diff --git a/BioInf/ViennaRNA/Bindings.hs b/BioInf/ViennaRNA/Bindings.hs --- a/BioInf/ViennaRNA/Bindings.hs +++ b/BioInf/ViennaRNA/Bindings.hs @@ -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 diff --git a/BioInf/ViennaRNA/Bindings/FFI/Centroid.chs b/BioInf/ViennaRNA/Bindings/FFI/Centroid.chs new file mode 100644 --- /dev/null +++ b/BioInf/ViennaRNA/Bindings/FFI/Centroid.chs @@ -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 + diff --git a/BioInf/ViennaRNA/Bindings/FFI/CoFold.chs b/BioInf/ViennaRNA/Bindings/FFI/CoFold.chs --- a/BioInf/ViennaRNA/Bindings/FFI/CoFold.chs +++ b/BioInf/ViennaRNA/Bindings/FFI/CoFold.chs @@ -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 #} diff --git a/BioInf/ViennaRNA/Bindings/FFI/Duplex.chs b/BioInf/ViennaRNA/Bindings/FFI/Duplex.chs new file mode 100644 --- /dev/null +++ b/BioInf/ViennaRNA/Bindings/FFI/Duplex.chs @@ -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 () + diff --git a/BioInf/ViennaRNA/Bindings/FFI/Fold.chs b/BioInf/ViennaRNA/Bindings/FFI/Fold.chs --- a/BioInf/ViennaRNA/Bindings/FFI/Fold.chs +++ b/BioInf/ViennaRNA/Bindings/FFI/Fold.chs @@ -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 diff --git a/BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs b/BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs --- a/BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs +++ b/BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs @@ -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 diff --git a/BioInf/ViennaRNA/Bindings/FFI/Utils.hs b/BioInf/ViennaRNA/Bindings/FFI/Utils.hs --- a/BioInf/ViennaRNA/Bindings/FFI/Utils.hs +++ b/BioInf/ViennaRNA/Bindings/FFI/Utils.hs @@ -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 diff --git a/C/ViennaRNA/2Dfold.c b/C/ViennaRNA/2Dfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/2Dfold.c @@ -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 +#include +#include +#include +#include +#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 +#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;icirc) ? 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;icirc) ? 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;icirc) ? 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)||(qE_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; uE_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 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; uMLclosing; + 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; uMLclosing; + 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 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 (uMAXLOOP) 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; iMLclosing)){ + 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= 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 (uMAXLOOP) 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= 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 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= 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; ik_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; jE_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 (uE_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 (uMAXLOOP) 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; iE_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); +} + diff --git a/C/ViennaRNA/2Dfold.h b/C/ViennaRNA/2Dfold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/2Dfold.h @@ -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 +#include + +/** + * @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 diff --git a/C/ViennaRNA/2Dpfold.c b/C/ViennaRNA/2Dpfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/2Dpfold.c @@ -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 +#include +#include +#include +#include +#include /* #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; uexpMLclosing * 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, (jQ_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: iQ_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], (jQ_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; kQ_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; lQ_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 (uQ_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; kQ_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 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 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; j1) ? 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= 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= 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; j1) ? 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= 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 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= 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= 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;iMAXLOOP) 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;iMAXLOOP) 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 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 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 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= 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= 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 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= 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= 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= 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, iexp_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(qmtexpMLbase, 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(kexpMLbase, 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; +} diff --git a/C/ViennaRNA/2Dpfold.h b/C/ViennaRNA/2Dpfold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/2Dpfold.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/LPfold.c b/C/ViennaRNA/LPfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/LPfold.c @@ -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 +#include +#include +#include +#include /* #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 +#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=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); l1) ? S1[i-1] : -1, (j0) 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=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, (l0)) + 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); ik; 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, (lQmax) { + 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 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; j10e-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; jexpMLclosing; + + 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 = (i5k+ulength) + temp += qm2[k+ulength+1][j3-1] * expMLbase[k+ulength-i5]; /* (..|-----|{}{}) */ + + if((i5k+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((l5-k5-1)+(j3-l3-1) + k-winSize+ulength0) /* 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+TURN0) /* oder so halt */ + for (k5=k+ulength+1; k5=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=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 = (i5k+ulength) + temp += qm2[k+ulength+1][j3-1] * expMLbase[k+ulength-i5]; /* (..|-----|{}{}) */ + + if((i5k+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=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 */} + diff --git a/C/ViennaRNA/LPfold.h b/C/ViennaRNA/LPfold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/LPfold.h @@ -0,0 +1,167 @@ +#ifndef VIENNA_RNA_PACKAGE_LPFOLD_H +#define VIENNA_RNA_PACKAGE_LPFOLD_H + +#include +#include + +#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 diff --git a/C/ViennaRNA/Lfold.c b/C/ViennaRNA/Lfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/Lfold.c @@ -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 +#include +#include +#include +#include +#include +#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; jlength-maxdist-4; j--) { + for (i=(length-maxdist-4>0)?length-maxdist-4:1 ; imatrices->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 (minqi+1)||(qMLbase); + 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, (jMLbase; + /* 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; j1) ? 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 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) 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, (ki+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(kMLbase == 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= 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)||(qMLclosing + 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;a0 && 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 diff --git a/C/ViennaRNA/Lfold.h b/C/ViennaRNA/Lfold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/Lfold.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/MEA.c b/C/ViennaRNA/MEA.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/MEA.c @@ -0,0 +1,288 @@ +/* + MEA.c + c Ivo L Hofacker, Vienna RNA package +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include /* #defines DBL_EPSILON */ +#include +#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; imodel_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; liA + 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]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;kstructure[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; lii >= 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; lii >= 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; lii >= 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()"); +} diff --git a/C/ViennaRNA/MEA.h b/C/ViennaRNA/MEA.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/MEA.h @@ -0,0 +1,36 @@ +#ifndef VIENNA_RNA_PACKAGE_MEA_H +#define VIENNA_RNA_PACKAGE_MEA_H + +#include +#include + +/** + * @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 diff --git a/C/ViennaRNA/PKplex.h b/C/ViennaRNA/PKplex.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/PKplex.h @@ -0,0 +1,25 @@ +#ifndef PKPLEX_H +#define PKPLEX_H + +#include + +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 diff --git a/C/ViennaRNA/PS_dot.c b/C/ViennaRNA/PS_dot.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/PS_dot.c @@ -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 +#include +#include +#include +#include +#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=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 +#include +#include + +#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 diff --git a/C/ViennaRNA/ProfileAln.c b/C/ViennaRNA/ProfileAln.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ProfileAln.c @@ -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 +#include +#include +#include +#include +#include +#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; +} + +/*---------------------------------------------------------------------------*/ diff --git a/C/ViennaRNA/ProfileAln.h b/C/ViennaRNA/ProfileAln.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ProfileAln.h @@ -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 diff --git a/C/ViennaRNA/ProfileDist.c b/C/ViennaRNA/ProfileDist.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ProfileDist.c @@ -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 +#include +#include +#include +#include +#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 ; k0)&&(j>0)) { + for(dist = 2.,k=0; k= 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 +#include +#include +#include +#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; k0)&&(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=0) { + switch (structure[i]) { + case '(': + for (j=0; j 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 + * weighted 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 diff --git a/C/ViennaRNA/aliLfold.c b/C/ViennaRNA/aliLfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/aliLfold.c @@ -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 +#include +#include +#include +#include +#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 +#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; ilength) 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=(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; jlength-maxdist-3; j--) { + for (i=(length-maxdist-2>0)?length-maxdist-2:1 ; 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=cv_fact*MINPSCORE) { /* we have a pair 2 consider */ + int new_c=0, stackEnergy=INF; + /* hairpin ----------------------------------------------*/ + for (new_c=s=0; sMLclosing; + 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 1) ? S5[s][i] : -1, (j < length) ? S3[s][j] : -1, P); + } + } + else{ + for (s=0; s1) ? 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]1) ? S5[s][i] : -1, -1, P); + } + } + else{ + for (s=0; s1) ? S5[s][i+1] : -1, S3[s][lastj-i], P); + } + } + else{ + for (s=0; s 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; ii0) { + 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 (cc1) ? S5[ss][i] : -1, (kMLbase == 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; ss1) ? S5[ss][i] : -1, (jj-2-TURN) vrna_message_error("backtrack failed in fML"); + continue; + } + + repeat1: + + /*----- begin of "repeat:" -----*/ + if (canonical) cij = c[i][j-i]; + + for (ss=0; ssstack[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= minq; q--) { + if (c[p][q-p]>=INF) continue; + for (ss=energy=0; ssMLclosing; + if(dangles){ + for (ss=0; ss0 && 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; i0; 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; sn_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; (j1) && (j': + 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); + } +} diff --git a/C/ViennaRNA/ali_plex.c b/C/ViennaRNA/ali_plex.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ali_plex.c @@ -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 +#include +#include +#include +#include +#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; s0; j--) { + int k,l,E,psc; + for (s=0; s=MINPSCORE) ? (n_seq*(P->DuplexInit + 2*extension_cost)) : INF; + if (psc1) ? S1[s][i-1] : -1, (j0 && 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; s1) ? S2[s][j-1] : -1, (i1 ) 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; s0 && j<=n4) { + int psc; + E = c[i][j]; traced=0; + st1[i-1] = '('; + st2[j-1] = ')'; + for (s=0; s0 && 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; s1) ? S1[s][i-1] : -1, (jDuplexInit + n_seq*2*extension_cost) { + vrna_message_error("backtrack failed in aliduplex"); + } else break; + } + } + if (i>1) i--; + if (j 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=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=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; smismatchI[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 (pscmismatchI[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 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 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; itemperature - 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; sDuplexInit - covscore(type,n_seq); + for (s=0; s1 ; k--) { + if(k= 1+j_flag; q--) { + if (p-k+l-q-2>MAXLOOP) break; + for(E=s=0;s1) ? S1[s][k-1] : -1, (l 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; si-MAXLOOP-2; k++) { + for (l=j-1; l>=1; l--) { + int LE; + if (i-k+l-j-2>MAXLOOP) break; + for (s=LE=0; s2) 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=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= 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; smismatchI[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 (pscmismatchI[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 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 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; i0 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; sn_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; +} diff --git a/C/ViennaRNA/ali_plex.h b/C/ViennaRNA/ali_plex.