -529, -958, -958, -838, -958},-{ -859,-1288,-1288,-1168,-1288},-{ -409, -838, -838, -718, -838}}},-/* UG.G@..UG */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..UG */-{{  DEF, -659, -809, -919, -809},-{ -769,-1378,-1528,-1638,-1528},-{ -529,-1138,-1288,-1398,-1288},-{ -709,-1318,-1468,-1578,-1468},-{ -599,-1208,-1358,-1468,-1358}},-/* UG.GC..UG */-{{  DEF, -659, -809, -919, -809},-{ -839,-1448,-1598,-1708,-1598},-{ -529,-1138,-1288,-1398,-1288},-{ -859,-1468,-1618,-1728,-1618},-{ -489,-1098,-1248,-1358,-1248}},-/* UG.GG..UG */-{{  DEF, -659, -809, -919, -809},-{-1009,-1618,-1768,-1878,-1768},-{ -409,-1018,-1168,-1278,-1168},-{ -969,-1578,-1728,-1838,-1728},-{ -599,-1208,-1358,-1468,-1358}},-/* UG.GU..UG */-{{  DEF, -659, -809, -919, -809},-{ -859,-1468,-1618,-1728,-1618},-{ -529,-1138,-1288,-1398,-1288},-{ -859,-1468,-1618,-1728,-1618},-{ -409,-1018,-1168,-1278,-1168}}},-/* UG.U@..UG */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..UG */-{{  DEF, -549, -439, -549, -359},-{ -769,-1268,-1158,-1268,-1078},-{ -529,-1028, -918,-1028, -838},-{ -709,-1208,-1098,-1208,-1018},-{ -599,-1098, -988,-1098, -908}},-/* UG.UC..UG */-{{  DEF, -549, -439, -549, -359},-{ -839,-1338,-1228,-1338,-1148},-{ -529,-1028, -918,-1028, -838},-{ -859,-1358,-1248,-1358,-1168},-{ -489, -988, -878, -988, -798}},-/* UG.UG..UG */-{{  DEF, -549, -439, -549, -359},-{-1009,-1508,-1398,-1508,-1318},-{ -409, -908, -798, -908, -718},-{ -969,-1468,-1358,-1468,-1278},-{ -599,-1098, -988,-1098, -908}},-/* UG.UU..UG */-{{  DEF, -549, -439, -549, -359},-{ -859,-1358,-1248,-1358,-1168},-{ -529,-1028, -918,-1028, -838},-{ -859,-1358,-1248,-1358,-1168},-{ -409, -908, -798, -908, -718}}}},-/* UG.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* UG.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UG.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UG.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* UG.A@..AU */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..AU */-{{  DEF, -719, -789, -959, -809},-{ -479,-1148,-1218,-1388,-1238},-{ -309, -978,-1048,-1218,-1068},-{ -389,-1058,-1128,-1298,-1148},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AC..AU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AG..AU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}},-/* UG.AU..AU */-{{  DEF, -719, -789, -959, -809},-{ -649,-1318,-1388,-1558,-1408},-{ -289, -958,-1028,-1198,-1048},-{ -739,-1408,-1478,-1648,-1498},-{ -379,-1048,-1118,-1288,-1138}}},-/* UG.C@..AU */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..AU */-{{  DEF, -479, -479, -359, -479},-{ -479, -908, -908, -788, -908},-{ -309, -738, -738, -618, -738},-{ -389, -818, -818, -698, -818},-{ -379, -808, -808, -688, -808}},-/* UG.CC..AU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}},-/* UG.CG..AU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}},-/* UG.CU..AU */-{{  DEF, -479, -479, -359, -479},-{ -649,-1078,-1078, -958,-1078},-{ -289, -718, -718, -598, -718},-{ -739,-1168,-1168,-1048,-1168},-{ -379, -808, -808, -688, -808}}},-/* UG.G@..AU */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..AU */-{{  DEF, -659, -809, -919, -809},-{ -479,-1088,-1238,-1348,-1238},-{ -309, -918,-1068,-1178,-1068},-{ -389, -998,-1148,-1258,-1148},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GC..AU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GG..AU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}},-/* UG.GU..AU */-{{  DEF, -659, -809, -919, -809},-{ -649,-1258,-1408,-1518,-1408},-{ -289, -898,-1048,-1158,-1048},-{ -739,-1348,-1498,-1608,-1498},-{ -379, -988,-1138,-1248,-1138}}},-/* UG.U@..AU */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..AU */-{{  DEF, -549, -439, -549, -359},-{ -479, -978, -868, -978, -788},-{ -309, -808, -698, -808, -618},-{ -389, -888, -778, -888, -698},-{ -379, -878, -768, -878, -688}},-/* UG.UC..AU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}},-/* UG.UG..AU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}},-/* UG.UU..AU */-{{  DEF, -549, -439, -549, -359},-{ -649,-1148,-1038,-1148, -958},-{ -289, -788, -678, -788, -598},-{ -739,-1238,-1128,-1238,-1048},-{ -379, -878, -768, -878, -688}}}},-/* UG.@@..UA */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* UG.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* UG.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* UG.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* UG.A@..UA */-{{{  DEF, -719, -789, -959, -809},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA..UA */-{{  DEF, -719, -789, -959, -809},-{ -449,-1118,-1188,-1358,-1208},-{ -479,-1148,-1218,-1388,-1238},-{ -429,-1098,-1168,-1338,-1188},-{ -329, -998,-1068,-1238,-1088}},-/* UG.AC..UA */-{{  DEF, -719, -789, -959, -809},-{ -679,-1348,-1418,-1588,-1438},-{ -559,-1228,-1298,-1468,-1318},-{ -729,-1398,-1468,-1638,-1488},-{ -189, -858, -928,-1098, -948}},-/* UG.AG..UA */-{{  DEF, -719, -789, -959, -809},-{ -939,-1608,-1678,-1848,-1698},-{ -249, -918, -988,-1158,-1008},-{ -939,-1608,-1678,-1848,-1698},-{ -329, -998,-1068,-1238,-1088}},-/* UG.AU..UA */-{{  DEF, -719, -789, -959, -809},-{ -639,-1308,-1378,-1548,-1398},-{ -229, -898, -968,-1138, -988},-{ -729,-1398,-1468,-1638,-1488},-{ -190, -859, -929,-1099, -949}}},-/* UG.C@..UA */-{{{  DEF, -479, -479, -359, -479},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA..UA */-{{  DEF, -479, -479, -359, -479},-{ -449, -878, -878, -758, -878},-{ -479, -908, -908, -788, -908},-{ -429, -858, -858, -738, -858},-{ -329, -758, -758, -638, -758}},-/* UG.CC..UA */-{{  DEF, -479, -479, -359, -479},-{ -679,-1108,-1108, -988,-1108},-{ -559, -988, -988, -868, -988},-{ -729,-1158,-1158,-1038,-1158},-{ -189, -618, -618, -498, -618}},-/* UG.CG..UA */-{{  DEF, -479, -479, -359, -479},-{ -939,-1368,-1368,-1248,-1368},-{ -249, -678, -678, -558, -678},-{ -939,-1368,-1368,-1248,-1368},-{ -329, -758, -758, -638, -758}},-/* UG.CU..UA */-{{  DEF, -479, -479, -359, -479},-{ -639,-1068,-1068, -948,-1068},-{ -229, -658, -658, -538, -658},-{ -729,-1158,-1158,-1038,-1158},-{ -190, -619, -619, -499, -619}}},-/* UG.G@..UA */-{{{  DEF, -659, -809, -919, -809},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA..UA */-{{  DEF, -659, -809, -919, -809},-{ -449,-1058,-1208,-1318,-1208},-{ -479,-1088,-1238,-1348,-1238},-{ -429,-1038,-1188,-1298,-1188},-{ -329, -938,-1088,-1198,-1088}},-/* UG.GC..UA */-{{  DEF, -659, -809, -919, -809},-{ -679,-1288,-1438,-1548,-1438},-{ -559,-1168,-1318,-1428,-1318},-{ -729,-1338,-1488,-1598,-1488},-{ -189, -798, -948,-1058, -948}},-/* UG.GG..UA */-{{  DEF, -659, -809, -919, -809},-{ -939,-1548,-1698,-1808,-1698},-{ -249, -858,-1008,-1118,-1008},-{ -939,-1548,-1698,-1808,-1698},-{ -329, -938,-1088,-1198,-1088}},-/* UG.GU..UA */-{{  DEF, -659, -809, -919, -809},-{ -639,-1248,-1398,-1508,-1398},-{ -229, -838, -988,-1098, -988},-{ -729,-1338,-1488,-1598,-1488},-{ -190, -799, -949,-1059, -949}}},-/* UG.U@..UA */-{{{  DEF, -549, -439, -549, -359},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA..UA */-{{  DEF, -549, -439, -549, -359},-{ -449, -948, -838, -948, -758},-{ -479, -978, -868, -978, -788},-{ -429, -928, -818, -928, -738},-{ -329, -828, -718, -828, -638}},-/* UG.UC..UA */-{{  DEF, -549, -439, -549, -359},-{ -679,-1178,-1068,-1178, -988},-{ -559,-1058, -948,-1058, -868},-{ -729,-1228,-1118,-1228,-1038},-{ -189, -688, -578, -688, -498}},-/* UG.UG..UA */-{{  DEF, -549, -439, -549, -359},-{ -939,-1438,-1328,-1438,-1248},-{ -249, -748, -638, -748, -558},-{ -939,-1438,-1328,-1438,-1248},-{ -329, -828, -718, -828, -638}},-/* UG.UU..UA */-{{  DEF, -549, -439, -549, -359},-{ -639,-1138,-1028,-1138, -948},-{ -229, -728, -618, -728, -538},-{ -729,-1228,-1118,-1228,-1038},-{ -190, -689, -579, -689, -499}}}},-/* UG.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UG.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* UG.A@.. @ */-{{{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AA.. @ */-{{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AC.. @ */-{{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AG.. @ */-{{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}},-/* UG.AU.. @ */-{{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859},-{ -100, -769, -839,-1009, -859}}},-/* UG.C@.. @ */-{{{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CA.. @ */-{{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CC.. @ */-{{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CG.. @ */-{{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}},-/* UG.CU.. @ */-{{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529},-{ -100, -529, -529, -409, -529}}},-/* UG.G@.. @ */-{{{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GA.. @ */-{{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GC.. @ */-{{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GG.. @ */-{{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}},-/* UG.GU.. @ */-{{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859},-{ -100, -709, -859, -969, -859}}},-/* UG.U@.. @ */-{{{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UA.. @ */-{{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UC.. @ */-{{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UG.. @ */-{{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}},-/* UG.UU.. @ */-{{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409},-{ -100, -599, -489, -599, -409}}}}},-{ /* noPair */ {{{{0}}}},-/* AU.@@..CG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* AU.@C..CG */-{{    0,    0,    0,    0,    0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* AU.@G..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* AU.@U..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* AU.A@..CG */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -569, -948,-1118,-1118,-1118},-{ -989,-1368,-1538,-1538,-1538},-{ -859,-1238,-1408,-1408,-1408}},-/* AU.AC..CG */-{{  DEF, -429, -599, -599, -599},-{ -999,-1378,-1548,-1548,-1548},-{ -499, -878,-1048,-1048,-1048},-{ -989,-1368,-1538,-1538,-1538},-{ -789,-1168,-1338,-1338,-1338}},-/* AU.AG..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -569, -948,-1118,-1118,-1118},-{ -989,-1368,-1538,-1538,-1538},-{ -859,-1238,-1408,-1408,-1408}},-/* AU.AU..CG */-{{  DEF, -429, -599, -599, -599},-{-1079,-1458,-1628,-1628,-1628},-{ -719,-1098,-1268,-1268,-1268},-{ -989,-1368,-1538,-1538,-1538},-{ -909,-1288,-1458,-1458,-1458}}},-/* AU.C@..CG */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -569, -778, -758, -758, -758},-{ -989,-1198,-1178,-1178,-1178},-{ -859,-1068,-1048,-1048,-1048}},-/* AU.CC..CG */-{{  DEF, -259, -239, -239, -239},-{ -999,-1208,-1188,-1188,-1188},-{ -499, -708, -688, -688, -688},-{ -989,-1198,-1178,-1178,-1178},-{ -789, -998, -978, -978, -978}},-/* AU.CG..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -569, -778, -758, -758, -758},-{ -989,-1198,-1178,-1178,-1178},-{ -859,-1068,-1048,-1048,-1048}},-/* AU.CU..CG */-{{  DEF, -259, -239, -239, -239},-{-1079,-1288,-1268,-1268,-1268},-{ -719, -928, -908, -908, -908},-{ -989,-1198,-1178,-1178,-1178},-{ -909,-1118,-1098,-1098,-1098}}},-/* AU.G@..CG */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -569, -858,-1208,-1208,-1208},-{ -989,-1278,-1628,-1628,-1628},-{ -859,-1148,-1498,-1498,-1498}},-/* AU.GC..CG */-{{  DEF, -339, -689, -689, -689},-{ -999,-1288,-1638,-1638,-1638},-{ -499, -788,-1138,-1138,-1138},-{ -989,-1278,-1628,-1628,-1628},-{ -789,-1078,-1428,-1428,-1428}},-/* AU.GG..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -569, -858,-1208,-1208,-1208},-{ -989,-1278,-1628,-1628,-1628},-{ -859,-1148,-1498,-1498,-1498}},-/* AU.GU..CG */-{{  DEF, -339, -689, -689, -689},-{-1079,-1368,-1718,-1718,-1718},-{ -719,-1008,-1358,-1358,-1358},-{ -989,-1278,-1628,-1628,-1628},-{ -909,-1198,-1548,-1548,-1548}}},-/* AU.U@..CG */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UA..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -569, -848, -848, -848, -848},-{ -989,-1268,-1268,-1268,-1268},-{ -859,-1138,-1138,-1138,-1138}},-/* AU.UC..CG */-{{  DEF, -329, -329, -329, -329},-{ -999,-1278,-1278,-1278,-1278},-{ -499, -778, -778, -778, -778},-{ -989,-1268,-1268,-1268,-1268},-{ -789,-1068,-1068,-1068,-1068}},-/* AU.UG..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -569, -848, -848, -848, -848},-{ -989,-1268,-1268,-1268,-1268},-{ -859,-1138,-1138,-1138,-1138}},-/* AU.UU..CG */-{{  DEF, -329, -329, -329, -329},-{-1079,-1358,-1358,-1358,-1358},-{ -719, -998, -998, -998, -998},-{ -989,-1268,-1268,-1268,-1268},-{ -909,-1188,-1188,-1188,-1188}}}},-/* AU.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* AU.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* AU.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* AU.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* AU.A@..GC */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA..GC */-{{  DEF, -429, -599, -599, -599},-{ -569, -948,-1118,-1118,-1118},-{ -769,-1148,-1318,-1318,-1318},-{ -759,-1138,-1308,-1308,-1308},-{ -549, -928,-1098,-1098,-1098}},-/* AU.AC..GC */-{{  DEF, -429, -599, -599, -599},-{ -929,-1308,-1478,-1478,-1478},-{ -359, -738, -908, -908, -908},-{ -789,-1168,-1338,-1338,-1338},-{ -549, -928,-1098,-1098,-1098}},-/* AU.AG..GC */-{{  DEF, -429, -599, -599, -599},-{ -609, -988,-1158,-1158,-1158},-{ -359, -738, -908, -908, -908},-{ -669,-1048,-1218,-1218,-1218},-{ -549, -928,-1098,-1098,-1098}},-/* AU.AU..GC */-{{  DEF, -429, -599, -599, -599},-{ -929,-1308,-1478,-1478,-1478},-{ -439, -818, -988, -988, -988},-{ -789,-1168,-1338,-1338,-1338},-{ -619, -998,-1168,-1168,-1168}}},-/* AU.C@..GC */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA..GC */-{{  DEF, -259, -239, -239, -239},-{ -569, -778, -758, -758, -758},-{ -769, -978, -958, -958, -958},-{ -759, -968, -948, -948, -948},-{ -549, -758, -738, -738, -738}},-/* AU.CC..GC */-{{  DEF, -259, -239, -239, -239},-{ -929,-1138,-1118,-1118,-1118},-{ -359, -568, -548, -548, -548},-{ -789, -998, -978, -978, -978},-{ -549, -758, -738, -738, -738}},-/* AU.CG..GC */-{{  DEF, -259, -239, -239, -239},-{ -609, -818, -798, -798, -798},-{ -359, -568, -548, -548, -548},-{ -669, -878, -858, -858, -858},-{ -549, -758, -738, -738, -738}},-/* AU.CU..GC */-{{  DEF, -259, -239, -239, -239},-{ -929,-1138,-1118,-1118,-1118},-{ -439, -648, -628, -628, -628},-{ -789, -998, -978, -978, -978},-{ -619, -828, -808, -808, -808}}},-/* AU.G@..GC */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA..GC */-{{  DEF, -339, -689, -689, -689},-{ -569, -858,-1208,-1208,-1208},-{ -769,-1058,-1408,-1408,-1408},-{ -759,-1048,-1398,-1398,-1398},-{ -549, -838,-1188,-1188,-1188}},-/* AU.GC..GC */-{{  DEF, -339, -689, -689, -689},-{ -929,-1218,-1568,-1568,-1568},-{ -359, -648, -998, -998, -998},-{ -789,-1078,-1428,-1428,-1428},-{ -549, -838,-1188,-1188,-1188}},-/* AU.GG..GC */-{{  DEF, -339, -689, -689, -689},-{ -609, -898,-1248,-1248,-1248},-{ -359, -648, -998, -998, -998},-{ -669, -958,-1308,-1308,-1308},-{ -549, -838,-1188,-1188,-1188}},-/* AU.GU..GC */-{{  DEF, -339, -689, -689, -689},-{ -929,-1218,-1568,-1568,-1568},-{ -439, -728,-1078,-1078,-1078},-{ -789,-1078,-1428,-1428,-1428},-{ -619, -908,-1258,-1258,-1258}}},-/* AU.U@..GC */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UA..GC */-{{  DEF, -329, -329, -329, -329},-{ -569, -848, -848, -848, -848},-{ -769,-1048,-1048,-1048,-1048},-{ -759,-1038,-1038,-1038,-1038},-{ -549, -828, -828, -828, -828}},-/* AU.UC..GC */-{{  DEF, -329, -329, -329, -329},-{ -929,-1208,-1208,-1208,-1208},-{ -359, -638, -638, -638, -638},-{ -789,-1068,-1068,-1068,-1068},-{ -549, -828, -828, -828, -828}},-/* AU.UG..GC */-{{  DEF, -329, -329, -329, -329},-{ -609, -888, -888, -888, -888},-{ -359, -638, -638, -638, -638},-{ -669, -948, -948, -948, -948},-{ -549, -828, -828, -828, -828}},-/* AU.UU..GC */-{{  DEF, -329, -329, -329, -329},-{ -929,-1208,-1208,-1208,-1208},-{ -439, -718, -718, -718, -718},-{ -789,-1068,-1068,-1068,-1068},-{ -619, -898, -898, -898, -898}}}},-/* AU.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* AU.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* AU.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* AU.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* AU.A@..GU */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA..GU */-{{  DEF, -429, -599, -599, -599},-{ -479, -858,-1028,-1028,-1028},-{ -309, -688, -858, -858, -858},-{ -389, -768, -938, -938, -938},-{ -379, -758, -928, -928, -928}},-/* AU.AC..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* AU.AG..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* AU.AU..GU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}}},-/* AU.C@..GU */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA..GU */-{{  DEF, -259, -239, -239, -239},-{ -479, -688, -668, -668, -668},-{ -309, -518, -498, -498, -498},-{ -389, -598, -578, -578, -578},-{ -379, -588, -568, -568, -568}},-/* AU.CC..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* AU.CG..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* AU.CU..GU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}}},-/* AU.G@..GU */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA..GU */-{{  DEF, -339, -689, -689, -689},-{ -479, -768,-1118,-1118,-1118},-{ -309, -598, -948, -948, -948},-{ -389, -678,-1028,-1028,-1028},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GC..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GG..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GU..GU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}}},-/* AU.U@..GU */-{{{  DEF, -329, -329, -329, -329},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UA..GU */-{{  DEF, -329, -329, -329, -329},-{ -479, -758, -758, -758, -758},-{ -309, -588, -588, -588, -588},-{ -389, -668, -668, -668, -668},-{ -379, -658, -658, -658, -658}},-/* AU.UC..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* AU.UG..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}},-/* AU.UU..GU */-{{  DEF, -329, -329, -329, -329},-{ -649, -928, -928, -928, -928},-{ -289, -568, -568, -568, -568},-{ -739,-1018,-1018,-1018,-1018},-{ -379, -658, -658, -658, -658}}}},-/* AU.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* AU.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* AU.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* AU.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* AU.A@..UG */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA..UG */-{{  DEF, -429, -599, -599, -599},-{ -769,-1148,-1318,-1318,-1318},-{ -529, -908,-1078,-1078,-1078},-{ -709,-1088,-1258,-1258,-1258},-{ -599, -978,-1148,-1148,-1148}},-/* AU.AC..UG */-{{  DEF, -429, -599, -599, -599},-{ -839,-1218,-1388,-1388,-1388},-{ -529, -908,-1078,-1078,-1078},-{ -859,-1238,-1408,-1408,-1408},-{ -489, -868,-1038,-1038,-1038}},-/* AU.AG..UG */-{{  DEF, -429, -599, -599, -599},-{-1009,-1388,-1558,-1558,-1558},-{ -409, -788, -958, -958, -958},-{ -969,-1348,-1518,-1518,-1518},-{ -599, -978,-1148,-1148,-1148}},-/* AU.AU..UG */-{{  DEF, -429, -599, -599, -599},-{ -859,-1238,-1408,-1408,-1408},-{ -529, -908,-1078,-1078,-1078},-{ -859,-1238,-1408,-1408,-1408},-{ -409, -788, -958, -958, -958}}},-/* AU.C@..UG */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA..UG */-{{  DEF, -259, -239, -239, -239},-{ -769, -978, -958, -958, -958},-{ -529, -738, -718, -718, -718},-{ -709, -918, -898, -898, -898},-{ -599, -808, -788, -788, -788}},-/* AU.CC..UG */-{{  DEF, -259, -239, -239, -239},-{ -839,-1048,-1028,-1028,-1028},-{ -529, -738, -718, -718, -718},-{ -859,-1068,-1048,-1048,-1048},-{ -489, -698, -678, -678, -678}},-/* AU.CG..UG */-{{  DEF, -259, -239, -239, -239},-{-1009,-1218,-1198,-1198,-1198},-{ -409, -618, -598, -598, -598},-{ -969,-1178,-1158,-1158,-1158},-{ -599, -808, -788, -788, -788}},-/* AU.CU..UG */-{{  DEF, -259, -239, -239, -239},-{ -859,-1068,-1048,-1048,-1048},-{ -529, -738, -718, -718, -718},-{ -859,-1068,-1048,-1048,-1048},-{ -409, -618, -598, -598, -598}}},-/* AU.G@..UG */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA..UG */-{{  DEF, -339, -689, -689, -689},-{ -769,-1058,-1408,-1408,-1408},-{ -529, -818,-1168,-1168,-1168},-{ -709, -998,-1348,-1348,-1348},-{ -599, -888,-1238,-1238,-1238}},-/* AU.GC..UG */-{{  DEF, -339, -689, -689, -689},-{ -839,-1128,-1478,-1478,-1478},-{ -529, 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-768}},-/* AU.UG..UG */-{{  DEF, -329, -329, -329, -329},-{-1009,-1288,-1288,-1288,-1288},-{ -409, -688, -688, -688, -688},-{ -969,-1248,-1248,-1248,-1248},-{ -599, -878, -878, -878, -878}},-/* AU.UU..UG */-{{  DEF, -329, -329, -329, -329},-{ -859,-1138,-1138,-1138,-1138},-{ -529, -808, -808, -808, -808},-{ -859,-1138,-1138,-1138,-1138},-{ -409, -688, -688, -688, -688}}}},-/* AU.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* AU.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* AU.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* AU.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* AU.A@..AU */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA..AU */-{{  DEF, -429, -599, -599, -599},-{ -479, -858,-1028,-1028,-1028},-{ -309, -688, -858, -858, -858},-{ -389, -768, -938, -938, -938},-{ -379, -758, -928, -928, -928}},-/* AU.AC..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* AU.AG..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}},-/* AU.AU..AU */-{{  DEF, -429, -599, -599, -599},-{ -649,-1028,-1198,-1198,-1198},-{ -289, -668, -838, -838, -838},-{ -739,-1118,-1288,-1288,-1288},-{ -379, -758, -928, -928, -928}}},-/* AU.C@..AU */-{{{  DEF, -259, -239, -239, -239},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA..AU */-{{  DEF, -259, -239, -239, -239},-{ -479, -688, -668, -668, -668},-{ -309, -518, -498, -498, -498},-{ -389, -598, -578, -578, -578},-{ -379, -588, -568, -568, -568}},-/* AU.CC..AU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* AU.CG..AU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}},-/* AU.CU..AU */-{{  DEF, -259, -239, -239, -239},-{ -649, -858, -838, -838, -838},-{ -289, -498, -478, -478, -478},-{ -739, -948, -928, -928, -928},-{ -379, -588, -568, -568, -568}}},-/* AU.G@..AU */-{{{  DEF, -339, -689, -689, -689},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA..AU */-{{  DEF, -339, -689, -689, -689},-{ -479, -768,-1118,-1118,-1118},-{ -309, -598, -948, -948, -948},-{ -389, -678,-1028,-1028,-1028},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GC..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GG..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ -739,-1028,-1378,-1378,-1378},-{ -379, -668,-1018,-1018,-1018}},-/* AU.GU..AU */-{{  DEF, -339, -689, -689, -689},-{ -649, -938,-1288,-1288,-1288},-{ -289, -578, -928, -928, -928},-{ 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*/-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* AU.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* AU.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* AU.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* AU.A@..UA */-{{{  DEF, -429, -599, -599, -599},-{ -100, -479, -649, -649, -649},-{ -100, 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-708},-{ -329, -608, -608, -608, -608}},-/* AU.UC..UA */-{{  DEF, -329, -329, -329, -329},-{ -679, -958, -958, -958, -958},-{ -559, -838, -838, -838, -838},-{ -729,-1008,-1008,-1008,-1008},-{ -189, -468, -468, -468, -468}},-/* AU.UG..UA */-{{  DEF, -329, -329, -329, -329},-{ -939,-1218,-1218,-1218,-1218},-{ -249, -528, -528, -528, -528},-{ -939,-1218,-1218,-1218,-1218},-{ -329, -608, -608, -608, -608}},-/* AU.UU..UA */-{{  DEF, -329, -329, -329, -329},-{ -639, -918, -918, -918, -918},-{ -229, -508, -508, -508, -508},-{ -729,-1008,-1008,-1008,-1008},-{ -190, -469, -469, -469, -469}}}},-/* AU.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* AU.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* AU.A@.. @ */-{{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AA.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AC.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AG.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}},-/* AU.AU.. @ */-{{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649},-{ -100, -479, -649, -649, -649}}},-/* AU.C@.. @ */-{{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CA.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CC.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CG.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}},-/* AU.CU.. @ */-{{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289},-{ -100, -309, -289, -289, -289}}},-/* AU.G@.. @ */-{{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GA.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GC.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GG.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}},-/* AU.GU.. @ */-{{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739},-{ -100, -389, -739, -739, -739}}},-/* AU.U@.. @ */-{{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UA.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UC.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UG.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}},-/* AU.UU.. @ */-{{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379},-{ -100, -379, -379, -379, -379}}}}},-{ /* noPair */ {{{{0}}}},-/* UA.@@..CG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* UA.@C..CG */-{{    0,    0,    0,    0,    0},-{ -949, -949, -949, -949, -949},-{ -449, -449, -449, -449, -449},-{ -939, -939, -939, -939, -939},-{ -739, -739, -739, -739, -739}},-/* UA.@G..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -519, -519, -519, -519, -519},-{ -939, -939, -939, -939, -939},-{ -809, -809, -809, -809, -809}},-/* UA.@U..CG */-{{    0,    0,    0,    0,    0},-{-1029,-1029,-1029,-1029,-1029},-{ -669, -669, -669, -669, -669},-{ -939, -939, -939, -939, -939},-{ -859, -859, -859, -859, -859}}},-/* UA.A@..CG */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..CG */-{{  DEF, -399, -629, -889, -589},-{-1079,-1428,-1658,-1918,-1618},-{ -569, -918,-1148,-1408,-1108},-{ -989,-1338,-1568,-1828,-1528},-{ -859,-1208,-1438,-1698,-1398}},-/* UA.AC..CG */-{{  DEF, -399, -629, -889, -589},-{ -999,-1348,-1578,-1838,-1538},-{ -499, -848,-1078,-1338,-1038},-{ -989,-1338,-1568,-1828,-1528},-{ -789,-1138,-1368,-1628,-1328}},-/* UA.AG..CG */-{{  DEF, -399, -629, -889, -589},-{-1079,-1428,-1658,-1918,-1618},-{ -569, -918,-1148,-1408,-1108},-{ -989,-1338,-1568,-1828,-1528},-{ -859,-1208,-1438,-1698,-1398}},-/* UA.AU..CG */-{{  DEF, -399, -629, -889, -589},-{-1079,-1428,-1658,-1918,-1618},-{ -719,-1068,-1298,-1558,-1258},-{ -989,-1338,-1568,-1828,-1528},-{ -909,-1258,-1488,-1748,-1448}}},-/* UA.C@..CG */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..CG */-{{  DEF, -429, -509, -199, -179},-{-1079,-1458,-1538,-1228,-1208},-{ -569, -948,-1028, -718, -698},-{ -989,-1368,-1448,-1138,-1118},-{ -859,-1238,-1318,-1008, -988}},-/* UA.CC..CG */-{{  DEF, -429, -509, -199, -179},-{ -999,-1378,-1458,-1148,-1128},-{ -499, -878, -958, -648, -628},-{ -989,-1368,-1448,-1138,-1118},-{ -789,-1168,-1248, -938, -918}},-/* UA.CG..CG */-{{  DEF, -429, -509, -199, -179},-{-1079,-1458,-1538,-1228,-1208},-{ -569, -948,-1028, -718, -698},-{ -989,-1368,-1448,-1138,-1118},-{ -859,-1238,-1318,-1008, -988}},-/* UA.CU..CG */-{{  DEF, -429, -509, -199, -179},-{-1079,-1458,-1538,-1228,-1208},-{ -719,-1098,-1178, -868, -848},-{ -989,-1368,-1448,-1138,-1118},-{ -909,-1288,-1368,-1058,-1038}}},-/* UA.G@..CG */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..CG */-{{  DEF, -379, -679, -889, -679},-{-1079,-1408,-1708,-1918,-1708},-{ -569, -898,-1198,-1408,-1198},-{ -989,-1318,-1618,-1828,-1618},-{ -859,-1188,-1488,-1698,-1488}},-/* UA.GC..CG */-{{  DEF, -379, -679, -889, -679},-{ -999,-1328,-1628,-1838,-1628},-{ -499, -828,-1128,-1338,-1128},-{ -989,-1318,-1618,-1828,-1618},-{ -789,-1118,-1418,-1628,-1418}},-/* UA.GG..CG */-{{  DEF, -379, -679, -889, -679},-{-1079,-1408,-1708,-1918,-1708},-{ -569, -898,-1198,-1408,-1198},-{ -989,-1318,-1618,-1828,-1618},-{ -859,-1188,-1488,-1698,-1488}},-/* UA.GU..CG */-{{  DEF, -379, -679, -889, -679},-{-1079,-1408,-1708,-1918,-1708},-{ -719,-1048,-1348,-1558,-1348},-{ -989,-1318,-1618,-1828,-1618},-{ -909,-1238,-1538,-1748,-1538}}},-/* UA.U@..CG */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..CG */-{{  DEF, -279, -139, -279, -140},-{-1079,-1308,-1168,-1308,-1169},-{ -569, -798, -658, -798, -659},-{ -989,-1218,-1078,-1218,-1079},-{ -859,-1088, -948,-1088, -949}},-/* UA.UC..CG */-{{  DEF, -279, -139, -279, -140},-{ -999,-1228,-1088,-1228,-1089},-{ -499, -728, -588, -728, -589},-{ -989,-1218,-1078,-1218,-1079},-{ -789,-1018, -878,-1018, -879}},-/* UA.UG..CG */-{{  DEF, -279, -139, -279, -140},-{-1079,-1308,-1168,-1308,-1169},-{ -569, -798, -658, -798, -659},-{ -989,-1218,-1078,-1218,-1079},-{ -859,-1088, -948,-1088, -949}},-/* UA.UU..CG */-{{  DEF, -279, -139, -279, -140},-{-1079,-1308,-1168,-1308,-1169},-{ -719, -948, -808, -948, -809},-{ -989,-1218,-1078,-1218,-1079},-{ -909,-1138, -998,-1138, -999}}}},-/* UA.@@..GC */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..GC */-{{    0,    0,    0,    0,    0},-{ -519, -519, -519, -519, -519},-{ -719, -719, -719, -719, -719},-{ -709, -709, -709, -709, -709},-{ -499, -499, -499, -499, -499}},-/* UA.@C..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -309, -309, -309, -309, -309},-{ -739, -739, -739, -739, -739},-{ -499, -499, -499, -499, -499}},-/* UA.@G..GC */-{{    0,    0,    0,    0,    0},-{ -559, -559, -559, -559, -559},-{ -309, -309, -309, -309, -309},-{ -619, -619, -619, -619, -619},-{ -499, -499, -499, -499, -499}},-/* UA.@U..GC */-{{    0,    0,    0,    0,    0},-{ -879, -879, -879, -879, -879},-{ -389, -389, -389, -389, -389},-{ -739, -739, -739, -739, -739},-{ -569, -569, -569, -569, -569}}},-/* UA.A@..GC */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..GC */-{{  DEF, -399, -629, -889, -589},-{ -569, -918,-1148,-1408,-1108},-{ -769,-1118,-1348,-1608,-1308},-{ -759,-1108,-1338,-1598,-1298},-{ -549, -898,-1128,-1388,-1088}},-/* UA.AC..GC */-{{  DEF, -399, -629, -889, -589},-{ -929,-1278,-1508,-1768,-1468},-{ -359, -708, -938,-1198, -898},-{ -789,-1138,-1368,-1628,-1328},-{ -549, -898,-1128,-1388,-1088}},-/* UA.AG..GC */-{{  DEF, -399, -629, -889, -589},-{ -609, -958,-1188,-1448,-1148},-{ -359, -708, -938,-1198, -898},-{ -669,-1018,-1248,-1508,-1208},-{ -549, -898,-1128,-1388,-1088}},-/* UA.AU..GC */-{{  DEF, -399, -629, -889, -589},-{ -929,-1278,-1508,-1768,-1468},-{ -439, -788,-1018,-1278, -978},-{ -789,-1138,-1368,-1628,-1328},-{ -619, -968,-1198,-1458,-1158}}},-/* UA.C@..GC */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..GC */-{{  DEF, -429, -509, -199, -179},-{ -569, -948,-1028, -718, -698},-{ -769,-1148,-1228, -918, -898},-{ -759,-1138,-1218, -908, -888},-{ -549, -928,-1008, -698, -678}},-/* UA.CC..GC */-{{  DEF, -429, -509, -199, -179},-{ -929,-1308,-1388,-1078,-1058},-{ -359, -738, -818, -508, -488},-{ -789,-1168,-1248, -938, -918},-{ -549, -928,-1008, -698, -678}},-/* UA.CG..GC */-{{  DEF, -429, -509, -199, -179},-{ -609, -988,-1068, -758, -738},-{ -359, -738, -818, -508, -488},-{ -669,-1048,-1128, -818, -798},-{ -549, -928,-1008, -698, -678}},-/* UA.CU..GC */-{{  DEF, -429, -509, -199, -179},-{ -929,-1308,-1388,-1078,-1058},-{ -439, -818, -898, -588, -568},-{ -789,-1168,-1248, -938, -918},-{ -619, -998,-1078, -768, -748}}},-/* UA.G@..GC */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..GC */-{{  DEF, -379, -679, -889, -679},-{ -569, -898,-1198,-1408,-1198},-{ -769,-1098,-1398,-1608,-1398},-{ -759,-1088,-1388,-1598,-1388},-{ -549, -878,-1178,-1388,-1178}},-/* UA.GC..GC */-{{  DEF, -379, -679, -889, -679},-{ -929,-1258,-1558,-1768,-1558},-{ -359, -688, -988,-1198, -988},-{ -789,-1118,-1418,-1628,-1418},-{ -549, -878,-1178,-1388,-1178}},-/* UA.GG..GC */-{{  DEF, -379, -679, -889, -679},-{ -609, -938,-1238,-1448,-1238},-{ -359, -688, -988,-1198, -988},-{ -669, -998,-1298,-1508,-1298},-{ -549, -878,-1178,-1388,-1178}},-/* UA.GU..GC */-{{  DEF, -379, -679, -889, -679},-{ -929,-1258,-1558,-1768,-1558},-{ -439, -768,-1068,-1278,-1068},-{ -789,-1118,-1418,-1628,-1418},-{ -619, -948,-1248,-1458,-1248}}},-/* UA.U@..GC */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..GC */-{{  DEF, -279, -139, -279, -140},-{ -569, -798, -658, -798, -659},-{ -769, -998, -858, -998, -859},-{ -759, -988, -848, -988, -849},-{ -549, -778, -638, -778, -639}},-/* UA.UC..GC */-{{  DEF, -279, -139, -279, -140},-{ -929,-1158,-1018,-1158,-1019},-{ -359, -588, -448, -588, -449},-{ -789,-1018, -878,-1018, -879},-{ -549, -778, -638, -778, -639}},-/* UA.UG..GC */-{{  DEF, -279, -139, -279, -140},-{ -609, -838, -698, -838, -699},-{ -359, -588, -448, -588, -449},-{ -669, -898, -758, -898, -759},-{ -549, -778, -638, -778, -639}},-/* UA.UU..GC */-{{  DEF, -279, -139, -279, -140},-{ -929,-1158,-1018,-1158,-1019},-{ -439, -668, -528, -668, -529},-{ -789,-1018, -878,-1018, -879},-{ -619, -848, -708, -848, -709}}}},-/* UA.@@..GU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..GU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* UA.@C..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UA.@G..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UA.@U..GU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* UA.A@..GU */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..GU */-{{  DEF, -399, -629, -889, -589},-{ -479, -828,-1058,-1318,-1018},-{ -309, -658, -888,-1148, -848},-{ -389, -738, -968,-1228, -928},-{ -379, -728, -958,-1218, -918}},-/* UA.AC..GU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}},-/* UA.AG..GU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}},-/* UA.AU..GU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}}},-/* UA.C@..GU */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..GU */-{{  DEF, -429, -509, -199, -179},-{ -479, -858, -938, -628, -608},-{ -309, -688, -768, -458, -438},-{ -389, -768, -848, -538, -518},-{ -379, -758, -838, -528, -508}},-/* UA.CC..GU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}},-/* UA.CG..GU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}},-/* UA.CU..GU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}}},-/* UA.G@..GU */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..GU */-{{  DEF, -379, -679, -889, -679},-{ -479, -808,-1108,-1318,-1108},-{ -309, -638, -938,-1148, -938},-{ -389, -718,-1018,-1228,-1018},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GC..GU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GG..GU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GU..GU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}}},-/* UA.U@..GU */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..GU */-{{  DEF, -279, -139, -279, -140},-{ -479, -708, -568, -708, -569},-{ -309, -538, -398, -538, -399},-{ -389, -618, -478, -618, -479},-{ -379, -608, -468, -608, -469}},-/* UA.UC..GU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}},-/* UA.UG..GU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}},-/* UA.UU..GU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}}}},-/* UA.@@..UG */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..UG */-{{    0,    0,    0,    0,    0},-{ -719, -719, -719, -719, -719},-{ -479, -479, -479, -479, -479},-{ -659, -659, -659, -659, -659},-{ -549, -549, -549, -549, -549}},-/* UA.@C..UG */-{{    0,    0,    0,    0,    0},-{ -789, -789, -789, -789, -789},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -439, -439, -439, -439, -439}},-/* UA.@G..UG */-{{    0,    0,    0,    0,    0},-{ -959, -959, -959, -959, -959},-{ -359, -359, -359, -359, -359},-{ -919, -919, -919, -919, -919},-{ -549, -549, -549, -549, -549}},-/* UA.@U..UG */-{{    0,    0,    0,    0,    0},-{ -809, -809, -809, -809, -809},-{ -479, -479, -479, -479, -479},-{ -809, -809, -809, -809, -809},-{ -359, -359, -359, -359, -359}}},-/* UA.A@..UG */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..UG */-{{  DEF, -399, -629, -889, -589},-{ -769,-1118,-1348,-1608,-1308},-{ -529, -878,-1108,-1368,-1068},-{ -709,-1058,-1288,-1548,-1248},-{ -599, -948,-1178,-1438,-1138}},-/* UA.AC..UG */-{{  DEF, -399, -629, -889, -589},-{ -839,-1188,-1418,-1678,-1378},-{ -529, -878,-1108,-1368,-1068},-{ -859,-1208,-1438,-1698,-1398},-{ -489, -838,-1068,-1328,-1028}},-/* UA.AG..UG */-{{  DEF, -399, -629, -889, -589},-{-1009,-1358,-1588,-1848,-1548},-{ -409, -758, -988,-1248, -948},-{ -969,-1318,-1548,-1808,-1508},-{ -599, -948,-1178,-1438,-1138}},-/* UA.AU..UG */-{{  DEF, -399, -629, -889, -589},-{ -859,-1208,-1438,-1698,-1398},-{ -529, -878,-1108,-1368,-1068},-{ -859,-1208,-1438,-1698,-1398},-{ -409, -758, -988,-1248, -948}}},-/* UA.C@..UG */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..UG */-{{  DEF, -429, -509, -199, -179},-{ -769,-1148,-1228, -918, -898},-{ -529, -908, -988, -678, -658},-{ -709,-1088,-1168, -858, -838},-{ -599, -978,-1058, -748, -728}},-/* UA.CC..UG */-{{  DEF, -429, -509, -199, -179},-{ -839,-1218,-1298, -988, -968},-{ -529, -908, -988, -678, -658},-{ -859,-1238,-1318,-1008, -988},-{ -489, -868, -948, -638, -618}},-/* UA.CG..UG */-{{  DEF, -429, -509, -199, -179},-{-1009,-1388,-1468,-1158,-1138},-{ -409, -788, -868, -558, -538},-{ -969,-1348,-1428,-1118,-1098},-{ -599, -978,-1058, -748, -728}},-/* UA.CU..UG */-{{  DEF, -429, -509, -199, -179},-{ -859,-1238,-1318,-1008, -988},-{ -529, -908, -988, -678, -658},-{ -859,-1238,-1318,-1008, -988},-{ -409, -788, -868, -558, -538}}},-/* UA.G@..UG */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..UG */-{{  DEF, -379, -679, -889, -679},-{ -769,-1098,-1398,-1608,-1398},-{ -529, -858,-1158,-1368,-1158},-{ -709,-1038,-1338,-1548,-1338},-{ -599, -928,-1228,-1438,-1228}},-/* UA.GC..UG */-{{  DEF, -379, -679, -889, -679},-{ -839,-1168,-1468,-1678,-1468},-{ -529, -858,-1158,-1368,-1158},-{ -859,-1188,-1488,-1698,-1488},-{ -489, -818,-1118,-1328,-1118}},-/* UA.GG..UG */-{{  DEF, -379, -679, -889, -679},-{-1009,-1338,-1638,-1848,-1638},-{ -409, -738,-1038,-1248,-1038},-{ -969,-1298,-1598,-1808,-1598},-{ -599, -928,-1228,-1438,-1228}},-/* UA.GU..UG */-{{  DEF, -379, -679, -889, -679},-{ -859,-1188,-1488,-1698,-1488},-{ -529, -858,-1158,-1368,-1158},-{ -859,-1188,-1488,-1698,-1488},-{ -409, -738,-1038,-1248,-1038}}},-/* UA.U@..UG */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..UG */-{{  DEF, -279, -139, -279, -140},-{ -769, -998, -858, -998, -859},-{ -529, -758, -618, -758, -619},-{ -709, -938, -798, -938, -799},-{ -599, -828, -688, -828, -689}},-/* UA.UC..UG */-{{  DEF, -279, -139, -279, -140},-{ -839,-1068, -928,-1068, -929},-{ -529, -758, -618, -758, -619},-{ -859,-1088, -948,-1088, -949},-{ -489, -718, -578, -718, -579}},-/* UA.UG..UG */-{{  DEF, -279, -139, -279, -140},-{-1009,-1238,-1098,-1238,-1099},-{ -409, -638, -498, -638, -499},-{ -969,-1198,-1058,-1198,-1059},-{ -599, -828, -688, -828, -689}},-/* UA.UU..UG */-{{  DEF, -279, -139, -279, -140},-{ -859,-1088, -948,-1088, -949},-{ -529, -758, -618, -758, -619},-{ -859,-1088, -948,-1088, -949},-{ -409, -638, -498, -638, -499}}}},-/* UA.@@..AU */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..AU */-{{    0,    0,    0,    0,    0},-{ -429, -429, -429, -429, -429},-{ -259, -259, -259, -259, -259},-{ -339, -339, -339, -339, -339},-{ -329, -329, -329, -329, -329}},-/* UA.@C..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UA.@G..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}},-/* UA.@U..AU */-{{    0,    0,    0,    0,    0},-{ -599, -599, -599, -599, -599},-{ -239, -239, -239, -239, -239},-{ -689, -689, -689, -689, -689},-{ -329, -329, -329, -329, -329}}},-/* UA.A@..AU */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..AU */-{{  DEF, -399, -629, -889, -589},-{ -479, -828,-1058,-1318,-1018},-{ -309, -658, -888,-1148, -848},-{ -389, -738, -968,-1228, -928},-{ -379, -728, -958,-1218, -918}},-/* UA.AC..AU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}},-/* UA.AG..AU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}},-/* UA.AU..AU */-{{  DEF, -399, -629, -889, -589},-{ -649, -998,-1228,-1488,-1188},-{ -289, -638, -868,-1128, -828},-{ -739,-1088,-1318,-1578,-1278},-{ -379, -728, -958,-1218, -918}}},-/* UA.C@..AU */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..AU */-{{  DEF, -429, -509, -199, -179},-{ -479, -858, -938, -628, -608},-{ -309, -688, -768, -458, -438},-{ -389, -768, -848, -538, -518},-{ -379, -758, -838, -528, -508}},-/* UA.CC..AU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}},-/* UA.CG..AU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}},-/* UA.CU..AU */-{{  DEF, -429, -509, -199, -179},-{ -649,-1028,-1108, -798, -778},-{ -289, -668, -748, -438, -418},-{ -739,-1118,-1198, -888, -868},-{ -379, -758, -838, -528, -508}}},-/* UA.G@..AU */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..AU */-{{  DEF, -379, -679, -889, -679},-{ -479, -808,-1108,-1318,-1108},-{ -309, -638, -938,-1148, -938},-{ -389, -718,-1018,-1228,-1018},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GC..AU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GG..AU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}},-/* UA.GU..AU */-{{  DEF, -379, -679, -889, -679},-{ -649, -978,-1278,-1488,-1278},-{ -289, -618, -918,-1128, -918},-{ -739,-1068,-1368,-1578,-1368},-{ -379, -708,-1008,-1218,-1008}}},-/* UA.U@..AU */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..AU */-{{  DEF, -279, -139, -279, -140},-{ -479, -708, -568, -708, -569},-{ -309, -538, -398, -538, -399},-{ -389, -618, -478, -618, -479},-{ -379, -608, -468, -608, -469}},-/* UA.UC..AU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}},-/* UA.UG..AU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}},-/* UA.UU..AU */-{{  DEF, -279, -139, -279, -140},-{ -649, -878, -738, -878, -739},-{ -289, -518, -378, -518, -379},-{ -739, -968, -828, -968, -829},-{ -379, -608, -468, -608, -469}}}},-/* UA.@@..UA */-{{{{    0,    0,    0,    0,    0},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A..UA */-{{    0,    0,    0,    0,    0},-{ -399, -399, -399, -399, -399},-{ -429, -429, -429, -429, -429},-{ -379, -379, -379, -379, -379},-{ -279, -279, -279, -279, -279}},-/* UA.@C..UA */-{{    0,    0,    0,    0,    0},-{ -629, -629, -629, -629, -629},-{ -509, -509, -509, -509, -509},-{ -679, -679, -679, -679, -679},-{ -139, -139, -139, -139, -139}},-/* UA.@G..UA */-{{    0,    0,    0,    0,    0},-{ -889, -889, -889, -889, -889},-{ -199, -199, -199, -199, -199},-{ -889, -889, -889, -889, -889},-{ -279, -279, -279, -279, -279}},-/* UA.@U..UA */-{{    0,    0,    0,    0,    0},-{ -589, -589, -589, -589, -589},-{ -179, -179, -179, -179, -179},-{ -679, -679, -679, -679, -679},-{ -140, -140, -140, -140, -140}}},-/* UA.A@..UA */-{{{  DEF, -399, -629, -889, -589},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA..UA */-{{  DEF, -399, -629, -889, -589},-{ -449, -798,-1028,-1288, -988},-{ -479, -828,-1058,-1318,-1018},-{ -429, -778,-1008,-1268, -968},-{ -329, -678, -908,-1168, -868}},-/* UA.AC..UA */-{{  DEF, -399, -629, -889, -589},-{ -679,-1028,-1258,-1518,-1218},-{ -559, -908,-1138,-1398,-1098},-{ -729,-1078,-1308,-1568,-1268},-{ -189, -538, -768,-1028, -728}},-/* UA.AG..UA */-{{  DEF, -399, -629, -889, -589},-{ -939,-1288,-1518,-1778,-1478},-{ -249, -598, -828,-1088, -788},-{ -939,-1288,-1518,-1778,-1478},-{ -329, -678, -908,-1168, -868}},-/* UA.AU..UA */-{{  DEF, -399, -629, -889, -589},-{ -639, -988,-1218,-1478,-1178},-{ -229, -578, -808,-1068, -768},-{ -729,-1078,-1308,-1568,-1268},-{ -190, -539, -769,-1029, -729}}},-/* UA.C@..UA */-{{{  DEF, -429, -509, -199, -179},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA..UA */-{{  DEF, -429, -509, -199, -179},-{ -449, -828, -908, -598, -578},-{ -479, -858, -938, -628, -608},-{ -429, -808, -888, -578, -558},-{ -329, -708, -788, -478, -458}},-/* UA.CC..UA */-{{  DEF, -429, -509, -199, -179},-{ -679,-1058,-1138, -828, -808},-{ -559, -938,-1018, -708, -688},-{ -729,-1108,-1188, -878, -858},-{ -189, -568, -648, -338, -318}},-/* UA.CG..UA */-{{  DEF, -429, -509, -199, -179},-{ -939,-1318,-1398,-1088,-1068},-{ -249, -628, -708, -398, -378},-{ -939,-1318,-1398,-1088,-1068},-{ -329, -708, -788, -478, -458}},-/* UA.CU..UA */-{{  DEF, -429, -509, -199, -179},-{ -639,-1018,-1098, -788, -768},-{ -229, -608, -688, -378, -358},-{ -729,-1108,-1188, -878, -858},-{ -190, -569, -649, -339, -319}}},-/* UA.G@..UA */-{{{  DEF, -379, -679, -889, -679},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA..UA */-{{  DEF, -379, -679, -889, -679},-{ -449, -778,-1078,-1288,-1078},-{ -479, -808,-1108,-1318,-1108},-{ -429, -758,-1058,-1268,-1058},-{ -329, -658, -958,-1168, -958}},-/* UA.GC..UA */-{{  DEF, -379, -679, -889, -679},-{ -679,-1008,-1308,-1518,-1308},-{ -559, -888,-1188,-1398,-1188},-{ -729,-1058,-1358,-1568,-1358},-{ -189, -518, -818,-1028, -818}},-/* UA.GG..UA */-{{  DEF, -379, -679, -889, -679},-{ -939,-1268,-1568,-1778,-1568},-{ -249, -578, -878,-1088, -878},-{ -939,-1268,-1568,-1778,-1568},-{ -329, -658, -958,-1168, -958}},-/* UA.GU..UA */-{{  DEF, -379, -679, -889, -679},-{ -639, -968,-1268,-1478,-1268},-{ -229, -558, -858,-1068, -858},-{ -729,-1058,-1358,-1568,-1358},-{ -190, -519, -819,-1029, -819}}},-/* UA.U@..UA */-{{{  DEF, -279, -139, -279, -140},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA..UA */-{{  DEF, -279, -139, -279, -140},-{ -449, -678, -538, -678, -539},-{ -479, -708, -568, -708, -569},-{ -429, -658, -518, -658, -519},-{ -329, -558, -418, -558, -419}},-/* UA.UC..UA */-{{  DEF, -279, -139, -279, -140},-{ -679, -908, -768, -908, -769},-{ -559, -788, -648, -788, -649},-{ -729, -958, -818, -958, -819},-{ -189, -418, -278, -418, -279}},-/* UA.UG..UA */-{{  DEF, -279, -139, -279, -140},-{ -939,-1168,-1028,-1168,-1029},-{ -249, -478, -338, -478, -339},-{ -939,-1168,-1028,-1168,-1029},-{ -329, -558, -418, -558, -419}},-/* UA.UU..UA */-{{  DEF, -279, -139, -279, -140},-{ -639, -868, -728, -868, -729},-{ -229, -458, -318, -458, -319},-{ -729, -958, -818, -958, -819},-{ -190, -419, -279, -419, -280}}}},-/* UA.@@.. @ */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@A.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@C.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@G.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}},-/* UA.@U.. @ */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF},-{  DEF,  DEF,  DEF,  DEF,  DEF}}},-/* UA.A@.. @ */-{{{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AA.. @ */-{{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AC.. @ */-{{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AG.. @ */-{{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}},-/* UA.AU.. @ */-{{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639},-{ -100, -449, -679, -939, -639}}},-/* UA.C@.. @ */-{{{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CA.. @ */-{{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CC.. @ */-{{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CG.. @ */-{{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}},-/* UA.CU.. @ */-{{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229},-{ -100, -479, -559, -249, -229}}},-/* UA.G@.. @ */-{{{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GA.. @ */-{{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GC.. @ */-{{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GG.. @ */-{{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}},-/* UA.GU.. @ */-{{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729},-{ -100, -429, -729, -939, -729}}},-/* UA.U@.. @ */-{{{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UA.. @ */-{{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UC.. @ */-{{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UG.. @ */-{{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}},-/* UA.UU.. @ */-{{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190},-{ -100, -329, -189, -329, -190}}}}},-{ /* noPair */ {{{{0}}}},-/*  @.@@..CG */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.@C..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -999, -999, -999, -999, -999},-{ -499, -499, -499, -499, -499},-{ -989, -989, -989, -989, -989},-{ -789, -789, -789, -789, -789}},-/*  @.@G..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.@U..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -719, -719, -719, -719, -719},-{ -989, -989, -989, -989, -989},-{ -909, -909, -909, -909, -909}}},-/*  @.A@..CG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.AC..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -999, -999, -999, -999, -999},-{ -499, -499, -499, -499, -499},-{ -989, -989, -989, -989, -989},-{ -789, -789, -789, -789, -789}},-/*  @.AG..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.AU..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -719, -719, -719, -719, -719},-{ -989, -989, -989, -989, -989},-{ -909, -909, -909, -909, -909}}},-/*  @.C@..CG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.CC..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -999, -999, -999, -999, -999},-{ -499, -499, -499, -499, -499},-{ -989, -989, -989, -989, -989},-{ -789, -789, -789, -789, -789}},-/*  @.CG..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.CU..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -719, -719, -719, -719, -719},-{ -989, -989, -989, -989, -989},-{ -909, -909, -909, -909, -909}}},-/*  @.G@..CG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.GC..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -999, -999, -999, -999, -999},-{ -499, -499, -499, -499, -499},-{ -989, -989, -989, -989, -989},-{ -789, -789, -789, -789, -789}},-/*  @.GG..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.GU..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -719, -719, -719, -719, -719},-{ -989, -989, -989, -989, -989},-{ -909, -909, -909, -909, -909}}},-/*  @.U@..CG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.UC..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -999, -999, -999, -999, -999},-{ -499, -499, -499, -499, -499},-{ -989, -989, -989, -989, -989},-{ -789, -789, -789, -789, -789}},-/*  @.UG..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -569, -569, -569, -569, -569},-{ -989, -989, -989, -989, -989},-{ -859, -859, -859, -859, -859}},-/*  @.UU..CG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1079,-1079,-1079,-1079,-1079},-{ -719, -719, -719, -719, -719},-{ -989, -989, -989, -989, -989},-{ -909, -909, -909, -909, -909}}}},-/*  @.@@..GC */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -569, -569, -569, -569, -569},-{ -769, -769, -769, -769, -769},-{ -759, -759, -759, -759, -759},-{ -549, -549, -549, -549, -549}},-/*  @.@C..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -359, -359, -359, -359, -359},-{ -789, -789, -789, -789, -789},-{ -549, -549, -549, -549, -549}},-/*  @.@G..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -609, -609, -609, -609, -609},-{ -359, -359, -359, -359, -359},-{ -669, -669, -669, -669, -669},-{ -549, -549, -549, -549, -549}},-/*  @.@U..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -439, -439, -439, -439, -439},-{ -789, -789, -789, -789, -789},-{ -619, -619, -619, -619, -619}}},-/*  @.A@..GC */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -569, -569, -569, -569, -569},-{ -769, -769, -769, -769, -769},-{ -759, -759, -759, -759, -759},-{ -549, -549, -549, -549, -549}},-/*  @.AC..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -359, -359, -359, -359, -359},-{ -789, -789, -789, -789, -789},-{ -549, -549, -549, -549, -549}},-/*  @.AG..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -609, -609, -609, -609, -609},-{ -359, -359, -359, -359, -359},-{ -669, -669, -669, -669, -669},-{ -549, -549, -549, -549, -549}},-/*  @.AU..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -439, -439, -439, -439, -439},-{ -789, -789, -789, -789, -789},-{ -619, -619, -619, -619, -619}}},-/*  @.C@..GC */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -569, -569, -569, -569, -569},-{ -769, -769, -769, -769, -769},-{ -759, -759, -759, -759, -759},-{ -549, -549, -549, -549, -549}},-/*  @.CC..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -359, -359, -359, -359, -359},-{ -789, -789, -789, -789, -789},-{ -549, -549, -549, -549, -549}},-/*  @.CG..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -609, -609, -609, -609, -609},-{ -359, -359, -359, -359, -359},-{ -669, -669, -669, -669, -669},-{ -549, -549, -549, -549, -549}},-/*  @.CU..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -439, -439, -439, -439, -439},-{ -789, -789, -789, -789, -789},-{ -619, -619, -619, -619, -619}}},-/*  @.G@..GC */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -569, -569, -569, -569, -569},-{ -769, -769, -769, -769, -769},-{ -759, -759, -759, -759, -759},-{ -549, -549, -549, -549, -549}},-/*  @.GC..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -359, -359, -359, -359, -359},-{ -789, -789, -789, -789, -789},-{ -549, -549, -549, -549, -549}},-/*  @.GG..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -609, -609, -609, -609, -609},-{ -359, -359, -359, -359, -359},-{ -669, -669, -669, -669, -669},-{ -549, -549, -549, -549, -549}},-/*  @.GU..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -439, -439, -439, -439, -439},-{ -789, -789, -789, -789, -789},-{ -619, -619, -619, -619, -619}}},-/*  @.U@..GC */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -569, -569, -569, -569, -569},-{ -769, -769, -769, -769, -769},-{ -759, -759, -759, -759, -759},-{ -549, -549, -549, -549, -549}},-/*  @.UC..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -359, -359, -359, -359, -359},-{ -789, -789, -789, -789, -789},-{ -549, -549, -549, -549, -549}},-/*  @.UG..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -609, -609, -609, -609, -609},-{ -359, -359, -359, -359, -359},-{ -669, -669, -669, -669, -669},-{ -549, -549, -549, -549, -549}},-/*  @.UU..GC */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -929, -929, -929, -929, -929},-{ -439, -439, -439, -439, -439},-{ -789, -789, -789, -789, -789},-{ -619, -619, -619, -619, -619}}}},-/*  @.@@..GU */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.@C..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.@G..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.@U..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.A@..GU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.AC..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.AG..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.AU..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.C@..GU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.CC..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.CG..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.CU..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.G@..GU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.GC..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.GG..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.GU..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.U@..GU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.UC..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.UG..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.UU..GU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}}},-/*  @.@@..UG */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -769, -769, -769, -769, -769},-{ -529, -529, -529, -529, -529},-{ -709, -709, -709, -709, -709},-{ -599, -599, -599, -599, -599}},-/*  @.@C..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -839, -839, -839, -839, -839},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -489, -489, -489, -489, -489}},-/*  @.@G..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1009,-1009,-1009,-1009,-1009},-{ -409, -409, -409, -409, -409},-{ -969, -969, -969, -969, -969},-{ -599, -599, -599, -599, -599}},-/*  @.@U..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -859, -859, -859, -859, -859},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -409, -409, -409, -409, -409}}},-/*  @.A@..UG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -769, -769, -769, -769, -769},-{ -529, -529, -529, -529, -529},-{ -709, -709, -709, -709, -709},-{ -599, -599, -599, -599, -599}},-/*  @.AC..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -839, -839, -839, -839, -839},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -489, -489, -489, -489, -489}},-/*  @.AG..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1009,-1009,-1009,-1009,-1009},-{ -409, -409, -409, -409, -409},-{ -969, -969, -969, -969, -969},-{ -599, -599, -599, -599, -599}},-/*  @.AU..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -859, -859, -859, -859, -859},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -409, -409, -409, -409, -409}}},-/*  @.C@..UG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -769, -769, -769, -769, -769},-{ -529, -529, -529, -529, -529},-{ -709, -709, -709, -709, -709},-{ -599, -599, -599, -599, -599}},-/*  @.CC..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -839, -839, -839, -839, -839},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -489, -489, -489, -489, -489}},-/*  @.CG..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1009,-1009,-1009,-1009,-1009},-{ -409, -409, -409, -409, -409},-{ -969, -969, -969, -969, -969},-{ -599, -599, -599, -599, -599}},-/*  @.CU..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -859, -859, -859, -859, -859},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -409, -409, -409, -409, -409}}},-/*  @.G@..UG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -769, -769, -769, -769, -769},-{ -529, -529, -529, -529, -529},-{ -709, -709, -709, -709, -709},-{ -599, -599, -599, -599, -599}},-/*  @.GC..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -839, -839, -839, -839, -839},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -489, -489, -489, -489, -489}},-/*  @.GG..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1009,-1009,-1009,-1009,-1009},-{ -409, -409, -409, -409, -409},-{ -969, -969, -969, -969, -969},-{ -599, -599, -599, -599, -599}},-/*  @.GU..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -859, -859, -859, -859, -859},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -409, -409, -409, -409, -409}}},-/*  @.U@..UG */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -769, -769, -769, -769, -769},-{ -529, -529, -529, -529, -529},-{ -709, -709, -709, -709, -709},-{ -599, -599, -599, -599, -599}},-/*  @.UC..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -839, -839, -839, -839, -839},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -489, -489, -489, -489, -489}},-/*  @.UG..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{-1009,-1009,-1009,-1009,-1009},-{ -409, -409, -409, -409, -409},-{ -969, -969, -969, -969, -969},-{ -599, -599, -599, -599, -599}},-/*  @.UU..UG */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -859, -859, -859, -859, -859},-{ -529, -529, -529, -529, -529},-{ -859, -859, -859, -859, -859},-{ -409, -409, -409, -409, -409}}}},-/*  @.@@..AU */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.@C..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.@G..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.@U..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.A@..AU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.AC..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.AG..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.AU..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.C@..AU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.CC..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.CG..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.CU..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.G@..AU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.GC..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.GG..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.GU..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}},-/*  @.U@..AU */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -479, -479, -479, -479, -479},-{ -309, -309, -309, -309, -309},-{ -389, -389, -389, -389, -389},-{ -379, -379, -379, -379, -379}},-/*  @.UC..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.UG..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}},-/*  @.UU..AU */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -649, -649, -649, -649, -649},-{ -289, -289, -289, -289, -289},-{ -739, -739, -739, -739, -739},-{ -379, -379, -379, -379, -379}}}},-/*  @.@@..UA */-{{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -449, -449, -449, -449, -449},-{ -479, -479, -479, -479, -479},-{ -429, -429, -429, -429, -429},-{ -329, -329, -329, -329, -329}},-/*  @.@C..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -679, -679, -679, -679, -679},-{ -559, -559, -559, -559, -559},-{ -729, -729, -729, -729, -729},-{ -189, -189, -189, -189, -189}},-/*  @.@G..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -939, -939, -939, -939, -939},-{ -249, -249, -249, -249, -249},-{ -939, -939, -939, -939, -939},-{ -329, -329, -329, -329, -329}},-/*  @.@U..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -639, -639, -639, -639, -639},-{ -229, -229, -229, -229, -229},-{ -729, -729, -729, -729, -729},-{ -190, -190, -190, -190, -190}}},-/*  @.A@..UA */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -449, -449, -449, -449, -449},-{ -479, -479, -479, -479, -479},-{ -429, -429, -429, -429, -429},-{ -329, -329, -329, -329, -329}},-/*  @.AC..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -679, -679, -679, -679, -679},-{ -559, -559, -559, -559, -559},-{ -729, -729, -729, -729, -729},-{ -189, -189, -189, -189, -189}},-/*  @.AG..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -939, -939, -939, -939, -939},-{ -249, -249, -249, -249, -249},-{ -939, -939, -939, -939, -939},-{ -329, -329, -329, -329, -329}},-/*  @.AU..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -639, -639, -639, -639, -639},-{ -229, -229, -229, -229, -229},-{ -729, -729, -729, -729, -729},-{ -190, -190, -190, -190, -190}}},-/*  @.C@..UA */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -449, -449, -449, -449, -449},-{ -479, -479, -479, -479, -479},-{ -429, -429, -429, -429, -429},-{ -329, -329, -329, -329, -329}},-/*  @.CC..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -679, -679, -679, -679, -679},-{ -559, -559, -559, -559, -559},-{ -729, -729, -729, -729, -729},-{ -189, -189, -189, -189, -189}},-/*  @.CG..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -939, -939, -939, -939, -939},-{ -249, -249, -249, -249, -249},-{ -939, -939, -939, -939, -939},-{ -329, -329, -329, -329, -329}},-/*  @.CU..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -639, -639, -639, -639, -639},-{ -229, -229, -229, -229, -229},-{ -729, -729, -729, -729, -729},-{ -190, -190, -190, -190, -190}}},-/*  @.G@..UA */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -449, -449, -449, -449, -449},-{ -479, -479, -479, -479, -479},-{ -429, -429, -429, -429, -429},-{ -329, -329, -329, -329, -329}},-/*  @.GC..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -679, -679, -679, -679, -679},-{ -559, -559, -559, -559, -559},-{ -729, -729, -729, -729, -729},-{ -189, -189, -189, -189, -189}},-/*  @.GG..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -939, -939, -939, -939, -939},-{ -249, -249, -249, -249, -249},-{ -939, -939, -939, -939, -939},-{ -329, -329, -329, -329, -329}},-/*  @.GU..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -639, -639, -639, -639, -639},-{ -229, -229, -229, -229, -229},-{ -729, -729, -729, -729, -729},-{ -190, -190, -190, -190, -190}}},-/*  @.U@..UA */-{{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -449, -449, -449, -449, -449},-{ -479, -479, -479, -479, -479},-{ -429, -429, -429, -429, -429},-{ -329, -329, -329, -329, -329}},-/*  @.UC..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -679, -679, -679, -679, -679},-{ -559, -559, -559, -559, -559},-{ -729, -729, -729, -729, -729},-{ -189, -189, -189, -189, -189}},-/*  @.UG..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -939, -939, -939, -939, -939},-{ -249, -249, -249, -249, -249},-{ -939, -939, -939, -939, -939},-{ -329, -329, -329, -329, -329}},-/*  @.UU..UA */-{{  DEF,  DEF,  DEF,  DEF,  DEF},-{ -639, -639, -639, -639, -639},-{ -229, -229, -229, -229, -229},-{ -729, -729, -729, -729, -729},-{ -190, -190, -190, -190, -190}}}},-/*  @.@@.. @ */-{{{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@A.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@C.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@G.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.@U.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}}},-/*  @.A@.. @ */-{{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AA.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AC.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AG.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.AU.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}}},-/*  @.C@.. @ */-{{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CA.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CC.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CG.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.CU.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}}},-/*  @.G@.. @ */-{{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GA.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GC.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GG.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.GU.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}}},-/*  @.U@.. @ */-{{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UA.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UC.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UG.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}},-/*  @.UU.. @ */-{{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100},-{ -100, -100, -100, -100, -100}}}}}};--
− include/PS_dot.h 
@@ -1,197 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_PS_DOT_H__-#define __VIENNA_RNA_PACKAGE_PS_DOT_H__--#include "data_structures.h"-#include "plot_layouts.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif--/**- *  \file PS_dot.h- *  \brief Various functions for plotting RNA secondary structures, dot-plots and other- *  visualizations- */--/* write PostScript drawing of structure to file with annotation */-int PS_rna_plot_snoop_a(char *string,-                        char *structure,-                        char *ssfile,-                        int *relative_access,-                        const char *seqs[]);--/**- *  \brief Produce a secondary structure graph in PostScript and write it to 'filename'.- *- *  Note that this function has changed from previous versions- *  and now expects the structure to be plotted in dot-bracket notation as an- *  argument. It does not make use of the global #base_pair array anymore.- *- *  \param string     The RNA sequence- *  \param structure  The secondary structure in dot-bracket notation- *  \param file       The filename of the postscript output- *  \return           1 on success, 0 otherwise- */-int PS_rna_plot(char *string,-                char *structure,-                char *file);--/**- *  \brief Produce a secondary structure graph in PostScript including additional- *  annotation macros and write it to 'filename'- *- *  Same as PS_rna_plot() but adds extra PostScript macros for various- *  annotations (see generated PS code). The 'pre' and 'post'- *  variables contain PostScript code that is verbatim copied in the- *  resulting PS file just before and after the structure plot.- *  If both arguments ('pre' and 'post') are NULL, no additional macros will- *  be printed into the PostScript.- *- *  \param string     The RNA sequence- *  \param structure  The secondary structure in dot-bracket notation- *  \param file       The filename of the postscript output- *  \param pre        PostScript code to appear before the secondary structure plot- *  \param post       PostScript code to appear after the secondary structure plot- *  \return           1 on success, 0 otherwise- */-int PS_rna_plot_a(char *string,-                  char *structure,-                  char *file,-                  char *pre,-                  char *post);--int PS_rna_plot_a_gquad(char *string,-                        char *structure,-                        char *ssfile,-                        char *pre,-                        char *post);--/**- *  \brief Produce a secondary structure graph in Graph Meta Language (gml) and write it to a file- *- *  If 'option' is an uppercase letter the RNA sequence is used to label nodes, if 'option' equals- *  \a 'X' or \a 'x' the resulting file will coordinates for an initial layout of the graph.- *- *  \param  string    The RNA sequence- *  \param  structure The secondary structure in dot-bracket notation- *  \param  ssfile    The filename of the gml output- *  \param  option    The option flag- *  \return           1 on success, 0 otherwise- */-int gmlRNA( char *string,-            char *structure,-            char *ssfile,-            char option);--/**- *  \brief  Produce a secondary structure graph in SStructView format- *- *  Write coord file for SStructView- *- *  \param  string    The RNA sequence- *  \param  structure The secondary structure in dot-bracket notation- *  \param  ssfile    The filename of the ssv output- *  \return           1 on success, 0 otherwise- */-int ssv_rna_plot( char *string,-                  char *structure,-                  char *ssfile);--/**- *  \brief Produce a secondary structure plot in SVG format and write it to a file- *- *  \param string     The RNA sequence- *  \param structure  The secondary structure in dot-bracket notation- *  \param ssfile     The filename of the svg output- *  \return           1 on success, 0 otherwise- */-int svg_rna_plot( char *string,-                  char *structure,-                  char *ssfile);--/**- *  \brief Produce a secondary structure plot for further editing in XRNA- *- *  \param string     The RNA sequence- *  \param structure  The secondary structure in dot-bracket notation- *  \param ssfile     The filename of the xrna output- *  \return           1 on success, 0 otherwise- */-int xrna_plot(char *string,-              char *structure,-              char *ssfile);--int PS_color_dot_plot(char *string,-                      cpair *pi,-                      char *filename);--int PS_color_dot_plot_turn( char *seq,-                            cpair *pi,-                            char *filename,-                            int winSize);--/**- *  \brief Produce a postscript dot-plot from two pair lists- *- *  This function reads two plist structures (e.g. base pair probabilities and a secondary structure)- *  as produced by assign_plist_from_pr() and assign_plist_from_db() and produces a postscript- *  "dot plot" that is written to 'filename'.\n- *  Using base pair probabilities in the first and mfe structure in the second plist, the resulting- *  "dot plot" represents each base pairing probability by a square of corresponding area in a upper- *  triangle matrix. The lower part of the matrix contains the minimum free energy structure.- *- *  \see assign_plist_from_pr(), assign_plist_from_db()- *- *  \param seq      The RNA sequence- *  \param filename A filename for the postscript output- *  \param pl       The base pair probability pairlist- *  \param mf       The mfe secondary structure pairlist- *  \param comment  A comment- *  \return         1 if postscript was successfully written, 0 otherwise- */-int PS_dot_plot_list( char *seq,-                      char *filename,-                      plist *pl,-                      plist *mf,-                      char *comment);--int PS_dot_plot_turn( char *seq,-                      struct plist *pl,-                      char *filename,-                      int winSize);--int PS_color_aln( const char *structure,-                  const char *filename,-                  const char *seqs[],-                  const char *names[]);--/**- * 	PS_color_aln for duplexes-*/-int aliPS_color_aln(const char *structure,-                    const char *filename, -                    const char *seqs[],-                    const char *names[]); ---/**- *  Wrapper to PS_dot_plot_list- *- *  \brief Produce postscript dot-plot- *- *  Reads base pair probabilities produced by pf_fold() from the- *  global array #pr and the pair list #base_pair produced by- *  fold() and produces a postscript "dot plot" that is written to- *  'filename'. The "dot plot" represents each base pairing- *  probability by a square of corresponding area in a upper triangle- *  matrix. The lower part of the matrix contains the minimum free energy- *  \note DO NOT USE THIS FUNCTION ANYMORE SINCE IT IS NOT THREADSAFE- *- *  \deprecated This function is deprecated and will be removed soon! Use \ref PS_dot_plot_list() instead!- */-DEPRECATED(int PS_dot_plot( char *string,-                            char *file));-#endif
− include/aln_util.h 
@@ -1,10 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_ALN_UTIL_H__-#define __VIENNA_RNA_PACKAGE_ALN_UTIL_H__--int read_clustal( FILE *clust,-                  char *AlignedSeqs[],-                  char *names[]);-/*@only@*/ /*@notnull@*/ char *consensus(const char *AS[]);-/*@only@*/ /*@notnull@*/ char *consens_mis(const char *AS[]);--#endif
− include/cofold.h 