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ali_plex.h @@ -0,0 +1,40 @@ +#ifndef VIENNA_RNA_PACKAGE_ALI_PLEX_H +#define VIENNA_RNA_PACKAGE_ALI_PLEX_H + +#include +/** +*** 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 diff --git a/C/ViennaRNA/alicircfold.inc b/C/ViennaRNA/alicircfold.inc new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alicircfold.inc @@ -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; iMLclosing; + if (fmmatrices->FcH = FcH; + vc->matrices->FcI = FcI; + vc->matrices->FcM = FcM; + vc->matrices->Fc = Fc; +} diff --git a/C/ViennaRNA/alifold.c b/C/ViennaRNA/alifold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alifold.c @@ -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 +#include +#include +#include +#include +#include + +#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 +#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 diff --git a/C/ViennaRNA/alifold.h b/C/ViennaRNA/alifold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alifold.h @@ -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 +#include +#include +#include +#include +#include +#include + +#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 QB matrix + * @param qm_p A pointer to the QM 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 diff --git a/C/ViennaRNA/alipfold.c b/C/ViennaRNA/alipfold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alipfold.c @@ -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 +#include +#include +#include +#include /* #defines FLT_MIN */ +#include + +#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 +#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; + } +} diff --git a/C/ViennaRNA/aln_util.c b/C/ViennaRNA/aln_util.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/aln_util.c @@ -0,0 +1,617 @@ +/* + aln_util.c + Helper functions frelated to alignments +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include + +#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;inum_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; nnfm) {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; i4) c=5; + bgfreq[c]++; + } + + for (i=0; i4) 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=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; spair[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; ipair[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=1)&&(j<=n)) { + if ((i>1)&&(jcv_fact*MINPSCORE)&&(ntypecv_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; j0) 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; s0; 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]; + } + } +} + diff --git a/C/ViennaRNA/aln_util.h b/C/ViennaRNA/aln_util.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/aln_util.h @@ -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 diff --git a/C/ViennaRNA/alphabet.c b/C/ViennaRNA/alphabet.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alphabet.c @@ -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 +#include +#include +#include +#include + +#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; kn) continue; + type = md->pair[S[i]][S[j]]; + while ((i>=1)&&(j<=n)) { + if ((i>1)&&(jpair[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; icirc){ + (*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; kn) continue; + type = md->pair[S[i]][S[j]]; + while ((i>=1)&&(j<=n)) { + if ((i>1)&&(jpair[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 + diff --git a/C/ViennaRNA/alphabet.h b/C/ViennaRNA/alphabet.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/alphabet.h @@ -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 + +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 diff --git a/C/ViennaRNA/boltzmann_sampling.c b/C/ViennaRNA/boltzmann_sampling.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/boltzmann_sampling.c @@ -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 +#include +#include +#include + +#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; iq1k = (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; k1) ? S1[i-1] : -1, (j 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 (startexp_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, (jexp_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= 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= 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, iexp_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 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; kexp_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 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 (ur){ 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 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; kr){ 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 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 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; spair[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; sr) { + *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; lpair[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; sexp_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=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) { + *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= 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, ipair[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); +} + diff --git a/C/ViennaRNA/boltzmann_sampling.h b/C/ViennaRNA/boltzmann_sampling.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/boltzmann_sampling.h @@ -0,0 +1,46 @@ +#ifndef VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H +#define VIENNA_RNA_PACKAGE_BOLTZMANN_SAMPLING_H + +#include + +/** + * @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 diff --git a/C/ViennaRNA/c_plex.c b/C/ViennaRNA/c_plex.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/c_plex.c @@ -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 +#include +#include +#include +#include +#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++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= 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 && lmismatchExt[type2][SS1[k-1]][SS2[l+1]]; + } + else if(k>1){ + E += P->dangle5[type2][SS1[k-1]]; + } + else if(ldangle3[type2][SS2[l+1]]; + } + if (E 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++=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(i1 && !(structure[j-2]=='|')){ + E -= P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]]; + } + else if (idangle3[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 (i1) 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 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(j1 && !(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(jdangle3[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(i1 && !(structure[j-2]=='|')){ + E+= P->mismatchExt[rtype[type]][SS2[j-1]][SS1[i+1]]+2*extension_cost; + } + else if (idangle3[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 (E1 ) 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 && jmismatchExt[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 (jdangle3[type][SS2[j+1]]+ extension_cost; + } + /* if (jdangle3[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 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 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; +} + + diff --git a/C/ViennaRNA/centroid.c b/C/ViennaRNA/centroid.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/centroid.c @@ -0,0 +1,204 @@ +/* + centroid structure prediction + + Ivo L Hofacker + Ronny Lorenz + Vienna RNA package +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include + +#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 + = \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; i0; 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 + = \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; i0.5) { + 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 + = \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; i0.5) { + 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 + +#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$ = \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$ = \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$ = \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 diff --git a/C/ViennaRNA/circfold.inc b/C/ViennaRNA/circfold.inc new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/circfold.inc @@ -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 (uMLclosing; + if (fmup_ml[1]){ + fm = fM_d3[i]+my_c[indx[length]+i+1]+E_MLstem(type, -1, S1[1], P) + P->MLclosing; + if (fmup_ml[i]){ + fm = fM_d3[i-1]+my_c[indx[length]+i+1]+E_MLstem(type, S1[i], S1[1], P) + P->MLclosing; + if (fmup_ml[length]){ + fm = E_MLstem(type, S1[length], -1, P) + my_c[indx[i]+1] + fM_d5[i+1] + P->MLclosing; + if (fmup_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 (fm0)?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; u0)?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; umatrices->FcH = FcH; + vc->matrices->FcI = FcI; + vc->matrices->FcM = FcM; + vc->matrices->Fc = Fc; +} + diff --git a/C/ViennaRNA/cofold.c b/C/ViennaRNA/cofold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/cofold.c @@ -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 +#include +#include +#include +#include +#include + +#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 +#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 (i0) { + 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 (exidxj + 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=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; plength) 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; imin_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 diff --git a/C/ViennaRNA/cofold.h b/C/ViennaRNA/cofold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/cofold.h @@ -0,0 +1,202 @@ +#ifndef VIENNA_RNA_PACKAGE_COFOLD_H +#define VIENNA_RNA_PACKAGE_COFOLD_H + +#include +#include +#include + +#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 RNAlib 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 diff --git a/C/ViennaRNA/color_output.inc b/C/ViennaRNA/color_output.inc new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/color_output.inc @@ -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 + diff --git a/C/ViennaRNA/commands.c b/C/ViennaRNA/commands.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/commands.c @@ -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 +#include +#include +#include +#include + +#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; +} diff --git a/C/ViennaRNA/commands.h b/C/ViennaRNA/commands.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/commands.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/constraints.c b/C/ViennaRNA/constraints.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints.c @@ -0,0 +1,59 @@ +/* constraints handling */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include + +#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); + } + } +} diff --git a/C/ViennaRNA/constraints.h b/C/ViennaRNA/constraints.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints.h @@ -0,0 +1,370 @@ +#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_H +#define VIENNA_RNA_PACKAGE_CONSTRAINTS_H + +#include + +/* include all structure constraint related headers */ +#include +#include +#include +#include +#include + +/** + * @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 diff --git a/C/ViennaRNA/constraints_SHAPE.c b/C/ViennaRNA/constraints_SHAPE.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_SHAPE.c @@ -0,0 +1,575 @@ +/* SHAPE reactivity data handling */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include + +#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); + } +} + diff --git a/C/ViennaRNA/constraints_SHAPE.h b/C/ViennaRNA/constraints_SHAPE.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_SHAPE.h @@ -0,0 +1,142 @@ +#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H +#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SHAPE_H + +#include + +/** + * @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 diff --git a/C/ViennaRNA/constraints_hard.c b/C/ViennaRNA/constraints_hard.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_hard.c @@ -0,0 +1,1056 @@ +/* constraints handling */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include + +#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 : 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 klength; + 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': /* 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': /* 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 diff --git a/C/ViennaRNA/constraints_hard.h b/C/ViennaRNA/constraints_hard.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_hard.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/constraints_ligand.c b/C/ViennaRNA/constraints_ligand.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_ligand.c @@ -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 +#include +#include +#include + +#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; +} + diff --git a/C/ViennaRNA/constraints_ligand.h b/C/ViennaRNA/constraints_ligand.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_ligand.h @@ -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 + +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 diff --git a/C/ViennaRNA/constraints_soft.c b/C/ViennaRNA/constraints_soft.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_soft.c @@ -0,0 +1,520 @@ +/* constraints handling */ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include + +#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; + } +} diff --git a/C/ViennaRNA/constraints_soft.h b/C/ViennaRNA/constraints_soft.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/constraints_soft.h @@ -0,0 +1,317 @@ +#ifndef VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H +#define VIENNA_RNA_PACKAGE_CONSTRAINTS_SOFT_H + +#include + +/** + * @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 diff --git a/C/ViennaRNA/convert_epars.c b/C/ViennaRNA/convert_epars.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/convert_epars.c @@ -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 +#include +#include +#include +#include + +#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 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); + } +} diff --git a/C/ViennaRNA/convert_epars.h b/C/ViennaRNA/convert_epars.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/convert_epars.h @@ -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 diff --git a/C/ViennaRNA/data_structures.c b/C/ViennaRNA/data_structures.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/data_structures.c @@ -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 +#include +#include +#include +#include +#include + +#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 +#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;sn_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;sn_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; ipair[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=1)&&(j<=n)) { + if ((i>1)&&(jcv_fact*MINPSCORE)&&(ntypecv_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; l0) ? 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]; + } + } + +} diff --git a/C/ViennaRNA/data_structures.h b/C/ViennaRNA/data_structures.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/data_structures.h @@ -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 +#include +#include +#include +#include +#include +#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= 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 diff --git a/C/ViennaRNA/dist_vars.c b/C/ViennaRNA/dist_vars.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/dist_vars.c @@ -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 */ + diff --git a/C/ViennaRNA/dist_vars.h b/C/ViennaRNA/dist_vars.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/dist_vars.h @@ -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 diff --git a/C/ViennaRNA/dp_matrices.c b/C/ViennaRNA/dp_matrices.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/dp_matrices.c @@ -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 +#include + +#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); +} + diff --git a/C/ViennaRNA/dp_matrices.h b/C/ViennaRNA/dp_matrices.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/dp_matrices.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/duplex.c b/C/ViennaRNA/duplex.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/duplex.c @@ -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 +#include +#include +#include +#include +#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 +#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, (j0 && 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, (i1 ) 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, (ithresh) 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]=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, (jDuplexInit) { + vrna_message_error("backtrack failed in fold duplex"); + } else break; + } + } + if (i>1) i--; + if (jenergy > ((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; s0; j--) { + int k,l,E,psc; + for (s=0; s=MINPSCORE) ? (n_seq*P->DuplexInit) : INF; + if (psc1) ? S1[s][i-1] : -1, (j0 && 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; s1) ? S2[s][j-1] : -1, (i1 ) 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; s0; i--) { + for (j=1; j<=n2; j++) { + int ii, jj, skip, Ed, psc; + + for (s=0; s1) ? S2[s][j-1] : -1, (ithresh) 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]=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; s0 && j<=n2) { + int psc; + E = c[i][j]; traced=0; + st1[i-1] = '('; + st2[j-1] = ')'; + for (s=0; s0 && 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; s1) ? S1[s][i-1] : -1, (jDuplexInit) { + vrna_message_error("backtrack failed in aliduplex"); + } else break; + } + } + if (i>1) i--; + if (j0 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; sn_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; +} diff --git a/C/ViennaRNA/duplex.h b/C/ViennaRNA/duplex.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/duplex.h @@ -0,0 +1,29 @@ +#ifndef VIENNA_RNA_PACKAGE_DUPLEX_H +#define VIENNA_RNA_PACKAGE_DUPLEX_H + +#include + +/** + * @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 diff --git a/C/ViennaRNA/edit_cost.h b/C/ViennaRNA/edit_cost.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/edit_cost.h @@ -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 */ + +}; + diff --git a/C/ViennaRNA/energy_const.h b/C/ViennaRNA/energy_const.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/energy_const.h @@ -0,0 +1,39 @@ +#ifndef VIENNA_RNA_PACKAGE_ENERGY_CONST_H +#define VIENNA_RNA_PACKAGE_ENERGY_CONST_H + +#include + +/** + * @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 diff --git a/C/ViennaRNA/energy_par.c b/C/ViennaRNA/energy_par.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/energy_par.c @@ -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" + diff --git a/C/ViennaRNA/energy_par.h b/C/ViennaRNA/energy_par.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/energy_par.h @@ -0,0 +1,100 @@ +/* + prototypes for energy_par.c +*/ + +#ifndef VIENNA_RNA_PACKAGE_ENERGY_PAR_H +#define VIENNA_RNA_PACKAGE_ENERGY_PAR_H + +#include + +#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 diff --git a/C/ViennaRNA/equilibrium_probs.c b/C/ViennaRNA/equilibrium_probs.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/equilibrium_probs.c @@ -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 +#include +#include +#include +#include /* #defines FLT_MAX ... */ +#include + +#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, (jexp_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 (lpair[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, (l1) ? S1[k-1] : -1, (lQmax) { + 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(lstartMAXLOOP) 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(lstartMAXLOOP) 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 = \sum_{a,b} p_a p_b d(S_a,S_b) + this can be computed from the pair probs p_ij as + = \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; icutoff) { + 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; spair[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(lstartMAXLOOP) + 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; spair[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(lstartMAXLOOP) + 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; spair[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) && (jup_ml[j+1] < n-j) + break; + + for (tmp3=1, s=0; sexp_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; sexp_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; spair[S[s][i]][S[s][j]]; if (typ==0) typ=7; + probs[ij] *= exp_E_ExtLoop(typ, (i>1) ? S5[s][i] : -1, (jTURN+1; l--) { + + /* 2. bonding k,l as substem of 2:loop enclosed by i,j */ + for (k=1; kpair[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; spair[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 (lpair[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; spair[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; spair[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); +} + diff --git a/C/ViennaRNA/equilibrium_probs.h b/C/ViennaRNA/equilibrium_probs.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/equilibrium_probs.h @@ -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 + +#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$ = \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$ = \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$ = \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$ = \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 diff --git a/C/ViennaRNA/eval.c b/C/ViennaRNA/eval.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/eval.c @@ -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 +#include +#include +#include +#include +#include +#include + +#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 ij) 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 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)) && (q1) && !pt[p-1]) ? s1[p-1] : -1; + mm3 = ((ON_SAME_STRAND(q, q + 1, cp)) && (qpair[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]]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+dang5model_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 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;cntpair[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; cntpair[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 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 (pq)) 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 (pmodel_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; +} + diff --git a/C/ViennaRNA/eval.h b/C/ViennaRNA/eval.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/eval.h @@ -0,0 +1,663 @@ +#ifndef VIENNA_RNA_PACKAGE_EVAL_H +#define VIENNA_RNA_PACKAGE_EVAL_H + +#include +#include +#include /* 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 diff --git a/C/ViennaRNA/exterior_loops.c b/C/ViennaRNA/exterior_loops.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/exterior_loops.c @@ -0,0 +1,1785 @@ +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include + +#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; +} diff --git a/C/ViennaRNA/exterior_loops.h b/C/ViennaRNA/exterior_loops.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/exterior_loops.h @@ -0,0 +1,175 @@ +#ifndef VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H +#define VIENNA_RNA_PACKAGE_EXTERIOR_LOOPS_H + +#include +#include + +/** + * @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; + + +/** + *

Compute the Energy contribution of an Exterior loop stem

+ * 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.
+ * 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); + +/** + *

Compute the energy contribution of a stem branching off a loop-region

+ * 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 immediately interior base pairs + * 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: + * 
+ *        3'  5'
+ *        |   |
+ *        X - Y
+ *  5'-si1     sj1-3'
+ *
+ * + * 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 internal-loop-penalty 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); + +/** + *

Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

+ * 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 diff --git a/C/ViennaRNA/file_formats.c b/C/ViennaRNA/file_formats.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_formats.c @@ -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 +#include +#include +#include +#include + +#include "ViennaRNA/fold_vars.h" +#include "ViennaRNA/utils.h" +#include "ViennaRNA/file_utils.h" +#include "ViennaRNA/constraints.h" +#if WITH_JSON_SUPPORT +# include +#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 diff --git a/C/ViennaRNA/file_formats.h b/C/ViennaRNA/file_formats.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_formats.h @@ -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 + +#include +#include + +/** + * @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 diff --git a/C/ViennaRNA/file_formats_msa.c b/C/ViennaRNA/file_formats_msa.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_formats_msa.c @@ -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 +#include +#include +#include +#include + +#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; +} diff --git a/C/ViennaRNA/file_formats_msa.h b/C/ViennaRNA/file_formats_msa.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_formats_msa.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/file_utils.c b/C/ViennaRNA/file_utils.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_utils.c @@ -0,0 +1,217 @@ +/* + file_utils.c + + c Ronny Lorenz + Vienna RNA package +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include "ViennaRNA/utils.h" +#include "ViennaRNA/file_utils.h" + +#define PRIVATE static +#define PUBLIC + +/* +################################# +# GLOBAL VARIABLES # +################################# +*/ + + +/* +################################# +# PRIVATE VARIABLES # +################################# +*/ +#ifdef _WIN32 +#ifdef __MINGW32__ +#include +#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; +} diff --git a/C/ViennaRNA/file_utils.h b/C/ViennaRNA/file_utils.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/file_utils.h @@ -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 diff --git a/C/ViennaRNA/findpath.c b/C/ViennaRNA/findpath.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/findpath.c @@ -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 +#include +#include +#include + +#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 +#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 (saddleEsequence)){ /* 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; di!=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 (enoldE)?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 (ipt != 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; cpt != NULL; cc++) free_intermediate(cc); + for (u=0; upt); + 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; ds; 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 diff --git a/C/ViennaRNA/findpath.h b/C/ViennaRNA/findpath.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/findpath.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/fold.c b/C/ViennaRNA/fold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/fold.c @@ -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 +#include +#include +#include +#include +#include + +#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 +#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 diff --git a/C/ViennaRNA/fold.h b/C/ViennaRNA/fold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/fold.h @@ -0,0 +1,320 @@ +#ifndef VIENNA_RNA_PACKAGE_FOLD_H +#define VIENNA_RNA_PACKAGE_FOLD_H + +#include +#include +#include +#include + +#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 diff --git a/C/ViennaRNA/fold_vars.h b/C/ViennaRNA/fold_vars.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/fold_vars.h @@ -0,0 +1,93 @@ +#ifndef VIENNA_RNA_PACKAGE_FOLD_VARS_H +#define VIENNA_RNA_PACKAGE_FOLD_VARS_H + +#include +/* 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 + + +/** + * \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 diff --git a/C/ViennaRNA/gquad.c b/C/ViennaRNA/gquad.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/gquad.c @@ -0,0 +1,1086 @@ +/* + gquad.c + + Ronny Lorenz 2012 + + Vienna RNA package +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include + +#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;imatrices->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;i0.) { + 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= (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); + } + } + } + } +} + diff --git a/C/ViennaRNA/gquad.h b/C/ViennaRNA/gquad.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/gquad.h @@ -0,0 +1,906 @@ +#ifndef VIENNA_RNA_PACKAGE_GQUAD_H +#define VIENNA_RNA_PACKAGE_GQUAD_H + +#include +#include + +#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;ajindx; + 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 diff --git a/C/ViennaRNA/grammar.h b/C/ViennaRNA/grammar.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/grammar.h @@ -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 + +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 diff --git a/C/ViennaRNA/hairpin_loops.c b/C/ViennaRNA/hairpin_loops.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/hairpin_loops.c @@ -0,0 +1,945 @@ +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#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; +} diff --git a/C/ViennaRNA/hairpin_loops.h b/C/ViennaRNA/hairpin_loops.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/hairpin_loops.h @@ -0,0 +1,303 @@ +#ifndef VIENNA_RNA_PACKAGE_HAIRPIN_LOOPS_H +#define VIENNA_RNA_PACKAGE_HAIRPIN_LOOPS_H + +#include +#include +#include +#include +#include + +#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:
+ * 
+ *        a3 a4
+ *      a2     a5
+ *      a1     a6
+ *        X - Y
+ *        |   |
+ *        5'  3'
+ *
+ * where X-Y marks the closing pair [e.g. a (G,C) 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 "a1.a2.a3.a4.a5.a6"
+ * @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 diff --git a/C/ViennaRNA/interior_loops.c b/C/ViennaRNA/interior_loops.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/interior_loops.c @@ -0,0 +1,1807 @@ +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#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); +} diff --git a/C/ViennaRNA/interior_loops.h b/C/ViennaRNA/interior_loops.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/interior_loops.h @@ -0,0 +1,532 @@ +#ifndef VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H +#define VIENNA_RNA_PACKAGE_INTERIOR_LOOPS_H + +#include +#include "ViennaRNA/energy_par.h" +#include +#include +#include + +#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 + */ + +/** + *

Compute the Energy of an interior-loop

+ * This function computes the free energy @f$\Delta G@f$ of an interior-loop with the + * following structure:
+ * 
+ *        3'  5'
+ *        |   |
+ *        U - V
+ *    a_n       b_1
+ *     .        .