@@ -1,182 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_COFOLD_H__-#define __VIENNA_RNA_PACKAGE_COFOLD_H__--#include "data_structures.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif--/**- *  \addtogroup cofold- *  \brief Predict structures formed by two molecules upon hybridization.- *- *  The function of an RNA molecule often depends on its interaction with- *  other RNAs. The following routines therefore allow to predict structures- *  formed by two RNA molecules upon hybridization.\n- *  One approach to co-folding two RNAs consists of concatenating the two- *  sequences and keeping track of the concatenation point in all energy- *  evaluations. Correspondingly, many of the cofold() and- *  co_pf_fold() routines below take one sequence string as argument- *  and use the the global variable #cut_point to mark the concatenation- *  point. Note that while the <i>RNAcofold</i> program uses the '&' character- *  to mark the chain break in its input, you should not use an '&' when using- *  the library routines (set #cut_point instead).\n- *  In a second approach to co-folding two RNAs, cofolding is seen as a- *  stepwise process. In the first step the probability of an unpaired region- *  is calculated and in a second step this probability of an unpaired region- *  is  multiplied with the probability of an interaction between the two RNAs.- *  This approach is implemented for the interaction between a long- *  target sequence and a short ligand RNA. Function pf_unstru() calculates- *  the partition function over all unpaired regions in the input- *  sequence. Function pf_interact(), which calculates the- *  partition function over all possible interactions between two- *  sequences, needs both sequence as separate strings as input.- *- */--/**- *  \addtogroup mfe_cofold- *  @{- *  \file cofold.h- * - *  \brief MFE version of cofolding routines- * - *  This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to- *  MFE Cofolding...- *  This also includes the Zuker suboptimals calculations, since they are implemented using the cofold- *  routines.- */--/**- *  \brief Compute the minimum free energy of two interacting RNA molecules- * - *  The code is analog to the fold() function. If #cut_point ==-1 results- *  should be the same as with fold().- * - *  \ingroup mfe_cofold- *- *  \param    sequence  The two sequences concatenated- *  \param    structure Will hold the barcket dot structure of the dimer molecule- *  \return   minimum free energy of the structure- */-float cofold( const char *sequence,-              char *structure);--/**- *  \brief Compute the minimum free energy of two interacting RNA molecules- * - */-float cofold_par( const char *string,-                  char *structure,-                  paramT *parameters,-                  int is_constrained);--/**- *  \brief Free memory occupied by cofold()- */-void      free_co_arrays(void);--/**- *  \brief Recalculate parameters- */-void      update_cofold_params(void);--void      update_cofold_params_par(paramT *parameters);---/**- *  \brief Export the arrays of partition function cofold (with gquadruplex support)- * - *  Export the cofold arrays for use e.g. in the concentration- *  Computations or suboptimal secondary structure backtracking- *- *  \param  f5_p    A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]- *  \param  c_p     A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j- *  \param  fML_p   A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem- *  \param  fM1_p   A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem- *  \param  fc_p    A pointer to the 'fc' array, i.e. array ...- *  \param  ggg_p   A pointer to the 'ggg' array, i.e. array containing best free energy of a gquadruplex delimited by [i,j]- *  \param  indx_p  A pointer to the indexing array used for accessing the energy matrices- *  \param  ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)- */-void export_cofold_arrays_gq( int **f5_p,-                              int **c_p,-                              int **fML_p,-                              int **fM1_p,-                              int **fc_p,-                              int **ggg_p,-                              int **indx_p,-                              char **ptype_p);--/**- *  \brief Export the arrays of partition function cofold- * - *  Export the cofold arrays for use e.g. in the concentration- *  Computations or suboptimal secondary structure backtracking- *- *  \param  f5_p    A pointer to the 'f5' array, i.e. array conatining best free energy in interval [1,j]- *  \param  c_p     A pointer to the 'c' array, i.e. array containing best free energy in interval [i,j] given that i pairs with j- *  \param  fML_p   A pointer to the 'M' array, i.e. array containing best free energy in interval [i,j] for any multiloop segment with at least one stem- *  \param  fM1_p   A pointer to the 'M1' array, i.e. array containing best free energy in interval [i,j] for multiloop segment with exactly one stem- *  \param  fc_p    A pointer to the 'fc' array, i.e. array ...- *  \param  indx_p  A pointer to the indexing array used for accessing the energy matrices- *  \param  ptype_p A pointer to the ptype array containing the base pair types for each possibility (i,j)- */-void export_cofold_arrays(int **f5_p,-                          int **c_p,-                          int **fML_p,-                          int **fM1_p,-                          int **fc_p,-                          int **indx_p,-                          char **ptype_p);---/**- *  @}- */--/**- *  \brief Compute Zuker type suboptimal structures- *- *  Compute Suboptimal structures according to M. Zuker, i.e. for every - *  possible base pair the minimum energy structure containing the resp. base pair. - *  Returns a list of these structures and their energies.- *- *  \ingroup subopt_zuker- *- *  \param  string  RNA sequence- *  \return         List of zuker suboptimal structures- */-SOLUTION  *zukersubopt(const char *string);--/**- *  \brief Compute Zuker type suboptimal structures- *- *  \ingroup subopt_zuker- *- */-SOLUTION  *zukersubopt_par( const char *string,-                            paramT *parameters);--/**- *  \brief get_monomer_free_energies- *- *  Export monomer free energies out of cofold arrays- * - *  \param e1 A pointer to a variable where the energy of molecule A will be written to- *  \param e2 A pointer to a variable where the energy of molecule B will be written to- */-void get_monomere_mfes( float *e1,-                        float *e2);---/**- *  allocate arrays for folding- *  \deprecated{This function is obsolete and will be removed soon!}- */-DEPRECATED(void initialize_cofold(int length));--#endif
− include/config.h 
@@ -1,163 +0,0 @@-/* config.h.  Generated from config.h.in by configure.  */-/* config.h.in.  Generated from configure.ac by autoheader.  */--/* Define to 1 if you have the `erand48' function. */-#define HAVE_ERAND48 1--/* Define to 1 if you have the <float.h> header file. */-#define HAVE_FLOAT_H 1--/* Define to 1 if you have the `floor' function. */-#define HAVE_FLOOR 1--/* Define to 1 if you have the <inttypes.h> header file. */-#define HAVE_INTTYPES_H 1--/* Define to 1 if you have the `m' library (-lm). */-#define HAVE_LIBM 1--/* Define to 1 if you have the <limits.h> header file. */-#define HAVE_LIMITS_H 1--/* Define to 1 if your system has a GNU libc compatible `malloc' function, and-   to 0 otherwise. */-#define HAVE_MALLOC 1--/* Define to 1 if you have the <malloc.h> header file. */-#define HAVE_MALLOC_H 1--/* Define to 1 if you have the <math.h> header file. */-#define HAVE_MATH_H 1--/* Define to 1 if you have the `memmove' function. */-#define HAVE_MEMMOVE 1--/* Define to 1 if you have the <memory.h> header file. */-#define HAVE_MEMORY_H 1--/* Define to 1 if you have the `memset' function. */-#define HAVE_MEMSET 1--/* Define to 1 if you have the `pow' function. */-#define HAVE_POW 1--/* Define to 1 if your system has a GNU libc compatible `realloc' function,-   and to 0 otherwise. */-#define HAVE_REALLOC 1--/* Define to 1 if you have the `rint' function. */-#define HAVE_RINT 1--/* Define to 1 if you have the `sqrt' function. */-#define HAVE_SQRT 1--/* Define to 1 if stdbool.h conforms to C99. */-#define HAVE_STDBOOL_H 1--/* Define to 1 if you have the <stdint.h> header file. */-#define HAVE_STDINT_H 1--/* Define to 1 if you have the <stdlib.h> header file. */-#define HAVE_STDLIB_H 1--/* Define to 1 if you have the `strchr' function. */-#define HAVE_STRCHR 1--/* Define to 1 if you have the `strdup' function. */-#define HAVE_STRDUP 1--/* Define to 1 if you have the <strings.h> header file. */-#define HAVE_STRINGS_H 1--/* Define to 1 if you have the <string.h> header file. */-#define HAVE_STRING_H 1--/* Define to 1 if you have the `strrchr' function. */-#define HAVE_STRRCHR 1--/* Define to 1 if you have the `strstr' function. */-#define HAVE_STRSTR 1--/* Define to 1 if you have the `strtol' function. */-#define HAVE_STRTOL 1--/* Define to 1 if you have the `strtoul' function. */-#define HAVE_STRTOUL 1--/* Define to 1 if you have the <sys/stat.h> header file. */-#define HAVE_SYS_STAT_H 1--/* Define to 1 if you have the <sys/types.h> header file. */-#define HAVE_SYS_TYPES_H 1--/* Define to 1 if you have the <unistd.h> header file. */-#define HAVE_UNISTD_H 1--/* Define to 1 if the system has the type `_Bool'. */-#define HAVE__BOOL 1--/* Define to 1 if your C compiler doesn't accept -c and -o together. */-/* #undef NO_MINUS_C_MINUS_O */--/* Name of package */-#define PACKAGE "ViennaRNA"--/* Define to the address where bug reports for this package should be sent. */-#define PACKAGE_BUGREPORT "rna@tbi.univie.ac.at"--/* Define to the full name of this package. */-#define PACKAGE_NAME "ViennaRNA"--/* Define to the full name and version of this package. */-#define PACKAGE_STRING "ViennaRNA 2.1.5"--/* Define to the one symbol short name of this package. */-#define PACKAGE_TARNAME "ViennaRNA"--/* Define to the home page for this package. */-#define PACKAGE_URL "http://www.tbi.univie.ac.a/~ivo/RNA"--/* Define to the version of this package. */-#define PACKAGE_VERSION "2.1.5"--/* Define to 1 if you have the ANSI C header files. */-#define STDC_HEADERS 1--/* only for gcc */-#define UNUSED __attribute__ ((unused))--/* Compute z-scores for RNALfold */-#define USE_SVM 1--/* Version number of package */-#define VERSION "2.1.5"--/* Analyse{Dists,Seqs} */-#define WITH_CLUSTER 1--/* Define if using the dmalloc debugging malloc package */-/* #undef WITH_DMALLOC */--/* Create the perl interface to RNAlib */-#define WITH_PERL_INTERFACE 1--/* Create the python interface to RNAlib */-/* #undef WITH_PYTHON_INTERFACE */--/* Define to empty if `const' does not conform to ANSI C. */-/* #undef const */--/* Define to `__inline__' or `__inline' if that's what the C compiler-   calls it, or to nothing if 'inline' is not supported under any name.  */-#ifndef __cplusplus-/* #undef inline */-#endif--/* Define to rpl_malloc if the replacement function should be used. */-/* #undef malloc */--/* Define to rpl_realloc if the replacement function should be used. */-/* #undef realloc */--/* Define to `unsigned int' if <sys/types.h> does not define. */-/* #undef size_t */
− include/data_structures.h 
@@ -1,774 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__-#define __VIENNA_RNA_PACKAGE_DATA_STRUCTURES_H__--#include "energy_const.h"-/**- *  \file data_structures.h- *  \brief All datastructures and typedefs shared among the Vienna RNA Package can be found here- */--/* to use floats instead of doubles in pf_fold() comment next line */-#define LARGE_PF-#ifdef  LARGE_PF-#define FLT_OR_DBL double-#else-#define FLT_OR_DBL float-#endif--#ifndef NBASES-#define NBASES 8-#endif--#ifndef MAXALPHA-/**- *  \brief Maximal length of alphabet- */-#define MAXALPHA              20-#endif--/**- *  \brief Maximum density of states discretization for subopt- */-#define MAXDOS                1000--#define   VRNA_GQUAD_MAX_STACK_SIZE     7-#define   VRNA_GQUAD_MIN_STACK_SIZE     2-#define   VRNA_GQUAD_MAX_LINKER_LENGTH  15-#define   VRNA_GQUAD_MIN_LINKER_LENGTH  1-#define   VRNA_GQUAD_MIN_BOX_SIZE       ((4*VRNA_GQUAD_MIN_STACK_SIZE)+(3*VRNA_GQUAD_MIN_LINKER_LENGTH))-#define   VRNA_GQUAD_MAX_BOX_SIZE       ((4*VRNA_GQUAD_MAX_STACK_SIZE)+(3*VRNA_GQUAD_MAX_LINKER_LENGTH))---/*-* ############################################################-* Here are the type definitions of various datastructures-* shared among the Vienna RNA Package-* ############################################################-*/--/**- *  \brief this datastructure is used as input parameter in functions of PS_dot.h and others- */-typedef struct plist {-  int i;-  int j;-  float p;-  int type;-} plist;--/**- *  \brief this datastructure is used as input parameter in functions of PS_dot.c- */-typedef struct cpair {-  int i,j,mfe;-  float p, hue, sat;-} cpair;--/**- *  \brief this is a workarround for the SWIG Perl Wrapper RNA plot function- *  that returns an array of type COORDINATE- */-typedef struct {-  float X; /* X coords */-  float Y; /* Y coords */-} COORDINATE;--/**- *  \brief  Stack of partial structures for backtracking- */-typedef struct sect {-  int  i;-  int  j;-  int ml;-} sect;--/**- *  \brief  Base pair- */-typedef struct bondT {-   unsigned int i;-   unsigned int j;-} bondT;--/**- *  \brief  Base pair with associated energy- */-typedef struct bondTEn {-   int i;-   int j;-   int energy;-} bondTEn;--/**- *  \brief The data structure that contains the complete model details used throughout the calculations- *- */-typedef struct{-  int     dangles;      /**<  \brief  Specifies the dangle model used in any energy evaluation (0,1,2 or 3)-                              \note   Some function do not implement all dangle model but only a subset of-                                      (0,1,2,3). Read the documentaion of the particular recurrences or-                                      energy evaluation function for information about the provided dangle-                                      model.-                        */-  int     special_hp;   /**<  \brief  Include special hairpin contributions for tri, tetra and hexaloops */-  int     noLP;         /**<  \brief  Only consider canonical structures, i.e. no 'lonely' base pairs */-  int     noGU;         /**<  \brief  Do not allow GU pairs */-  int     noGUclosure;  /**<  \brief  Do not allow loops to be closed by GU pair */-  int     logML;        /**<  \brief  Use logarithmic scaling for multi loops */-  int     circ;         /**<  \brief  Assume molecule to be circular */-  int     gquad;        /**<  \brief  Include G-quadruplexes in structure prediction */-} model_detailsT;--/**- *  \brief The datastructure that contains temperature scaled energy parameters.- */-typedef struct{-  int id;-  int stack[NBPAIRS+1][NBPAIRS+1];-  int hairpin[31];-  int bulge[MAXLOOP+1];-  int internal_loop[MAXLOOP+1];-  int mismatchExt[NBPAIRS+1][5][5];-  int mismatchI[NBPAIRS+1][5][5];-  int mismatch1nI[NBPAIRS+1][5][5];-  int mismatch23I[NBPAIRS+1][5][5];-  int mismatchH[NBPAIRS+1][5][5];-  int mismatchM[NBPAIRS+1][5][5];-  int dangle5[NBPAIRS+1][5];-  int dangle3[NBPAIRS+1][5];-  int int11[NBPAIRS+1][NBPAIRS+1][5][5];-  int int21[NBPAIRS+1][NBPAIRS+1][5][5][5];-  int int22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];-  int ninio[5];-  double  lxc;-  int     MLbase;-  int     MLintern[NBPAIRS+1];-  int     MLclosing;-  int     TerminalAU;-  int     DuplexInit;-  int     Tetraloop_E[200];-  char    Tetraloops[1401];-  int     Triloop_E[40];-  char    Triloops[241];-  int     Hexaloop_E[40];-  char    Hexaloops[1801];-  int     TripleC;-  int     MultipleCA;-  int     MultipleCB;-  int     gquad [VRNA_GQUAD_MAX_STACK_SIZE + 1]-                [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];--  double  temperature;            /**<  \brief  Temperature used for loop contribution scaling */--  model_detailsT model_details;   /**<  \brief  Model details to be used in the recursions */--}  paramT;--/**- *  \brief  The datastructure that contains temperature scaled Boltzmann weights of the energy parameters.- */-typedef struct{-  int     id;-  double  expstack[NBPAIRS+1][NBPAIRS+1];-  double  exphairpin[31];-  double  expbulge[MAXLOOP+1];-  double  expinternal[MAXLOOP+1];-  double  expmismatchExt[NBPAIRS+1][5][5];-  double  expmismatchI[NBPAIRS+1][5][5];-  double  expmismatch23I[NBPAIRS+1][5][5];-  double  expmismatch1nI[NBPAIRS+1][5][5];-  double  expmismatchH[NBPAIRS+1][5][5];-  double  expmismatchM[NBPAIRS+1][5][5];-  double  expdangle5[NBPAIRS+1][5];-  double  expdangle3[NBPAIRS+1][5];-  double  expint11[NBPAIRS+1][NBPAIRS+1][5][5];-  double  expint21[NBPAIRS+1][NBPAIRS+1][5][5][5];-  double  expint22[NBPAIRS+1][NBPAIRS+1][5][5][5][5];-  double  expninio[5][MAXLOOP+1];-  double  lxc;-  double  expMLbase;-  double  expMLintern[NBPAIRS+1];-  double  expMLclosing;-  double  expTermAU;-  double  expDuplexInit;-  double  exptetra[40];-  double  exptri[40];-  double  exphex[40];-  char    Tetraloops[1401];-  double  expTriloop[40];-  char    Triloops[241];-  char    Hexaloops[1801];-  double  expTripleC;-  double  expMultipleCA;-  double  expMultipleCB;-  double  expgquad[VRNA_GQUAD_MAX_STACK_SIZE + 1]-                  [3*VRNA_GQUAD_MAX_LINKER_LENGTH + 1];--  double  kT;-  double  pf_scale;     /**<  \brief    Scaling factor to avoid over-/underflows */--  double  temperature;  /**<  \brief    Temperature used for loop contribution scaling */-  double  alpha;        /**<  \brief    Scaling factor for the thermodynamic temperature-                              \details  This allows for temperature scaling in Boltzmann-                                        factors independently from the energy contributions.-                                        The resulting Boltzmann factors are then computed by-                                        \f$ e^{-E/(\alpha \cdot K \cdot T)} \f$-                        */--  model_detailsT model_details; /**<  \brief  Model details to be used in the recursions */--}  pf_paramT;----/*-* ############################################################-* SUBOPT data structures-* ############################################################-*/---/**- *  \brief  Base pair data structure used in subopt.c- */-typedef struct {-  int i;-  int j;-} PAIR;--/**- *  \brief  Sequence interval stack element used in subopt.c- */-typedef struct {-    int i;-    int j;-    int array_flag;-} INTERVAL;--/**- *  \brief  Solution element from subopt.c- */-typedef struct {-  float energy;       /**< \brief Free Energy of structure in kcal/mol */-  char *structure;    /**< \brief Structure in dot-bracket notation */-} SOLUTION;--/*-* ############################################################-* COFOLD data structures-* ############################################################-*/--/**- *  \brief  - */-typedef struct cofoldF {-  /* free energies for: */-  double F0AB;  /**< \brief Null model without DuplexInit */-  double FAB;   /**< \brief all states with DuplexInit correction */-  double FcAB;  /**< \brief true hybrid states only */-  double FA;    /**< \brief monomer A */-  double FB;    /**< \brief monomer B */-} cofoldF;--/**- *  \brief  - */-typedef struct ConcEnt {-  double A0;    /**< \brief start concentration A */-  double B0;    /**< \brief start concentration B */-  double ABc;   /**< \brief End concentration AB */-  double AAc;-  double BBc;-  double Ac;-  double Bc;-} ConcEnt;--/**- *  \brief  - */-typedef struct pairpro{-  struct plist *AB;-  struct plist *AA;-  struct plist *A;-  struct plist *B;-  struct plist *BB;-}pairpro;--/**- *  \brief A base pair info structure- *- *  For each base pair (i,j) with i,j in [0, n-1] the structure lists:- *  - its probability 'p'- *  - an entropy-like measure for its well-definedness 'ent'- *  - the frequency of each type of pair in 'bp[]'- *    + 'bp[0]' contains the number of non-compatible sequences- *    + 'bp[1]' the number of CG pairs, etc.- */-typedef struct {-   unsigned i;    /**<  \brief  nucleotide position i */ -   unsigned j;    /**<  \brief  nucleotide position j */-   float p;       /**< \brief  Probability */-   float ent;     /**< \brief  Pseudo entropy for \f$ p(i,j) = S_i + S_j - p_ij*ln(p_ij) \f$ */-   short bp[8];   /**< \brief  Frequencies of pair_types */-   char comp;     /**< \brief  1 iff pair is in mfe structure */-} pair_info;---/*-* ############################################################-* FINDPATH data structures-* ############################################################-*/--/**- *  \brief  - */-typedef struct move {-  int i;  /* i,j>0 insert; i,j<0 delete */-  int j;-  int when;  /* 0 if still available, else resulting distance from start */-  int E;-} move_t;--/**- *  \brief  - */-typedef struct intermediate {-  short *pt;      /**<  \brief  pair table */-  int Sen;        /**<  \brief  saddle energy so far */-  int curr_en;    /**<  \brief  current energy */-  move_t *moves;  /**<  \brief  remaining moves to target */-} intermediate_t;--/**- *  \brief  - */-typedef struct path {-  double en;-  char *s;-} path_t;--/*-* ############################################################-* RNAup data structures-* ############################################################-*/--/**- *  \brief contributions to p_u- */-typedef struct pu_contrib {-  double **H; /**<  \brief  hairpin loops */-  double **I; /**<  \brief  interior loops */-  double **M; /**<  \brief  multi loops */-  double **E; /**<  \brief  exterior loop */-  int length; /**<  \brief  length of the input sequence */-  int w;      /**<  \brief  longest unpaired region */-} pu_contrib;--/**- *  \brief  - */-typedef struct interact {-  double *Pi;       /**<  \brief  probabilities of interaction */-  double *Gi;       /**<  \brief  free energies of interaction */-  double Gikjl;     /**<  \brief  full free energy for interaction between [k,i] k<i-                                  in longer seq and [j,l] j<l in shorter seq */-  double Gikjl_wo;  /**<  \brief  Gikjl without contributions for prob_unpaired */-  int i;            /**<  \brief  k<i in longer seq */-  int k;            /**<  \brief  k<i in longer seq */-  int j;            /**<  \brief  j<l in shorter seq */-  int l;            /**<  \brief  j<l in shorter seq */-  int length;       /**<  \brief  length of longer sequence */-} interact;--/**- *  \brief  Collection of all free_energy of beeing unpaired values for output- */-typedef struct pu_out {-  int len;            /**<  \brief  sequence length */-  int u_vals;         /**<  \brief  number of different -u values */-  int contribs;       /**<  \brief  [-c "SHIME"] */-  char **header;      /**<  \brief  header line */-  double **u_values;  /**<  \brief  (the -u values * [-c "SHIME"]) * seq len */-} pu_out;--/**- *  \brief  constraints for cofolding - */-typedef struct constrain{-  int *indx;-  char *ptype;-} constrain;--/*-* ############################################################-* RNAduplex data structures-* ############################################################-*/--/**- *  \brief  - */-typedef struct {-  int i;-  int j;-  int end;-  char *structure;-  double energy;-  double energy_backtrack;-  double opening_backtrack_x;-  double opening_backtrack_y;-  int offset;-  double dG1;-  double dG2;-  double ddG;-  int tb;-  int te;-  int qb;-  int qe;-} duplexT;--/*-* ############################################################-* RNAsnoop data structures-* ############################################################-*/--/**- *  \brief  - */-typedef struct node {-  int k;-  int energy;-  struct node *next;-} folden;--/**- *  \brief  - */-typedef struct {-  int i;-  int j;-  int u;-  char *structure;-  float energy;-  float Duplex_El;-  float Duplex_Er;-  float Loop_E;-  float Loop_D;-  float pscd;-  float psct;-  float pscg;-  float Duplex_Ol;-  float Duplex_Or;-  float Duplex_Ot;-  float fullStemEnergy;-} snoopT;--------/*-* ############################################################-* PKplex data structures-* ############################################################-*/--/**- *  \brief  - */-typedef struct dupVar{-  int i;-  int j;-  int end;-  char *pk_helix;-  char *structure;-  double energy;-  int offset;-  double dG1;-  double dG2;-  double ddG;-  int tb;-  int te;-  int qb;-  int qe;-  int inactive;-  int processed;-} dupVar;----/*-* ############################################################-* 2Dfold data structures-* ############################################################-*/--/**- *  \brief Solution element returned from TwoDfoldList- *- *  This element contains free energy and structure for the appropriate- *  kappa (k), lambda (l) neighborhood- *  The datastructure contains two integer attributes 'k' and 'l'- *  as well as an attribute 'en' of type float representing the free energy- *  in kcal/mol and an attribute 's' of type char* containg the secondary- *  structure representative,- *- *  A value of #INF in k denotes the end of a list- *- *  \see  TwoDfoldList()- */-typedef struct{-  int k;          /**<  \brief  Distance to first reference */-  int l;          /**<  \brief  Distance to second reference */-  float en;       /**<  \brief  Free energy in kcal/mol */-  char *s;        /**<  \brief  MFE representative structure in dot-bracket notation */-} TwoDfold_solution;--/**- *  \brief Variables compound for 2Dfold MFE folding- *- *  \see get_TwoDfold_variables(), destroy_TwoDfold_variables(), TwoDfoldList()- */-typedef struct{-  paramT          *P;             /**<  \brief  Precomputed energy parameters and model details */-  int             do_backtrack;   /**<  \brief  Flag whether to do backtracing of the structure(s) or not */-  char            *ptype;         /**<  \brief  Precomputed array of pair types */-  char            *sequence;      /**<  \brief  The input sequence  */-  short           *S, *S1;        /**<  \brief  The input sequences in numeric form */-  unsigned int    maxD1;          /**<  \brief  Maximum allowed base pair distance to first reference */-  unsigned int    maxD2;          /**<  \brief  Maximum allowed base pair distance to second reference */---  unsigned int    *mm1;           /**<  \brief  Maximum matching matrix, reference struct 1 disallowed */-  unsigned int    *mm2;           /**<  \brief  Maximum matching matrix, reference struct 2 disallowed */--  int             *my_iindx;      /**<  \brief  Index for moving in quadratic distancy dimensions */--  double          temperature;--  unsigned int    *referenceBPs1; /**<  \brief  Matrix containing number of basepairs of reference structure1 in interval [i,j] */-  unsigned int    *referenceBPs2; /**<  \brief  Matrix containing number of basepairs of reference structure2 in interval [i,j] */-  unsigned int    *bpdist;        /**<  \brief  Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */--  short           *reference_pt1;-  short           *reference_pt2;-  int             circ;-  int             dangles;-  unsigned int    seq_length;--  int             ***E_F5;-  int             ***E_F3;-  int             ***E_C;-  int             ***E_M;-  int             ***E_M1;-  int             ***E_M2;--  int             **E_Fc;-  int             **E_FcH;-  int             **E_FcI;-  int             **E_FcM;--  int             **l_min_values;-  int             **l_max_values;-  int             *k_min_values;-  int             *k_max_values;--  int             **l_min_values_m;-  int             **l_max_values_m;-  int             *k_min_values_m;-  int             *k_max_values_m;--  int             **l_min_values_m1;-  int             **l_max_values_m1;-  int             *k_min_values_m1;-  int             *k_max_values_m1;--  int             **l_min_values_f;-  int             **l_max_values_f;-  int             *k_min_values_f;-  int             *k_max_values_f;--  int             **l_min_values_f3;-  int             **l_max_values_f3;-  int             *k_min_values_f3;-  int             *k_max_values_f3;--  int             **l_min_values_m2;-  int             **l_max_values_m2;-  int             *k_min_values_m2;-  int             *k_max_values_m2;--  int             *l_min_values_fc;-  int             *l_max_values_fc;-  int             k_min_values_fc;-  int             k_max_values_fc;--  int             *l_min_values_fcH;-  int             *l_max_values_fcH;-  int             k_min_values_fcH;-  int             k_max_values_fcH;--  int             *l_min_values_fcI;-  int             *l_max_values_fcI;-  int             k_min_values_fcI;-  int             k_max_values_fcI;--  int             *l_min_values_fcM;-  int             *l_max_values_fcM;-  int             k_min_values_fcM;-  int             k_max_values_fcM;--  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */-  int             *E_F5_rem;-  int             *E_F3_rem;-  int             *E_C_rem;-  int             *E_M_rem;-  int             *E_M1_rem;-  int             *E_M2_rem;--  int             E_Fc_rem;-  int             E_FcH_rem;-  int             E_FcI_rem;-  int             E_FcM_rem;--#ifdef COUNT_STATES-  unsigned long             ***N_F5;-  unsigned long             ***N_C;-  unsigned long             ***N_M;-  unsigned long             ***N_M1;-#endif-} TwoDfold_vars;--/**- *  \brief Solution element returned from TwoDpfoldList- *- *  This element contains the partition function for the appropriate- *  kappa (k), lambda (l) neighborhood- *  The datastructure contains two integer attributes 'k' and 'l'- *  as well as an attribute 'q' of type #FLT_OR_DBL- *- *  A value of #INF in k denotes the end of a list- *- *  \see  TwoDpfoldList()- */-typedef struct{-  int k;          /**<  \brief  Distance to first reference */-  int l;          /**<  \brief  Distance to second reference */-  FLT_OR_DBL  q;  /**<  \brief  partition function */-} TwoDpfold_solution;--/**- *  \brief  Variables compound for 2Dfold partition function folding- *- *  \see    get_TwoDpfold_variables(), get_TwoDpfold_variables_from_MFE(),- *          destroy_TwoDpfold_variables(), TwoDpfoldList()- */-typedef struct{--  unsigned int    alloc;-  char            *ptype;         /**<  \brief  Precomputed array of pair types */-  char            *sequence;      /**<  \brief  The input sequence  */-  short           *S, *S1;        /**<  \brief  The input sequences in numeric form */-  unsigned int    maxD1;          /**<  \brief  Maximum allowed base pair distance to first reference */-  unsigned int    maxD2;          /**<  \brief  Maximum allowed base pair distance to second reference */--  double          temperature;    /* temperature in last call to scale_pf_params */-  double          init_temp;      /* temperature in last call to scale_pf_params */-  FLT_OR_DBL      *scale;-  FLT_OR_DBL      pf_scale;-  pf_paramT       *pf_params;     /* holds all [unscaled] pf parameters */--  int             *my_iindx;      /**<  \brief  Index for moving in quadratic distancy dimensions */-  int             *jindx;         /**<  \brief  Index for moving in the triangular matrix qm1 */--  short           *reference_pt1;-  short           *reference_pt2;--  unsigned int    *referenceBPs1; /**<  \brief  Matrix containing number of basepairs of reference structure1 in interval [i,j] */-  unsigned int    *referenceBPs2; /**<  \brief  Matrix containing number of basepairs of reference structure2 in interval [i,j] */-  unsigned int    *bpdist;        /**<  \brief  Matrix containing base pair distance of reference structure 1 and 2 on interval [i,j] */--  unsigned int    *mm1;           /**<  \brief  Maximum matching matrix, reference struct 1 disallowed */-  unsigned int    *mm2;           /**<  \brief  Maximum matching matrix, reference struct 2 disallowed */--  int             circ;-  int             dangles;-  unsigned int    seq_length;--  FLT_OR_DBL      ***Q;-  FLT_OR_DBL      ***Q_B;-  FLT_OR_DBL      ***Q_M;-  FLT_OR_DBL      ***Q_M1;-  FLT_OR_DBL      ***Q_M2;--  FLT_OR_DBL      **Q_c;-  FLT_OR_DBL      **Q_cH;-  FLT_OR_DBL      **Q_cI;-  FLT_OR_DBL      **Q_cM;--  int             **l_min_values;-  int             **l_max_values;-  int             *k_min_values;-  int             *k_max_values;--  int             **l_min_values_b;-  int             **l_max_values_b;-  int             *k_min_values_b;-  int             *k_max_values_b;--  int             **l_min_values_m;-  int             **l_max_values_m;-  int             *k_min_values_m;-  int             *k_max_values_m;--  int             **l_min_values_m1;-  int             **l_max_values_m1;-  int             *k_min_values_m1;-  int             *k_max_values_m1;--  int             **l_min_values_m2;-  int             **l_max_values_m2;-  int             *k_min_values_m2;-  int             *k_max_values_m2;--  int             *l_min_values_qc;-  int             *l_max_values_qc;-  int             k_min_values_qc;-  int             k_max_values_qc;--  int             *l_min_values_qcH;-  int             *l_max_values_qcH;-  int             k_min_values_qcH;-  int             k_max_values_qcH;--  int             *l_min_values_qcI;-  int             *l_max_values_qcI;-  int             k_min_values_qcI;-  int             k_max_values_qcI;--  int             *l_min_values_qcM;-  int             *l_max_values_qcM;-  int             k_min_values_qcM;-  int             k_max_values_qcM;--  /* auxilary arrays for remaining set of coarse graining (k,l) > (k_max, l_max) */-  FLT_OR_DBL      *Q_rem;-  FLT_OR_DBL      *Q_B_rem;-  FLT_OR_DBL      *Q_M_rem;-  FLT_OR_DBL      *Q_M1_rem;-  FLT_OR_DBL      *Q_M2_rem;--  FLT_OR_DBL      Q_c_rem;-  FLT_OR_DBL      Q_cH_rem;-  FLT_OR_DBL      Q_cI_rem;-  FLT_OR_DBL      Q_cM_rem;--} TwoDpfold_vars;--#endif
− include/energy_const.h 
@@ -1,33 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__-#define __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__--#include <limits.h>--/**- *  \file energy_const.h- *  energy constants- */--/** The gas constant */-#define GASCONST 1.98717  /* in [cal/K] */-/** 0 deg Celsius in Kelvin */-#define K0  273.15-/** Infinity as used in minimization routines */-#define INF 10000000 /* (INT_MAX/10) */--#define EMAX (INF/10)-/** forbidden */-#define FORBIDDEN 9999-/** bonus contribution */-#define BONUS 10000-/** The number of distinguishable base pairs */-#define NBPAIRS 7-/** The minimum loop length */-#define TURN 3-/** The maximum loop length */-#define MAXLOOP 30--#define   VRNA_GQUAD_MISMATCH_PENALTY   300   /* penalty for incompatible nucleotides in an alignment that destruct a gquad layer */-#define   VRNA_GQUAD_MISMATCH_NUM_ALI   1   /* maximum number of mismatching sequences in the alignment when gquad should be formed */--#endif
− include/energy_par.h 
@@ -1,100 +0,0 @@-/*-   prototypes for energy_par.c-*/--#ifndef __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__-#define __VIENNA_RNA_PACKAGE_ENERGY_PAR_H__--#include "energy_const.h"--#define PUBLIC---extern double lxc37;   /* parameter for logarithmic loop-			  energy extrapolation            */--extern int stack37[NBPAIRS+1][NBPAIRS+1];-extern int stackdH[NBPAIRS+1][NBPAIRS+1]; /* stack enthalpies */-extern int entropies[NBPAIRS+1][NBPAIRS+1];  /* not used anymore */--extern int hairpin37[31];-extern int hairpindH[31];-extern int bulge37[31];-extern int bulgedH[31];-extern int internal_loop37[31];-extern int internal_loopdH[31];-extern int internal2_energy;-extern int old_mismatch_37[NBPAIRS+1][5][5];-extern int mismatchI37[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatchIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatch1nI37[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatch23I37[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatch1nIdH[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatch23IdH[NBPAIRS+1][5][5];  /* interior loop mismatches */-extern int mismatchH37[NBPAIRS+1][5][5];  /* same for hairpins */-extern int mismatchM37[NBPAIRS+1][5][5];  /* same for multiloops */-extern int mismatchHdH[NBPAIRS+1][5][5];  /* same for hairpins */-extern int mismatchMdH[NBPAIRS+1][5][5];  /* same for multiloops */-extern int mismatchExt37[NBPAIRS+1][5][5];-extern int mismatchExtdH[NBPAIRS+1][5][5];--extern int dangle5_37[NBPAIRS+1][5];      /* 5' dangle exterior of pair */-extern int dangle3_37[NBPAIRS+1][5];      /* 3' dangle */-extern int dangle3_dH[NBPAIRS+1][5];       /* corresponding enthalpies */-extern int dangle5_dH[NBPAIRS+1][5];--extern int int11_37[NBPAIRS+1][NBPAIRS+1][5][5]; /* 1x1 interior loops */-extern int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5];--extern int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5]; /* 2x1 interior loops */-extern int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5];--extern int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5]; /* 2x2 interior loops */-extern int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5];--/* constants for linearly destabilizing contributions for multi-loops-   F = ML_closing + ML_intern*(k-1) + ML_BASE*u  */-extern int ML_BASE37;-extern int ML_BASEdH;-extern int ML_closing37;-extern int ML_closingdH;-extern int ML_intern37;-extern int ML_interndH;--extern int TripleC37;-extern int TripleCdH;-extern int MultipleCA37;-extern int MultipleCAdH;-extern int MultipleCB37;-extern int MultipleCBdH;--/* Ninio-correction for asymmetric internal loops with branches n1 and n2 */-/*    ninio_energy = min{max_ninio, |n1-n2|*F_ninio[min{4.0, n1, n2}] } */-extern int  MAX_NINIO;                   /* maximum correction */-extern int ninio37;-extern int niniodH;-/* penalty for helices terminated by AU (actually not GC) */-extern int TerminalAU37;-extern int TerminalAUdH;-/* penalty for forming bi-molecular duplex */-extern int DuplexInit37;-extern int DuplexInitdH;-/* stabilizing contribution due to special hairpins of size 4 (tetraloops) */-extern char Tetraloops[];  /* string containing the special tetraloops */-extern int  Tetraloop37[];  /* Bonus energy for special tetraloops */-extern int  TetraloopdH[];-extern char Triloops[];    /* string containing the special triloops */-extern int  Triloop37[]; /* Bonus energy for special Triloops */-extern int  TriloopdH[]; /* Bonus energy for special Triloops */-extern char Hexaloops[];    /* string containing the special triloops */-extern int  Hexaloop37[]; /* Bonus energy for special Triloops */-extern int  HexaloopdH[]; /* Bonus energy for special Triloops */--extern int GQuadAlpha37;-extern int GQuadAlphadH;-extern int GQuadBeta37;-extern int GQuadBetadH;--extern double Tmeasure;       /* temperature of param measurements */--#endif
− include/fold.h 
@@ -1,604 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_FOLD_H__-#define __VIENNA_RNA_PACKAGE_FOLD_H__--#include "data_structures.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif--/**- *  \addtogroup mfe_fold- *  \ingroup folding_routines- *  \brief This section covers all functions and variables related to the calculation- *  of minimum free energy (MFE) structures.- *- *  The library provides a fast dynamic programming minimum free energy- *  folding algorithm as described in \cite zuker:1981.- *  All relevant parts that directly implement the "Zuker & Stiegler" algorithm for single- *  sequences are described in this section.- *- *  Folding of circular RNA sequences is handled as a post-processing step of the forward- *  recursions. See \cite hofacker:2006 for further details.- *- *  Nevertheless, the RNAlib also- *  provides interfaces for the prediction of consensus MFE structures of sequence alignments,- *  MFE structure for two hybridized sequences, local optimal structures and many more. For- *  those more specialized variants of MFE folding routines, please consult the appropriate- *  subsections (Modules) as listed above.- *  - *  \file fold.h- *  \brief MFE calculations and energy evaluations for single RNA sequences- * - *  This file includes (almost) all function declarations within the RNAlib that are related to- *  MFE folding...- */--/**- *  \defgroup eval Energy evaluation- *  @{- *    \brief This module contains all functions and variables related to energy evaluation- *    of sequence/structure pairs.- *- *- *  @}- */--/**- *  \defgroup mfe_fold Calculating Minimum Free Energy Structures- *  @{- *    \brief This module contains all functions and variables related to the calculation- *    of global minimum free energy structures for single sequences.- *- *    The library provides a fast dynamic programming minimum free energy- *    folding algorithm as described by \ref zuker_81 "Zuker & Stiegler (1981)".- *  @}- */--/** \brief if nonzero use logarithmic ML energy in energy_of_struct  */-extern  int logML;--/** \brief do ML decomposition uniquely (for subopt)  */-extern  int uniq_ML;--/** \brief set to first pos of second seq for cofolding  */-extern  int cut_point;--/**- *  \brief verbose info from energy_of_struct- *  \ingroup eval- */-extern  int eos_debug;---/**- *  \brief Compute minimum free energy and an appropriate secondary- *  structure of an RNA sequence- * - *  The first parameter given, the RNA sequence, must be \a uppercase and should only contain- *  an alphabet \f$\Sigma\f$ that is understood by the RNAlib\n- *  (e.g. \f$ \Sigma = \{A,U,C,G\} \f$)\n- *- *  The second parameter, \a structure, must always point to an allocated- *  block of memory with a size of at least \f$\mathrm{strlen}(\mathrm{sequence})+1\f$- *- *  If the third parameter is NULL, global model detail settings are assumed for the folding- *  recursions. Otherwise, the provided parameters are used.- *- *  The fourth parameter indicates whether a secondary structure constraint in enhanced dot-bracket- *  notation is passed through the structure parameter or not. If so, the characters " | x < > " are- *  recognized to mark bases that are paired, unpaired, paired upstream, or downstream, respectively.- *  Matching brackets " ( ) " denote base pairs, dots "." are used for unconstrained bases.- *- *  To indicate that the RNA sequence is circular and thus has to be post-processed, set the last- *  parameter to non-zero- *- *  After a successful call of fold_par(), a backtracked secondary structure (in dot-bracket notation)- *  that exhibits the minimum of free energy will be written to the memory \a structure is pointing to.- *  The function returns the minimum of free energy for any fold of the sequence given.- *- *  \note OpenMP: Passing NULL to the 'parameters' argument involves access to several global model- *        detail variables and thus is not to be considered threadsafe- *- *  \ingroup mfe_fold- *- *  \see fold(), circfold(), #model_detailsT, set_energy_model(), get_scaled_parameters()- *- *  \param sequence       RNA sequence- *  \param structure      A pointer to the character array where the- *                        secondary structure in dot-bracket notation will be written to- *  \param parameters     A data structure containing the prescaled energy contributions- *                        and the model details. (NULL may be passed, see OpenMP notes above)- *  \param is_constrained Switch to indicate that a structure contraint is passed via the structure argument (0==off)- *  \param is_circular    Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off)- *- *  \return the minimum free energy (MFE) in kcal/mol- */-float fold_par( const char *sequence,-                char *structure,-                paramT *parameters,-                int is_constrained,-                int is_circular);--/**- *  \brief Compute minimum free energy and an appropriate secondary structure of an RNA sequence- *- *  This function essentially does the same thing as fold_par(). However, it takes its model details,- *  i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs- *  from the current global settings within the library- *- *  Use fold_par() for a completely threadsafe variant- *- *  \ingroup mfe_fold- *- *  \see fold_par(), circfold()- *- *  \param sequence RNA sequence- *  \param structure A pointer to the character array where the- *         secondary structure in dot-bracket notation will be written to- *  \return the minimum free energy (MFE) in kcal/mol- */-float fold( const char *sequence,-            char *structure);--/**- *  \brief Compute minimum free energy and an appropriate secondary structure of a circular RNA sequence- *- *  This function essentially does the same thing as fold_par(). However, it takes its model details,- *  i.e. #temperature, #dangles, #tetra_loop, #noGU, #no_closingGU, #fold_constrained, #noLonelyPairs- *  from the current global settings within the library- *- *  Use fold_par() for a completely threadsafe variant- *- *  \ingroup mfe_fold- *- *  \see fold_par(), circfold()- *- *  \param sequence RNA sequence- *  \param structure A pointer to the character array where the- *         secondary structure in dot-bracket notation will be written to- *  \return the minimum free energy (MFE) in kcal/mol- */-float circfold( const char *sequence,-                char *structure);---/**- *  \addtogroup eval Energy evaluation- *  \ingroup folding_routines- *  @{- *    \brief This module contains all functions and variables related to energy evaluation- *    of sequence/structure pairs.- *  @}- */--/**- *  \brief Calculate the free energy of an already folded RNA using global model detail settings- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \note OpenMP: This function relies on several global model settings variables and thus is- *        not to be considered threadsafe. See energy_of_struct_par() for a completely threadsafe- *        implementation.- *- *  \ingroup eval- *- *  \see energy_of_struct_par(), energy_of_circ_structure()- *- *  \param string     RNA sequence- *  \param structure  secondary structure in dot-bracket notation- *  \param verbosity_level a flag to turn verbose output on/off- *  \return          the free energy of the input structure given the input sequence in kcal/mol- */-float energy_of_structure(const char *string,-                          const char *structure,-                          int verbosity_level);--/**- *  \brief Calculate the free energy of an already folded RNA- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \ingroup eval- *- *  \see energy_of_circ_structure(), energy_of_structure_pt(), get_scaled_parameters()- *- *  \param string           RNA sequence in uppercase letters- *  \param structure        Secondary structure in dot-bracket notation- *  \param parameters       A data structure containing the prescaled energy contributions and the model details.- *  \param verbosity_level  A flag to turn verbose output on/off- *  \return                The free energy of the input structure given the input sequence in kcal/mol- */-float energy_of_struct_par( const char *string,-                            const char *structure,-                            paramT *parameters,-                            int verbosity_level);--/**- *  \brief Calculate the free energy of an already folded  circular RNA- *- *  \note OpenMP: This function relies on several global model settings variables and thus is- *        not to be considered threadsafe. See energy_of_circ_struct_par() for a completely threadsafe- *        implementation.- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \ingroup eval- *- *  \see energy_of_circ_struct_par(), energy_of_struct_par()- *- *  \param string           RNA sequence- *  \param structure        Secondary structure in dot-bracket notation- *  \param verbosity_level  A flag to turn verbose output on/off- *  \return                The free energy of the input structure given the input sequence in kcal/mol- */-float energy_of_circ_structure( const char *string,-                                const char *structure,-                                int verbosity_level);--/**- *  \brief Calculate the free energy of an already folded circular RNA- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \ingroup eval- *- *  \see energy_of_struct_par(), get_scaled_parameters()- *- *  \param string           RNA sequence- *  \param structure        Secondary structure in dot-bracket notation- *  \param parameters       A data structure containing the prescaled energy contributions and the model details.- *  \param verbosity_level  A flag to turn verbose output on/off- *  \return                The free energy of the input structure given the input sequence in kcal/mol- */-float energy_of_circ_struct_par(const char *string,-                                const char *structure,-                                paramT *parameters,-                                int verbosity_level);---float energy_of_gquad_structure(const char *string,-                                const char *structure,-                                int verbosity_level);--float energy_of_gquad_struct_par( const char *string,-                                  const char *structure,-                                  paramT *parameters,-                                  int verbosity_level);--/**- *  \brief Calculate the free energy of an already folded RNA- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \note OpenMP: This function relies on several global model settings variables and thus is- *        not to be considered threadsafe. See energy_of_struct_pt_par() for a completely threadsafe- *        implementation.- *- *  \ingroup eval- *- *  \see make_pair_table(), energy_of_struct_pt_par()- *- *  \param string     RNA sequence- *  \param ptable     the pair table of the secondary structure- *  \param s          encoded RNA sequence- *  \param s1         encoded RNA sequence- *  \param verbosity_level a flag to turn verbose output on/off- *  \return          the free energy of the input structure given the input sequence in 10kcal/mol- */-int energy_of_structure_pt( const char *string,-                            short *ptable,-                            short *s,-                            short *s1,-                            int verbosity_level);--/**- *  \brief Calculate the free energy of an already folded RNA- *- *  If verbosity level is set to a value >0, energies of structure elements are printed to stdout- *- *  \ingroup eval- *- *  \see make_pair_table(), energy_of_struct_par(), get_scaled_parameters()- *- *  \param string           RNA sequence in uppercase letters- *  \param ptable           The pair table of the secondary structure- *  \param s                Encoded RNA sequence- *  \param s1               Encoded RNA sequence- *  \param parameters       A data structure containing the prescaled energy contributions and the model details.- *  \param verbosity_level  A flag to turn verbose output on/off- *  \return                The free energy of the input structure given the input sequence in 10kcal/mol- */-int energy_of_struct_pt_par(const char *string,-                            short *ptable,-                            short *s,-                            short *s1,-                            paramT *parameters,-                            int verbosity_level);--/**- *  \brief Free arrays for mfe folding- *- *  \ingroup mfe_fold- *- */-void  free_arrays(void);---/**- *  \brief Create a dot-backet/parenthesis structure from backtracking stack- * - *  \note This function is threadsafe- */-void  parenthesis_structure(char *structure,-                            bondT *bp,-                            int length);--/**- *  \brief Create a dot-backet/parenthesis structure from backtracking stack- *  obtained by zuker suboptimal calculation in cofold.c- * - *  \note This function is threadsafe- */-void parenthesis_zuker( char *structure,-                        bondT *bp,-                        int length);--void letter_structure(char *structure,-                      bondT *bp,-                      int length);---/**- *  \brief Recalculate energy parameters- *- *  \ingroup mfe_fold- */-void  update_fold_params(void);--/**- *- *  \ingroup mfe_fold- * - */-void update_fold_params_par(paramT *parameters);--/**- *- *  \ingroup mfe_fold- * - */-char  *backtrack_fold_from_pair(char *sequence,-                                int i,-                                int j);--/** - * \brief Calculate energy of a move (closing or opening of a base pair)- *- *  If the parameters m1 and m2 are negative, it is deletion (opening)- *  of a base pair, otherwise it is insertion (opening).- *- *  \see              make_pair_table(), energy_of_move()- *  \param string     RNA sequence- *  \param structure  secondary structure in dot-bracket notation- *  \param m1         first coordinate of base pair- *  \param m2         second coordinate of base pair- *  \returns          energy change of the move in kcal/mol- */-float energy_of_move( const char *string,-                      const char *structure,-                      int m1,-                      int m2);---/**- * - * \brief Calculate energy of a move (closing or opening of a base pair)- *- *  If the parameters m1 and m2 are negative, it is deletion (opening)- *  of a base pair, otherwise it is insertion (opening).- *- *  \see              make_pair_table(), energy_of_move()- *  \param pt         the pair table of the secondary structure- *  \param s          encoded RNA sequence- *  \param s1         encoded RNA sequence- *  \param m1         first coordinate of base pair- *  \param m2         second coordinate of base pair- *  \returns          energy change of the move in 10cal/mol- */-int energy_of_move_pt(short *pt,-                   short *s,-                   short *s1,-                   int m1,-                   int m2);--/**- * \brief Calculate energy of a loop- *- *  \param ptable     the pair table of the secondary structure- *  \param s          encoded RNA sequence- *  \param s1         encoded RNA sequence- *  \param i          position of covering base pair- *  \returns          free energy of the loop in 10cal/mol- */-int   loop_energy(short *ptable,-                  short *s,-                  short *s1,-                  int i);--/**- *- *  \ingroup mfe_fold- * - */-void export_fold_arrays(int **f5_p,-                        int **c_p,-                        int **fML_p,-                        int **fM1_p,-                        int **indx_p,-                        char **ptype_p);--/**- *- *  \ingroup mfe_fold- * - */-void export_fold_arrays_par(int **f5_p,-                            int **c_p,-                            int **fML_p,-                            int **fM1_p,-                            int **indx_p,-                            char **ptype_p,-                            paramT **P_p);--/**- *- *  \ingroup mfe_fold- * - */-void export_circfold_arrays(int *Fc_p,-                            int *FcH_p,-                            int *FcI_p,-                            int *FcM_p,-                            int **fM2_p,-                            int **f5_p,-                            int **c_p,-                            int **fML_p,-                            int **fM1_p,-                            int **indx_p,-                            char **ptype_p);--/**- *- *  \ingroup mfe_fold- * - */-void export_circfold_arrays_par(int *Fc_p,-                                int *FcH_p,-                                int *FcI_p,-                                int *FcM_p,-                                int **fM2_p,-                                int **f5_p,-                                int **c_p,-                                int **fML_p,-                                int **fM1_p,-                                int **indx_p,-                                char **ptype_p,-                                paramT **P_p);---/**- *  \brief Create a plist from a dot-bracket string- * - *  The dot-bracket string is parsed and for each base pair an- *  entry in the plist is created. The probability of each pair in- *  the list is set by a function parameter.- * - *  The end of the plist is marked by sequence positions i as well as j- *  equal to 0. This condition should be used to stop looping over its- *  entries- * - *  This function is threadsafe- * - *  \param pl     A pointer to the plist that is to be created- *  \param struc  The secondary structure in dot-bracket notation- *  \param pr     The probability for each base pair- */-void assign_plist_from_db(plist **pl,-                          const char *struc,-                          float pr);--/* finally moved the loop energy function declarations to this header...  */-/* BUT: The functions only exist for backward compatibility reasons!      */-/* You better include "loop_energies.h" and call the functions:           */-/* E_Hairpin() and E_IntLoop() which are (almost) threadsafe as they get  */-/* a pointer to the energy parameter datastructure as additional argument */--/**- *  \deprecated {This function is deprecated and will be removed soon.- *  Use \ref E_IntLoop() instead!}- */-DEPRECATED(int LoopEnergy(int n1,-                          int n2,-                          int type,-                          int type_2,-                          int si1,-                          int sj1,-                          int sp1,-                          int sq1));--/**- *  \deprecated {This function is deprecated and will be removed soon.- *  Use \ref E_Hairpin() instead!}- */-DEPRECATED(int HairpinE(int size,-                        int type,-                        int si1,-                        int sj1,-                        const char *string));--/**- *  Allocate arrays for folding\n- *  \deprecated {This function is deprecated and will be removed soon!}- * - */-DEPRECATED(void initialize_fold(int length));--/**- *  Calculate the free energy of an already folded RNA- * - *  \note This function is not entirely threadsafe! Depending on the state of the global- *  variable \ref eos_debug it prints energy information to stdout or not...\n- * - *  \deprecated This function is deprecated and should not be used in future programs!- *  Use \ref energy_of_structure() instead!- * - *  \see              energy_of_structure, energy_of_circ_struct(), energy_of_struct_pt()- *  \param string     RNA sequence- *  \param structure  secondary structure in dot-bracket notation- *  \return          the free energy of the input structure given the input sequence in kcal/mol- */-DEPRECATED(float energy_of_struct(const char *string,-                                  const char *structure));--/**- *  Calculate the free energy of an already folded RNA- * - *  \note This function is not entirely threadsafe! Depending on the state of the global- *  variable \ref eos_debug it prints energy information to stdout or not...\n- * - *  \deprecated This function is deprecated and should not be used in future programs!- *  Use \ref energy_of_structure_pt() instead!- * - *  \see              make_pair_table(), energy_of_structure()- *  \param string     RNA sequence- *  \param ptable     the pair table of the secondary structure- *  \param s          encoded RNA sequence- *  \param s1         encoded RNA sequence- *  \return          the free energy of the input structure given the input sequence in 10kcal/mol- */-DEPRECATED(int energy_of_struct_pt( const char *string,-                                    short *ptable,-                                    short *s,-                                    short *s1));--/**- *  Calculate the free energy of an already folded  circular RNA- * - *  \note This function is not entirely threadsafe! Depending on the state of the global- *  variable \ref eos_debug it prints energy information to stdout or not...\n- * - *  \deprecated This function is deprecated and should not be used in future programs- *  Use \ref energy_of_circ_structure() instead!- * - *  \see              energy_of_circ_structure(), energy_of_struct(), energy_of_struct_pt()- *  \param string     RNA sequence- *  \param structure  secondary structure in dot-bracket notation- *  \return          the free energy of the input structure given the input sequence in kcal/mol- */-DEPRECATED(float energy_of_circ_struct( const char *string,-                                        const char *structure));--#endif
− include/fold_vars.h 
@@ -1,217 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_FOLD_VARS_H__-#define __VIENNA_RNA_PACKAGE_FOLD_VARS_H__--#include "data_structures.h"--/**- *  \file fold_vars.h- *  \brief Here all all declarations of the global variables used throughout RNAlib- */---#define PUBLIC-#define PRIVATE static--/**- *  \brief Global switch to activate/deactivate folding with structure constraints- */-extern int    fold_constrained;--/**- *  \brief Global switch to avoid/allow helices of length 1- * - *  Disallow all pairs which can only occur as lonely pairs (i.e. as helix- *  of length 1). This avoids lonely base pairs in the predicted structures in- *  most cases.- */-extern int    noLonelyPairs;--/**- *  \brief Switch the energy model for dangling end contributions (0, 1, 2, 3)- * - *  If set to 0 no stabilizing energies are assigned to bases adjacent to- *  helices in free ends and multiloops (so called dangling ends). Normally- *  (dangles = 1) dangling end energies are assigned only to unpaired- *  bases and a base cannot participate simultaneously in two dangling ends. In- *  the partition function algorithm pf_fold() these checks are neglected.- *  If #dangles is set to 2, all folding routines will follow this convention.- *  This treatment of dangling ends gives more favorable energies to helices- *  directly adjacent to one another, which can be beneficial since such- *  helices often do engage in stabilizing interactions through co-axial- *  stacking.\n- *  If dangles = 3 co-axial stacking is explicitly included for- *  adjacent helices in mutli-loops. The option affects only mfe folding- *  and energy evaluation (fold() and energy_of_structure()), as- *  well as suboptimal folding (subopt()) via re-evaluation of energies.- *  Co-axial stacking with one intervening mismatch is not considered so far.- * - *  Default is 2 in most algorithms, partition function algorithms can only handle 0 and 2- */-extern int  dangles;--/**- *  \brief Global switch to forbid/allow GU base pairs at all- */-extern int  noGU;--/**- *  \brief GU allowed only inside stacks if set to 1- */-extern int  no_closingGU;--/**- *  \brief Include special stabilizing energies for some tri-, tetra- and hexa-loops;- * - *  default is 1.- */-extern int  tetra_loop;--/**- *  \brief 0 = BP; 1=any mit GC; 2=any mit AU-parameter- * - *  If set to 1 or 2: fold sequences from an artificial alphabet ABCD..., where A- *  pairs B, C pairs D, etc. using either GC (1) or AU parameters (2);- *  default is 0, you probably don't want to change it.- */-extern int  energy_set;--/**- *  \brief backward compatibility variable.. this does not effect anything- */-extern int  circ;--/**- *  \brief generate comma seperated output- */-extern int  csv;--/**- *  use old alifold energies (with gaps)- */-extern int oldAliEn;-/**- *  use ribosum matrices- */-extern int ribo;            --/**- *  warning this variable will vanish in the future- *  ribosums will be compiled in instead- */-extern char *RibosumFile;   --/**- *  \brief contains allowed non standard base pairs- * - *  Lists additional base pairs that will be allowed to form in addition to- *  GC, CG, AU, UA, GU and UG. Nonstandard base pairs are given a stacking- *  energy of 0.- */-extern char *nonstandards;--/**- *  \brief Rescale energy parameters to a temperature in degC.- * - *  Default is 37C. You have to call the update_..._params() functions after- *  changing this parameter.- */-extern double temperature;--/**- *  interior loops of size 2 get energy 0.8Kcal and- *  no mismatches, default 1- */-extern int  james_rule;--/**- *  use logarithmic multiloop energy function- */-extern int  logML;--/**- *  \brief Marks the position (starting from 1) of the first- *  nucleotide of the second molecule within the concatenated sequence.- * - *  To evaluate the energy of a duplex structure (a structure formed by two- *  strands), concatenate the to sequences and set it to the- *  first base of the second strand in the concatenated sequence.- *  The default value of -1 stands for single molecule folding. The- *  cut_point variable is also used by PS_rna_plot() and- *  PS_dot_plot() to mark the chain break in postscript plots.- */-extern int  cut_point;--/**- *  \brief Contains a list of base pairs after a call to fold().- * - *  base_pair[0].i contains the total number of pairs.- *  \deprecated Do not use this variable anymore!- */-extern bondT  *base_pair;--/**- *  \brief A pointer to the base pair probability matrix- * - *  \deprecated Do not use this variable anymore!- */-extern FLT_OR_DBL *pr;--/**- *  \brief index array to move through pr.- * - *  The probability for base i and j to form a pair is in pr[iindx[i]-j].- *  \deprecated Do not use this variable anymore!- */-extern int   *iindx;--/**- *  \brief A scaling factor used by pf_fold() to avoid overflows.- * - *  Should be set to approximately \f$exp{((-F/kT)/length)}\f$, where \f$F\f$ is an estimate- *  for the ensemble free energy, for example the minimum free energy. You must- *  call update_pf_params() after changing this parameter.\n- *  If pf_scale is -1 (the default) , an estimate will be provided- *  automatically when computing partition functions, e.g. pf_fold()- *  The automatic estimate is usually insufficient for sequences more- *  than a few hundred bases long.- */-extern double pf_scale;--/**- *  \brief do backtracking, i.e. compute secondary structures or base pair probabilities- * - *  If 0, do not calculate pair probabilities in pf_fold(); this is about- *  twice as fast. Default is 1.- */-extern int    do_backtrack;--/**- *  \brief A backtrack array marker for inverse_fold()- * - *  If set to 'C': force (1,N) to be paired,- *  'M' fold as if the sequence were inside a multi-loop. Otherwise ('F') the- *  usual mfe structure is computed.- */-extern char backtrack_type;--/**- *  \brief Allow G-quadruplex formation- */-extern int gquad;---char * option_string(void);--/**- * \brief Set default model details- *- *  Use this function if you wish to initialize a #model_detailsT data structure with- *  its default values, i.e. the global model settings- *- *  \see- *- *  \param md A pointer to the data structure that shall be initialized- */-void set_model_details(model_detailsT *md);--#endif
− include/gquad.h 