+ *     .        .
+ *     .        .
+ *    a_1       b_m
+ *        X - Y
+ *        |   |
+ *        5'  3'
+ *
+ * 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:
+ * 5'-mismatch: a_1
+ * 3'-mismatch: b_m
+ * and for the enclosed base pair (V,U):
+ * 5'-mismatch: b_1
+ * 3'-mismatch: a_n
+ * @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); + +/** + *

Compute Boltzmann weight @f$e^{-\Delta G/kT} @f$ of interior loop

+ * 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 diff --git a/C/ViennaRNA/intl11.h b/C/ViennaRNA/intl11.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl11.h @@ -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} + } + }}; diff --git a/C/ViennaRNA/intl11dH.h b/C/ViennaRNA/intl11dH.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl11dH.h @@ -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} + } + }}; diff --git a/C/ViennaRNA/intl21.h b/C/ViennaRNA/intl21.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl21.h @@ -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, 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, 110, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + } + ,{{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 150, 150, 150, 150, 150} + } + } + ,{{{ 250, 250, 250, 230, 230} + ,{ 250, 250, 230, 230, 230} + ,{ 250, 230, 250, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 250, 250, 230, 230, 230} + } + ,{{ 250, 250, 230, 110, 230} + ,{ 250, 250, 230, 110, 230} + ,{ 230, 230, 170, 110, 230} + ,{ 110, 80, 110, 110, 110} + ,{ 230, 230, 230, 110, 230} + } + ,{{ 250, 250, 250, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 250, 230, 250, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 250, 250, 230, 230, 230} + } + ,{{ 230, 170, 230, 110, 230} + ,{ 230, 170, 230, 80, 230} + ,{ 230, 110, 230, 110, 230} + ,{ 120, 120, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + } + ,{{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 220, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 170, 150, 170, 150, 140} + } + } + ,{{{ 300, 300, 300, 300, 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} + } + } + ,{{{ 300, 300, 300, 300, 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} + } + } + ,{{{ 300, 300, 300, 300, 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} + } + } + } +,{{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ 250, 250, 230, 230, 230} + ,{ 250, 250, 230, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 230, 230, 230, 230, 230} + } + ,{{ 250, 250, 230, 230, 230} + ,{ 250, 250, 230, 210, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 120, 120, 110, 110, 110} + ,{ 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, 190, 230, 230} + } + ,{{ 230, 110, 230, 110, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + } + ,{{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 150, 150, 150, 150, 150} + } + } + ,{{{ 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, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 230, 230, 230, 230, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 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, 230, 230} + } + ,{{ 230, 110, 230, 110, 230} + ,{ 230, 110, 230, 110, 230} + ,{ 230, 110, 230, 110, 230} + ,{ 110, 110, 110, 110, 110} + ,{ 230, 110, 230, 110, 230} + } + ,{{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 230, 150} + ,{ 230, 230, 230, 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, 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, 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, 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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} 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+ ,{ 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} 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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} + } + } + 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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, 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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} + } + } + ,{{{ 300, 300, 300, 300, 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, 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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} + } + } + }}; diff --git a/C/ViennaRNA/intl21dH.h b/C/ViennaRNA/intl21dH.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl21dH.h @@ -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} + 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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, 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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, 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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} + } + } + ,{{{ 850, 850, 850, 850, 850} + ,{ 850, 850, 850, 850, 850} + ,{ 850, 850, 850, 850, 850} + ,{ 850, 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} + } + } + }}; diff --git a/C/ViennaRNA/intl22.h b/C/ViennaRNA/intl22.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl22.h @@ -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, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + } + ,{{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, 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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120} + ,{ 130, 100, 130, 100, 110} + ,{ 170, 100, 130, 100, 170} + } + ,{{ 220, 130, 220, 130, 140} + ,{ 220, 130, 220, 130, 140} + ,{ 130, 100, 130, 100, 120} + ,{ 70, -70, 70, -70, 0} + ,{ 130, 100, 130, 100, 120} + } + ,{{ 190, 110, 190, 100, 170} + ,{ 190, 110, 190, 100, 110} + ,{ 130, 100, 130, 100, 120} + ,{ 130, 100, 130, 100, 110} + ,{ 170, 100, 130, 100, 170} + } + ,{{ 130, 100, 130, 100, 120} + ,{ 70, 70, 70, -10, 60} + ,{ 130, 100, 130, 100, 120} + ,{ 20, -40, -10, -40, 20} + ,{ 130, 100, 130, 100, 120} + } + ,{{ 140, 110, 140, 110, 120} + ,{ 130, 100, 130, 100, 110} + ,{ 140, 110, 140, 110, 120} + ,{ 130, 100, 130, 100, 110} + ,{ 30, -20, -10, 30, 20} + } + } + ,{{{ 170, 90, 170, 140, 170} + ,{ 170, 70, 170, -10, 170} + ,{ 150, 80, 150, -40, 150} + ,{ 140, 10, 140, 80, 140} + ,{ 150, 90, 150, 140, 150} + } + ,{{ 170, 10, 170, -10, 170} + ,{ 170, -20, 170, -10, 170} + ,{ 150, -40, 150, -40, 150} + ,{ -30, -170, -30, -90, -30} + ,{ 150, 10, 150, -40, 150} + } + ,{{ 150, 70, 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,{ 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, 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} + ,{ 270, 230, 270, 130, 270} + ,{ 270, 230, 270, 130, 270} + ,{ 140, 100, 140, 130, 140} + ,{ 270, 230, 270, 130, 270} + } + 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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, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, 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, 190, 150, 150} + ,{ 170, 170, 150, 150, 150} + ,{ 220, 220, 190, 130, 140} + ,{ 170, 170, 150, 150, 150} + ,{ 140, 140, 120, 140, 120} + } + ,{{ 150, 130, 110, 110, 150} + ,{ 150, 130, 110, 110, 150} + ,{ 130, 130, 110, 100, 110} + ,{ 90, 10, 70, 10, 90} + ,{ 130, 130, 100, 100, 110} + } + ,{{ 220, 220, 190, 150, 150} + ,{ 150, 150, 150, 150, 150} + ,{ 220, 220, 190, 130, 140} + ,{ 170, 170, 150, 150, 150} + ,{ 140, 140, 120, 120, 120} + } + ,{{ 140, 130, 100, 100, 140} + ,{ 90, 10, 70, 10, 90} + ,{ 130, 130, 100, 100, 110} + ,{ 140, -10, 20, 80, 140} + ,{ 130, 130, 100, 100, 110} + } + ,{{ 170, 170, 170, 150, 150} + ,{ 170, 170, 150, 150, 150} + ,{ 170, 140, 170, 120, 120} + ,{ 170, 170, 150, 150, 150} + ,{ 140, 