@@ -1,725 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_GQUAD_H__-#define __VIENNA_RNA_PACKAGE_GQUAD_H__--#include "data_structures.h"--#ifndef INLINE-#ifdef __GNUC__-# define INLINE inline-#else-# define INLINE-#endif-#endif--/**- *  \file gquad.h- *  \brief Various functions related to G-quadruplex computations- */---int         E_gquad(int L,-                    int l[3],-                    paramT *P);--FLT_OR_DBL exp_E_gquad( int L,-                        int l[3],-                        pf_paramT *pf);--int         E_gquad_ali(int i,-                        int L,-                        int l[3],-                        const short **S,-                        int n_seq,-                        paramT *P);---void        E_gquad_ali_en( int i,-                            int L,-                            int l[3],-                            const short **S,-                            int n_seq,-                            int en[2],-                            paramT *P);--/**- *  \brief Get a triangular matrix prefilled with minimum free energy- *  contributions of G-quadruplexes.- *- *  At each position ij in the matrix, the minimum free energy of any- *  G-quadruplex delimited by i and j is stored. If no G-quadruplex formation- *  is possible, the matrix element is set to INF.- *  Access the elements in the matrix via matrix[indx[j]+i]. To get- *  the integer array indx see get_jindx().- *- *  \see get_jindx(), encode_sequence()- *- *  \param S  The encoded sequence- *  \param P  A pointer to the data structure containing the precomputed energy contributions- *  \return   A pointer to the G-quadruplex contribution matrix-*/-int         *get_gquad_matrix(short *S, paramT *P);--int         *get_gquad_ali_matrix(short *S_cons,-                                  short **S,-                                  int n_seq,-                                  paramT *P);--FLT_OR_DBL  *get_gquad_pf_matrix( short *S,-                                  FLT_OR_DBL *scale,-                                  pf_paramT *pf);--int         **get_gquad_L_matrix( short *S,-                                  int start,-                                  int maxdist,-                                  int **g,-                                  paramT *P);--void        get_gquad_pattern_mfe(short *S,-                                  int i,-                                  int j,-                                  paramT *P,-                                  int *L,-                                  int l[3]);--void-get_gquad_pattern_exhaustive( short *S,-                              int i,-                              int j,-                              paramT *P,-                              int *L,-                              int *l,-                              int threshold);--void        get_gquad_pattern_pf( short *S,-                                  int i,-                                  int j,-                                  pf_paramT *pf,-                                  int *L,-                                  int l[3]);--plist       *get_plist_gquad_from_pr( short *S,-                                      int gi,-                                      int gj,-                                      FLT_OR_DBL *G,-                                      FLT_OR_DBL *probs,-                                      FLT_OR_DBL *scale,-                                      pf_paramT *pf);-plist       *get_plist_gquad_from_pr_max(short *S,-                                      int gi,-                                      int gj,-                                      FLT_OR_DBL *G,-                                      FLT_OR_DBL *probs,-                                      FLT_OR_DBL *scale,-                                      int *L,-                                      int l[3],-                                      pf_paramT *pf);--plist       *get_plist_gquad_from_db( const char *structure,-                                      float pr);--int         get_gquad_count(short *S,-                            int i,-                            int j);--int         get_gquad_layer_count(short *S,-                            int i,-                            int j);---/**- *  given a dot-bracket structure (possibly) containing gquads encoded- *  by '+' signs, find first gquad, return end position or 0 if none found- *  Upon return L and l[] contain the number of stacked layers, as well as- *  the lengths of the linker regions.  - *  To parse a string with many gquads, call parse_gquad repeatedly e.g.- *  end1 = parse_gquad(struc, &L, l); ... ;- *  end2 = parse_gquad(struc+end1, &L, l); end2+=end1; ... ;- *  end3 = parse_gquad(struc+end2, &L, l); end3+=end2; ... ; - */-int         parse_gquad(const char *struc, int *L, int l[3]);----/**- *  backtrack an interior loop like enclosed g-quadruplex- *  with closing pair (i,j)- *- *  \param c      The total contribution the loop should resemble- *  \param i      position i of enclosing pair- *  \param j      position j of enclosing pair- *  \param type   base pair type of enclosing pair (must be reverse type)- *  \param S      integer encoded sequence- *  \param ggg    triangular matrix containing g-quadruplex contributions- *  \param index  the index for accessing the triangular matrix- *  \param p      here the 5' position of the gquad is stored- *  \param q      here the 3' position of the gquad is stored- *  \param P      the datastructure containing the precalculated contibutions- *- *  \return       1 on success, 0 if no gquad found- */-INLINE  PRIVATE int backtrack_GQuad_IntLoop(int c,-                                            int i,-                                            int j,-                                            int type,-                                            short *S,-                                            int *ggg,-                                            int *index,-                                            int *p,-                                            int *q,-                                            paramT *P){--  int energy, dangles, k, l, maxl, minl, c0, l1;-  short si, sj;--  dangles = P->model_details.dangles;-  si      = S[i + 1];-  sj      = S[j - 1];-  energy  = 0;--  if(dangles == 2)-    energy += P->mismatchI[type][si][sj];--  if(type > 2)-    energy += P->TerminalAU;--  k = i + 1;-  if(S[k] == 3){-    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minl  = j - i + k - MAXLOOP - 2;-      c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minl  = MAX2(c0, minl);-      c0    = j - 3;-      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxl  = MIN2(c0, maxl);-      for(l = minl; l < maxl; l++){-        if(S[l] != 3) continue;-        if(c == energy + ggg[index[l] + k] + P->internal_loop[j - l - 1]){-          *p = k; *q = l;-          return 1;-        }-      }-    }-  }--  for(k = i + 2;-      k < j - VRNA_GQUAD_MIN_BOX_SIZE;-      k++){-    l1    = k - i - 1;-    if(l1>MAXLOOP) break;-    if(S[k] != 3) continue;-    minl  = j - i + k - MAXLOOP - 2;-    c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minl  = MAX2(c0, minl);-    c0    = j - 1;-    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    maxl  = MIN2(c0, maxl);-    for(l = minl; l < maxl; l++){-      if(S[l] != 3) continue;-      if(c == energy + ggg[index[l] + k] + P->internal_loop[l1 + j - l - 1]){-        *p = k; *q = l;-        return 1;-      }-    }-  }--  l = j - 1;-  if(S[l] == 3)-    for(k = i + 4;-        k < j - VRNA_GQUAD_MIN_BOX_SIZE;-        k++){-      l1    = k - i - 1;-      if(l1>MAXLOOP) break;-      if(S[k] != 3) continue;-      if(c == energy + ggg[index[l] + k] + P->internal_loop[l1]){-        *p = k; *q = l;-        return 1;-      }-    }--  return 0;-}--/**- *  backtrack an interior loop like enclosed g-quadruplex- *  with closing pair (i,j) with underlying Lfold matrix- *- *  \param c      The total contribution the loop should resemble- *  \param i      position i of enclosing pair- *  \param j      position j of enclosing pair- *  \param type   base pair type of enclosing pair (must be reverse type)- *  \param S      integer encoded sequence- *  \param ggg    triangular matrix containing g-quadruplex contributions- *  \param p      here the 5' position of the gquad is stored- *  \param q      here the 3' position of the gquad is stored- *  \param P      the datastructure containing the precalculated contibutions- *- *  \return       1 on success, 0 if no gquad found- */-INLINE  PRIVATE int backtrack_GQuad_IntLoop_L(int c,-                                              int i,-                                              int j,-                                              int type,-                                              short *S,-                                              int **ggg,-                                              int maxdist,-                                              int *p,-                                              int *q,-                                              paramT *P){--  int energy, dangles, k, l, maxl, minl, c0, l1;-  short si, sj;--  dangles = P->model_details.dangles;-  si      = S[i + 1];-  sj      = S[j - 1];-  energy  = 0;--  if(dangles == 2)-    energy += P->mismatchI[type][si][sj];--  if(type > 2)-    energy += P->TerminalAU;--  k = i + 1;-  if(S[k] == 3){-    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minl  = j - i + k - MAXLOOP - 2;-      c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minl  = MAX2(c0, minl);-      c0    = j - 3;-      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxl  = MIN2(c0, maxl);-      for(l = minl; l < maxl; l++){-        if(S[l] != 3) continue;-        if(c == energy + ggg[k][l - k] + P->internal_loop[j - l - 1]){-          *p = k; *q = l;-          return 1;-        }-      }-    }-  }--  for(k = i + 2;-      k < j - VRNA_GQUAD_MIN_BOX_SIZE;-      k++){-    l1    = k - i - 1;-    if(l1>MAXLOOP) break;-    if(S[k] != 3) continue;-    minl  = j - i + k - MAXLOOP - 2;-    c0    = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minl  = MAX2(c0, minl);-    c0    = j - 1;-    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    maxl  = MIN2(c0, maxl);-    for(l = minl; l < maxl; l++){-      if(S[l] != 3) continue;-      if(c == energy + ggg[k][l - k] + P->internal_loop[l1 + j - l - 1]){-        *p = k; *q = l;-        return 1;-      }-    }-  }--  l = j - 1;-  if(S[l] == 3)-    for(k = i + 4;-        k < j - VRNA_GQUAD_MIN_BOX_SIZE;-        k++){-      l1    = k - i - 1;-      if(l1>MAXLOOP) break;-      if(S[k] != 3) continue;-      if(c == energy + ggg[k][l - k] + P->internal_loop[l1]){-        *p = k; *q = l;-        return 1;-      }-    }--  return 0;-}--INLINE PRIVATE-int-E_GQuad_IntLoop(int i,-                int j,-                int type,-                short *S,-                int *ggg,-                int *index,-                paramT *P){--  int energy, ge, en1, en2, dangles, p, q, l1, minq, maxq;-  int c0, c1, c2, c3, up, d53, d5, d3;-  short si, sj;--  dangles = P->model_details.dangles;-  si      = S[i + 1];-  sj      = S[j - 1];-  energy  = 0;--  if(dangles == 2)-    energy += P->mismatchI[type][si][sj];--  if(type > 2)-    energy += P->TerminalAU;--  ge = INF;--  p = i + 1;-  if(S[p] == 3){-    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minq  = j - i + p - MAXLOOP - 2;-      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minq  = MAX2(c0, minq);-      c0    = j - 3;-      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxq  = MIN2(c0, maxq);-      for(q = minq; q < maxq; q++){-        if(S[q] != 3) continue;-        c0  = energy + ggg[index[q] + p] + P->internal_loop[j - q - 1];-        ge  = MIN2(ge, c0);-      }-    }-  }--  for(p = i + 2;-      p < j - VRNA_GQUAD_MIN_BOX_SIZE;-      p++){-    l1    = p - i - 1;-    if(l1>MAXLOOP) break;-    if(S[p] != 3) continue;-    minq  = j - i + p - MAXLOOP - 2;-    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minq  = MAX2(c0, minq);-    c0    = j - 1;-    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    maxq  = MIN2(c0, maxq);-    for(q = minq; q < maxq; q++){-      if(S[q] != 3) continue;-      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];-      ge   = MIN2(ge, c0);-    }-  }--  q = j - 1;-  if(S[q] == 3)-    for(p = i + 4;-        p < j - VRNA_GQUAD_MIN_BOX_SIZE;-        p++){-      l1    = p - i - 1;-      if(l1>MAXLOOP) break;-      if(S[p] != 3) continue;-      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1];-      ge  = MIN2(ge, c0);-    }--#if 0-  /* here comes the additional stuff for the odd dangle models */-  if(dangles % 1){-    en1 = energy + P->dangle5[type][si];-    en2 = energy + P->dangle5[type][sj];-    en3 = energy + P->mismatchI[type][si][sj];--    /* first case with 5' dangle (i.e. j-1) onto enclosing pair */-    p = i + 1;-    if(S[p] == 3){-      if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){-        minq  = j - i + p - MAXLOOP - 2;-        c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-        minq  = MAX2(c0, minq);-        c0    = j - 4;-        maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-        maxq  = MIN2(c0, maxq);-        for(q = minq; q < maxq; q++){-          if(S[q] != 3) continue;-          c0  = en1 + ggg[index[q] + p] + P->internal_loop[j - q - 1];-          ge  = MIN2(ge, c0);-        }-      }-    }--    for(p = i + 2; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++){-      l1    = p - i - 1;-      if(l1>MAXLOOP) break;-      if(S[p] != 3) continue;-      minq  = j - i + p - MAXLOOP - 2;-      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minq  = MAX2(c0, minq);-      c0    = j - 2;-      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxq  = MIN2(c0, maxq);-      for(q = minq; q < maxq; q++){-        if(S[q] != 3) continue;-        c0  = en1 + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];-        ge   = MIN2(ge, c0);-      }-    }--    q = j - 2;-    if(S[q] == 3)-      for(p = i + 4; p < j - VRNA_GQUAD_MIN_BOX_SIZE; p++){-        l1    = p - i - 1;-        if(l1>MAXLOOP) break;-        if(S[p] != 3) continue;-        c0  = en1 + ggg[index[q] + p] + P->internal_loop[l1 + 1];-        ge  = MIN2(ge, c0);-      }--    /* second case with 3' dangle (i.e. i+1) onto enclosing pair */--  }-#endif-  return ge;-}--INLINE PRIVATE-int *-E_GQuad_IntLoop_exhaustive( int i,-                            int j,-                            int **p_p,-                            int **q_p,-                            int type,-                            short *S,-                            int *ggg,-                            int threshold,-                            int *index,-                            paramT *P){--  int energy, *ge, en1, en2, dangles, p, q, l1, minq, maxq;-  int c0, c1, c2, c3, up, d53, d5, d3;-  short si, sj;-  int cnt = 0;--  dangles = P->model_details.dangles;-  si      = S[i + 1];-  sj      = S[j - 1];-  energy  = 0;--  if(dangles == 2)-    energy += P->mismatchI[type][si][sj];--  if(type > 2)-    energy += P->TerminalAU;--  /* guess how many gquads are possible in interval [i+1,j-1] */-  *p_p  = (int *)space(sizeof(int) * 256);-  *q_p  = (int *)space(sizeof(int) * 256);-  ge    = (int *)space(sizeof(int) * 256);--  p = i + 1;-  if(S[p] == 3){-    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minq  = j - i + p - MAXLOOP - 2;-      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minq  = MAX2(c0, minq);-      c0    = j - 3;-      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxq  = MIN2(c0, maxq);-      for(q = minq; q < maxq; q++){-        if(S[q] != 3) continue;-        c0  = energy + ggg[index[q] + p] + P->internal_loop[j - q - 1];-        if(c0 <= threshold){-          ge[cnt]       = energy + P->internal_loop[j - q - 1];-          (*p_p)[cnt]   = p;-          (*q_p)[cnt++] = q;-        }-      }-    }-  }--  for(p = i + 2;-      p < j - VRNA_GQUAD_MIN_BOX_SIZE;-      p++){-    l1    = p - i - 1;-    if(l1>MAXLOOP) break;-    if(S[p] != 3) continue;-    minq  = j - i + p - MAXLOOP - 2;-    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minq  = MAX2(c0, minq);-    c0    = j - 1;-    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    maxq  = MIN2(c0, maxq);-    for(q = minq; q < maxq; q++){-      if(S[q] != 3) continue;-      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1 + j - q - 1];-        if(c0 <= threshold){-          ge[cnt]       = energy + P->internal_loop[l1 + j - q - 1];-          (*p_p)[cnt]   = p;-          (*q_p)[cnt++] = q;-        }-    }-  }--  q = j - 1;-  if(S[q] == 3)-    for(p = i + 4;-        p < j - VRNA_GQUAD_MIN_BOX_SIZE;-        p++){-      l1    = p - i - 1;-      if(l1>MAXLOOP) break;-      if(S[p] != 3) continue;-      c0  = energy + ggg[index[q] + p] + P->internal_loop[l1];-        if(c0 <= threshold){-          ge[cnt]       = energy + P->internal_loop[l1];-          (*p_p)[cnt]   = p;-          (*q_p)[cnt++] = q;-        }-    }---  (*p_p)[cnt] = -1;--  return ge;-}--INLINE PRIVATE-int-E_GQuad_IntLoop_L(int i,-                  int j,-                  int type,-                  short *S,-                  int **ggg,-                  int maxdist,-                  paramT *P){--  int energy, ge, en1, en2, dangles, p, q, l1, minq, maxq;-  int c0, c1, c2, c3, up, d53, d5, d3;-  short si, sj;--  dangles = P->model_details.dangles;-  si      = S[i + 1];-  sj      = S[j - 1];-  energy  = 0;--  if(dangles == 2)-    energy += P->mismatchI[type][si][sj];--  if(type > 2)-    energy += P->TerminalAU;--  ge = INF;--  p = i + 1;-  if(S[p] == 3){-    if(p < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minq  = j - i + p - MAXLOOP - 2;-      c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minq  = MAX2(c0, minq);-      c0    = j - 3;-      maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxq  = MIN2(c0, maxq);-      for(q = minq; q < maxq; q++){-        if(S[q] != 3) continue;-        c0  = energy + ggg[p][q-p] + P->internal_loop[j - q - 1];-        ge  = MIN2(ge, c0);-      }-    }-  }--  for(p = i + 2;-      p < j - VRNA_GQUAD_MIN_BOX_SIZE;-      p++){-    l1    = p - i - 1;-    if(l1>MAXLOOP) break;-    if(S[p] != 3) continue;-    minq  = j - i + p - MAXLOOP - 2;-    c0    = p + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minq  = MAX2(c0, minq);-    c0    = j - 1;-    maxq  = p + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    maxq  = MIN2(c0, maxq);-    for(q = minq; q < maxq; q++){-      if(S[q] != 3) continue;-      c0  = energy + ggg[p][q - p] + P->internal_loop[l1 + j - q - 1];-      ge   = MIN2(ge, c0);-    }-  }--  q = j - 1;-  if(S[q] == 3)-    for(p = i + 4;-        p < j - VRNA_GQUAD_MIN_BOX_SIZE;-        p++){-      l1    = p - i - 1;-      if(l1>MAXLOOP) break;-      if(S[p] != 3) continue;-      c0  = energy + ggg[p][q - p] + P->internal_loop[l1];-      ge  = MIN2(ge, c0);-    }--  return ge;-}--INLINE PRIVATE-FLT_OR_DBL-exp_E_GQuad_IntLoop(int i,-                    int j,-                    int type,-                    short *S,-                    FLT_OR_DBL *G,-                    int *index,-                    pf_paramT *pf){--  int k, l, minl, maxl, u, r;-  FLT_OR_DBL q, qe, *expintern;-  short si, sj;--  q         = 0;-  si        = S[i + 1];-  sj        = S[j - 1];-  qe        = pf->expmismatchI[type][si][sj];-  expintern = pf->expinternal;--  if(type > 2)-    qe *= pf->expTermAU;--  k = i + 1;-  if(S[k] == 3){-    if(k < j - VRNA_GQUAD_MIN_BOX_SIZE){-      minl  = j - i + k - MAXLOOP - 2;-      u     = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-      minl  = MAX2(u, minl);-      u     = j - 3;-      maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-      maxl  = MIN2(u, maxl);-      for(l = minl; l < maxl; l++){-        if(S[l] != 3) continue;-        if(G[index[k]-l] == 0.) continue;-        q += qe * G[index[k]-l] * expintern[j - l - 1];-      }-    }-  }---  for(k = i + 2;-      k <= j - VRNA_GQUAD_MIN_BOX_SIZE;-      k++){-    u = k - i - 1;-    if(u > MAXLOOP) break;-    if(S[k] != 3) continue;-    minl  = j - i + k - MAXLOOP - 2;-    r     = k + VRNA_GQUAD_MIN_BOX_SIZE - 1;-    minl  = MAX2(r, minl);-    maxl  = k + VRNA_GQUAD_MAX_BOX_SIZE + 1;-    r     = j - 1;-    maxl  = MIN2(r, maxl);-    for(l = minl; l < maxl; l++){-      if(S[l] != 3) continue;-      if(G[index[k]-l] == 0.) continue;-      q += qe * G[index[k]-l] * expintern[u + j - l - 1];-    }-  }--  l = j - 1;-  if(S[l] == 3)-    for(k = i + 4; k < j - VRNA_GQUAD_MIN_BOX_SIZE; k++){-      u    = k - i - 1;-      if(u>MAXLOOP) break;-      if(S[k] != 3) continue;-      if(G[index[k]-l] == 0.) continue;-      q += qe * G[index[k]-l] * expintern[u];-    }--  return q;-}--#endif
− include/intl11.h 
@@ -1,393 +0,0 @@-PUBLIC int int11_37[NBPAIRS+1][NBPAIRS+1][5][5] =-{{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{    90,    90,    50,    50,    50}-  ,{    90,    90,    50,    50,    50}-  ,{    50,    50,    50,    50,    50}-  ,{    50,    50,    50,  -140,    50}-  ,{    50,    50,    50,    50,    40}-  }- ,{{    90,    90,    50,    50,    60}-  ,{    90,    90,   -40,    50,    50}-  ,{    60,    30,    50,    50,    60}-  ,{    50,   -10,    50,  -220,    50}-  ,{    50,    50,     0,    50,   -10}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,    60,    50,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   -20,   120,  -140,   120}-  ,{   120,   120,   100,   120,   110}-  }- ,{{   220,   220,   170,   120,   120}-  ,{   220,   220,   130,   120,   120}-  ,{   170,   120,   170,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   110}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,    80}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- ,{{   220,   220,   170,   120,   120}-  ,{   220,   220,   130,   120,   120}-  ,{   170,   120,   170,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{    90,    90,    60,    50,    50}-  ,{    90,    90,    30,   -10,    50}-  ,{    50,   -40,    50,    50,     0}-  ,{    50,    50,    50,  -220,    50}-  ,{    60,    50,    60,    50,   -10}-  }- ,{{    80,    80,    50,    50,    50}-  ,{    80,    80,    50,    50,    50}-  ,{    50,    50,    50,    50,    50}-  ,{    50,    50,    50,  -230,    50}-  ,{    50,    50,    50,    50,   -60}-  }- ,{{   190,   190,   120,   150,   150}-  ,{   190,   190,   120,   150,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   150,   120,   120,   120,   150}-  }- ,{{   160,   160,   120,   120,   120}-  ,{   160,   160,   120,   100,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,    70}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,    80}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- ,{{   190,   190,   120,   150,   150}-  ,{   190,   190,   120,   150,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   150,   120,   120,   120,   150}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,    60,   120,   -20,   120}-  ,{   120,    50,   120,   120,   100}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   110}-  }- ,{{   190,   190,   120,   120,   150}-  ,{   190,   190,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   150,   150,   120,  -140,   120}-  ,{   150,   120,   120,   120,   150}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   120}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   120}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   220,   220,   170,   120,   120}-  ,{   220,   220,   120,   120,   120}-  ,{   170,   130,   170,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   110}-  }- ,{{   160,   160,   120,   120,   120}-  ,{   160,   160,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   100,   120,  -140,   120}-  ,{   120,   120,   120,   120,    70}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- ,{{   220,   220,   190,   190,   190}-  ,{   220,   220,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,    80}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,    80}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   120}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   120}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   150}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- ,{{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   150}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   170}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   220,   220,   170,   120,   120}-  ,{   220,   220,   120,   120,   120}-  ,{   170,   130,   170,   120,   120}-  ,{   120,   120,   120,  -140,   120}-  ,{   120,   120,   120,   120,   120}-  }- ,{{   190,   190,   120,   120,   150}-  ,{   190,   190,   120,   120,   120}-  ,{   120,   120,   120,   120,   120}-  ,{   150,   150,   120,  -140,   120}-  ,{   150,   120,   120,   120,   150}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   220,   220,   190,   190,   190}-  ,{   220,   220,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   160}-  }- ,{{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- ,{{   220,   220,   190,   190,   190}-  ,{   220,   220,   190,   190,   190}-  ,{   190,   190,   190,   190,   190}-  ,{   190,   190,   190,   -70,   190}-  ,{   190,   190,   190,   190,   190}-  }- }};
− include/intl11dH.h 
@@ -1,393 +0,0 @@-PUBLIC int int11_dH[NBPAIRS+1][NBPAIRS+1][5][5] =-{{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1840, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  }- ,{{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1840, -1050}-  ,{ -1050, -1050, -1050, -1050, -1390}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1840, -1050}-  ,{ -1050, -1050, -1050, -1050, -1390}-  }- ,{{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1050, -1050}-  ,{ -1050, -1050, -1050, -1840, -1050}-  ,{ -1050, -1050, -1050, -1050, -1730}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550, -1230}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550, -1230}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550, -1230}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -730}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -730}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550, -1230}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -730}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -730}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- }-,{{{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  ,{   INF,   INF,   INF,   INF,   INF}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  }- ,{{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550,  -550,  -550}-  ,{  -550,  -550,  -550, -1340,  -550}-  ,{  -550,  -550,  -550,  -550,  -890}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,  -390}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- ,{{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  ,{   -50,   -50,   -50,  -830,   -50}-  ,{   -50,   -50,   -50,   -50,   -50}-  }- }};
− include/intl21.h 
@@ -1,1993 +0,0 @@-PUBLIC int int21_37[NBPAIRS+1][NBPAIRS+1][5][5][5] =-{{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   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230,   150}-   ,{   230,   230,   230,   230,   150}-   ,{   150,   150,   150,   150,   150}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   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,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   250,   300,   210,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   120,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   190,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   250,   370,   210,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   120,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   190,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   300,   300,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   370,   370,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   ,{   300,   300,   300,   300,   300}-   }-  ,{{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   300,   190,   300,   190,   300}-   ,{   190,   190,   190,   190,   190}-   ,{   300,   190,   300,   190,   300}-   }-  ,{{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   300,   300,   300,   300,   220}-   ,{   220,   220,   220,   220,   220}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- ,{{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   ,{   370,   370,   370,   370,   370}-   }-  ,{{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   370,   260,   370,   260,   370}-   ,{   260,   260,   260,   260,   260}-   ,{   370,   260,   370,   260,   370}-   }-  ,{{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   370,   370,   370,   370,   300}-   ,{   300,   300,   300,   300,   300}-   }-  }- }};
− include/intl21dH.h 
@@ -1,1993 +0,0 @@-PUBLIC int int21_dH[NBPAIRS+1][NBPAIRS+1][5][5][5] =-{{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,   350,   350,  -230,   350}-   ,{   350,   350,   350,  -230,   350}-   ,{   350,   350,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,   350,   350,  -230,   350}-   }-  ,{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,  -230,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   }-  ,{{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{  -670,  -670,  -670,  -670,  -670}-   }-  }- ,{{{   780,   640,   780,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   780,   350,   780,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   640,   640,   350,   350,   350}-   }-  ,{{   350,   350,   350,   250,   350}-   ,{   350,   260,   350,   250,   350}-   ,{   350,   350,  -250,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,   350,   350,  -230,   350}-   }-  ,{{   780,   640,   780,   350,   350}-   ,{   350,   160,   350,   350,   350}-   ,{   780,   350,   780,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   640,   640,   350,   350,   350}-   }-  ,{{   350,  -160,   350,  -230,   350}-   ,{   350,  -160,   350,  -410,   350}-   ,{   350,  -230,   350,  -230,   350}-   ,{  -230,  -310,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   }-  ,{{   580,   350,   580,   350,  -580}-   ,{   350,   350,   350,   350,  -670}-   ,{   580,   350,   580,   350,  -580}-   ,{   350,   350,   350,   350,  -670}-   ,{  -670,  -670,  -690,  -670,  -700}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   690,   690,   350,   350,   350}-   ,{   690,   690,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   690,   690,   350,   350,   350}-   ,{   690,   690,   350,   240,   350}-   ,{   350,   350,   350,   350,   350}-   ,{  -230,  -500,  -230,  -230,  -230}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   130,   350,   350}-   }-  ,{{   350,  -230,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   }-  ,{{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{  -670,  -670,  -670,  -670,  -670}-   }-  }- ,{{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   ,{   350,   350,   350,   350,   350}-   }-  ,{{   350,  -230,   350,  -230,   350}-   ,{   350,  -230,   350,  -230,   350}-   ,{   350,  -230,   350,  -230,   350}-   ,{  -230,  -230,  -230,  -230,  -230}-   ,{   350,  -230,   350,  -230,   350}-   }-  ,{{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{   350,   350,   350,   350,  -670}-   ,{  -670,  -670,  -670,  -670,  -670}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   690,   850,   240,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,  -500,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   130,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   690,   850,   240,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,  -500,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   130,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,   690,  1350,   240,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,  -500,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,   130,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,  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280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-  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1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   850,   850,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-  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1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{  1350,  1350,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- }-,{{{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  ,{{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   ,{   INF,   INF,   INF,   INF,   INF}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   ,{   850,   850,   850,   850,   850}-   }-  ,{{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   850,   280,   850,   280,   850}-   ,{   280,   280,   280,   280,   280}-   ,{   850,   280,   850,   280,   850}-   }-  ,{{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{   850,   850,   850,   850,  -160}-   ,{  -160,  -160,  -160,  -160,  -160}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- ,{{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   ,{  1350,  1350,  1350,  1350,  1350}-   }-  ,{{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{  1350,   780,  1350,   780,  1350}-   ,{   780,   780,   780,   780,   780}-   ,{  1350,   780,  1350,   780,  1350}-   }-  ,{{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{  1350,  1350,  1350,  1350,   340}-   ,{   340,   340,   340,   340,   340}-   }-  }- }};
− include/intl22.h 
@@ -1,9993 +0,0 @@-PUBLIC int int22_37[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =-{{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   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80}-    }-   }-  ,{{{   200,   160,   200,   110,   200}-    ,{   200,   160,   200,    60,   200}-    ,{   180,   140,   180,   110,   180}-    ,{   200,   160,   200,    60,   200}-    ,{   170,   130,   170,    90,   170}-    }-   ,{{   160,   120,   160,    20,   160}-    ,{   160,   120,   160,    20,   160}-    ,{   150,   110,   150,    20,   150}-    ,{    60,    20,    60,   -70,    60}-    ,{   150,   110,   150,    20,   150}-    }-   ,{{   200,   160,   200,   110,   200}-    ,{   200,   160,   200,    60,   200}-    ,{   180,   140,   180,   110,   180}-    ,{   200,   160,   200,    60,   200}-    ,{   170,   130,   170,    90,   170}-    }-   ,{{   150,   110,   150,    20,   150}-    ,{    60,    20,    60,   -70,    60}-    ,{   150,   110,   150,    20,   150}-    ,{    10,   -30,    10,     0,    10}-    ,{   150,   110,   150,    20,   150}-    }-   ,{{   200,   160,   200,    90,   200}-    ,{   200,   160,   200,    60,   200}-    ,{   170,   130,   170,    90,   170}-    ,{   200,   160,   200,    60,   200}-    ,{   100,   100,    80,   -50,    80}-    }-   }-  ,{{{   180,   150,   180,   150,   170}-    ,{   180,   150,   180,   150,   170}-    ,{   170,   140,   170,   140,   150}-    ,{   180,   150,   180,   150,   170}-    ,{   150,   120,   150,   120,   140}-    }-   ,{{   140,   110,   140,   110,   130}-    ,{   140,   110,   140,   110,   130}-    ,{   140,   110,   140,   110,   120}-    ,{   110,    20,   110,    20,    90}-    ,{   140,   110,   140,   110,   120}-    }-   ,{{   180,   150,   180,   150,   170}-    ,{   180,   150,   180,   150,   170}-    ,{   170,   140,   170,   140,   150}-    ,{   180,   150,   180,   150,   170}-    ,{   150,   120,   150,   120,   140}-    }-   ,{{   140,   110,   140,   110,   120}-    ,{   110,    20,   110,    20,    90}-    ,{   140,   110,   140,   110,   120}-    ,{   -10,   -40,   -10,   -40,   -20}-    ,{   140,   110,   140,   110,   120}-    }-   ,{{   180,   150,   180,   150,   170}-    ,{   180,   150,   180,   150,   170}-    ,{   150,   120,   150,   120,   140}-    ,{   180,   150,   180,   150,   170}-    ,{    60,    30,    60,    30,    50}-    }-   }-  ,{{{   200,   110,   200,    80,   200}-    ,{   200,    60,   200,    10,   200}-    ,{   180,   110,   180,   -10,   180}-    ,{   200,    60,   200,    80,   200}-    ,{   170,    90,   170,    20,   170}-    }-   ,{{   160,    20,   160,     0,   160}-    ,{   160,    20,   160,   -30,   160}-    ,{   150,    20,   150,   -40,   150}-    ,{    60,   -70,    60,     0,    60}-    ,{   150,    20,   150,   -40,   150}-    }-   ,{{   200,   110,   200,    10,   200}-    ,{   200,    60,   200,    10,   200}-    ,{   180,   110,   180,   -10,   180}-    ,{   200,    60,   200,    10,   200}-    ,{   170,    90,   170,   -20,   170}-    }-   ,{{   150,    20,   150,    80,   150}-    ,{    60,   -70,    60,     0,    60}-    ,{   150,    20,   150,   -40,   150}-    ,{    80,     0,    10,    80,    10}- 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150,    10,   150,   -40,   150}-    }-   ,{{   150,    70,   150,    20,   150}-    ,{   140,    70,   140,   -50,   140}-    ,{   150,    70,   150,   -40,   150}-    ,{   140,    10,   140,   -50,   140}-    ,{   150,    70,   150,    20,   150}-    }-   ,{{   150,    10,   150,    80,   150}-    ,{    30,   -50,    30,   -30,    30}-    ,{   150,    10,   150,   -40,   150}-    ,{    80,   -30,    10,    80,    10}-    ,{   150,    10,   150,   -40,   150}-    }-   ,{{   150,    90,   150,   140,   150}-    ,{   140,    10,   140,   -50,   140}-    ,{   150,    80,   150,   -50,   150}-    ,{   140,    10,   140,   -50,   140}-    ,{   140,    90,    70,   140,    70}-    }-   }-  ,{{{   140,   130,   140,   130,   140}-    ,{   140,   130,   140,   130,   140}-    ,{   120,   110,   120,   110,    30}-    ,{   110,   100,   110,   100,    70}-    ,{   120,   100,   120,   100,    30}-    }-   ,{{   140,   130,   140,   130,   140}-    ,{   140,   130,   140,   130,   140}-    ,{   120,   100,   120,   100,    30}-    ,{    50,   -70,     0,   -70,    50}-    ,{   120,   100,   120,   100,    30}-    }-   ,{{   120,   100,   120,   100,    30}-    ,{   110,   100,   110,   100,    30}-    ,{   120,   100,   120,   100,    30}-    ,{   110,   100,   110,   100,    20}-    ,{   120,   100,   120,   100,    30}-    }-   ,{{   140,   100,   120,   100,   140}-    ,{   140,   -10,    50,   -10,   140}-    ,{   120,   100,   120,   100,    30}-    ,{    70,   -40,   -60,   -40,    70}-    ,{   120,   100,   120,   100,    30}-    }-   ,{{   120,   110,   120,   110,    30}-    ,{   110,   100,   110,   100,    20}-    ,{   120,   110,   120,   110,    30}-    ,{   110,   100,   110,   100,    20}-    ,{    40,    30,    40,    30,   -60}-    }-   }-  }- ,{{{{   300,   290,   300,   260,   300}-    ,{   300,   270,   300,   260,   300}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   290,   290,   270,   220,   270}-    }-   ,{{   300,   270,   300,   260,   300}-    ,{   300,   270,   300,   260,   300}-    ,{   270,   230,   270,   220,   270}-    ,{   230,   150,   230,   140,   220}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   270,   230,   270,   220,   270}-    ,{   270,   190,   270,   180,   260}-    ,{   270,   230,   270,   220,   270}-    ,{   210,   130,   140,   210,   150}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   290,   290,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   290,   290,   270,   220,   270}-    }-   }-  ,{{{   300,   290,   300,   190,   300}-    ,{   300,   270,   300,   170,   300}-    ,{   270,   230,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   290,   290,   270,   190,   270}-    }-   ,{{   300,   270,   300,   170,   300}-    ,{   300,   270,   300,   170,   300}-    ,{   270,   230,   270,   130,   270}-    ,{   190,   150,   190,    50,   190}-    ,{   270,   230,   270,   130,   270}-    }-   ,{{   270,   230,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   270,   230,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   270,   230,   270,   190,   270}-    }-   ,{{   270,   230,   270,   130,   270}-    ,{   230,   190,   230,    90,   230}-    ,{   270,   230,   270,   130,   270}-    ,{   140,   100,   140,   130,   140}-    ,{   270,   230,   270,   130,   270}-    }-   ,{{   290,   290,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   270,   230,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   290,   290,   270,   130,   270}-    }-   }-  ,{{{   290,   260,   290,   260,   270}-    ,{   290,   260,   290,   260,   270}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    }-   ,{{   290,   260,   290,   260,   270}-    ,{   290,   260,   290,   260,   270}-    ,{   250,   220,   250,   220,   240}-    ,{   230,   140,   230,   140,   220}-    ,{   250,   220,   250,   220,   240}-    }-   ,{{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    }-   ,{{   270,   220,   270,   220,   260}-    ,{   270,   180,   270,   180,   260}-    ,{   250,   220,   250,   220,   240}-    ,{   120,    90,   120,    90,   110}-    ,{   250,   220,   250,   220,   240}-    }-   ,{{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    ,{   250,   220,   250,   220,   240}-    }-   }-  ,{{{   300,   190,   300,   210,   300}-    ,{   300,   170,   300,   170,   300}-    ,{   270,   190,   270,    80,   270}-    ,{   270,   130,   270,   210,   270}-    ,{   270,   190,   270,   210,   270}-    }-   ,{{   300,   170,   300,   130,   300}-    ,{   300,   170,   300,   110,   300}-    ,{   270,   130,   270,    80,   270}-    ,{   190,    50,   190,   130,   190}-    ,{   270,   130,   270,    80,   270}-    }-   ,{{   270,   190,   270,    80,   270}-    ,{   270,   130,   270,    80,   270}-    ,{   270,   190,   270,    80,   270}-    ,{   270,   130,   270,    80,   270}-    ,{   270,   190,   270,    80,   270}-    }-   ,{{   270,   130,   270,   210,   270}-    ,{   230,    90,   230,   170,   230}-    ,{   270,   130,   270,    80,   270}-    ,{   210,   130,   140,   210,   140}-    ,{   270,   130,   270,    80,   270}-    }-   ,{{   270,   190,   270,   210,   270}-    ,{   270,   130,   270,    80,   270}-    ,{   270,   190,   270,    80,   270}-    ,{   270,   130,   270,    80,   270}-    ,{   270,   130,   270,   210,   270}-    }-   }-  ,{{{   270,   260,   270,   260,   240}-    ,{   270,   260,   270,   260,   240}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    }-   ,{{   270,   260,   270,   260,   240}-    ,{   270,   260,   270,   260,   240}-    ,{   240,   220,   240,   220,   150}-    ,{   220,   140,   220,   140,    70}-    ,{   240,   220,   240,   220,   150}-    }-   ,{{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    }-   ,{{   260,   220,   260,   220,   150}-    ,{   260,   180,   260,   180,   110}-    ,{   240,   220,   240,   220,   150}-    ,{   150,    90,   110,    90,   150}-    ,{   240,   220,   240,   220,   150}-    }-   ,{{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    ,{   240,   220,   240,   220,   150}-    }-   }-  }- ,{{{{   310,   260,   310,   220,   300}-    ,{   310,   230,   310,   220,   300}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   260,   260,   240,   190,   240}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   200,   160,   200,   160,   200}-    ,{   240,   200,   240,   190,   240}-    ,{   150,    60,   150,    60,   130}-    ,{   240,   200,   240,   190,   240}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    }-   ,{{   310,   230,   310,   220,   300}-    ,{   310,   230,   310,   220,   300}-    ,{   240,   200,   240,   190,   240}-    ,{   180,   100,   110,   180,   120}-    ,{   240,   200,   240,   190,   240}-    }-   ,{{   260,   260,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   260,   260,   240,   190,   240}-    }-   }-  ,{{{   270,   260,   270,   160,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   260,   260,   240,   160,   240}-    }-   ,{{   240,   200,   240,   100,   240}-    ,{   200,   160,   200,    70,   200}-    ,{   240,   200,   240,   100,   240}-    ,{   100,    60,   100,   -30,   100}-    ,{   240,   200,   240,   100,   240}-    }-   ,{{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    }-   ,{{   270,   230,   270,   130,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   240,   200,   240,   100,   240}-    ,{   110,    70,   110,   100,   110}-    ,{   240,   200,   240,   100,   240}-    }-   ,{{   260,   260,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   260,   260,   240,   100,   240}-    }-   }-  ,{{{   310,   220,   310,   220,   300}-    ,{   310,   220,   310,   220,   300}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   190,   160,   190,   160,   170}-    ,{   220,   190,   220,   190,   210}-    ,{   150,    60,   150,    60,   130}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   310,   220,   310,   220,   300}-    ,{   310,   220,   310,   220,   300}-    ,{   220,   190,   220,   190,   210}-    ,{    90,    60,    90,    60,    80}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    }-   }-  ,{{{   270,   160,   270,   210,   270}-    ,{   270,   130,   270,   210,   270}-    ,{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,   180,   240}-    ,{   240,   160,   240,   180,   240}-    }-   ,{{   240,   100,   240,    50,   240}-    ,{   200,    70,   200,    10,   200}-    ,{   240,   100,   240,    50,   240}-    ,{   100,   -30,   100,    40,   100}-    ,{   240,   100,   240,    50,   240}-    }-   ,{{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   160,   240,    50,   240}-    }-   ,{{   270,   130,   270,   210,   270}-    ,{   270,   130,   270,   210,   270}-    ,{   240,   100,   240,    50,   240}-    ,{   180,   100,   110,   180,   110}-    ,{   240,   100,   240,    50,   240}-    }-   ,{{   240,   160,   240,   180,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   100,   240,   180,   240}-    }-   }-  ,{{{   300,   220,   300,   220,   150}-    ,{   300,   220,   300,   220,   150}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   210,   190,   210,   190,   140}-    ,{   170,   160,   170,   160,   140}-    ,{   210,   190,   210,   190,   120}-    ,{   130,    60,   130,    60,   -10}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   300,   220,   300,   220,   150}-    ,{   300,   220,   300,   220,   150}-    ,{   210,   190,   210,   190,   120}-    ,{   120,    60,    80,    60,   120}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    }-   }-  }- ,{{{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   220,   180,   220,   170,   220}-    ,{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   170,   220}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   210,   170,   210,   170,   210}-    ,{   160,    70,   160,    70,   140}-    ,{   210,   170,   210,   170,   210}-    }-   ,{{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   170,   220}-    ,{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   170,   220}-    }-   ,{{   230,   170,   230,   170,   210}-    ,{   230,   140,   230,   140,   210}-    ,{   210,   170,   210,   170,   210}-    ,{   130,    60,    60,   130,    70}-    ,{   210,   170,   210,   170,   210}-    }-   ,{{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   180,   220}-    ,{   220,   180,   220,   170,   220}-    ,{   220,   180,   220,   180,   220}-    ,{   150,   150,   130,    80,   130}-    }-   }-  ,{{{   240,   200,   240,   140,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   220,   180,   220,   140,   220}-    ,{   220,   180,   220,    90,   220}-    ,{   220,   180,   220,   140,   220}-    }-   ,{{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   210,   170,   210,    80,   210}-    ,{   110,    70,   110,   -20,   110}-    ,{   210,   170,   210,    80,   210}-    }-   ,{{   220,   180,   220,   140,   220}-    ,{   220,   180,   220,    90,   220}-    ,{   220,   180,   220,   140,   220}-    ,{   220,   180,   220,    90,   220}-    ,{   220,   180,   220,   140,   220}-    }-   ,{{   210,   170,   210,    80,   210}-    ,{   180,   140,   180,    50,   180}-    ,{   210,   170,   210,    80,   210}-    ,{    60,    20,    60,    60,    60}-    ,{   210,   170,   210,    80,   210}-    }-   ,{{   220,   180,   220,   140,   220}-    ,{   220,   180,   220,    90,   220}-    ,{   220,   180,   220,   140,   220}-    ,{   220,   180,   220,    90,   220}-    ,{   150,   150,   130,     0,   130}-    }-   }-  ,{{{   230,   190,   230,   190,   210}-    ,{   230,   190,   230,   190,   210}-    ,{   200,   170,   200,   170,   190}-    ,{   210,   180,   210,   180,   190}-    ,{   200,   170,   200,   170,   190}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   200,   170,   200,   170,   180}-    ,{   160,    70,   160,    70,   140}-    ,{   200,   170,   200,   170,   180}-    }-   ,{{   210,   180,   210,   180,   190}-    ,{   210,   180,   210,   180,   190}-    ,{   200,   170,   200,   170,   190}-    ,{   210,   180,   210,   180,   190}-    ,{   200,   170,   200,   170,   190}-    }-   ,{{   230,   170,   230,   170,   210}-    ,{   230,   140,   230,   140,   210}-    ,{   200,   170,   200,   170,   180}-    ,{    50,    20,    50,    20,    30}-    ,{   200,   170,   200,   170,   180}-    }-   ,{{   210,   180,   210,   180,   190}-    ,{   210,   180,   210,   180,   190}-    ,{   200,   170,   200,   170,   190}-    ,{   210,   180,   210,   180,   190}-    ,{   110,    80,   110,    80,   100}-    }-   }-  ,{{{   240,   140,   240,   130,   240}-    ,{   240,   100,   240,   120,   240}-    ,{   220,   140,   220,    30,   220}-    ,{   220,    90,   220,   130,   220}-    ,{   220,   140,   220,    70,   220}-    }-   ,{{   240,   100,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   210,    80,   210,    20,   210}-    ,{   110,   -20,   110,    50,   110}-    ,{   210,    80,   210,    20,   210}-    }-   ,{{   220,   140,   220,    30,   220}-    ,{   220,    90,   220,    30,   220}-    ,{   220,   140,   220,    30,   220}-    ,{   220,    90,   220,    30,   220}-    ,{   220,   140,   220,    30,   220}-    }-   ,{{   210,    80,   210,   130,   210}-    ,{   180,    50,   180,   120,   180}-    ,{   210,    80,   210,    20,   210}-    ,{   130,    60,    60,   130,    60}-    ,{   210,    80,   210,    20,   210}-    }-   ,{{   220,   140,   220,    70,   220}-    ,{   220,    90,   220,    30,   220}-    ,{   220,   140,   220,    30,   220}-    ,{   220,    90,   220,    30,   220}-    ,{   130,     0,   130,    70,   130}-    }-   }-  ,{{{   210,   190,   210,   190,   180}-    ,{   210,   190,   210,   190,   180}-    ,{   190,   170,   190,   170,   100}-    ,{   190,   180,   190,   180,   100}-    ,{   190,   170,   190,   170,   100}-    }-   ,{{   210,   190,   210,   190,   180}-    ,{   210,   190,   210,   190,   180}-    ,{   180,   170,   180,   170,    90}-    ,{   140,    70,   140,    70,     0}-    ,{   180,   170,   180,   170,    90}-    }-   ,{{   190,   180,   190,   180,   100}-    ,{   190,   180,   190,   180,   100}-    ,{   190,   170,   190,   170,   100}-    ,{   190,   180,   190,   180,   100}-    ,{   190,   170,   190,   170,   100}-    }-   ,{{   210,   170,   210,   170,    90}-    ,{   210,   140,   210,   140,    60}-    ,{   180,   170,   180,   170,    90}-    ,{    70,    20,    30,    20,    70}-    ,{   180,   170,   180,   170,    90}-    }-   ,{{   190,   180,   190,   180,   100}-    ,{   190,   180,   190,   180,   100}-    ,{   190,   170,   190,   170,   100}-    ,{   190,   180,   190,   180,   100}-    ,{   100,    80,   100,    80,    10}-    }-   }-  }- ,{{{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   190,   150,   190,   150,   190}-    ,{   180,    90,   180,    90,   160}-    ,{   190,   150,   190,   150,   190}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    }-   ,{{   190,   150,   190,   150,   190}-    ,{   190,   100,   190,   100,   170}-    ,{   190,   150,   190,   150,   190}-    ,{   150,    80,    80,   150,    90}-    ,{   190,   150,   190,   150,   190}-    }-   ,{{   240,   200,   240,   190,   240}-    ,{   240,   200,   240,   190,   240}-    ,{   210,   170,   210,   160,   210}-    ,{   240,   200,   240,   190,   240}-    ,{   170,   170,   150,   110,   150}-    }-   }-  ,{{{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    }-   ,{{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   190,   150,   190,    60,   190}-    ,{   130,    90,   130,     0,   130}-    ,{   190,   150,   190,    60,   190}-    }-   ,{{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   240,   200,   240,   160,   240}-    }-   ,{{   190,   150,   190,    80,   190}-    ,{   140,   100,   140,    10,   140}-    ,{   190,   150,   190,    60,   190}-    ,{    80,    40,    80,    80,    80}-    ,{   190,   150,   190,    60,   190}-    }-   ,{{   240,   200,   240,   130,   240}-    ,{   240,   200,   240,   100,   240}-    ,{   210,   170,   210,   130,   210}-    ,{   240,   200,   240,   100,   240}-    ,{   170,   170,   150,    20,   150}-    }-   }-  ,{{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   180,   150,   180,   150,   160}-    ,{   180,    90,   180,    90,   160}-    ,{   180,   150,   180,   150,   160}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    }-   ,{{   190,   150,   190,   150,   170}-    ,{   190,   100,   190,   100,   170}-    ,{   180,   150,   180,   150,   160}-    ,{    70,    40,    70,    40,    50}-    ,{   180,   150,   180,   150,   160}-    }-   ,{{   220,   190,   220,   190,   210}-    ,{   220,   190,   220,   190,   210}-    ,{   190,   160,   190,   160,   180}-    ,{   220,   190,   220,   190,   210}-    ,{   140,   110,   140,   110,   120}-    }-   }-  ,{{{   240,   160,   240,   150,   240}-    ,{   240,   100,   240,    80,   240}-    ,{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,   150,   240}-    ,{   240,   160,   240,    90,   240}-    }-   ,{{   240,   100,   240,    70,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   190,    60,   190,     0,   190}-    ,{   130,     0,   130,    70,   130}-    ,{   190,    60,   190,     0,   190}-    }-   ,{{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   160,   240,    50,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   240,   160,   240,    50,   240}-    }-   ,{{   190,    80,   190,   150,   190}-    ,{   140,    10,   140,    80,   140}-    ,{   190,    60,   190,     0,   190}-    ,{   150,    80,    80,   150,    80}-    ,{   190,    60,   190,     0,   190}-    }-   ,{{   240,   130,   240,    90,   240}-    ,{   240,   100,   240,    50,   240}-    ,{   210,   130,   210,    20,   210}-    ,{   240,   100,   240,    50,   240}-    ,{   150,    20,   150,    90,   150}-    }-   }-  ,{{{   210,   190,   210,   190,   180}-    ,{   210,   190,   210,   190,   180}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   210,   190,   210,   190,   180}-    ,{   210,   190,   210,   190,   180}-    ,{   160,   150,   160,   150,    70}-    ,{   160,    90,   160,    90,    10}-    ,{   160,   150,   160,   150,    70}-    }-   ,{{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    }-   ,{{   170,   150,   170,   150,    90}-    ,{   170,   100,   170,   100,    20}-    ,{   160,   150,   160,   150,    70}-    ,{    90,    40,    50,    40,    90}-    ,{   160,   150,   160,   150,    70}-    }-   ,{{   210,   190,   210,   190,   120}-    ,{   210,   190,   210,   190,   120}-    ,{   180,   160,   180,   160,    90}-    ,{   210,   190,   210,   190,   120}-    ,{   120,   110,   120,   110,    30}-    }-   }-  }- ,{{{{   310,   290,   310,   260,   300}-    ,{   310,   270,   310,   260,   300}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   290,   290,   270,   220,   270}-    }-   ,{{   300,   270,   300,   260,   300}-    ,{   300,   270,   300,   260,   300}-    ,{   270,   230,   270,   220,   270}-    ,{   230,   150,   230,   140,   220}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   310,   230,   310,   220,   300}-    ,{   310,   230,   310,   220,   300}-    ,{   270,   230,   270,   220,   270}-    ,{   210,   130,   140,   210,   150}-    ,{   270,   230,   270,   220,   270}-    }-   ,{{   290,   290,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   270,   230,   270,   220,   270}-    ,{   290,   290,   270,   220,   270}-    }-   }-  ,{{{   300,   290,   300,   190,   300}-    ,{   300,   270,   300,   170,   300}-    ,{   270,   230,   270,   190,   270}-    ,{   270,   230,   270,   130,   270}-    ,{   290,   290,   270,   190,   270}-    }-   ,{{   300,   270,   300,   170,   300}-    ,{   300,   270,   300,   170,   300}-    ,{   270,   230,   270,   130,   270}-    ,{   190,   150,   190,    50,   190}-    ,{   270,   230,   270,   130,  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120,   120,    90,   -20,    90}-    ,{   120,   120,    90,    50,    90}-    }-   ,{{   150,   150,   120,    10,   120}-    ,{   150,   150,   120,    10,   120}-    ,{   120,   120,    90,   -10,    90}-    ,{   -50,   -50,   -80,  -190,   -80}-    ,{   120,   120,    90,   -10,    90}-    }-   ,{{   120,   120,    90,    50,    90}-    ,{   120,   120,    90,   -20,    90}-    ,{   120,   120,    90,    50,    90}-    ,{   120,   120,    90,   -20,    90}-    ,{   120,   120,    90,    50,    90}-    }-   ,{{   120,   120,    90,   -10,    90}-    ,{    10,    10,   -20,  -130,   -20}-    ,{   120,   120,    90,   -10,    90}-    ,{   -20,   -20,   -50,   -20,   -50}-    ,{   120,   120,    90,   -10,    90}-    }-   ,{{   130,   130,   100,    50,   100}-    ,{   120,   120,    90,   -20,    90}-    ,{   130,   130,   100,    50,   100}-    ,{   120,   120,    90,   -20,    90}-    ,{   110,   110,    20,   -90,    20}-    }-   }-  ,{{{   130,   120,   120,   120,   130}-    ,{   130,   120,   120,   120,   130}-    ,{   110,   100,   100,   100,   110}-    ,{   100,    90,    90,    90,   100}-    ,{   100,   100,   100,   100,   100}-    }-   ,{{   130,   120,   120,   120,   130}-    ,{   130,   120,   120,   120,   130}-    ,{   100,   100,   100,   100,   100}-    ,{   -10,   -80,   -20,   -80,   -10}-    ,{   100,   100,   100,   100,   100}-    }-   ,{{   100,   100,   100,   100,   100}-    ,{   100,    90,    90,    90,   100}-    ,{   100,   100,   100,   100,   100}-    ,{   100,    90,    90,    90,   100}-    ,{   100,   100,   100,   100,   100}-    }-   ,{{   100,   100,   100,   100,   100}-    ,{    50,   -10,    50,   -10,    50}-    ,{   100,   100,   100,   100,   100}-    ,{   -40,   -40,   -40,   -40,   -40}-    ,{   100,   100,   100,   100,   100}-    }-   ,{{   110,   100,   100,   100,   110}-    ,{   100,    90,    90,    90,   100}-    ,{   110,   100,   100,   100,   110}-    ,{   100,    90,    90,    90,   100}-    ,{    30,    20,    20,    20,    30}-    }-   }-  ,{{{   120,   -10,   120,    80,   120}-    ,{   120,   -50,   120,   -20,   120}-    ,{   100,   -10,   100,   -40,   100}-    ,{    90,   -80,    90,    80,    90}-    ,{    90,   -20,    90,    10,    90}-    }-   ,{{   120,   -50,   120,   -20,   120}-    ,{   120,   -50,   120,   -20,   120}-    ,{    90,   -80,    90,   -40,    90}-    ,{   -80,  -260,   -80,   -90,   -80}-    ,{    90,   -80,    90,   -40,    90}-    }-   ,{{    90,   -20,    90,   -40,    90}-    ,{    90,   -80,    90,   -50,    90}-    ,{    90,   -20,    90,   -40,    90}-    ,{    90,   -80,    90,   -50,    90}-    ,{    90,   -20,    90,   -40,    90}-    }-   ,{{    90,   -80,    90,    80,    90}-    ,{   -20,  -190,   -20,   -20,   -20}-    ,{    90,   -80,    90,   -40,    90}-    ,{    80,   -90,   -50,    80,   -50}-    ,{    90,   -80,    90,   -40,    90}-    }-   ,{{   100,   -10,   100,    10,   100}-    ,{    90,   -80,    90,   -50,    90}-    ,{   100,   -10,   100,   -40,   100}-    ,{    90,   -80,    90,   -50,    90}-    ,{    20,  -150,    20,    10,    20}-    }-   }-  ,{{{   120,   120,   120,   120,   110}-    ,{   120,   120,   120,   120,   110}-    ,{   100,   100,   100,   100,    30}-    ,{    90,    90,    90,    90,    20}-    ,{   100,   100,   100,   100,    20}-    }-   ,{{   120,   120,   120,   120,   110}-    ,{   120,   120,   120,   120,   110}-    ,{   100,   100,   100,   100,    20}-    ,{   -20,   -80,   -20,   -80,  -150}-    ,{   100,   100,   100,   100,    20}-    }-   ,{{   100,   100,   100,   100,    20}-    ,{    90,    90,    90,    90,    20}-    ,{   100,   100,   100,   100,    20}-    ,{    90,    90,    90,    90,    20}-    ,{   100,   100,   100,   100,    20}-    }-   ,{{   100,   100,   100,   100,    20}-    ,{    50,   -10,    50,   -10,   -90}-    ,{   100,   100,   100,   100,    20}-    ,{    10,   -40,   -40,   -40,    10}-    ,{   100,   100,   100,   100,    20}-    }-   ,{{   100,   100,   100,   100,    30}-    ,{    90,    90,    90,    90,    20}-    ,{   100,   100,   100,   100,    30}-    ,{    90,    90,    90,    90,    20}-    ,{    20,    20,    20,    20,   -50}-    }-   }-  }- ,{{{{   300,   300,   250,   250,   260}-    ,{   280,   280,   250,   250,   260}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   300,   300,   220,   220,   220}-    }-   ,{{   280,   280,   250,   250,   260}-    ,{   280,   280,   250,   250,   260}-    ,{   240,   240,   220,   220,   220}-    ,{   200,   160,   200,   140,   200}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   240,   240,   240,   220,   240}-    ,{   240,   200,   240,   180,   240}-    ,{   240,   240,   220,   220,   220}-    ,{   210,   110,    90,   210,   140}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   300,   300,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   300,   300,   220,   220,   220}-    }-   }-  ,{{{   300,   300,   250,   160,   250}-    ,{   280,   280,   250,   140,   250}-    ,{   240,   240,   210,   160,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   300,   300,   210,   160,   210}-    }-   ,{{   280,   280,   250,   140,   250}-    ,{   280,   280,   250,   140,   250}-    ,{   240,   240,   210,   100,   210}-    ,{   160,   160,   130,    20,   130}-    ,{   240,   240,   210,   100,   210}-    }-   ,{{   240,   240,   210,   160,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   240,   240,   210,   160,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   240,   240,   210,   160,   210}-    }-   ,{{   240,   240,   210,   100,   210}-    ,{   200,   200,   170,    60,   170}-    ,{   240,   240,   210,   100,   210}-    ,{   110,   110,    80,   100,    80}-    ,{   240,   240,   210,   100,   210}-    }-   ,{{   300,   300,   210,   160,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   240,   240,   210,   160,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   300,   300,   210,   100,   210}-    }-   }-  ,{{{   260,   250,   250,   250,   260}-    ,{   260,   250,   250,   250,   260}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   260,   250,   250,   250,   260}-    ,{   260,   250,   250,   250,   260}-    ,{   220,   220,   220,   220,   220}-    ,{   200,   140,   200,   140,   200}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   240,   220,   240,   220,   240}-    ,{   240,   180,   240,   180,   240}-    ,{   220,   220,   220,   220,   220}-    ,{    90,    90,    90,    90,    90}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    }-   }-  ,{{{   250,   100,   250,   210,   250}-    ,{   250,    70,   250,   170,   250}-    ,{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,   210,   210}-    ,{   210,   100,   210,   210,   210}-    }-   ,{{   250,    70,   250,   130,   250}-    ,{   250,    70,   250,   110,   250}-    ,{   210,    40,   210,    80,   210}-    ,{   130,   -40,   130,   130,   130}-    ,{   210,    40,   210,    80,   210}-    }-   ,{{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,   100,   210,    80,   210}-    }-   ,{{   210,    40,   210,   210,   210}-    ,{   170,     0,   170,   170,   170}-    ,{   210,    40,   210,    80,   210}-    ,{   210,    40,    80,   210,    80}-    ,{   210,    40,   210,    80,   210}-    }-   ,{{   210,   100,   210,   210,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,    40,   210,   210,   210}-    }-   }-  ,{{{   250,   250,   250,   250,   240}-    ,{   250,   250,   250,   250,   240}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    }-   ,{{   250,   250,   250,   250,   240}-    ,{   250,   250,   250,   250,   240}-    ,{   220,   220,   220,   220,   140}-    ,{   200,   140,   200,   140,    60}-    ,{   220,   220,   220,   220,   140}-    }-   ,{{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    }-   ,{{   240,   220,   240,   220,   140}-    ,{   240,   180,   240,   180,   100}-    ,{   220,   220,   220,   220,   140}-    ,{   140,    90,    90,    90,   140}-    ,{   220,   220,   220,   220,   140}-    }-   ,{{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    ,{   220,   220,   220,   220,   140}-    }-   }-  }- ,{{{{   280,   270,   280,   220,   280}-    ,{   280,   240,   280,   220,   280}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   270,   270,   190,   190,   190}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   190,   190,   150,   150,   160}-    ,{   210,   210,   190,   190,   190}-    ,{   120,    80,   110,    50,   120}-    ,{   210,   210,   190,   190,   190}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    }-   ,{{   280,   240,   280,   220,   280}-    ,{   280,   240,   280,   220,   280}-    ,{   210,   210,   190,   190,   190}-    ,{   180,    80,    60,   180,   110}-    ,{   210,   210,   190,   190,   190}-    }-   ,{{   270,   270,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   270,   270,   190,   190,   190}-    }-   }-  ,{{{   270,   270,   210,   130,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   270,   270,   180,   130,   180}-    }-   ,{{   210,   210,   180,    70,   180}-    ,{   190,   190,   150,    40,   150}-    ,{   210,   210,   180,    70,   180}-    ,{    80,    80,    50,   -60,    50}-    ,{   210,   210,   180,    70,   180}-    }-   ,{{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,   130,   180}-    }-   ,{{   240,   240,   210,   100,   210}-    ,{   240,   240,   210,   100,   210}-    ,{   210,   210,   180,    70,   180}-    ,{    80,    80,    50,    70,    50}-    ,{   210,   210,   180,    70,   180}-    }-   ,{{   270,   270,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   270,   270,   180,    70,   180}-    }-   }-  ,{{{   280,   220,   280,   220,   280}-    ,{   280,   220,   280,   220,   280}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    }-   ,{{   190,   190,   190,   190,   190}-    ,{   160,   150,   150,   150,   160}-    ,{   190,   190,   190,   190,   190}-    ,{   120,    50,   110,    50,   120}-    ,{   190,   190,   190,   190,   190}-    }-   ,{{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    }-   ,{{   280,   220,   280,   220,   280}-    ,{   280,   220,   280,   220,   280}-    ,{   190,   190,   190,   190,   190}-    ,{    60,    60,    60,    60,    60}-    ,{   190,   190,   190,   190,   190}-    }-   ,{{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    }-   }-  ,{{{   210,    70,   210,   210,   210}-    ,{   210,    40,   210,   210,   210}-    ,{   180,    70,   180,    50,   180}-    ,{   180,    10,   180,   180,   180}-    ,{   180,    70,   180,   180,   180}-    }-   ,{{   180,    10,   180,    50,   180}-    ,{   150,   -20,   150,    10,   150}-    ,{   180,    10,   180,    50,   180}-    ,{    50,  -120,    50,    40,    50}-    ,{   180,    10,   180,    50,   180}-    }-   ,{{   180,    70,   180,    50,   180}-    ,{   180,    10,   180,    50,   180}-    ,{   180,    70,   180,    50,   180}-    ,{   180,    10,   180,    50,   180}-    ,{   180,    70,   180,    50,   180}-    }-   ,{{   210,    40,   210,   210,   210}-    ,{   210,    40,   210,   210,   210}-    ,{   180,    10,   180,    50,   180}-    ,{   180,    10,    50,   180,    50}-    ,{   180,    10,   180,    50,   180}-    }-   ,{{   180,    70,   180,   180,   180}-    ,{   180,    10,   180,    50,   180}-    ,{   180,    70,   180,    50,   180}-    ,{   180,    10,   180,    50,   180}-    ,{   180,    10,   180,   180,   180}-    }-   }-  ,{{{   280,   220,   280,   220,   140}-    ,{   280,   220,   280,   220,   140}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    }-   ,{{   190,   190,   190,   190,   140}-    ,{   150,   150,   150,   150,   140}-    ,{   190,   190,   190,   190,   110}-    ,{   110,    50,   110,    50,   -20}-    ,{   190,   190,   190,   190,   110}-    }-   ,{{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    }-   ,{{   280,   220,   280,   220,   140}-    ,{   280,   220,   280,   220,   140}-    ,{   190,   190,   190,   190,   110}-    ,{   110,    60,    60,    60,   110}-    ,{   190,   190,   190,   190,   110}-    }-   ,{{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    ,{   190,   190,   190,   190,   110}-    }-   }-  }- ,{{{{   210,   210,   190,   190,   200}-    ,{   210,   210,   190,   190,   200}-    ,{   190,   190,   170,   170,   170}-    ,{   200,   200,   170,   170,   180}-    ,{   190,   190,   170,   170,   170}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   190,   190,   160,   160,   170}-    ,{   130,    90,   120,    60,   130}-    ,{   190,   190,   160,   160,   170}-    }-   ,{{   200,   200,   170,   170,   180}-    ,{   200,   200,   170,   170,   180}-    ,{   190,   190,   170,   170,   170}-    ,{   200,   200,   170,   170,   180}-    ,{   190,   190,   170,   170,   170}-    }-   ,{{   200,   190,   190,   160,   200}-    ,{   200,   160,   190,   130,   200}-    ,{   190,   190,   160,   160,   170}-    ,{   130,    40,    10,   130,    70}-    ,{   190,   190,   160,   160,   170}-    }-   ,{{   200,   200,   170,   170,   180}-    ,{   200,   200,   170,   170,   180}-    ,{   190,   190,   170,   170,   170}-    ,{   200,   200,   170,   170,   180}-    ,{   160,   160,    80,    80,    80}-    }-   }-  ,{{{   210,   210,   180,   110,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   190,   190,   160,   110,   160}-    ,{   200,   200,   170,    60,   170}-    ,{   190,   190,   160,   110,   160}-    }-   ,{{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   190,   190,   160,    50,   160}-    ,{    90,    90,    60,   -50,    60}-    ,{   190,   190,   160,    50,   160}-    }-   ,{{   200,   200,   170,   110,   170}-    ,{   200,   200,   170,    60,   170}-    ,{   190,   190,   160,   110,   160}-    ,{   200,   200,   170,    60,   170}-    ,{   190,   190,   160,   110,   160}-    }-   ,{{   190,   190,   160,    50,   160}-    ,{   160,   160,   130,    20,   130}-    ,{   190,   190,   160,    50,   160}-    ,{    40,    40,    10,    30,    10}-    ,{   190,   190,   160,    50,   160}-    }-   ,{{   200,   200,   170,   110,   170}-    ,{   200,   200,   170,    60,   170}-    ,{   190,   190,   160,   110,   160}-    ,{   200,   200,   170,    60,   170}-    ,{   160,   160,    70,   -30,    70}-    }-   }-  ,{{{   200,   190,   190,   190,   200}-    ,{   200,   190,   190,   190,   200}-    ,{   170,   170,   170,   170,   170}-    ,{   180,   170,   170,   170,   180}-    ,{   170,   170,   170,   170,   170}-    }-   ,{{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   170,   160,   160,   160,   170}-    ,{   130,    60,   120,    60,   130}-    ,{   170,   160,   160,   160,   170}-    }-   ,{{   180,   170,   170,   170,   180}-    ,{   180,   170,   170,   170,   180}-    ,{   170,   170,   170,   170,   170}-    ,{   180,   170,   170,   170,   180}-    ,{   170,   170,   170,   170,   170}-    }-   ,{{   200,   160,   190,   160,   200}-    ,{   200,   130,   190,   130,   200}-    ,{   170,   160,   160,   160,  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100}-    ,{   170,   170,   170,   170,    90}-    }-   ,{{   190,   160,   190,   160,    90}-    ,{   190,   130,   190,   130,    60}-    ,{   160,   160,   160,   160,    90}-    ,{    70,    10,    10,    10,    70}-    ,{   160,   160,   160,   160,    90}-    }-   ,{{   170,   170,   170,   170,   100}-    ,{   170,   170,   170,   170,   100}-    ,{   170,   170,   170,   170,    90}-    ,{   170,   170,   170,   170,   100}-    ,{    80,    80,    80,    80,     0}-    }-   }-  }- ,{{{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   170,   170,   140,   140,   150}-    ,{   150,   110,   140,    80,   150}-    ,{   170,   170,   140,   140,   150}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    }-   ,{{   170,   170,   150,   150,   160}-    ,{   160,   120,   150,    90,   160}-    ,{   170,   170,   140,   140,   150}-    ,{   150,    60,    30,   150,    90}-    ,{   170,   170,   140,   140,   150}-    }-   ,{{   210,   210,   190,   190,   190}-    ,{   210,   210,   190,   190,   190}-    ,{   180,   180,   160,   160,   160}-    ,{   210,   210,   190,   190,   190}-    ,{   190,   190,   100,   100,   110}-    }-   }-  ,{{{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,   130,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,   130,   180}-    }-   ,{{   210,   210,   180,    70,   180}-    ,{   210,   210,   180,    70,   180}-    ,{   170,   170,   140,    30,   140}-    ,{   110,   110,    80,   -30,    80}-    ,{   170,   170,   140,    30,  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250,   280}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   300,   300,   220,   220,   220}-    }-   ,{{   280,   280,   250,   250,   260}-    ,{   280,   280,   250,   250,   260}-    ,{   240,   240,   220,   220,   220}-    ,{   200,   160,   200,   140,   200}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   280,   240,   280,   220,   280}-    ,{   280,   240,   280,   220,   280}-    ,{   240,   240,   220,   220,   220}-    ,{   210,   110,    90,   210,   140}-    ,{   240,   240,   220,   220,   220}-    }-   ,{{   300,   300,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   240,   240,   220,   220,   220}-    ,{   300,   300,   220,   220,   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220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    ,{   220,   220,   220,   220,   220}-    }-   }-  ,{{{   250,   100,   250,   210,   250}-    ,{   250,    70,   250,   210,   250}-    ,{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,   210,   210}-    ,{   210,   100,   210,   210,   210}-    }-   ,{{   250,    70,   250,   130,   250}-    ,{   250,    70,   250,   110,   250}-    ,{   210,    40,   210,    80,   210}-    ,{   130,   -40,   130,   130,   130}-    ,{   210,    40,   210,    80,   210}-    }-   ,{{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,   100,   210,    80,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,   100,   210,    80,   210}-    }-   ,{{   210,    40,   210,   210,   210}-    ,{   210,    40,   210,   210,   210}-    ,{   210,    40,   210,    80,   210}-    ,{   210,    40,    80,   210,    80}- 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320,   260,   320}-    ,{   370,   370,   340,   340,   340}-    }-   ,{{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   370,   370,   340,   360,   340}-    }-   ,{{   370,   370,   360,   340,   360}-    ,{   360,   330,   360,   300,   360}-    ,{   370,   370,   340,   340,   340}-    ,{   340,   260,   210,   340,   340}-    ,{   370,   370,   340,   340,   340}-    }-   ,{{   430,   430,   340,   360,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   430,   430,   340,   340,   340}-    }-   }-  ,{{{   430,   430,   370,   360,   370}-    ,{   410,   410,   370,   330,   370}-    ,{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   300,   340}-    ,{   430,   430,   340,   360,   340}-    }-   ,{{   410,   410,   370,   330,   370}-    ,{   410,   410,   370,   330,   370}-    ,{   370,   370,   340,   300,   340}-    ,{   290,   290,   260,   220,   260}-    ,{   370,   370,   340,   300,   340}-    }-   ,{{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   300,   340}-    ,{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   300,   340}-    ,{   370,   370,   340,   360,   340}-    }-   ,{{   370,   370,   340,   300,   340}-    ,{   330,   330,   300,   260,   300}-    ,{   370,   370,   340,   300,   340}-    ,{   300,   240,   210,   300,   210}-    ,{   370,   370,   340,   300,   340}-    }-   ,{{   430,   430,   340,   360,   340}-    ,{   370,   370,   340,   300,   340}-    ,{   370,   370,   340,   360,   340}-    ,{   370,   370,   340,   300,   340}-    ,{   430,   430,   340,   300,   340}-    }-   }-  ,{{{   370,   370,   370,   370,   370}-    ,{   370,   370,   370,   370,   370}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,  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310}-    ,{   310,   310,   310,   310,   310}-    ,{   280,   280,   280,   280,   280}-    ,{   310,   310,   310,   310,   310}-    ,{   220,   220,   220,   220,   220}-    }-   }-  ,{{{   310,   290,   310,   280,   310}-    ,{   310,   230,   310,   210,   310}-    ,{   310,   290,   310,   180,   310}-    ,{   310,   230,   310,   280,   310}-    ,{   310,   290,   310,   220,   310}-    }-   ,{{   310,   230,   310,   200,   310}-    ,{   310,   230,   310,   180,   310}-    ,{   260,   180,   260,   130,   260}-    ,{   200,   120,   200,   200,   200}-    ,{   260,   180,   260,   130,   260}-    }-   ,{{   310,   290,   310,   180,   310}-    ,{   310,   230,   310,   180,   310}-    ,{   310,   290,   310,   180,   310}-    ,{   310,   230,   310,   180,   310}-    ,{   310,   290,   310,   180,   310}-    }-   ,{{   280,   200,   260,   280,   260}-    ,{   210,   130,   210,   210,   210}-    ,{   260,   180,   260,   130,   260}-    ,{   280,   200,   150,   280,   150}- 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  INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF, 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  INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   240,   240,   220,   230,   220}-    ,{   240,   240,   220,   210,   220}-    ,{   230,   220,   210,   230,   210}-    ,{   240,   240,   220,   210,   220}-    ,{   210,   210,   190,   210,   190}-    }-   ,{{   200,   200,   180,   170,   180}-    ,{   200,   200,   180,   170,   180}-    ,{   190,   190,   180,   170,   180}-    ,{   140,   100,   140,    80,   140}-    ,{   190,   190,   180,   170,   180}-    }-   ,{{   240,   240,   220,   230,   220}-    ,{   240,   240,   220,   210,   220}-    ,{   230,   220,   210,   230,   210}-    ,{   240,   240,   220,   210,   220}-    ,{   210,   210,   190,   210,   190}-    }-   ,{{   190,   190,   180,   170,   180}-    ,{   140,   100,   140,    80,   140}-    ,{   190,   190,   180,   170,   180}-    ,{   130,    50,    30,   130,    70}-    ,{   190,   190,   180,   170,   180}-    }-   ,{{   240,   240,   220,   210,   220}-    ,{   240,   240,   220,   210,   220}-    ,{   210,   210,   190,   210,   190}-    ,{   240,   240,   220,   210,   220}-    ,{   180,   180,   100,    90,   100}-    }-   }-  ,{{{   240,   240,   220,   230,   220}-    ,{   240,   240,   220,   180,   220}-    ,{   230,   220,   210,   230,   210}-    ,{   240,   240,   220,   180,   220}-    ,{   210,   210,   190,   210,   190}-    }-   ,{{   200,   200,   180,   140,   180}-    ,{   200,   200,   180,   140,   180}-    ,{   190,   190,   180,   140,   180}-    ,{   100,   100,    90,    50,    90}-    ,{   190,   190,   180,   140,   180}-    }-   ,{{   240,   240,   220,   230,   220}-    ,{   240,   240,   220,   180,   220}-    ,{   230,   220,   210,   230,   210}-    ,{   240,   240,   220,   180,   220}-    ,{   210,   210,   190,   210,   190}-    }-   ,{{   190,   190,   180,   140,   180}-    ,{   100,   100,    90,    50,    90}-    ,{   190,   190,   180,   140,   180}-    ,{   120,    50,    30,   120,    30}-    ,{   190,   190,   180,   140,   180}-    }-   ,{{   240,   240,   220,   210,   220}-    ,{   240,   240,   220,   180,   220}-    ,{   210,   210,   190,   210,   190}-    ,{   240,   240,   220,   180,   220}-    ,{   180,   180,   100,    60,   100}-    }-   }-  ,{{{   220,   210,   220,   210,   220}-    ,{   220,   210,   220,   210,   220}-    ,{   200,   200,   200,   200,   200}-    ,{   220,   210,   220,   210,   220}-    ,{   190,   180,   190,  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  50,   210}-    ,{   220,   110,   220,   130,   220}-    ,{   190,   140,   190,    70,   190}-    }-   ,{{   180,    70,   180,    60,   180}-    ,{   180,    70,   180,    20,   180}-    ,{   180,    70,   180,    20,   180}-    ,{    90,   -20,    90,    60,    90}-    ,{   180,    70,   180,    20,   180}-    }-   ,{{   220,   160,   220,    60,   220}-    ,{   220,   110,   220,    60,   220}-    ,{   210,   160,   210,    50,   210}-    ,{   220,   110,   220,    60,   220}-    ,{   190,   140,   190,    30,   190}-    }-   ,{{   180,    70,   180,   130,   180}-    ,{    90,   -20,    90,    60,    90}-    ,{   180,    70,   180,    20,   180}-    ,{   130,    50,    30,   130,    30}-    ,{   180,    70,   180,    20,   180}-    }-   ,{{   220,   140,   220,    70,   220}-    ,{   220,   110,   220,    60,   220}-    ,{   190,   140,   190,    30,   190}-    ,{   220,   110,   220,    60,   220}-    ,{   100,     0,   100,    70,   100}-    }-   }-  ,{{{   220,   210,   220,   210,   150}-    ,{   220,   210,   220,   210,   150}-    ,{   200,   200,   200,   200,   110}-    ,{   220,   210,   220,   210,   130}-    ,{   190,   180,   190,   180,   100}-    }-   ,{{   180,   170,   180,   170,   150}-    ,{   180,   170,   180,   170,   150}-    ,{   170,   170,   170,   170,    80}-    ,{   140,    80,   140,    80,     0}-    ,{   170,   170,   170,   170,    80}-    }-   ,{{   220,   210,   220,   210,   130}-    ,{   220,   210,   220,   210,   130}-    ,{   200,   200,   200,   200,   110}-    ,{   220,   210,   220,   210,   130}-    ,{   190,   180,   190,   180,   100}-    }-   ,{{   170,   170,   170,   170,    80}-    ,{   140,    80,   140,    80,     0}-    ,{   170,   170,   170,   170,    80}-    ,{    70,    20,    30,    20,    70}-    ,{   170,   170,   170,   170,    80}-    }-   ,{{   220,   210,   220,   210,   130}-    ,{   220,   210,   220,   210,   130}-    ,{   190,   180,   190,   180,   100}-    ,{   220,   210,   220,   210,   130}-    ,{   100,    90,   100,    90,    10}-    }-   }-  }- ,{{{{   210,   210,   200,   200,   200}-    ,{   210,   210,   200,   190,   200}-    ,{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   160,   170}-    ,{   190,   190,   170,   190,   170}-    }-   ,{{   210,   210,   200,   190,   200}-    ,{   210,   210,   200,   190,   200}-    ,{   190,   190,   170,   160,   170}-    ,{    50,    10,    50,   -10,    50}-    ,{   190,   190,   170,   160,   170}-    }-   ,{{   190,   190,   170,   190,   170}-    ,{   180,   180,   170,   160,   170}-    ,{   190,   190,   170,   190,   170}-    ,{   180,   180,   170,   160,   170}-    ,{   190,   190,   170,   190,   170}-    }-   ,{{   190,   190,   170,   160,   170}-    ,{   110,    70,   110,    50,   110}-    ,{   190,   190,   170,   160,   170}-    ,{   130,    50,    30,   130,    70}-    ,{   190,   190,   170,   160,   170}-    }-   ,{{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   160,   170}-    ,{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   160,   170}-    ,{   170,   170,   100,    90,   100}-    }-   }-  ,{{{   210,   210,   200,   200,   200}-    ,{   210,   210,   200,   160,   200}-    ,{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   130,   170}-    ,{   190,   190,   170,   190,   170}-    }-   ,{{   210,   210,   200,   160,   200}-    ,{   210,   210,   200,   160,   200}-    ,{   190,   190,   170,   130,   170}-    ,{    10,    10,     0,   -40,     0}-    ,{   190,   190,   170,   130,   170}-    }-   ,{{   190,   190,   170,   190,   170}-    ,{   180,   180,   170,   130,   170}-    ,{   190,   190,   170,   190,   170}-    ,{   180,   180,   170,   130,   170}-    ,{   190,   190,   170,   190,   170}-    }-   ,{{   190,   190,   170,   130,   170}-    ,{    70,    70,    60,    20,    60}-    ,{   190,   190,   170,   130,   170}-    ,{   120,    50,    30,   120,    30}-    ,{   190,   190,   170,   130,   170}-    }-   ,{{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   130,   170}-    ,{   200,   190,   180,   200,   180}-    ,{   180,   180,   170,   130,   170}-    ,{   170,   170,   100,    60,   100}-    }-   }-  ,{{{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   170,   170,   170,   170,   170}-    ,{   160,   160,   160,   160,   160}-    ,{   170,   160,   170,   160,   170}-    }-   ,{{   190,   190,   190,   190,   190}-    ,{   190,   190,   190,   190,   190}-    ,{   170,   160,   170,   160,   170}-    ,{    50,   -10,    50,   -10,    50}-    ,{   170,   160,   170,   160,   170}-    }-   ,{{   170,   160,   170,   160,   170}-    ,{   160,   160,   160,   160,   160}-    ,{   170,   160,   170,   160,   170}-    ,{   160,   160,   160,   160,   160}-    ,{   170,   160,   170,   160,   170}-    }-   ,{{   170,   160,   170,   160,   170}-    ,{   110,    50,   110,    50,   110}-    ,{   170,   160,   170,   160,  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 170}-    ,{    60,   -50,    60,    30,    60}-    ,{   170,    60,   170,    10,   170}-    ,{   130,    50,    30,   130,    30}-    ,{   170,    60,   170,    10,   170}-    }-   ,{{   180,   130,   180,    70,   180}-    ,{   170,    60,   170,    10,   170}-    ,{   180,   130,   180,    20,   180}-    ,{   170,    60,   170,    10,   170}-    ,{   100,   -10,   100,    70,   100}-    }-   }-  ,{{{   190,   190,   190,   190,   160}-    ,{   190,   190,   190,   190,   160}-    ,{   170,   170,   170,   170,    80}-    ,{   160,   160,   160,   160,    70}-    ,{   170,   160,   170,   160,    80}-    }-   ,{{   190,   190,   190,   190,   160}-    ,{   190,   190,   190,   190,   160}-    ,{   170,   160,   170,   160,    80}-    ,{    50,   -10,    50,   -10,  -100}-    ,{   170,   160,   170,   160,    80}-    }-   ,{{   170,   160,   170,   160,    80}-    ,{   160,   160,   160,   160,    70}-    ,{   170,   160,   170,   160,    80}-    ,{   160,   160,   160,   160,    70}-    ,{   170,   160,   170,   160,    80}-    }-   ,{{   170,   160,   170,   160,    80}-    ,{   110,    50,   110,    50,   -30}-    ,{   170,   160,   170,   160,    80}-    ,{    70,    20,    30,    20,    70}-    ,{   170,   160,   170,   160,    80}-    }-   ,{{   170,   170,   170,   170,    80}-    ,{   160,   160,   160,   160,    70}-    ,{   170,   170,   170,   170,    80}-    ,{   160,   160,   160,   160,    70}-    ,{    90,    90,    90,    90,     0}-    }-   }-  }- ,{{{{   370,   370,   330,   320,   330}-    ,{   340,   340,   330,   320,   330}-    ,{   310,   310,   290,   310,   290}-    ,{   310,   310,   290,   280,   290}-    ,{   370,   370,   290,   310,   290}-    }-   ,{{   340,   340,   330,   320,   330}-    ,{   340,   340,   330,   320,   330}-    ,{   310,   310,   290,   280,   290}-    ,{   270,   230,   270,   200,   270}-    ,{   310,   310,   290,   280,   290}-    }-   ,{{   310,   310,   290,   310,   290}-    ,{   310,   310,   290,   280,   290}-    ,{   310,   310,   290,   310,   290}-    ,{   310,   310,   290,   280,   290}-    ,{   310,   310,   290,   310,   290}-    }-   ,{{   310,   310,   310,   280,   310}-    ,{   310,   270,   310,   240,   310}-    ,{   310,   310,   290,   280,   290}-    ,{   260,   180,   160,   260,   200}-    ,{   310,   310,   290,   280,   290}-    }-   ,{{   370,   370,   290,   310,   290}-    ,{   310,   310,   290,   280,   290}-    ,{   310,   310,   290,   310,   290}-    ,{   310,   310,   290,   280,   290}-    ,{   370,   370,   290,   280,   290}-    }-   }-  ,{{{   370,   370,   330,   310,   330}-    ,{   340,   340,   330,   290,   330}-    ,{   310,   310,   290,   310,   290}-    ,{   310,   310,   290,   250,   290}-    ,{   370,   370,   290,   310,   290}-    }-   ,{{   340,   340,   330,   290,   330}-    ,{   340,   340,   330,   290,   330}-    ,{   310,   310,   290,   250,   290}-    ,{   230,   230,   210,   170,   210}-    ,{   310,   310,   290,   250,  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 290}-    ,{   270,   200,   270,   200,   270}-    ,{   290,   280,   290,   280,   290}-    }-   ,{{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    }-   ,{{   310,   280,   310,   280,   310}-    ,{   310,   240,   310,   240,   310}-    ,{   290,   280,   290,   280,   290}-    ,{   160,   150,   160,   150,   160}-    ,{   290,   280,   290,   280,   290}-    }-   ,{{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    ,{   290,   280,   290,   280,   290}-    }-   }-  ,{{{   330,   240,   330,   260,   330}-    ,{   330,   220,   330,   220,   330}-    ,{   290,   240,   290,   130,   290}-    ,{   290,   180,   290,   260,   290}-    ,{   290,   240,   290,   260,   290}-    }-   ,{{   330,   220,   330,   180,   330}-    ,{   330,   220,   330,   170,   330}-    ,{   290,   180,   290,   130,   290}-    ,{   210,   100,   210,   180,   210}-    ,{   290,   180,   290,   130,   290}-    }-   ,{{   290,   240,   290,   130,   290}-    ,{   290,   180,   290,   130,   290}-    ,{   290,   240,   290,   130,   290}-    ,{   290,   180,   290,   130,   290}-    ,{   290,   240,   290,   130,   290}-    }-   ,{{   290,   180,   290,   260,   290}-    ,{   250,   140,   250,   220,   250}-    ,{   290,   180,   290,   130,   290}-    ,{   260,   180,   160,   260,   160}-    ,{   290,   180,   290,   130,   290}-    }-   ,{{   290,   240,   290,   260,   290}-    ,{   290,   180,   290,   130,   290}-    ,{   290,   240,   290,   130,   290}-    ,{   290,   180,   290,   130,   290}-    ,{   290,   180,   290,   260,   290}-    }-   }-  ,{{{   320,   320,   320,   320,   290}-    ,{   320,   320,   320,   320,   290}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    }-   ,{{   320,   320,   320,   320,   290}-    ,{   320,   320,   320,   320,   290}-    ,{   290,   280,   290,   280,   200}-    ,{   270,   200,   270,   200,   120}-    ,{   290,   280,   290,   280,   200}-    }-   ,{{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    }-   ,{{   310,   280,   310,   280,   200}-    ,{   310,   240,   310,   240,   160}-    ,{   290,   280,   290,   280,   200}-    ,{   200,   150,   160,   150,   200}-    ,{   290,   280,   290,   280,   200}-    }-   ,{{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    ,{   290,   280,   290,   280,   200}-    }-   }-  }- ,{{{{   350,   340,   350,   280,   350}-    ,{   350,   310,   350,   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240,   130,   240,    80,   240}-    }-   ,{{   250,   190,   250,    90,   250}-    ,{   250,   140,   250,    90,   250}-    ,{   240,   190,   240,    80,   240}-    ,{   250,   140,   250,    90,   250}-    ,{   240,   190,   240,    80,   240}-    }-   ,{{   240,   130,   240,   190,   240}-    ,{   210,   100,   210,   180,   210}-    ,{   240,   130,   240,    80,   240}-    ,{   190,   110,    90,   190,    90}-    ,{   240,   130,   240,    80,   240}-    }-   ,{{   250,   190,   250,   120,   250}-    ,{   250,   140,   250,    90,   250}-    ,{   240,   190,   240,    80,   240}-    ,{   250,   140,   250,    90,   250}-    ,{   150,    40,   150,   120,   150}-    }-   }-  ,{{{   260,   250,   260,   250,   230}-    ,{   260,   250,   260,   250,   230}-    ,{   240,   230,   240,   230,   150}-    ,{   240,   240,   240,   240,   150}-    ,{   240,   230,   240,   230,   150}-    }-   ,{{   260,   250,   260,   250,   230}-    ,{   260,   250,   260,   250,   230}-    ,{   230,   230,   230,   230,   140}-    ,{   190,   130,   190,   130,    40}-    ,{   230,   230,   230,   230,   140}-    }-   ,{{   240,   240,   240,   240,   150}-    ,{   240,   240,   240,   240,   150}-    ,{   240,   230,   240,   230,   150}-    ,{   240,   240,   240,   240,   150}-    ,{   240,   230,   240,   230,   150}-    }-   ,{{   260,   230,   260,   230,   140}-    ,{   260,   200,   260,   200,   110}-    ,{   230,   230,   230,   230,   140}-    ,{   120,    80,    80,    80,   120}-    ,{   230,   230,   230,   230,   140}-    }-   ,{{   240,   240,   240,   240,   150}-    ,{   240,   240,   240,   240,   150}-    ,{   240,   230,   240,   230,   150}-    ,{   240,   240,   240,   240,   150}-    ,{   150,   140,   150,   140,    60}-    }-   }-  }- ,{{{{   280,   280,   260,   280,   260}-    ,{   280,   280,   260,   250,   260}-    ,{   280,   280,   260,   280,   260}-    ,{   280,   280,   260,   250,   260}-    ,{   280,   280,   260,   280,   260}-    }-   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280,   280,   260,   220,   260}-    ,{   280,   280,   260,   280,   260}-    }-   ,{{   280,   280,   260,   220,   260}-    ,{   280,   280,   260,   220,   260}-    ,{   230,   230,   220,   180,   220}-    ,{   170,   170,   160,   120,   160}-    ,{   230,   230,   220,   180,   220}-    }-   ,{{   280,   280,   260,   280,   260}-    ,{   280,   280,   260,   220,   260}-    ,{   280,   280,   260,   280,   260}-    ,{   280,   280,   260,   220,   260}-    ,{   280,   280,   260,   280,   260}-    }-   ,{{   230,   230,   220,   200,   220}-    ,{   180,   180,   170,   130,   170}-    ,{   230,   230,   220,   180,   220}-    ,{   200,   120,   110,   200,   110}-    ,{   230,   230,   220,   180,   220}-    }-   ,{{   280,   280,   260,   250,   260}-    ,{   280,   280,   260,   220,   260}-    ,{   250,   250,   230,   250,   230}-    ,{   280,   280,   260,   220,   260}-    ,{   250,   250,   180,   140,   180}-    }-   }-  ,{{{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    }-   ,{{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   210,   210,   210,   210,   210}-    ,{   210,   150,   210,   150,   210}-    ,{   210,   210,   210,   210,   210}-    }-   ,{{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    }-   ,{{   220,   210,   220,   210,   220}-    ,{   220,   160,   220,   160,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   100,   100,   100,   100,   100}-    ,{   210,   210,   210,   210,   210}-    }-   ,{{   260,   250,   260,   250,   260}-    ,{   260,   250,   260,   250,   260}-    ,{   230,   220,   230,   220,   230}-    ,{   260,   250,   260,   250,   260}-    ,{   170,   170,   170,   170,   170}-    }-   }-  ,{{{   260,   210,   260,   210,   260}-    ,{   260,   150,   260,   140,   260}-    ,{   260,   210,   260,   100,   260}-    ,{   260,   150,   260,   210,   260}-    ,{   260,   210,   260,   150,   260}-    }-   ,{{   260,   150,   260,   130,   260}-    ,{   260,   150,   260,   100,   260}-    ,{   220,   110,   220,    60,   220}-    ,{   160,    50,   160,   130,   160}-    ,{   220,   110,   220,    60,   220}-    }-   ,{{   260,   210,   260,   100,   260}-    ,{   260,   150,   260,   100,   260}-    ,{   260,   210,   260,   100,   260}-    ,{   260,   150,   260,   100,   260}-    ,{   260,   210,   260,   100,   260}-    }-   ,{{   220,   130,   220,   210,   220}-    ,{   170,    60,   170,   140,   170}-    ,{   220,   110,   220,    60,   220}-    ,{   210,   130,   110,   210,   110}-    ,{   220,   110,   220,    60,   220}-    }-   ,{{   260,   180,   260,   150,   260}-    ,{   260,   150,   260,   100,   260}-    ,{   230,   180,   230,    70,   230}-    ,{   260,   150,   260,   100,   260}-    ,{   180,    70,   180,   150,   180}-    }-   }-  ,{{{   260,   250,   260,   250,   230}-    ,{   260,   250,   260,   250,   230}-    ,{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    }-   ,{{   260,   250,   260,   250,   230}-    ,{   260,   250,   260,   250,   230}-    ,{   210,   210,   210,   210,   120}-    ,{   210,   150,   210,   150,    60}-    ,{   210,   210,   210,   210,   120}-    }-   ,{{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    ,{   260,   250,   260,   250,   170}-    }-   ,{{   220,   210,   220,   210,   140}-    ,{   220,   160,   220,   160,    70}-    ,{   210,   210,   210,   210,   120}-    ,{   140,   100,   100,   100,   140}-    ,{   210,   210,   210,   210,   120}-    }-   ,{{   260,   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100}-    ,{   190,   140,   190,   140,   100}-    }-   ,{{   210,   170,   210,   170,   190}-    ,{   210,   170,   210,   170,   190}-    ,{   190,   140,   190,   140,   100}-    ,{    70,   -30,    70,   -30,   -70}-    ,{   190,   140,   190,   140,   100}-    }-   ,{{   190,   140,   190,   140,   100}-    ,{   180,   140,   180,   140,   100}-    ,{   190,   140,   190,   140,   100}-    ,{   180,   140,   180,   140,   100}-    ,{   190,   140,   190,   140,   100}-    }-   ,{{   190,   140,   190,   140,   100}-    ,{   130,    30,   130,    30,   -10}-    ,{   190,   140,   190,   140,   100}-    ,{    90,     0,    50,     0,    90}-    ,{   190,   140,   190,   140,   100}-    }-   ,{{   190,   150,   190,   150,   110}-    ,{   180,   140,   180,   140,   100}-    ,{   190,   150,   190,   150,   110}-    ,{   180,   140,   180,   140,   100}-    ,{   110,    70,   110,    70,    30}-    }-   }-  }- ,{{{{   370,   370,   340,   300,   340}-    ,{   340,   340,   340,   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280,   170,   280,   120,   280}-    }-   ,{{   280,   230,   280,   120,   280}-    ,{   280,   170,   280,   120,   280}-    ,{   280,   230,   280,   120,   280}-    ,{   280,   170,   280,   120,   280}-    ,{   280,   230,   280,   120,   280}-    }-   ,{{   310,   200,   310,   280,   310}-    ,{   310,   200,   310,   280,   310}-    ,{   280,   170,   280,   120,   280}-    ,{   250,   170,   150,   250,   150}-    ,{   280,   170,   280,   120,   280}-    }-   ,{{   280,   230,   280,   250,   280}-    ,{   280,   170,   280,   120,   280}-    ,{   280,   230,   280,   120,   280}-    ,{   280,   170,   280,   120,   280}-    ,{   280,   170,   280,   250,   280}-    }-   }-  ,{{{   370,   260,   370,   260,   220}-    ,{   370,   260,   370,   260,   220}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    }-   ,{{   280,   230,   280,   230,   220}-    ,{   240,   200,   240,   200,   220}-    ,{   280,   230,   280,   230,   190}-    ,{   200,   100,   200,   100,    60}-    ,{   280,   230,   280,   230,   190}-    }-   ,{{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    }-   ,{{   370,   260,   370,   260,   220}-    ,{   370,   260,   370,   260,   220}-    ,{   280,   230,   280,   230,   190}-    ,{   190,   100,   150,   100,   190}-    ,{   280,   230,   280,   230,   190}-    }-   ,{{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    ,{   280,   230,   280,   230,   190}-    }-   }-  }- ,{{{{   280,   280,   280,   230,   280}-    ,{   280,   280,   280,   230,   280}-    ,{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   220,   260}-    }-   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260,   260,   260,   170,   260}-    ,{   260,   260,   260,   220,   260}-    }-   ,{{   280,   280,   280,   180,   280}-    ,{   280,   280,   280,   180,   280}-    ,{   250,   250,   250,   160,   250}-    ,{   150,   150,   150,    60,   150}-    ,{   250,   250,   250,   160,   250}-    }-   ,{{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   170,   260}-    ,{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   170,   260}-    ,{   260,   260,   260,   220,   260}-    }-   ,{{   250,   250,   250,   160,   250}-    ,{   220,   220,   220,   130,   220}-    ,{   250,   250,   250,   160,   250}-    ,{   140,   100,   100,   140,   100}-    ,{   250,   250,   250,   160,   250}-    }-   ,{{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   170,   260}-    ,{   260,   260,   260,   220,   260}-    ,{   260,   260,   260,   170,   260}-    ,{   230,   230,   170,    70,   170}-    }-   }-  ,{{{   280,   230,   280,   230,   250}-    ,{   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INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   310,   300,   270,   310,   290}-    ,{   300,   300,   270,   270,   290}-    ,{   310,   290,   250,   310,   250}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    }-   ,{{   290,   270,   230,   230,   290}-    ,{   290,   270,   230,   230,   290}-    ,{   260,   260,   220,   220,   220}-    ,{   190,   170,   190,   130,   190}-    ,{   260,   260,   220,   220,   220}-    }-   ,{{   310,   300,   270,   310,   270}-    ,{   300,   300,   270,   270,   270}-    ,{   310,   290,   250,   310,   250}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    }-   ,{{   260,   260,   220,   220,   220}-    ,{   190,   170,   190,   130,   190}-    ,{   260,   260,   220,   220,   220}-    ,{   210,   130,    80,   210,   210}-    ,{   260,   260,   220,   220,   220}-    }-   ,{{   300,   300,   270,   300,   270}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    ,{   300,   300,   270,   270,   270}-    ,{   240,   240,   150,   150,   150}-    }-   }-  ,{{{   310,   300,   270,   310,   270}-    ,{   300,   300,   270,   270,   270}-    ,{   310,   290,   250,   310,   250}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    }-   ,{{   270,   270,   230,   230,   230}-    ,{   270,   270,   230,   230,   230}-    ,{   260,   260,   220,   220,   220}-    ,{   170,   170,   130,   130,   130}-    ,{   260,   260,   220,   220,   220}-    }-   ,{{   310,   300,   270,   310,   270}-    ,{   300,   300,   270,   270,   270}-    ,{   310,   290,   250,   310,   250}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    }-   ,{{   260,   260,   220,   220,   220}-    ,{   170,   170,   130,   130,   130}-    ,{   260,   260,   220,   220,   220}-    ,{   210,   110,    80,   210,    80}-    ,{   260,   260,   220,   220,   220}-    }-   ,{{   300,   300,   270,   300,   270}-    ,{   300,   300,   270,   270,   270}-    ,{   300,   270,   240,   300,   240}-    ,{   300,   300,   270,   270,   270}-    ,{   240,   240,   150,   150,   150}-    }-   }-  ,{{{   270,   270,   270,   270,   270}-    ,{   270,   270,   270,   270,   270}-    ,{   250,   250,   250,   250,   250}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    }-   ,{{   230,   230,   230,   230,   230}-    ,{   230,   230,   230,   230,   230}-    ,{   220,   220,   220,   220,   220}-    ,{   190,   130,   190,   130,   190}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   270,   270,   270,   270,   270}-    ,{   270,   270,   270,   270,   270}-    ,{   250,   250,   250,   250,   250}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   190,   130,   190,   130,   190}-    ,{   220,   220,   220,   220,   220}-    ,{    80,    80,    80,    80,    80}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   270,   270,   270,   270,   270}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    ,{   270,   270,   270,   270,   270}-    ,{   150,   150,   150,   150,   150}-    }-   }-  ,{{{   270,   230,   270,   210,   270}-    ,{   270,   190,   270,   140,   270}-    ,{   250,   230,   250,   120,   250}-    ,{   270,   190,   270,   210,   270}-    ,{   240,   220,   240,   150,   240}-    }-   ,{{   230,   150,   230,   130,   230}-    ,{   230,   150,   230,   100,   230}-    ,{   220,   140,   220,    90,   220}-    ,{   130,    50,   130,   130,   130}-    ,{   220,   140,   220,    90,   220}-    }-   ,{{   270,   230,   270,   140,   270}-    ,{   270,   190,   270,   140,   270}-    ,{   250,   230,   250,   120,   250}-    ,{   270,   190,   270,   140,   270}-    ,{   240,   220,   240,   110,   240}-    }-   ,{{   220,   140,   220,   210,   220}-    ,{   130,    50,   130,   130,   130}-    ,{   220,   140,   220,    90,   220}-    ,{   210,   130,    80,   210,    80}-    ,{   220,   140,   220,    90,   220}-    }-   ,{{   270,   220,   270,   150,   270}-    ,{   270,   190,   270,   140,   270}-    ,{   240,   220,   240,   110,   240}-    ,{   270,   190,   270,   140,   270}-    ,{   150,    70,   150,   150,   150}-    }-   }-  ,{{{   290,   270,   270,   270,   290}-    ,{   290,   270,   270,   270,   290}-    ,{   250,   250,   250,   250,   250}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    }-   ,{{   290,   230,   230,   230,   290}-    ,{   290,   230,   230,   230,   290}-    ,{   220,   220,   220,   220,   220}-    ,{   190,   130,   190,   130,   130}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   270,   270,   270,   270,   270}-    ,{   270,   270,   270,   270,   270}-    ,{   250,   250,   250,   250,   250}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   190,   130,   190,   130,   130}-    ,{   220,   220,   220,   220,   220}-    ,{   210,    80,    80,    80,   210}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   270,   270,   270,   270,   270}-    ,{   270,   270,   270,   270,   270}-    ,{   240,   240,   240,   240,   240}-    ,{   270,   270,   270,   270,   270}-    ,{   150,   150,   150,   150,   150}-    }-   }-  }- ,{{{{   300,   280,   240,   280,   300}-    ,{   300,   280,   240,   240,   300}-    ,{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    }-   ,{{   300,   280,   240,   240,   300}-    ,{   300,   280,   240,   240,   300}-    ,{   250,   250,   220,   220,   220}-    ,{   100,    70,   100,    40,   100}-    ,{   250,   250,   220,   220,   220}-    }-   ,{{   280,   250,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    }-   ,{{   250,   250,   220,   220,   220}-    ,{   160,   140,   160,   100,   160}-    ,{   250,   250,   220,   220,   220}-    ,{   210,   130,    80,   210,   210}-    ,{   250,   250,   220,   220,   220}-    }-   ,{{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   240,   240,   140,   140,   140}-    }-   }-  ,{{{   280,   280,   240,   280,   240}-    ,{   280,   280,   240,   240,   240}-    ,{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    }-   ,{{   280,   280,   240,   240,   240}-    ,{   280,   280,   240,   240,   240}-    ,{   250,   250,   220,   220,   220}-    ,{    70,    70,    40,    40,    40}-    ,{   250,   250,   220,   220,   220}-    }-   ,{{   280,   250,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   250,   220,   280,   220}-    }-   ,{{   250,   250,   220,   220,   220}-    ,{   140,   140,   100,   100,   100}-    ,{   250,   250,   220,   220,   220}-    ,{   210,   110,    80,   210,    80}-    ,{   250,   250,   220,   220,   220}-    }-   ,{{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   280,   260,   220,   280,   220}-    ,{   250,   250,   210,   210,   210}-    ,{   240,   240,   140,   140,   140}-    }-   }-  ,{{{   240,   240,   240,   240,   240}-    ,{   240,   240,   240,   240,   240}-    ,{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   240,   240,   240,   240,   240}-    ,{   240,   240,   240,   240,   240}-    ,{   220,   220,   220,   220,   220}-    ,{   100,    40,   100,    40,   100}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   160,   100,   160,   100,   160}-    ,{   220,   220,   220,   220,   220}-    ,{    80,    80,    80,    80,    80}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   140,   140,   140,   140,   140}-    }-   }-  ,{{{   240,   200,   240,   210,   240}-    ,{   240,   160,   240,   110,   240}-    ,{   220,   200,   220,    90,   220}-    ,{   210,   130,   210,   210,   210}-    ,{   220,   200,   220,   140,   220}-    }-   ,{{   240,   160,   240,   110,   240}-    ,{   240,   160,   240,   110,   240}-    ,{   220,   140,   220,    90,   220}-    ,{    40,   -40,    40,    40,    40}-    ,{   220,   140,   220,    90,   220}-    }-   ,{{   220,   200,   220,    90,   220}-    ,{   210,   130,   210,    80,   210}-    ,{   220,   200,   220,    90,   220}-    ,{   210,   130,   210,    80,   210}-    ,{   220,   200,   220,    90,   220}-    }-   ,{{   220,   140,   220,   210,   220}-    ,{   100,    20,   100,   100,   100}-    ,{   220,   140,   220,    90,   220}-    ,{   210,   130,    80,   210,    80}-    ,{   220,   140,   220,    90,   220}-    }-   ,{{   220,   200,   220,   140,   220}-    ,{   210,   130,   210,    80,   210}-    ,{   220,   200,   220,    90,   220}-    ,{   210,   130,   210,    80,   210}-    ,{   140,    90,   140,   140,   140}-    }-   }-  ,{{{   300,   240,   240,   240,   300}-    ,{   300,   240,   240,   240,   300}-    ,{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   300,   240,   240,   240,   300}-    ,{   300,   240,   240,   240,   300}-    ,{   220,   220,   220,   220,   220}-    ,{   100,    40,   100,    40,    50}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    ,{   210,   210,   210,   210,   210}-    ,{   220,   220,   220,   220,   220}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{   160,   100,   160,   100,   140}- 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340,   260,   340,   210,   340}-    }-   ,{{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    }-   ,{{   340,   260,   340,   340,   340}-    ,{   300,   220,   300,   300,   300}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   260,   210,   340,   210}-    ,{   340,   260,   340,   210,   340}-    }-   ,{{   340,   320,   340,   340,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   260,   340,   340,   340}-    }-   }-  ,{{{   430,   370,   370,   370,   430}-    ,{   430,   370,   370,   370,   430}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   430,   370,   370,   370,   430}-    ,{   430,   370,   370,   370,   430}-    ,{   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340,   340}-    ,{   400,   370,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   430,   430,   340,   340,   340}-    }-   }-  ,{{{   430,   430,   370,   400,   370}-    ,{   410,   410,   370,   370,   370}-    ,{   400,   370,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   430,   430,   340,   400,   340}-    }-   ,{{   410,   410,   370,   370,   370}-    ,{   410,   410,   370,   370,   370}-    ,{   370,   370,   340,   340,   340}-    ,{   290,   290,   260,   260,   260}-    ,{   370,   370,   340,   340,   340}-    }-   ,{{   400,   370,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   400,   370,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   400,   370,   340,   400,   340}-    }-   ,{{   370,   370,   340,   340,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   340,   240,   210,   340,   210}-    ,{   370,   370,   340,   340,   340}-    }-   ,{{   430,   430,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   400,   370,   340,   400,   340}-    ,{   370,   370,   340,   340,   340}-    ,{   430,   430,   340,   340,   340}-    }-   }-  ,{{{   400,   370,   400,   370,   400}-    ,{   400,   370,   400,   370,   400}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   370,   370,   370,   370,   370}-    ,{   370,   370,   370,   370,   370}-    ,{   340,   340,   340,   340,   340}-    ,{   320,   260,   320,   260,   320}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   400,   340,   400,   340,   400}-    ,{   400,   340,   400,   340,   400}-    ,{   340,   340,   340,   340,   340}-    ,{   210,   210,   210,   210,   210}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   }-  ,{{{   370,   320,   370,   340,   370}-    ,{   370,   290,   370,   340,   370}-    ,{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   340,   340}-    ,{   340,   320,   340,   340,   340}-    }-   ,{{   370,   290,   370,   260,   370}-    ,{   370,   290,   370,   240,   370}-    ,{   340,   260,   340,   210,   340}-    ,{   260,   180,   260,   260,   260}-    ,{   340,   260,   340,   210,   340}-    }-   ,{{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    }-   ,{{   340,   260,   340,   340,   340}-    ,{   340,   260,   340,   340,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   260,   210,   340,   210}-    ,{   340,   260,   340,   210,   340}-    }-   ,{{   340,   320,   340,   340,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   320,   340,   210,   340}-    ,{   340,   260,   340,   210,   340}-    ,{   340,   260,   340,   340,   340}-    }-   }-  ,{{{   430,   370,   400,   370,   430}-    ,{   430,   370,   400,   370,   430}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   430,   370,   370,   370,   430}-    ,{   430,   370,   370,   370,   430}-    ,{   340,   340,   340,   340,   340}-    ,{   320,   260,   320,   260,   260}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   400,   340,   400,   340,   340}-    ,{   400,   340,   400,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   210,   210,   210,   340}-    ,{   340,   340,   340,   340,   340}-    }-   ,{{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    ,{   340,   340,   340,   340,   340}-    }-   }-  }- }};
− include/intl22dH.h 
@@ -1,9993 +0,0 @@-PUBLIC int int22_dH[NBPAIRS+1][NBPAIRS+1][5][5][5][5] =-{{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   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30,  -110}-    ,{    80,  -230,  -110,    80,   -60}-    ,{    80,  -120,    30,    30,    80}-    ,{   -30,  -340,  -220,   -30,  -170}-    }-   ,{{  -120,  -460,  -290,  -120,  -230}-    ,{  -120,  -460,  -310,  -120,  -260}-    ,{  -430,  -770,  -620,  -430,  -570}-    ,{  -230,  -670,  -290,  -980,  -230}-    ,{  -430,  -770,  -620,  -430,  -570}-    }-   ,{{    30,  -290,  -170,    30,  -110}-    ,{    30,  -310,  -170,    30,  -110}-    ,{    20,  -290,  -170,    20,  -120}-    ,{    30,  -310,  -170,    30,  -110}-    ,{   -30,  -340,  -220,   -30,  -170}-    }-   ,{{    80,  -120,    30,  -430,    80}-    ,{  -520,  -960,  -580, -1270,  -520}-    ,{  -430,  -770,  -620,  -430,  -570}-    ,{    80,  -120,    30,  -430,    80}-    ,{  -430,  -770,  -620,  -430,  -570}-    }-   ,{{    80,  -230,  -110,    80,   -60}-    ,{    30,  -310,  -170,    30,  -110}-    ,{    80,  -230,  -110,    80,   -60}-    ,{    30,  -310,  -170,    30,  -110}-    ,{  -860,  -860,  -960, -1410,  -900}-    }-   }-  ,{{{    30,  -120,    30,  -520,    30}-    ,{  -170,  -310,  -170,  -810,  -170}-    ,{  -110,  -260,  -110,  -520,  -110}-    ,{    30,  -120,    30,  -810,    30}-    ,{  -220,  -370,  -220,  -630,  -220}-    }-   ,{{  -310,  -460,  -310,  -960,  -310}-    ,{  -310,  -460,  -310,  -960,  -310}-    ,{  -620,  -770,  -620, -1270,  -620}-    ,{  -530,  -670,  -530, -1170,  -530}-    ,{  -620,  -770,  -620, -1270,  -620}-    }-   ,{{  -170,  -310,  -170,  -580,  -170}-    ,{  -170,  -310,  -170,  -810,  -170}-    ,{  -170,  -320,  -170,  -580,  -170}-    ,{  -170,  -310,  -170,  -810,  -170}-    ,{  -220,  -370,  -220,  -630,  -220}-    }-   ,{{    30,  -120,    30, -1270,    30}-    ,{  -810,  -960,  -810, -1460,  -810}-    ,{  -620,  -770,  -620, -1270,  -620}-    ,{    30,  -120,    30, -1870,    30}-    ,{  -620,  -770,  -620, -1270,  -620}-    }-   ,{{  -110,  -260,  -110,  -520,  -110}-    ,{  -170,  -310,  -170,  -810,  -170}-    ,{  -110,  -260,  -110,  -520,  -110}-    ,{  -170,  -310,  -170,  -810,  -170}-    ,{  -860,  -860,  -960, -1600,  -960}-    }-   }-  ,{{{    80,  -430,    20,  -430,    80}-    ,{  -110,  -620,  -170,  -620,  -110}-    ,{   -60,  -570,  -120,  -570,   -60}-    ,{    80,  -430,    20,  -430,    80}-    ,{  -170,  -680,  -230,  -680,  -170}-    }-   ,{{  -230,  -770,  -290,  -770,  -230}-    ,{  -260,  -770,  -320,  -770,  -260}-    ,{  -570, -1080,  -630, -1080,  -570}-    ,{  -230,  -980,  -290,  -980,  -230}-    ,{  -570, -1080,  -630, -1080,  -570}-    }-   ,{{  -110,  -620,  -170,  -620,  -110}-    ,{  -110,  -620,  -170,  -620,  -110}-    ,{  -120,  -630,  -180,  -630,  -120}-    ,{  -110,  -620,  -170,  -620,  -110}-    ,{  -170,  -680,  -230,  -680,  -170}-    }-   ,{{    80,  -430,    20,  -430,    80}-    ,{  -520, -1270,  -580, -1270,  -520}-    ,{  -570, -1080,  -630, -1080,  -570}-    ,{    80,  -430,    20,  -430,    80}-    ,{  -570, -1080,  -630, -1080,  -570}-    }-   ,{{   -60,  -570,  -120,  -570,  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30}-    ,{  -430,  -980,  -620,  -430,  -620}-    }-   ,{{    80,  -230,  -110,    80,  -110}-    ,{    30,  -530,  -170,    30,  -170}-    ,{    80,  -230,  -110,    80,  -110}-    ,{    30,  -530,  -170,    30,  -170}-    ,{  -960, -1320,  -960, -2010,  -960}-    }-   }-  ,{{{   -30,  -430,   -30,  -430,  -860}-    ,{  -220,  -620,  -220,  -620,  -860}-    ,{  -170,  -570,  -170,  -570,  -900}-    ,{   -30,  -430,   -30,  -430,  -960}-    ,{  -280,  -680,  -280,  -680, -1010}-    }-   ,{{  -340,  -770,  -340,  -770,  -860}-    ,{  -370,  -770,  -370,  -770,  -860}-    ,{  -680, -1080,  -680, -1080, -1410}-    ,{  -340,  -980,  -340,  -980, -1320}-    ,{  -680, -1080,  -680, -1080, -1410}-    }-   ,{{  -220,  -620,  -220,  -620,  -960}-    ,{  -220,  -620,  -220,  -620,  -960}-    ,{  -230,  -630,  -230,  -630,  -960}-    ,{  -220,  -620,  -220,  -620,  -960}-    ,{  -280,  -680,  -280,  -680, -1010}-    }-   ,{{   -30,  -430,   -30,  -430, -1410}-    ,{  -630, -1270,  -630, -1270, -1600}-    ,{  -680, -1080,  -680, -1080, -1410}-    ,{   -30,  -430,   -30,  -430, -2010}-    ,{  -680, -1080,  -680, -1080, -1410}-    }-   ,{{  -170,  -570,  -170,  -570,  -900}-    ,{  -220,  -620,  -220,  -620,  -960}-    ,{  -170,  -570,  -170,  -570,  -900}-    ,{  -220,  -620,  -220,  -620,  -960}-    ,{ -1010, -1410, -1010, -1410, -1750}-    }-   }-  }- ,{{{{   540,   180,    30,   540,   180}-    ,{    10,  -580,  -150,    10,   -90}-    ,{   540,  -350,  -600,   540,  -540}-    ,{   180,   180,    30,  -320,   180}-    ,{   -90,  -740,   -90,  -260,  -540}-    }-   ,{{   -90,  -350,  -150,  -100,   -90}-    ,{   -90,  -580,  -150,  -200,   -90}-    ,{  -100,  -350,  -600,  -100,  -540}-    ,{  -630, -1790,  -630, -1790, -1040}-    ,{  -400,  -740,  -600,  -400,  -540}-    }-   ,{{   540,  -660,  -510,   540,  -400}-    ,{    10,  -660,  -510,    10,  -400}-    ,{   540,  -940,  -820,   540,  -760}-    ,{  -320,  -660,  -510,  -320,  -460}-    ,{  -260,  -940,  -820,  -260,  -550}-    }-   ,{{   180,   180,    30,  -400,   180}-    ,{  -500, -1070,  -500, -1080,  -570}-    ,{  -400,  -740,  -600,  -400,  -540}-    ,{   180,   180,    30,  -430,   180}-    ,{  -400,  -740,  -600,  -400,  -540}-    }-   ,{{   -90,  -660,   -90,  -210,  -460}-    ,{  -320,  -660,  -510,  -320,  -460}-    ,{  -210, -1250, -1130,  -210, -1070}-    ,{  -320,  -660,  -510,  -320,  -460}-    ,{   -90,  -830,   -90,  -810,  -800}-    }-   }-  ,{{{   540,   180,   -90,   540,    30}-    ,{    10,  -580,  -220,    10,  -150}-    ,{   540,  -740,  -600,   540,  -600}-    ,{   180,   180,  -390, -1160,    30}-    ,{   -90,  -740,   -90,  -810,  -600}-    }-   ,{{  -100,  -580,  -220,  -100,  -150}-    ,{  -150,  -580,  -220,  -970,  -150}-    ,{  -100,  -740,  -600,  -100,  -600}-    ,{ -1340, -2010, -1650, -1980, -1340}-    ,{  -600,  -740,  -600, -1240,  -600}-    }-   ,{{   540,  -660,  -510,   540,  -510}-    ,{    10,  -660, -1150,    10,  -510}-    ,{   540,  -960,  -820,   540,  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-460}-    ,{  -460,  -970,  -750,  -970,  -460}-    ,{  -760, -1270,  -820, -1270,  -760}-    ,{  -460,  -970,  -520,  -970,  -460}-    ,{  -550, -1270,  -820, -1270,  -550}-    }-   ,{{   180,  -430,    20,  -430,   180}-    ,{  -500, -1070,  -500, -1320,  -570}-    ,{  -540, -1050,  -600, -1050,  -540}-    ,{   180,  -430,    20,  -430,   180}-    ,{  -540, -1050,  -600, -1050,  -540}-    }-   ,{{  -460,  -830,  -520,  -970,  -460}-    ,{  -460,  -970,  -520,  -970,  -460}-    ,{ -1070, -1580, -1130, -1580, -1070}-    ,{  -460,  -970,  -520,  -970,  -460}-    ,{  -830,  -830, -1710, -1260, -1460}-    }-   }-  ,{{{    30,  -350,    30,  -200,    30}-    ,{  -150,  -870,  -150,  -200,  -150}-    ,{  -210,  -350,  -600,  -210,  -600}-    ,{    30,  -870,    30,  -320,    30}-    ,{  -260,  -940,  -600,  -260,  -600}-    }-   ,{{  -150,  -350,  -150,  -200,  -150}-    ,{  -150, -1600,  -150,  -200,  -150}-    ,{  -350,  -350,  -600,  -440,  -600}-    ,{ -1340, -3070, -1340, -2390, -1340}-    ,{  -400,  -960,  -600,  -400,  -600}-    }-   ,{{  -260,  -870,  -510,  -260,  -510}-    ,{  -320, -1110,  -510,  -320,  -510}-    ,{  -620,  -940,  -820,  -620,  -820}-    ,{  -320,  -870,  -510,  -320,  -510}-    ,{  -260,  -940,  -820,  -260,  -820}-    }-   ,{{    30,  -960,    30,  -400,    30}-    ,{  -860, -1880,  -860, -1080,  -860}-    ,{  -400,  -960,  -600,  -400,  -600}-    ,{    30, -1370,    30, -2280,    30}-    ,{  -400,  -960,  -600,  -400,  -600}-    }-   ,{{  -210,  -870,  -510,  -210,  -510}-    ,{  -320,  -870,  -510,  -320,  -510}-    ,{  -210, -1250, -1130,  -210, -1130}-    ,{  -320,  -870,  -510,  -320,  -510}-    ,{  -800, -1360,  -800, -1550,  -800}-    }-   }-  ,{{{  -200,  -430,  -200,  -430,  -230}-    ,{  -200,  -600,  -200,  -600,  -400}-    ,{  -650, -1050,  -650, -1050, -1390}-    ,{  -230,  -430,  -570,  -430,  -230}-    ,{  -650, -1050,  -650, -1050, -1390}-    }-   ,{{  -200,  -600,  -200,  -600, -1390}-    ,{  -200,  -600,  -200,  -600, -1490}-    ,{  -650, -1050,  -650, -1050, -1390}-    ,{ -1150, -1790, -1150, -1790, -1520}-    ,{  -650, -1050,  -650, -1050, -1390}-    }-   ,{{  -400,  -970,  -570,  -970,  -400}-    ,{  -400,  -970,  -570,  -970,  -400}-    ,{  -870, -1270,  -870, -1270, -1610}-    ,{  -570,  -970,  -570,  -970, -1300}-    ,{  -870, -1270,  -870, -1270, -1610}-    }-   ,{{  -230,  -430,  -650,  -430,  -230}-    ,{ -1300, -1320, -1750, -1320, -1300}-    ,{  -650, -1050,  -650, -1050, -1390}-    ,{  -230,  -430,  -880,  -430,  -230}-    ,{  -650, -1050,  -650, -1050, -1390}-    }-   ,{{  -570,  -970,  -570,  -970, -1300}-    ,{  -570,  -970,  -570,  -970, -1300}-    ,{ -1180, -1580, -1180, -1580, -1920}-    ,{  -570,  -970,  -570,  -970, -1300}-    ,{  -860, -1260,  -860, -1260, -2350}-    }-   }-  }- ,{{{{   240,    40,   190,  -270,   240}-    ,{  -590, -1030,  -650,  -870,  -590}-    ,{  -870, -1180, -1060,  -870, -1010}-    ,{   240,    40,   190,  -270,   240}-    ,{  -870,  -970, -1060,  -870, -1010}-    }-   ,{{  -780, -1210,  -840,  -870,  -780}-    ,{ -1050, -1370, -1240, -1050, -1190}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{  -780, -1220,  -840, -1530,  -780}-    ,{  -870, -1210, -1060,  -870, -1010}-    }-   ,{{  -870, -1180, -1060,  -870, -1010}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{  -870, -1180, -1060,  -870, -1010}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{  -870, -1180, -1060,  -870, -1010}-    }-   ,{{   240,    40,   190,  -270,   240}-    ,{  -590, -1030,  -650, -1340,  -590}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{   240,    40,   190,  -270,   240}-    ,{  -870, -1210, -1060,  -870, -1010}-    }-   ,{{  -870,  -970, -1060,  -870, -1010}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{  -870, -1180, -1060,  -870, -1010}-    ,{  -870, -1210, -1060,  -870, -1010}-    ,{  -970,  -970, -1060, -1520, -1010}-    }-   }-  ,{{{   190,    40,   190, -1470,   190}-    ,{  -890, -1030,  -890, -1530,  -890}-    ,{ -1060, -1210, -1060, -1470, -1060}-    ,{   190,    40,   190, -1710,   190}-    ,{  -970,  -970, -1060, -1470, -1060}-    }-   ,{{ -1060, -1210, -1060, -1710, -1060}-    ,{ -1240, -1370, -1240, -1890, -1240}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{ -1080, -1220, -1080, -1720, -1080}-    ,{ -1060, -1210, -1060, -1710, -1060}-    }-   ,{{ -1060, -1210, -1060, -1470, -1060}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{ -1060, -1210, -1060, -1470, -1060}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{ -1060, -1210, -1060, -1470, -1060}-    }-   ,{{   190,    40,   190, -1530,   190}-    ,{  -890, -1030,  -890, -1530,  -890}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{   190,    40,   190, -1710,   190}-    ,{ -1060, -1210, -1060, -1710, -1060}-    }-   ,{{  -970,  -970, -1060, -1470, -1060}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{ -1060, -1210, -1060, -1470, -1060}-    ,{ -1060, -1210, -1060, -1710, -1060}-    ,{  -970,  -970, -1060, -1710, -1060}-    }-   }-  ,{{{   240,  -270,   180,  -270,   240}-    ,{  -590, -1340,  -650, -1340,  -590}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{   240,  -270,   180,  -270,   240}-    ,{ -1010, -1520, -1070, -1520, -1010}-    }-   ,{{  -780, -1520,  -840, -1520,  -780}-    ,{ -1190, -1700, -1250, -1700, -1190}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{  -780, -1530,  -840, -1530,  -780}-    ,{ -1010, -1520, -1070, -1520, -1010}-    }-   ,{{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    }-   ,{{   240,  -270,   180,  -270,   240}-    ,{  -590, -1340,  -650, -1340,  -590}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{   240,  -270,   180,  -270,   240}-    ,{ -1010, -1520, -1070, -1520, -1010}-    }-   ,{{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    ,{ -1010, -1520, -1070, -1520, -1010}-    }-   }-  ,{{{   190, -1180,   190,  -870,   190}-    ,{  -870, -1250,  -890,  -870,  -890}-    ,{  -870, -1180, -1060,  -870, -1060}-    ,{   190, -1420,   190,  -870,   190}-    ,{  -870, -1180, -1060,  -870, -1060}-    }-   ,{{  -870, -1420, -1060,  -870, -1060}-    ,{ -1050, -1600, -1240, -1050, -1240}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{ -1080, -1440, -1080, -2130, -1080}-    ,{  -870, -1420, -1060,  -870, -1060}-    }-   ,{{  -870, -1180, -1060,  -870, -1060}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{  -870, -1180, -1060,  -870, -1060}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{  -870, -1180, -1060,  -870, -1060}-    }-   ,{{   190, -1250,   190,  -870,   190}-    ,{  -890, -1250,  -890, -1940,  -890}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{   190, -1420,   190, -2120,   190}-    ,{  -870, -1420, -1060,  -870, -1060}-    }-   ,{{  -870, -1180, -1060,  -870, -1060}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{  -870, -1180, -1060,  -870, -1060}-    ,{  -870, -1420, -1060,  -870, -1060}-    ,{ -1060, -1420, -1060, -2120, -1060}-    }-   }-  ,{{{   130,  -270,   130,  -270, -1680}-    ,{  -700, -1340,  -700, -1340, -1680}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{   130,  -270,   130,  -270, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    }-   ,{{  -890, -1520,  -890, -1520, -1790}-    ,{ -1300, -1700, -1300, -1700, -1790}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{  -890, -1530,  -890, -1530, -1870}-    ,{ -1120, -1520, -1120, -1520, -1850}-    }-   ,{{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    }-   ,{{   130,  -270,   130,  -270, -1680}-    ,{  -700, -1340,  -700, -1340, -1680}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{   130,  -270,   130,  -270, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    }-   ,{{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    ,{ -1120, -1520, -1120, -1520, -1850}-    }-   }-  }- ,{{{{   800,   600,   740,   290,   800}-    ,{   200,  -140,     0,   200,    50}-    ,{  -310,  -630,  -510,  -310,  -450}-    ,{   800,   600,   740,   290,   800}-    ,{  -310,  -410,  -510,  -310,  -450}-    }-   ,{{   200,  -140,     0,   200,    50}-    ,{   200,  -140,     0,   200,    50}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{  -550,  -990,  -610, -1300,  -550}-    ,{  -310,  -650,  -510,  -310,  -450}-    }-   ,{{  -310,  -630,  -510,  -310,  -450}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{  -310,  -630,  -510,  -310,  -450}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{  -310,  -630,  -510,  -310,  -450}-    }-   ,{{   800,   600,   740,   290,   800}-    ,{  -720, -1160,  -780, -1470,  -720}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{   800,   600,   740,   290,   800}-    ,{  -310,  -650,  -510,  -310,  -450}-    }-   ,{{  -310,  -410,  -510,  -310,  -450}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{  -310,  -630,  -510,  -310,  -450}-    ,{  -310,  -650,  -510,  -310,  -450}-    ,{  -410,  -410,  -510,  -960,  -450}-    }-   }-  ,{{{   740,   600,   740,  -640,   740}-    ,{     0,  -140,     0,  -640,     0}-    ,{  -510,  -650,  -510,  -910,  -510}-    ,{   740,   600,   740, -1150,   740}-    ,{  -410,  -410,  -510,  -910,  -510}-    }-   ,{{     0,  -140,     0,  -640,     0}-    ,{     0,  -140,     0,  -640,     0}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{  -850,  -990,  -850, -1490,  -850}-    ,{  -510,  -650,  -510, -1150,  -510}-    }-   ,{{  -510,  -650,  -510,  -910,  -510}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{  -510,  -650,  -510,  -910,  -510}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{  -510,  -650,  -510,  -910,  -510}-    }-   ,{{   740,   600,   740, -1150,   740}-    ,{ -1020, -1160, -1020, -1660, -1020}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{   740,   600,   740, -1150,   740}-    ,{  -510,  -650,  -510, -1150,  -510}-    }-   ,{{  -410,  -410,  -510,  -910,  -510}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{  -510,  -650,  -510,  -910,  -510}-    ,{  -510,  -650,  -510, -1150,  -510}-    ,{  -410,  -410,  -510, -1150,  -510}-    }-   }-  ,{{{   800,   290,   740,   290,   800}-    ,{    50,  -450,     0,  -450,    50}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{   800,   290,   740,   290,   800}-    ,{  -450,  -960,  -510,  -960,  -450}-    }-   ,{{    50,  -450,     0,  -450,    50}-    ,{    50,  -450,     0,  -450,    50}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -550, -1300,  -610, -1300,  -550}-    ,{  -450,  -960,  -510,  -960,  -450}-    }-   ,{{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    }-   ,{{   800,   290,   740,   290,   800}-    ,{  -720, -1470,  -780, -1470,  -720}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{   800,   290,   740,   290,   800}-    ,{  -450,  -960,  -510,  -960,  -450}-    }-   ,{{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    ,{  -450,  -960,  -510,  -960,  -450}-    }-   }-  ,{{{   740,  -360,   740,   200,   740}-    ,{   200,  -360,     0,   200,     0}-    ,{  -310,  -630,  -510,  -310,  -510}-    ,{   740,  -870,   740,  -310,   740}-    ,{  -310,  -630,  -510,  -310,  -510}-    }-   ,{{   200,  -360,     0,   200,     0}-    ,{   200,  -360,     0,   200,     0}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{  -850, -1210,  -850, -1900,  -850}-    ,{  -310,  -870,  -510,  -310,  -510}-    }-   ,{{  -310,  -630,  -510,  -310,  -510}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{  -310,  -630,  -510,  -310,  -510}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{  -310,  -630,  -510,  -310,  -510}-    }-   ,{{   740,  -870,   740,  -310,   740}-    ,{ -1020, -1380, -1020, -2070, -1020}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{   740,  -870,   740, -1560,   740}-    ,{  -310,  -870,  -510,  -310,  -510}-    }-   ,{{  -310,  -630,  -510,  -310,  -510}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{  -310,  -630,  -510,  -310,  -510}-    ,{  -310,  -870,  -510,  -310,  -510}-    ,{  -510,  -870,  -510, -1560,  -510}-    }-   }-  ,{{{   690,   290,   690,   290,  -550}-    ,{   -50,  -450,   -50,  -450,  -550}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{   690,   290,   690,   290, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    }-   ,{{   -50,  -450,   -50,  -450,  -550}-    ,{   -50,  -450,   -50,  -450,  -550}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -660, -1300,  -660, -1300, -1640}-    ,{  -560,  -960,  -560,  -960, -1300}-    }-   ,{{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    }-   ,{{   690,   290,   690,   290, -1300}-    ,{  -830, -1470,  -830, -1470, -1810}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{   690,   290,   690,   290, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    }-   ,{{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    ,{  -560,  -960,  -560,  -960, -1300}-    }-   }-  }- ,{{{{  1170,   970,  1120,   780,  1170}-    ,{   780,   440,   580,   780,   640}-    ,{   480,   170,   280,   480,   340}-    ,{  1170,   970,  1120,   660,  1170}-    ,{   480,   170,   280,   480,   340}-    }-   ,{{   780,   440,   580,   780,   640}-    ,{   780,   440,   580,   780,   640}-    ,{   470,   130,   270,   470,   330}-    ,{  -510,  -950,  -570, -1260,  -510}-    ,{   470,   130,   270,   470,   330}-    }-   ,{{   490,   170,   290,   490,   340}-    ,{   490,   140,   290,   490,   340}-    ,{   480,   170,   280,   480,   340}-    ,{   490,   140,   290,   490,   340}-    ,{   480,   170,   280,   480,   340}-    }-   ,{{  1170,   970,  1120,   660,  1170}-    ,{  -330,  -770,  -390, -1080,  -330}-    ,{   470,   130,   270,   470,   330}-    ,{  1170,   970,  1120,   660,  1170}-    ,{   470,   130,   270,   470,   330}-    }-   ,{{   490,   170,   290,   490,   340}-    ,{   490,   140,   290,   490,   340}-    ,{   480,   170,   280,   480,   340}-    ,{   490,   140,   290,   490,   340}-    ,{  -600,  -600,  -690, -1150,  -640}-    }-   }-  ,{{{  1120,   970,  1120,   -60,  1120}-    ,{   580,   440,   580,   -60,   580}-    ,{   280,   140,   280,  -120,   280}-    ,{  1120,   970,  1120,  -350,  1120}-    ,{   280,   140,   280,  -120,   280}-    }-   ,{{   580,   440,   580,   -60,   580}-    ,{   580,   440,   580,   -60,   580}-    ,{   270,   130,   270,  -370,   270}-    ,{  -800,  -950,  -800, -1450,  -800}-    ,{   270,   130,   270,  -370,   270}-    }-   ,{{   290,   140,   290,  -120,   290}-    ,{   290,   140,   290,  -350,   290}-    ,{   280,   140,   280,  -120,   280}-    ,{   290,   140,   290,  -350,   290}-    ,{   280,   140,   280,  -120,   280}-    }-   ,{{  1120,   970,  1120,  -370,  1120}-    ,{  -620,  -770,  -620, -1270,  -620}-    ,{   270,   130,   270,  -370,   270}-    ,{  1120,   970,  1120,  -780,  1120}-    ,{   270,   130,   270,  -370,   270}-    }-   ,{{   290,   140,   290,  -120,   290}-    ,{   290,   140,   290,  -350,   290}-    ,{   280,   140,   280,  -120,   280}-    ,{   290,   140,   290,  -350,   290}-    ,{  -600,  -600,  -690, -1340,  -690}-    }-   }-  ,{{{  1170,   660,  1110,   660,  1170}-    ,{   640,   130,   580,   130,   640}-    ,{   340,  -170,   280,  -170,   340}-    ,{  1170,   660,  1110,   660,  1170}-    ,{   340,  -170,   280,  -170,   340}-    }-   ,{{   640,   130,   580,   130,   640}-    ,{   640,   130,   580,   130,   640}-    ,{   330,  -180,   270,  -180,   330}-    ,{  -510, -1260,  -570, -1260,  -510}-    ,{   330,  -180,   270,  -180,   330}-    }-   ,{{   340,  -160,   280,  -160,   340}-    ,{   340,  -160,   280,  -160,   340}-    ,{   340,  -170,   280,  -170,   340}-    ,{   340,  -160,   280,  -160,   340}-    ,{   340,  -170,   280,  -170,   340}-    }-   ,{{  1170,   660,  1110,   660,  1170}-    ,{  -330, -1080,  -390, -1080,  -330}-    ,{   330,  -180,   270,  -180,   330}-    ,{  1170,   660,  1110,   660,  1170}-    ,{   330,  -180,   270,  -180,   330}-    }-   ,{{   340,  -160,   280,  -160,   340}-    ,{   340,  -160,   280,  -160,   340}-    ,{   340,  -170,   280,  -170,   340}-    ,{   340,  -160,   280,  -160,   340}-    ,{  -640, -1150,  -700, -1150,  -640}-    }-   }-  ,{{{  1120,   220,  1120,   780,  1120}-    ,{   780,   220,   580,   780,   580}-    ,{   480,   170,   280,   480,   280}-    ,{  1120,   -70,  1120,   490,  1120}-    ,{   480,   170,   280,   480,   280}-    }-   ,{{   780,   220,   580,   780,   580}-    ,{   780,   220,   580,   780,   580}-    ,{   470,   -80,   270,   470,   270}-    ,{  -800, -1160,  -800, -1860,  -800}-    ,{   470,   -80,   270,   470,   270}-    }-   ,{{   490,   170,   290,   490,   290}-    ,{   490,   -70,   290,   490,   290}-    ,{   480,   170,   280,   480,   280}-    ,{   490,   -70,   290,   490,   290}-    ,{   480,   170,   280,   480,   280}-    }-   ,{{  1120,   -80,  1120,   470,  1120}-    ,{  -620,  -980,  -620, -1680,  -620}-    ,{   470,   -80,   270,   470,   270}-    ,{  1120,  -490,  1120, -1190,  1120}-    ,{   470,   -80,   270,   470,   270}-    }-   ,{{   490,   170,   290,   490,   290}-    ,{   490,   -70,   290,   490,   290}-    ,{   480,   170,   280,   480,   280}-    ,{   490,   -70,   290,   490,   290}-    ,{  -690, -1050,  -690, -1750,  -690}-    }-   }-  ,{{{  1060,   660,  1060,   660,    40}-    ,{   530,   130,   530,   130,    40}-    ,{   230,  -170,   230,  -170,  -500}-    ,{  1060,   660,  1060,   660,  -500}-    ,{   230,  -170,   230,  -170,  -500}-    }-   ,{{   530,   130,   530,   130,    40}-    ,{   530,   130,   530,   130,    40}-    ,{   220,  -180,   220,  -180,  -510}-    ,{  -620, -1260,  -620, -1260, -1590}-    ,{   220,  -180,   220,  -180,  -510}-    }-   ,{{   230,  -160,   230,  -160,  -500}-    ,{   230,  -160,   230,  -160,  -500}-    ,{   230,  -170,   230,  -170,  -500}-    ,{   230,  -160,   230,  -160,  -500}-    ,{   230,  -170,   230,  -170,  -500}-    }-   ,{{  1060,   660,  1060,   660,  -510}-    ,{  -440, -1080,  -440, -1080, -1410}-    ,{   220,  -180,   220,  -180,  -510}-    ,{  1060,   660,  1060,   660,  -920}-    ,{   220,  -180,   220,  -180,  -510}-    }-   ,{{   230,  -160,   230,  -160,  -500}-    ,{   230,  -160,   230,  -160,  -500}-    ,{   230,  -170,   230,  -170,  -500}-    ,{   230,  -160,   230,  -160,  -500}-    ,{  -750, -1150,  -750, -1150, -1480}-    }-   }-  }- ,{{{{  1350,  1160,  1300,   850,  1350}-    ,{   850,   500,   650,   850,   700}-    ,{   720,   400,   520,   720,   570}-    ,{  1350,  1160,  1300,   850,  1350}-    ,{   590,   270,   390,   590,   440}-    }-   ,{{   850,   500,   650,   850,   700}-    ,{   850,   500,   650,   850,   700}-    ,{   570,   220,   370,   570,   420}-    ,{  -460,  -900,  -520, -1210,  -460}-    ,{   570,   220,   370,   570,   420}-    }-   ,{{   720,   400,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   720,   400,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   590,   270,   390,   590,   440}-    }-   ,{{  1350,  1160,  1300,   850,  1350}-    ,{  -760, -1200,  -820, -1510,  -760}-    ,{   570,   220,   370,   570,   420}-    ,{  1350,  1160,  1300,   850,  1350}-    ,{   570,   220,   370,   570,   420}-    }-   ,{{   720,   370,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   280,   -40,    80,   280,   130}-    ,{   720,   370,   520,   720,   570}-    ,{  -320,  -320,  -420,  -870,  -360}-    }-   }-  ,{{{  1300,  1160,  1300,   120,  1300}-    ,{   650,   500,   650,     0,   650}-    ,{   520,   370,   520,   120,   520}-    ,{  1300,  1160,  1300,  -120,  1300}-    ,{   390,   240,   390,   -10,   390}-    }-   ,{{   650,   500,   650,     0,   650}-    ,{   650,   500,   650,     0,   650}-    ,{   370,   220,   370,  -270,   370}-    ,{  -750,  -900,  -750, -1400,  -750}-    ,{   370,   220,   370,  -270,   370}-    }-   ,{{   520,   370,   520,   120,   520}-    ,{   520,   370,   520,  -120,   520}-    ,{   520,   370,   520,   120,   520}-    ,{   520,   370,   520,  -120,   520}-    ,{   390,   240,   390,   -10,   390}-    }-   ,{{  1300,  1160,  1300,  -270,  1300}-    ,{ -1050, -1200, -1050, -1700, -1050}-    ,{   370,   220,   370,  -270,   370}-    ,{  1300,  1160,  1300,  -590,  1300}-    ,{   370,   220,   370,  -270,   370}-    }-   ,{{   520,   370,   520,  -120,   520}-    ,{   520,   370,   520,  -120,   520}-    ,{    80,   -60,    80,  -320,    80}-    ,{   520,   370,   520,  -120,   520}-    ,{  -320,  -320,  -420, -1060,  -420}-    }-   }-  ,{{{  1350,   850,  1290,   850,  1350}-    ,{   700,   190,   640,   190,   700}-    ,{   570,    60,   510,    60,   570}-    ,{  1350,   850,  1290,   850,  1350}-    ,{   440,   -60,   380,   -60,   440}-    }-   ,{{   700,   190,   640,   190,   700}-    ,{   700,   190,   640,   190,   700}-    ,{   420,   -80,   360,   -80,   420}-    ,{  -460, -1210,  -520, -1210,  -460}-    ,{   420,   -80,   360,   -80,   420}-    }-   ,{{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   440,   -60,   380,   -60,   440}-    }-   ,{{  1350,   850,  1290,   850,  1350}-    ,{  -760, -1510,  -820, -1510,  -760}-    ,{   420,   -80,   360,   -80,   420}-    ,{  1350,   850,  1290,   850,  1350}-    ,{   420,   -80,   360,   -80,   420}-    }-   ,{{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   130,  -370,    70,  -370,   130}-    ,{   570,    60,   510,    60,   570}-    ,{  -360,  -870,  -420,  -870,  -360}-    }-   }-  ,{{{  1300,   400,  1300,   850,  1300}-    ,{   850,   290,   650,   850,   650}-    ,{   720,   400,   520,   720,   520}-    ,{  1300,   160,  1300,   720,  1300}-    ,{   590,   270,   390,   590,   390}-    }-   ,{{   850,   290,   650,   850,   650}-    ,{   850,   290,   650,   850,   650}-    ,{   570,    10,   370,   570,   370}-    ,{  -750, -1110,  -750, -1810,  -750}-    ,{   570,    10,   370,   570,   370}-    }-   ,{{   720,   400,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   720,   400,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   590,   270,   390,   590,   390}-    }-   ,{{  1300,    10,  1300,   570,  1300}-    ,{ -1050, -1410, -1050, -2110, -1050}-    ,{   570,    10,   370,   570,   370}-    ,{  1300,  -310,  1300, -1000,  1300}-    ,{   570,    10,   370,   570,   370}-    }-   ,{{   720,   160,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   280,   -40,    80,   280,    80}-    ,{   720,   160,   520,   720,   520}-    ,{  -420,  -780,  -420, -1470,  -420}-    }-   }-  ,{{{  1250,   850,  1250,   850,   100}-    ,{   590,   190,   590,   190,   100}-    ,{   460,    60,   460,    60,  -270}-    ,{  1250,   850,  1250,   850,  -270}-    ,{   330,   -60,   330,   -60,  -400}-    }-   ,{{   590,   190,   590,   190,   100}-    ,{   590,   190,   590,   190,   100}-    ,{   310,   -80,   310,   -80,  -420}-    ,{  -570, -1210,  -570, -1210, -1540}-    ,{   310,   -80,   310,   -80,  -420}-    }-   ,{{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   330,   -60,   330,   -60,  -400}-    }-   ,{{  1250,   850,  1250,   850,  -420}-    ,{  -870, -1510,  -870, -1510, -1840}-    ,{   310,   -80,   310,   -80,  -420}-    ,{  1250,   850,  1250,   850,  -740}-    ,{   310,   -80,   310,   -80,  -420}-    }-   ,{{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{    20,  -370,    20,  -370,  -710}-    ,{   460,    60,   460,    60,  -270}-    ,{  -470,  -870,  -470,  -870, -1210}-    }-   }-  }- ,{{{{  1350,  1160,  1300,   850,  1350}-    ,{   850,   500,   650,   850,   700}-    ,{   720,   400,   520,   720,   570}-    ,{  1350,  1160,  1300,   850,  1350}-    ,{   590,   270,   390,   590,   440}-    }-   ,{{   850,   500,   650,   850,   700}-    ,{   850,   500,   650,   850,   700}-    ,{   570,   220,   370,   570,   420}-    ,{  -230,  -670,  -290,  -980,  -230}-    ,{   570,   220,   370,   570,   420}-    }-   ,{{   720,   400,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   720,   400,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   590,   270,   390,   590,   440}-    }-   ,{{  1350,  1160,  1300,   850,  1350}-    ,{  -330,  -770,  -390, -1080,  -330}-    ,{   570,   220,   370,   570,   420}-    ,{  1350,  1160,  1300,   850,  1350}-    ,{   570,   220,   370,   570,   420}-    }-   ,{{   720,   370,   520,   720,   570}-    ,{   720,   370,   520,   720,   570}-    ,{   480,   170,   280,   480,   340}-    ,{   720,   370,   520,   720,   570}-    ,{   -90,  -320,   -90,  -810,  -360}-    }-   }-  ,{{{  1300,  1160,  1300,   540,  1300}-    ,{   650,   500,   650,    10,   650}-    ,{   540,   370,   520,   540,   520}-    ,{  1300,  1160,  1300,  -120,  1300}-    ,{   390,   240,   390,   -10,   390}-    }-   ,{{   650,   500,   650,     0,   650}-    ,{   650,   500,   650,     0,   650}-    ,{   370,   220,   370,  -100,   370}-    ,{  -530,  -670,  -530, -1170,  -530}-    ,{   370,   220,   370,  -270,   370}-    }-   ,{{   540,   370,   520,   540,   520}-    ,{   520,   370,   520,    10,   520}-    ,{   540,   370,   520,   540,   520}-    ,{   520,   370,   520,  -120,   520}-    ,{   390,   240,   390,   -10,   390}-    }-   ,{{  1300,  1160,  1300,  -270,  1300}-    ,{  -620,  -770,  -620, -1270,  -620}-    ,{   370,   220,   370,  -270,   370}-    ,{  1300,  1160,  1300,  -590,  1300}-    ,{   370,   220,   370,  -270,   370}-    }-   ,{{   520,   370,   520,  -120,   520}-    ,{   520,   370,   520,  -120,   520}-    ,{   280,   140,   280,  -120,   280}-    ,{   520,   370,   520,  -120,   520}-    ,{   -90,  -320,   -90,  -810,  -420}-    }-   }-  ,{{{  1350,   850,  1290,   850,  1350}-    ,{   700,   190,   640,   190,   700}-    ,{   570,    60,   510,    60,   570}-    ,{  1350,   850,  1290,   850,  1350}-    ,{   440,   -60,   380,   -60,   440}-    }-   ,{{   700,   190,   640,   190,   700}-    ,{   700,   190,   640,   190,   700}-    ,{   420,   -80,   360,   -80,   420}-    ,{  -230,  -980,  -290,  -980,  -230}-    ,{   420,   -80,   360,   -80,   420}-    }-   ,{{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   440,   -60,   380,   -60,   440}-    }-   ,{{  1350,   850,  1290,   850,  1350}-    ,{  -330, -1070,  -390, -1080,  -330}-    ,{   420,   -80,   360,   -80,   420}-    ,{  1350,   850,  1290,   850,  1350}-    ,{   420,   -80,   360,   -80,   420}-    }-   ,{{   570,    60,   510,    60,   570}-    ,{   570,    60,   510,    60,   570}-    ,{   340,  -170,   280,  -170,   340}-    ,{   570,    60,   510,    60,   570}-    ,{  -360,  -830,  -420,  -870,  -360}-    }-   }-  ,{{{  1300,   400,  1300,   850,  1300}-    ,{   850,   290,   650,   850,   650}-    ,{   720,   400,   520,   720,   520}-    ,{  1300,   160,  1300,   720,  1300}-    ,{   590,   270,   390,   590,   390}-    }-   ,{{   850,   290,   650,   850,   650}-    ,{   850,   290,   650,   850,   650}-    ,{   570,    10,   370,   570,   370}-    ,{  -530,  -890,  -530, -1580,  -530}-    ,{   570,    10,   370,   570,   370}-    }-   ,{{   720,   400,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   720,   400,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   590,   270,   390,   590,   390}-    }-   ,{{  1300,    10,  1300,   570,  1300}-    ,{  -620,  -980,  -620, -1080,  -620}-    ,{   570,    10,   370,   570,   370}-    ,{  1300,  -310,  1300, -1000,  1300}-    ,{   570,    10,   370,   570,   370}-    }-   ,{{   720,   170,   520,   720,   520}-    ,{   720,   160,   520,   720,   520}-    ,{   480,   170,   280,   480,   280}-    ,{   720,   160,   520,   720,   520}-    ,{  -420,  -780,  -420, -1470,  -420}-    }-   }-  ,{{{  1250,   850,  1250,   850,   100}-    ,{   590,   190,   590,   190,   100}-    ,{   460,    60,   460,    60,  -270}-    ,{  1250,   850,  1250,   850,  -230}-    ,{   330,   -60,   330,   -60,  -400}-    }-   ,{{   590,   190,   590,   190,   100}-    ,{   590,   190,   590,   190,   100}-    ,{   310,   -80,   310,   -80,  -420}-    ,{  -340,  -980,  -340,  -980, -1320}-    ,{   310,   -80,   310,   -80,  -420}-    }-   ,{{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   330,   -60,   330,   -60,  -400}-    }-   ,{{  1250,   850,  1250,   850,  -230}-    ,{  -440, -1080,  -440, -1080, -1300}-    ,{   310,   -80,   310,   -80,  -420}-    ,{  1250,   850,  1250,   850,  -230}-    ,{   310,   -80,   310,   -80,  -420}-    }-   ,{{   460,    60,   460,    60,  -270}-    ,{   460,    60,   460,    60,  -270}-    ,{   230,  -170,   230,  -170,  -500}-    ,{   460,    60,   460,    60,  -270}-    ,{  -470,  -870,  -470,  -870, -1210}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   540,   -90,   540,   180,   -90}-    ,{   540,  -100,   540,   180,   -90}-    ,{   180,   -90,  -460,   180,  -460}-    ,{    30,  -150,  -260,    30,  -210}-    ,{  -200,  -200,  -400,  -230,  -570}-    }-   ,{{   180,  -350,  -660,   180,  -660}-    ,{   180,  -580,  -660,   180,  -660}-    ,{  -430,  -600,  -970,  -430,  -830}-    ,{  -350,  -350,  -870,  -960,  -870}-    ,{  -430,  -600,  -970,  -430,  -970}-    }-   ,{{    30,  -150,  -510,    30,   -90}-    ,{   -90,  -220,  -510,  -390,   -90}-    ,{    20,  -600,  -520,    20,  -520}-    ,{    30,  -150,  -510,    30,  -510}-    ,{  -200,  -200,  -570,  -650,  -570}-    }-   ,{{   540,  -100,   540,  -400,  -210}-    ,{   540,  -100,   540, -1240,  -810}-    ,{  -430,  -600,  -970,  -430,  -970}-    ,{  -200,  -200,  -260,  -400,  -210}-    ,{  -430,  -600,  -970,  -430,  -970}-    }-   ,{{   180,   -90,  -400,   180,  -460}-    ,{    30,  -150,  -510,    30,  -510}-    ,{   180,   -90,  -460,   180,  -460}-    ,{    30,  -150,  -510,    30,  -510}-    ,{  -230, -1390,  -400,  -230, -1300}-    }-   }-  ,{{{    10,   -90,    10,  -500,  -320}-    ,{    10,  -150,    10,  -860,  -510}-    ,{   -90,   -90,  -460,  -500,  -460}-    ,{  -150,  -150,  -320,  -860,  -320}-    ,{  -200,  -200,  -400, -1300,  -570}-    }-   ,{{  -580,  -580,  -660, -1070,  -660}-    ,{  -580,  -580,  -660, -1340,  -660}-    ,{  -600,  -600,  -970, -1070,  -970}-    ,{  -870, -1600, -1110, -1880,  -870}-    ,{  -600,  -600,  -970, -1320,  -970}-    }-   ,{{  -150,  -150,  -510,  -500,  -510}-    ,{  -220,  -220, -1150,  -860,  -510}-    ,{  -500, -1070,  -750,  -500,  -520}-    ,{  -150,  -150,  -510,  -860,  -510}-    ,{  -200,  -200,  -570, -1750,  -570}-    }-   ,{{    10,  -200,    10, -1080,  -320}-    ,{    10,  -970,    10, -2450, -1160}-    ,{  -600,  -600,  -970, -1320,  -970}-    ,{  -200,  -200,  -320, -1080,  -320}-    ,{  -600,  -600,  -970, -1320,  -970}-    }-   ,{{   -90,   -90,  -400,  -570,  -460}-    ,{  -150,  -150,  -510,  -860,  -510}-    ,{   -90,   -90,  -460,  -570,  -460}-    ,{  -150,  -150,  -510,  -860,  -510}-    ,{  -400, -1490,  -400, -1300, -1300}-    }-   }-  ,{{{   540,  -100,   540,  -400,  -210}-    ,{   540,  -100,   540,  -600, -1130}-    ,{  -540,  -540,  -760,  -540, -1070}-    ,{  -210,  -350,  -620,  -400,  -210}-    ,{  -650,  -650,  -870,  -650, -1180}-    }-   ,{{  -350,  -350,  -940,  -740, -1250}-    ,{  -740,  -740,  -960,  -740, -1270}-    ,{ -1050, -1050, -1270, -1050, -1580}-    ,{  -350,  -350,  -940,  -960, -1250}-    ,{ -1050, -1050, -1270, -1050, -1580}-    }-   ,{{  -600,  -600,  -820,  -600, -1130}-    ,{  -600,  -600,  -820,  -600, -1130}-    ,{  -600,  -600,  -820,  -600, -1130}-    ,{  -600,  -600,  -820,  -600, -1130}-    ,{  -650,  -650,  -870,  -650, -1180}-    }-   ,{{   540,  -100,   540,  -400,  -210}-    ,{   540,  -100,   540, -1240, -1530}-    ,{ -1050, -1050, -1270, -1050, -1580}-    ,{  -210,  -440,  -620,  -400,  -210}-    ,{ -1050, -1050, -1270, -1050, -1580}-    }-   ,{{  -540,  -540,  -760,  -540, -1070}-    ,{  -600,  -600,  -820,  -600, -1130}-    ,{  -540,  -540,  -760,  -540, -1070}-    ,{  -600,  -600,  -820,  -600, -1130}-    ,{ -1390, -1390, -1610, -1390, -1920}-    }-   }-  ,{{{   180,  -630,  -320,   180,  -320}-    ,{   180, -1340,  -510,   180,  -510}-    ,{   180,  -630,  -460,   180,  -460}-    ,{    30, -1340,  -320,    30,  -320}-    ,{  -230, -1150,  -570,  -230,  -570}-    }-   ,{{   180, -1790,  -660,   180,  -660}-    ,{   180, -2010,  -660,   180,  -660}-    ,{  -430, -1790,  -970,  -430,  -970}-    ,{  -870, -3070,  -870, -1370,  -870}-    ,{  -430, -1790,  -970,  -430,  -970}-    }-   ,{{    30,  -630,  -510,    30,  -510}-    ,{  -390, -1650,  -510,  -390,  -510}-    ,{    20,  -630,  -520,    20,  -520}-    ,{    30, -1340,  -510,    30,  -510}-    ,{  -570, -1150,  -570,  -880,  -570}-    }-   ,{{  -320, -1790,  -320,  -430,  -320}-    ,{ -1160, -1980, -1160, -1870, -1160}-    ,{  -430, -1790,  -970,  -430,  -970}-    ,{  -320, -2390,  -320, -2280,  -320}-    ,{  -430, -1790,  -970,  -430,  -970}-    }-   ,{{   180, -1040,  -460,   180,  -460}-    ,{    30, -1340,  -510,    30,  -510}-    ,{   180, -1040,  -460,   180,  -460}-    ,{    30, -1340,  -510,    30,  -510}-    ,{  -230, -1520, -1300,  -230, -1300}-    }-   }-  ,{{{   -90,  -400,  -260,  -400,   -90}-    ,{   -90,  -600,  -820,  -600,   -90}-    ,{  -540,  -540,  -550,  -540,  -830}-    ,{  -260,  -400,  -260,  -400,  -800}-    ,{  -650,  -650,  -870,  -650,  -860}-    }-   ,{{  -740,  -740,  -940,  -740,  -830}-    ,{  -740,  -740,  -960,  -740, -1240}-    ,{  -830, -1050, -1270, -1050,  -830}-    ,{  -940,  -960,  -940,  -960, -1360}-    ,{ -1050, -1050, -1270, -1050, -1260}-    }-   ,{{   -90,  -600,  -820,  -600,   -90}-    ,{   -90,  -600,  -820,  -600,   -90}-    ,{  -600,  -600,  -820,  -600, -1710}-    ,{  -600,  -600,  -820,  -600,  -800}-    ,{  -650,  -650,  -870,  -650,  -860}-    }-   ,{{  -260,  -400,  -260,  -400,  -810}-    ,{  -810, -1240, -1220, -1240,  -810}-    ,{ -1050, -1050, -1270, -1050, -1260}-    ,{  -260,  -400,  -260,  -400, -1550}-    ,{ -1050, -1050, -1270, -1050, -1260}-    }-   ,{{  -540,  -540,  -550,  -540,  -800}-    ,{  -600,  -600,  -820,  -600,  -800}-    ,{  -540,  -540,  -550,  -540, -1460}-    ,{  -600,  -600,  -820,  -600,  -800}-    ,{ -1390, -1390, -1610, -1390, -2350}-    }-   }-  }- ,{{{{    50,    50,  -320,    50,  -320}-    ,{    50,  -130,  -490,    50,  -490}-    ,{  -400,  -580,  -940,  -400,  -940}-    ,{    50,    50,  -320,  -320,  -320}-    ,{  -400,  -540,  -940,  -400,  -940}-    }-   ,{{    50,  -130,  -490,    50,  -490}-    ,{    50,  -130,  -490,    50,  -490}-    ,{  -400,  -580,  -940,  -400,  -940}-    ,{ -1320, -1320, -1680, -1770, -1680}-    ,{  -400,  -580,  -940,  -400,  -940}-    }-   ,{{  -320,  -490,  -860,  -320,  -860}-    ,{  -320,  -490,  -860,  -320,  -860}-    ,{  -620,  -800, -1160,  -620, -1160}-    ,{  -320,  -490,  -860,  -320,  -860}-    ,{  -620,  -800, -1160,  -620, -1160}-    }-   ,{{    50,    50,  -320,  -400,  -320}-    ,{  -840,  -840, -1210, -1290, -1210}-    ,{  -400,  -580,  -940,  -400,  -940}-    ,{    50,    50,  -320,  -400,  -320}-    ,{  -400,  -580,  -940,  -400,  -940}-    }-   ,{{  -320,  -490,  -860,  -320,  -860}-    ,{  -320,  -490,  -860,  -320,  -860}-    ,{  -930, -1110, -1470,  -930, -1470}-    ,{  -320,  -490,  -860,  -320,  -860}-    ,{  -540,  -540, -1150, -1230, -1150}-    }-   }-  ,{{{    50,    50,  -320,  -840,  -320}-    ,{  -130,  -130,  -490,  -840,  -490}-    ,{  -580,  -580,  -940, -1270,  -940}-    ,{    50,    50,  -320, -1210,  -320}-    ,{  -540,  -540,  -940, -1270,  -940}-    }-   ,{{  -130,  -130,  -490,  -840,  -490}-    ,{  -130,  -130,  -490,  -840,  -490}-    ,{  -580,  -580,  -940, -1290,  -940}-    ,{ -1320, -1320, -1680, -2030, -1680}-    ,{  -580,  -580,  -940, -1290,  -940}-    }-   ,{{  -490,  -490,  -860, -1210,  -860}-    ,{  -490,  -490,  -860, -1210,  -860}-    ,{  -800,  -800, -1160, -1270, -1160}-    ,{  -490,  -490,  -860, -1210,  -860}-    ,{  -800,  -800, -1160, -1270, -1160}-    }-   ,{{    50,    50,  -320, -1290,  -320}-    ,{  -840,  -840, -1210, -1560, -1210}-    ,{  -580,  -580,  -940, -1290,  -940}-    ,{    50,    50,  -320, -1920,  -320}-    ,{  -580,  -580,  -940, -1290,  -940}-    }-   ,{{  -490,  -490,  -860, -1210,  -860}-    ,{  -490,  -490,  -860, -1210,  -860}-    ,{ -1110, -1110, -1470, -1580, -1470}-    ,{  -490,  -490,  -860, -1210,  -860}-    ,{  -540,  -540, -1150, -1500, -1150}-    }-   }-  ,{{{  -400,  -400,  -620,  -400,  -930}-    ,{  -580,  -580,  -800,  -580, -1110}-    ,{ -1030, -1030, -1250, -1030, -1560}-    ,{  -400,  -400,  -620,  -400,  -930}-    ,{ -1030, -1030, -1250, -1030, -1560}-    }-   ,{{  -580,  -580,  -800,  -580, -1110}-    ,{  -580,  -580,  -800,  -580, -1110}-    ,{ -1030, -1030, -1250, -1030, -1560}-    ,{ -1750, -1770, -1750, -1770, -2060}-    ,{ -1030, -1030, -1250, -1030, -1560}-    }-   ,{{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{ -1250, -1250, -1470, -1250, -1780}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{ -1250, -1250, -1470, -1250, -1780}-    }-   ,{{  -400,  -400,  -620,  -400,  -930}-    ,{ -1270, -1290, -1270, -1290, -1580}-    ,{ -1030, -1030, -1250, -1030, -1560}-    ,{  -400,  -400,  -620,  -400,  -930}-    ,{ -1030, -1030, -1250, -1030, -1560}-    }-   ,{{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{ -1560, -1560, -1780, -1560, -2090}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{ -1230, -1230, -1450, -1230, -1760}-    }-   }-  ,{{{    50, -1320,  -320,    50,  -320}-    ,{    50, -1320,  -490,    50,  -490}-    ,{  -400, -1750,  -940,  -400,  -940}-    ,{  -320, -1680,  -320,  -320,  -320}-    ,{  -400, -1750,  -940,  -400,  -940}-    }-   ,{{    50, -1320,  -490,    50,  -490}-    ,{    50, -1320,  -490,    50,  -490}-    ,{  -400, -1770,  -940,  -400,  -940}-    ,{ -1680, -2510, -1680, -2390, -1680}-    ,{  -400, -1770,  -940,  -400,  -940}-    }-   ,{{  -320, -1680,  -860,  -320,  -860}-    ,{  -320, -1680,  -860,  -320,  -860}-    ,{  -620, -1750, -1160,  -620, -1160}-    ,{  -320, -1680,  -860,  -320,  -860}-    ,{  -620, -1750, -1160,  -620, -1160}-    }-   ,{{  -320, -1770,  -320,  -400,  -320}-    ,{ -1210, -2030, -1210, -1920, -1210}-    ,{  -400, -1770,  -940,  -400,  -940}-    ,{  -320, -2390,  -320, -2280,  -320}-    ,{  -400, -1770,  -940,  -400,  -940}-    }-   ,{{  -320, -1680,  -860,  -320,  -860}-    ,{  -320, -1680,  -860,  -320,  -860}-    ,{  -930, -2060, -1470,  -930, -1470}-    ,{  -320, -1680,  -860,  -320,  -860}-    ,{ -1150, -1970, -1150, -1860, -1150}-    }-   }-  ,{{{  -400,  -400,  -620,  -400,  -540}-    ,{  -540,  -580,  -800,  -580,  -540}-    ,{ -1030, -1030, -1250, -1030, -1230}-    ,{  -400,  -400,  -620,  -400, -1150}-    ,{ -1030, -1030, -1250, -1030, -1230}-    }-   ,{{  -540,  -580,  -800,  -580,  -540}-    ,{  -540,  -580,  -800,  -580,  -540}-    ,{ -1030, -1030, -1250, -1030, -1230}-    ,{ -1750, -1770, -1750, -1770, -1970}-    ,{ -1030, -1030, -1250, -1030, -1230}-    }-   ,{{  -940,  -940, -1160,  -940, -1150}-    ,{  -940,  -940, -1160,  -940, -1150}-    ,{ -1250, -1250, -1470, -1250, -1450}-    ,{  -940,  -940, -1160,  -940, -1150}-    ,{ -1250, -1250, -1470, -1250, -1450}-    }-   ,{{  -400,  -400,  -620,  -400, -1230}-    ,{ -1270, -1290, -1270, -1290, -1500}-    ,{ -1030, -1030, -1250, -1030, -1230}-    ,{  -400,  -400,  -620,  -400, -1860}-    ,{ -1030, -1030, -1250, -1030, -1230}-    }-   ,{{  -940,  -940, -1160,  -940, -1150}-    ,{  -940,  -940, -1160,  -940, -1150}-    ,{ -1560, -1560, -1780, -1560, -1760}-    ,{  -940,  -940, -1160,  -940, -1150}-    ,{ -1230, -1230, -1450, -1230, -1440}-    }-   }-  }- ,{{{{   210,   210,  -160,  -240,  -160}-    ,{  -870,  -870, -1230,  -870, -1230}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{   210,   210,  -160,  -240,  -160}-    ,{  -800,  -800, -1410,  -870, -1410}-    }-   ,{{  -870, -1040, -1410,  -870, -1410}-    ,{ -1050, -1220, -1590, -1050, -1590}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{ -1060, -1060, -1420, -1510, -1420}-    ,{  -870, -1040, -1410,  -870, -1410}-    }-   ,{{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    }-   ,{{   210,   210,  -160,  -240,  -160}-    ,{  -870,  -870, -1230, -1320, -1230}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{   210,   210,  -160,  -240,  -160}-    ,{  -870, -1040, -1410,  -870, -1410}-    }-   ,{{  -800,  -800, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -870, -1040, -1410,  -870, -1410}-    ,{  -800,  -800, -1410, -1490, -1410}-    }-   }-  ,{{{   210,   210,  -160, -1520,  -160}-    ,{  -870,  -870, -1230, -1580, -1230}-    ,{ -1040, -1040, -1410, -1520, -1410}-    ,{   210,   210,  -160, -1760,  -160}-    ,{  -800,  -800, -1410, -1520, -1410}-    }-   ,{{ -1040, -1040, -1410, -1760, -1410}-    ,{ -1220, -1220, -1590, -1940, -1590}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{ -1060, -1060, -1420, -1770, -1420}-    ,{ -1040, -1040, -1410, -1760, -1410}-    }-   ,{{ -1040, -1040, -1410, -1520, -1410}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{ -1040, -1040, -1410, -1520, -1410}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{ -1040, -1040, -1410, -1520, -1410}-    }-   ,{{   210,   210,  -160, -1580,  -160}-    ,{  -870,  -870, -1230, -1580, -1230}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{   210,   210,  -160, -1760,  -160}-    ,{ -1040, -1040, -1410, -1760, -1410}-    }-   ,{{  -800,  -800, -1410, -1520, -1410}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{ -1040, -1040, -1410, -1520, -1410}-    ,{ -1040, -1040, -1410, -1760, -1410}-    ,{  -800,  -800, -1410, -1760, -1410}-    }-   }-  ,{{{  -240,  -240,  -460,  -240,  -770}-    ,{ -1300, -1320, -1300, -1320, -1610}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{  -240,  -240,  -460,  -240,  -770}-    ,{ -1490, -1490, -1710, -1490, -2020}-    }-   ,{{ -1490, -1490, -1490, -1490, -1800}-    ,{ -1670, -1670, -1890, -1670, -2200}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1510, -1490, -1510, -1800}-    ,{ -1490, -1490, -1710, -1490, -2020}-    }-   ,{{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    }-   ,{{  -240,  -240,  -460,  -240,  -770}-    ,{ -1300, -1320, -1300, -1320, -1610}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{  -240,  -240,  -460,  -240,  -770}-    ,{ -1490, -1490, -1710, -1490, -2020}-    }-   ,{{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    ,{ -1490, -1490, -1710, -1490, -2020}-    }-   }-  ,{{{  -160, -1990,  -160,  -870,  -160}-    ,{  -870, -2060, -1230,  -870, -1230}-    ,{  -870, -1990, -1410,  -870, -1410}-    ,{  -160, -2230,  -160,  -870,  -160}-    ,{  -870, -1990, -1410,  -870, -1410}-    }-   ,{{  -870, -2230, -1410,  -870, -1410}-    ,{ -1050, -2410, -1590, -1050, -1590}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{ -1420, -2250, -1420, -2130, -1420}-    ,{  -870, -2230, -1410,  -870, -1410}-    }-   ,{{  -870, -1990, -1410,  -870, -1410}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{  -870, -1990, -1410,  -870, -1410}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{  -870, -1990, -1410,  -870, -1410}-    }-   ,{{  -160, -2060,  -160,  -870,  -160}-    ,{ -1230, -2060, -1230, -1940, -1230}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{  -160, -2230,  -160, -2120,  -160}-    ,{  -870, -2230, -1410,  -870, -1410}-    }-   ,{{  -870, -1990, -1410,  -870, -1410}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{  -870, -1990, -1410,  -870, -1410}-    ,{  -870, -2230, -1410,  -870, -1410}-    ,{ -1410, -2230, -1410, -2120, -1410}-    }-   }-  ,{{{  -240,  -240,  -460,  -240, -1520}-    ,{ -1300, -1320, -1300, -1320, -1520}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{  -240,  -240,  -460,  -240, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    }-   ,{{ -1490, -1490, -1490, -1490, -1640}-    ,{ -1640, -1670, -1890, -1670, -1640}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1510, -1490, -1510, -1710}-    ,{ -1490, -1490, -1710, -1490, -1700}-    }-   ,{{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    }-   ,{{  -240,  -240,  -460,  -240, -1520}-    ,{ -1300, -1320, -1300, -1320, -1520}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{  -240,  -240,  -460,  -240, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    }-   ,{{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    ,{ -1490, -1490, -1710, -1490, -1700}-    }-   }-  }- ,{{{{   760,   760,   400,   310,   400}-    ,{   200,  -430,  -340,   200,  -340}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{   760,   760,   400,   310,   400}-    ,{  -250,  -250,  -850,  -310,  -850}-    }-   ,{{   200,  -430,  -340,   200,  -340}-    ,{   200,  -430,  -340,   200,  -340}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -830,  -830, -1190, -1280, -1190}-    ,{  -310,  -490,  -850,  -310,  -850}-    }-   ,{{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    }-   ,{{   760,   760,   400,   310,   400}-    ,{ -1000, -1000, -1360, -1450, -1360}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{   760,   760,   400,   310,   400}-    ,{  -310,  -490,  -850,  -310,  -850}-    }-   ,{{  -250,  -250,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -310,  -490,  -850,  -310,  -850}-    ,{  -250,  -250,  -850,  -940,  -850}-    }-   }-  ,{{{   760,   760,   400,  -690,   400}-    ,{  -340,  -490,  -340,  -690,  -340}-    ,{  -490,  -490,  -850,  -960,  -850}-    ,{   760,   760,   400, -1200,   400}-    ,{  -250,  -250,  -850,  -960,  -850}-    }-   ,{{  -340,  -490,  -340,  -690,  -340}-    ,{  -340, -2040,  -340,  -690,  -340}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{  -830,  -830, -1190, -1540, -1190}-    ,{  -490,  -490,  -850, -1200,  -850}-    }-   ,{{  -490,  -490,  -850,  -960,  -850}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{  -490,  -490,  -850,  -960,  -850}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{  -490,  -490,  -850,  -960,  -850}-    }-   ,{{   760,   760,   400, -1200,   400}-    ,{ -1000, -1000, -1360, -1710, -1360}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{   760,   760,   400, -1200,   400}-    ,{  -490,  -490,  -850, -1200,  -850}-    }-   ,{{  -250,  -250,  -850,  -960,  -850}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{  -490,  -490,  -850,  -960,  -850}-    ,{  -490,  -490,  -850, -1200,  -850}-    ,{  -250,  -250,  -850, -1200,  -850}-    }-   }-  ,{{{   310,   310,    90,   310,  -220}-    ,{  -430,  -430,  -650,  -430,  -960}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{   310,   310,    90,   310,  -220}-    ,{  -940,  -940, -1160,  -940, -1470}-    }-   ,{{  -430,  -430,  -650,  -430,  -960}-    ,{  -430,  -430,  -650,  -430,  -960}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{ -1260, -1280, -1260, -1280, -1570}-    ,{  -940,  -940, -1160,  -940, -1470}-    }-   ,{{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    }-   ,{{   310,   310,    90,   310,  -220}-    ,{ -1430, -1450, -1430, -1450, -1740}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{   310,   310,    90,   310,  -220}-    ,{  -940,  -940, -1160,  -940, -1470}-    }-   ,{{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    ,{  -940,  -940, -1160,  -940, -1470}-    }-   }-  ,{{{   400, -1170,   400,   200,   400}-    ,{   200, -1170,  -340,   200,  -340}-    ,{  -310, -1440,  -850,  -310,  -850}-    ,{   400, -1680,   400,  -310,   400}-    ,{  -310, -1440,  -850,  -310,  -850}-    }-   ,{{   200, -1170,  -340,   200,  -340}-    ,{   200, -1170,  -340,   200,  -340}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{ -1190, -2020, -1190, -1900, -1190}-    ,{  -310, -1680,  -850,  -310,  -850}-    }-   ,{{  -310, -1440,  -850,  -310,  -850}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{  -310, -1440,  -850,  -310,  -850}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{  -310, -1440,  -850,  -310,  -850}-    }-   ,{{   400, -1680,   400,  -310,   400}-    ,{ -1360, -2190, -1360, -2070, -1360}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{   400, -1680,   400, -1560,   400}-    ,{  -310, -1680,  -850,  -310,  -850}-    }-   ,{{  -310, -1440,  -850,  -310,  -850}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{  -310, -1440,  -850,  -310,  -850}-    ,{  -310, -1680,  -850,  -310,  -850}-    ,{  -850, -1680,  -850, -1560,  -850}-    }-   }-  ,{{{   310,   310,    90,   310,  -390}-    ,{  -390,  -430,  -650,  -430,  -390}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{   310,   310,    90,   310, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    }-   ,{{  -390,  -430,  -650,  -430,  -390}-    ,{  -390,  -430,  -650,  -430,  -390}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{ -1260, -1280, -1260, -1280, -1480}-    ,{  -940,  -940, -1160,  -940, -1140}-    }-   ,{{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    }-   ,{{   310,   310,    90,   310, -1140}-    ,{ -1430, -1450, -1430, -1450, -1650}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{   310,   310,    90,   310, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    }-   ,{{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    ,{  -940,  -940, -1160,  -940, -1140}-    }-   }-  }- ,{{{{  1140,  1140,   770,   780,   770}-    ,{   780,   600,   240,   780,   240}-    ,{   480,   300,   -60,   480,   -60}-    ,{  1140,  1140,   770,   690,   770}-    ,{   480,   300,   -60,   480,   -60}-    }-   ,{{   780,   600,   240,   780,   240}-    ,{   780,   600,   240,   780,   240}-    ,{   470,   290,   -70,   470,   -70}-    ,{  -780,  -780, -1150, -1230, -1150}-    ,{   470,   290,   -70,   470,   -70}-    }-   ,{{   490,   310,   -50,   490,   -50}-    ,{   490,   310,   -50,   490,   -50}-    ,{   480,   300,   -60,   480,   -60}-    ,{   490,   310,   -50,   490,   -50}-    ,{   480,   300,   -60,   480,   -60}-    }-   ,{{  1140,  1140,   770,   690,   770}-    ,{  -600,  -600,  -970, -1050,  -970}-    ,{   470,   290,   -70,   470,   -70}-    ,{  1140,  1140,   770,   690,   770}-    ,{   470,   290,   -70,   470,   -70}-    }-   ,{{   490,   310,   -50,   490,   -50}-    ,{   490,   310,   -50,   490,   -50}-    ,{   480,   300,   -60,   480,   -60}-    ,{   490,   310,   -50,   490,   -50}-    ,{  -430,  -430, -1040, -1120, -1040}-    }-   }-  ,{{{  1140,  1140,   770,  -110,   770}-    ,{   600,   600,   240,  -110,   240}-    ,{   300,   300,   -60,  -170,   -60}-    ,{  1140,  1140,   770,  -400,   770}-    ,{   300,   300,   -60,  -170,   -60}-    }-   ,{{   600,   600,   240,  -110,   240}-    ,{   600,   600,   240,  -110,   240}-    ,{   290,   290,   -70,  -420,   -70}-    ,{  -780,  -780, -1150, -1500, -1150}-    ,{   290,   290,   -70,  -420,   -70}-    }-   ,{{   310,   310,   -50,  -170,   -50}-    ,{   310,   310,   -50,  -400,   -50}-    ,{   300,   300,   -60,  -170,   -60}-    ,{   310,   310,   -50,  -400,   -50}-    ,{   300,   300,   -60,  -170,   -60}-    }-   ,{{  1140,  1140,   770,  -420,   770}-    ,{  -600,  -600,  -970, -1320,  -970}-    ,{   290,   290,   -70,  -420,   -70}-    ,{  1140,  1140,   770,  -830,   770}-    ,{   290,   290,   -70,  -420,   -70}-    }-   ,{{   310,   310,   -50,  -170,   -50}-    ,{   310,   310,   -50,  -400,   -50}-    ,{   300,   300,   -60,  -170,   -60}-    ,{   310,   310,   -50,  -400,   -50}-    ,{  -430,  -430, -1040, -1390, -1040}-    }-   }-  ,{{{   690,   690,   470,   690,   160}-    ,{   150,   150,   -60,   150,  -370}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{   690,   690,   470,   690,   160}-    ,{  -140,  -140,  -360,  -140,  -670}-    }-   ,{{   150,   150,   -60,   150,  -370}-    ,{   150,   150,   -60,   150,  -370}-    ,{  -150,  -150,  -370,  -150,  -680}-    ,{ -1210, -1230, -1210, -1230, -1520}-    ,{  -150,  -150,  -370,  -150,  -680}-    }-   ,{{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    }-   ,{{   690,   690,   470,   690,   160}-    ,{ -1030, -1050, -1030, -1050, -1340}-    ,{  -150,  -150,  -370,  -150,  -680}-    ,{   690,   690,   470,   690,   160}-    ,{  -150,  -150,  -370,  -150,  -680}-    }-   ,{{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{ -1120, -1120, -1340, -1120, -1650}-    }-   }-  ,{{{   780,  -580,   770,   780,   770}-    ,{   780,  -580,   240,   780,   240}-    ,{   480,  -640,   -60,   480,   -60}-    ,{   770,  -880,   770,   490,   770}-    ,{   480,  -640,   -60,   480,   -60}-    }-   ,{{   780,  -580,   240,   780,   240}-    ,{   780,  -580,   240,   780,   240}-    ,{   470,  -890,   -70,   470,   -70}-    ,{ -1150, -1970, -1150, -1860, -1150}-    ,{   470,  -890,   -70,   470,   -70}-    }-   ,{{   490,  -640,   -50,   490,   -50}-    ,{   490,  -880,   -50,   490,   -50}-    ,{   480,  -640,   -60,   480,   -60}-    ,{   490,  -880,   -50,   490,   -50}-    ,{   480,  -640,   -60,   480,   -60}-    }-   ,{{   770,  -890,   770,   470,   770}-    ,{  -970, -1790,  -970, -1680,  -970}-    ,{   470,  -890,   -70,   470,   -70}-    ,{   770, -1300,   770, -1190,   770}-    ,{   470,  -890,   -70,   470,   -70}-    }-   ,{{   490,  -640,   -50,   490,   -50}-    ,{   490,  -880,   -50,   490,   -50}-    ,{   480,  -640,   -60,   480,   -60}-    ,{   490,  -880,   -50,   490,   -50}-    ,{ -1040, -1860, -1040, -1750, -1040}-    }-   }-  ,{{{   690,   690,   470,   690,   190}-    ,{   190,   150,   -60,   150,   190}-    ,{  -140,  -140,  -360,  -140,  -350}-    ,{   690,   690,   470,   690,  -340}-    ,{  -140,  -140,  -360,  -140,  -350}-    }-   ,{{   190,   150,   -60,   150,   190}-    ,{   190,   150,   -60,   150,   190}-    ,{  -150,  -150,  -370,  -150,  -360}-    ,{ -1210, -1230, -1210, -1230, -1440}-    ,{  -150,  -150,  -370,  -150,  -360}-    }-   ,{{  -140,  -140,  -360,  -140,  -340}-    ,{  -140,  -140,  -360,  -140,  -340}-    ,{  -140,  -140,  -360,  -140,  -350}-    ,{  -140,  -140,  -360,  -140,  -340}-    ,{  -140,  -140,  -360,  -140,  -350}-    }-   ,{{   690,   690,   470,   690,  -360}-    ,{ -1030, -1050, -1030, -1050, -1260}-    ,{  -150,  -150,  -370,  -150,  -360}-    ,{   690,   690,   470,   690,  -770}-    ,{  -150,  -150,  -370,  -150,  -360}-    }-   ,{{  -140,  -140,  -360,  -140,  -340}-    ,{  -140,  -140,  -360,  -140,  -340}-    ,{  -140,  -140,  -360,  -140,  -350}-    ,{  -140,  -140,  -360,  -140,  -340}-    ,{ -1120, -1120, -1340, -1120, -1330}-    }-   }-  }- ,{{{{  1320,  1320,   960,   870,   960}-    ,{   850,   670,   300,   850,   300}-    ,{   720,   540,   170,   720,   170}-    ,{  1320,  1320,   960,   870,   960}-    ,{   590,   410,    40,   590,    40}-    }-   ,{{   850,   670,   300,   850,   300}-    ,{   850,   670,   300,   850,   300}-    ,{   570,   390,    20,   570,    20}-    ,{  -730,  -730, -1100, -1180, -1100}-    ,{   570,   390,    20,   570,    20}-    }-   ,{{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   590,   410,    40,   590,    40}-    }-   ,{{  1320,  1320,   960,   870,   960}-    ,{ -1030, -1030, -1400, -1480, -1400}-    ,{   570,   390,    20,   570,    20}-    ,{  1320,  1320,   960,   870,   960}-    ,{   570,   390,    20,   570,    20}-    }-   ,{{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   280,   100,  -260,   280,  -260}-    ,{   720,   540,   170,   720,   170}-    ,{  -160,  -160,  -760,  -850,  -760}-    }-   }-  ,{{{  1320,  1320,   960,    70,   960}-    ,{   670,   670,   300,   -40,   300}-    ,{   540,   540,   170,    70,   170}-    ,{  1320,  1320,   960,  -170,   960}-    ,{   410,   410,    40,   -60,    40}-    }-   ,{{   670,   670,   300,   -40,   300}-    ,{   670,   670,   300,   -40,   300}-    ,{   390,   390,    20,  -320,    20}-    ,{  -730,  -730, -1100, -1450, -1100}-    ,{   390,   390,    20,  -320,    20}-    }-   ,{{   540,   540,   170,    70,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   540,   540,   170,    70,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   410,   410,    40,   -60,    40}-    }-   ,{{  1320,  1320,   960,  -320,   960}-    ,{ -1030, -1030, -1400, -1750, -1400}-    ,{   390,   390,    20,  -320,    20}-    ,{  1320,  1320,   960,  -640,   960}-    ,{   390,   390,    20,  -320,    20}-    }-   ,{{   540,   540,   170,  -170,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   100,   100,  -260,  -370,  -260}-    ,{   540,   540,   170,  -170,   170}-    ,{  -160,  -160,  -760, -1110,  -760}-    }-   }-  ,{{{   870,   870,   650,   870,   340}-    ,{   220,   220,     0,   220,  -310}-    ,{    90,    90,  -130,    90,  -440}-    ,{   870,   870,   650,   870,   340}-    ,{   -40,   -40,  -260,   -40,  -570}-    }-   ,{{   220,   220,     0,   220,  -310}-    ,{   220,   220,     0,   220,  -310}-    ,{   -60,   -60,  -280,   -60,  -590}-    ,{ -1160, -1180, -1160, -1180, -1470}-    ,{   -60,   -60,  -280,   -60,  -590}-    }-   ,{{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{   -40,   -40,  -260,   -40,  -570}-    }-   ,{{   870,   870,   650,   870,   340}-    ,{ -1460, -1480, -1460, -1480, -1770}-    ,{   -60,   -60,  -280,   -60,  -590}-    ,{   870,   870,   650,   870,   340}-    ,{   -60,   -60,  -280,   -60,  -590}-    }-   ,{{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{  -350,  -350,  -570,  -350,  -880}-    ,{    90,    90,  -130,    90,  -440}-    ,{  -850,  -850, -1070,  -850, -1380}-    }-   }-  ,{{{   960,  -410,   960,   850,   960}-    ,{   850,  -520,   300,   850,   300}-    ,{   720,  -410,   170,   720,   170}-    ,{   960,  -650,   960,   720,   960}-    ,{   590,  -540,    40,   590,    40}-    }-   ,{{   850,  -520,   300,   850,   300}-    ,{   850,  -520,   300,   850,   300}-    ,{   570,  -800,    20,   570,    20}-    ,{ -1100, -1920, -1100, -1810, -1100}-    ,{   570,  -800,    20,   570,    20}-    }-   ,{{   720,  -410,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   720,  -410,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   590,  -540,    40,   590,    40}-    }-   ,{{   960,  -800,   960,   570,   960}-    ,{ -1400, -2220, -1400, -2110, -1400}-    ,{   570,  -800,    20,   570,    20}-    ,{   960, -1120,   960, -1000,   960}-    ,{   570,  -800,    20,   570,    20}-    }-   ,{{   720,  -650,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   280,  -850,  -260,   280,  -260}-    ,{   720,  -650,   170,   720,   170}-    ,{  -760, -1590,  -760, -1470,  -760}-    }-   }-  ,{{{   870,   870,   650,   870,   250}-    ,{   250,   220,     0,   220,   250}-    ,{    90,    90,  -130,    90,  -110}-    ,{   870,   870,   650,   870,  -110}-    ,{   -40,   -40,  -260,   -40,  -240}-    }-   ,{{   250,   220,     0,   220,   250}-    ,{   250,   220,     0,   220,   250}-    ,{   -60,   -60,  -280,   -60,  -260}-    ,{ -1160, -1180, -1160, -1180, -1390}-    ,{   -60,   -60,  -280,   -60,  -260}-    }-   ,{{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{   -40,   -40,  -260,   -40,  -240}-    }-   ,{{   870,   870,   650,   870,  -260}-    ,{ -1460, -1480, -1460, -1480, -1690}-    ,{   -60,   -60,  -280,   -60,  -260}-    ,{   870,   870,   650,   870,  -580}-    ,{   -60,   -60,  -280,   -60,  -260}-    }-   ,{{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{  -350,  -350,  -570,  -350,  -550}-    ,{    90,    90,  -130,    90,  -110}-    ,{  -850,  -850, -1070,  -850, -1050}-    }-   }-  }- ,{{{{  1320,  1320,   960,   870,   960}-    ,{   850,   670,   540,   850,   300}-    ,{   720,   540,   170,   720,   170}-    ,{  1320,  1320,   960,   870,   960}-    ,{   590,   410,    40,   590,    40}-    }-   ,{{   850,   670,   300,   850,   300}-    ,{   850,   670,   300,   850,   300}-    ,{   570,   390,    20,   570,    20}-    ,{  -350,  -350,  -870,  -960,  -870}-    ,{   570,   390,    20,   570,    20}-    }-   ,{{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   590,   410,    40,   590,    40}-    }-   ,{{  1320,  1320,   960,   870,   960}-    ,{   540,  -100,   540, -1050,  -810}-    ,{   570,   390,    20,   570,    20}-    ,{  1320,  1320,   960,   870,   960}-    ,{   570,   390,    20,   570,    20}-    }-   ,{{   720,   540,   170,   720,   170}-    ,{   720,   540,   170,   720,   170}-    ,{   480,   300,   -60,   480,   -60}-    ,{   720,   540,   170,   720,   170}-    ,{  -160,  -160,  -400,  -230,  -760}-    }-   }-  ,{{{  1320,  1320,   960,    70,   960}-    ,{   670,   670,   300,   -40,   300}-    ,{   540,   540,   170,    70,   170}-    ,{  1320,  1320,   960,  -170,   960}-    ,{   410,   410,    40,   -60,    40}-    }-   ,{{   670,   670,   300,   -40,   300}-    ,{   670,   670,   300,   -40,   300}-    ,{   390,   390,    20,  -320,    20}-    ,{  -730,  -730, -1100, -1450,  -870}-    ,{   390,   390,    20,  -320,    20}-    }-   ,{{   540,   540,   170,    70,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   540,   540,   170,    70,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   410,   410,    40,   -60,    40}-    }-   ,{{  1320,  1320,   960,  -320,   960}-    ,{    10,  -600,    10, -1320,  -970}-    ,{   390,   390,    20,  -320,    20}-    ,{  1320,  1320,   960,  -640,   960}-    ,{   390,   390,    20,  -320,    20}-    }-   ,{{   540,   540,   170,  -170,   170}-    ,{   540,   540,   170,  -170,   170}-    ,{   300,   300,   -60,  -170,   -60}-    ,{   540,   540,   170,  -170,   170}-    ,{  -160,  -160,  -400, -1110,  -760}-    }-   }-  ,{{{   870,   870,   650,   870,   340}-    ,{   540,   220,   540,   220,  -310}-    ,{    90,    90,  -130,    90,  -440}-    ,{   870,   870,   650,   870,   340}-    ,{   -40,   -40,  -260,   -40,  -570}-    }-   ,{{   220,   220,     0,   220,  -310}-    ,{   220,   220,     0,   220,  -310}-    ,{   -60,   -60,  -280,   -60,  -590}-    ,{  -350,  -350,  -940,  -960, -1250}-    ,{   -60,   -60,  -280,   -60,  -590}-    }-   ,{{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{   -40,   -40,  -260,   -40,  -570}-    }-   ,{{   870,   870,   650,   870,   340}-    ,{   540,  -100,   540, -1050, -1340}-    ,{   -60,   -60,  -280,   -60,  -590}-    ,{   870,   870,   650,   870,   340}-    ,{   -60,   -60,  -280,   -60,  -590}-    }-   ,{{    90,    90,  -130,    90,  -440}-    ,{    90,    90,  -130,    90,  -440}-    ,{  -140,  -140,  -360,  -140,  -670}-    ,{    90,    90,  -130,    90,  -440}-    ,{  -850,  -850, -1070,  -850, -1380}-    }-   }-  ,{{{   960,  -410,   960,   850,   960}-    ,{   850,  -520,   300,   850,   300}-    ,{   720,  -410,   170,   720,   170}-    ,{   960,  -650,   960,   720,   960}-    ,{   590,  -540,    40,   590,    40}-    }-   ,{{   850,  -520,   300,   850,   300}-    ,{   850,  -520,   300,   850,   300}-    ,{   570,  -800,    20,   570,    20}-    ,{  -870, -1920,  -870, -1370,  -870}-    ,{   570,  -800,    20,   570,    20}-    }-   ,{{   720,  -410,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   720,  -410,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   590,  -540,    40,   590,    40}-    }-   ,{{   960,  -800,   960,   570,   960}-    ,{  -970, -1790,  -970, -1680,  -970}-    ,{   570,  -800,    20,   570,    20}-    ,{   960, -1120,   960, -1000,   960}-    ,{   570,  -800,    20,   570,    20}-    }-   ,{{   720,  -640,   170,   720,   170}-    ,{   720,  -650,   170,   720,   170}-    ,{   480,  -640,   -60,   480,   -60}-    ,{   720,  -650,   170,   720,   170}-    ,{  -230, -1520,  -760,  -230,  -760}-    }-   }-  ,{{{   870,   870,   650,   870,   250}-    ,{   250,   220,     0,   220,   250}-    ,{    90,    90,  -130,    90,  -110}-    ,{   870,   870,   650,   870,  -110}-    ,{   -40,   -40,  -260,   -40,  -240}-    }-   ,{{   250,   220,     0,   220,   250}-    ,{   250,   220,     0,   220,   250}-    ,{   -60,   -60,  -280,   -60,  -260}-    ,{  -940,  -960,  -940,  -960, -1360}-    ,{   -60,   -60,  -280,   -60,  -260}-    }-   ,{{    90,    90,  -130,    90,   -90}-    ,{    90,    90,  -130,    90,   -90}-    ,{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{   -40,   -40,  -260,   -40,  -240}-    }-   ,{{   870,   870,   650,   870,  -260}-    ,{  -810, -1050, -1030, -1050,  -810}-    ,{   -60,   -60,  -280,   -60,  -260}-    ,{   870,   870,   650,   870,  -580}-    ,{   -60,   -60,  -280,   -60,  -260}-    }-   ,{{    90,    90,  -130,    90,  -110}-    ,{    90,    90,  -130,    90,  -110}-    ,{  -140,  -140,  -360,  -140,  -350}-    ,{    90,    90,  -130,    90,  -110}-    ,{  -850,  -850, -1070,  -850, -1050}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   240,  -780,  -870,   240,  -870}-    ,{   190, -1060, -1060,   190,  -970}-    ,{   240,  -780, -1010,   240, -1010}-    ,{   190,  -870,  -870,   190,  -870}-    ,{   130,  -890, -1120,   130, -1120}-    }-   ,{{    40, -1210, -1180,    40,  -970}-    ,{    40, -1210, -1210,    40,  -970}-    ,{  -270, -1520, -1520,  -270, -1520}-    ,{ -1180, -1420, -1180, -1250, -1180}-    ,{  -270, -1520, -1520,  -270, -1520}-    }-   ,{{   190,  -840, -1060,   190, -1060}-    ,{   190, -1060, -1060,   190, -1060}-    ,{   180,  -840, -1070,   180, -1070}-    ,{   190, -1060, -1060,   190, -1060}-    ,{   130,  -890, -1120,   130, -1120}-    }-   ,{{  -270,  -870,  -870,  -270,  -870}-    ,{ -1470, -1710, -1470, -1530, -1470}-    ,{  -270, -1520, -1520,  -270, -1520}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{  -270, -1520, -1520,  -270, -1520}-    }-   ,{{   240,  -780, -1010,   240, -1010}-    ,{   190, -1060, -1060,   190, -1060}-    ,{   240,  -780, -1010,   240, -1010}-    ,{   190, -1060, -1060,   190, -1060}-    ,{ -1680, -1790, -1850, -1680, -1850}-    }-   }-  ,{{{  -590, -1050,  -870,  -590,  -870}-    ,{  -890, -1240, -1060,  -890, -1060}-    ,{  -590, -1190, -1010,  -590, -1010}-    ,{  -870, -1050,  -870,  -890,  -870}-    ,{  -700, -1300, -1120,  -700, -1120}-    }-   ,{{ -1030, -1370, -1210, -1030, -1210}-    ,{ -1030, -1370, -1210, -1030, -1210}-    ,{ -1340, -1700, -1520, -1340, -1520}-    ,{ -1250, -1600, -1420, -1250, -1420}-    ,{ -1340, -1700, -1520, -1340, -1520}-    }-   ,{{  -650, -1240, -1060,  -650, -1060}-    ,{  -890, -1240, -1060,  -890, -1060}-    ,{  -650, -1250, -1070,  -650, -1070}-    ,{  -890, -1240, -1060,  -890, -1060}-    ,{  -700, -1300, -1120,  -700, -1120}-    }-   ,{{  -870, -1050,  -870, -1340,  -870}-    ,{ -1530, -1890, -1710, -1530, -1710}-    ,{ -1340, -1700, -1520, -1340, -1520}-    ,{  -870, -1050,  -870, -1940,  -870}-    ,{ -1340, -1700, -1520, -1340, -1520}-    }-   ,{{  -590, -1190, -1010,  -590, -1010}-    ,{  -890, -1240, -1060,  -890, -1060}-    ,{  -590, -1190, -1010,  -590, -1010}-    ,{  -890, -1240, -1060,  -890, -1060}-    ,{ -1680, -1790, -1850, -1680, -1850}-    }-   }-  ,{{{  -870,  -870,  -870,  -870,  -870}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1010, -1010, -1010, -1010, -1010}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{ -1120, -1120, -1120, -1120, -1120}-    }-   ,{{ -1180, -1210, -1180, -1210, -1180}-    ,{ -1210, -1210, -1210, -1210, -1210}-    ,{ -1520, -1520, -1520, -1520, -1520}-    ,{ -1180, -1420, -1180, -1420, -1180}-    ,{ -1520, -1520, -1520, -1520, -1520}-    }-   ,{{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1070, -1070, -1070, -1070, -1070}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1120, -1120, -1120, -1120, -1120}-    }-   ,{{  -870,  -870,  -870,  -870,  -870}-    ,{ -1470, -1710, -1470, -1710, -1470}-    ,{ -1520, -1520, -1520, -1520, -1520}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{ -1520, -1520, -1520, -1520, -1520}-    }-   ,{{ -1010, -1010, -1010, -1010, -1010}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1010, -1010, -1010, -1010, -1010}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1850, -1850, -1850, -1850, -1850}-    }-   }-  ,{{{   240,  -780,  -870,   240,  -870}-    ,{   190, -1080, -1060,   190, -1060}-    ,{   240,  -780, -1010,   240, -1010}-    ,{   190, -1080,  -870,   190,  -870}-    ,{   130,  -890, -1120,   130, -1120}-    }-   ,{{    40, -1220, -1210,    40, -1210}-    ,{    40, -1220, -1210,    40, -1210}-    ,{  -270, -1530, -1520,  -270, -1520}-    ,{ -1420, -1440, -1420, -1420, -1420}-    ,{  -270, -1530, -1520,  -270, -1520}-    }-   ,{{   190,  -840, -1060,   190, -1060}-    ,{   190, -1080, -1060,   190, -1060}-    ,{   180,  -840, -1070,   180, -1070}-    ,{   190, -1080, -1060,   190, -1060}-    ,{   130,  -890, -1120,   130, -1120}-    }-   ,{{  -270, -1530,  -870,  -270,  -870}-    ,{ -1710, -1720, -1710, -1710, -1710}-    ,{  -270, -1530, -1520,  -270, -1520}-    ,{  -870, -2130,  -870, -2120,  -870}-    ,{  -270, -1530, -1520,  -270, -1520}-    }-   ,{{   240,  -780, -1010,   240, -1010}-    ,{   190, -1080, -1060,   190, -1060}-    ,{   240,  -780, -1010,   240, -1010}-    ,{   190, -1080, -1060,   190, -1060}-    ,{ -1850, -1870, -1850, -1850, -1850}-    }-   }-  ,{{{  -870,  -870,  -870,  -870,  -970}-    ,{  -970, -1060, -1060, -1060,  -970}-    ,{ -1010, -1010, -1010, -1010, -1010}-    ,{  -870,  -870,  -870,  -870, -1060}-    ,{ -1120, -1120, -1120, -1120, -1120}-    }-   ,{{  -970, -1210, -1180, -1210,  -970}-    ,{  -970, -1210, -1210, -1210,  -970}-    ,{ -1520, -1520, -1520, -1520, -1520}-    ,{ -1180, -1420, -1180, -1420, -1420}-    ,{ -1520, -1520, -1520, -1520, -1520}-    }-   ,{{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1070, -1070, -1070, -1070, -1070}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1120, -1120, -1120, -1120, -1120}-    }-   ,{{  -870,  -870,  -870,  -870, -1520}-    ,{ -1470, -1710, -1470, -1710, -1710}-    ,{ -1520, -1520, -1520, -1520, -1520}-    ,{  -870,  -870,  -870,  -870, -2120}-    ,{ -1520, -1520, -1520, -1520, -1520}-    }-   ,{{ -1010, -1010, -1010, -1010, -1010}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1010, -1010, -1010, -1010, -1010}-    ,{ -1060, -1060, -1060, -1060, -1060}-    ,{ -1850, -1850, -1850, -1850, -1850}-    }-   }-  }- ,{{{{   210,  -870,  -870,   210,  -800}-    ,{   210, -1040, -1040,   210,  -800}-    ,{  -240, -1490, -1490,  -240, -1490}-    ,{  -160,  -870,  -870,  -160,  -870}-    ,{  -240, -1490, -1490,  -240, -1490}-    }-   ,{{   210, -1040, -1040,   210,  -800}-    ,{   210, -1040, -1040,   210,  -800}-    ,{  -240, -1490, -1490,  -240, -1490}-    ,{ -1990, -2230, -1990, -2060, -1990}-    ,{  -240, -1490, -1490,  -240, -1490}-    }-   ,{{  -160, -1410, -1410,  -160, -1410}-    ,{  -160, -1410, -1410,  -160, -1410}-    ,{  -460, -1490, -1710,  -460, -1710}-    ,{  -160, -1410, -1410,  -160, -1410}-    ,{  -460, -1490, -1710,  -460, -1710}-    }-   ,{{  -240,  -870,  -870,  -240,  -870}-    ,{ -1520, -1760, -1520, -1580, -1520}-    ,{  -240, -1490, -1490,  -240, -1490}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{  -240, -1490, -1490,  -240, -1490}-    }-   ,{{  -160, -1410, -1410,  -160, -1410}-    ,{  -160, -1410, -1410,  -160, -1410}-    ,{  -770, -1800, -2020,  -770, -2020}-    ,{  -160, -1410, -1410,  -160, -1410}-    ,{ -1520, -1640, -1700, -1520, -1700}-    }-   }-  ,{{{  -870, -1050,  -870,  -870,  -870}-    ,{  -870, -1220, -1040,  -870, -1040}-    ,{ -1300, -1670, -1490, -1300, -1490}-    ,{  -870, -1050,  -870, -1230,  -870}-    ,{ -1300, -1640, -1490, -1300, -1490}-    }-   ,{{  -870, -1220, -1040,  -870, -1040}-    ,{  -870, -1220, -1040,  -870, -1040}-    ,{ -1320, -1670, -1490, -1320, -1490}-    ,{ -2060, -2410, -2230, -2060, -2230}-    ,{ -1320, -1670, -1490, -1320, -1490}-    }-   ,{{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1300, -1890, -1710, -1300, -1710}-    ,{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1300, -1890, -1710, -1300, -1710}-    }-   ,{{  -870, -1050,  -870, -1320,  -870}-    ,{ -1580, -1940, -1760, -1580, -1760}-    ,{ -1320, -1670, -1490, -1320, -1490}-    ,{  -870, -1050,  -870, -1940,  -870}-    ,{ -1320, -1670, -1490, -1320, -1490}-    }-   ,{{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1610, -2200, -2020, -1610, -2020}-    ,{ -1230, -1590, -1410, -1230, -1410}-    ,{ -1520, -1640, -1700, -1520, -1700}-    }-   }-  ,{{{  -870,  -870,  -870,  -870,  -870}-    ,{ -1040, -1040, -1040, -1040, -1040}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{ -1040, -1040, -1040, -1040, -1040}-    ,{ -1040, -1040, -1040, -1040, -1040}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{ -1990, -2230, -1990, -2230, -1990}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1710, -1710, -1710, -1710, -1710}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1710, -1710, -1710, -1710, -1710}-    }-   ,{{  -870,  -870,  -870,  -870,  -870}-    ,{ -1520, -1760, -1520, -1760, -1520}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{  -870,  -870,  -870,  -870,  -870}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -2020, -2020, -2020, -2020, -2020}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1700, -1700, -1700, -1700, -1700}-    }-   }-  ,{{{   210, -1060,  -870,   210,  -870}-    ,{   210, -1060, -1040,   210, -1040}-    ,{  -240, -1490, -1490,  -240, -1490}-    ,{  -160, -1420,  -870,  -160,  -870}-    ,{  -240, -1490, -1490,  -240, -1490}-    }-   ,{{   210, -1060, -1040,   210, -1040}-    ,{   210, -1060, -1040,   210, -1040}-    ,{  -240, -1510, -1490,  -240, -1490}-    ,{ -2230, -2250, -2230, -2230, -2230}-    ,{  -240, -1510, -1490,  -240, -1490}-    }-   ,{{  -160, -1420, -1410,  -160, -1410}-    ,{  -160, -1420, -1410,  -160, -1410}-    ,{  -460, -1490, -1710,  -460, -1710}-    ,{  -160, -1420, -1410,  -160, -1410}-    ,{  -460, -1490, -1710,  -460, -1710}-    }-   ,{{  -240, -1510,  -870,  -240,  -870}-    ,{ -1760, -1770, -1760, -1760, -1760}-    ,{  -240, -1510, -1490,  -240, -1490}-    ,{  -870, -2130,  -870, -2120,  -870}-    ,{  -240, -1510, -1490,  -240, -1490}-    }-   ,{{  -160, -1420, -1410,  -160, -1410}-    ,{  -160, -1420, -1410,  -160, -1410}-    ,{  -770, -1800, -2020,  -770, -2020}-    ,{  -160, -1420, -1410,  -160, -1410}-    ,{ -1700, -1710, -1700, -1700, -1700}-    }-   }-  ,{{{  -800,  -870,  -870,  -870,  -800}-    ,{  -800, -1040, -1040, -1040,  -800}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{  -870,  -870,  -870,  -870, -1410}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{  -800, -1040, -1040, -1040,  -800}-    ,{  -800, -1040, -1040, -1040,  -800}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{ -1990, -2230, -1990, -2230, -2230}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1710, -1710, -1710, -1710, -1710}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1710, -1710, -1710, -1710, -1710}-    }-   ,{{  -870,  -870,  -870,  -870, -1490}-    ,{ -1520, -1760, -1520, -1760, -1760}-    ,{ -1490, -1490, -1490, -1490, -1490}-    ,{  -870,  -870,  -870,  -870, -2120}-    ,{ -1490, -1490, -1490, -1490, -1490}-    }-   ,{{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -2020, -2020, -2020, -2020, -2020}-    ,{ -1410, -1410, -1410, -1410, -1410}-    ,{ -1700, -1700, -1700, -1700, -1700}-    }-   }-  }- ,{{{{  -710,  -710,  -710,  -710,  -710}-    ,{  -710, -1780, -1540,  -710, -1540}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710,  -710,  -710,  -710,  -710}-    ,{  -710, -1730, -1960,  -710, -1960}-    }-   ,{{  -710, -1960, -1730,  -710, -1730}-    ,{  -890, -2140, -2140,  -890, -1900}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{ -1730, -1970, -1730, -1800, -1730}-    ,{  -710, -1960, -1960,  -710, -1960}-    }-   ,{{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    }-   ,{{  -710,  -710,  -710,  -710,  -710}-    ,{ -1540, -1780, -1540, -1610, -1540}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{  -710,  -710,  -710,  -710,  -710}-    ,{  -710, -1960, -1960,  -710, -1960}-    }-   ,{{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1960, -1960,  -710, -1960}-    ,{ -1780, -1900, -1960, -1780, -1960}-    }-   }-  ,{{{  -710,  -890,  -710, -1540,  -710}-    ,{ -1610, -1960, -1780, -1610, -1780}-    ,{ -1540, -2140, -1960, -1540, -1960}-    ,{  -710,  -890,  -710, -1780,  -710}-    ,{ -1540, -1900, -1960, -1540, -1960}-    }-   ,{{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1960, -2320, -2140, -1960, -2140}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1800, -2150, -1970, -1800, -1970}-    ,{ -1780, -2140, -1960, -1780, -1960}-    }-   ,{{ -1540, -2140, -1960, -1540, -1960}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1540, -2140, -1960, -1540, -1960}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1540, -2140, -1960, -1540, -1960}-    }-   ,{{  -710,  -890,  -710, -1610,  -710}-    ,{ -1610, -1960, -1780, -1610, -1780}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{  -710,  -890,  -710, -1780,  -710}-    ,{ -1780, -2140, -1960, -1780, -1960}-    }-   ,{{ -1540, -1900, -1960, -1540, -1960}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1540, -2140, -1960, -1540, -1960}-    ,{ -1780, -2140, -1960, -1780, -1960}-    ,{ -1780, -1900, -1960, -1780, -1960}-    }-   }-  ,{{{  -710,  -710,  -710,  -710,  -710}-    ,{ -1540, -1780, -1540, -1780, -1540}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{  -710,  -710,  -710,  -710,  -710}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1730, -1960, -1730, -1960, -1730}-    ,{ -2140, -2140, -2140, -2140, -2140}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1730, -1970, -1730, -1970, -1730}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{  -710,  -710,  -710,  -710,  -710}-    ,{ -1540, -1780, -1540, -1780, -1540}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{  -710,  -710,  -710,  -710,  -710}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   }-  ,{{{  -710, -1730,  -710,  -710,  -710}-    ,{  -710, -1800, -1780,  -710, -1780}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1970,  -710,  -710,  -710}-    ,{  -710, -1730, -1960,  -710, -1960}-    }-   ,{{  -710, -1970, -1960,  -710, -1960}-    ,{  -890, -2150, -2140,  -890, -2140}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{ -1970, -1990, -1970, -1970, -1970}-    ,{  -710, -1970, -1960,  -710, -1960}-    }-   ,{{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    }-   ,{{  -710, -1800,  -710,  -710,  -710}-    ,{ -1780, -1800, -1780, -1780, -1780}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{  -710, -1970,  -710, -1960,  -710}-    ,{  -710, -1970, -1960,  -710, -1960}-    }-   ,{{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{  -710, -1730, -1960,  -710, -1960}-    ,{  -710, -1970, -1960,  -710, -1960}-    ,{ -1960, -1970, -1960, -1960, -1960}-    }-   }-  ,{{{  -710,  -710,  -710,  -710, -1780}-    ,{ -1540, -1780, -1540, -1780, -1780}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{  -710,  -710,  -710,  -710, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1730, -1960, -1730, -1960, -1900}-    ,{ -1900, -2140, -2140, -2140, -1900}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1730, -1970, -1730, -1970, -1970}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{  -710,  -710,  -710,  -710, -1780}-    ,{ -1540, -1780, -1540, -1780, -1780}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{  -710,  -710,  -710,  -710, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   ,{{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    ,{ -1960, -1960, -1960, -1960, -1960}-    }-   }-  }- ,{{{{   360,   -70,  -150,   360,  -150}-    ,{   360,   -70,  -890,   360,  -650}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{  -150, -1180, -1400,  -150, -1400}-    }-   ,{{   360,   -70,  -890,   360,  -650}-    ,{   360,   -70,  -890,   360,  -650}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{ -1500, -1600, -1500, -1570, -1500}-    ,{  -150, -1400, -1400,  -150, -1400}-    }-   ,{{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    }-   ,{{  -150,  -150,  -150,  -150,  -150}-    ,{ -1670, -1910, -1670, -1740, -1670}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{  -150, -1400, -1400,  -150, -1400}-    }-   ,{{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1400, -1400,  -150, -1400}-    ,{ -1230, -1340, -1400, -1230, -1400}-    }-   }-  ,{{{   -30,   -70,  -150,   -30,  -150}-    ,{   -30,   -70,  -890,   -30,  -890}-    ,{  -990, -1580, -1400,  -990, -1400}-    ,{  -150,  -330,  -150, -1230,  -150}-    ,{  -990, -1340, -1400,  -990, -1400}-    }-   ,{{   -30,   -70,  -890,   -30,  -890}-    ,{   -30,   -70,  -890,   -30,  -890}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{ -1570, -1600, -1740, -1570, -1740}-    ,{ -1230, -1580, -1400, -1230, -1400}-    }-   ,{{  -990, -1580, -1400,  -990, -1400}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{  -990, -1580, -1400,  -990, -1400}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{  -990, -1580, -1400,  -990, -1400}-    }-   ,{{  -150,  -330,  -150, -1230,  -150}-    ,{ -1740, -2090, -1910, -1740, -1910}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{  -150,  -330,  -150, -1230,  -150}-    ,{ -1230, -1580, -1400, -1230, -1400}-    }-   ,{{  -990, -1340, -1400,  -990, -1400}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{  -990, -1580, -1400,  -990, -1400}-    ,{ -1230, -1580, -1400, -1230, -1400}-    ,{ -1230, -1340, -1400, -1230, -1400}-    }-   }-  ,{{{  -150,  -150,  -150,  -150,  -150}-    ,{  -890,  -890,  -890,  -890,  -890}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -890,  -890,  -890,  -890,  -890}-    ,{  -890,  -890,  -890,  -890,  -890}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1500, -1740, -1500, -1740, -1500}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -150,  -150,  -150,  -150,  -150}-    ,{ -1670, -1910, -1670, -1910, -1670}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   }-  ,{{{   360,  -910,  -150,   360,  -150}-    ,{   360,  -910,  -890,   360,  -890}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1420,  -150,  -150,  -150}-    ,{  -150, -1180, -1400,  -150, -1400}-    }-   ,{{   360,  -910,  -890,   360,  -890}-    ,{   360,  -910,  -890,   360,  -890}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{ -1740, -3040, -1740, -1740, -1740}-    ,{  -150, -1420, -1400,  -150, -1400}-    }-   ,{{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    }-   ,{{  -150, -1420,  -150,  -150,  -150}-    ,{ -1910, -1930, -1910, -1910, -1910}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{  -150, -1420,  -150, -1400,  -150}-    ,{  -150, -1420, -1400,  -150, -1400}-    }-   ,{{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{  -150, -1180, -1400,  -150, -1400}-    ,{  -150, -1420, -1400,  -150, -1400}-    ,{ -1400, -1420, -1400, -1400, -1400}-    }-   }-  ,{{{  -150,  -150,  -150,  -150,  -650}-    ,{  -650,  -890,  -890,  -890,  -650}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -650,  -890,  -890,  -890,  -650}-    ,{  -650,  -890,  -890,  -890,  -650}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1500, -1740, -1500, -1740, -1740}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -150,  -150,  -150,  -150, -1400}-    ,{ -1670, -1910, -1670, -1910, -1910}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   }-  }- ,{{{{   940,   220,   220,   940,   220}-    ,{   940,  -310,  -310,   940,   -70}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,   220,   220,   650,   220}-    ,{   640,  -380,  -610,   640,  -610}-    }-   ,{{   940,  -310,  -310,   940,   -70}-    ,{   940,  -310,  -310,   940,   -70}-    ,{   630,  -620,  -620,   630,  -620}-    ,{ -1460, -1700, -1460, -1520, -1460}-    ,{   630,  -620,  -620,   630,  -620}-    }-   ,{{   650,  -380,  -600,   650,  -600}-    ,{   650,  -600,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,  -600,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    }-   ,{{   630,   220,   220,   630,   220}-    ,{ -1280, -1520, -1280, -1340, -1280}-    ,{   630,  -620,  -620,   630,  -620}-    ,{   220,   220,   220,   220,   220}-    ,{   630,  -620,  -620,   630,  -620}-    }-   ,{{   650,  -380,  -600,   650,  -600}-    ,{   650,  -600,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,  -600,  -600,   650,  -600}-    ,{ -1410, -1530, -1590, -1410, -1590}-    }-   }-  ,{{{   220,    40,   220,  -130,   220}-    ,{  -130,  -490,  -310,  -130,  -310}-    ,{  -190,  -790,  -610,  -190,  -610}-    ,{   220,    40,   220,  -430,   220}-    ,{  -190,  -790,  -610,  -190,  -610}-    }-   ,{{  -130,  -490,  -310,  -130,  -310}-    ,{  -130,  -490,  -310,  -130,  -310}-    ,{  -440,  -800,  -620,  -440,  -620}-    ,{ -1520, -1880, -1700, -1520, -1700}-    ,{  -440,  -800,  -620,  -440,  -620}-    }-   ,{{  -190,  -780,  -600,  -190,  -600}-    ,{  -430,  -780,  -600,  -430,  -600}-    ,{  -190,  -790,  -610,  -190,  -610}-    ,{  -430,  -780,  -600,  -430,  -600}-    ,{  -190,  -790,  -610,  -190,  -610}-    }-   ,{{   220,    40,   220,  -440,   220}-    ,{ -1340, -1700, -1520, -1340, -1520}-    ,{  -440,  -800,  -620,  -440,  -620}-    ,{   220,    40,   220,  -850,   220}-    ,{  -440,  -800,  -620,  -440,  -620}-    }-   ,{{  -190,  -780,  -600,  -190,  -600}-    ,{  -430,  -780,  -600,  -430,  -600}-    ,{  -190,  -790,  -610,  -190,  -610}-    ,{  -430,  -780,  -600,  -430,  -600}-    ,{ -1410, -1530, -1590, -1410, -1590}-    }-   }-  ,{{{   220,   220,   220,   220,   220}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{   220,   220,   220,   220,   220}-    ,{  -610,  -610,  -610,  -610,  -610}-    }-   ,{{  -310,  -310,  -310,  -310,  -310}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -620,  -620,  -620,  -620,  -620}-    ,{ -1460, -1700, -1460, -1700, -1460}-    ,{  -620,  -620,  -620,  -620,  -620}-    }-   ,{{  -600,  -600,  -600,  -600,  -600}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    }-   ,{{   220,   220,   220,   220,   220}-    ,{ -1280, -1520, -1280, -1520, -1280}-    ,{  -620,  -620,  -620,  -620,  -620}-    ,{   220,   220,   220,   220,   220}-    ,{  -620,  -620,  -620,  -620,  -620}-    }-   ,{{  -600,  -600,  -600,  -600,  -600}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{ -1590, -1590, -1590, -1590, -1590}-    }-   }-  ,{{{   940,  -320,   220,   940,   220}-    ,{   940,  -320,  -310,   940,  -310}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,  -620,   220,   650,   220}-    ,{   640,  -380,  -610,   640,  -610}-    }-   ,{{   940,  -320,  -310,   940,  -310}-    ,{   940,  -320,  -310,   940,  -310}-    ,{   630,  -630,  -620,   630,  -620}-    ,{ -1700, -1710, -1700, -1700, -1700}-    ,{   630,  -630,  -620,   630,  -620}-    }-   ,{{   650,  -380,  -600,   650,  -600}-    ,{   650,  -620,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,  -620,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    }-   ,{{   630,  -630,   220,   630,   220}-    ,{ -1520, -1530, -1520, -1520, -1520}-    ,{   630,  -630,  -620,   630,  -620}-    ,{   220, -1040,   220, -1030,   220}-    ,{   630,  -630,  -620,   630,  -620}-    }-   ,{{   650,  -380,  -600,   650,  -600}-    ,{   650,  -620,  -600,   650,  -600}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   650,  -620,  -600,   650,  -600}-    ,{ -1590, -1600, -1590, -1590, -1590}-    }-   }-  ,{{{   220,   220,   220,   220,   -70}-    ,{   -70,  -310,  -310,  -310,   -70}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{   220,   220,   220,   220,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    }-   ,{{   -70,  -310,  -310,  -310,   -70}-    ,{   -70,  -310,  -310,  -310,   -70}-    ,{  -620,  -620,  -620,  -620,  -620}-    ,{ -1460, -1700, -1460, -1700, -1700}-    ,{  -620,  -620,  -620,  -620,  -620}-    }-   ,{{  -600,  -600,  -600,  -600,  -600}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    }-   ,{{   220,   220,   220,   220,  -620}-    ,{ -1280, -1520, -1280, -1520, -1520}-    ,{  -620,  -620,  -620,  -620,  -620}-    ,{   220,   220,   220,   220, -1030}-    ,{  -620,  -620,  -620,  -620,  -620}-    }-   ,{{  -600,  -600,  -600,  -600,  -600}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -600,  -600,  -600,  -600,  -600}-    ,{ -1590, -1590, -1590, -1590, -1590}-    }-   }-  }- ,{{{{  1010,   410,   410,  1010,   410}-    ,{  1010,  -240,  -240,  1010,     0}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,   410,   410,   880,   410}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{  1010,  -240,  -240,  1010,     0}-    ,{  1010,  -240,  -240,  1010,     0}-    ,{   730,  -520,  -520,   730,  -520}-    ,{ -1410, -1650, -1410, -1470, -1410}-    ,{   730,  -520,  -520,   730,  -520}-    }-   ,{{   880,  -150,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{   730,   410,   410,   730,   410}-    ,{ -1710, -1950, -1710, -1770, -1710}-    ,{   730,  -520,  -520,   730,  -520}-    ,{   410,   410,   410,   410,   410}-    ,{   730,  -520,  -520,   730,  -520}-    }-   ,{{   880,  -370,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   440,  -590,  -810,   440,  -810}-    ,{   880,  -370,  -370,   880,  -370}-    ,{ -1140, -1250, -1310, -1140, -1310}-    }-   }-  ,{{{   410,   230,   410,    40,   410}-    ,{   -70,  -420,  -240,   -70,  -240}-    ,{    40,  -550,  -370,    40,  -370}-    ,{   410,   230,   410,  -200,   410}-    ,{   -90,  -680,  -500,   -90,  -500}-    }-   ,{{   -70,  -420,  -240,   -70,  -240}-    ,{   -70,  -420,  -240,   -70,  -240}-    ,{  -350,  -700,  -520,  -350,  -520}-    ,{ -1470, -1830, -1650, -1470, -1650}-    ,{  -350,  -700,  -520,  -350,  -520}-    }-   ,{{    40,  -550,  -370,    40,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{    40,  -550,  -370,    40,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{   -90,  -680,  -500,   -90,  -500}-    }-   ,{{   410,   230,   410,  -350,   410}-    ,{ -1770, -2130, -1950, -1770, -1950}-    ,{  -350,  -700,  -520,  -350,  -520}-    ,{   410,   230,   410,  -670,   410}-    ,{  -350,  -700,  -520,  -350,  -520}-    }-   ,{{  -200,  -550,  -370,  -200,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{  -400,  -990, 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 -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -810,  -810,  -810,  -810,  -810}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{ -1310, -1310, -1310, -1310, -1310}-    }-   }-  ,{{{  1010,  -150,   410,  1010,   410}-    ,{  1010,  -260,  -240,  1010,  -240}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,   410,   880,   410}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{  1010,  -260,  -240,  1010,  -240}-    ,{  1010,  -260,  -240,  1010,  -240}-    ,{   730,  -540,  -520,   730,  -520}-    ,{ -1650, -1660, -1650, -1650, -1650}-    ,{   730,  -540,  -520,   730,  -520}-    }-   ,{{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{   730,  -540,   410,   730,   410}-    ,{ -1950, -1960, -1950, -1950, -1950}-    ,{   730,  -540,  -520,   730,  -520}-    ,{   410,  -860,   410,  -840,   410}-    ,{   730,  -540,  -520,   730,  -520}-    }-   ,{{   880,  -390,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   440,  -590,  -810,   440,  -810}-    ,{   880,  -390,  -370,   880,  -370}-    ,{ -1310, -1330, -1310, -1310, -1310}-    }-   }-  ,{{{   410,   410,   410,   410,     0}-    ,{     0,  -240,  -240,  -240,     0}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{   410,   410,   410,   410,  -370}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{     0,  -240,  -240,  -240,     0}-    ,{     0,  -240,  -240,  -240,     0}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{ -1410, -1650, -1410, -1650, -1650}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{   410,   410,   410,   410,  -520}-    ,{ -1710, -1950, -1710, -1950, -1950}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{   410,   410,   410,   410,  -840}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -810,  -810,  -810,  -810,  -810}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{ -1310, -1310, -1310, -1310, -1310}-    }-   }-  }- ,{{{{  1010,   410,   410,  1010,   410}-    ,{  1010,   -70,  -240,  1010,     0}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,   410,   410,   880,   410}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{  1010,   -70,  -240,  1010,     0}-    ,{  1010,   -70,  -240,  1010,     0}-    ,{   730,  -520,  -520,   730,  -520}-    ,{ -1180, -1420, -1180, -1250, -1180}-    ,{   730,  -520,  -520,   730,  -520}-    }-   ,{{   880,  -150,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{   730,   410,   410,   730,   410}-    ,{ -1280, -1520, -1280, -1340, -1280}-    ,{   730,  -520,  -520,   730,  -520}-    ,{   410,   410,   410,   410,   410}-    ,{   730,  -520,  -520,   730,  -520}-    }-   ,{{   880,  -370,  -370,   880,  -370}-    ,{   880,  -370,  -370,   880,  -370}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   880,  -370,  -370,   880,  -370}-    ,{ -1140, -1250, -1310, -1140, -1310}-    }-   }-  ,{{{   410,   230,   410,    40,   410}-    ,{   -30,   -70,  -240,   -30,  -240}-    ,{    40,  -550,  -370,    40,  -370}-    ,{   410,   230,   410,  -200,   410}-    ,{   -90,  -680,  -500,   -90,  -500}-    }-   ,{{   -30,   -70,  -240,   -30,  -240}-    ,{   -30,   -70,  -240,   -30,  -240}-    ,{  -350,  -700,  -520,  -350,  -520}-    ,{ -1250, -1600, -1420, -1250, -1420}-    ,{  -350,  -700,  -520,  -350,  -520}-    }-   ,{{    40,  -550,  -370,    40,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{    40,  -550,  -370,    40,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{   -90,  -680,  -500,   -90,  -500}-    }-   ,{{   410,   230,   410,  -350,   410}-    ,{ -1340, -1700, -1520, -1340, -1520}-    ,{  -350,  -700,  -520,  -350,  -520}-    ,{   410,   230,   410,  -670,   410}-    ,{  -350,  -700,  -520,  -350,  -520}-    }-   ,{{  -190,  -550,  -370,  -190,  -370}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{  -190,  -790,  -610,  -190,  -610}-    ,{  -200,  -550,  -370,  -200,  -370}-    ,{ -1140, -1250, -1310, -1140, -1310}-    }-   }-  ,{{{   410,   410,   410,   410,   410}-    ,{  -240,  -240,  -240,  -240,  -240}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{   410,   410,   410,   410,   410}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{  -240,  -240,  -240,  -240,  -240}-    ,{  -240,  -240,  -240,  -240,  -240}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{ -1180, -1420, -1180, -1420, -1180}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{   410,   410,   410,   410,   410}-    ,{ -1280, -1520, -1280, -1520, -1280}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{   410,   410,   410,   410,   410}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{ -1310, -1310, -1310, -1310, -1310}-    }-   }-  ,{{{  1010,  -150,   410,  1010,   410}-    ,{  1010,  -260,  -240,  1010,  -240}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,   410,   880,   410}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{  1010,  -260,  -240,  1010,  -240}-    ,{  1010,  -260,  -240,  1010,  -240}-    ,{   730,  -540,  -520,   730,  -520}-    ,{ -1420, -1440, -1420, -1420, -1420}-    ,{   730,  -540,  -520,   730,  -520}-    }-   ,{{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   880,  -150,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   750,  -280,  -500,   750,  -500}-    }-   ,{{   730,  -540,   410,   730,   410}-    ,{ -1520, -1530, -1520, -1520, -1520}-    ,{   730,  -540,  -520,   730,  -520}-    ,{   410,  -860,   410,  -840,   410}-    ,{   730,  -540,  -520,   730,  -520}-    }-   ,{{   880,  -380,  -370,   880,  -370}-    ,{   880,  -390,  -370,   880,  -370}-    ,{   640,  -380,  -610,   640,  -610}-    ,{   880,  -390,  -370,   880,  -370}-    ,{ -1310, -1330, -1310, -1310, -1310}-    }-   }-  ,{{{   410,   410,   410,   410,     0}-    ,{     0,  -240,  -240,  -240,     0}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{   410,   410,   410,   410,  -370}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{     0,  -240,  -240,  -240,     0}-    ,{     0,  -240,  -240,  -240,     0}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{ -1180, -1420, -1180, -1420, -1420}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -500,  -500,  -500,  -500,  -500}-    }-   ,{{   410,   410,   410,   410,  -520}-    ,{ -1280, -1520, -1280, -1520, -1520}-    ,{  -520,  -520,  -520,  -520,  -520}-    ,{   410,   410,   410,   410,  -840}-    ,{  -520,  -520,  -520,  -520,  -520}-    }-   ,{{  -370,  -370,  -370,  -370,  -370}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{  -610,  -610,  -610,  -610,  -610}-    ,{  -370,  -370,  -370,  -370,  -370}-    ,{ -1310, -1310, -1310, -1310, -1310}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   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INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{   800,   200,  -310,   800,  -310}-    ,{   740,     0,  -510,   740,  -410}-    ,{   800,    50,  -450,   800,  -450}-    ,{   740,   200,  -310,   740,  -310}-    ,{   690,   -50,  -560,   690,  -560}-    }-   ,{{   600,  -140,  -630,   600,  -410}-    ,{   600,  -140,  -650,   600,  -410}-    ,{   290,  -450,  -960,   290,  -960}-    ,{  -360,  -360,  -630,  -870,  -630}-    ,{   290,  -450,  -960,   290,  -960}-    }-   ,{{   740,     0,  -510,   740,  -510}-    ,{   740,     0,  -510,   740,  -510}-    ,{   740,     0,  -510,   740,  -510}-    ,{   740,     0,  -510,   740,  -510}-    ,{   690,   -50,  -560,   690,  -560}-    }-   ,{{   290,   200,  -310,   290,  -310}-    ,{  -640,  -640,  -910, -1150,  -910}-    ,{   290,  -450,  -960,   290,  -960}-    ,{   200,   200,  -310,  -310,  -310}-    ,{   290,  -450,  -960,   290,  -960}-    }-   ,{{   800,    50,  -450,   800,  -450}-    ,{   740,     0,  -510,   740,  -510}-    ,{   800,    50,  -450,   800,  -450}-    ,{   740,     0,  -510,   740,  -510}-    ,{  -550,  -550, -1300, -1300, -1300}-    }-   }-  ,{{{   200,   200,  -310,  -720,  -310}-    ,{     0,     0,  -510, -1020,  -510}-    ,{    50,    50,  -450,  -720,  -450}-    ,{   200,   200,  -310, -1020,  -310}-    ,{   -50,   -50,  -560,  -830,  -560}-    }-   ,{{  -140,  -140,  -650, -1160,  -650}-    ,{  -140,  -140,  -650, -1160,  -650}-    ,{  -450,  -450,  -960, -1470,  -960}-    ,{  -360,  -360,  -870, -1380,  -870}-    ,{  -450,  -450,  -960, -1470,  -960}-    }-   ,{{     0,     0,  -510,  -780,  -510}-    ,{     0,     0,  -510, -1020,  -510}-    ,{     0,     0,  -510,  -780,  -510}-    ,{     0,     0,  -510, -1020,  -510}-    ,{   -50,   -50,  -560,  -830,  -560}-    }-   ,{{   200,   200,  -310, -1470,  -310}-    ,{  -640,  -640, -1150, -1660, -1150}-    ,{  -450,  -450,  -960, -1470,  -960}-    ,{   200,   200,  -310, -2070,  -310}-    ,{  -450,  -450,  -960, -1470,  -960}-    }-   ,{{    50,    50,  -450,  -720,  -450}-    ,{     0,     0,  -510, -1020,  -510}-    ,{    50,    50,  -450,  -720,  -450}-    ,{     0,     0,  -510, -1020,  -510}-    ,{  -550,  -550, -1300, -1810, -1300}-    }-   }-  ,{{{  -310,  -310,  -310,  -310,  -310}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -450,  -450,  -450,  -450,  -450}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -560,  -560,  -560,  -560,  -560}-    }-   ,{{  -630,  -650,  -630,  -650,  -630}-    ,{  -650,  -650,  -650,  -650,  -650}-    ,{  -960,  -960,  -960,  -960,  -960}-    ,{  -630,  -870,  -630,  -870,  -630}-    ,{  -960,  -960,  -960,  -960,  -960}-    }-   ,{{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -560,  -560,  -560,  -560,  -560}-    }-   ,{{  -310,  -310,  -310,  -310,  -310}-    ,{  -910, -1150,  -910, -1150,  -910}-    ,{  -960,  -960,  -960,  -960,  -960}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -960,  -960,  -960,  -960,  -960}-    }-   ,{{  -450,  -450,  -450,  -450,  -450}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -450,  -450,  -450,  -450,  -450}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{ -1300, -1300, -1300, -1300, -1300}-    }-   }-  ,{{{   800,  -550,  -310,   800,  -310}-    ,{   740,  -850,  -510,   740,  -510}-    ,{   800,  -550,  -450,   800,  -450}-    ,{   740,  -850,  -310,   740,  -310}-    ,{   690,  -660,  -560,   690,  -560}-    }-   ,{{   600,  -990,  -650,   600,  -650}-    ,{   600,  -990,  -650,   600,  -650}-    ,{   290, -1300,  -960,   290,  -960}-    ,{  -870, -1210,  -870,  -870,  -870}-    ,{   290, -1300,  -960,   290,  -960}-    }-   ,{{   740,  -610,  -510,   740,  -510}-    ,{   740,  -850,  -510,   740,  -510}-    ,{   740,  -610,  -510,   740,  -510}-    ,{   740,  -850,  -510,   740,  -510}-    ,{   690,  -660,  -560,   690,  -560}-    }-   ,{{   290, -1300,  -310,   290,  -310}-    ,{ -1150, -1490, -1150, -1150, -1150}-    ,{   290, -1300,  -960,   290,  -960}-    ,{  -310, -1900,  -310, -1560,  -310}-    ,{   290, -1300,  -960,   290,  -960}-    }-   ,{{   800,  -550,  -450,   800,  -450}-    ,{   740,  -850,  -510,   740,  -510}-    ,{   800,  -550,  -450,   800,  -450}-    ,{   740,  -850,  -510,   740,  -510}-    ,{ -1300, -1640, -1300, -1300, -1300}-    }-   }-  ,{{{  -310,  -310,  -310,  -310,  -410}-    ,{  -410,  -510,  -510,  -510,  -410}-    ,{  -450,  -450,  -450,  -450,  -450}-    ,{  -310,  -310,  -310,  -310,  -510}-    ,{  -560,  -560,  -560,  -560,  -560}-    }-   ,{{  -410,  -650,  -630,  -650,  -410}-    ,{  -410,  -650,  -650,  -650,  -410}-    ,{  -960,  -960,  -960,  -960,  -960}-    ,{  -630,  -870,  -630,  -870,  -870}-    ,{  -960,  -960,  -960,  -960,  -960}-    }-   ,{{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -560,  -560,  -560,  -560,  -560}-    }-   ,{{  -310,  -310,  -310,  -310,  -960}-    ,{  -910, -1150,  -910, -1150, -1150}-    ,{  -960,  -960,  -960,  -960,  -960}-    ,{  -310,  -310,  -310,  -310, -1560}-    ,{  -960,  -960,  -960,  -960,  -960}-    }-   ,{{  -450,  -450,  -450,  -450,  -450}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{  -450,  -450,  -450,  -450,  -450}-    ,{  -510,  -510,  -510,  -510,  -510}-    ,{ -1300, -1300, -1300, -1300, -1300}-    }-   }-  }- ,{{{{   760,   200,  -310,   760,  -250}-    ,{   760,  -340,  -490,   760,  -250}-    ,{   310,  -430,  -940,   310,  -940}-    ,{   400,   200,  -310,   400,  -310}-    ,{   310,  -390,  -940,   310,  -940}-    }-   ,{{   760,  -430,  -490,   760,  -250}-    ,{   760,  -490,  -490,   760,  -250}-    ,{   310,  -430,  -940,   310,  -940}-    ,{ -1170, -1170, -1440, -1680, -1440}-    ,{   310,  -430,  -940,   310,  -940}-    }-   ,{{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{    90,  -650, -1160,    90, -1160}-    ,{   400,  -340,  -850,   400,  -850}-    ,{    90,  -650, -1160,    90, -1160}-    }-   ,{{   310,   200,  -310,   310,  -310}-    ,{  -690,  -690,  -960, -1200,  -960}-    ,{   310,  -430,  -940,   310,  -940}-    ,{   200,   200,  -310,  -310,  -310}-    ,{   310,  -430,  -940,   310,  -940}-    }-   ,{{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{  -220,  -960, -1470,  -220, -1470}-    ,{   400,  -340,  -850,   400,  -850}-    ,{  -390,  -390, -1140, -1140, -1140}-    }-   }-  ,{{{   200,   200,  -310, -1000,  -310}-    ,{  -340,  -340,  -490, -1000,  -490}-    ,{  -430,  -430,  -940, -1430,  -940}-    ,{   200,   200,  -310, -1360,  -310}-    ,{  -390,  -390,  -940, -1430,  -940}-    }-   ,{{  -430,  -430,  -490, -1000,  -490}-    ,{  -490, -2040,  -490, -1000,  -490}-    ,{  -430,  -430,  -940, -1450,  -940}-    ,{ -1170, -1170, -1680, -2190, -1680}-    ,{  -430,  -430,  -940, -1450,  -940}-    }-   ,{{  -340,  -340,  -850, -1360,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -650,  -650, -1160, -1430, -1160}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -650,  -650, -1160, -1430, -1160}-    }-   ,{{   200,   200,  -310, -1450,  -310}-    ,{  -690,  -690, -1200, -1710, -1200}-    ,{  -430,  -430,  -940, -1450,  -940}-    ,{   200,   200,  -310, -2070,  -310}-    ,{  -430,  -430,  -940, -1450,  -940}-    }-   ,{{  -340,  -340,  -850, -1360,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -960,  -960, -1470, -1740, -1470}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -390,  -390, -1140, -1650, -1140}-    }-   }-  ,{{{  -310,  -310,  -310,  -310,  -310}-    ,{  -490,  -490,  -490,  -490,  -490}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -490,  -490,  -490,  -490,  -490}-    ,{  -490,  -490,  -490,  -490,  -490}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{ -1440, -1680, -1440, -1680, -1440}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1160, -1160, -1160, -1160, -1160}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1160, -1160, -1160, -1160, -1160}-    }-   ,{{  -310,  -310,  -310,  -310,  -310}-    ,{  -960, -1200,  -960, -1200,  -960}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{  -310,  -310,  -310,  -310,  -310}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1470, -1470, -1470, -1470, -1470}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1140, -1140, -1140, -1140, -1140}-    }-   }-  ,{{{   760,  -830,  -310,   760,  -310}-    ,{   760,  -830,  -490,   760,  -490}-    ,{   310, -1260,  -940,   310,  -940}-    ,{   400, -1190,  -310,   400,  -310}-    ,{   310, -1260,  -940,   310,  -940}-    }-   ,{{   760,  -830,  -490,   760,  -490}-    ,{   760,  -830,  -490,   760,  -490}-    ,{   310, -1280,  -940,   310,  -940}-    ,{ -1680, -2020, -1680, -1680, -1680}-    ,{   310, -1280,  -940,   310,  -940}-    }-   ,{{   400, -1190,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{    90, -1260, -1160,    90, -1160}-    ,{   400, -1190,  -850,   400,  -850}-    ,{    90, -1260, -1160,    90, -1160}-    }-   ,{{   310, -1280,  -310,   310,  -310}-    ,{ -1200, -1540, -1200, -1200, -1200}-    ,{   310, -1280,  -940,   310,  -940}-    ,{  -310, -1900,  -310, -1560,  -310}-    ,{   310, -1280,  -940,   310,  -940}-    }-   ,{{   400, -1190,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{  -220, -1570, -1470,  -220, -1470}-    ,{   400, -1190,  -850,   400,  -850}-    ,{ -1140, -1480, -1140, -1140, -1140}-    }-   }-  ,{{{  -250,  -310,  -310,  -310,  -250}-    ,{  -250,  -490,  -490,  -490,  -250}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{  -310,  -310,  -310,  -310,  -850}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -250,  -490,  -490,  -490,  -250}-    ,{  -250,  -490,  -490,  -490,  -250}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{ -1440, -1680, -1440, -1680, -1680}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1160, -1160, -1160, -1160, -1160}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1160, -1160, -1160, -1160, -1160}-    }-   ,{{  -310,  -310,  -310,  -310,  -940}-    ,{  -960, -1200,  -960, -1200, -1200}-    ,{  -940,  -940,  -940,  -940,  -940}-    ,{  -310,  -310,  -310,  -310, -1560}-    ,{  -940,  -940,  -940,  -940,  -940}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1470, -1470, -1470, -1470, -1470}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{ -1140, -1140, -1140, -1140, -1140}-    }-   }-  }- ,{{{{   360,   360,  -150,  -150,  -150}-    ,{   -30,   -30,  -990,  -150,  -990}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{   360,   360,  -150,  -150,  -150}-    ,{  -150,  -650, -1400,  -150, -1400}-    }-   ,{{   -70,   -70, -1180,  -150, -1180}-    ,{   -70,   -70, -1580,  -330, -1340}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -910,  -910, -1180, -1420, -1180}-    ,{  -150,  -890, -1400,  -150, -1400}-    }-   ,{{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    }-   ,{{   360,   360,  -150,  -150,  -150}-    ,{   -30,   -30,  -990, -1230,  -990}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{   360,   360,  -150,  -150,  -150}-    ,{  -150,  -890, -1400,  -150, -1400}-    }-   ,{{  -150,  -650, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -150,  -890, -1400,  -150, -1400}-    ,{  -650,  -650, -1400, -1400, -1400}-    }-   }-  ,{{{   360,   360,  -150, -1670,  -150}-    ,{   -30,   -30, -1230, -1740, -1230}-    ,{  -890,  -890, -1400, -1670, -1400}-    ,{   360,   360,  -150, -1910,  -150}-    ,{  -650,  -650, -1400, -1670, -1400}-    }-   ,{{   -70,   -70, -1400, -1910, -1400}-    ,{   -70,   -70, -1580, -2090, -1580}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{  -910,  -910, -1420, -1930, -1420}-    ,{  -890,  -890, -1400, -1910, -1400}-    }-   ,{{  -890,  -890, -1400, -1670, -1400}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{  -890,  -890, -1400, -1670, -1400}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{  -890,  -890, -1400, -1670, -1400}-    }-   ,{{   360,   360,  -150, -1740,  -150}-    ,{   -30,   -30, -1230, -1740, -1230}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{   360,   360,  -150, -1910,  -150}-    ,{  -890,  -890, -1400, -1910, -1400}-    }-   ,{{  -650,  -650, -1400, -1670, -1400}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{  -890,  -890, -1400, -1670, -1400}-    ,{  -890,  -890, -1400, -1910, -1400}-    ,{  -650,  -650, -1400, -1910, -1400}-    }-   }-  ,{{{  -150,  -150,  -150,  -150,  -150}-    ,{  -990, -1230,  -990, -1230,  -990}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1180, -1400, -1180, -1400, -1180}-    ,{ -1580, -1580, -1580, -1580, -1580}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1180, -1420, -1180, -1420, -1180}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -150,  -150,  -150,  -150,  -150}-    ,{  -990, -1230,  -990, -1230,  -990}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150,  -150}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   }-  ,{{{  -150, -1500,  -150,  -150,  -150}-    ,{  -150, -1570, -1230,  -150, -1230}-    ,{  -150, -1500, -1400,  -150, -1400}-    ,{  -150, -1740,  -150,  -150,  -150}-    ,{  -150, -1500, -1400,  -150, -1400}-    }-   ,{{  -150, -1600, -1400,  -150, -1400}-    ,{  -330, -1600, -1580,  -330, -1580}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{ -1420, -3040, -1420, -1420, -1420}-    ,{  -150, -1740, -1400,  -150, -1400}-    }-   ,{{  -150, -1500, -1400,  -150, -1400}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{  -150, -1500, -1400,  -150, -1400}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{  -150, -1500, -1400,  -150, -1400}-    }-   ,{{  -150, -1570,  -150,  -150,  -150}-    ,{ -1230, -1570, -1230, -1230, -1230}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{  -150, -1740,  -150, -1400,  -150}-    ,{  -150, -1740, -1400,  -150, -1400}-    }-   ,{{  -150, -1500, -1400,  -150, -1400}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{  -150, -1500, -1400,  -150, -1400}-    ,{  -150, -1740, -1400,  -150, -1400}-    ,{ -1400, -1740, -1400, -1400, -1400}-    }-   }-  ,{{{  -150,  -150,  -150,  -150, -1230}-    ,{  -990, -1230,  -990, -1230, -1230}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1180, -1400, -1180, -1400, -1340}-    ,{ -1340, -1580, -1580, -1580, -1340}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1180, -1420, -1180, -1420, -1420}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{  -150,  -150,  -150,  -150, -1230}-    ,{  -990, -1230,  -990, -1230, -1230}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{  -150,  -150,  -150,  -150, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   ,{{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    ,{ -1400, -1400, -1400, -1400, -1400}-    }-   }-  }- ,{{{{   910,   910,   400,   910,   400}-    ,{   910,   170,  -340,   910,  -100}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   910,   910,   400,   400,   400}-    ,{   400,  -100,  -850,   400,  -850}-    }-   ,{{   910,   170,  -340,   910,  -100}-    ,{   910,   170,  -340,   910,  -100}-    ,{   400,  -340,  -850,   400,  -850}-    ,{  -680,  -680,  -950, -1190,  -950}-    ,{   400,  -340,  -850,   400,  -850}-    }-   ,{{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    }-   ,{{   910,   910,   400,   400,   400}-    ,{  -850,  -850, -1120, -1360, -1120}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   910,   910,   400,   400,   400}-    ,{   400,  -340,  -850,   400,  -850}-    }-   ,{{   400,  -100,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{   400,  -340,  -850,   400,  -850}-    ,{  -100,  -100,  -850,  -850,  -850}-    }-   }-  ,{{{   910,   910,   400,  -850,   400}-    ,{   170,   170,  -340,  -850,  -340}-    ,{  -340,  -340,  -850, -1120,  -850}-    ,{   910,   910,   400, -1360,   400}-    ,{  -100,  -100,  -850, -1120,  -850}-    }-   ,{{   170,   170,  -340,  -850,  -340}-    ,{   170,   170,  -340,  -850,  -340}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -680,  -680, -1190, -1700, -1190}-    ,{  -340,  -340,  -850, -1360,  -850}-    }-   ,{{  -340,  -340,  -850, -1120,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -340,  -340,  -850, -1120,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -340,  -340,  -850, -1120,  -850}-    }-   ,{{   910,   910,   400, -1360,   400}-    ,{  -850,  -850, -1360, -1870, -1360}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{   910,   910,   400, -1360,   400}-    ,{  -340,  -340,  -850, -1360,  -850}-    }-   ,{{  -100,  -100,  -850, -1120,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -340,  -340,  -850, -1120,  -850}-    ,{  -340,  -340,  -850, -1360,  -850}-    ,{  -100,  -100,  -850, -1360,  -850}-    }-   }-  ,{{{   400,   400,   400,   400,   400}-    ,{  -340,  -340,  -340,  -340,  -340}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{   400,   400,   400,   400,   400}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -340,  -340,  -340,  -340,  -340}-    ,{  -340,  -340,  -340,  -340,  -340}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -950, -1190,  -950, -1190,  -950}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{   400,   400,   400,   400,   400}-    ,{ -1120, -1360, -1120, -1360, -1120}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{   400,   400,   400,   400,   400}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   }-  ,{{{   910,  -680,   400,   910,   400}-    ,{   910,  -680,  -340,   910,  -340}-    ,{   400,  -950,  -850,   400,  -850}-    ,{   400, -1190,   400,   400,   400}-    ,{   400,  -950,  -850,   400,  -850}-    }-   ,{{   910,  -680,  -340,   910,  -340}-    ,{   910,  -680,  -340,   910,  -340}-    ,{   400, -1190,  -850,   400,  -850}-    ,{ -1190, -1530, -1190, -1190, -1190}-    ,{   400, -1190,  -850,   400,  -850}-    }-   ,{{   400,  -950,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{   400,  -950,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{   400,  -950,  -850,   400,  -850}-    }-   ,{{   400, -1190,   400,   400,   400}-    ,{ -1360, -1700, -1360, -1360, -1360}-    ,{   400, -1190,  -850,   400,  -850}-    ,{   400, -1190,   400,  -850,   400}-    ,{   400, -1190,  -850,   400,  -850}-    }-   ,{{   400,  -950,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{   400,  -950,  -850,   400,  -850}-    ,{   400, -1190,  -850,   400,  -850}-    ,{  -850, -1190,  -850,  -850,  -850}-    }-   }-  ,{{{   400,   400,   400,   400,  -100}-    ,{  -100,  -340,  -340,  -340,  -100}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{   400,   400,   400,   400,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -100,  -340,  -340,  -340,  -100}-    ,{  -100,  -340,  -340,  -340,  -100}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -950, -1190,  -950, -1190, -1190}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{   400,   400,   400,   400,  -850}-    ,{ -1120, -1360, -1120, -1360, -1360}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{   400,   400,   400,   400,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   ,{{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    ,{  -850,  -850,  -850,  -850,  -850}-    }-   }-  }- ,{{{{  1490,  1280,   780,  1490,   780}-    ,{  1490,   750,   240,  1490,   480}-    ,{  1200,   450,   -50,  1200,   -50}-    ,{  1280,  1280,   780,  1200,   780}-    ,{  1200,   450,   -50,  1200,   -50}-    }-   ,{{  1490,   750,   240,  1490,   480}-    ,{  1490,   750,   240,  1490,   480}-    ,{  1190,   440,   -60,  1190,   -60}-    ,{  -630,  -630,  -900, -1140,  -900}-    ,{  1190,   440,   -60,  1190,   -60}-    }-   ,{{  1200,   460,   -50,  1200,   -50}-    ,{  1200,   460,   -50,  1200,   -50}-    ,{  1200,   450,   -50,  1200,   -50}-    ,{  1200,   460,   -50,  1200,   -50}-    ,{  1200,   450,   -50,  1200,   -50}-    }-   ,{{  1280,  1280,   780,  1190,   780}-    ,{  -450,  -450,  -720,  -960,  -720}-    ,{  1190,   440,   -60,  1190,   -60}-    ,{  1280,  1280,   780,   780,   780}-    ,{  1190,   440,   -60,  1190,   -60}-    }-   ,{{  1200,   460,   -50,  1200,   -50}-    ,{  1200,   460,   -50,  1200,   -50}-    ,{  1200,   450,   -50,  1200,   -50}-    ,{  1200,   460,   -50,  1200,   -50}-    ,{  -280,  -280, -1030, -1030, -1030}-    }-   }-  ,{{{  1280,  1280,   780,  -260,   780}-    ,{   750,   750,   240,  -260,   240}-    ,{   450,   450,   -50,  -320,   -50}-    ,{  1280,  1280,   780,  -560,   780}-    ,{   450,   450,   -50,  -320,   -50}-    }-   ,{{   750,   750,   240,  -260,   240}-    ,{   750,   750,   240,  -260,   240}-    ,{   440,   440,   -60,  -570,   -60}-    ,{  -630,  -630, -1140, -1650, -1140}-    ,{   440,   440,   -60,  -570,   -60}-    }-   ,{{   460,   460,   -50,  -320,   -50}-    ,{   460,   460,   -50,  -560,   -50}-    ,{   450,   450,   -50,  -320,   -50}-    ,{   460,   460,   -50,  -560,   -50}-    ,{   450,   450,   -50,  -320,   -50}-    }-   ,{{  1280,  1280,   780,  -570,   780}-    ,{  -450,  -450,  -960, -1470,  -960}-    ,{   440,   440,   -60,  -570,   -60}-    ,{  1280,  1280,   780,  -980,   780}-    ,{   440,   440,   -60,  -570,   -60}-    }-   ,{{   460,   460,   -50,  -320,   -50}-    ,{   460,   460,   -50,  -560,   -50}-    ,{   450,   450,   -50,  -320,   -50}-    ,{   460,   460,   -50,  -560,   -50}-    ,{  -280,  -280, -1030, -1540, -1030}-    }-   }-  ,{{{   780,   780,   780,   780,   780}-    ,{   240,   240,   240,   240,   240}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   780,   780,   780,   780,   780}-    ,{   -50,   -50,   -50,   -50,   -50}-    }-   ,{{   240,   240,   240,   240,   240}-    ,{   240,   240,   240,   240,   240}-    ,{   -60,   -60,   -60,   -60,   -60}-    ,{  -900, -1140,  -900, -1140,  -900}-    ,{   -60,   -60,   -60,   -60,   -60}-    }-   ,{{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    }-   ,{{   780,   780,   780,   780,   780}-    ,{  -720,  -960,  -720,  -960,  -720}-    ,{   -60,   -60,   -60,   -60,   -60}-    ,{   780,   780,   780,   780,   780}-    ,{   -60,   -60,   -60,   -60,   -60}-    }-   ,{{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{ -1030, -1030, -1030, -1030, -1030}-    }-   }-  ,{{{  1490,   -90,   780,  1490,   780}-    ,{  1490,   -90,   240,  1490,   240}-    ,{  1200,  -150,   -50,  1200,   -50}-    ,{  1200,  -390,   780,  1200,   780}-    ,{  1200,  -150,   -50,  1200,   -50}-    }-   ,{{  1490,   -90,   240,  1490,   240}-    ,{  1490,   -90,   240,  1490,   240}-    ,{  1190,  -400,   -60,  1190,   -60}-    ,{ -1140, -1480, -1140, -1140, -1140}-    ,{  1190,  -400,   -60,  1190,   -60}-    }-   ,{{  1200,  -150,   -50,  1200,   -50}-    ,{  1200,  -390,   -50,  1200,   -50}-    ,{  1200,  -150,   -50,  1200,   -50}-    ,{  1200,  -390,   -50,  1200,   -50}-    ,{  1200,  -150,   -50,  1200,   -50}-    }-   ,{{  1190,  -400,   780,  1190,   780}-    ,{  -960, -1300,  -960,  -960,  -960}-    ,{  1190,  -400,   -60,  1190,   -60}-    ,{   780,  -810,   780,  -470,   780}-    ,{  1190,  -400,   -60,  1190,   -60}-    }-   ,{{  1200,  -150,   -50,  1200,   -50}-    ,{  1200,  -390,   -50,  1200,   -50}-    ,{  1200,  -150,   -50,  1200,   -50}-    ,{  1200,  -390,   -50,  1200,   -50}-    ,{ -1030, -1370, -1030, -1030, -1030}-    }-   }-  ,{{{   780,   780,   780,   780,   480}-    ,{   480,   240,   240,   240,   480}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   780,   780,   780,   780,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    }-   ,{{   480,   240,   240,   240,   480}-    ,{   480,   240,   240,   240,   480}-    ,{   -60,   -60,   -60,   -60,   -60}-    ,{  -900, -1140,  -900, -1140, -1140}-    ,{   -60,   -60,   -60,   -60,   -60}-    }-   ,{{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    }-   ,{{   780,   780,   780,   780,   -60}-    ,{  -720,  -960,  -720,  -960,  -960}-    ,{   -60,   -60,   -60,   -60,   -60}-    ,{   780,   780,   780,   780,  -470}-    ,{   -60,   -60,   -60,   -60,   -60}-    }-   ,{{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{ -1030, -1030, -1030, -1030, -1030}-    }-   }-  }- ,{{{{  1560,  1470,   960,  1560,   960}-    ,{  1560,   820,   310,  1560,   550}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1470,  1470,   960,  1430,   960}-    ,{  1300,   560,    50,  1300,    50}-    }-   ,{{  1560,   820,   310,  1560,   550}-    ,{  1560,   820,   310,  1560,   550}-    ,{  1280,   540,    30,  1280,    30}-    ,{  -580,  -580,  -850, -1090,  -850}-    ,{  1280,   540,    30,  1280,    30}-    }-   ,{{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1300,   560,    50,  1300,    50}-    }-   ,{{  1470,  1470,   960,  1280,   960}-    ,{  -880,  -880, -1150, -1390, -1150}-    ,{  1280,   540,    30,  1280,    30}-    ,{  1470,  1470,   960,   960,   960}-    ,{  1280,   540,    30,  1280,    30}-    }-   ,{{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{   990,   250,  -260,   990,  -260}-    ,{  1430,   690,   180,  1430,   180}-    ,{   -10,   -10,  -760,  -760,  -760}-    }-   }-  ,{{{  1470,  1470,   960,   -90,   960}-    ,{   820,   820,   310,  -200,   310}-    ,{   690,   690,   180,   -90,   180}-    ,{  1470,  1470,   960,  -330,   960}-    ,{   560,   560,    50,  -220,    50}-    }-   ,{{   820,   820,   310,  -200,   310}-    ,{   820,   820,   310,  -200,   310}-    ,{   540,   540,    30,  -480,    30}-    ,{  -580,  -580, -1090, -1600, -1090}-    ,{   540,   540,    30,  -480,    30}-    }-   ,{{   690,   690,   180,   -90,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   690,   690,   180,   -90,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   560,   560,    50,  -220,    50}-    }-   ,{{  1470,  1470,   960,  -480,   960}-    ,{  -880,  -880, -1390, -1900, -1390}-    ,{   540,   540,    30,  -480,    30}-    ,{  1470,  1470,   960,  -800,   960}-    ,{   540,   540,    30,  -480,    30}-    }-   ,{{   690,   690,   180,  -330,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   250,   250,  -260,  -530,  -260}-    ,{   690,   690,   180,  -330,   180}-    ,{   -10,   -10,  -760, -1270,  -760}-    }-   }-  ,{{{   960,   960,   960,   960,   960}-    ,{   310,   310,   310,   310,   310}-    ,{   180,   180,   180,   180,   180}-    ,{   960,   960,   960,   960,   960}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   310,   310,   310,   310,   310}-    ,{   310,   310,   310,   310,   310}-    ,{    30,    30,    30,    30,    30}-    ,{  -850, -1090,  -850, -1090,  -850}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   960,   960,   960,   960,   960}-    ,{ -1150, -1390, -1150, -1390, -1150}-    ,{    30,    30,    30,    30,    30}-    ,{   960,   960,   960,   960,   960}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{  -260,  -260,  -260,  -260,  -260}-    ,{   180,   180,   180,   180,   180}-    ,{  -760,  -760,  -760,  -760,  -760}-    }-   }-  ,{{{  1560,    80,   960,  1560,   960}-    ,{  1560,   -30,   310,  1560,   310}-    ,{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   960,  1430,   960}-    ,{  1300,   -50,    50,  1300,    50}-    }-   ,{{  1560,   -30,   310,  1560,   310}-    ,{  1560,   -30,   310,  1560,   310}-    ,{  1280,  -310,    30,  1280,    30}-    ,{ -1090, -1430, -1090, -1090, -1090}-    ,{  1280,  -310,    30,  1280,    30}-    }-   ,{{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  1300,   -50,    50,  1300,    50}-    }-   ,{{  1280,  -310,   960,  1280,   960}-    ,{ -1390, -1730, -1390, -1390, -1390}-    ,{  1280,  -310,    30,  1280,    30}-    ,{   960,  -630,   960,  -290,   960}-    ,{  1280,  -310,    30,  1280,    30}-    }-   ,{{  1430,  -160,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{   990,  -360,  -260,   990,  -260}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  -760, -1100,  -760,  -760,  -760}-    }-   }-  ,{{{   960,   960,   960,   960,   550}-    ,{   550,   310,   310,   310,   550}-    ,{   180,   180,   180,   180,   180}-    ,{   960,   960,   960,   960,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   550,   310,   310,   310,   550}-    ,{   550,   310,   310,   310,   550}-    ,{    30,    30,    30,    30,    30}-    ,{  -850, -1090,  -850, -1090, -1090}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   960,   960,   960,   960,    30}-    ,{ -1150, -1390, -1150, -1390, -1390}-    ,{    30,    30,    30,    30,    30}-    ,{   960,   960,   960,   960,  -290}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{  -260,  -260,  -260,  -260,  -260}-    ,{   180,   180,   180,   180,   180}-    ,{  -760,  -760,  -760,  -760,  -760}-    }-   }-  }- ,{{{{  1560,  1470,   960,  1560,   960}-    ,{  1560,   820,   310,  1560,   550}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1470,  1470,   960,  1430,   960}-    ,{  1300,   560,    50,  1300,    50}-    }-   ,{{  1560,   820,   310,  1560,   550}-    ,{  1560,   820,   310,  1560,   550}-    ,{  1280,   540,    30,  1280,    30}-    ,{  -360,  -360,  -630,  -870,  -630}-    ,{  1280,   540,    30,  1280,    30}-    }-   ,{{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1300,   560,    50,  1300,    50}-    }-   ,{{  1470,  1470,   960,  1280,   960}-    ,{   -30,   -30,  -720,  -960,  -720}-    ,{  1280,   540,    30,  1280,    30}-    ,{  1470,  1470,   960,   960,   960}-    ,{  1280,   540,    30,  1280,    30}-    }-   ,{{  1430,   690,   180,  1430,   180}-    ,{  1430,   690,   180,  1430,   180}-    ,{  1200,   450,   -50,  1200,   -50}-    ,{  1430,   690,   180,  1430,   180}-    ,{   -10,   -10,  -760,  -760,  -760}-    }-   }-  ,{{{  1470,  1470,   960,   -90,   960}-    ,{   820,   820,   310,  -200,   310}-    ,{   690,   690,   180,   -90,   180}-    ,{  1470,  1470,   960,  -330,   960}-    ,{   560,   560,    50,  -220,    50}-    }-   ,{{   820,   820,   310,  -200,   310}-    ,{   820,   820,   310,  -200,   310}-    ,{   540,   540,    30,  -480,    30}-    ,{  -360,  -360,  -870, -1380,  -870}-    ,{   540,   540,    30,  -480,    30}-    }-   ,{{   690,   690,   180,   -90,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   690,   690,   180,   -90,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   560,   560,    50,  -220,    50}-    }-   ,{{  1470,  1470,   960,  -480,   960}-    ,{   -30,   -30,  -960, -1470,  -960}-    ,{   540,   540,    30,  -480,    30}-    ,{  1470,  1470,   960,  -800,   960}-    ,{   540,   540,    30,  -480,    30}-    }-   ,{{   690,   690,   180,  -320,   180}-    ,{   690,   690,   180,  -330,   180}-    ,{   450,   450,   -50,  -320,   -50}-    ,{   690,   690,   180,  -330,   180}-    ,{   -10,   -10,  -760, -1270,  -760}-    }-   }-  ,{{{   960,   960,   960,   960,   960}-    ,{   310,   310,   310,   310,   310}-    ,{   180,   180,   180,   180,   180}-    ,{   960,   960,   960,   960,   960}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   310,   310,   310,   310,   310}-    ,{   310,   310,   310,   310,   310}-    ,{    30,    30,    30,    30,    30}-    ,{  -630,  -870,  -630,  -870,  -630}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   960,   960,   960,   960,   960}-    ,{  -720,  -960,  -720,  -960,  -720}-    ,{    30,    30,    30,    30,    30}-    ,{   960,   960,   960,   960,   960}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   180,   180,   180,   180,   180}-    ,{  -760,  -760,  -760,  -760,  -760}-    }-   }-  ,{{{  1560,    80,   960,  1560,   960}-    ,{  1560,   -30,   310,  1560,   310}-    ,{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   960,  1430,   960}-    ,{  1300,   -50,    50,  1300,    50}-    }-   ,{{  1560,   -30,   310,  1560,   310}-    ,{  1560,   -30,   310,  1560,   310}-    ,{  1280,  -310,    30,  1280,    30}-    ,{  -870, -1210,  -870,  -870,  -870}-    ,{  1280,  -310,    30,  1280,    30}-    }-   ,{{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  1430,    80,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  1300,   -50,    50,  1300,    50}-    }-   ,{{  1280,  -310,   960,  1280,   960}-    ,{  -960, -1300,  -960,  -960,  -960}-    ,{  1280,  -310,    30,  1280,    30}-    ,{   960,  -630,   960,  -290,   960}-    ,{  1280,  -310,    30,  1280,    30}-    }-   ,{{  1430,  -150,   180,  1430,   180}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  1200,  -150,   -50,  1200,   -50}-    ,{  1430,  -160,   180,  1430,   180}-    ,{  -760, -1100,  -760,  -760,  -760}-    }-   }-  ,{{{   960,   960,   960,   960,   550}-    ,{   550,   310,   310,   310,   550}-    ,{   180,   180,   180,   180,   180}-    ,{   960,   960,   960,   960,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   550,   310,   310,   310,   550}-    ,{   550,   310,   310,   310,   550}-    ,{    30,    30,    30,    30,    30}-    ,{  -630,  -870,  -630,  -870,  -870}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{    50,    50,    50,    50,    50}-    }-   ,{{   960,   960,   960,   960,    30}-    ,{  -720,  -960,  -720,  -960,  -960}-    ,{    30,    30,    30,    30,    30}-    ,{   960,   960,   960,   960,  -290}-    ,{    30,    30,    30,    30,    30}-    }-   ,{{   180,   180,   180,   180,   180}-    ,{   180,   180,   180,   180,   180}-    ,{   -50,   -50,   -50,   -50,   -50}-    ,{   180,   180,   180,   180,   180}-    ,{  -760,  -760,  -760,  -760,  -760}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{  1170,   780,   490,  1170,   490}-    ,{  1120,   580,   290,  1120,   290}-    ,{  1170,   640,   340,  1170,   340}-    ,{  1120,   780,   490,  1120,   490}-    ,{  1060,   530,   230,  1060,   230}-    }-   ,{{   970,   440,   170,   970,   170}-    ,{   970,   440,   140,   970,   140}-    ,{   660,   130,  -160,   660,  -160}-    ,{   220,   220,   170,   -80,   170}-    ,{   660,   130,  -160,   660,  -160}-    }-   ,{{  1120,   580,   290,  1120,   290}-    ,{  1120,   580,   290,  1120,   290}-    ,{  1110,   580,   280,  1110,   280}-    ,{  1120,   580,   290,  1120,   290}-    ,{  1060,   530,   230,  1060,   230}-    }-   ,{{   780,   780,   490,   660,   490}-    ,{   -60,   -60,  -120,  -370,  -120}-    ,{   660,   130,  -160,   660,  -160}-    ,{   780,   780,   490,   470,   490}-    ,{   660,   130,  -160,   660,  -160}-    }-   ,{{  1170,   640,   340,  1170,   340}-    ,{  1120,   580,   290,  1120,   290}-    ,{  1170,   640,   340,  1170,   340}-    ,{  1120,   580,   290,  1120,   290}-    ,{    40,    40,  -500,  -510,  -500}-    }-   }-  ,{{{   780,   780,   490,  -330,   490}-    ,{   580,   580,   290,  -620,   290}-    ,{   640,   640,   340,  -330,   340}-    ,{   780,   780,   490,  -620,   490}-    ,{   530,   530,   230,  -440,   230}-    }-   ,{{   440,   440,   140,  -770,   140}-    ,{   440,   440,   140,  -770,   140}-    ,{   130,   130,  -160, -1080,  -160}-    ,{   220,   220,   -70,  -980,   -70}-    ,{   130,   130,  -160, -1080,  -160}-    }-   ,{{   580,   580,   290,  -390,   290}-    ,{   580,   580,   290,  -620,   290}-    ,{   580,   580,   280,  -390,   280}-    ,{   580,   580,   290,  -620,   290}-    ,{   530,   530,   230,  -440,   230}-    }-   ,{{   780,   780,   490, -1080,   490}-    ,{   -60,   -60,  -350, -1270,  -350}-    ,{   130,   130,  -160, -1080,  -160}-    ,{   780,   780,   490, -1680,   490}-    ,{   130,   130,  -160, -1080,  -160}-    }-   ,{{   640,   640,   340,  -330,   340}-    ,{   580,   580,   290,  -620,   290}-    ,{   640,   640,   340,  -330,   340}-    ,{   580,   580,   290,  -620,   290}-    ,{    40,    40,  -500, -1410,  -500}-    }-   }-  ,{{{   480,   470,   480,   470,   480}-    ,{   280,   270,   280,   270,   280}-    ,{   340,   330,   340,   330,   340}-    ,{   480,   470,   480,   470,   480}-    ,{   230,   220,   230,   220,   230}-    }-   ,{{   170,   130,   170,   130,   170}-    ,{   140,   130,   140,   130,   140}-    ,{  -170,  -180,  -170,  -180,  -170}-    ,{   170,   -80,   170,   -80,   170}-    ,{  -170,  -180,  -170,  -180,  -170}-    }-   ,{{   280,   270,   280,   270,   280}-    ,{   280,   270,   280,   270,   280}-    ,{   280,   270,   280,   270,   280}-    ,{   280,   270,   280,   270,   280}-    ,{   230,   220,   230,   220,   230}-    }-   ,{{   480,   470,   480,   470,   480}-    ,{  -120,  -370,  -120,  -370,  -120}-    ,{  -170,  -180,  -170,  -180,  -170}-    ,{   480,   470,   480,   470,   480}-    ,{  -170,  -180,  -170,  -180,  -170}-    }-   ,{{   340,   330,   340,   330,   340}-    ,{   280,   270,   280,   270,   280}-    ,{   340,   330,   340,   330,   340}-    ,{   280,   270,   280,   270,   280}-    ,{  -500,  -510,  -500,  -510,  -500}-    }-   }-  ,{{{  1170,  -510,   490,  1170,   490}-    ,{  1120,  -800,   290,  1120,   290}-    ,{  1170,  -510,   340,  1170,   340}-    ,{  1120,  -800,   490,  1120,   490}-    ,{  1060,  -620,   230,  1060,   230}-    }-   ,{{   970,  -950,   140,   970,   140}-    ,{   970,  -950,   140,   970,   140}-    ,{   660, -1260,  -160,   660,  -160}-    ,{   -70, -1160,   -70,  -490,   -70}-    ,{   660, -1260,  -160,   660,  -160}-    }-   ,{{  1120,  -570,   290,  1120,   290}-    ,{  1120,  -800,   290,  1120,   290}-    ,{  1110,  -570,   280,  1110,   280}-    ,{  1120,  -800,   290,  1120,   290}-    ,{  1060,  -620,   230,  1060,   230}-    }-   ,{{   660, -1260,   490,   660,   490}-    ,{  -350, -1450,  -350,  -780,  -350}-    ,{   660, -1260,  -160,   660,  -160}-    ,{   490, -1860,   490, -1190,   490}-    ,{   660, -1260,  -160,   660,  -160}-    }-   ,{{  1170,  -510,   340,  1170,   340}-    ,{  1120,  -800,   290,  1120,   290}-    ,{  1170,  -510,   340,  1170,   340}-    ,{  1120,  -800,   290,  1120,   290}-    ,{  -500, -1590,  -500,  -920,  -500}-    }-   }-  ,{{{   480,   470,   480,   470,  -600}-    ,{   280,   270,   280,   270,  -600}-    ,{   340,   330,   340,   330,  -640}-    ,{   480,   470,   480,   470,  -690}-    ,{   230,   220,   230,   220,  -750}-    }-   ,{{   170,   130,   170,   130,  -600}-    ,{   140,   130,   140,   130,  -600}-    ,{  -170,  -180,  -170,  -180, -1150}-    ,{   170,   -80,   170,   -80, -1050}-    ,{  -170,  -180,  -170,  -180, -1150}-    }-   ,{{   280,   270,   280,   270,  -690}-    ,{   280,   270,   280,   270,  -690}-    ,{   280,   270,   280,   270,  -700}-    ,{   280,   270,   280,   270,  -690}-    ,{   230,   220,   230,   220,  -750}-    }-   ,{{   480,   470,   480,   470, -1150}-    ,{  -120,  -370,  -120,  -370, -1340}-    ,{  -170,  -180,  -170,  -180, -1150}-    ,{   480,   470,   480,   470, -1750}-    ,{  -170,  -180,  -170,  -180, -1150}-    }-   ,{{   340,   330,   340,   330,  -640}-    ,{   280,   270,   280,   270,  -690}-    ,{   340,   330,   340,   330,  -640}-    ,{   280,   270,   280,   270,  -690}-    ,{  -500,  -510,  -500,  -510, -1480}-    }-   }-  }- ,{{{{  1140,   780,   490,  1140,   490}-    ,{  1140,   600,   310,  1140,   310}-    ,{   690,   150,  -140,   690,  -140}-    ,{   780,   780,   490,   770,   490}-    ,{   690,   190,  -140,   690,  -140}-    }-   ,{{  1140,   600,   310,  1140,   310}-    ,{  1140,   600,   310,  1140,   310}-    ,{   690,   150,  -140,   690,  -140}-    ,{  -580,  -580,  -640,  -890,  -640}-    ,{   690,   150,  -140,   690,  -140}-    }-   ,{{   770,   240,   -50,   770,   -50}-    ,{   770,   240,   -50,   770,   -50}-    ,{   470,   -60,  -360,   470,  -360}-    ,{   770,   240,   -50,   770,   -50}-    ,{   470,   -60,  -360,   470,  -360}-    }-   ,{{   780,   780,   490,   690,   490}-    ,{  -110,  -110,  -170,  -420,  -170}-    ,{   690,   150,  -140,   690,  -140}-    ,{   780,   780,   490,   470,   490}-    ,{   690,   150,  -140,   690,  -140}-    }-   ,{{   770,   240,   -50,   770,   -50}-    ,{   770,   240,   -50,   770,   -50}-    ,{   160,  -370,  -670,   160,  -670}-    ,{   770,   240,   -50,   770,   -50}-    ,{   190,   190,  -340,  -360,  -340}-    }-   }-  ,{{{   780,   780,   490,  -600,   490}-    ,{   600,   600,   310,  -600,   310}-    ,{   150,   150,  -140, -1030,  -140}-    ,{   780,   780,   490,  -970,   490}-    ,{   190,   190,  -140, -1030,  -140}-    }-   ,{{   600,   600,   310,  -600,   310}-    ,{   600,   600,   310,  -600,   310}-    ,{   150,   150,  -140, -1050,  -140}-    ,{  -580,  -580,  -880, -1790,  -880}-    ,{   150,   150,  -140, -1050,  -140}-    }-   ,{{   240,   240,   -50,  -970,   -50}-    ,{   240,   240,   -50,  -970,   -50}-    ,{   -60,   -60,  -360, -1030,  -360}-    ,{   240,   240,   -50,  -970,   -50}-    ,{   -60,   -60,  -360, -1030,  -360}-    }-   ,{{   780,   780,   490, -1050,   490}-    ,{  -110,  -110,  -400, -1320,  -400}-    ,{   150,   150,  -140, -1050,  -140}-    ,{   780,   780,   490, -1680,   490}-    ,{   150,   150,  -140, -1050,  -140}-    }-   ,{{   240,   240,   -50,  -970,   -50}-    ,{   240,   240,   -50,  -970,   -50}-    ,{  -370,  -370,  -670, -1340,  -670}-    ,{   240,   240,   -50,  -970,   -50}-    ,{   190,   190,  -340, -1260,  -340}-    }-   }-  ,{{{   480,   470,   480,   470,   480}-    ,{   300,   290,   300,   290,   300}-    ,{  -140,  -150,  -140,  -150,  -140}-    ,{   480,   470,   480,   470,   480}-    ,{  -140,  -150,  -140,  -150,  -140}-    }-   ,{{   300,   290,   300,   290,   300}-    ,{   300,   290,   300,   290,   300}-    ,{  -140,  -150,  -140,  -150,  -140}-    ,{  -640,  -890,  -640,  -890,  -640}-    ,{  -140,  -150,  -140,  -150,  -140}-    }-   ,{{   -60,   -70,   -60,   -70,   -60}-    ,{   -60,   -70,   -60,   -70,   -60}-    ,{  -360,  -370,  -360,  -370,  -360}-    ,{   -60,   -70,   -60,   -70,   -60}-    ,{  -360,  -370,  -360,  -370,  -360}-    }-   ,{{   480,   470,   480,   470,   480}-    ,{  -170,  -420,  -170,  -420,  -170}-    ,{  -140,  -150,  -140,  -150,  -140}-    ,{   480,   470,   480,   470,   480}-    ,{  -140,  -150,  -140,  -150,  -140}-    }-   ,{{   -60,   -70,   -60,   -70,   -60}-    ,{   -60,   -70,   -60,   -70,   -60}-    ,{  -670,  -680,  -670,  -680,  -670}-    ,{   -60,   -70,   -60,   -70,   -60}-    ,{  -350,  -360,  -350,  -360,  -350}-    }-   }-  ,{{{  1140,  -780,   490,  1140,   490}-    ,{  1140,  -780,   310,  1140,   310}-    ,{   690, -1210,  -140,   690,  -140}-    ,{   770, -1150,   490,   770,   490}-    ,{   690, -1210,  -140,   690,  -140}-    }-   ,{{  1140,  -780,   310,  1140,   310}-    ,{  1140,  -780,   310,  1140,   310}-    ,{   690, -1230,  -140,   690,  -140}-    ,{  -880, -1970,  -880, -1300,  -880}-    ,{   690, -1230,  -140,   690,  -140}-    }-   ,{{   770, -1150,   -50,   770,   -50}-    ,{   770, -1150,   -50,   770,   -50}-    ,{   470, -1210,  -360,   470,  -360}-    ,{   770, -1150,   -50,   770,   -50}-    ,{   470, -1210,  -360,   470,  -360}-    }-   ,{{   690, -1230,   490,   690,   490}-    ,{  -400, -1500,  -400,  -830,  -400}-    ,{   690, -1230,  -140,   690,  -140}-    ,{   490, -1860,   490, -1190,   490}-    ,{   690, -1230,  -140,   690,  -140}-    }-   ,{{   770, -1150,   -50,   770,   -50}-    ,{   770, -1150,   -50,   770,   -50}-    ,{   160, -1520,  -670,   160,  -670}-    ,{   770, -1150,   -50,   770,   -50}-    ,{  -340, -1440,  -340,  -770,  -340}-    }-   }-  ,{{{   480,   470,   480,   470,  -430}-    ,{   300,   290,   300,   290,  -430}-    ,{  -140,  -150,  -140,  -150, -1120}-    ,{   480,   470,   480,   470, -1040}-    ,{  -140,  -150,  -140,  -150, -1120}-    }-   ,{{   300,   290,   300,   290,  -430}-    ,{   300,   290,   300,   290,  -430}-    ,{  -140,  -150,  -140,  -150, -1120}-    ,{  -640,  -890,  -640,  -890, -1860}-    ,{  -140,  -150,  -140,  -150, -1120}-    }-   ,{{   -60,   -70,   -60,   -70, -1040}-    ,{   -60,   -70,   -60,   -70, -1040}-    ,{  -360,  -370,  -360,  -370, -1340}-    ,{   -60,   -70,   -60,   -70, -1040}-    ,{  -360,  -370,  -360,  -370, -1340}-    }-   ,{{   480,   470,   480,   470, -1120}-    ,{  -170,  -420,  -170,  -420, -1390}-    ,{  -140,  -150,  -140,  -150, -1120}-    ,{   480,   470,   480,   470, -1750}-    ,{  -140,  -150,  -140,  -150, -1120}-    }-   ,{{   -60,   -70,   -60,   -70, -1040}-    ,{   -60,   -70,   -60,   -70, -1040}-    ,{  -670,  -680,  -670,  -680, -1650}-    ,{   -60,   -70,   -60,   -70, -1040}-    ,{  -350,  -360,  -350,  -360, -1330}-    }-   }-  }- ,{{{{   940,   940,   650,   630,   650}-    ,{   220,  -130,  -190,   220,  -190}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   940,   940,   650,   630,   650}-    ,{   220,   -70,  -600,   220,  -600}-    }-   ,{{   220,  -310,  -380,   220,  -380}-    ,{    40,  -490,  -780,    40,  -780}-    ,{   220,  -310,  -600,   220,  -600}-    ,{  -320,  -320,  -380,  -630,  -380}-    ,{   220,  -310,  -600,   220,  -600}-    }-   ,{{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    }-   ,{{   940,   940,   650,   630,   650}-    ,{  -130,  -130,  -190,  -440,  -190}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   940,   940,   650,   630,   650}-    ,{   220,  -310,  -600,   220,  -600}-    }-   ,{{   220,   -70,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   220,  -310,  -600,   220,  -600}-    ,{   -70,   -70,  -600,  -620,  -600}-    }-   }-  ,{{{   940,   940,   650, -1280,   650}-    ,{  -130,  -130,  -430, -1340,  -430}-    ,{  -310,  -310,  -600, -1280,  -600}-    ,{   940,   940,   650, -1520,   650}-    ,{   -70,   -70,  -600, -1280,  -600}-    }-   ,{{  -310,  -310,  -600, -1520,  -600}-    ,{  -490,  -490,  -780, -1700,  -780}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{  -320,  -320,  -620, -1530,  -620}-    ,{  -310,  -310,  -600, -1520,  -600}-    }-   ,{{  -310,  -310,  -600, -1280,  -600}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{  -310,  -310,  -600, -1280,  -600}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{  -310,  -310,  -600, -1280,  -600}-    }-   ,{{   940,   940,   650, -1340,   650}-    ,{  -130,  -130,  -430, -1340,  -430}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{   940,   940,   650, -1520,   650}-    ,{  -310,  -310,  -600, -1520,  -600}-    }-   ,{{   -70,   -70,  -600, -1280,  -600}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{  -310,  -310,  -600, -1280,  -600}-    ,{  -310,  -310,  -600, -1520,  -600}-    ,{   -70,   -70,  -600, -1520,  -600}-    }-   }-  ,{{{   640,   630,   640,   630,   640}-    ,{  -190,  -440,  -190,  -440,  -190}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{   640,   630,   640,   630,   640}-    ,{  -610,  -620,  -610,  -620,  -610}-    }-   ,{{  -380,  -620,  -380,  -620,  -380}-    ,{  -790,  -800,  -790,  -800,  -790}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -380,  -630,  -380,  -630,  -380}-    ,{  -610,  -620,  -610,  -620,  -610}-    }-   ,{{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    }-   ,{{   640,   630,   640,   630,   640}-    ,{  -190,  -440,  -190,  -440,  -190}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{   640,   630,   640,   630,   640}-    ,{  -610,  -620,  -610,  -620,  -610}-    }-   ,{{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    ,{  -610,  -620,  -610,  -620,  -610}-    }-   }-  ,{{{   650, -1460,   650,   220,   650}-    ,{   220, -1520,  -430,   220,  -430}-    ,{   220, -1460,  -600,   220,  -600}-    ,{   650, -1700,   650,   220,   650}-    ,{   220, -1460,  -600,   220,  -600}-    }-   ,{{   220, -1700,  -600,   220,  -600}-    ,{    40, -1880,  -780,    40,  -780}-    ,{   220, -1700,  -600,   220,  -600}-    ,{  -620, -1710,  -620, -1040,  -620}-    ,{   220, -1700,  -600,   220,  -600}-    }-   ,{{   220, -1460,  -600,   220,  -600}-    ,{   220, -1700,  -600,   220,  -600}-    ,{   220, -1460,  -600,   220,  -600}-    ,{   220, -1700,  -600,   220,  -600}-    ,{   220, -1460,  -600,   220,  -600}-    }-   ,{{   650, -1520,   650,   220,   650}-    ,{  -430, -1520,  -430,  -850,  -430}-    ,{   220, -1700,  -600,   220,  -600}-    ,{   650, -1700,   650, -1030,   650}-    ,{   220, -1700,  -600,   220,  -600}-    }-   ,{{   220, -1460,  -600,   220,  -600}-    ,{   220, -1700,  -600,   220,  -600}-    ,{   220, -1460,  -600,   220,  -600}-    ,{   220, -1700,  -600,   220,  -600}-    ,{  -600, -1700,  -600, -1030,  -600}-    }-   }-  ,{{{   640,   630,   640,   630, -1410}-    ,{  -190,  -440,  -190,  -440, -1410}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{   640,   630,   640,   630, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    }-   ,{{  -380,  -620,  -380,  -620, -1530}-    ,{  -790,  -800,  -790,  -800, -1530}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -380,  -630,  -380,  -630, -1600}-    ,{  -610,  -620,  -610,  -620, -1590}-    }-   ,{{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    }-   ,{{   640,   630,   640,   630, -1410}-    ,{  -190,  -440,  -190,  -440, -1410}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{   640,   630,   640,   630, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    }-   ,{{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    ,{  -610,  -620,  -610,  -620, -1590}-    }-   }-  }- ,{{{{  1490,  1490,  1200,  1280,  1200}-    ,{  1280,   750,   460,  1280,   460}-    ,{   780,   240,   -50,   780,   -50}-    ,{  1490,  1490,  1200,  1190,  1200}-    ,{   780,   480,   -50,   780,   -50}-    }-   ,{{  1280,   750,   460,  1280,   460}-    ,{  1280,   750,   460,  1280,   460}-    ,{   780,   240,   -50,   780,   -50}-    ,{   -90,   -90,  -150,  -400,  -150}-    ,{   780,   240,   -50,   780,   -50}-    }-   ,{{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    }-   ,{{  1490,  1490,  1200,  1190,  1200}-    ,{  -260,  -260,  -320,  -570,  -320}-    ,{   780,   240,   -50,   780,   -50}-    ,{  1490,  1490,  1200,  1190,  1200}-    ,{   780,   240,   -50,   780,   -50}-    }-   ,{{   780,   480,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   780,   240,   -50,   780,   -50}-    ,{   480,   480,   -50,   -60,   -50}-    }-   }-  ,{{{  1490,  1490,  1200,  -450,  1200}-    ,{   750,   750,   460,  -450,   460}-    ,{   240,   240,   -50,  -720,   -50}-    ,{  1490,  1490,  1200,  -960,  1200}-    ,{   480,   480,   -50,  -720,   -50}-    }-   ,{{   750,   750,   460,  -450,   460}-    ,{   750,   750,   460,  -450,   460}-    ,{   240,   240,   -50,  -960,   -50}-    ,{   -90,   -90,  -390, -1300,  -390}-    ,{   240,   240,   -50,  -960,   -50}-    }-   ,{{   240,   240,   -50,  -720,   -50}-    ,{   240,   240,   -50,  -960,   -50}-    ,{   240,   240,   -50,  -720,   -50}-    ,{   240,   240,   -50,  -960,   -50}-    ,{   240,   240,   -50,  -720,   -50}-    }-   ,{{  1490,  1490,  1200,  -960,  1200}-    ,{  -260,  -260,  -560, -1470,  -560}-    ,{   240,   240,   -50,  -960,   -50}-    ,{  1490,  1490,  1200,  -960,  1200}-    ,{   240,   240,   -50,  -960,   -50}-    }-   ,{{   480,   480,   -50,  -720,   -50}-    ,{   240,   240,   -50,  -960,   -50}-    ,{   240,   240,   -50,  -720,   -50}-    ,{   240,   240,   -50,  -960,   -50}-    ,{   480,   480,   -50,  -960,   -50}-    }-   }-  ,{{{  1200,  1190,  1200,  1190,  1200}-    ,{   450,   440,   450,   440,   450}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{  1200,  1190,  1200,  1190,  1200}-    ,{   -50,   -60,   -50,   -60,   -50}-    }-   ,{{   450,   440,   450,   440,   450}-    ,{   450,   440,   450,   440,   450}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{  -150,  -400,  -150,  -400,  -150}-    ,{   -50,   -60,   -50,   -60,   -50}-    }-   ,{{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    }-   ,{{  1200,  1190,  1200,  1190,  1200}-    ,{  -320,  -570,  -320,  -570,  -320}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{  1200,  1190,  1200,  1190,  1200}-    ,{   -50,   -60,   -50,   -60,   -50}-    }-   ,{{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    ,{   -50,   -60,   -50,   -60,   -50}-    }-   }-  ,{{{  1280,  -630,  1200,  1280,  1200}-    ,{  1280,  -630,   460,  1280,   460}-    ,{   780,  -900,   -50,   780,   -50}-    ,{  1200, -1140,  1200,   780,  1200}-    ,{   780,  -900,   -50,   780,   -50}-    }-   ,{{  1280,  -630,   460,  1280,   460}-    ,{  1280,  -630,   460,  1280,   460}-    ,{   780, -1140,   -50,   780,   -50}-    ,{  -390, -1480,  -390,  -810,  -390}-    ,{   780, -1140,   -50,   780,   -50}-    }-   ,{{   780,  -900,   -50,   780,   -50}-    ,{   780, -1140,   -50,   780,   -50}-    ,{   780,  -900,   -50,   780,   -50}-    ,{   780, -1140,   -50,   780,   -50}-    ,{   780,  -900,   -50,   780,   -50}-    }-   ,{{  1200, -1140,  1200,   780,  1200}-    ,{  -560, -1650,  -560,  -980,  -560}-    ,{   780, -1140,   -50,   780,   -50}-    ,{  1200, -1140,  1200,  -470,  1200}-    ,{   780, -1140,   -50,   780,   -50}-    }-   ,{{   780,  -900,   -50,   780,   -50}-    ,{   780, -1140,   -50,   780,   -50}-    ,{   780,  -900,   -50,   780,   -50}-    ,{   780, -1140,   -50,   780,   -50}-    ,{   -50, -1140,   -50,  -470,   -50}-    }-   }-  ,{{{  1200,  1190,  1200,  1190,  -280}-    ,{   450,   440,   450,   440,  -280}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{  1200,  1190,  1200,  1190, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    }-   ,{{   450,   440,   450,   440,  -280}-    ,{   450,   440,   450,   440,  -280}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{  -150,  -400,  -150,  -400, -1370}-    ,{   -50,   -60,   -50,   -60, -1030}-    }-   ,{{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    }-   ,{{  1200,  1190,  1200,  1190, -1030}-    ,{  -320,  -570,  -320,  -570, -1540}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{  1200,  1190,  1200,  1190, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    }-   ,{{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    ,{   -50,   -60,   -50,   -60, -1030}-    }-   }-  }- ,{{{{  1870,  1870,  1570,  1870,  1570}-    ,{  1870,  1340,  1040,  1870,  1040}-    ,{  1570,  1040,   740,  1570,   740}-    ,{  1870,  1870,  1570,  1570,  1570}-    ,{  1570,  1040,   740,  1570,   740}-    }-   ,{{  1870,  1340,  1040,  1870,  1040}-    ,{  1870,  1340,  1040,  1870,  1040}-    ,{  1560,  1030,   730,  1560,   730}-    ,{   -50,   -50,  -110,  -360,  -110}-    ,{  1560,  1030,   730,  1560,   730}-    }-   ,{{  1570,  1040,   750,  1570,   750}-    ,{  1570,  1040,   750,  1570,   750}-    ,{  1570,  1040,   740,  1570,   740}-    ,{  1570,  1040,   750,  1570,   750}-    ,{  1570,  1040,   740,  1570,   740}-    }-   ,{{  1870,  1870,  1570,  1560,  1570}-    ,{   130,   130,    70,  -180,    70}-    ,{  1560,  1030,   730,  1560,   730}-    ,{  1870,  1870,  1570,  1560,  1570}-    ,{  1560,  1030,   730,  1560,   730}-    }-   ,{{  1570,  1040,   750,  1570,   750}-    ,{  1570,  1040,   750,  1570,   750}-    ,{  1570,  1040,   740,  1570,   740}-    ,{  1570,  1040,   750,  1570,   750}-    ,{   300,   300,  -230,  -250,  -230}-    }-   }-  ,{{{  1870,  1870,  1570,   130,  1570}-    ,{  1340,  1340,  1040,   130,  1040}-    ,{  1040,  1040,   740,    70,   740}-    ,{  1870,  1870,  1570,  -160,  1570}-    ,{  1040,  1040,   740,    70,   740}-    }-   ,{{  1340,  1340,  1040,   130,  1040}-    ,{  1340,  1340,  1040,   130,  1040}-    ,{  1030,  1030,   730,  -180,   730}-    ,{   -50,   -50,  -340, -1260,  -340}-    ,{  1030,  1030,   730,  -180,   730}-    }-   ,{{  1040,  1040,   750,    70,   750}-    ,{  1040,  1040,   750,  -160,   750}-    ,{  1040,  1040,   740,    70,   740}-    ,{  1040,  1040,   750,  -160,   750}-    ,{  1040,  1040,   740,    70,   740}-    }-   ,{{  1870,  1870,  1570,  -180,  1570}-    ,{   130,   130,  -160, -1080,  -160}-    ,{  1030,  1030,   730,  -180,   730}-    ,{  1870,  1870,  1570,  -590,  1570}-    ,{  1030,  1030,   730,  -180,   730}-    }-   ,{{  1040,  1040,   750,    70,   750}-    ,{  1040,  1040,   750,  -160,   750}-    ,{  1040,  1040,   740,    70,   740}-    ,{  1040,  1040,   750,  -160,   750}-    ,{   300,   300,  -230, -1150,  -230}-    }-   }-  ,{{{  1570,  1560,  1570,  1560,  1570}-    ,{  1040,  1030,  1040,  1030,  1040}-    ,{   740,   730,   740,   730,   740}-    ,{  1570,  1560,  1570,  1560,  1570}-    ,{   740,   730,   740,   730,   740}-    }-   ,{{  1040,  1030,  1040,  1030,  1040}-    ,{  1040,  1030,  1040,  1030,  1040}-    ,{   730,   720,   730,   720,   730}-    ,{  -110,  -360,  -110,  -360,  -110}-    ,{   730,   720,   730,   720,   730}-    }-   ,{{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    }-   ,{{  1570,  1560,  1570,  1560,  1570}-    ,{    70,  -180,    70,  -180,    70}-    ,{   730,   720,   730,   720,   730}-    ,{  1570,  1560,  1570,  1560,  1570}-    ,{   730,   720,   730,   720,   730}-    }-   ,{{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{   740,   730,   740,   730,   740}-    ,{  -240,  -250,  -240,  -250,  -240}-    }-   }-  ,{{{  1870,   -50,  1570,  1870,  1570}-    ,{  1870,   -50,  1040,  1870,  1040}-    ,{  1570,  -110,   740,  1570,   740}-    ,{  1570,  -340,  1570,  1570,  1570}-    ,{  1570,  -110,   740,  1570,   740}-    }-   ,{{  1870,   -50,  1040,  1870,  1040}-    ,{  1870,   -50,  1040,  1870,  1040}-    ,{  1560,  -360,   730,  1560,   730}-    ,{  -340, -1440,  -340,  -770,  -340}-    ,{  1560,  -360,   730,  1560,   730}-    }-   ,{{  1570,  -110,   750,  1570,   750}-    ,{  1570,  -340,   750,  1570,   750}-    ,{  1570,  -110,   740,  1570,   740}-    ,{  1570,  -340,   750,  1570,   750}-    ,{  1570,  -110,   740,  1570,   740}-    }-   ,{{  1570,  -360,  1570,  1560,  1570}-    ,{  -160, -1260,  -160,  -590,  -160}-    ,{  1560,  -360,   730,  1560,   730}-    ,{  1570,  -770,  1570,  -100,  1570}-    ,{  1560,  -360,   730,  1560,   730}-    }-   ,{{  1570,  -110,   750,  1570,   750}-    ,{  1570,  -340,   750,  1570,   750}-    ,{  1570,  -110,   740,  1570,   740}-    ,{  1570,  -340,   750,  1570,   750}-    ,{  -230, -1330,  -230,  -660,  -230}-    }-   }-  ,{{{  1570,  1560,  1570,  1560,   300}-    ,{  1040,  1030,  1040,  1030,   300}-    ,{   740,   730,   740,   730,  -240}-    ,{  1570,  1560,  1570,  1560,  -230}-    ,{   740,   730,   740,   730,  -240}-    }-   ,{{  1040,  1030,  1040,  1030,   300}-    ,{  1040,  1030,  1040,  1030,   300}-    ,{   730,   720,   730,   720,  -250}-    ,{  -110,  -360,  -110,  -360, -1330}-    ,{   730,   720,   730,   720,  -250}-    }-   ,{{   740,   730,   740,   730,  -230}-    ,{   740,   730,   740,   730,  -230}-    ,{   740,   730,   740,   730,  -240}-    ,{   740,   730,   740,   730,  -230}-    ,{   740,   730,   740,   730,  -240}-    }-   ,{{  1570,  1560,  1570,  1560,  -250}-    ,{    70,  -180,    70,  -180, -1150}-    ,{   730,   720,   730,   720,  -250}-    ,{  1570,  1560,  1570,  1560,  -660}-    ,{   730,   720,   730,   720,  -250}-    }-   ,{{   740,   730,   740,   730,  -230}-    ,{   740,   730,   740,   730,  -230}-    ,{   740,   730,   740,   730,  -240}-    ,{   740,   730,   740,   730,  -230}-    ,{  -240,  -250,  -240,  -250, -1220}-    }-   }-  }- ,{{{{  2050,  2050,  1760,  1930,  1760}-    ,{  1930,  1400,  1110,  1930,  1110}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  2050,  2050,  1760,  1800,  1760}-    ,{  1670,  1140,   850,  1670,   850}-    }-   ,{{  1930,  1400,  1110,  1930,  1110}-    ,{  1930,  1400,  1110,  1930,  1110}-    ,{  1650,  1120,   830,  1650,   830}-    ,{     0,     0,   -60,  -310,   -60}-    ,{  1650,  1120,   830,  1650,   830}-    }-   ,{{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1670,  1140,   850,  1670,   850}-    }-   ,{{  2050,  2050,  1760,  1740,  1760}-    ,{  -300,  -300,  -360,  -610,  -360}-    ,{  1650,  1120,   830,  1650,   830}-    ,{  2050,  2050,  1760,  1740,  1760}-    ,{  1650,  1120,   830,  1650,   830}-    }-   ,{{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1360,   830,   540,  1360,   540}-    ,{  1800,  1270,   980,  1800,   980}-    ,{   570,   570,    40,    20,    40}-    }-   }-  ,{{{  2050,  2050,  1760,   300,  1760}-    ,{  1400,  1400,  1110,   190,  1110}-    ,{  1270,  1270,   980,   300,   980}-    ,{  2050,  2050,  1760,    60,  1760}-    ,{  1140,  1140,   850,   180,   850}-    }-   ,{{  1400,  1400,  1110,   190,  1110}-    ,{  1400,  1400,  1110,   190,  1110}-    ,{  1120,  1120,   830,   -80,   830}-    ,{     0,     0,  -290, -1210,  -290}-    ,{  1120,  1120,   830,   -80,   830}-    }-   ,{{  1270,  1270,   980,   300,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{  1270,  1270,   980,   300,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{  1140,  1140,   850,   180,   850}-    }-   ,{{  2050,  2050,  1760,   -80,  1760}-    ,{  -300,  -300,  -590, -1510,  -590}-    ,{  1120,  1120,   830,   -80,   830}-    ,{  2050,  2050,  1760,  -400,  1760}-    ,{  1120,  1120,   830,   -80,   830}-    }-   ,{{  1270,  1270,   980,    60,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{   830,   830,   540,  -130,   540}-    ,{  1270,  1270,   980,    60,   980}-    ,{   570,   570,    40,  -870,    40}-    }-   }-  ,{{{  1750,  1740,  1750,  1740,  1750}-    ,{  1100,  1090,  1100,  1090,  1100}-    ,{   970,   960,   970,   960,   970}-    ,{  1750,  1740,  1750,  1740,  1750}-    ,{   840,   830,   840,   830,   840}-    }-   ,{{  1100,  1090,  1100,  1090,  1100}-    ,{  1100,  1090,  1100,  1090,  1100}-    ,{   820,   810,   820,   810,   820}-    ,{   -60,  -310,   -60,  -310,   -60}-    ,{   820,   810,   820,   810,   820}-    }-   ,{{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   840,   830,   840,   830,   840}-    }-   ,{{  1750,  1740,  1750,  1740,  1750}-    ,{  -360,  -610,  -360,  -610,  -360}-    ,{   820,   810,   820,   810,   820}-    ,{  1750,  1740,  1750,  1740,  1750}-    ,{   820,   810,   820,   810,   820}-    }-   ,{{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   530,   520,   530,   520,   530}-    ,{   970,   960,   970,   960,   970}-    ,{    30,    20,    30,    20,    30}-    }-   }-  ,{{{  1930,   130,  1760,  1930,  1760}-    ,{  1930,    10,  1110,  1930,  1110}-    ,{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,  1760,  1800,  1760}-    ,{  1670,     0,   850,  1670,   850}-    }-   ,{{  1930,    10,  1110,  1930,  1110}-    ,{  1930,    10,  1110,  1930,  1110}-    ,{  1650,  -260,   830,  1650,   830}-    ,{  -290, -1390,  -290,  -720,  -290}-    ,{  1650,  -260,   830,  1650,   830}-    }-   ,{{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1670,     0,   850,  1670,   850}-    }-   ,{{  1760,  -260,  1760,  1650,  1760}-    ,{  -590, -1690,  -590, -1020,  -590}-    ,{  1650,  -260,   830,  1650,   830}-    ,{  1760,  -580,  1760,    80,  1760}-    ,{  1650,  -260,   830,  1650,   830}-    }-   ,{{  1800,  -110,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1360,  -310,   540,  1360,   540}-    ,{  1800,  -110,   980,  1800,   980}-    ,{    40, -1050,    40,  -380,    40}-    }-   }-  ,{{{  1750,  1740,  1750,  1740,   360}-    ,{  1100,  1090,  1100,  1090,   360}-    ,{   970,   960,   970,   960,     0}-    ,{  1750,  1740,  1750,  1740,     0}-    ,{   840,   830,   840,   830,  -130}-    }-   ,{{  1100,  1090,  1100,  1090,   360}-    ,{  1100,  1090,  1100,  1090,   360}-    ,{   820,   810,   820,   810,  -150}-    ,{   -60,  -310,   -60,  -310, -1280}-    ,{   820,   810,   820,   810,  -150}-    }-   ,{{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   840,   830,   840,   830,  -130}-    }-   ,{{  1750,  1740,  1750,  1740,  -150}-    ,{  -360,  -610,  -360,  -610, -1580}-    ,{   820,   810,   820,   810,  -150}-    ,{  1750,  1740,  1750,  1740,  -470}-    ,{   820,   810,   820,   810,  -150}-    }-   ,{{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   530,   520,   530,   520,  -440}-    ,{   970,   960,   970,   960,     0}-    ,{    30,    20,    30,    20,  -940}-    }-   }-  }- ,{{{{  2050,  2050,  1760,  1930,  1760}-    ,{  1930,  1400,  1110,  1930,  1110}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  2050,  2050,  1760,  1800,  1760}-    ,{  1670,  1140,   850,  1670,   850}-    }-   ,{{  1930,  1400,  1110,  1930,  1110}-    ,{  1930,  1400,  1110,  1930,  1110}-    ,{  1650,  1120,   830,  1650,   830}-    ,{   220,   220,   170,   -80,   170}-    ,{  1650,  1120,   830,  1650,   830}-    }-   ,{{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1670,  1140,   850,  1670,   850}-    }-   ,{{  2050,  2050,  1760,  1740,  1760}-    ,{   130,   130,    70,  -180,    70}-    ,{  1650,  1120,   830,  1650,   830}-    ,{  2050,  2050,  1760,  1740,  1760}-    ,{  1650,  1120,   830,  1650,   830}-    }-   ,{{  1800,  1270,   980,  1800,   980}-    ,{  1800,  1270,   980,  1800,   980}-    ,{  1570,  1040,   740,  1570,   740}-    ,{  1800,  1270,   980,  1800,   980}-    ,{   570,   570,    40,    20,    40}-    }-   }-  ,{{{  2050,  2050,  1760,   300,  1760}-    ,{  1400,  1400,  1110,   190,  1110}-    ,{  1270,  1270,   980,   300,   980}-    ,{  2050,  2050,  1760,    60,  1760}-    ,{  1140,  1140,   850,   180,   850}-    }-   ,{{  1400,  1400,  1110,   190,  1110}-    ,{  1400,  1400,  1110,   190,  1110}-    ,{  1120,  1120,   830,   -80,   830}-    ,{   220,   220,   -70,  -980,   -70}-    ,{  1120,  1120,   830,   -80,   830}-    }-   ,{{  1270,  1270,   980,   300,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{  1270,  1270,   980,   300,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{  1140,  1140,   850,   180,   850}-    }-   ,{{  2050,  2050,  1760,   -80,  1760}-    ,{   130,   130,  -160, -1080,  -160}-    ,{  1120,  1120,   830,   -80,   830}-    ,{  2050,  2050,  1760,  -400,  1760}-    ,{  1120,  1120,   830,   -80,   830}-    }-   ,{{  1270,  1270,   980,    70,   980}-    ,{  1270,  1270,   980,    60,   980}-    ,{  1040,  1040,   740,    70,   740}-    ,{  1270,  1270,   980,    60,   980}-    ,{   570,   570,    40,  -870,    40}-    }-   }-  ,{{{  1750,  1740,  1750,  1740,  1750}-    ,{  1100,  1090,  1100,  1090,  1100}-    ,{   970,   960,   970,   960,   970}-    ,{  1750,  1740,  1750,  1740,  1750}-    ,{   840,   830,   840,   830,   840}-    }-   ,{{  1100,  1090,  1100,  1090,  1100}-    ,{  1100,  1090,  1100,  1090,  1100}-    ,{   820,   810,   820,   810,   820}-    ,{   170,   -80,   170,   -80,   170}-    ,{   820,   810,   820,   810,   820}-    }-   ,{{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   840,   830,   840,   830,   840}-    }-   ,{{  1750,  1740,  1750,  1740,  1750}-    ,{    70,  -180,    70,  -180,    70}-    ,{   820,   810,   820,   810,   820}-    ,{  1750,  1740,  1750,  1740,  1750}-    ,{   820,   810,   820,   810,   820}-    }-   ,{{   970,   960,   970,   960,   970}-    ,{   970,   960,   970,   960,   970}-    ,{   740,   730,   740,   730,   740}-    ,{   970,   960,   970,   960,   970}-    ,{    30,    20,    30,    20,    30}-    }-   }-  ,{{{  1930,   130,  1760,  1930,  1760}-    ,{  1930,    10,  1110,  1930,  1110}-    ,{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,  1760,  1800,  1760}-    ,{  1670,     0,   850,  1670,   850}-    }-   ,{{  1930,    10,  1110,  1930,  1110}-    ,{  1930,    10,  1110,  1930,  1110}-    ,{  1650,  -260,   830,  1650,   830}-    ,{   -70, -1160,   -70,  -490,   -70}-    ,{  1650,  -260,   830,  1650,   830}-    }-   ,{{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1800,   130,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1670,     0,   850,  1670,   850}-    }-   ,{{  1760,  -260,  1760,  1650,  1760}-    ,{  -160, -1260,  -160,  -590,  -160}-    ,{  1650,  -260,   830,  1650,   830}-    ,{  1760,  -580,  1760,    80,  1760}-    ,{  1650,  -260,   830,  1650,   830}-    }-   ,{{  1800,  -110,   980,  1800,   980}-    ,{  1800,  -110,   980,  1800,   980}-    ,{  1570,  -110,   740,  1570,   740}-    ,{  1800,  -110,   980,  1800,   980}-    ,{    40, -1050,    40,  -380,    40}-    }-   }-  ,{{{  1750,  1740,  1750,  1740,   360}-    ,{  1100,  1090,  1100,  1090,   360}-    ,{   970,   960,   970,   960,     0}-    ,{  1750,  1740,  1750,  1740,     0}-    ,{   840,   830,   840,   830,  -130}-    }-   ,{{  1100,  1090,  1100,  1090,   360}-    ,{  1100,  1090,  1100,  1090,   360}-    ,{   820,   810,   820,   810,  -150}-    ,{   170,   -80,   170,   -80, -1050}-    ,{   820,   810,   820,   810,  -150}-    }-   ,{{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   840,   830,   840,   830,  -130}-    }-   ,{{  1750,  1740,  1750,  1740,  -150}-    ,{    70,  -180,    70,  -180, -1150}-    ,{   820,   810,   820,   810,  -150}-    ,{  1750,  1740,  1750,  1740,  -470}-    ,{   820,   810,   820,   810,  -150}-    }-   ,{{   970,   960,   970,   960,     0}-    ,{   970,   960,   970,   960,     0}-    ,{   740,   730,   740,   730,  -240}-    ,{   970,   960,   970,   960,     0}-    ,{    30,    20,    30,    20,  -940}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{  1350,   850,   720,  1350,   720}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1350,   700,   570,  1350,   570}-    ,{  1300,   850,   720,  1300,   720}-    ,{  1250,   590,   460,  1250,   460}-    }-   ,{{  1160,   500,   400,  1160,   370}-    ,{  1160,   500,   370,  1160,   370}-    ,{   850,   190,    60,   850,    60}-    ,{   400,   290,   400,    10,   160}-    ,{   850,   190,    60,   850,    60}-    }-   ,{{  1300,   650,   520,  1300,   520}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1290,   640,   510,  1290,   510}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1250,   590,   460,  1250,   460}-    }-   ,{{   850,   850,   720,   850,   720}-    ,{   120,     0,   120,  -270,  -120}-    ,{   850,   190,    60,   850,    60}-    ,{   850,   850,   720,   570,   720}-    ,{   850,   190,    60,   850,    60}-    }-   ,{{  1350,   700,   570,  1350,   570}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1350,   700,   570,  1350,   570}-    ,{  1300,   650,   520,  1300,   520}-    ,{   100,   100,  -270,  -420,  -270}-    }-   }-  ,{{{   850,   850,   720,  -760,   720}-    ,{   650,   650,   520, -1050,   520}-    ,{   700,   700,   570,  -760,   570}-    ,{   850,   850,   720, -1050,   720}-    ,{   590,   590,   460,  -870,   460}-    }-   ,{{   500,   500,   370, -1200,   370}-    ,{   500,   500,   370, -1200,   370}-    ,{   190,   190,    60, -1510,    60}-    ,{   290,   290,   160, -1410,   160}-    ,{   190,   190,    60, -1510,    60}-    }-   ,{{   650,   650,   520,  -820,   520}-    ,{   650,   650,   520, -1050,   520}-    ,{   640,   640,   510,  -820,   510}-    ,{   650,   650,   520, -1050,   520}-    ,{   590,   590,   460,  -870,   460}-    }-   ,{{   850,   850,   720, -1510,   720}-    ,{     0,     0,  -120, -1700,  -120}-    ,{   190,   190,    60, -1510,    60}-    ,{   850,   850,   720, -2110,   720}-    ,{   190,   190,    60, -1510,    60}-    }-   ,{{   700,   700,   570,  -760,   570}-    ,{   650,   650,   520, -1050,   520}-    ,{   700,   700,   570,  -760,   570}-    ,{   650,   650,   520, -1050,   520}-    ,{   100,   100,  -270, -1840,  -270}-    }-   }-  ,{{{   720,   570,   720,   570,   280}-    ,{   520,   370,   520,   370,    80}-    ,{   570,   420,   570,   420,   130}-    ,{   720,   570,   720,   570,   280}-    ,{   460,   310,   460,   310,    20}-    }-   ,{{   400,   220,   400,   220,   -40}-    ,{   370,   220,   370,   220,   -60}-    ,{    60,   -80,    60,   -80,  -370}-    ,{   400,    10,   400,    10,   -40}-    ,{    60,   -80,    60,   -80,  -370}-    }-   ,{{   520,   370,   520,   370,    80}-    ,{   520,   370,   520,   370,    80}-    ,{   510,   360,   510,   360,    70}-    ,{   520,   370,   520,   370,    80}-    ,{   460,   310,   460,   310,    20}-    }-   ,{{   720,   570,   720,   570,   280}-    ,{   120,  -270,   120,  -270,  -320}-    ,{    60,   -80,    60,   -80,  -370}-    ,{   720,   570,   720,   570,   280}-    ,{    60,   -80,    60,   -80,  -370}-    }-   ,{{   570,   420,   570,   420,   130}-    ,{   520,   370,   520,   370,    80}-    ,{   570,   420,   570,   420,   130}-    ,{   520,   370,   520,   370,    80}-    ,{  -270,  -420,  -270,  -420,  -710}-    }-   }-  ,{{{  1350,  -460,   720,  1350,   720}-    ,{  1300,  -750,   520,  1300,   520}-    ,{  1350,  -460,   570,  1350,   570}-    ,{  1300,  -750,   720,  1300,   720}-    ,{  1250,  -570,   460,  1250,   460}-    }-   ,{{  1160,  -900,   370,  1160,   370}-    ,{  1160,  -900,   370,  1160,   370}-    ,{   850, -1210,    60,   850,    60}-    ,{   160, -1110,   160,  -310,   160}-    ,{   850, -1210,    60,   850,    60}-    }-   ,{{  1300,  -520,   520,  1300,   520}-    ,{  1300,  -750,   520,  1300,   520}-    ,{  1290,  -520,   510,  1290,   510}-    ,{  1300,  -750,   520,  1300,   520}-    ,{  1250,  -570,   460,  1250,   460}-    }-   ,{{   850, -1210,   720,   850,   720}-    ,{  -120, -1400,  -120,  -590,  -120}-    ,{   850, -1210,    60,   850,    60}-    ,{   720, -1810,   720, -1000,   720}-    ,{   850, -1210,    60,   850,    60}-    }-   ,{{  1350,  -460,   570,  1350,   570}-    ,{  1300,  -750,   520,  1300,   520}-    ,{  1350,  -460,   570,  1350,   570}-    ,{  1300,  -750,   520,  1300,   520}-    ,{  -270, -1540,  -270,  -740,  -270}-    }-   }-  ,{{{   590,   570,   590,   570,  -320}-    ,{   390,   370,   390,   370,  -320}-    ,{   440,   420,   440,   420,  -360}-    ,{   590,   570,   590,   570,  -420}-    ,{   330,   310,   330,   310,  -470}-    }-   ,{{   270,   220,   270,   220,  -320}-    ,{   240,   220,   240,   220,  -320}-    ,{   -60,   -80,   -60,   -80,  -870}-    ,{   270,    10,   270,    10,  -780}-    ,{   -60,   -80,   -60,   -80,  -870}-    }-   ,{{   390,   370,   390,   370,  -420}-    ,{   390,   370,   390,   370,  -420}-    ,{   380,   360,   380,   360,  -420}-    ,{   390,   370,   390,   370,  -420}-    ,{   330,   310,   330,   310,  -470}-    }-   ,{{   590,   570,   590,   570,  -870}-    ,{   -10,  -270,   -10,  -270, -1060}-    ,{   -60,   -80,   -60,   -80,  -870}-    ,{   590,   570,   590,   570, -1470}-    ,{   -60,   -80,   -60,   -80,  -870}-    }-   ,{{   440,   420,   440,   420,  -360}-    ,{   390,   370,   390,   370,  -420}-    ,{   440,   420,   440,   420,  -360}-    ,{   390,   370,   390,   370,  -420}-    ,{  -400,  -420,  -400,  -420, -1210}-    }-   }-  }- ,{{{{  1320,   850,   720,  1320,   720}-    ,{  1320,   670,   540,  1320,   540}-    ,{   870,   220,    90,   870,    90}-    ,{   960,   850,   720,   960,   720}-    ,{   870,   250,    90,   870,    90}-    }-   ,{{  1320,   670,   540,  1320,   540}-    ,{  1320,   670,   540,  1320,   540}-    ,{   870,   220,    90,   870,    90}-    ,{  -410,  -520,  -410,  -800,  -650}-    ,{   870,   220,    90,   870,    90}-    }-   ,{{   960,   300,   170,   960,   170}-    ,{   960,   300,   170,   960,   170}-    ,{   650,     0,  -130,   650,  -130}-    ,{   960,   300,   170,   960,   170}-    ,{   650,     0,  -130,   650,  -130}-    }-   ,{{   870,   850,   720,   870,   720}-    ,{    70,   -40,    70,  -320,  -170}-    ,{   870,   220,    90,   870,    90}-    ,{   850,   850,   720,   570,   720}-    ,{   870,   220,    90,   870,    90}-    }-   ,{{   960,   300,   170,   960,   170}-    ,{   960,   300,   170,   960,   170}-    ,{   340,  -310,  -440,   340,  -440}-    ,{   960,   300,   170,   960,   170}-    ,{   250,   250,  -110,  -260,  -110}-    }-   }-  ,{{{   850,   850,   720, -1030,   720}-    ,{   670,   670,   540, -1030,   540}-    ,{   220,   220,    90, -1460,    90}-    ,{   850,   850,   720, -1400,   720}-    ,{   250,   250,    90, -1460,    90}-    }-   ,{{   670,   670,   540, -1030,   540}-    ,{   670,   670,   540, -1030,   540}-    ,{   220,   220,    90, -1480,    90}-    ,{  -520,  -520,  -650, -2220,  -650}-    ,{   220,   220,    90, -1480,    90}-    }-   ,{{   300,   300,   170, -1400,   170}-    ,{   300,   300,   170, -1400,   170}-    ,{     0,     0,  -130, -1460,  -130}-    ,{   300,   300,   170, -1400,   170}-    ,{     0,     0,  -130, -1460,  -130}-    }-   ,{{   850,   850,   720, -1480,   720}-    ,{   -40,   -40,  -170, -1750,  -170}-    ,{   220,   220,    90, -1480,    90}-    ,{   850,   850,   720, -2110,   720}-    ,{   220,   220,    90, -1480,    90}-    }-   ,{{   300,   300,   170, -1400,   170}-    ,{   300,   300,   170, -1400,   170}-    ,{  -310,  -310,  -440, -1770,  -440}-    ,{   300,   300,   170, -1400,   170}-    ,{   250,   250,  -110, -1690,  -110}-    }-   }-  ,{{{   720,   570,   720,   570,   280}-    ,{   540,   390,   540,   390,   100}-    ,{    90,   -60,    90,   -60,  -350}-    ,{   720,   570,   720,   570,   280}-    ,{    90,   -60,    90,   -60,  -350}-    }-   ,{{   540,   390,   540,   390,   100}-    ,{   540,   390,   540,   390,   100}-    ,{    90,   -60,    90,   -60,  -350}-    ,{  -410,  -800,  -410,  -800,  -850}-    ,{    90,   -60,    90,   -60,  -350}-    }-   ,{{   170,    20,   170,    20,  -260}-    ,{   170,    20,   170,    20,  -260}-    ,{  -130,  -280,  -130,  -280,  -570}-    ,{   170,    20,   170,    20,  -260}-    ,{  -130,  -280,  -130,  -280,  -570}-    }-   ,{{   720,   570,   720,   570,   280}-    ,{    70,  -320,    70,  -320,  -370}-    ,{    90,   -60,    90,   -60,  -350}-    ,{   720,   570,   720,   570,   280}-    ,{    90,   -60,    90,   -60,  -350}-    }-   ,{{   170,    20,   170,    20,  -260}-    ,{   170,    20,   170,    20,  -260}-    ,{  -440,  -590,  -440,  -590,  -880}-    ,{   170,    20,   170,    20,  -260}-    ,{  -110,  -260,  -110,  -260,  -550}-    }-   }-  ,{{{  1320,  -730,   720,  1320,   720}-    ,{  1320,  -730,   540,  1320,   540}-    ,{   870, -1160,    90,   870,    90}-    ,{   960, -1100,   720,   960,   720}-    ,{   870, -1160,    90,   870,    90}-    }-   ,{{  1320,  -730,   540,  1320,   540}-    ,{  1320,  -730,   540,  1320,   540}-    ,{   870, -1180,    90,   870,    90}-    ,{  -650, -1920,  -650, -1120,  -650}-    ,{   870, -1180,    90,   870,    90}-    }-   ,{{   960, -1100,   170,   960,   170}-    ,{   960, -1100,   170,   960,   170}-    ,{   650, -1160,  -130,   650,  -130}-    ,{   960, -1100,   170,   960,   170}-    ,{   650, -1160,  -130,   650,  -130}-    }-   ,{{   870, -1180,   720,   870,   720}-    ,{  -170, -1450,  -170,  -640,  -170}-    ,{   870, -1180,    90,   870,    90}-    ,{   720, -1810,   720, -1000,   720}-    ,{   870, -1180,    90,   870,    90}-    }-   ,{{   960, -1100,   170,   960,   170}-    ,{   960, -1100,   170,   960,   170}-    ,{   340, -1470,  -440,   340,  -440}-    ,{   960, -1100,   170,   960,   170}-    ,{  -110, -1390,  -110,  -580,  -110}-    }-   }-  ,{{{   590,   570,   590,   570,  -160}-    ,{   410,   390,   410,   390,  -160}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{   590,   570,   590,   570,  -760}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{   410,   390,   410,   390,  -160}-    ,{   410,   390,   410,   390,  -160}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{  -540,  -800,  -540,  -800, -1590}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{    40,    20,    40,    20,  -760}-    ,{    40,    20,    40,    20,  -760}-    ,{  -260,  -280,  -260,  -280, -1070}-    ,{    40,    20,    40,    20,  -760}-    ,{  -260,  -280,  -260,  -280, -1070}-    }-   ,{{   590,   570,   590,   570,  -850}-    ,{   -60,  -320,   -60,  -320, -1110}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{   590,   570,   590,   570, -1470}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{    40,    20,    40,    20,  -760}-    ,{    40,    20,    40,    20,  -760}-    ,{  -570,  -590,  -570,  -590, -1380}-    ,{    40,    20,    40,    20,  -760}-    ,{  -240,  -260,  -240,  -260, -1050}-    }-   }-  }- ,{{{{  1010,  1010,   880,   730,   880}-    ,{   410,   -70,    40,   410,  -200}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  1010,  1010,   880,   730,   880}-    ,{   410,     0,  -370,   410,  -370}-    }-   ,{{   410,  -240,  -150,   410,  -370}-    ,{   230,  -420,  -550,   230,  -550}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  -150,  -260,  -150,  -540,  -390}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{  1010,  1010,   880,   730,   880}-    ,{    40,   -70,    40,  -350,  -200}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  1010,  1010,   880,   730,   880}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{   410,     0,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{     0,     0,  -370,  -520,  -370}-    }-   }-  ,{{{  1010,  1010,   880, -1710,   880}-    ,{   -70,   -70,  -200, -1770,  -200}-    ,{  -240,  -240,  -370, -1710,  -370}-    ,{  1010,  1010,   880, -1950,   880}-    ,{     0,     0,  -370, -1710,  -370}-    }-   ,{{  -240,  -240,  -370, -1950,  -370}-    ,{  -420,  -420,  -550, -2130,  -550}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{  -260,  -260,  -390, -1960,  -390}-    ,{  -240,  -240,  -370, -1950,  -370}-    }-   ,{{  -240,  -240,  -370, -1710,  -370}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{  -240,  -240,  -370, -1710,  -370}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{  -240,  -240,  -370, -1710,  -370}-    }-   ,{{  1010,  1010,   880, -1770,   880}-    ,{   -70,   -70,  -200, -1770,  -200}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{  1010,  1010,   880, -1950,   880}-    ,{  -240,  -240,  -370, -1950,  -370}-    }-   ,{{     0,     0,  -370, -1710,  -370}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{  -240,  -240,  -370, -1710,  -370}-    ,{  -240,  -240,  -370, -1950,  -370}-    ,{     0,     0,  -370, -1950,  -370}-    }-   }-  ,{{{   880,   730,   880,   730,   440}-    ,{    40,  -350,    40,  -350,  -400}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{   880,   730,   880,   730,   440}-    ,{  -370,  -520,  -370,  -520,  -810}-    }-   ,{{  -150,  -520,  -150,  -520,  -590}-    ,{  -550,  -700,  -550,  -700,  -990}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -150,  -540,  -150,  -540,  -590}-    ,{  -370,  -520,  -370,  -520,  -810}-    }-   ,{{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    }-   ,{{   880,   730,   880,   730,   440}-    ,{    40,  -350,    40,  -350,  -400}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{   880,   730,   880,   730,   440}-    ,{  -370,  -520,  -370,  -520,  -810}-    }-   ,{{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    ,{  -370,  -520,  -370,  -520,  -810}-    }-   }-  ,{{{   880, -1410,   880,   410,   880}-    ,{   410, -1470,  -200,   410,  -200}-    ,{   410, -1410,  -370,   410,  -370}-    ,{   880, -1650,   880,   410,   880}-    ,{   410, -1410,  -370,   410,  -370}-    }-   ,{{   410, -1650,  -370,   410,  -370}-    ,{   230, -1830,  -550,   230,  -550}-    ,{   410, -1650,  -370,   410,  -370}-    ,{  -390, -1660,  -390,  -860,  -390}-    ,{   410, -1650,  -370,   410,  -370}-    }-   ,{{   410, -1410,  -370,   410,  -370}-    ,{   410, -1650,  -370,   410,  -370}-    ,{   410, -1410,  -370,   410,  -370}-    ,{   410, -1650,  -370,   410,  -370}-    ,{   410, -1410,  -370,   410,  -370}-    }-   ,{{   880, -1470,   880,   410,   880}-    ,{  -200, -1470,  -200,  -670,  -200}-    ,{   410, -1650,  -370,   410,  -370}-    ,{   880, -1650,   880,  -840,   880}-    ,{   410, -1650,  -370,   410,  -370}-    }-   ,{{   410, -1410,  -370,   410,  -370}-    ,{   410, -1650,  -370,   410,  -370}-    ,{   410, -1410,  -370,   410,  -370}-    ,{   410, -1650,  -370,   410,  -370}-    ,{  -370, -1650,  -370,  -840,  -370}-    }-   }-  ,{{{   750,   730,   750,   730, -1140}-    ,{   -90,  -350,   -90,  -350, -1140}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{   750,   730,   750,   730, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -280,  -520,  -280,  -520, -1250}-    ,{  -680,  -700,  -680,  -700, -1250}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -280,  -540,  -280,  -540, -1330}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{   750,   730,   750,   730, -1140}-    ,{   -90,  -350,   -90,  -350, -1140}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{   750,   730,   750,   730, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   }-  }- ,{{{{  1560,  1560,  1430,  1470,  1430}-    ,{  1470,   820,   690,  1470,   690}-    ,{   960,   310,   180,   960,   180}-    ,{  1560,  1560,  1430,  1280,  1430}-    ,{   960,   550,   180,   960,   180}-    }-   ,{{  1470,   820,   690,  1470,   690}-    ,{  1470,   820,   690,  1470,   690}-    ,{   960,   310,   180,   960,   180}-    ,{    80,   -30,    80,  -310,  -160}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{  1560,  1560,  1430,  1280,  1430}-    ,{   -90,  -200,   -90,  -480,  -330}-    ,{   960,   310,   180,   960,   180}-    ,{  1560,  1560,  1430,  1280,  1430}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{   960,   550,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   550,   550,   180,    30,   180}-    }-   }-  ,{{{  1560,  1560,  1430,  -880,  1430}-    ,{   820,   820,   690,  -880,   690}-    ,{   310,   310,   180, -1150,   180}-    ,{  1560,  1560,  1430, -1390,  1430}-    ,{   550,   550,   180, -1150,   180}-    }-   ,{{   820,   820,   690,  -880,   690}-    ,{   820,   820,   690,  -880,   690}-    ,{   310,   310,   180, -1390,   180}-    ,{   -30,   -30,  -160, -1730,  -160}-    ,{   310,   310,   180, -1390,   180}-    }-   ,{{   310,   310,   180, -1150,   180}-    ,{   310,   310,   180, -1390,   180}-    ,{   310,   310,   180, -1150,   180}-    ,{   310,   310,   180, -1390,   180}-    ,{   310,   310,   180, -1150,   180}-    }-   ,{{  1560,  1560,  1430, -1390,  1430}-    ,{  -200,  -200,  -330, -1900,  -330}-    ,{   310,   310,   180, -1390,   180}-    ,{  1560,  1560,  1430, -1390,  1430}-    ,{   310,   310,   180, -1390,   180}-    }-   ,{{   550,   550,   180, -1150,   180}-    ,{   310,   310,   180, -1390,   180}-    ,{   310,   310,   180, -1150,   180}-    ,{   310,   310,   180, -1390,   180}-    ,{   550,   550,   180, -1390,   180}-    }-   }-  ,{{{  1430,  1280,  1430,  1280,   990}-    ,{   690,   540,   690,   540,   250}-    ,{   180,    30,   180,    30,  -260}-    ,{  1430,  1280,  1430,  1280,   990}-    ,{   180,    30,   180,    30,  -260}-    }-   ,{{   690,   540,   690,   540,   250}-    ,{   690,   540,   690,   540,   250}-    ,{   180,    30,   180,    30,  -260}-    ,{    80,  -310,    80,  -310,  -360}-    ,{   180,    30,   180,    30,  -260}-    }-   ,{{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    }-   ,{{  1430,  1280,  1430,  1280,   990}-    ,{   -90,  -480,   -90,  -480,  -530}-    ,{   180,    30,   180,    30,  -260}-    ,{  1430,  1280,  1430,  1280,   990}-    ,{   180,    30,   180,    30,  -260}-    }-   ,{{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    ,{   180,    30,   180,    30,  -260}-    }-   }-  ,{{{  1470,  -580,  1430,  1470,  1430}-    ,{  1470,  -580,   690,  1470,   690}-    ,{   960,  -850,   180,   960,   180}-    ,{  1430, -1090,  1430,   960,  1430}-    ,{   960,  -850,   180,   960,   180}-    }-   ,{{  1470,  -580,   690,  1470,   690}-    ,{  1470,  -580,   690,  1470,   690}-    ,{   960, -1090,   180,   960,   180}-    ,{  -160, -1430,  -160,  -630,  -160}-    ,{   960, -1090,   180,   960,   180}-    }-   ,{{   960,  -850,   180,   960,   180}-    ,{   960, -1090,   180,   960,   180}-    ,{   960,  -850,   180,   960,   180}-    ,{   960, -1090,   180,   960,   180}-    ,{   960,  -850,   180,   960,   180}-    }-   ,{{  1430, -1090,  1430,   960,  1430}-    ,{  -330, -1600,  -330,  -800,  -330}-    ,{   960, -1090,   180,   960,   180}-    ,{  1430, -1090,  1430,  -290,  1430}-    ,{   960, -1090,   180,   960,   180}-    }-   ,{{   960,  -850,   180,   960,   180}-    ,{   960, -1090,   180,   960,   180}-    ,{   960,  -850,   180,   960,   180}-    ,{   960, -1090,   180,   960,   180}-    ,{   180, -1090,   180,  -290,   180}-    }-   }-  ,{{{  1300,  1280,  1300,  1280,   -10}-    ,{   560,   540,   560,   540,   -10}-    ,{    50,    30,    50,    30,  -760}-    ,{  1300,  1280,  1300,  1280,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{   560,   540,   560,   540,   -10}-    ,{   560,   540,   560,   540,   -10}-    ,{    50,    30,    50,    30,  -760}-    ,{   -50,  -310,   -50,  -310, -1100}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{  1300,  1280,  1300,  1280,  -760}-    ,{  -220,  -480,  -220,  -480, -1270}-    ,{    50,    30,    50,    30,  -760}-    ,{  1300,  1280,  1300,  1280,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   }-  }- ,{{{{  2050,  1930,  1800,  2050,  1800}-    ,{  2050,  1400,  1270,  2050,  1270}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1930,  1930,  1800,  1760,  1800}-    ,{  1750,  1100,   970,  1750,   970}-    }-   ,{{  2050,  1400,  1270,  2050,  1270}-    ,{  2050,  1400,  1270,  2050,  1270}-    ,{  1740,  1090,   960,  1740,   960}-    ,{   130,    10,   130,  -260,  -110}-    ,{  1740,  1090,   960,  1740,   960}-    }-   ,{{  1760,  1110,   980,  1760,   980}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    }-   ,{{  1930,  1930,  1800,  1740,  1800}-    ,{   300,   190,   300,   -80,    60}-    ,{  1740,  1090,   960,  1740,   960}-    ,{  1930,  1930,  1800,  1650,  1800}-    ,{  1740,  1090,   960,  1740,   960}-    }-   ,{{  1760,  1110,   980,  1760,   980}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1760,  1110,   980,  1760,   980}-    ,{   360,   360,     0,  -150,     0}-    }-   }-  ,{{{  1930,  1930,  1800,  -300,  1800}-    ,{  1400,  1400,  1270,  -300,  1270}-    ,{  1100,  1100,   970,  -360,   970}-    ,{  1930,  1930,  1800,  -590,  1800}-    ,{  1100,  1100,   970,  -360,   970}-    }-   ,{{  1400,  1400,  1270,  -300,  1270}-    ,{  1400,  1400,  1270,  -300,  1270}-    ,{  1090,  1090,   960,  -610,   960}-    ,{    10,    10,  -110, -1690,  -110}-    ,{  1090,  1090,   960,  -610,   960}-    }-   ,{{  1110,  1110,   980,  -360,   980}-    ,{  1110,  1110,   980,  -590,   980}-    ,{  1100,  1100,   970,  -360,   970}-    ,{  1110,  1110,   980,  -590,   980}-    ,{  1100,  1100,   970,  -360,   970}-    }-   ,{{  1930,  1930,  1800,  -610,  1800}-    ,{   190,   190,    60, -1510,    60}-    ,{  1090,  1090,   960,  -610,   960}-    ,{  1930,  1930,  1800, -1020,  1800}-    ,{  1090,  1090,   960,  -610,   960}-    }-   ,{{  1110,  1110,   980,  -360,   980}-    ,{  1110,  1110,   980,  -590,   980}-    ,{  1100,  1100,   970,  -360,   970}-    ,{  1110,  1110,   980,  -590,   980}-    ,{   360,   360,     0, -1580,     0}-    }-   }-  ,{{{  1800,  1650,  1800,  1650,  1360}-    ,{  1270,  1120,  1270,  1120,   830}-    ,{   970,   820,   970,   820,   530}-    ,{  1800,  1650,  1800,  1650,  1360}-    ,{   970,   820,   970,   820,   530}-    }-   ,{{  1270,  1120,  1270,  1120,   830}-    ,{  1270,  1120,  1270,  1120,   830}-    ,{   960,   810,   960,   810,   520}-    ,{   130,  -260,   130,  -260,  -310}-    ,{   960,   810,   960,   810,   520}-    }-   ,{{   980,   830,   980,   830,   540}-    ,{   980,   830,   980,   830,   540}-    ,{   970,   820,   970,   820,   530}-    ,{   980,   830,   980,   830,   540}-    ,{   970,   820,   970,   820,   530}-    }-   ,{{  1800,  1650,  1800,  1650,  1360}-    ,{   300,   -80,   300,   -80,  -130}-    ,{   960,   810,   960,   810,   520}-    ,{  1800,  1650,  1800,  1650,  1360}-    ,{   960,   810,   960,   810,   520}-    }-   ,{{   980,   830,   980,   830,   540}-    ,{   980,   830,   980,   830,   540}-    ,{   970,   820,   970,   820,   530}-    ,{   980,   830,   980,   830,   540}-    ,{     0,  -150,     0,  -150,  -440}-    }-   }-  ,{{{  2050,     0,  1800,  2050,  1800}-    ,{  2050,     0,  1270,  2050,  1270}-    ,{  1750,   -60,   970,  1750,   970}-    ,{  1800,  -290,  1800,  1760,  1800}-    ,{  1750,   -60,   970,  1750,   970}-    }-   ,{{  2050,     0,  1270,  2050,  1270}-    ,{  2050,     0,  1270,  2050,  1270}-    ,{  1740,  -310,   960,  1740,   960}-    ,{  -110, -1390,  -110,  -580,  -110}-    ,{  1740,  -310,   960,  1740,   960}-    }-   ,{{  1760,   -60,   980,  1760,   980}-    ,{  1760,  -290,   980,  1760,   980}-    ,{  1750,   -60,   970,  1750,   970}-    ,{  1760,  -290,   980,  1760,   980}-    ,{  1750,   -60,   970,  1750,   970}-    }-   ,{{  1800,  -310,  1800,  1740,  1800}-    ,{    60, -1210,    60,  -400,    60}-    ,{  1740,  -310,   960,  1740,   960}-    ,{  1800,  -720,  1800,    80,  1800}-    ,{  1740,  -310,   960,  1740,   960}-    }-   ,{{  1760,   -60,   980,  1760,   980}-    ,{  1760,  -290,   980,  1760,   980}-    ,{  1750,   -60,   970,  1750,   970}-    ,{  1760,  -290,   980,  1760,   980}-    ,{     0, -1280,     0,  -470,     0}-    }-   }-  ,{{{  1670,  1650,  1670,  1650,   570}-    ,{  1140,  1120,  1140,  1120,   570}-    ,{   840,   820,   840,   820,    30}-    ,{  1670,  1650,  1670,  1650,    40}-    ,{   840,   820,   840,   820,    30}-    }-   ,{{  1140,  1120,  1140,  1120,   570}-    ,{  1140,  1120,  1140,  1120,   570}-    ,{   830,   810,   830,   810,    20}-    ,{     0,  -260,     0,  -260, -1050}-    ,{   830,   810,   830,   810,    20}-    }-   ,{{   850,   830,   850,   830,    40}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    }-   ,{{  1670,  1650,  1670,  1650,    20}-    ,{   180,   -80,   180,   -80,  -870}-    ,{   830,   810,   830,   810,    20}-    ,{  1670,  1650,  1670,  1650,  -380}-    ,{   830,   810,   830,   810,    20}-    }-   ,{{   850,   830,   850,   830,    40}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    ,{   850,   830,   850,   830,    40}-    ,{  -130,  -150,  -130,  -150,  -940}-    }-   }-  }- ,{{{{  2120,  2120,  1990,  2120,  1990}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  2120,  2120,  1990,  1990,  1990}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  1470,  1340,  2120,  1340}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{   180,    60,   180,  -210,   -60}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  2120,  1990,  1840,  1990}-    ,{  -120,  -230,  -120,  -510,  -360}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{  2120,  2120,  1990,  1840,  1990}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1550,   900,   770,  1550,   770}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{   640,   640,   270,   120,   270}-    }-   }-  ,{{{  2120,  2120,  1990,  -120,  1990}-    ,{  1470,  1470,  1340,  -230,  1340}-    ,{  1340,  1340,  1210,  -120,  1210}-    ,{  2120,  2120,  1990,  -360,  1990}-    ,{  1210,  1210,  1080,  -250,  1080}-    }-   ,{{  1470,  1470,  1340,  -230,  1340}-    ,{  1470,  1470,  1340,  -230,  1340}-    ,{  1190,  1190,  1060,  -510,  1060}-    ,{    60,    60,   -60, -1640,   -60}-    ,{  1190,  1190,  1060,  -510,  1060}-    }-   ,{{  1340,  1340,  1210,  -120,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{  1340,  1340,  1210,  -120,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{  1210,  1210,  1080,  -250,  1080}-    }-   ,{{  2120,  2120,  1990,  -510,  1990}-    ,{  -230,  -230,  -360, -1940,  -360}-    ,{  1190,  1190,  1060,  -510,  1060}-    ,{  2120,  2120,  1990,  -830,  1990}-    ,{  1190,  1190,  1060,  -510,  1060}-    }-   ,{{  1340,  1340,  1210,  -360,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{   900,   900,   770,  -560,   770}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{   640,   640,   270, -1300,   270}-    }-   }-  ,{{{  1990,  1840,  1990,  1840,  1550}-    ,{  1340,  1190,  1340,  1190,   900}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1990,  1840,  1990,  1840,  1550}-    ,{  1080,   930,  1080,   930,   640}-    }-   ,{{  1340,  1190,  1340,  1190,   900}-    ,{  1340,  1190,  1340,  1190,   900}-    ,{  1060,   910,  1060,   910,   620}-    ,{   180,  -210,   180,  -210,  -260}-    ,{  1060,   910,  1060,   910,   620}-    }-   ,{{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1080,   930,  1080,   930,   640}-    }-   ,{{  1990,  1840,  1990,  1840,  1550}-    ,{  -120,  -510,  -120,  -510,  -560}-    ,{  1060,   910,  1060,   910,   620}-    ,{  1990,  1840,  1990,  1840,  1550}-    ,{  1060,   910,  1060,   910,   620}-    }-   ,{{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{   770,   620,   770,   620,   330}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{   270,   120,   270,   120,  -170}-    }-   }-  ,{{{  2120,   180,  1990,  2120,  1990}-    ,{  2120,    60,  1340,  2120,  1340}-    ,{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1990,  1990,  1990}-    ,{  1860,    50,  1080,  1860,  1080}-    }-   ,{{  2120,    60,  1340,  2120,  1340}-    ,{  2120,    60,  1340,  2120,  1340}-    ,{  1840,  -210,  1060,  1840,  1060}-    ,{   -60, -1340,   -60,  -530,   -60}-    ,{  1840,  -210,  1060,  1840,  1060}-    }-   ,{{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1860,    50,  1080,  1860,  1080}-    }-   ,{{  1990,  -210,  1990,  1840,  1990}-    ,{  -360, -1640,  -360,  -830,  -360}-    ,{  1840,  -210,  1060,  1840,  1060}-    ,{  1990,  -530,  1990,   270,  1990}-    ,{  1840,  -210,  1060,  1840,  1060}-    }-   ,{{  1990,   -60,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1550,  -260,   770,  1550,   770}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{   270, -1000,   270,  -200,   270}-    }-   }-  ,{{{  1860,  1840,  1860,  1840,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1860,  1840,  1860,  1840,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1210,  1190,  1210,  1190,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{   930,   910,   930,   910,   120}-    ,{    50,  -210,    50,  -210, -1000}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1860,  1840,  1860,  1840,   120}-    ,{  -250,  -510,  -250,  -510, -1300}-    ,{   930,   910,   930,   910,   120}-    ,{  1860,  1840,  1860,  1840,  -200}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   640,   620,   640,   620,  -170}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   140,   120,   140,   120,  -670}-    }-   }-  }- ,{{{{  2120,  2120,  1990,  2120,  1990}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  2120,  2120,  1990,  1990,  1990}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  1470,  1340,  2120,  1340}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{   400,   290,   400,    10,   160}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  2120,  1990,  1840,  1990}-    ,{   300,   190,   300,   -80,    60}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{  2120,  2120,  1990,  1840,  1990}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{   640,   640,   270,   120,   270}-    }-   }-  ,{{{  2120,  2120,  1990,  -120,  1990}-    ,{  1470,  1470,  1340,  -230,  1340}-    ,{  1340,  1340,  1210,  -120,  1210}-    ,{  2120,  2120,  1990,  -360,  1990}-    ,{  1210,  1210,  1080,  -250,  1080}-    }-   ,{{  1470,  1470,  1340,  -230,  1340}-    ,{  1470,  1470,  1340,  -230,  1340}-    ,{  1190,  1190,  1060,  -510,  1060}-    ,{   290,   290,   160, -1410,   160}-    ,{  1190,  1190,  1060,  -510,  1060}-    }-   ,{{  1340,  1340,  1210,  -120,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{  1340,  1340,  1210,  -120,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{  1210,  1210,  1080,  -250,  1080}-    }-   ,{{  2120,  2120,  1990,  -510,  1990}-    ,{   190,   190,    60, -1510,    60}-    ,{  1190,  1190,  1060,  -510,  1060}-    ,{  2120,  2120,  1990,  -830,  1990}-    ,{  1190,  1190,  1060,  -510,  1060}-    }-   ,{{  1340,  1340,  1210,  -360,  1210}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{  1100,  1100,   970,  -360,   970}-    ,{  1340,  1340,  1210,  -360,  1210}-    ,{   640,   640,   270, -1300,   270}-    }-   }-  ,{{{  1990,  1840,  1990,  1840,  1550}-    ,{  1340,  1190,  1340,  1190,   900}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1990,  1840,  1990,  1840,  1550}-    ,{  1080,   930,  1080,   930,   640}-    }-   ,{{  1340,  1190,  1340,  1190,   900}-    ,{  1340,  1190,  1340,  1190,   900}-    ,{  1060,   910,  1060,   910,   620}-    ,{   400,    10,   400,    10,   -40}-    ,{  1060,   910,  1060,   910,   620}-    }-   ,{{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{  1080,   930,  1080,   930,   640}-    }-   ,{{  1990,  1840,  1990,  1840,  1550}-    ,{   300,   -80,   300,   -80,  -130}-    ,{  1060,   910,  1060,   910,   620}-    ,{  1990,  1840,  1990,  1840,  1550}-    ,{  1060,   910,  1060,   910,   620}-    }-   ,{{  1210,  1060,  1210,  1060,   770}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{   970,   820,   970,   820,   530}-    ,{  1210,  1060,  1210,  1060,   770}-    ,{   270,   120,   270,   120,  -170}-    }-   }-  ,{{{  2120,   180,  1990,  2120,  1990}-    ,{  2120,    60,  1340,  2120,  1340}-    ,{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1990,  1990,  1990}-    ,{  1860,    50,  1080,  1860,  1080}-    }-   ,{{  2120,    60,  1340,  2120,  1340}-    ,{  2120,    60,  1340,  2120,  1340}-    ,{  1840,  -210,  1060,  1840,  1060}-    ,{   160, -1110,   160,  -310,   160}-    ,{  1840,  -210,  1060,  1840,  1060}-    }-   ,{{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1990,   180,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1860,    50,  1080,  1860,  1080}-    }-   ,{{  1990,  -210,  1990,  1840,  1990}-    ,{    60, -1210,    60,  -400,    60}-    ,{  1840,  -210,  1060,  1840,  1060}-    ,{  1990,  -530,  1990,   270,  1990}-    ,{  1840,  -210,  1060,  1840,  1060}-    }-   ,{{  1990,   -60,  1210,  1990,  1210}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{  1750,   -60,   970,  1750,   970}-    ,{  1990,   -60,  1210,  1990,  1210}-    ,{   270, -1000,   270,  -200,   270}-    }-   }-  ,{{{  1860,  1840,  1860,  1840,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1860,  1840,  1860,  1840,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1210,  1190,  1210,  1190,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{   930,   910,   930,   910,   120}-    ,{   270,    10,   270,    10,  -780}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1860,  1840,  1860,  1840,   120}-    ,{   180,   -80,   180,   -80,  -870}-    ,{   930,   910,   930,   910,   120}-    ,{  1860,  1840,  1860,  1840,  -200}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   840,   820,   840,   820,    30}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   140,   120,   140,   120,  -670}-    }-   }-  }- }-,{{{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-   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 ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  ,{{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   ,{{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    ,{   INF,   INF,   INF,   INF,   INF}-    }-   }-  }- ,{{{{  1350,   850,   720,  1350,   720}-    ,{  1300,   650,   540,  1300,   520}-    ,{  1350,   700,   570,  1350,   570}-    ,{  1300,   850,   720,  1300,   720}-    ,{  1250,   590,   460,  1250,   460}-    }-   ,{{  1160,   500,   400,  1160,   370}-    ,{  1160,   500,   370,  1160,   370}-    ,{   850,   190,    60,   850,    60}-    ,{   400,   290,   400,    10,   170}-    ,{   850,   190,    60,   850,    60}-    }-   ,{{  1300,   650,   520,  1300,   520}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1290,   640,   510,  1290,   510}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1250,   590,   460,  1250,   460}-    }-   ,{{   850,   850,   720,   850,   720}-    ,{   540,     0,   540,  -270,  -120}-    ,{   850,   190,    60,   850,    60}-    ,{   850,   850,   720,   570,   720}-    ,{   850,   190,    60,   850,    60}-    }-   ,{{  1350,   700,   570,  1350,   570}-    ,{  1300,   650,   520,  1300,   520}-    ,{  1350,   700,   570,  1350,   570}-    ,{  1300,   650,   520,  1300,   520}-    ,{   100,   100,  -270,  -230,  -270}-    }-   }-  ,{{{   850,   850,   720,  -330,   720}-    ,{   650,   650,   520,  -620,   520}-    ,{   700,   700,   570,  -330,   570}-    ,{   850,   850,   720,  -620,   720}-    ,{   590,   590,   460,  -440,   460}-    }-   ,{{   500,   500,   370,  -770,   370}-    ,{   500,   500,   370,  -770,   370}-    ,{   190,   190,    60, -1070,    60}-    ,{   290,   290,   160,  -980,   160}-    ,{   190,   190,    60, -1080,    60}-    }-   ,{{   650,   650,   520,  -390,   520}-    ,{   650,   650,   520,  -620,   520}-    ,{   640,   640,   510,  -390,   510}-    ,{   650,   650,   520,  -620,   520}-    ,{   590,   590,   460,  -440,   460}-    }-   ,{{   850,   850,   720, -1080,   720}-    ,{    10,     0,    10, -1270,  -120}-    ,{   190,   190,    60, -1080,    60}-    ,{   850,   850,   720, -1080,   720}-    ,{   190,   190,    60, -1080,    60}-    }-   ,{{   700,   700,   570,  -330,   570}-    ,{   650,   650,   520,  -620,   520}-    ,{   700,   700,   570,  -330,   570}-    ,{   650,   650,   520,  -620,   520}-    ,{   100,   100,  -270, -1300,  -270}-    }-   }-  ,{{{   720,   570,   720,   570,   480}-    ,{   540,   370,   540,   370,   280}-    ,{   570,   420,   570,   420,   340}-    ,{   720,   570,   720,   570,   480}-    ,{   460,   310,   460,   310,   230}-    }-   ,{{   400,   220,   400,   220,   170}-    ,{   370,   220,   370,   220,   140}-    ,{    60,   -80,    60,   -80,  -170}-    ,{   400,    10,   400,    10,   170}-    ,{    60,   -80,    60,   -80,  -170}-    }-   ,{{   520,   370,   520,   370,   280}-    ,{   520,   370,   520,   370,   280}-    ,{   510,   360,   510,   360,   280}-    ,{   520,   370,   520,   370,   280}-    ,{   460,   310,   460,   310,   230}-    }-   ,{{   720,   570,   720,   570,   480}-    ,{   540,  -100,   540,  -270,  -120}-    ,{    60,   -80,    60,   -80,  -170}-    ,{   720,   570,   720,   570,   480}-    ,{    60,   -80,    60,   -80,  -170}-    }-   ,{{   570,   420,   570,   420,   340}-    ,{   520,   370,   520,   370,   280}-    ,{   570,   420,   570,   420,   340}-    ,{   520,   370,   520,   370,   280}-    ,{  -270,  -420,  -270,  -420,  -500}-    }-   }-  ,{{{  1350,  -230,   720,  1350,   720}-    ,{  1300,  -530,   520,  1300,   520}-    ,{  1350,  -230,   570,  1350,   570}-    ,{  1300,  -530,   720,  1300,   720}-    ,{  1250,  -340,   460,  1250,   460}-    }-   ,{{  1160,  -670,   370,  1160,   370}-    ,{  1160,  -670,   370,  1160,   370}-    ,{   850,  -980,    60,   850,    60}-    ,{   160,  -890,   160,  -310,   160}-    ,{   850,  -980,    60,   850,    60}-    }-   ,{{  1300,  -290,   520,  1300,   520}-    ,{  1300,  -530,   520,  1300,   520}-    ,{  1290,  -290,   510,  1290,   510}-    ,{  1300,  -530,   520,  1300,   520}-    ,{  1250,  -340,   460,  1250,   460}-    }-   ,{{   850,  -980,   720,   850,   720}-    ,{  -120, -1170,  -120,  -590,  -120}-    ,{   850,  -980,    60,   850,    60}-    ,{   720, -1580,   720, -1000,   720}-    ,{   850,  -980,    60,   850,    60}-    }-   ,{{  1350,  -230,   570,  1350,   570}-    ,{  1300,  -530,   520,  1300,   520}-    ,{  1350,  -230,   570,  1350,   570}-    ,{  1300,  -530,   520,  1300,   520}-    ,{  -230, -1320,  -270,  -230,  -270}-    }-   }-  ,{{{   590,   570,   590,   570,   -90}-    ,{   390,   370,   390,   370,   -90}-    ,{   440,   420,   440,   420,  -360}-    ,{   590,   570,   590,   570,  -420}-    ,{   330,   310,   330,   310,  -470}-    }-   ,{{   270,   220,   270,   220,  -320}-    ,{   240,   220,   240,   220,  -320}-    ,{   -60,   -80,   -60,   -80,  -830}-    ,{   270,    10,   270,    10,  -780}-    ,{   -60,   -80,   -60,   -80,  -870}-    }-   ,{{   390,   370,   390,   370,   -90}-    ,{   390,   370,   390,   370,   -90}-    ,{   380,   360,   380,   360,  -420}-    ,{   390,   370,   390,   370,  -420}-    ,{   330,   310,   330,   310,  -470}-    }-   ,{{   590,   570,   590,   570,  -810}-    ,{   -10,  -270,   -10,  -270,  -810}-    ,{   -60,   -80,   -60,   -80,  -870}-    ,{   590,   570,   590,   570, -1470}-    ,{   -60,   -80,   -60,   -80,  -870}-    }-   ,{{   440,   420,   440,   420,  -360}-    ,{   390,   370,   390,   370,  -420}-    ,{   440,   420,   440,   420,  -360}-    ,{   390,   370,   390,   370,  -420}-    ,{  -400,  -420,  -400,  -420, -1210}-    }-   }-  }- ,{{{{  1320,   850,   720,  1320,   720}-    ,{  1320,   670,   540,  1320,   540}-    ,{   870,   220,    90,   870,    90}-    ,{   960,   850,   720,   960,   720}-    ,{   870,   250,    90,   870,    90}-    }-   ,{{  1320,   670,   540,  1320,   540}-    ,{  1320,   670,   540,  1320,   540}-    ,{   870,   220,    90,   870,    90}-    ,{  -410,  -520,  -410,  -800,  -640}-    ,{   870,   220,    90,   870,    90}-    }-   ,{{   960,   300,   170,   960,   170}-    ,{   960,   300,   170,   960,   170}-    ,{   650,     0,  -130,   650,  -130}-    ,{   960,   300,   170,   960,   170}-    ,{   650,     0,  -130,   650,  -130}-    }-   ,{{   870,   850,   720,   870,   720}-    ,{    70,   -40,    70,  -320,  -170}-    ,{   870,   220,    90,   870,    90}-    ,{   850,   850,   720,   570,   720}-    ,{   870,   220,    90,   870,    90}-    }-   ,{{   960,   300,   170,   960,   170}-    ,{   960,   300,   170,   960,   170}-    ,{   340,  -310,  -440,   340,  -440}-    ,{   960,   300,   170,   960,   170}-    ,{   250,   250,   -90,  -260,  -110}-    }-   }-  ,{{{   850,   850,   720,   540,   720}-    ,{   670,   670,   540,    10,   540}-    ,{   540,   220,    90,   540,    90}-    ,{   850,   850,   720,  -970,   720}-    ,{   250,   250,    90,  -810,    90}-    }-   ,{{   670,   670,   540,  -100,   540}-    ,{   670,   670,   540,  -600,   540}-    ,{   220,   220,    90,  -100,    90}-    ,{  -520,  -520,  -650, -1790,  -650}-    ,{   220,   220,    90, -1050,    90}-    }-   ,{{   540,   300,   170,   540,   170}-    ,{   300,   300,   170,    10,   170}-    ,{   540,     0,  -130,   540,  -130}-    ,{   300,   300,   170,  -970,   170}-    ,{     0,     0,  -130, -1030,  -130}-    }-   ,{{   850,   850,   720, -1050,   720}-    ,{   -40,   -40,  -170, -1320,  -170}-    ,{   220,   220,    90, -1050,    90}-    ,{   850,   850,   720, -1680,   720}-    ,{   220,   220,    90, -1050,    90}-    }-   ,{{   300,   300,   170,  -810,   170}-    ,{   300,   300,   170,  -970,   170}-    ,{  -310,  -310,  -440, -1340,  -440}-    ,{   300,   300,   170,  -970,   170}-    ,{   250,   250,   -90,  -810,  -110}-    }-   }-  ,{{{   720,   570,   720,   570,   480}-    ,{   540,   390,   540,   390,   300}-    ,{    90,   -60,    90,   -60,  -140}-    ,{   720,   570,   720,   570,   480}-    ,{    90,   -60,    90,   -60,  -140}-    }-   ,{{   540,   390,   540,   390,   300}-    ,{   540,   390,   540,   390,   300}-    ,{    90,   -60,    90,   -60,  -140}-    ,{  -410,  -800,  -410,  -800,  -640}-    ,{    90,   -60,    90,   -60,  -140}-    }-   ,{{   170,    20,   170,    20,   -60}-    ,{   170,    20,   170,    20,   -60}-    ,{  -130,  -280,  -130,  -280,  -360}-    ,{   170,    20,   170,    20,   -60}-    ,{  -130,  -280,  -130,  -280,  -360}-    }-   ,{{   720,   570,   720,   570,   480}-    ,{    70,  -320,    70,  -320,  -170}-    ,{    90,   -60,    90,   -60,  -140}-    ,{   720,   570,   720,   570,   480}-    ,{    90,   -60,    90,   -60,  -140}-    }-   ,{{   170,    20,   170,    20,   -60}-    ,{   170,    20,   170,    20,   -60}-    ,{  -440,  -590,  -440,  -590,  -670}-    ,{   170,    20,   170,    20,   -60}-    ,{  -110,  -260,  -110,  -260,  -350}-    }-   }-  ,{{{  1320,  -350,   720,  1320,   720}-    ,{  1320,  -730,   540,  1320,   540}-    ,{   870,  -350,    90,   870,    90}-    ,{   960,  -870,   720,   960,   720}-    ,{   870,  -940,    90,   870,    90}-    }-   ,{{  1320,  -350,   540,  1320,   540}-    ,{  1320,  -730,   540,  1320,   540}-    ,{   870,  -350,    90,   870,    90}-    ,{  -650, -1920,  -650, -1120,  -650}-    ,{   870,  -960,    90,   870,    90}-    }-   ,{{   960,  -870,   170,   960,   170}-    ,{   960, -1100,   170,   960,   170}-    ,{   650,  -940,  -130,   650,  -130}-    ,{   960,  -870,   170,   960,   170}-    ,{   650,  -940,  -130,   650,  -130}-    }-   ,{{   870,  -960,   720,   870,   720}-    ,{  -170, -1450,  -170,  -640,  -170}-    ,{   870,  -960,    90,   870,    90}-    ,{   720, -1370,   720, -1000,   720}-    ,{   870,  -960,    90,   870,    90}-    }-   ,{{   960,  -870,   170,   960,   170}-    ,{   960,  -870,   170,   960,   170}-    ,{   340, -1250,  -440,   340,  -440}-    ,{   960,  -870,   170,   960,   170}-    ,{  -110, -1360,  -110,  -580,  -110}-    }-   }-  ,{{{   590,   570,   590,   570,  -160}-    ,{   410,   390,   410,   390,  -160}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{   590,   570,   590,   570,  -230}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{   410,   390,   410,   390,  -160}-    ,{   410,   390,   410,   390,  -160}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{  -540,  -800,  -540,  -800, -1520}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{    40,    20,    40,    20,  -400}-    ,{    40,    20,    40,    20,  -400}-    ,{  -260,  -280,  -260,  -280, -1070}-    ,{    40,    20,    40,    20,  -760}-    ,{  -260,  -280,  -260,  -280, -1070}-    }-   ,{{   590,   570,   590,   570,  -230}-    ,{   -60,  -320,   -60,  -320, -1110}-    ,{   -40,   -60,   -40,   -60,  -850}-    ,{   590,   570,   590,   570,  -230}-    ,{   -40,   -60,   -40,   -60,  -850}-    }-   ,{{    40,    20,    40,    20,  -760}-    ,{    40,    20,    40,    20,  -760}-    ,{  -570,  -590,  -570,  -590, -1380}-    ,{    40,    20,    40,    20,  -760}-    ,{  -240,  -260,  -240,  -260, -1050}-    }-   }-  }- ,{{{{  1010,  1010,   880,   730,   880}-    ,{   410,   -30,    40,   410,  -190}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  1010,  1010,   880,   730,   880}-    ,{   410,     0,  -370,   410,  -370}-    }-   ,{{   410,   -70,  -150,   410,  -370}-    ,{   230,   -70,  -550,   230,  -550}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  -150,  -260,  -150,  -540,  -380}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{  1010,  1010,   880,   730,   880}-    ,{    40,   -30,    40,  -350,  -190}-    ,{   410,  -240,  -370,   410,  -370}-    ,{  1010,  1010,   880,   730,   880}-    ,{   410,  -240,  -370,   410,  -370}-    }-   ,{{   410,     0,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{   410,  -240,  -370,   410,  -370}-    ,{     0,     0,  -370,  -520,  -370}-    }-   }-  ,{{{  1010,  1010,   880, -1280,   880}-    ,{   -30,   -30,  -200, -1340,  -200}-    ,{  -240,  -240,  -370, -1280,  -370}-    ,{  1010,  1010,   880, -1520,   880}-    ,{     0,     0,  -370, -1280,  -370}-    }-   ,{{   -70,   -70,  -370, -1520,  -370}-    ,{   -70,   -70,  -550, -1700,  -550}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{  -260,  -260,  -390, -1530,  -390}-    ,{  -240,  -240,  -370, -1520,  -370}-    }-   ,{{  -240,  -240,  -370, -1280,  -370}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{  -240,  -240,  -370, -1280,  -370}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{  -240,  -240,  -370, -1280,  -370}-    }-   ,{{  1010,  1010,   880, -1340,   880}-    ,{   -30,   -30,  -200, -1340,  -200}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{  1010,  1010,   880, -1520,   880}-    ,{  -240,  -240,  -370, -1520,  -370}-    }-   ,{{     0,     0,  -370, -1280,  -370}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{  -240,  -240,  -370, -1280,  -370}-    ,{  -240,  -240,  -370, -1520,  -370}-    ,{     0,     0,  -370, -1520,  -370}-    }-   }-  ,{{{   880,   730,   880,   730,   640}-    ,{    40,  -350,    40,  -350,  -190}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{   880,   730,   880,   730,   640}-    ,{  -370,  -520,  -370,  -520,  -610}-    }-   ,{{  -150,  -520,  -150,  -520,  -380}-    ,{  -550,  -700,  -550,  -700,  -790}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -150,  -540,  -150,  -540,  -380}-    ,{  -370,  -520,  -370,  -520,  -610}-    }-   ,{{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    }-   ,{{   880,   730,   880,   730,   640}-    ,{    40,  -350,    40,  -350,  -190}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{   880,   730,   880,   730,   640}-    ,{  -370,  -520,  -370,  -520,  -610}-    }-   ,{{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    ,{  -370,  -520,  -370,  -520,  -610}-    }-   }-  ,{{{   880, -1180,   880,   410,   880}-    ,{   410, -1250,  -200,   410,  -200}-    ,{   410, -1180,  -370,   410,  -370}-    ,{   880, -1420,   880,   410,   880}-    ,{   410, -1180,  -370,   410,  -370}-    }-   ,{{   410, -1420,  -370,   410,  -370}-    ,{   230, -1600,  -550,   230,  -550}-    ,{   410, -1420,  -370,   410,  -370}-    ,{  -390, -1440,  -390,  -860,  -390}-    ,{   410, -1420,  -370,   410,  -370}-    }-   ,{{   410, -1180,  -370,   410,  -370}-    ,{   410, -1420,  -370,   410,  -370}-    ,{   410, -1180,  -370,   410,  -370}-    ,{   410, -1420,  -370,   410,  -370}-    ,{   410, -1180,  -370,   410,  -370}-    }-   ,{{   880, -1250,   880,   410,   880}-    ,{  -200, -1250,  -200,  -670,  -200}-    ,{   410, -1420,  -370,   410,  -370}-    ,{   880, -1420,   880,  -840,   880}-    ,{   410, -1420,  -370,   410,  -370}-    }-   ,{{   410, -1180,  -370,   410,  -370}-    ,{   410, -1420,  -370,   410,  -370}-    ,{   410, -1180,  -370,   410,  -370}-    ,{   410, -1420,  -370,   410,  -370}-    ,{  -370, -1420,  -370,  -840,  -370}-    }-   }-  ,{{{   750,   730,   750,   730, -1140}-    ,{   -90,  -350,   -90,  -350, -1140}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{   750,   730,   750,   730, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -280,  -520,  -280,  -520, -1250}-    ,{  -680,  -700,  -680,  -700, -1250}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -280,  -540,  -280,  -540, -1330}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{   750,   730,   750,   730, -1140}-    ,{   -90,  -350,   -90,  -350, -1140}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{   750,   730,   750,   730, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   ,{{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    ,{  -500,  -520,  -500,  -520, -1310}-    }-   }-  }- ,{{{{  1560,  1560,  1430,  1470,  1430}-    ,{  1470,   820,   690,  1470,   690}-    ,{   960,   310,   180,   960,   180}-    ,{  1560,  1560,  1430,  1280,  1430}-    ,{   960,   550,   180,   960,   180}-    }-   ,{{  1470,   820,   690,  1470,   690}-    ,{  1470,   820,   690,  1470,   690}-    ,{   960,   310,   180,   960,   180}-    ,{    80,   -30,    80,  -310,  -150}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{  1560,  1560,  1430,  1280,  1430}-    ,{   -90,  -200,   -90,  -480,  -320}-    ,{   960,   310,   180,   960,   180}-    ,{  1560,  1560,  1430,  1280,  1430}-    ,{   960,   310,   180,   960,   180}-    }-   ,{{   960,   550,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   960,   310,   180,   960,   180}-    ,{   550,   550,   180,    30,   180}-    }-   }-  ,{{{  1560,  1560,  1430,   -30,  1430}-    ,{   820,   820,   690,   -30,   690}-    ,{   310,   310,   180,  -720,   180}-    ,{  1560,  1560,  1430,  -960,  1430}-    ,{   550,   550,   180,  -720,   180}-    }-   ,{{   820,   820,   690,   -30,   690}-    ,{   820,   820,   690,   -30,   690}-    ,{   310,   310,   180,  -960,   180}-    ,{   -30,   -30,  -160, -1300,  -160}-    ,{   310,   310,   180,  -960,   180}-    }-   ,{{   310,   310,   180,  -720,   180}-    ,{   310,   310,   180,  -960,   180}-    ,{   310,   310,   180,  -720,   180}-    ,{   310,   310,   180,  -960,   180}-    ,{   310,   310,   180,  -720,   180}-    }-   ,{{  1560,  1560,  1430,  -960,  1430}-    ,{  -200,  -200,  -330, -1470,  -330}-    ,{   310,   310,   180,  -960,   180}-    ,{  1560,  1560,  1430,  -960,  1430}-    ,{   310,   310,   180,  -960,   180}-    }-   ,{{   550,   550,   180,  -720,   180}-    ,{   310,   310,   180,  -960,   180}-    ,{   310,   310,   180,  -720,   180}-    ,{   310,   310,   180,  -960,   180}-    ,{   550,   550,   180,  -960,   180}-    }-   }-  ,{{{  1430,  1280,  1430,  1280,  1200}-    ,{   690,   540,   690,   540,   450}-    ,{   180,    30,   180,    30,   -50}-    ,{  1430,  1280,  1430,  1280,  1200}-    ,{   180,    30,   180,    30,   -50}-    }-   ,{{   690,   540,   690,   540,   450}-    ,{   690,   540,   690,   540,   450}-    ,{   180,    30,   180,    30,   -50}-    ,{    80,  -310,    80,  -310,  -150}-    ,{   180,    30,   180,    30,   -50}-    }-   ,{{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    }-   ,{{  1430,  1280,  1430,  1280,  1200}-    ,{   -90,  -480,   -90,  -480,  -320}-    ,{   180,    30,   180,    30,   -50}-    ,{  1430,  1280,  1430,  1280,  1200}-    ,{   180,    30,   180,    30,   -50}-    }-   ,{{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    ,{   180,    30,   180,    30,   -50}-    }-   }-  ,{{{  1470,  -360,  1430,  1470,  1430}-    ,{  1470,  -360,   690,  1470,   690}-    ,{   960,  -630,   180,   960,   180}-    ,{  1430,  -870,  1430,   960,  1430}-    ,{   960,  -630,   180,   960,   180}-    }-   ,{{  1470,  -360,   690,  1470,   690}-    ,{  1470,  -360,   690,  1470,   690}-    ,{   960,  -870,   180,   960,   180}-    ,{  -160, -1210,  -160,  -630,  -160}-    ,{   960,  -870,   180,   960,   180}-    }-   ,{{   960,  -630,   180,   960,   180}-    ,{   960,  -870,   180,   960,   180}-    ,{   960,  -630,   180,   960,   180}-    ,{   960,  -870,   180,   960,   180}-    ,{   960,  -630,   180,   960,   180}-    }-   ,{{  1430,  -870,  1430,   960,  1430}-    ,{  -330, -1380,  -330,  -800,  -330}-    ,{   960,  -870,   180,   960,   180}-    ,{  1430,  -870,  1430,  -290,  1430}-    ,{   960,  -870,   180,   960,   180}-    }-   ,{{   960,  -630,   180,   960,   180}-    ,{   960,  -870,   180,   960,   180}-    ,{   960,  -630,   180,   960,   180}-    ,{   960,  -870,   180,   960,   180}-    ,{   180,  -870,   180,  -290,   180}-    }-   }-  ,{{{  1300,  1280,  1300,  1280,   -10}-    ,{   560,   540,   560,   540,   -10}-    ,{    50,    30,    50,    30,  -760}-    ,{  1300,  1280,  1300,  1280,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{   560,   540,   560,   540,   -10}-    ,{   560,   540,   560,   540,   -10}-    ,{    50,    30,    50,    30,  -760}-    ,{   -50,  -310,   -50,  -310, -1100}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{  1300,  1280,  1300,  1280,  -760}-    ,{  -220,  -480,  -220,  -480, -1270}-    ,{    50,    30,    50,    30,  -760}-    ,{  1300,  1280,  1300,  1280,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   ,{{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    ,{    50,    30,    50,    30,  -760}-    }-   }-  }- ,{{{{  2050,  1930,  1800,  2050,  1800}-    ,{  2050,  1400,  1270,  2050,  1270}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1930,  1930,  1800,  1760,  1800}-    ,{  1750,  1100,   970,  1750,   970}-    }-   ,{{  2050,  1400,  1270,  2050,  1270}-    ,{  2050,  1400,  1270,  2050,  1270}-    ,{  1740,  1090,   960,  1740,   960}-    ,{   130,    10,   130,  -260,  -110}-    ,{  1740,  1090,   960,  1740,   960}-    }-   ,{{  1760,  1110,   980,  1760,   980}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    }-   ,{{  1930,  1930,  1800,  1740,  1800}-    ,{   300,   190,   300,   -80,    70}-    ,{  1740,  1090,   960,  1740,   960}-    ,{  1930,  1930,  1800,  1650,  1800}-    ,{  1740,  1090,   960,  1740,   960}-    }-   ,{{  1760,  1110,   980,  1760,   980}-    ,{  1760,  1110,   980,  1760,   980}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1760,  1110,   980,  1760,   980}-    ,{   360,   360,     0,  -150,     0}-    }-   }-  ,{{{  1930,  1930,  1800,   130,  1800}-    ,{  1400,  1400,  1270,   130,  1270}-    ,{  1100,  1100,   970,    70,   970}-    ,{  1930,  1930,  1800,  -160,  1800}-    ,{  1100,  1100,   970,    70,   970}-    }-   ,{{  1400,  1400,  1270,   130,  1270}-    ,{  1400,  1400,  1270,   130,  1270}-    ,{  1090,  1090,   960,  -180,   960}-    ,{    10,    10,  -110, -1260,  -110}-    ,{  1090,  1090,   960,  -180,   960}-    }-   ,{{  1110,  1110,   980,    70,   980}-    ,{  1110,  1110,   980,  -160,   980}-    ,{  1100,  1100,   970,    70,   970}-    ,{  1110,  1110,   980,  -160,   980}-    ,{  1100,  1100,   970,    70,   970}-    }-   ,{{  1930,  1930,  1800,  -180,  1800}-    ,{   190,   190,    60, -1080,    60}-    ,{  1090,  1090,   960,  -180,   960}-    ,{  1930,  1930,  1800,  -590,  1800}-    ,{  1090,  1090,   960,  -180,   960}-    }-   ,{{  1110,  1110,   980,    70,   980}-    ,{  1110,  1110,   980,  -160,   980}-    ,{  1100,  1100,   970,    70,   970}-    ,{  1110,  1110,   980,  -160,   980}-    ,{   360,   360,     0, -1150,     0}-    }-   }-  ,{{{  1800,  1650,  1800,  1650,  1570}-    ,{  1270,  1120,  1270,  1120,  1040}-    ,{   970,   820,   970,   820,   740}-    ,{  1800,  1650,  1800,  1650,  1570}-    ,{   970,   820,   970,   820,   740}-    }-   ,{{  1270,  1120,  1270,  1120,  1040}-    ,{  1270,  1120,  1270,  1120,  1040}-    ,{   960,   810,   960,   810,   730}-    ,{   130,  -260,   130,  -260,  -110}-    ,{   960,   810,   960,   810,   730}-    }-   ,{{   980,   830,   980,   830,   740}-    ,{   980,   830,   980,   830,   740}-    ,{   970,   820,   970,   820,   740}-    ,{   980,   830,   980,   830,   740}-    ,{   970,   820,   970,   820,   740}-    }-   ,{{  1800,  1650,  1800,  1650,  1570}-    ,{   300,   -80,   300,   -80,    70}-    ,{   960,   810,   960,   810,   730}-    ,{  1800,  1650,  1800,  1650,  1570}-    ,{   960,   810,   960,   810,   730}-    }-   ,{{   980,   830,   980,   830,   740}-    ,{   980,   830,   980,   830,   740}-    ,{   970,   820,   970,   820,   740}-    ,{   980,   830,   980,   830,   740}-    ,{     0,  -150,     0,  -150,  -240}-    }-   }-  ,{{{  2050,   220,  1800,  2050,  1800}-    ,{  2050,   220,  1270,  2050,  1270}-    ,{  1750,   170,   970,  1750,   970}-    ,{  1800,   -70,  1800,  1760,  1800}-    ,{  1750,   170,   970,  1750,   970}-    }-   ,{{  2050,   220,  1270,  2050,  1270}-    ,{  2050,   220,  1270,  2050,  1270}-    ,{  1740,   -80,   960,  1740,   960}-    ,{  -110, -1160,  -110,  -580,  -110}-    ,{  1740,   -80,   960,  1740,   960}-    }-   ,{{  1760,   170,   980,  1760,   980}-    ,{  1760,   -70,   980,  1760,   980}-    ,{  1750,   170,   970,  1750,   970}-    ,{  1760,   -70,   980,  1760,   980}-    ,{  1750,   170,   970,  1750,   970}-    }-   ,{{  1800,   -80,  1800,  1740,  1800}-    ,{    60,  -980,    60,  -400,    60}-    ,{  1740,   -80,   960,  1740,   960}-    ,{  1800,  -490,  1800,    80,  1800}-    ,{  1740,   -80,   960,  1740,   960}-    }-   ,{{  1760,   170,   980,  1760,   980}-    ,{  1760,   -70,   980,  1760,   980}-    ,{  1750,   170,   970,  1750,   970}-    ,{  1760,   -70,   980,  1760,   980}-    ,{     0, -1050,     0,  -470,     0}-    }-   }-  ,{{{  1670,  1650,  1670,  1650,   570}-    ,{  1140,  1120,  1140,  1120,   570}-    ,{   840,   820,   840,   820,    30}-    ,{  1670,  1650,  1670,  1650,    40}-    ,{   840,   820,   840,   820,    30}-    }-   ,{{  1140,  1120,  1140,  1120,   570}-    ,{  1140,  1120,  1140,  1120,   570}-    ,{   830,   810,   830,   810,    20}-    ,{     0,  -260,     0,  -260, -1050}-    ,{   830,   810,   830,   810,    20}-    }-   ,{{   850,   830,   850,   830,    40}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    }-   ,{{  1670,  1650,  1670,  1650,    20}-    ,{   180,   -80,   180,   -80,  -870}-    ,{   830,   810,   830,   810,    20}-    ,{  1670,  1650,  1670,  1650,  -380}-    ,{   830,   810,   830,   810,    20}-    }-   ,{{   850,   830,   850,   830,    40}-    ,{   850,   830,   850,   830,    40}-    ,{   840,   820,   840,   820,    30}-    ,{   850,   830,   850,   830,    40}-    ,{  -130,  -150,  -130,  -150,  -940}-    }-   }-  }- ,{{{{  2120,  2120,  1990,  2120,  1990}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  2120,  2120,  1990,  1990,  1990}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  1470,  1340,  2120,  1340}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{   180,    60,   180,  -210,   -60}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  2120,  1990,  1840,  1990}-    ,{  -120,  -230,  -120,  -510,  -360}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{  2120,  2120,  1990,  1840,  1990}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1550,   900,   770,  1550,   770}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{   640,   640,   270,   120,   270}-    }-   }-  ,{{{  2120,  2120,  1990,   300,  1990}-    ,{  1470,  1470,  1340,   190,  1340}-    ,{  1340,  1340,  1210,   300,  1210}-    ,{  2120,  2120,  1990,    60,  1990}-    ,{  1210,  1210,  1080,   180,  1080}-    }-   ,{{  1470,  1470,  1340,   190,  1340}-    ,{  1470,  1470,  1340,   190,  1340}-    ,{  1190,  1190,  1060,   -80,  1060}-    ,{    60,    60,   -60, -1210,   -60}-    ,{  1190,  1190,  1060,   -80,  1060}-    }-   ,{{  1340,  1340,  1210,   300,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{  1340,  1340,  1210,   300,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{  1210,  1210,  1080,   180,  1080}-    }-   ,{{  2120,  2120,  1990,   -80,  1990}-    ,{  -230,  -230,  -360, -1510,  -360}-    ,{  1190,  1190,  1060,   -80,  1060}-    ,{  2120,  2120,  1990,  -400,  1990}-    ,{  1190,  1190,  1060,   -80,  1060}-    }-   ,{{  1340,  1340,  1210,    60,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{   900,   900,   770,  -130,   770}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{   640,   640,   270,  -870,   270}-    }-   }-  ,{{{  1990,  1840,  1990,  1840,  1750}-    ,{  1340,  1190,  1340,  1190,  1100}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1990,  1840,  1990,  1840,  1750}-    ,{  1080,   930,  1080,   930,   840}-    }-   ,{{  1340,  1190,  1340,  1190,  1100}-    ,{  1340,  1190,  1340,  1190,  1100}-    ,{  1060,   910,  1060,   910,   820}-    ,{   180,  -210,   180,  -210,   -60}-    ,{  1060,   910,  1060,   910,   820}-    }-   ,{{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1080,   930,  1080,   930,   840}-    }-   ,{{  1990,  1840,  1990,  1840,  1750}-    ,{  -120,  -510,  -120,  -510,  -360}-    ,{  1060,   910,  1060,   910,   820}-    ,{  1990,  1840,  1990,  1840,  1750}-    ,{  1060,   910,  1060,   910,   820}-    }-   ,{{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{   770,   620,   770,   620,   530}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{   270,   120,   270,   120,    30}-    }-   }-  ,{{{  2120,   400,  1990,  2120,  1990}-    ,{  2120,   290,  1340,  2120,  1340}-    ,{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1990,  1990,  1990}-    ,{  1860,   270,  1080,  1860,  1080}-    }-   ,{{  2120,   290,  1340,  2120,  1340}-    ,{  2120,   290,  1340,  2120,  1340}-    ,{  1840,    10,  1060,  1840,  1060}-    ,{   -60, -1110,   -60,  -530,   -60}-    ,{  1840,    10,  1060,  1840,  1060}-    }-   ,{{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1860,   270,  1080,  1860,  1080}-    }-   ,{{  1990,    10,  1990,  1840,  1990}-    ,{  -360, -1410,  -360,  -830,  -360}-    ,{  1840,    10,  1060,  1840,  1060}-    ,{  1990,  -310,  1990,   270,  1990}-    ,{  1840,    10,  1060,  1840,  1060}-    }-   ,{{  1990,   160,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1550,   -40,   770,  1550,   770}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{   270,  -780,   270,  -200,   270}-    }-   }-  ,{{{  1860,  1840,  1860,  1840,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1860,  1840,  1860,  1840,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1210,  1190,  1210,  1190,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{   930,   910,   930,   910,   120}-    ,{    50,  -210,    50,  -210, -1000}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1860,  1840,  1860,  1840,   120}-    ,{  -250,  -510,  -250,  -510, -1300}-    ,{   930,   910,   930,   910,   120}-    ,{  1860,  1840,  1860,  1840,  -200}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   640,   620,   640,   620,  -170}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   140,   120,   140,   120,  -670}-    }-   }-  }- ,{{{{  2120,  2120,  1990,  2120,  1990}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  2120,  2120,  1990,  1990,  1990}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  1470,  1340,  2120,  1340}-    ,{  2120,  1470,  1340,  2120,  1340}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{   400,   290,   400,    10,   170}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1860,  1210,  1080,  1860,  1080}-    }-   ,{{  2120,  2120,  1990,  1840,  1990}-    ,{   540,   190,   540,   -80,    70}-    ,{  1840,  1190,  1060,  1840,  1060}-    ,{  2120,  2120,  1990,  1840,  1990}-    ,{  1840,  1190,  1060,  1840,  1060}-    }-   ,{{  1990,  1340,  1210,  1990,  1210}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{  1750,  1100,   970,  1750,   970}-    ,{  1990,  1340,  1210,  1990,  1210}-    ,{   640,   640,   270,   120,   270}-    }-   }-  ,{{{  2120,  2120,  1990,   540,  1990}-    ,{  1470,  1470,  1340,   190,  1340}-    ,{  1340,  1340,  1210,   540,  1210}-    ,{  2120,  2120,  1990,    60,  1990}-    ,{  1210,  1210,  1080,   180,  1080}-    }-   ,{{  1470,  1470,  1340,   190,  1340}-    ,{  1470,  1470,  1340,   190,  1340}-    ,{  1190,  1190,  1060,   -80,  1060}-    ,{   290,   290,   160,  -980,   160}-    ,{  1190,  1190,  1060,   -80,  1060}-    }-   ,{{  1340,  1340,  1210,   540,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{  1340,  1340,  1210,   540,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{  1210,  1210,  1080,   180,  1080}-    }-   ,{{  2120,  2120,  1990,   -80,  1990}-    ,{   190,   190,    60, -1080,    60}-    ,{  1190,  1190,  1060,   -80,  1060}-    ,{  2120,  2120,  1990,  -400,  1990}-    ,{  1190,  1190,  1060,   -80,  1060}-    }-   ,{{  1340,  1340,  1210,    70,  1210}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{  1100,  1100,   970,    70,   970}-    ,{  1340,  1340,  1210,    60,  1210}-    ,{   640,   640,   270,  -810,   270}-    }-   }-  ,{{{  1990,  1840,  1990,  1840,  1750}-    ,{  1340,  1190,  1340,  1190,  1100}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1990,  1840,  1990,  1840,  1750}-    ,{  1080,   930,  1080,   930,   840}-    }-   ,{{  1340,  1190,  1340,  1190,  1100}-    ,{  1340,  1190,  1340,  1190,  1100}-    ,{  1060,   910,  1060,   910,   820}-    ,{   400,    10,   400,    10,   170}-    ,{  1060,   910,  1060,   910,   820}-    }-   ,{{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{  1080,   930,  1080,   930,   840}-    }-   ,{{  1990,  1840,  1990,  1840,  1750}-    ,{   540,   -80,   540,   -80,    70}-    ,{  1060,   910,  1060,   910,   820}-    ,{  1990,  1840,  1990,  1840,  1750}-    ,{  1060,   910,  1060,   910,   820}-    }-   ,{{  1210,  1060,  1210,  1060,   970}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{   970,   820,   970,   820,   740}-    ,{  1210,  1060,  1210,  1060,   970}-    ,{   270,   120,   270,   120,    30}-    }-   }-  ,{{{  2120,   400,  1990,  2120,  1990}-    ,{  2120,   290,  1340,  2120,  1340}-    ,{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1990,  1990,  1990}-    ,{  1860,   270,  1080,  1860,  1080}-    }-   ,{{  2120,   290,  1340,  2120,  1340}-    ,{  2120,   290,  1340,  2120,  1340}-    ,{  1840,    10,  1060,  1840,  1060}-    ,{   160,  -890,   160,  -310,   160}-    ,{  1840,    10,  1060,  1840,  1060}-    }-   ,{{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1990,   400,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1860,   270,  1080,  1860,  1080}-    }-   ,{{  1990,    10,  1990,  1840,  1990}-    ,{    60,  -980,    60,  -400,    60}-    ,{  1840,    10,  1060,  1840,  1060}-    ,{  1990,  -310,  1990,   270,  1990}-    ,{  1840,    10,  1060,  1840,  1060}-    }-   ,{{  1990,   170,  1210,  1990,  1210}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{  1750,   170,   970,  1750,   970}-    ,{  1990,   160,  1210,  1990,  1210}-    ,{   270,  -780,   270,  -200,   270}-    }-   }-  ,{{{  1860,  1840,  1860,  1840,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1860,  1840,  1860,  1840,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1210,  1190,  1210,  1190,   640}-    ,{  1210,  1190,  1210,  1190,   640}-    ,{   930,   910,   930,   910,   120}-    ,{   270,    10,   270,    10,  -780}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   950,   930,   950,   930,   140}-    }-   ,{{  1860,  1840,  1860,  1840,   120}-    ,{   180,   -80,   180,   -80,  -810}-    ,{   930,   910,   930,   910,   120}-    ,{  1860,  1840,  1860,  1840,  -200}-    ,{   930,   910,   930,   910,   120}-    }-   ,{{  1080,  1060,  1080,  1060,   270}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   840,   820,   840,   820,    30}-    ,{  1080,  1060,  1080,  1060,   270}-    ,{   140,   120,   140,   120,  -670}-    }-   }-  }- }};
− include/list.h 
@@ -1,65 +0,0 @@-/*-  $Log: list.h,v $-  Revision 1.2  2000/10/10 08:50:01  ivo-  some annotation for lclint--  Revision 1.1  1997/08/04 21:05:32  walter-  Initial revision--*/--#ifndef	__LIST_H-#define	__LIST_H--/*---------------------- Macros and type definitions ----------------------*/--typedef struct LST_BUCKET {-  struct LST_BUCKET *next;-}-LST_BUCKET;--typedef struct {-  int count;			/* Number of elements currently in list */-  LST_BUCKET *head;		/* Pointer to head element of list      */-  LST_BUCKET *z;		/* Pointer to last node of list         */-  LST_BUCKET hz[2];		/* Space for head and z nodes           */-}-LIST;--/* Return a pointer to the user space given the address of the header of- * a node.- */--#define	LST_USERSPACE(h)	((void*)((LST_BUCKET*)(h) + 1))--/* Return a pointer to the header of a node, given the address of the- * user space.- */--#define	LST_HEADER(n)		((LST_BUCKET*)(n) - 1)--/* Return a pointer to the user space of the list's head node. This user- * space does not actually exist, but it is useful to be able to address- * it to enable insertion at the start of the list.- */--#define	LST_HEAD(l)		LST_USERSPACE((l)->head)--/* Determine if a list is empty- */--#define	LST_EMPTY(l)		((l)->count == 0)--/*-------------------------- Function Prototypes --------------------------*/--/*@only@*//*@out@*/ void *lst_newnode (int size);-void lst_freenode (/*@only@*/ void *node);-/*@only@*//*@out@*/  LIST *lst_init (void);-void lst_kill (LIST * l, void (*freeNode) ());-void lst_insertafter (LIST * l, /*@keep@*/ void *node, void *after);-void *lst_deletenext (/*@only@*/ LIST * l, void *node);-/*@dependent@*/ void *lst_first (LIST * l);-/*@dependent@*/ void *lst_next (void *prev);-void lst_mergesort (LIST * l, int (*cmp_func) ());--#endif
− include/loop_energies.h 
@@ -1,660 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__-#define __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__--#include <stdio.h>-#include <stdlib.h>-#include <math.h>-#include <ctype.h>-#include <string.h>-#include "params.h"-#include "fold_vars.h"-#include "energy_par.h"--#ifdef __GNUC__-# define INLINE inline-#else-# define INLINE-#endif--/**- *  \file loop_energies.h- *  \brief Energy evaluation for MFE and partition function calculations- * - *  <P>- *  This file contains functions for the calculation of the free energy \f$\Delta G\f$- *  of a hairpin- [ E_Hairpin() ] or interior-loop [ E_IntLoop()] .<BR>- *  The unit of the free energy returned is \f$10^{-2} * \mathrm{kcal}/\mathrm{mol}\f$- *  </P>- *  <P>- *  In case of computing the partition function, this file also supplies functions- *  which return the Boltzmann weights \f$e^{-\Delta G/kT} \f$ for a hairpin- [ exp_E_Hairpin() ]- *  or interior-loop [ exp_E_IntLoop() ].- *  </P>- */--/**- *  \def E_MLstem(A,B,C,D)- *  <H2>Compute the Energy contribution of a Multiloop stem</H2>- *  This definition is a wrapper for the E_Stem() funtion.- *  It is substituted by an E_Stem() funtion call with argument- *  extLoop=0, so the energy contribution returned reflects a- *  stem introduced in a multiloop.<BR>- *  As for the parameters B (si1) and C (sj1) of the substituted- *  E_Stem() function, you can inhibit to take 5'-, 3'-dangles- *  or mismatch contributions to be taken into account by passing- *  -1 to these parameters.- * - *  \see    E_Stem()- *  \param  A The pair type of the stem-closing pair- *  \param  B The 5'-mismatching nucleotide- *  \param  C The 3'-mismatching nucleotide- *  \param  D The datastructure containing scaled energy parameters- *  \return   The energy contribution of the introduced multiloop stem- */-INLINE  PRIVATE int E_MLstem( int type,-                              int si1,-                              int sj1,-                              paramT *P);--/**- *  \def exp_E_MLstem(A,B,C,D)- *  This is the partition function variant of \ref E_MLstem()- *  \see E_MLstem()- *  \return The Boltzmann weighted energy contribution of the introduced multiloop stem- */-INLINE  PRIVATE double exp_E_MLstem(int type,-                                    int si1,-                                    int sj1,-                                    pf_paramT *P);--/**- *  \def E_ExtLoop(A,B,C,D)- *  <H2>Compute the Energy contribution of an Exterior loop stem</H2>- *  This definition is a wrapper for the E_Stem() funtion.- *  It is substituted by an E_Stem() funtion call with argument- *  extLoop=1, so the energy contribution returned reflects a- *  stem introduced in an exterior-loop.<BR>- *  As for the parameters B (si1) and C (sj1) of the substituted- *  E_Stem() function, you can inhibit to take 5'-, 3'-dangles- *  or mismatch contributions to be taken into account by passing- *  -1 to these parameters.- * - *  \see    E_Stem()- *  \param  A The pair type of the stem-closing pair- *  \param  B The 5'-mismatching nucleotide- *  \param  C The 3'-mismatching nucleotide- *  \param  D The datastructure containing scaled energy parameters- *  \return   The energy contribution of the introduced exterior-loop stem- */-INLINE  PRIVATE int E_ExtLoop(int type,-                              int si1,-                              int sj1,-                              paramT *P);--/**- *  \def exp_E_ExtLoop(A,B,C,D)- *  This is the partition function variant of \ref E_ExtLoop()- *  \see E_ExtLoop()- *  \return The Boltzmann weighted energy contribution of the introduced exterior-loop stem- */-INLINE  PRIVATE double exp_E_ExtLoop( int type,-                                      int si1,-                                      int sj1,-                                      pf_paramT *P);--/**- *  <H2>Compute the Energy of an interior-loop</H2>- *  This function computes the free energy \f$\Delta G\f$ of an interior-loop with the- *  following structure: <BR>- *  <PRE>- *        3'  5'- *        |   |- *        U - V- *    a_n       b_1- *     .        .- *     .        .- *     .        .- *    a_1       b_m- *        X - Y- *        |   |- *        5'  3'- *  </PRE>- *  This general structure depicts an interior-loop that is closed by the base pair (X,Y).- *  The enclosed base pair is (V,U) which leaves the unpaired bases a_1-a_n and b_1-b_n- *  that constitute the loop. In this example, the length of the interior-loop is \f$(n+m)\f$- *  where n or m may be 0 resulting in a bulge-loop or base pair stack.- *  The mismatching nucleotides for the closing pair (X,Y) are:<BR>- *  5'-mismatch: a_1<BR>- *  3'-mismatch: b_m<BR>- *  and for the enclosed base pair (V,U):<BR>- *  5'-mismatch: b_1<BR>- *  3'-mismatch: a_n<BR>- *  \note Base pairs are always denoted in 5'->3' direction. Thus the enclosed base pair- *  must be 'turned arround' when evaluating the free energy of the interior-loop- *  \see scale_parameters()- *  \see paramT- *  \note This function is threadsafe- * - *  \param  n1      The size of the 'left'-loop (number of unpaired nucleotides)- *  \param  n2      The size of the 'right'-loop (number of unpaired nucleotides)- *  \param  type    The pair type of the base pair closing the interior loop- *  \param  type_2  The pair type of the enclosed base pair- *  \param  si1     The 5'-mismatching nucleotide of the closing pair- *  \param  sj1     The 3'-mismatching nucleotide of the closing pair- *  \param  sp1     The 3'-mismatching nucleotide of the enclosed pair- *  \param  sq1     The 5'-mismatching nucleotide of the enclosed pair- *  \param  P       The datastructure containing scaled energy parameters- *  \return The Free energy of the Interior-loop in dcal/mol- */-INLINE  PRIVATE int E_IntLoop(int n1,-                              int n2,-                              int type,-                              int type_2,-                              int si1,-                              int sj1,-                              int sp1,-                              int sq1,-                              paramT *P);---/**- *  <H2>Compute the Energy of a hairpin-loop</H2>- *  To evaluate the free energy of a hairpin-loop, several parameters have to be known.- *  A general hairpin-loop has this structure:<BR>- *  <PRE>- *        a3 a4- *      a2     a5- *      a1     a6- *        X - Y- *        |   |- *        5'  3'- *  </PRE>- *  where X-Y marks the closing pair [e.g. a <B>(G,C)</B> pair]. The length of this loop is 6 as there are- *  six unpaired nucleotides (a1-a6) enclosed by (X,Y). The 5' mismatching nucleotide is- *  a1 while the 3' mismatch is a6. The nucleotide sequence of this loop is &quot;a1.a2.a3.a4.a5.a6&quot; <BR>- *  \note The parameter sequence should contain the sequence of the loop in capital letters of the nucleic acid- *  alphabet if the loop size is below 7. This is useful for unusually stable tri-, tetra- and hexa-loops- *  which are treated differently (based on experimental data) if they are tabulated.- *  @see scale_parameters()- *  @see paramT- *  \warning Not (really) thread safe! A threadsafe implementation will replace this function in a future release!\n- *  Energy evaluation may change due to updates in global variable "tetra_loop"- * - *  \param  size  The size of the loop (number of unpaired nucleotides)- *  \param  type  The pair type of the base pair closing the hairpin- *  \param  si1   The 5'-mismatching nucleotide- *  \param  sj1   The 3'-mismatching nucleotide- *  \param  string  The sequence of the loop- *  \param  P     The datastructure containing scaled energy parameters- *  \return The Free energy of the Hairpin-loop in dcal/mol- */-INLINE  PRIVATE int E_Hairpin(int size,-                              int type,-                              int si1,-                              int sj1,-                              const char *string,-                              paramT *P);--/**- *  <H2>Compute the energy contribution of a stem branching off a loop-region</H2>- *  This function computes the energy contribution of a stem that branches off- *  a loop region. This can be the case in multiloops, when a stem branching off- *  increases the degree of the loop but also <I>immediately interior base pairs</I>- *  of an exterior loop contribute free energy.- *  To switch the bahavior of the function according to the evaluation of a multiloop-- *  or exterior-loop-stem, you pass the flag 'extLoop'.- *  The returned energy contribution consists of a TerminalAU penalty if the pair type- *  is greater than 2, dangling end contributions of mismatching nucleotides adjacent to- *  the stem if only one of the si1, sj1 parameters is greater than 0 and mismatch energies- *  if both mismatching nucleotides are positive values.- *  Thus, to avoid incooperating dangling end or mismatch energies just pass a negative number,- *  e.g. -1 to the mismatch argument.- * - *  This is an illustration of how the energy contribution is assembled:- *  <PRE>- *        3'  5'- *        |   |- *        X - Y- *  5'-si1     sj1-3'- *  </PRE>- * - *  Here, (X,Y) is the base pair that closes the stem that branches off a loop region.- *  The nucleotides si1 and sj1 are the 5'- and 3'- mismatches, respectively. If the base pair- *  type of (X,Y) is greater than 2 (i.e. an A-U or G-U pair, the TerminalAU penalty will be- *  included in the energy contribution returned. If si1 and sj1 are both nonnegative numbers,- *  mismatch energies will also be included. If one of sij or sj1 is a negtive value, only- *  5' or 3' dangling end contributions are taken into account. To prohibit any of these mismatch- *  contributions to be incoorporated, just pass a negative number to both, si1 and sj1.- *  In case the argument extLoop is 0, the returned energy contribution also includes- *  the <I>internal-loop-penalty</I> of a multiloop stem with closing pair type.- * - *  \see    E_MLstem()- *  \see    E_ExtLoop()- *  \note   This function is threadsafe- * - *  \param  type    The pair type of the first base pair un the stem- *  \param  si1     The 5'-mismatching nucleotide- *  \param  sj1     The 3'-mismatching nucleotide- *  \param  extLoop A flag that indicates whether the contribution reflects the one of an exterior loop or not- *  \param  P       The datastructure containing scaled energy parameters- *  \return         The Free energy of the branch off the loop in dcal/mol- * - */-INLINE  PRIVATE int E_Stem( int type,-                            int si1,-                            int sj1,-                            int extLoop,-                            paramT *P);--/**- *  <H2>Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region</H2>- *  This is the partition function variant of \ref E_Stem()- *  \see E_Stem()- *  \note This function is threadsafe- * - *  \return The Boltzmann weighted energy contribution of the branch off the loop- */-INLINE  PRIVATE double exp_E_Stem(int type,-                                  int si1,-                                  int sj1,-                                  int extLoop,-                                  pf_paramT *P);--/**- *  <H2>Compute Boltzmann weight \f$e^{-\Delta G/kT} \f$ of a hairpin loop</H2>- *  multiply by scale[u+2]- *  @see get_scaled_pf_parameters()- *  @see pf_paramT- *  @see E_Hairpin()- *  \warning Not (really) thread safe! A threadsafe implementation will replace this function in a future release!\n- *  Energy evaluation may change due to updates in global variable "tetra_loop"- * - *  \param  u       The size of the loop (number of unpaired nucleotides)- *  \param  type    The pair type of the base pair closing the hairpin- *  \param  si1     The 5'-mismatching nucleotide- *  \param  sj1     The 3'-mismatching nucleotide- *  \param  string  The sequence of the loop- *  \param  P       The datastructure containing scaled Boltzmann weights of the energy parameters- *  \return The Boltzmann weight of the Hairpin-loop- */-INLINE  PRIVATE double exp_E_Hairpin( int u,-                                      int type,-                                      short si1,-                                      short sj1,-                                      const char *string,-                                      pf_paramT *P);--/**- *  <H2>Compute Boltzmann weight \f$e^{-\Delta G/kT} \f$ of interior loop</H2>- *  multiply by scale[u1+u2+2] for scaling- *  @see get_scaled_pf_parameters()- *  @see pf_paramT- *  @see E_IntLoop()- *  \note This function is threadsafe- * - *  \param  u1      The size of the 'left'-loop (number of unpaired nucleotides)- *  \param  u2      The size of the 'right'-loop (number of unpaired nucleotides)- *  \param  type    The pair type of the base pair closing the interior loop- *  \param  type2   The pair type of the enclosed base pair- *  \param  si1     The 5'-mismatching nucleotide of the closing pair- *  \param  sj1     The 3'-mismatching nucleotide of the closing pair- *  \param  sp1     The 3'-mismatching nucleotide of the enclosed pair- *  \param  sq1     The 5'-mismatching nucleotide of the enclosed pair- *  \param  P       The datastructure containing scaled Boltzmann weights of the energy parameters- *  \return The Boltzmann weight of the Interior-loop- */-INLINE  PRIVATE double  exp_E_IntLoop(int u1,-                                      int u2,-                                      int type,-                                      int type2,-                                      short si1,-                                      short sj1,-                                      short sp1,-                                      short sq1,-                                      pf_paramT *P);---/*-#################################-# BEGIN OF FUNCTION DEFINITIONS #-#################################-*/-INLINE  PRIVATE int E_Hairpin(int size, int type, int si1, int sj1, const char *string, paramT *P){-  int energy;--  energy = (size <= 30) ? P->hairpin[size] : P->hairpin[30]+(int)(P->lxc*log((size)/30.));-  if (P->model_details.special_hp){-    if (size == 4) { /* check for tetraloop bonus */-      char tl[7]={0}, *ts;-      strncpy(tl, string, 6);-      if ((ts=strstr(P->Tetraloops, tl)))-        return (P->Tetraloop_E[(ts - P->Tetraloops)/7]);-    }-    else if (size == 6) {-      char tl[9]={0}, *ts;-      strncpy(tl, string, 8);-      if ((ts=strstr(P->Hexaloops, tl)))-        return (energy = P->Hexaloop_E[(ts - P->Hexaloops)/9]);-    }-    else if (size == 3) {-      char tl[6]={0,0,0,0,0,0}, *ts;-      strncpy(tl, string, 5);-      if ((ts=strstr(P->Triloops, tl))) {-        return (P->Triloop_E[(ts - P->Triloops)/6]);-      }-      return (energy + (type>2 ? P->TerminalAU : 0));-    }-  }-  energy += P->mismatchH[type][si1][sj1];--  return energy;-}--INLINE  PRIVATE int E_IntLoop(int n1, int n2, int type, int type_2, int si1, int sj1, int sp1, int sq1, paramT *P){-  /* compute energy of degree 2 loop (stack bulge or interior) */-  int nl, ns, energy;-  energy = INF;--  if (n1>n2) { nl=n1; ns=n2;}-  else {nl=n2; ns=n1;}--  if (nl == 0)-    return P->stack[type][type_2];  /* stack */--  if (ns==0) {                      /* bulge */-    energy = (nl<=MAXLOOP)?P->bulge[nl]:-      (P->bulge[30]+(int)(P->lxc*log(nl/30.)));-    if (nl==1) energy += P->stack[type][type_2];-    else {-      if (type>2) energy += P->TerminalAU;-      if (type_2>2) energy += P->TerminalAU;-    }-    return energy;-  }-  else {                            /* interior loop */-    if (ns==1) {-      if (nl==1)                    /* 1x1 loop */-        return P->int11[type][type_2][si1][sj1];-      if (nl==2) {                  /* 2x1 loop */-        if (n1==1)-          energy = P->int21[type][type_2][si1][sq1][sj1];-        else-          energy = P->int21[type_2][type][sq1][si1][sp1];-        return energy;-      }-      else {  /* 1xn loop */-        energy = (nl+1<=MAXLOOP)?(P->internal_loop[nl+1]) : (P->internal_loop[30]+(int)(P->lxc*log((nl+1)/30.)));-        energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);-        energy += P->mismatch1nI[type][si1][sj1] + P->mismatch1nI[type_2][sq1][sp1];-        return energy;-      }-    }-    else if (ns==2) {-      if(nl==2)      {              /* 2x2 loop */-        return P->int22[type][type_2][si1][sp1][sq1][sj1];}-      else if (nl==3){              /* 2x3 loop */-        energy = P->internal_loop[5]+P->ninio[2];-        energy += P->mismatch23I[type][si1][sj1] + P->mismatch23I[type_2][sq1][sp1];-        return energy;-      }--    }-    { /* generic interior loop (no else here!)*/-      energy = (n1+n2<=MAXLOOP)?(P->internal_loop[n1+n2]) : (P->internal_loop[30]+(int)(P->lxc*log((n1+n2)/30.)));--      energy += MIN2(MAX_NINIO, (nl-ns)*P->ninio[2]);--      energy += P->mismatchI[type][si1][sj1] + P->mismatchI[type_2][sq1][sp1];-    }-  }-  return energy;-}--INLINE  PRIVATE int E_Stem(int type, int si1, int sj1, int extLoop, paramT *P){-  int energy = 0;-  int d5 = (si1 >= 0) ? P->dangle5[type][si1] : 0;-  int d3 = (sj1 >= 0) ? P->dangle3[type][sj1] : 0;--  if(type > 2)-    energy += P->TerminalAU;--  if(si1 >= 0 && sj1 >= 0)-    energy += (extLoop) ? P->mismatchExt[type][si1][sj1] : P->mismatchM[type][si1][sj1];-  else-    energy += d5 + d3;--  if(!extLoop) energy += P->MLintern[type];-  return energy;-}--INLINE  PRIVATE int E_ExtLoop(int type, int si1, int sj1, paramT *P){-  int energy = 0;-  if(si1 >= 0 && sj1 >= 0){-    energy += P->mismatchExt[type][si1][sj1];-  }-  else if (si1 >= 0){-    energy += P->dangle5[type][si1];-  }-  else if (sj1 >= 0){-    energy += P->dangle3[type][sj1];-  }--  if(type > 2)-    energy += P->TerminalAU;--  return energy;-}--INLINE  PRIVATE int E_MLstem(int type, int si1, int sj1, paramT *P){-  int energy = 0;-  if(si1 >= 0 && sj1 >= 0){-    energy += P->mismatchM[type][si1][sj1];-  }-  else if (si1 >= 0){-    energy += P->dangle5[type][si1];-  }-  else if (sj1 >= 0){-    energy += P->dangle3[type][sj1];-  }--  if(type > 2)-    energy += P->TerminalAU;--  energy += P->MLintern[type];--  return energy;-}--INLINE  PRIVATE double exp_E_Hairpin(int u, int type, short si1, short sj1, const char *string, pf_paramT *P){-  double q, kT;-  kT = P->kT;   /* kT in cal/mol  */--  if(u <= 30)-    q = P->exphairpin[u];-  else-    q = P->exphairpin[30] * exp( -(P->lxc*log( u/30.))*10./kT);--  if(u < 3) return q; /* should only be the case when folding alignments */--  if(P->model_details.special_hp){-    if(u==4) {-      char tl[7]={0,0,0,0,0,0,0}, *ts;-      strncpy(tl, string, 6);-      if ((ts=strstr(P->Tetraloops, tl))){-        if(type != 7)-          return (P->exptetra[(ts-P->Tetraloops)/7]);-        else-          q *= P->exptetra[(ts-P->Tetraloops)/7];-      }-    }-    if (u==6) {-      char tl[9]={0,0,0,0,0,0,0,0,0}, *ts;-      strncpy(tl, string, 8);-      if ((ts=strstr(P->Hexaloops, tl)))-        return  (P->exphex[(ts-P->Hexaloops)/9]);-    }-    if (u==3) {-      char tl[6]={0,0,0,0,0,0}, *ts;-      strncpy(tl, string, 5);-      if ((ts=strstr(P->Triloops, tl)))-        return (P->exptri[(ts-P->Triloops)/6]);-      if (type>2)-        return q *= P->expTermAU;-    }-  }-  /* no mismatches for tri-loops */-  q *= P->expmismatchH[type][si1][sj1];--  return q;-}--INLINE  PRIVATE double exp_E_IntLoop(int u1, int u2, int type, int type2, short si1, short sj1, short sp1, short sq1, pf_paramT *P){-  int ul, us, no_close = 0;-  double z = 0.;--  if ((no_closingGU) && ((type2==3)||(type2==4)||(type==3)||(type==4)))-    no_close = 1;--  if (u1>u2) { ul=u1; us=u2;}-  else {ul=u2; us=u1;}--  if (ul==0) /* stack */-    z = P->expstack[type][type2];-  else if(!no_close){-    if (us==0) {                      /* bulge */-      z = P->expbulge[ul];-      if (ul==1) z *= P->expstack[type][type2];-      else {-        if (type>2) z *= P->expTermAU;-        if (type2>2) z *= P->expTermAU;-      }-      return z;-    }-    else if (us==1) {-      if (ul==1){                    /* 1x1 loop */-        return P->expint11[type][type2][si1][sj1];-      }-      if (ul==2) {                  /* 2x1 loop */-        if (u1==1)-          return P->expint21[type][type2][si1][sq1][sj1];-        else-          return P->expint21[type2][type][sq1][si1][sp1];-      }-      else {  /* 1xn loop */-        z = P->expinternal[ul+us] * P->expmismatch1nI[type][si1][sj1] * P->expmismatch1nI[type2][sq1][sp1];-        return z * P->expninio[2][ul-us];-      }-    }-    else if (us==2) {-      if(ul==2) /* 2x2 loop */-        return P->expint22[type][type2][si1][sp1][sq1][sj1];-      else if(ul==3){              /* 2x3 loop */-        z = P->expinternal[5]*P->expmismatch23I[type][si1][sj1]*P->expmismatch23I[type2][sq1][sp1];-        return z * P->expninio[2][1];-      }-    }-    /* generic interior loop (no else here!)*/-    z = P->expinternal[ul+us] * P->expmismatchI[type][si1][sj1] * P->expmismatchI[type2][sq1][sp1];-    return z * P->expninio[2][ul-us];--  }-  return z;-}--INLINE  PRIVATE double exp_E_Stem(int type, int si1, int sj1, int extLoop, pf_paramT *P){-  double energy = 1.0;-  double d5 = (si1 >= 0) ? P->expdangle5[type][si1] : 1.;-  double d3 = (sj1 >= 0) ? P->expdangle3[type][sj1] : 1.;--  if(type > 2)-    energy *= P->expTermAU;--  if(si1 >= 0 && sj1 >= 0)-    energy *= (extLoop) ? P->expmismatchExt[type][si1][sj1] : P->expmismatchM[type][si1][sj1];-  else-    energy *= d5 * d3;--  if(!extLoop) energy *= P->expMLintern[type];-  return energy;-}--INLINE  PRIVATE double exp_E_MLstem(int type, int si1, int sj1, pf_paramT *P){-  double energy = 1.0;-  if(si1 >= 0 && sj1 >= 0){-    energy *= P->expmismatchM[type][si1][sj1];-  }-  else if(si1 >= 0){-    energy *= P->expdangle5[type][si1];-  }-  else if(sj1 >= 0){-    energy *= P->expdangle3[type][sj1];-  }--  if(type > 2)-    energy *= P->expTermAU;--  energy *= P->expMLintern[type];-  return energy;-}--INLINE  PRIVATE double exp_E_ExtLoop(int type, int si1, int sj1, pf_paramT *P){-  double energy = 1.0;-  if(si1 >= 0 && sj1 >= 0){-    energy *= P->expmismatchExt[type][si1][sj1];-  }-  else if(si1 >= 0){-    energy *= P->expdangle5[type][si1];-  }-  else if(sj1 >= 0){-    energy *= P->expdangle3[type][sj1];-  }--  if(type > 2)-    energy *= P->expTermAU;--  return energy;-}--INLINE  PRIVATE int     E_IntLoop_Co(int type, int type_2, int i, int j, int p, int q, int cutpoint, short si1, short sj1, short sp1, short sq1, int dangles, paramT *P){-  int energy = 0;-  if(type > 2)   energy += P->TerminalAU;-  if(type_2 > 2) energy += P->TerminalAU;--  if(!dangles) return energy;--  int ci = (i>=cutpoint)||((i+1)<cutpoint);-  int cj = ((j-1)>=cutpoint)||(j<cutpoint);-  int cp = ((p-1)>=cutpoint)||(p<cutpoint);-  int cq = (q>=cutpoint)||((q+1)<cutpoint);--  int d3    = ci  ? P->dangle3[type][si1]   : 0;-  int d5    = cj  ? P->dangle5[type][sj1]   : 0;-  int d5_2  = cp  ? P->dangle5[type_2][sp1] : 0;-  int d3_2  = cq  ? P->dangle3[type_2][sq1] : 0;--  int tmm   = (cj && ci) ? P->mismatchExt[type][sj1][si1]   : d5 + d3;-  int tmm_2 = (cp && cq) ? P->mismatchExt[type_2][sp1][sq1] : d5_2 + d3_2;--  if(dangles == 2) return energy + tmm + tmm_2;--  /* now we may have non-double dangles only */-  if(i+2 < p){-    if(q+2 < j){ energy += tmm + tmm_2;}-    else if(q+2 == j){ energy += (cj && cq) ? MIN2(tmm + d5_2, tmm_2 + d3) : tmm + tmm_2;}-    else energy += d3 + d5_2;-  }-  else if(i+2 == p){-    if(q+2 < j){ energy += (ci && cp) ? MIN2(tmm + d3_2, tmm_2 + d5) : tmm + tmm_2;}-    else if(q+2 == j){-      energy += MIN2(tmm, MIN2(tmm_2, MIN2(d5 + d5_2, d3 + d3_2)));-    }-    else energy += MIN2(d3, d5_2);-  }-  else{-    if(q+2 < j){ energy += d5 + d3_2;}-    else if(q+2 == j){ energy += MIN2(d5, d3_2);}-  }-  return energy;-}--#endif