140, 30, 140, 30} + } + } + ,{{{ 220, 220, 190, 140, 140} + ,{ 170, 170, 140, 40, 140} + ,{ 220, 220, 190, 70, 130} + ,{ 170, 170, 140, 30, 140} + ,{ 140, 140, 110, 140, 110} + } + ,{{ 130, 130, 110, 70, 100} + ,{ 130, 130, 100, 40, 100} + ,{ 130, 130, 110, 70, 100} + ,{ 70, -20, 70, -50, 10} + ,{ 130, 130, 100, -10, 100} + } + ,{{ 220, 220, 190, 70, 140} + ,{ 140, 60, 50, 30, 140} + ,{ 220, 220, 190, 70, 130} + ,{ 170, 170, 140, 30, 140} + ,{ 140, 140, 110, 50, 110} + } + ,{{ 130, 130, 100, -10, 100} + ,{ 10, 0, -100, -70, 10} + ,{ 130, 130, 100, -10, 100} + ,{ -10, -10, -50, -30, -50} + ,{ 130, 130, 100, -10, 100} + } + ,{{ 170, 170, 140, 140, 140} + ,{ 170, 170, 140, 30, 140} + ,{ 140, 140, 110, 60, 110} + ,{ 170, 170, 140, 30, 140} + ,{ 140, 140, 30, 140, 20} + } + } + ,{{{ 150, 150, 150, 150, 150} + ,{ 150, 150, 150, 150, 150} + ,{ 140, 130, 130, 130, 140} + ,{ 150, 150, 150, 150, 150} + ,{ 120, 120, 120, 120, 120} + } + ,{{ 110, 110, 110, 110, 110} + ,{ 110, 110, 110, 110, 110} + ,{ 110, 100, 100, 100, 110} + ,{ 80, -40, 70, 10, 80} + ,{ 110, 100, 100, 100, 110} + } + ,{{ 150, 150, 150, 150, 150} + ,{ 150, 150, 150, 150, 150} + ,{ 140, 130, 130, 130, 140} + ,{ 150, 150, 150, 150, 150} + ,{ 120, 120, 120, 120, 120} + } + ,{{ 110, 100, 100, 100, 110} + ,{ 80, -70, -60, 10, 80} + ,{ 110, 100, 100, 100, 110} + ,{ -40, -40, -40, -40, -50} + ,{ 110, 100, 100, 100, 110} + } + ,{{ 150, 150, 150, 150, 150} + ,{ 150, 150, 150, 150, 150} + ,{ 120, 120, 120, 120, 120} + ,{ 150, 150, 150, 150, 150} + ,{ 30, 30, 30, 30, 30} + } + } + ,{{{ 140, 70, 140, 80, 140} + ,{ 140, 10, 140, 10, 140} + ,{ 130, 70, 130, 20, 130} + ,{ 140, -30, 140, 80, 140} + ,{ 110, 50, 110, 70, 110} + } + ,{{ 100, -30, 100, -30, 100} + ,{ 100, -30, 100, -30, 100} + ,{ 100, -70, 100, -40, 100} + ,{ 10, -170, 10, -30, 10} + ,{ 100, -70, 100, -40, 100} + } + ,{{ 140, 70, 140, 10, 140} + ,{ 140, 10, 140, -30, 140} + ,{ 130, 70, 130, -10, 130} + ,{ 140, -30, 140, 10, 140} + ,{ 110, 0, 110, -60, 110} + } + ,{{ 100, -70, 100, 80, 100} + ,{ 10, -160, 10, 0, 10} + ,{ 100, -70, 100, -40, 100} + ,{ 80, -90, -50, 80, -50} + ,{ 100, -70, 100, -40, 100} + } + ,{{ 140, 50, 140, 70, 140} + ,{ 140, -30, 140, 10, 140} + ,{ 110, 0, 110, 20, 110} + ,{ 140, -30, 140, 10, 140} + ,{ 70, 50, 20, 70, 20} + } + } + ,{{{ 170, 150, 170, 150, 150} + ,{ 150, 150, 150, 150, 150} + ,{ 170, 130, 170, 130, 30} + ,{ 150, 150, 150, 150, 140} + ,{ 120, 120, 120, 120, 40} + } + ,{{ 150, 110, 110, 110, 150} + ,{ 150, 110, 110, 110, 150} + ,{ 100, 100, 100, 100, -20} + ,{ 90, 10, 70, 10, 90} + ,{ 100, 100, 100, 100, 30} + } + ,{{ 150, 150, 150, 150, 70} + ,{ 150, 150, 150, 150, 0} + ,{ 130, 130, 130, 130, -10} + ,{ 150, 150, 150, 150, 70} + ,{ 120, 120, 120, 120, 40} + } + ,{{ 140, 100, 100, 100, 140} + ,{ 90, 10, 70, 10, 90} + ,{ 100, 100, 100, 100, 30} + ,{ 140, -40, 20, -40, 140} + ,{ 100, 100, 100, 100, 30} + } + ,{{ 170, 150, 170, 150, 70} + ,{ 150, 150, 150, 150, 70} + ,{ 170, 120, 170, 120, 20} + ,{ 150, 150, 150, 150, 70} + ,{ 30, 30, 30, 30, -60} + } + } + } + ,{{{{ 150, 150, 120, 120, 130} + ,{ 150, 150, 120, 120, 130} + ,{ 130, 130, 100, 100, 110} + ,{ 120, 120, 90, 90, 100} + ,{ 120, 120, 100, 100, 100} + } + ,{{ 150, 150, 120, 120, 130} + ,{ 150, 150, 120, 120, 130} + ,{ 120, 120, 100, 100, 100} + ,{ -10, -50, -20, -80, -10} + ,{ 120, 120, 100, 100, 100} + } + ,{{ 120, 120, 100, 100, 100} + ,{ 120, 120, 90, 90, 100} + ,{ 120, 120, 100, 100, 100} + ,{ 120, 120, 90, 90, 100} + ,{ 120, 120, 100, 100, 100} + } + ,{{ 120, 120, 100, 100, 100} + ,{ 50, 10, 50, -10, 50} + ,{ 120, 120, 100, 100, 100} + ,{ 80, -20, -40, 80, 10} + ,{ 120, 120, 100, 100, 100} + } + ,{{ 130, 130, 100, 100, 110} + ,{ 120, 120, 90, 90, 100} + ,{ 130, 130, 100, 100, 110} + ,{ 120, 120, 90, 90, 100} + ,{ 110, 110, 20, 20, 30} + } + } + ,{{{ 150, 150, 120, 50, 120} + ,{ 150, 150, 120, 10, 120} + ,{ 130, 130, 100, 50, 100} + ,{ 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, 170} + ,{ 20, 10, 10, 10, 20} + ,{ 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} + ,{ 80, 80, 80, 80, 80} + } + } + ,{{{ 180, 50, 180, 130, 180} + ,{ 180, 10, 180, 120, 180} + ,{ 160, 50, 160, 30, 160} + ,{ 170, 0, 170, 130, 170} + ,{ 160, 50, 160, 70, 160} + } + ,{{ 180, 10, 180, 50, 180} + ,{ 180, 10, 180, 50, 180} + ,{ 160, -10, 160, 20, 160} + ,{ 60, -110, 60, 50, 60} + ,{ 160, -10, 160, 20, 160} + } + ,{{ 170, 50, 170, 30, 170} + ,{ 170, 0, 170, 30, 170} + ,{ 160, 50, 160, 30, 160} + ,{ 170, 0, 170, 30, 170} + ,{ 160, 50, 160, 30, 160} + } + ,{{ 160, -10, 160, 130, 160} + ,{ 130, -40, 130, 120, 130} + ,{ 160, -10, 160, 20, 160} + ,{ 130, -30, 10, 130, 10} + ,{ 160, -10, 160, 20, 160} + } + ,{{ 170, 50, 170, 70, 170} + ,{ 170, 0, 170, 30, 170} + ,{ 160, 50, 160, 30, 160} + ,{ 170, 0, 170, 30, 170} + ,{ 70, -100, 70, 70, 70} + } + } + ,{{{ 190, 190, 190, 190, 170} + ,{ 190, 190, 190, 190, 170} + ,{ 170, 170, 170, 170, 90} + ,{ 170, 170, 170, 170, 100} + ,{ 170, 170, 170, 170, 90} + } + ,{{ 190, 190, 190, 190, 170} + ,{ 190, 190, 190, 190, 170} + ,{ 160, 160, 160, 160, 90} + ,{ 120, 60, 120, 60, -10} + ,{ 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} + ,{ 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, 140} + } + ,{{ 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} + } + ,{{ 170, 170, 140, 50, 140} + ,{ 120, 120, 90, -20, 90} + ,{ 170, 170, 140, 30, 140} + ,{ 60, 60, 30, 50, 30} + ,{ 170, 170, 140, 30, 140} + } + ,{{ 210, 210, 180, 100, 180} + ,{ 210, 210, 180, 70, 180} + ,{ 180, 180, 150, 100, 150} + ,{ 210, 210, 180, 70, 180} + ,{ 190, 190, 100, -10, 100} + } + } + ,{{{ 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} + ,{ 190, 190, 190, 190, 190} + ,{ 150, 140, 140, 140, 150} + ,{ 150, 80, 140, 80, 150} + ,{ 150, 140, 140, 140, 150} + } + ,{{ 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} + } + ,{{ 160, 140, 150, 140, 160} + ,{ 160, 90, 150, 90, 160} + ,{ 150, 140, 140, 140, 150} + ,{ 40, 30, 30, 30, 40} + ,{ 150, 140, 140, 140, 150} + } + ,{{ 190, 190, 190, 190, 190} + ,{ 190, 190, 190, 190, 190} + ,{ 160, 160, 160, 160, 160} + ,{ 190, 190, 190, 190, 190} + ,{ 110, 100, 100, 100, 110} + } + } + ,{{{ 180, 70, 180, 150, 180} + ,{ 180, 10, 180, 80, 180} + ,{ 180, 70, 180, 50, 180} + ,{ 180, 10, 180, 150, 180} + ,{ 180, 70, 180, 90, 180} + } + ,{{ 180, 10, 180, 70, 180} + ,{ 180, 10, 180, 50, 180} + ,{ 140, -30, 140, 0, 140} + ,{ 80, -90, 80, 70, 80} + ,{ 140, -30, 140, 0, 140} + } + ,{{ 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} + } + ,{{ 150, -10, 140, 150, 140} + ,{ 90, -80, 90, 80, 90} + ,{ 140, -30, 140, 0, 140} + ,{ 150, -10, 30, 150, 30} + ,{ 140, -30, 140, 0, 140} + } + ,{{ 180, 40, 180, 90, 180} + ,{ 180, 10, 180, 50, 180} + ,{ 150, 40, 150, 20, 150} + ,{ 180, 10, 180, 50, 180} + ,{ 100, -70, 100, 90, 100} + } + } + ,{{{ 190, 190, 190, 190, 170} + ,{ 190, 190, 190, 190, 170} + ,{ 190, 190, 190, 190, 110} + ,{ 190, 190, 190, 190, 110} + ,{ 190, 190, 190, 190, 110} + } + ,{{ 190, 190, 190, 190, 170} + ,{ 190, 190, 190, 190, 170} + ,{ 140, 140, 140, 140, 70} + ,{ 140, 80, 140, 80, 10} + ,{ 140, 140, 140, 140, 70} + } + ,{{ 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} + } + ,{{ 150, 140, 150, 140, 90} + ,{ 150, 90, 150, 90, 20} + ,{ 140, 140, 140, 140, 70} + ,{ 90, 30, 30, 30, 90} + ,{ 140, 140, 140, 140, 70} + } + ,{{ 190, 190, 190, 190, 110} + ,{ 190, 190, 190, 190, 110} + ,{ 160, 160, 160, 160, 80} + ,{ 190, 190, 190, 190, 110} + ,{ 100, 100, 100, 100, 30} + } + } + } + ,{{{{ 300, 300, 280, 250, 280} + ,{ 280, 280, 280, 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, 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} + ,{ 240, 240, 210, 100, 210} + ,{ 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, 140, 210} + } + } + ,{{{ 280, 250, 280, 250, 280} + ,{ 280, 250, 280, 250, 280} + ,{ 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} + } + ,{{ 280, 220, 280, 220, 280} + ,{ 280, 220, 280, 220, 280} + ,{ 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, 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} + ,{ 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, 50, 210, 210, 210} + } + } + ,{{{ 280, 250, 280, 250, 240} + ,{ 280, 250, 280, 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, 90} + ,{ 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, 220, 280, 220, 140} + ,{ 280, 220, 280, 220, 140} + ,{ 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} + } + } + } + } +,{{{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, 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, 270, 270, 290} + ,{ 300, 300, 270, 270, 290} + ,{ 290, 290, 250, 270, 250} + ,{ 300, 300, 270, 270, 270} + ,{ 270, 270, 240, 260, 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} + } + ,{{ 300, 300, 270, 270, 270} + ,{ 300, 300, 270, 270, 270} + ,{ 290, 290, 250, 270, 250} + ,{ 300, 300, 270, 270, 270} + ,{ 270, 270, 240, 260, 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, 270, 270} + ,{ 300, 300, 270, 270, 270} + ,{ 270, 270, 240, 260, 240} + ,{ 300, 300, 270, 270, 270} + ,{ 240, 240, 150, 150, 150} + } + } + ,{{{ 300, 300, 270, 270, 270} + ,{ 300, 300, 270, 230, 270} + ,{ 290, 290, 250, 270, 250} + ,{ 300, 300, 270, 230, 270} + ,{ 270, 270, 240, 260, 240} + } + ,{{ 270, 270, 230, 190, 230} + ,{ 270, 270, 230, 190, 230} + ,{ 260, 260, 220, 180, 220} + ,{ 170, 170, 130, 90, 130} + ,{ 260, 260, 220, 180, 220} + } + ,{{ 300, 300, 270, 270, 270} + ,{ 300, 300, 270, 230, 270} + ,{ 290, 290, 250, 270, 250} + ,{ 300, 300, 270, 230, 270} + ,{ 270, 270, 240, 260, 240} + } + ,{{ 260, 260, 220, 180, 220} + ,{ 170, 170, 130, 90, 130} + ,{ 260, 260, 220, 180, 220} + ,{ 170, 110, 80, 170, 80} + ,{ 260, 260, 220, 180, 220} + } + ,{{ 300, 300, 270, 260, 270} + ,{ 300, 300, 270, 230, 270} + ,{ 270, 270, 240, 260, 240} + ,{ 300, 300, 270, 230, 270} + ,{ 240, 240, 150, 110, 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, 240, 300} + ,{ 300, 280, 240, 240, 300} + ,{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 210, 210} + ,{ 250, 250, 220, 240, 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} + } + ,{{ 250, 250, 220, 240, 220} + ,{ 250, 250, 210, 210, 210} + ,{ 250, 250, 220, 240, 220} + ,{ 250, 250, 210, 210, 210} + ,{ 250, 250, 220, 240, 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} + } + ,{{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 210, 210} + ,{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 210, 210} + ,{ 240, 240, 140, 140, 140} + } + } + ,{{{ 280, 280, 240, 240, 240} + ,{ 280, 280, 240, 200, 240} + ,{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 170, 210} + ,{ 250, 250, 220, 240, 220} + } + ,{{ 280, 280, 240, 200, 240} + ,{ 280, 280, 240, 200, 240} + ,{ 250, 250, 220, 180, 220} + ,{ 70, 70, 40, 0, 40} + ,{ 250, 250, 220, 180, 220} + } + ,{{ 250, 250, 220, 240, 220} + ,{ 250, 250, 210, 170, 210} + ,{ 250, 250, 220, 240, 220} + ,{ 250, 250, 210, 170, 210} + ,{ 250, 250, 220, 240, 220} + } + ,{{ 250, 250, 220, 180, 220} + ,{ 140, 140, 100, 60, 100} + ,{ 250, 250, 220, 180, 220} + ,{ 170, 110, 80, 170, 80} + ,{ 250, 250, 220, 180, 220} + } + ,{{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 170, 210} + ,{ 260, 260, 220, 240, 220} + ,{ 250, 250, 210, 170, 210} + ,{ 240, 240, 140, 100, 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, 60, 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, 40} + ,{ 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, 100} + ,{ 220, 220, 220, 220, 220} + ,{ 210, 80, 80, 80, 210} + ,{ 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} + } + } + } + ,{{{{ 430, 430, 370, 370, 430} + ,{ 430, 410, 370, 370, 430} + ,{ 370, 370, 340, 360, 340} + ,{ 370, 370, 340, 340, 340} + ,{ 430, 430, 340, 360, 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} + } + ,{{ 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, 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} + } + ,{{ 360, 340, 360, 340, 360} + ,{ 360, 300, 360, 300, 360} + ,{ 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, 300, 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} + ,{ 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} + ,{ 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} + } + ,{{ 360, 340, 360, 340, 340} + ,{ 360, 300, 360, 300, 300} + ,{ 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} + } + } + } + ,{{{{ 400, 400, 400, 360, 400} + ,{ 400, 370, 400, 360, 400} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 330, 310} + } + ,{{ 360, 360, 310, 360, 330} + ,{ 360, 360, 270, 360, 330} + ,{ 340, 340, 310, 310, 310} + ,{ 230, 220, 230, 170, 230} + ,{ 340, 340, 310, 310, 310} + } + ,{{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 310} + } + ,{{ 400, 370, 400, 340, 400} + ,{ 400, 370, 400, 340, 400} + ,{ 340, 340, 310, 310, 310} + ,{ 310, 230, 180, 310, 310} + ,{ 340, 340, 310, 310, 310} + } + ,{{ 400, 400, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 310, 310} + } + } + ,{{{ 400, 400, 340, 360, 340} + ,{ 370, 370, 340, 360, 340} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 400, 400, 310, 330, 310} + } + ,{{ 360, 360, 310, 360, 310} + ,{ 360, 360, 270, 360, 270} + ,{ 340, 340, 310, 270, 310} + ,{ 220, 220, 170, 130, 170} + ,{ 340, 340, 310, 270, 310} + } + ,{{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + } + ,{{ 370, 370, 340, 300, 340} + ,{ 370, 370, 340, 300, 340} + ,{ 340, 340, 310, 270, 310} + ,{ 270, 210, 180, 270, 180} + ,{ 340, 340, 310, 270, 310} + } + ,{{ 400, 400, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 400, 400, 310, 270, 310} + } + } + ,{{{ 400, 340, 400, 340, 400} + ,{ 400, 340, 400, 340, 400} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 310, 310, 310, 310, 310} + ,{ 270, 270, 270, 270, 270} + ,{ 310, 310, 310, 310, 310} + ,{ 230, 170, 230, 170, 230} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 400, 340, 400, 340, 400} + ,{ 400, 340, 400, 340, 400} + ,{ 310, 310, 310, 310, 310} + ,{ 180, 180, 180, 180, 180} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + } + ,{{{ 340, 290, 340, 340, 340} + ,{ 340, 260, 340, 340, 340} + ,{ 310, 290, 310, 180, 310} + ,{ 310, 230, 310, 310, 310} + ,{ 310, 290, 310, 310, 310} + } + ,{{ 310, 230, 310, 180, 310} + ,{ 270, 190, 270, 140, 270} + ,{ 310, 230, 310, 180, 310} + ,{ 170, 20, 170, 170, 170} + ,{ 310, 230, 310, 180, 310} + } + ,{{ 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} + } + ,{{ 340, 260, 340, 340, 340} + ,{ 340, 260, 340, 340, 340} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 230, 180, 310, 180} + ,{ 310, 230, 310, 180, 310} + } + ,{{ 310, 290, 310, 310, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 290, 310, 180, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 230, 310, 310, 310} + } + } + ,{{{ 400, 340, 400, 340, 340} + ,{ 400, 340, 400, 340, 340} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 330, 310, 310, 310, 330} + ,{ 330, 270, 270, 270, 330} + ,{ 310, 310, 310, 310, 310} + ,{ 230, 170, 230, 170, 170} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 400, 340, 400, 340, 340} + ,{ 400, 340, 400, 340, 340} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 180, 180, 180, 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, 310} + ,{ 310, 310, 310, 310, 310} + } + } + } + ,{{{{ 370, 340, 310, 310, 370} + ,{ 370, 340, 310, 310, 370} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 320, 320, 290, 310, 290} + } + ,{{ 370, 340, 310, 310, 370} + ,{ 370, 340, 310, 310, 370} + ,{ 320, 320, 280, 280, 280} + ,{ 240, 220, 240, 180, 240} + ,{ 320, 320, 280, 280, 280} + } + ,{{ 330, 330, 290, 310, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 320, 320, 290, 310, 290} + } + ,{{ 320, 320, 310, 280, 310} + ,{ 310, 290, 310, 250, 310} + ,{ 320, 320, 280, 280, 280} + ,{ 260, 180, 130, 260, 260} + ,{ 320, 320, 280, 280, 280} + } + ,{{ 330, 330, 290, 310, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 290, 290, 200, 200, 200} + } + } + ,{{{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 250, 290} + ,{ 320, 320, 290, 310, 290} + } + ,{{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 320, 320, 280, 240, 280} + ,{ 220, 220, 180, 140, 180} + ,{ 320, 320, 280, 240, 280} + } + ,{{ 330, 330, 290, 310, 290} + ,{ 330, 330, 290, 250, 290} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 250, 290} + ,{ 320, 320, 290, 310, 290} + } + ,{{ 320, 320, 280, 240, 280} + ,{ 290, 290, 250, 210, 250} + ,{ 320, 320, 280, 240, 280} + ,{ 220, 170, 130, 220, 130} + ,{ 320, 320, 280, 240, 280} + } + ,{{ 330, 330, 290, 310, 290} + ,{ 330, 330, 290, 250, 290} + ,{ 320, 320, 290, 310, 290} + ,{ 330, 330, 290, 250, 290} + ,{ 290, 290, 200, 160, 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, 290, 160, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 290, 270, 290, 160, 290} + } + ,{{ 280, 200, 280, 260, 280} + ,{ 250, 170, 250, 250, 250} + ,{ 280, 200, 280, 150, 280} + ,{ 260, 180, 130, 260, 130} + ,{ 280, 200, 280, 150, 280} + } + ,{{ 290, 270, 290, 200, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 290, 270, 290, 160, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 200, 120, 200, 200, 200} + } + } + ,{{{ 370, 310, 310, 310, 370} + ,{ 370, 310, 310, 310, 370} + ,{ 290, 290, 290, 290, 290} + ,{ 290, 290, 290, 290, 290} + ,{ 290, 290, 290, 290, 290} + } + ,{{ 370, 310, 310, 310, 370} + ,{ 370, 310, 310, 310, 370} + ,{ 280, 280, 280, 280, 280} + ,{ 240, 180, 240, 180, 180} + ,{ 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, 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, 330, 370} + ,{ 370, 340, 310, 310, 370} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 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} + } + ,{{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 340, 340, 310, 330, 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, 310, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 310, 310, 280, 300, 280} + ,{ 340, 340, 310, 310, 310} + ,{ 320, 320, 220, 220, 220} + } + } + ,{{{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + } + ,{{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 300, 300, 260, 220, 260} + ,{ 240, 240, 200, 160, 200} + ,{ 300, 300, 260, 220, 260} + } + ,{{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 340, 340, 310, 330, 310} + } + ,{{ 300, 300, 260, 240, 260} + ,{ 250, 250, 210, 170, 210} + ,{ 300, 300, 260, 220, 260} + ,{ 240, 190, 150, 240, 150} + ,{ 300, 300, 260, 220, 260} + } + ,{{ 340, 340, 310, 300, 310} + ,{ 340, 340, 310, 270, 310} + ,{ 310, 310, 280, 300, 280} + ,{ 340, 340, 310, 270, 310} + ,{ 320, 320, 220, 180, 220} 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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} 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,{ 120, 120, 120, 120, 120} + } + } + } + ,{{{{ 280, 210, 210, 280, 270} + ,{ 270, 210, 210, 240, 270} + ,{ 280, 190, 190, 280, 190} + ,{ 210, 180, 180, 210, 180} + ,{ 280, 190, 190, 280, 190} + } + ,{{ 270, 210, 210, 240, 270} + ,{ 270, 210, 210, 240, 270} + ,{ 220, 190, 190, 220, 190} + ,{ 70, 10, 70, 40, 70} + ,{ 220, 190, 190, 220, 190} + } + ,{{ 280, 190, 190, 280, 190} + ,{ 210, 180, 180, 210, 180} + ,{ 280, 190, 190, 280, 190} + ,{ 210, 180, 180, 210, 180} + ,{ 280, 190, 190, 280, 190} + } + ,{{ 220, 190, 190, 220, 190} + ,{ 130, 70, 130, 100, 130} + ,{ 220, 190, 190, 220, 190} + ,{ 210, 50, 50, 210, 180} + ,{ 220, 190, 190, 220, 190} + } + ,{{ 280, 190, 190, 280, 190} + ,{ 210, 180, 180, 210, 180} + ,{ 280, 190, 190, 280, 190} + ,{ 210, 180, 180, 210, 180} + ,{ 140, 140, 110, 140, 110} + } + } + ,{{{ 280, 190, 210, 280, 210} + ,{ 240, 190, 210, 240, 210} + ,{ 280, 160, 190, 280, 190} + ,{ 210, 150, 180, 210, 180} + ,{ 280, 150, 190, 280, 190} + } + ,{{ 240, 190, 210, 240, 210} 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180, 180} + ,{ 190, 190, 190, 190, 190} + } + ,{{ 190, 190, 190, 190, 190} + ,{ 130, 70, 130, 70, 130} + ,{ 190, 190, 190, 190, 190} + ,{ 50, 50, 50, 50, 50} + ,{ 190, 190, 190, 190, 190} + } + ,{{ 190, 190, 190, 190, 190} + ,{ 180, 180, 180, 180, 180} + ,{ 190, 190, 190, 190, 190} + ,{ 180, 180, 180, 180, 180} + ,{ 110, 110, 110, 110, 110} + } + } + ,{{{ 210, 120, 210, 180, 210} + ,{ 210, 80, 210, 80, 210} + ,{ 190, 120, 190, 60, 190} + ,{ 180, 50, 180, 180, 180} + ,{ 190, 110, 190, 110, 190} + } + ,{{ 210, 80, 210, 80, 210} + ,{ 210, 80, 210, 80, 210} + ,{ 190, 50, 190, 60, 190} + ,{ 10, -120, 10, 10, 10} + ,{ 190, 50, 190, 60, 190} + } + ,{{ 190, 110, 190, 60, 190} + ,{ 180, 50, 180, 50, 180} + ,{ 190, 110, 190, 60, 190} + ,{ 180, 50, 180, 50, 180} + ,{ 190, 110, 190, 60, 190} + } + ,{{ 190, 50, 190, 180, 190} + ,{ 70, -60, 70, 70, 70} + ,{ 190, 50, 190, 60, 190} + ,{ 180, 40, 50, 180, 50} + ,{ 190, 50, 190, 60, 190} + } + ,{{ 190, 120, 190, 110, 190} + ,{ 180, 50, 180, 50, 180} + 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330, 310, 400, 310} + } + ,{{ 400, 360, 340, 370, 400} + ,{ 400, 360, 340, 370, 400} + ,{ 340, 310, 310, 340, 310} + ,{ 290, 230, 290, 260, 290} + ,{ 340, 310, 310, 340, 310} + } + ,{{ 400, 310, 310, 400, 310} + ,{ 340, 310, 310, 340, 310} + ,{ 400, 310, 310, 400, 310} + ,{ 340, 310, 310, 340, 310} + ,{ 400, 310, 310, 400, 310} + } + ,{{ 360, 360, 330, 340, 330} + ,{ 360, 360, 330, 300, 330} + ,{ 340, 310, 310, 340, 310} + ,{ 340, 180, 180, 340, 310} + ,{ 340, 310, 310, 340, 310} + } + ,{{ 400, 330, 310, 400, 310} + ,{ 340, 310, 310, 340, 310} + ,{ 400, 310, 310, 400, 310} + ,{ 340, 310, 310, 340, 310} + ,{ 340, 330, 310, 340, 310} + } + } + ,{{{ 400, 360, 340, 400, 340} + ,{ 370, 360, 340, 370, 340} + ,{ 400, 270, 310, 400, 310} + ,{ 340, 270, 310, 340, 310} + ,{ 400, 330, 310, 400, 310} + } + ,{{ 370, 360, 340, 370, 340} + ,{ 370, 360, 340, 370, 340} + ,{ 340, 270, 310, 340, 310} + ,{ 260, 190, 230, 260, 230} + ,{ 340, 270, 310, 340, 310} + } + ,{{ 400, 270, 310, 400, 310} + ,{ 340, 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180, 180, 180} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + } + ,{{{ 340, 230, 340, 310, 340} + ,{ 340, 220, 340, 270, 340} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 170, 310, 310, 310} + ,{ 310, 230, 310, 310, 310} + } + ,{{ 340, 220, 340, 230, 340} + ,{ 340, 220, 340, 210, 340} + ,{ 310, 170, 310, 180, 310} + ,{ 230, 20, 230, 230, 230} + ,{ 310, 170, 310, 180, 310} + } + ,{{ 310, 230, 310, 180, 310} + ,{ 310, 170, 310, 180, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 170, 310, 180, 310} + ,{ 310, 230, 310, 180, 310} + } + ,{{ 310, 170, 310, 310, 310} + ,{ 270, 130, 270, 270, 270} + ,{ 310, 170, 310, 180, 310} + ,{ 310, 170, 180, 310, 180} + ,{ 310, 170, 310, 180, 310} + } + ,{{ 310, 230, 310, 310, 310} + ,{ 310, 170, 310, 180, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 170, 310, 180, 310} + ,{ 310, 170, 310, 310, 310} + } + } + ,{{{ 400, 340, 340, 340, 400} + ,{ 400, 340, 340, 340, 400} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 400, 340, 340, 340, 400} + ,{ 400, 340, 340, 340, 400} + ,{ 310, 310, 310, 310, 310} + ,{ 290, 230, 