− include/naview.h 
@@ -1,16 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_NAVIEW_H__-#define __VIENNA_RNA_PACKAGE_NAVIEW_H__--/**- *  \file naview.h- *- */--/**- *- */-int naview_xy_coordinates(short *pair_table,-                          float *X,-                          float *Y);--#endif
− include/pair_mat.h 
@@ -1,148 +0,0 @@-#include <ctype.h>-#include "utils.h"-#include "fold_vars.h"--#define NBASES 8-/*@notnull@*/--static const char Law_and_Order[] = "_ACGUTXKI";-static int BP_pair[NBASES][NBASES]=-/* _  A  C  G  U  X  K  I */-{{ 0, 0, 0, 0, 0, 0, 0, 0},- { 0, 0, 0, 0, 5, 0, 0, 5},- { 0, 0, 0, 1, 0, 0, 0, 0},- { 0, 0, 2, 0, 3, 0, 0, 0},- { 0, 6, 0, 4, 0, 0, 0, 6},- { 0, 0, 0, 0, 0, 0, 2, 0},- { 0, 0, 0, 0, 0, 1, 0, 0},- { 0, 6, 0, 0, 5, 0, 0, 0}};--#define MAXALPHA 20       /* maximal length of alphabet */--static short alias[MAXALPHA+1];-static int pair[MAXALPHA+1][MAXALPHA+1];-/* rtype[pair[i][j]]:=pair[j][i] */-static int rtype[8] = {0, 2, 1, 4, 3, 6, 5, 7};--#ifdef _OPENMP-#pragma omp threadprivate(Law_and_Order, BP_pair, alias, pair, rtype)-#endif--/* for backward compatibility */-#define ENCODE(c) encode_char(c)--static int encode_char(char c) {-  /* return numerical representation of base used e.g. in pair[][] */-  int code;-  if (energy_set>0) code = (int) (c-'A')+1;-  else {-    const char *pos;-    pos = strchr(Law_and_Order, c);-    if (pos==NULL) code=0;-    else code = (int) (pos-Law_and_Order);-    if (code>5) code = 0;-    if (code>4) code--; /* make T and U equivalent */-  }-  return code;-}--/*@+boolint +charint@*/-/*@null@*/-extern char *nonstandards;-extern void   nrerror(const char message[]);-static void make_pair_matrix(void)-{-   int i,j;--   if (energy_set==0) {-      for (i=0; i<5; i++) alias[i] = (short) i;-      alias[5] = 3; /* X <-> G */-      alias[6] = 2; /* K <-> C */-      alias[7] = 0; /* I <-> default base '@' */-      for (i=0; i<NBASES; i++) {-          for (j=0; j<NBASES; j++)-            pair[i][j] = BP_pair[i][j];-      }-      if (noGU) pair[3][4] = pair[4][3] =0;-      if (nonstandards!=NULL) {  /* allow nonstandard bp's */-         for (i=0; i<(int)strlen(nonstandards); i+=2)-            pair[encode_char(nonstandards[i])]-              [encode_char(nonstandards[i+1])]=7;-      }-      for (i=0; i<NBASES; i++) {-          for (j=0; j<NBASES; j++)-           rtype[pair[i][j]] = pair[j][i];-      }-   } else {-      for (i=0; i<=MAXALPHA; i++) {-         for (j=0; j<=MAXALPHA; j++)-            pair[i][j] = 0;-      }-      if (energy_set==1) {-         for (i=1; i<MAXALPHA;) {-            alias[i++] = 3;  /* A <-> G */-            alias[i++] = 2;  /* B <-> C */-         }-         for (i=1; i<MAXALPHA; i++) {-            pair[i][i+1] = 2;    /* AB <-> GC */-            i++;-            pair[i][i-1] = 1;    /* BA <-> CG */-         }-      }-      else if (energy_set==2) {-        for (i=1; i<MAXALPHA;) {-            alias[i++] = 1;  /* A <-> A*/-            alias[i++] = 4;  /* B <-> U */-         }-         for (i=1; i<MAXALPHA; i++) {-            pair[i][i+1] = 5;    /* AB <-> AU */-            i++;-            pair[i][i-1] = 6;    /* BA <-> UA */-         }-      }-      else if (energy_set==3) {-        for (i=1; i<MAXALPHA-2; ) {-          alias[i++] = 3;  /* A <-> G */-          alias[i++] = 2;  /* B <-> C */-          alias[i++] = 1;  /* C <-> A */-          alias[i++] = 4;  /* D <-> U */-        }-        for (i=1; i<MAXALPHA-2; i++) {-          pair[i][i+1] = 2;    /* AB <-> GC */-          i++;-          pair[i][i-1] = 1;    /* BA <-> CG */-          i++;-          pair[i][i+1] = 5;    /* CD <-> AU */-          i++;-          pair[i][i-1] = 6;    /* DC <-> UA */-        }-      }-      else nrerror("What energy_set are YOU using??");-      for (i=0; i<=MAXALPHA; i++) {-        for (j=0; j<=MAXALPHA; j++)-          rtype[pair[i][j]] = pair[j][i];-      }-   }-}--static short *encode_sequence(const char *sequence, short how){-  unsigned int i,l = (unsigned int)strlen(sequence);-  short         *S = (short *) space(sizeof(short)*(l+2));--  switch(how){-    /* standard encoding as always used for S */-    case 0:   for(i=1; i<=l; i++) /* make numerical encoding of sequence */-                S[i]= (short) encode_char(toupper(sequence[i-1]));-              S[l+1] = S[1];-              S[0] = (short) l;-              break;-    /* encoding for mismatches of nostandard bases (normally used for S1) */-    case 1:   for(i=1; i<=l; i++)-                S[i] = alias[(short) encode_char(toupper(sequence[i-1]))];-              S[l+1] = S[1];-              S[0] = S[l];-              break;-  }--  return S;-}
− include/params.h 
@@ -1,134 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_PARAMS_H__-#define __VIENNA_RNA_PACKAGE_PARAMS_H__--#include "energy_const.h"-#include "data_structures.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif--/**- *  \addtogroup energy_parameters- *  \brief All relevant functions to retrieve and copy precalculated energy parameter sets as well as- *  reading/writing the energy parameter set from/to file(s).- *- *  This module covers all relevant functions for precalculation of the energy parameters- *  necessary for the folding routines provided by RNAlib. Furthermore, the energy parameter set- *  in the RNAlib can be easily exchanged by a user-defined one. It is also possible to write the- *  current energy parameter set into a text file.- *  @{- *- *  \file params.h- */--/**- * \brief Get precomputed energy contributions for all the known loop types- *- *  \note OpenMP: This function relies on several global model settings variables and thus is- *        not to be considered threadsafe. See get_scaled_parameters() for a completely threadsafe- *        implementation.- *- * \return     A set of precomputed energy contributions- */-paramT *scale_parameters(void);--/**- * \brief Get precomputed energy contributions for all the known loop types- *- *  Call this function to retrieve precomputed energy contributions, i.e. scaled- *  according to the temperature passed. Furthermore, this function assumes a- *  data structure that contains the model details as well, such that subsequent- *  folding recursions are able to retrieve the correct model settings- *- *  \see #model_detailsT, set_model_details()- *- *  \param temperature  The temperature in degrees Celcius- *  \param md           The model details- *  \return             precomputed energy contributions and model settings- */-paramT *get_scaled_parameters(double temperature,-                              model_detailsT md);--paramT *get_parameter_copy(paramT *par);--/**- *  get a datastructure of type \ref pf_paramT which contains- *  the Boltzmann weights of several energy parameters scaled- *  according to the current temperature- *  \return The datastructure containing Boltzmann weights for use in partition function calculations- */-pf_paramT *get_scaled_pf_parameters(void);--/**- *  \brief Get precomputed Boltzmann factors of the loop type- *  dependent energy contributions with independent thermodynamic- *  temperature- *- *  This function returns a data structure that contains- *  all necessary precalculated Boltzmann factors for each- *  loop type contribution.<br>- *  In contrast to get_scaled_pf_parameters(), this function- *  enables setting of independent temperatures for both, the- *  individual energy contributions as well as the thermodynamic- *  temperature used in- *  \f$ exp(-\Delta G / kT) \f$- *- *  \see get_scaled_pf_parameters(), get_boltzmann_factor_copy()- *- *  \param  temperature   The temperature in degrees Celcius used for (re-)scaling the energy contributions- *  \param  betaScale     A scaling value that is used as a multiplication factor for the absolute- *                        temperature of the system- *  \param  md            The model details to be used- *  \param  pf_scale      The scaling factor for the Boltzmann factors- *  \return               A set of precomputed Boltzmann factors- */-pf_paramT *get_boltzmann_factors( double temperature,-                                  double betaScale,-                                  model_detailsT md,-                                  double pf_scale);--/**- *  \brief Get a copy of already precomputed Boltzmann factors- *- *  \see get_boltzmann_factors(), get_scaled_pf_parameters()- *- *  \param  parameters  The input data structure that shall be copied- *  \return             A copy of the provided Boltzmann factor dataset- */-pf_paramT *get_boltzmann_factor_copy(pf_paramT *parameters);--/**- *  \brief Get precomputed Boltzmann factors of the loop type- *  dependent energy contributions (alifold variant)- *- */-pf_paramT *get_scaled_alipf_parameters(unsigned int n_seq);--/**- *  \brief Get precomputed Boltzmann factors of the loop type- *  dependent energy contributions (alifold variant) with- *  independent thermodynamic temperature- *- */-PUBLIC pf_paramT *get_boltzmann_factors_ali(unsigned int n_seq,-                                            double temperature,-                                            double betaScale,-                                            model_detailsT md,-                                            double pf_scale);--/**- *  @}- */--DEPRECATED(paramT     *copy_parameters(void));-DEPRECATED(paramT     *set_parameters(paramT *dest));-DEPRECATED(pf_paramT  *scale_pf_parameters(void));-DEPRECATED(pf_paramT  *copy_pf_param(void));-DEPRECATED(pf_paramT  *set_pf_param(paramT *dest));----#endif
− include/part_func.h 
@@ -1,443 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_H__-#define __VIENNA_RNA_PACKAGE_PART_FUNC_H__--#include "data_structures.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif---/**- *  \addtogroup pf_fold- *  \brief This section provides information about all functions and variables related to- *  the calculation of the partition function and base pair probabilities.- *- *  Instead of the minimum free energy structure the partition function of all possible structures- *  and from that the pairing probability for every possible pair can be calculated, using a dynamic- *  programming algorithm as described in \cite mccaskill:1990. - *- *  @{- *    \file part_func.h- *    \brief Partition function of single RNA sequences- * - *    This file includes (almost) all function declarations within the <b>RNAlib</b> that are related to- *    Partion function folding...- *  @}- */--/**- *  \brief Flag indicating that auxilary arrays are needed throughout the computations. This is essential for stochastic backtracking- *- *  Set this variable to 1 prior to a call of pf_fold() to ensure that all matrices needed for stochastic backtracking- *  are filled in the forward recursions- *- *  \ingroup subopt_stochbt- *- *  \see pbacktrack(), pbacktrack_circ- */-extern  int st_back;--/*-#################################################-# PARTITION FUNCTION COMPUTATION                #-#################################################-*/--/**- *  \brief Compute the partition function \f$Q\f$ for a given RNA sequence- *- *  If \a structure is not a NULL pointer on input, it contains on- *  return a string consisting of the letters " . , | { } ( ) " denoting- *  bases that are essentially unpaired, weakly paired, strongly paired without- *  preference, weakly upstream (downstream) paired, or strongly up-- *  (down-)stream paired bases, respectively.- *  If #fold_constrained is not 0, the \a structure string is- *  interpreted on input as a list of constraints for the folding. The- *  character "x" marks bases that must be unpaired, matching brackets " ( ) "- *  denote base pairs, all other characters are ignored. Any pairs- *  conflicting with the constraint will be forbidden. This is usually sufficient- *  to ensure the constraints are honored.- *  If tha parameter calculate_bppm is set to 0 base pairing probabilities will not- *  be computed (saving CPU time), otherwise after calculations took place #pr will- *  contain the probability that bases \a i and \a j pair.- * - *  \ingroup pf_fold- *- *  \note           The global array #pr is deprecated and the user who wants the calculated- *                  base pair probabilities for further computations is advised to use the function- *                  export_bppm()- *  \post           After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.- *                  Depending on whether the global variable #do_backtrack was set the base pair probabilities are already- *                  computed and may be accessed for further usage via the export_bppm() function.- *                  A call of free_pf_arrays() will free all memory allocated by this function.- *                  Successive calls will first free previously allocated memory before starting the computation.- *  \see            pf_fold(), pf_circ_fold(), bppm_to_structure(), export_bppm(), get_boltzmann_factors(), free_pf_arrays()- *  \param[in]      sequence        The RNA sequence input- *  \param[in,out]  structure       A pointer to a char array where a base pair probability information can be stored in a- *                                  pseudo-dot-bracket notation (may be NULL, too)- *  \param[in]      parameters      Data structure containing the precalculated Boltzmann factors- *  \param[in]      calculate_bppm  Switch to Base pair probability calculations on/off (0==off)- *  \param[in]      is_constrained  Switch to indicate that a structure contraint is passed via the structure argument (0==off)- *  \param[in]      is_circular     Switch to (de-)activate postprocessing steps in case RNA sequence is circular (0==off)- *  \return         The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol- */-float   pf_fold_par(  const char *sequence,-                      char *structure,-                      pf_paramT *parameters,-                      int calculate_bppm,-                      int is_constrained,-                      int is_circular);--/**- *  \brief Compute the partition function \f$Q\f$ of an RNA sequence- * - *  If \a structure is not a NULL pointer on input, it contains on- *  return a string consisting of the letters " . , | { } ( ) " denoting- *  bases that are essentially unpaired, weakly paired, strongly paired without- *  preference, weakly upstream (downstream) paired, or strongly up-- *  (down-)stream paired bases, respectively.- *  If #fold_constrained is not 0, the \a structure string is- *  interpreted on input as a list of constraints for the folding. The- *  character "x" marks bases that must be unpaired, matching brackets " ( ) "- *  denote base pairs, all other characters are ignored. Any pairs- *  conflicting with the constraint will be forbidden. This is usually sufficient- *  to ensure the constraints are honored.- *  If #do_backtrack has been set to 0 base pairing probabilities will not- *  be computed (saving CPU time), otherwise #pr will contain the probability- *  that bases \a i and \a j pair.- * - *  \ingroup pf_fold- *- *  \note   The global array #pr is deprecated and the user who wants the calculated- *          base pair probabilities for further computations is advised to use the function- *          export_bppm().- *  \note   \b OpenMP:- *          This function is not entirely threadsafe. While the recursions are working on their- *          own copies of data the model details for the recursions are determined from the global- *          settings just before entering the recursions. Consider using pf_fold_par() for a- *          really threadsafe implementation.- *  \pre    This function takes its model details from the global variables provided in \e RNAlib- *  \post   After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.- *          Depending on whether the global variable #do_backtrack was set the base pair probabilities are already- *          computed and may be accessed for further usage via the export_bppm() function.- *          A call of free_pf_arrays() will free all memory allocated by this function.- *          Successive calls will first free previously allocated memory before starting the computation.- *  \see    pf_fold_par(), pf_circ_fold(), bppm_to_structure(), export_bppm()- *  \param sequence   The RNA sequence input- *  \param structure  A pointer to a char array where a base pair probability information can be stored in a pseudo-dot-bracket notation (may be NULL, too)- *  \return           The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol- */-float   pf_fold(const char *sequence,-                char *structure);--/**- *  \brief Compute the partition function of a circular RNA sequence- * - *  \ingroup pf_fold- *- *  \note           The global array #pr is deprecated and the user who wants the calculated- *                  base pair probabilities for further computations is advised to use the function- *                  export_bppm().- *  \note           \b OpenMP:- *                  This function is not entirely threadsafe. While the recursions are working on their- *                  own copies of data the model details for the recursions are determined from the global- *                  settings just before entering the recursions. Consider using pf_fold_par() for a- *                  really threadsafe implementation.- *  \pre            This function takes its model details from the global variables provided in \e RNAlib- *  \post           After successful run the hidden folding matrices are filled with the appropriate Boltzmann factors.- *                  Depending on whether the global variable #do_backtrack was set the base pair probabilities are already- *                  computed and may be accessed for further usage via the export_bppm() function.- *                  A call of free_pf_arrays() will free all memory allocated by this function.- *                  Successive calls will first free previously allocated memory before starting the computation.- *  \see            pf_fold_par(), pf_fold()- *  \param[in]      sequence   The RNA sequence input- *  \param[in,out]  structure  A pointer to a char array where a base pair probability information can be- *                  stored in a pseudo-dot-bracket notation (may be NULL, too)- *  \return         The Gibbs free energy of the ensemble (\f$G = -RT \cdot \log(Q) \f$) in kcal/mol- */-float   pf_circ_fold( const char *sequence,-                      char *structure);--/**- *  \brief Sample a secondary structure from the Boltzmann ensemble according its probability\n- *- *  \ingroup subopt_stochbt- *  \pre    pf_fold_par() or pf_fold() have to be called first to fill the partition function matrices- *- *  \param  sequence  The RNA sequence- *  \return           A sampled secondary structure in dot-bracket notation- */-char    *pbacktrack(char *sequence);--/**- *  \brief Sample a secondary structure of a circular RNA from the Boltzmann ensemble according its probability- * - *  This function does the same as \ref pbacktrack() but assumes the RNA molecule to be circular- *- *  \ingroup subopt_stochbt- *  \pre    pf_fold_par() or pf_fold_circ() have to be called first to fill the partition function matrices- *- *  \param  sequence  The RNA sequence- *  \return           A sampled secondary structure in dot-bracket notation- */-char    *pbacktrack_circ(char *sequence);--/**- *  \brief Free arrays for the partition function recursions- *- *  Call this function if you want to free all allocated memory associated with- *  the partition function forward recursion.- *  \note Successive calls of pf_fold(), pf_circ_fold() already check if they should free- *  any memory from a previous run.- *  \note <b>OpenMP notice:</b><br>- *  This function should be called before leaving a thread in order to avoid leaking memory- *  - *  \ingroup pf_fold- *- *  \post   All memory allocated by pf_fold_par(), pf_fold() or pf_circ_fold() will be free'd- *  \see    pf_fold_par(), pf_fold(), pf_circ_fold()- */-void  free_pf_arrays(void);--/**- *  \brief Recalculate energy parameters- * - *  Call this function to recalculate the pair matrix and energy parameters- *  after a change in folding parameters like #temperature- *- *  \ingroup pf_fold- *- */-void  update_pf_params(int length);--/**- *  \brief Recalculate energy parameters- * - *  \ingroup pf_fold- *- */-void update_pf_params_par(int length, pf_paramT *parameters);--/**- *  \brief Get a pointer to the base pair probability array- *  \ingroup  pf_fold- *- *  Accessing the base pair probabilities for a pair (i,j) is achieved by- *  \code- *  FLT_OR_DBL *pr  = export_bppm();- *  pr_ij           = pr[iindx[i]-j];- *  \endcode- *- *  \pre      Call pf_fold_par(), pf_fold() or pf_circ_fold() first to fill the base pair probability array- *- *  \see pf_fold(), pf_circ_fold(), get_iindx()- *- *  \return A pointer to the base pair probability array- */-FLT_OR_DBL  *export_bppm(void);--/*-#################################################-# OTHER PARTITION FUNCTION RELATED DECLARATIONS #-#################################################-*/--/**- *  \brief Create a plist from a probability matrix- * - *  The probability matrix given is parsed and all pair probabilities above- *  the given threshold are used to create an entry in the plist- * - *  The end of the plist is marked by sequence positions i as well as j- *  equal to 0. This condition should be used to stop looping over its- *  entries- * - *  \note This function is threadsafe- *  \ingroup            pf_fold- *  \param[out] pl      A pointer to the plist that is to be created- *  \param[in]  probs   The probability matrix used for creting the plist- *  \param[in]  length  The length of the RNA sequence- *  \param[in]  cutoff  The cutoff value- */-void  assign_plist_from_pr( plist **pl,-                            FLT_OR_DBL *probs,-                            int length,-                            double cutoff);--/* this doesn't work if free_pf_arrays() is called before */-void assign_plist_gquad_from_pr(plist **pl,-                                int length,-                                double cut_off);--char *get_centroid_struct_gquad_pr(int length,-                                  double *dist);--/**- *  \brief Get the pointers to (almost) all relavant computation arrays used in partition function computation- *- *  \ingroup    pf_fold- *  \pre        In order to assign meaningful pointers, you have to call pf_fold_par() or pf_fold() first!- *  \see        pf_fold_par(), pf_fold(), pf_circ_fold()- *  \param[out] S_p       A pointer to the 'S' array (integer representation of nucleotides)- *  \param[out] S1_p      A pointer to the 'S1' array (2nd integer representation of nucleotides)- *  \param[out] ptype_p   A pointer to the pair type matrix- *  \param[out] qb_p      A pointer to the Q<sup>B</sup> matrix- *  \param[out] qm_p      A pointer to the Q<sup>M</sup> matrix- *  \param[out] q1k_p     A pointer to the 5' slice of the Q matrix (\f$q1k(k) = Q(1, k)\f$)- *  \param[out] qln_p     A pointer to the 3' slice of the Q matrix (\f$qln(l) = Q(l, n)\f$)- *  \return     Non Zero if everything went fine, 0 otherwise- */-int get_pf_arrays(short **S_p,-                  short **S1_p,-                  char **ptype_p,-                  FLT_OR_DBL **qb_p,-                  FLT_OR_DBL **qm_p,-                  FLT_OR_DBL **q1k_p,-                  FLT_OR_DBL **qln_p);--/**- *  \brief Get the free energy of a subsequence from the q[] array- */-double get_subseq_F(int i, int j);--/**- *  \brief Get the centroid structure of the ensemble- * - *  This function is a threadsafe replacement for \ref centroid() with a 'plist' input- * - *  The centroid is the structure with the minimal average distance to all other structures- *  \n \f$ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} \f$ \n- *  Thus, the centroid is simply the structure containing all pairs with \f$p_ij>0.5\f$- *  The distance of the centroid to the ensemble is written to the memory adressed by \a dist.- *- *  \ingroup            centroid_fold- *  \param[in]  length  The length of the sequence- *  \param[out] dist    A pointer to the distance variable where the centroid distance will be written to- *  \param[in]  pl      A pair list containing base pair probability information about the ensemble- *  \return             The centroid structure of the ensemble in dot-bracket notation- */-char  *get_centroid_struct_pl(int length,-                              double *dist,-                              plist *pl);--/**- *  \brief Get the centroid structure of the ensemble- * - *  This function is a threadsafe replacement for \ref centroid() with a probability array input- * - *  The centroid is the structure with the minimal average distance to all other structures- *  \n \f$ <d(S)> = \sum_{(i,j) \in S} (1-p_{ij}) + \sum_{(i,j) \notin S} p_{ij} \f$ \n- *  Thus, the centroid is simply the structure containing all pairs with \f$p_ij>0.5\f$- *  The distance of the centroid to the ensemble is written to the memory adressed by \a dist.- * - *  \ingroup              centroid_fold- *  \param[in]    length  The length of the sequence- *  \param[out]   dist    A pointer to the distance variable where the centroid distance will be written to- *  \param[in]    pr      A upper triangular matrix containing base pair probabilities (access via iindx \ref get_iindx() )- *  \return               The centroid structure of the ensemble in dot-bracket notation- */-char  *get_centroid_struct_pr(int length,-                              double *dist,-                              FLT_OR_DBL *pr);--/**- *  \brief Get the mean base pair distance of the last partition function computation- * - *  \note To ensure thread-safety, use the function mean_bp_distance_pr() instead!- *- *  \ingroup pf_fold- *- *  \see mean_bp_distance_pr()- * - *  \param    length- *  \return  mean base pair distance in thermodynamic ensemble- */-double  mean_bp_distance(int length);--/**- *  \brief Get the mean base pair distance in the thermodynamic ensemble- * - *  This is a threadsafe implementation of \ref mean_bp_dist() !- * - *  \f$<d> = \sum_{a,b} p_a p_b d(S_a,S_b)\f$\n- *  this can be computed from the pair probs \f$p_ij\f$ as\n- *  \f$<d> = \sum_{ij} p_{ij}(1-p_{ij})\f$- * - *  \note This function is threadsafe- * - *  \ingroup pf_fold- *- *  \param length The length of the sequence- *  \param pr     The matrix containing the base pair probabilities- *  \return       The mean pair distance of the structure ensemble- */-double  mean_bp_distance_pr(int length,-                            FLT_OR_DBL *pr);--/**- *  \brief Create a dot-bracket like structure string from base pair probability matrix- */-void  bppm_to_structure(char *structure,-                        FLT_OR_DBL *pr,-                        unsigned int length);--plist *stackProb(double cutoff);--/**- *  \brief Get a pseudo dot bracket notation for a given probability information- */-char    bppm_symbol(const float *x);---/*-#################################################-# DEPRECATED FUNCTIONS                          #-#################################################-*/--/**- *  \brief Allocate space for pf_fold()- * - *  \deprecated This function is obsolete and will be removed soon!- */-DEPRECATED(void init_pf_fold(int length));--/**- *  \deprecated This function is deprecated and should not be used anymore as it is not threadsafe!- *  \see get_centroid_struct_pl(), get_centroid_struct_pr()- */-DEPRECATED(char *centroid(int length,-                          double *dist));     /* mean pair distance of ensemble */--/**- *  get the mean pair distance of ensemble- * - *  \deprecated This function is not threadsafe and should not be used anymore. Use \ref mean_bp_distance() instead!- */-DEPRECATED(double mean_bp_dist(int length));--/**- *  \deprecated Use \ref exp_E_IntLoop() from loop_energies.h instead- */-DEPRECATED(double expLoopEnergy(int u1,-                                int u2,-                                int type,-                                int type2,-                                short si1,-                                short sj1,-                                short sp1,-                                short sq1));--/**- *  \deprecated Use exp_E_Hairpin() from loop_energies.h instead- */-DEPRECATED(double expHairpinEnergy( int u,-                                    int type,-                                    short si1,-                                    short sj1,-                                    const char *string));--#endif
− include/part_func_co.h 
@@ -1,235 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__-#define __VIENNA_RNA_PACKAGE_PART_FUNC_CO_H__--#include "data_structures.h"--#ifdef __GNUC__-#define DEPRECATED(func) func __attribute__ ((deprecated))-#else-#define DEPRECATED(func) func-#endif--/**- *  \addtogroup pf_cofold- *  \brief Partition Function Cofolding- *- *  To simplify the implementation the partition function computation is done- *  internally in a null model that does not include the duplex initiation- *  energy, i.e. the entropic penalty for producing a dimer from two- *  monomers). The resulting free energies and pair probabilities are initially- *  relative to that null model. In a second step the free energies can be- *  corrected to include the dimerization penalty, and the pair probabilities- *  can be divided into the conditional pair probabilities given that a re- *  dimer is formed or not formed. See \cite bernhart:2006 for further details.- *  @{- *  \file part_func_co.h- * - *  \brief Partition function for two RNA sequences- * - *  As for folding one RNA molecule, this computes the partition function- *  of all possible structures and the base pair probabilities. Uses the- *  same global #pf_scale variable to avoid overflows.- * - *  To simplify the implementation the partition function computation is done- *  internally in a null model that does not include the duplex initiation- *  energy, i.e. the entropic penalty for producing a dimer from two- *  monomers). The resulting free energies and pair probabilities are initially- *  relative to that null model. In a second step the free energies can be- *  corrected to include the dimerization penalty, and the pair probabilities- *  can be divided into the conditional pair probabilities given that a re- *  dimer is formed or not formed.- * - *  After computing the partition functions of all possible dimeres one- *  can compute the probabilities of base pairs, the concentrations out of- *  start concentrations and sofar and soaway.- * - *  Dimer formation is inherently concentration dependent. Given the free- *  energies of the monomers A and B and dimers AB, AA, and BB one can compute- *  the equilibrium concentrations, given input concentrations of A and B, see- *  e.g. Dimitrov & Zuker (2004)- */--/**- *  \brief Toggles no intrabp in 2nd mol- */-extern int    mirnatog;--/**- *  \brief Free energies of the two monomers- */-extern double F_monomer[2];--/**- *  \brief Calculate partition function and base pair probabilities- *- *  This is the cofold partition function folding. The second molecule starts- *  at the #cut_point nucleotide.- *- *  \note OpenMP: Since this function relies on the global parameters- *        #do_backtrack, #dangles, #temperature and #pf_scale it is not- *        threadsafe according to concurrent changes in these variables!- *        Use co_pf_fold_par() instead to circumvent this issue.- *- *  \see co_pf_fold_par()- *- *  \param  sequence  Concatenated RNA sequences- *  \param  structure Will hold the structure or constraints- *  \return           cofoldF structure containing a set of energies needed for- *                    concentration computations.- */-cofoldF co_pf_fold( char *sequence,-                    char *structure);--/**- *  \brief Calculate partition function and base pair probabilities- *- *  This is the cofold partition function folding. The second molecule starts- *  at the #cut_point nucleotide.- *- *  \see get_boltzmann_factors(), co_pf_fold()- *- *  \param sequence       Concatenated RNA sequences- *  \param structure      Pointer to the structure constraint- *  \param parameters     Data structure containing the precalculated Boltzmann factors- *  \param calculate_bppm Switch to turn Base pair probability calculations on/off (0==off)- *  \param is_constrained Switch to indicate that a structure contraint is passed via the- *                        structure argument (0==off)- *  \return               cofoldF structure containing a set of energies needed for- *                        concentration computations.- */-cofoldF co_pf_fold_par( char *sequence,-                        char *structure,-                        pf_paramT *parameters,-                        int calculate_bppm,-                        int is_constrained);--/**- *  \brief Get a pointer to the base pair probability array- * - *  Accessing the base pair probabilities for a pair (i,j) is achieved by- *  \verbatim FLT_OR_DBL *pr = export_bppm(); pr_ij = pr[iindx[i]-j]; \endverbatim- * - *  \see get_iindx()- *  \return A pointer to the base pair probability array- */-FLT_OR_DBL *export_co_bppm(void);--/**- *  \brief Free the memory occupied by co_pf_fold()- */-void    free_co_pf_arrays(void);--/**- *  \brief Recalculate energy parameters- *- *  This function recalculates all energy parameters given- *  the current model settings.- *- *  \note This function relies on the global variables #pf_scale, #dangles and- *        #temperature. Thus it might not be threadsafe in certain situations.- *        Use update_co_pf_params_par() instead.- *- *  \see get_boltzmann_factors(), update_co_pf_params_par()- *- *  \param    length      Length of the current RNA sequence- */-void    update_co_pf_params(int length);--/**- *  \brief Recalculate energy parameters- *- *  This function recalculates all energy parameters given- *  the current model settings.- *  It's second argument can either be NULL or a data structure- *  containing the precomputed Boltzmann factors. In the first- *  scenario, the necessary data structure will be created automatically- *  according to the current global model settings, i.e. this- *  mode might not be threadsafe.- *  However, if the provided data structure is not NULL, threadsafety- *  for the model parameters #dangles, #pf_scale and #temperature is regained, since their- *  values are taken from this data structure during subsequent calculations.- *- *  \see get_boltzmann_factors(), update_co_pf_params()- *- *  \param    length      Length of the current RNA sequence- *  \param    parameters  data structure containing the precomputed Boltzmann factors- */-void    update_co_pf_params_par(int length,-                                pf_paramT *parameters);--/**- *  \brief Compute Boltzmann probabilities of dimerization without homodimers- * - *  Given the pair probabilities and free energies (in the null model) for a- *  dimer AB and the two constituent monomers A and B, compute the conditional pair- *  probabilities given that a dimer AB actually forms.- *  Null model pair probabilities are given as a list as produced by- *  assign_plist_from_pr(), the dimer probabilities 'prAB' are modified in place.- * - *  \param FAB      free energy of dimer AB- *  \param FEA      free energy of monomer A- *  \param FEB      free energy of monomer B- *  \param prAB     pair probabilities for dimer- *  \param prA      pair probabilities monomer- *  \param prB      pair probabilities monomer- *  \param Alength  Length of molecule A- */-void    compute_probabilities(double FAB,-                              double FEA,-                              double FEB,-                              struct plist  *prAB,-                              struct plist  *prA,-                              struct plist  *prB,-                              int Alength);--/**- *  \brief Given two start monomer concentrations a and b, compute the- *  concentrations in thermodynamic equilibrium of all dimers and the monomers.- * - *  This function takes an array  'startconc' of input concentrations with alternating- *  entries for the initial concentrations of molecules A and B (terminated by- *  two zeroes), then computes the resulting equilibrium concentrations- *  from the free energies for the dimers. Dimer free energies should be the- *  dimer-only free energies, i.e. the FcAB entries from the #cofoldF struct.- * - *  \param FEAB       Free energy of AB dimer (FcAB entry)- *  \param FEAA       Free energy of AA dimer (FcAB entry)- *  \param FEBB       Free energy of BB dimer (FcAB entry)- *  \param FEA        Free energy of monomer A- *  \param FEB        Free energy of monomer B- *  \param startconc  List of start concentrations [a0],[b0],[a1],[b1],...,[an][bn],[0],[0]- *  \return ConcEnt array containing the equilibrium energies and start concentrations- */-ConcEnt *get_concentrations(double FEAB,-                            double FEAA,-                            double FEBB,-                            double FEA,-                            double FEB,-                            double *startconc);---/**- *  @}- */--/*-#################################################-# DEPRECATED FUNCTIONS                          #-#################################################-*/--/**- *  DO NOT USE THIS FUNCTION ANYMORE- *  \deprecated{ This function is deprecated and will be removed soon!}- *  use \ref assign_plist_from_pr() instead!- */-DEPRECATED(plist  *get_plist( struct plist *pl,-                              int length,-                              double cut_off));-/**- *  DO NOT USE THIS FUNCTION ANYMORE- *  \deprecated{ This function is deprecated and will be removed soon!}- */-DEPRECATED(void   init_co_pf_fold(int length));--#endif
− include/plot_layouts.h 
@@ -1,106 +0,0 @@-/**- * \file plot_layouts.h- *- * \brief Secondary structure plot layout algorithms- *- *  c Ronny Lorenz- *    The ViennaRNA Package- */-#ifndef __VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H__-#define __VIENNA_RNA_PACKAGE_PLOT_LAYOUTS_H__--#include "data_structures.h"-#include "naview.h"--#ifndef PI-#define  PI       3.141592654-#endif-#define  PIHALF       PI/2.---/**- *  \brief Definition of Plot type <i>simple</i>- *- *  This is the plot type definition for several RNA structure plotting functions telling- *  them to use <b>Simple</b> plotting algorithm- *- *  \see rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()- */-#define VRNA_PLOT_TYPE_SIMPLE     0--/**- *  \brief Definition of Plot type <i>Naview</i>- *- *  This is the plot type definition for several RNA structure plotting functions telling- *  them to use <b>Naview</b> plotting algorithm- *- *  \see rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()- */-#define VRNA_PLOT_TYPE_NAVIEW     1--/**- *  \brief Definition of Plot type <i>Circular</i>- *- *  This is the plot type definition for several RNA structure plotting functions telling- *  them to produce a <b>Circular plot</b>- *- *  \see rna_plot_type, PS_rna_plot_a(), PS_rna_plot(), svg_rna_plot(), gmlRNA(), ssv_rna_plot(), xrna_plot()- */-#define VRNA_PLOT_TYPE_CIRCULAR   2---/**- *  \brief Switch for changing the secondary structure layout algorithm- *- *  Current possibility are 0 for a simple radial drawing or 1 for the modified- *  radial drawing taken from the \e naview program of \ref bruccoleri_88 "Bruccoleri & Heinrich (1988)".- *- *  \note To provide thread safety please do not rely on this global variable in future implementations- *  but pass a plot type flag directly to the function that decides which layout algorithm it may use!- *- *  \see #VRNA_PLOT_TYPE_SIMPLE, #VRNA_PLOT_TYPE_NAVIEW, #VRNA_PLOT_TYPE_CIRCULAR- *- */-extern int rna_plot_type;--/**- *  \brief Calculate nucleotide coordinates for secondary structure plot the <i>Simple way</i>- *- *  \see make_pair_table(), rna_plot_type, simple_circplot_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(),- *  PS_rna_plot, svg_rna_plot()- *- *  \param  pair_table  The pair table of the secondary structure- *  \param  X           a pointer to an array with enough allocated space to hold the x coordinates- *  \param  Y           a pointer to an array with enough allocated space to hold the y coordinates- *  \return             length of sequence on success, 0 otherwise- */-int simple_xy_coordinates(short *pair_table,-                          float *X,-                          float *Y);--/**- *  \brief Calculate nucleotide coordinates for <i>Circular Plot</i>- *- *  This function calculates the coordinates of nucleotides mapped in equal distancies onto a unit circle.- *- *  \note In order to draw nice arcs using quadratic bezier curves that connect base pairs one may calculate- *  a second tangential point \f$P^t\f$ in addition to the actual R<sup>2</sup> coordinates.- *  the simplest way to do so may be to compute a radius scaling factor \f$rs\f$ in the interval \f$[0,1]\f$ that- *  weights the proportion of base pair span to the actual length of the sequence. This scaling factor- *  can then be used to calculate the coordinates for \f$P^t\f$, i.e. \f$ P^{t}_x[i] = X[i] * rs\f$- *  and \f$P^{t}_y[i] = Y[i] * rs\f$.- *- *  \see make_pair_table(), rna_plot_type, simple_xy_coordinates(), naview_xy_coordinates(), PS_rna_plot_a(),- *  PS_rna_plot, svg_rna_plot()- *- *  \param  pair_table  The pair table of the secondary structure- *  \param  x           a pointer to an array with enough allocated space to hold the x coordinates- *  \param  y           a pointer to an array with enough allocated space to hold the y coordinates- *  \return             length of sequence on success, 0 otherwise- */-int simple_circplot_coordinates(short *pair_table,-                                float *x,-                                float *y);---#endif
− include/subopt.h 
@@ -1,117 +0,0 @@-/* subopt.h */-#ifndef __VIENNA_RNA_PACKAGE_SUBOPT_H__-#define __VIENNA_RNA_PACKAGE_SUBOPT_H__--#include "data_structures.h"--#define MAXDOS 1000--/**- *  \addtogroup subopt_fold Enumerating Suboptimal Structures- *  \ingroup folding_routines- *  @{- *    \file subopt.h- *    \brief RNAsubopt and density of states declarations- *- *  @}- */--/**- *  \addtogroup subopt_wuchty- *  @{- *- *  @}- */--/**- *  \brief Returns list of subopt structures or writes to fp- * - *  This function produces <b>all</b> suboptimal secondary structures within- *  'delta' * 0.01 kcal/mol of the optimum. The results are either- *  directly written to a 'fp' (if 'fp' is not NULL), or- *  (fp==NULL) returned in a #SOLUTION * list terminated- *  by an entry were the 'structure' pointer is NULL.- *- *  \ingroup subopt_wuchty- *- *  \param  seq- *  \param  structure- *  \param  delta- *  \param  fp- *  \return- */-SOLUTION *subopt (char *seq,-                  char *structure,-                  int delta,-                  FILE *fp);--/**- *  \brief Returns list of subopt structures or writes to fp- * - *  \ingroup subopt_wuchty- */-SOLUTION *subopt_par( char *seq,-                      char *structure,-                      paramT *parameters,-                      int delta,-                      int is_constrained,-                      int is_circular,-                      FILE *fp);--/**- *  \brief Returns list of circular subopt structures or writes to fp- * - *  This function is similar to subopt() but calculates secondary structures- *  assuming the RNA sequence to be circular instead of linear- * - *  \ingroup subopt_wuchty- *- *  \param  seq- *  \param  sequence- *  \param  delta- *  \param  fp- *  \return- */-SOLUTION *subopt_circ ( char *seq,-                        char *sequence,-                        int delta,-                        FILE *fp);--/**- *  \brief Sort output by energy- * - *  \ingroup subopt_wuchty- *- */-extern  int     subopt_sorted;---/**- *  \brief printing threshold for use with logML- * - *  \ingroup subopt_wuchty- *- */-extern  double  print_energy;--/**- *  \addtogroup dos- *  @{- */--/**- *  \brief The Density of States- *- *  This array contains the density of states for an RNA sequences after a call to subopt_par(),- *  subopt() or subopt_circ().- *- *  \pre  Call one of the functions subopt_par(), subopt() or subopt_circ() prior accessing the contents- *        of this array- *  \see  subopt_par(), subopt(), subopt_circ()- *- */-extern  int     density_of_states[MAXDOS+1];--/** @} */ /* End of group dos */--#endif
− include/utils.h 
@@ -1,615 +0,0 @@-#ifndef __VIENNA_RNA_PACKAGE_UTILS_H__-#define __VIENNA_RNA_PACKAGE_UTILS_H__--/**- *  \file utils.h- *  \brief Various utility- and helper-functions used throughout the Vienna RNA package- */--/**- *  Output flag of \ref get_input_line():  "An ERROR has occured, maybe EOF"- */-#define VRNA_INPUT_ERROR                  1U-/**- *  Output flag of \ref get_input_line():  "the user requested quitting the program"- */-#define VRNA_INPUT_QUIT                   2U-/**- *  Output flag of \ref get_input_line():  "something was read"- */-#define VRNA_INPUT_MISC                   4U--/** Input/Output flag of \ref get_input_line():\n- *  if used as input option this tells get_input_line() that the data to be read should comply- *  with the FASTA format- * - *  the function will return this flag if a fasta header was read- */-#define VRNA_INPUT_FASTA_HEADER           8U--/** Input flag for get_input_line():\n- *  Tell get_input_line() that we assume to read a nucleotide sequence- * - */-#define VRNA_INPUT_SEQUENCE               16U--/** Input flag for get_input_line():\n- *  Tell get_input_line() that we assume to read a structure constraint- * - */-#define VRNA_INPUT_CONSTRAINT             32U--/**- *  Input switch for \ref get_input_line():- *  "do not trunkate the line by eliminating white spaces at end of line"- */-#define VRNA_INPUT_NO_TRUNCATION          256U--/**- *  Input switch for read_record():  "do fill rest array"- */-#define VRNA_INPUT_NO_REST                512U--/**- *  Input switch for read_record():  "never allow data to span more than one line"- */-#define VRNA_INPUT_NO_SPAN                1024U--/**- *  Input switch for read_record():  "do not skip empty lines"- */-#define VRNA_INPUT_NOSKIP_BLANK_LINES     2048U--/**- *  Output flag for read_record():  "read an empty line"- */-#define VRNA_INPUT_BLANK_LINE             4096U--/**- *  Input switch for \ref get_input_line():  "do not skip comment lines"- */-#define VRNA_INPUT_NOSKIP_COMMENTS        128U--/**- *  Output flag for read_record():  "read a comment"- */-#define VRNA_INPUT_COMMENT                8192U-----/**- *  pipe sign '|' switch for structure constraints (paired with another base)- */-#define VRNA_CONSTRAINT_PIPE              1U-/**- *  dot '.' switch for structure constraints (no constraint at all)- */-#define VRNA_CONSTRAINT_DOT               2U-/**- *  'x' switch for structure constraint (base must not pair)- */-#define VRNA_CONSTRAINT_X                 4U-/**- *  angle brackets '<', '>' switch for structure constraint (paired downstream/upstream)- */-#define VRNA_CONSTRAINT_ANG_BRACK         8U-/**- *  round brackets '(',')' switch for structure constraint (base i pairs base j)- */-#define VRNA_CONSTRAINT_RND_BRACK         16U-/**- *  constraint may span over several lines- */-#define VRNA_CONSTRAINT_MULTILINE         32U-/**- *  do not print the header information line- */-#define VRNA_CONSTRAINT_NO_HEADER         64U-/**- *  placeholder for all constraining characters- */-#define VRNA_CONSTRAINT_ALL              128U-/**- *  '+' switch for structure constraint (base is involved in a gquad)- */-#define VRNA_CONSTRAINT_G                256U----/**- * Tell a function that an input is assumed to span several lines if used as input-option- * A function might also be returning this state telling that it has read data from- * multiple lines.- *- * \see extract_record_rest_structure(), read_record(), getConstraint()- *- */-#define VRNA_OPTION_MULTILINE             32U---/**- *  Get the minimum of two comparable values- */-#define MIN2(A, B)      ((A) < (B) ? (A) : (B))-/**- *  Get the maximum of two comparable values- */-#define MAX2(A, B)      ((A) > (B) ? (A) : (B))-/**- *  Get the minimum of three comparable values- */-#define MIN3(A, B, C)   (MIN2(  (MIN2((A),(B))) ,(C)))-/**- *  Get the maximum of three comparable values- */-#define MAX3(A, B, C)   (MAX2(  (MAX2((A),(B))) ,(C)))---/**- * Stringify a macro after expansion- */-#define XSTR(s) STR(s)-/**- * Stringify a macro argument- */-#define STR(s) #s--#ifndef FILENAME_MAX_LENGTH-/**- *  \brief Maximum length of filenames that are generated by our programs- *- *  This definition should be used throughout the complete ViennaRNA package- *  wherever a static array holding filenames of output files is declared.- */-#define FILENAME_MAX_LENGTH   80-/**- *  \brief Maximum length of id taken from fasta header for filename generation- *- *  this has to be smaller than FILENAME_MAX_LENGTH since in most cases,- *  some suffix will be appended to the ID- */-#define FILENAME_ID_LENGTH    42-#endif---#ifdef HAVE_CONFIG_H-#include <config.h>-#ifndef HAVE_STRDUP-char *strdup(const char *s);-#endif-#endif-#ifdef WITH_DMALLOC-/* use dmalloc library to check for memory management bugs */-#include "dmalloc.h"-#define space(S) calloc(1,(S))-#else--/**- *  \brief Allocate space safely- *- *  \param size The size of the memory to be allocated in bytes- *  \return     A pointer to the allocated memory- */-/*@only@*/ /*@notnull@*/-void  *space(unsigned size) /*@ensures MaxSet(result) == (size-1);@*/;--/**- *  \brief Reallocate space safely- *- *  \param p    A pointer to the memory region to be reallocated- *  \param size The size of the memory to be allocated in bytes- *  \return     A pointer to the newly allocated memory- */-/*@only@*/ /*@notnull@*/-void  *xrealloc(/*@null@*/ /*@only@*/ /*@out@*/ /*@returned@*/ void *p,-                unsigned size) /*@modifies *p @*/ /*@ensures MaxSet(result) == (size-1) @*/;-#endif--/**- *  \brief Die with an error message- *- *  \see warn_user()- *  \param message The error message to be printed before exiting with 'FAILURE'- */-/*@exits@*/-void nrerror(const char message[]);--/**- *  \brief Print a warning message- *- *  Print a warning message to \e stderr- *- *  \param  message   The warning message- */-void warn_user(const char message[]);--/**- *  \brief  Make random number seeds- */-void   init_rand(void);--/**- * \brief Current 48 bit random number- *- *  This variable is used by urn(). These should be set to some- *  random number seeds before the first call to urn().- *- *  \see urn()- */-extern unsigned short xsubi[3];--/**- *  \brief get a random number from [0..1]- *- *  \note Usually implemented by calling \e erand48().- *  \return   A random number in range [0..1]- */-double urn(void);--/**- *  \brief Generates a pseudo random integer in a specified range- *- *  \param from   The first number in range- *  \param to     The last number in range- *  \return       A pseudo random number in range [from, to]- */-int    int_urn(int from, int to);--void   filecopy(FILE *from, FILE *to); /* inefficient `cp' */--/**- *  \brief Get a timestamp- *- *  Returns a string containing the current date in the format- *  \verbatim Fri Mar 19 21:10:57 1993\endverbatim- *- *  \return A string containing the timestamp- */-/*@observer@*/-char  *time_stamp(void);--/**- *  \brief Create a random string using characters from a specified symbol set- *- *  \param l        The length of the sequence- *  \param symbols  The symbol set- *  \return         A random string of length 'l' containing characters from the symbolset- */-/*@only@*/ /*@notnull@*/-char  *random_string(int l, const char symbols[]);--/**- *  \brief Calculate hamming distance between two sequences- *- *  Calculate the number of positions in which - *  \param s1   The first sequence- *  \param s2   The second sequence- *  \return     The hamming distance between s1 and s2- */-int   hamming(const char *s1, const char *s2);--/**- *  \brief Calculate hamming distance between two sequences up to a specified length- *- *  This function is similar to hamming() but instead of comparing both sequences- *  up to their actual length only the first 'n' characters are taken into account- *  \param s1   The first sequence- *  \param s2   The second sequence- *  \return     The hamming distance between s1 and s2- */-int   hamming_bound(const char *s1, const char *s2, int n);--/**- *  \brief Read a line of arbitrary length from a stream- *- *  Returns a pointer to the resulting string. The necessary memory is- *  allocated and should be released using \e free() when the string is- *  no longer needed.- *- *  \param  fp  A file pointer to the stream where the function should read from- *  \return     A pointer to the resulting string- */-/*@only@*/ /*@null@*/-char  *get_line(FILE *fp);--int skip_comment_lines(char **line);--/**- *  Retrieve a line from 'stdin' savely while skipping comment characters and- *  other features- *  This function returns the type of input it has read if recognized.- *  An option argument allows to switch between different reading modes.\n- *  Currently available options are:\n- *  #VRNA_INPUT_NOPRINT_COMMENTS, #VRNA_INPUT_NOSKIP_COMMENTS, #VRNA_INPUT_NOELIM_WS_SUFFIX- * - *  pass a collection of options as one value like this:- *  \verbatim get_input_line(string, option_1 | option_2 | option_n) \endverbatim- * - *  If the function recognizes the type of input, it will report it in the return- *  value. It also reports if a user defined 'quit' command (@-sign on 'stdin')- *  was given. Possible return values are:\n- *  #VRNA_INPUT_FASTA_HEADER, #VRNA_INPUT_ERROR, #VRNA_INPUT_MISC, #VRNA_INPUT_QUIT- * - *  \param string   A pointer to the character array that contains the line read- *  \param options  A collection of options for switching the functions behavior- *  \return         A flag with information about what has been read- */-unsigned int get_input_line(char **string,-                            unsigned int options);--unsigned int get_multi_input_line(char **string,-                                  unsigned int options);--/**- *  \brief  Get a data record from stdin- * - *  This function may be used to obtain complete datasets from stdin. A dataset is always- *  defined to contain at least a sequence. If data on stdin starts with a fasta header,- *  i.e. a line like- *  \verbatim >some header info \endverbatim- *  then read_record() will assume that the sequence that follows the header may span- *  over several lines. To disable this behavior and to assign a single line to the argument- *  'sequence' one can pass VRNA_INPUT_NO_SPAN in the 'options' argument.- *  If no fasta header is read in the beginning of a data block, a sequence must not span over- *  multiple lines!\n- *  Unless the options #VRNA_INPUT_NOSKIP_COMMENTS or #VRNA_INPUT_NOSKIP_BLANK_LINES are passed,- *  a sequence may be interrupted by lines starting with a comment character or empty lines.\n- *  A sequence is regarded as completely read if it was either assumed to not span over multiple- *  lines, a secondary structure or structure constraint follows the sequence on the next line- *  or a new header marks the beginning of a new sequence...\n- *  All lines following the sequence (this includes comments) and not initiating a new dataset are- *  available through the line-array 'rest'. Here one can usually find the structure constraint or- *  other information belonging to the current dataset. Filling of 'rest' may be prevented by- *  passing #VRNA_INPUT_NO_REST to the options argument.\n- * - *  \note This function will exit any program with an error message if no sequence could be read!- * - *  The main purpose of this function is to be able to easily parse blocks of data from stdin- *  in the header of a loop where all calculations for the appropriate data is done inside the- *  loop. The loop may be then left on certain return values, e.g.:- *  \verbatim-char *id, *seq, **rest;-int  i;-while(!(read_record(&id, &seq, &rest, 0) & (VRNA_INPUT_ERROR | VRNA_INPUT_QUIT))){-  if(id) printf("%s\n", id);-  printf("%s\n", seq);-  if(rest)-    for(i=0;rest[i];i++)-      printf("%s\n", rest[i]);-} \endverbatim- * - *  In the example above, the while loop will be terminated when read_record() returns either an- *  error or a user initiated quit request.\n- *  As long as data is read from stdin, the id is printed if it is available for the current block- *  of data. The sequence will be printed in any case and if some more lines belong to the current- *  block of data each line will be printed as well.- * - *  \note Do not forget to free the memory occupied by header, sequence and rest!- * - *  \param  header    A pointer which will be set such that it points to the header of the record- *  \param  sequence  A pointer which will be set such that it points to the sequence of the record- *  \param  rest      A pointer which will be set such that it points to an array of lines which also belong to the record- *  \param  options   Some options which may be passed to alter the behavior of the function, use 0 for no options- *  \return           A flag with information about what the function actually did read- */-unsigned int read_record( char **header,-                          char **sequence,-                          char  ***rest,-                          unsigned int options);---/* \brief Extract a dot-bracket structure string from (multiline)character array- *- * This function extracts a dot-bracket structure string from the 'rest' array as- * returned by read_record() and returns it. All occurences of comments within the- * 'lines' array will be skipped as long as they do not break the structure string.- * If no structure could be read, this function returns NULL.- *- * \see read_record()- *- * \param lines   The (multiline) character array to be parsed- * \param length  The assumed length of the dot-bracket string (passing a value < 1 results in no length limit)- * \param option  Some options which may be passed to alter the behavior of the function, use 0 for no options- * \return        The dot-bracket string read from lines or NULL- */-char *extract_record_rest_structure(const char **lines,-                                    unsigned int length,-                                    unsigned int option);--/**- *  \brief Pack secondary secondary structure, 5:1 compression using base 3 encoding- *- *  Returns a binary string encoding of the secondary structure using- *  a 5:1 compression scheme. The string is NULL terminated and can- *  therefore be used with standard string functions such as strcmp().- *  Useful for programs that need to keep many structures in memory.- *- *  \param struc    The secondary structure in dot-bracket notation- *  \return         The binary encoded structure- */-char *pack_structure(const char *struc);--/**- *  \brief Unpack secondary structure previously packed with pack_structure()- *- *  Translate a compressed binary string produced by pack_structure() back into- *  the familiar dot-bracket notation.- *- *  \param packed   The binary encoded packed secondary structure- *  \return         The unpacked secondary structure in dot-bracket notation- */-char *unpack_structure(const char *packed);--/**- *  \brief Create a pair table of a secondary structure- *- *  Returns a newly allocated table, such that table[i]=j if (i.j) pair- *  or 0 if i is unpaired, table[0] contains the length of the structure.- *- *  \param  structure The secondary structure in dot-bracket notation- *  \return           A pointer to the created pair_table- */-short *make_pair_table(const char *structure);--short *make_pair_table_pk(const char *structure);--/**- *  \brief Get an exact copy of a pair table- *- *  \param pt The pair table to be copied- *  \return   A pointer to the copy of 'pt' - */-short *copy_pair_table(const short *pt);--/**-***Pair table for snoop align-***-***-**/-short *alimake_pair_table(const char *structure);--/**-*** returns a newly allocated table, such that:  table[i]=j if (i.j) pair or-*** 0 if i is unpaired, table[0] contains the length of the structure.-*** The special pseudoknotted H/ACA-mRNA structure is taken into account.-**/-short *make_pair_table_snoop(const char *structure);--/**- *  \brief Compute the "base pair" distance between two secondary structures s1 and s2.- * - *  The sequences should have the same length.- *  dist = number of base pairs in one structure but not in the other- *  same as edit distance with open-pair close-pair as move-set- * - *  \param str1   First structure in dot-bracket notation- *  \param str2   Second structure in dot-bracket notation- *  \return       The base pair distance between str1 and str2- */--int *make_loop_index_pt(short *pt);---int bp_distance(const char *str1,-                const char *str2);--/**- *  \brief Print a line to \e stdout that asks for an input sequence- *- *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions- */-void print_tty_input_seq(void);--/**- *  \brief Print a line with a user defined string and a ruler to stdout.- *- *  (usually this is used to ask for user input)- *  There will also be a ruler (scale line) printed that helps orientation of the sequence positions- * - *  \param s A user defined string that will be printed to stdout- */-void print_tty_input_seq_str(const char *s);--/**- *  \brief Print structure constraint characters to stdout- *  (full constraint support)- *- */-void print_tty_constraint_full(void);--/**- *  \brief Print structure constraint characters to stdout.- *  (constraint support is specified by option parameter)- *- *  Currently available options are:\n- *  #VRNA_CONSTRAINT_PIPE (paired with another base)\n- *  #VRNA_CONSTRAINT_DOT (no constraint at all)\n- *  #VRNA_CONSTRAINT_X (base must not pair)\n- *  #VRNA_CONSTRAINT_ANG_BRACK (paired downstream/upstream)\n- *  #VRNA_CONSTRAINT_RND_BRACK (base i pairs base j)\n- * - *  pass a collection of options as one value like this:- *  \verbatim print_tty_constraint(option_1 | option_2 | option_n) \endverbatim- * - *  \param option Option switch that tells which constraint help will be printed- */-void print_tty_constraint(unsigned int option);--/**- *  \brief Convert a DNA input sequence to RNA alphabet- *- *  This function substitudes <i>T</i> and <i>t</i> with <i>U</i> and <i>u</i>, respectively- * - *  \param sequence The sequence to be converted- */-void str_DNA2RNA(char *sequence);--/**- *  \brief Convert an input sequence to uppercase- * - *  \param sequence The sequence to be converted- */-void  str_uppercase(char *sequence);--/**- *  \brief Get an index mapper array (iindx) for accessing the energy matrices, e.g. in partition function related functions.- *- *  Access of a position "(i,j)" is then accomplished by using \verbatim (i,j) ~ iindx[i]-j \endverbatim- *  This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout- *  the ViennaRNAPackage- * - *  Consult the implemented code to find out about the mapping formula ;)- * - *  \see get_indx()- *  \param length The length of the RNA sequence- *  \return       The mapper array- */-int   *get_iindx(unsigned int length);--/**- *  \brief Get an index mapper array (indx) for accessing the energy matrices, e.g. in MFE related functions.- *- *  Access of a position "(i,j)" is then accomplished by using \verbatim (i,j) ~ indx[j]+i \endverbatim- *  This function is necessary as most of the two-dimensional energy matrices are actually one-dimensional arrays throughout- *  the ViennaRNAPackage- * - *  Consult the implemented code to find out about the mapping formula ;)- * - *  \see get_iindx()- *  \param length The length of the RNA sequence- *  \return       The mapper array- * - */-int   *get_indx(unsigned int length);--void getConstraint( char **cstruc,-                    const char **lines,-                    unsigned int option);--/**- *  \brief Insert constraining pair types according to constraint structure string- *- *  \see get_indx(), get_iindx()- *- *  \param constraint     The structure constraint string- *  \param length         The actual length of the sequence (constraint may be shorter)- *  \param ptype          A pointer to the basepair type array- *  \param min_loop_size  The minimal loop size (usually \ref TURN )- *  \param idx_type       Define the access type for base pair type array (0 = indx, 1 = iindx)- */-void constrain_ptypes(const char *constraint,-                      unsigned int length,-                      char *ptype,-                      int *BP,-                      int min_loop_size,-                      unsigned int idx_type);--unsigned int  *make_referenceBP_array(short *reference_pt,-                                      unsigned int turn);--unsigned int  *compute_BPdifferences( short *pt1,-                                      short *pt2,-                                      unsigned int turn);--#endif
+ tests/properties.hs view
@@ -0,0 +1,119 @@++module Main where++import Test.Tasty+import Test.Tasty.HUnit+import Test.Tasty.Silver as S+import Test.Tasty.Silver.Interactive as SI+import Test.Tasty.TH+import Data.Array ((!))+import Debug.Trace++import BioInf.ViennaRNA.Bindings as V++++a =~ b = abs (b - a) <= 0.01++++case_mfe_001 :: Assertion+case_mfe_001 = do+  (e,s) <- V.mfe "cccaaaggg"+  assertBool "energy" $ e =~ (-1.2)+  assertBool "structure" $ s == "(((...)))"++case_mfe_002 :: Assertion+case_mfe_002 = do+  (e,s) <- V.mfe "uguagcuagcuagcuagcuacguacguagcuagc"+  assertBool "energy" $ e =~ (-14.0)+  assertBool "structure" $ s == "............(((((((((....)))))))))"++-- RNAfold webserver test sequence, allowing for isolated base pairs++case_mfe_003 :: Assertion+case_mfe_003 = do+  (e,s) <- V.mfe "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+  assertBool "energy" $ e =~ (-29.90)+  assertBool "structure" $ s == "(((((((..(((.((((.(....(((((.(((((....)))).)..).))))....).)))).))))))))))."++--case_circmfe_001 :: Assertion+--case_circmfe_001 = do+--  (e,s) <- V.circmfe "GGGCUAUUAGCUCAGUUGGUUAGAGCGCA&CCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+--  assertBool "energy" $ e =~ (-19.50)+--  assertBool "structure" $ s == ".((((((..(((.((((.(....(((((.(((((....)))).)..).))))....).)))).))))))))).."++case_eos_001 :: Assertion+case_eos_001 = do+  e <- V.eos "ACGAUCAGAGAUCAGAGCAUACGACAGCAG" "..((((...))))...((........)).."+  assertBool "eos" $ e =~ (-2.90)++case_eosTemp_37_001 :: Assertion+case_eosTemp_37_001 = do+  e <- V.eosTemp 37 "ACGAUCAGAGAUCAGAGCAUACGACAGCAG" "..((((...))))...((........)).."+  assertBool "eos" $ e =~ (-2.90)++case_eosTemp_20_001 :: Assertion+case_eosTemp_20_001 = do+  e <- V.eosTemp 20 "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA" "((((((((((((.....)))))((.(.(((((.......))))).).))(((((.......))))))))))))."+  assertBool "eos" $ e =~ (-40.86)++-- TODO more on @arr@ checks !++case_part_001 :: Assertion+case_part_001 = do+  (e,s,arr) <- V.part "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+  assertBool "energy" $ e =~ (-31.43)+  assertBool "structure" $ s == "(((((((..(((.{{{{,|,,.,({({((((({(....})))}).,,,)|||,,..}.}}}),))))))))))."+  assertBool "1,13" $ arr ! (1,13) =~ 0.010+  assertBool "4,70" $ arr ! (4,70) =~ 0.999++case_duplexfold_001 :: Assertion+case_duplexfold_001 = do+  d <- V.duplexFold "ACGATCAGAGATCAGAGCATACGACAGCAG" "ACGAAAAAAAGAGCATACGACAGCAG"+  assertBool "energy" $ energy d =~ (-4.10)+  assertBool "structure" $ structure d == ".((...((...((.&.))...))...))."++case_mfeTemp_37_001 :: Assertion+case_mfeTemp_37_001 = do+  (e,s) <- V.mfeTemp 37 "cccaaaggg"+  assertBool "energy" $ e =~ (-1.2)+  assertBool "structure" $ s == "(((...)))"++case_mfeTemp_37_002 :: Assertion+case_mfeTemp_37_002 = do+  (e,s) <- V.mfeTemp 37 "uguagcuagcuagcuagcuacguacguagcuagc"+  assertBool "energy" $ e =~ (-14.0)+  assertBool "structure" $ s == "............(((((((((....)))))))))"++case_mfeTemp_37_003 :: Assertion+case_mfeTemp_37_003 = do+  (e,s) <- V.mfeTemp 37 "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+  assertBool "energy" $ e =~ (-28.90)+  assertBool "structure" $ s == "(((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))."++case_mfeTemp_20_001 :: Assertion+case_mfeTemp_20_001 = do+  (e,s) <- V.mfeTemp 20 "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+  assertBool "energy" $ e =~ (-39.29)+  assertBool "structure" $ s == "(((((((..((((.........)))).(((((.......))))).....(((((.......))))))))))))."++++case_centroidTemp_37_001 :: Assertion+case_centroidTemp_37_001 = do+  (e,s) <- V.centroidTemp 37 "cccaaaggg"+  assertBool "energy" $ e =~ (-1.2)+  assertBool "structure" $ s == "(((...)))"++case_centroidTemp_37_003 :: Assertion+case_centroidTemp_37_003 = do+  (e,s) <- V.centroidTemp 37 "GGGCUAUUAGCUCAGUUGGUUAGAGCGCACCCCUGAUAAGGGUGAGGUCGCUGAUUCGAAUUCAGCAUAGCCCA"+  assertBool "energy" $ e =~ (-28.10)+  assertBool "structure" $ s == "(((((((..((((.........)))).(((((.(....)))))).....(((((.......))))))))))))."++++main :: IO ()+main = $(defaultMainGenerator)+