290, 230, 230} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 330, 310, 330, 310, 310} + ,{ 330, 270, 330, 270, 270} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 180, 180, 180, 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, 310} + ,{ 310, 310, 310, 310, 310} + } + } + } + ,{{{{ 370, 310, 370, 370, 370} + ,{ 370, 310, 370, 340, 370} + ,{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 300, 280, 370, 280} + } + ,{{ 310, 280, 280, 310, 300} + ,{ 300, 240, 240, 270, 300} + ,{ 310, 280, 280, 310, 280} + ,{ 200, 140, 200, 170, 200} + ,{ 310, 280, 280, 310, 280} + } + ,{{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + } + ,{{ 370, 310, 370, 340, 370} + ,{ 370, 310, 370, 340, 370} + ,{ 310, 280, 280, 310, 280} + ,{ 310, 150, 150, 310, 280} + ,{ 310, 280, 280, 310, 280} + } + ,{{ 370, 300, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 310, 300, 280, 310, 280} + } + } + ,{{{ 370, 300, 310, 370, 310} + ,{ 340, 270, 310, 340, 310} + ,{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 300, 280, 370, 280} + } + ,{{ 310, 240, 280, 310, 280} + ,{ 270, 210, 240, 270, 240} + ,{ 310, 240, 280, 310, 280} + ,{ 170, 110, 140, 170, 140} + ,{ 310, 240, 280, 310, 280} + } + ,{{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + } + ,{{ 340, 270, 310, 340, 310} + ,{ 340, 270, 310, 340, 310} + ,{ 310, 240, 280, 310, 280} + ,{ 310, 110, 150, 310, 150} + ,{ 310, 240, 280, 310, 280} + } + ,{{ 370, 300, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 310, 300, 280, 310, 280} + } + } + ,{{{ 370, 310, 370, 310, 370} + ,{ 370, 310, 370, 310, 370} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 240, 240, 240, 240, 240} + ,{ 280, 280, 280, 280, 280} + ,{ 200, 140, 200, 140, 200} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 370, 310, 370, 310, 370} + ,{ 370, 310, 370, 310, 370} + ,{ 280, 280, 280, 280, 280} + ,{ 150, 150, 150, 150, 150} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + } + ,{{{ 310, 200, 310, 310, 310} + ,{ 310, 170, 310, 310, 310} + ,{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 280, 280} + ,{ 280, 200, 280, 280, 280} + } + ,{{ 280, 140, 280, 150, 280} + ,{ 240, 110, 240, 110, 240} + ,{ 280, 140, 280, 150, 280} + ,{ 140, 10, 140, 140, 140} + ,{ 280, 140, 280, 150, 280} + } + ,{{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 200, 280, 150, 280} + } + ,{{ 310, 170, 310, 310, 310} + ,{ 310, 170, 310, 310, 310} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 140, 150, 280, 150} + ,{ 280, 140, 280, 150, 280} + } + ,{{ 280, 200, 280, 280, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 140, 280, 280, 280} + } + } + ,{{{ 370, 310, 370, 310, 310} + ,{ 370, 310, 370, 310, 310} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 300, 280, 280, 280, 300} + ,{ 300, 240, 240, 240, 300} + ,{ 280, 280, 280, 280, 280} + ,{ 200, 140, 200, 140, 140} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 370, 310, 370, 310, 310} + ,{ 370, 310, 370, 310, 310} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 150, 150, 150, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + } + } + ,{{{{ 350, 280, 280, 350, 340} + ,{ 340, 280, 280, 310, 340} + ,{ 350, 260, 260, 350, 260} + ,{ 290, 260, 260, 290, 260} + ,{ 350, 260, 260, 350, 260} + } + ,{{ 340, 280, 280, 310, 340} + ,{ 340, 280, 280, 310, 340} + ,{ 280, 250, 250, 280, 250} + ,{ 210, 150, 210, 180, 210} + ,{ 280, 250, 250, 280, 250} + } + ,{{ 350, 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250, 280, 250} + ,{ 260, 70, 100, 260, 100} + ,{ 280, 220, 250, 280, 250} + } + ,{{ 350, 230, 260, 350, 260} + ,{ 290, 230, 260, 290, 260} + ,{ 350, 220, 260, 350, 260} + ,{ 290, 230, 260, 290, 260} + ,{ 200, 190, 170, 200, 170} + } + } + ,{{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 250, 250, 250, 250, 250} + ,{ 210, 150, 210, 150, 210} + ,{ 250, 250, 250, 250, 250} + } + ,{{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + } + ,{{ 280, 250, 280, 250, 280} + ,{ 280, 220, 280, 220, 280} + ,{ 250, 250, 250, 250, 250} + ,{ 100, 100, 100, 100, 100} + ,{ 250, 250, 250, 250, 250} + } + ,{{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 170, 170, 170, 170, 170} + } + } + ,{{{ 280, 180, 280, 230, 280} + ,{ 280, 140, 280, 220, 280} + ,{ 260, 180, 260, 130, 260} + ,{ 260, 130, 260, 230, 260} + ,{ 260, 180, 260, 170, 260} + } + ,{{ 280, 140, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 250, 120, 250, 120, 250} + ,{ 150, 20, 150, 150, 150} + ,{ 250, 120, 250, 120, 250} + } + ,{{ 260, 180, 260, 130, 260} + ,{ 260, 130, 260, 130, 260} + ,{ 260, 180, 260, 130, 260} + ,{ 260, 130, 260, 130, 260} + ,{ 260, 180, 260, 130, 260} + } + ,{{ 250, 120, 250, 230, 250} + ,{ 220, 90, 220, 220, 220} + ,{ 250, 120, 250, 120, 250} + ,{ 230, 100, 100, 230, 100} + ,{ 250, 120, 250, 120, 250} + } + ,{{ 260, 180, 260, 170, 260} + ,{ 260, 130, 260, 130, 260} + ,{ 260, 180, 260, 130, 260} + ,{ 260, 130, 260, 130, 260} + ,{ 170, 30, 170, 170, 170} + } + } + ,{{{ 340, 280, 280, 280, 340} + ,{ 340, 280, 280, 280, 340} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + } + ,{{ 340, 280, 280, 280, 340} + ,{ 340, 280, 280, 280, 340} + ,{ 250, 250, 250, 250, 250} + ,{ 210, 150, 210, 150, 150} + ,{ 250, 250, 250, 250, 250} + } + ,{{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + } + ,{{ 280, 250, 280, 250, 250} + ,{ 280, 220, 280, 220, 220} + ,{ 250, 250, 250, 250, 250} + ,{ 230, 100, 100, 100, 230} + ,{ 250, 250, 250, 250, 250} + } + ,{{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 260, 260, 260, 260} + ,{ 170, 170, 170, 170, 170} + } + } + } + ,{{{{ 370, 280, 280, 370, 340} + ,{ 340, 280, 280, 310, 340} + ,{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + } + ,{{ 340, 280, 280, 310, 340} + ,{ 340, 280, 280, 310, 340} + ,{ 260, 230, 230, 260, 230} + ,{ 230, 170, 230, 200, 230} + ,{ 260, 230, 230, 260, 230} + } + ,{{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 370, 280, 280, 370, 280} + } + ,{{ 280, 230, 240, 280, 250} + ,{ 240, 180, 240, 210, 240} + ,{ 260, 230, 230, 260, 230} + ,{ 280, 120, 120, 280, 250} + ,{ 260, 230, 230, 260, 230} + } + ,{{ 340, 280, 280, 340, 280} + ,{ 310, 280, 280, 310, 280} + ,{ 340, 250, 250, 340, 250} + ,{ 310, 280, 280, 310, 280} + ,{ 220, 220, 190, 220, 190} + } + } + ,{{{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + } + ,{{ 310, 240, 280, 310, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 260, 200, 230, 260, 230} + ,{ 200, 140, 170, 200, 170} + ,{ 260, 200, 230, 260, 230} + } + ,{{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 370, 240, 280, 370, 280} + } + ,{{ 280, 200, 230, 280, 230} + ,{ 210, 150, 180, 210, 180} + ,{ 260, 200, 230, 260, 230} + ,{ 280, 90, 120, 280, 120} + ,{ 260, 200, 230, 260, 230} + } + ,{{ 340, 240, 280, 340, 280} + ,{ 310, 240, 280, 310, 280} + ,{ 340, 210, 250, 340, 250} + ,{ 310, 240, 280, 310, 280} + ,{ 220, 220, 190, 220, 190} + } + } + ,{{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 230, 230, 230, 230, 230} + ,{ 230, 170, 230, 170, 230} + ,{ 230, 230, 230, 230, 230} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 240, 230, 240, 230, 240} + ,{ 240, 180, 240, 180, 240} + ,{ 230, 230, 230, 230, 230} + ,{ 120, 120, 120, 120, 120} + ,{ 230, 230, 230, 230, 230} + } + ,{{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 250, 250, 250, 250, 250} + ,{ 280, 280, 280, 280, 280} + ,{ 190, 190, 190, 190, 190} + } + } + ,{{{ 280, 200, 280, 250, 280} + ,{ 280, 140, 280, 180, 280} + ,{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 250, 280} + ,{ 280, 200, 280, 190, 280} + } + ,{{ 280, 140, 280, 170, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 230, 100, 230, 100, 230} + ,{ 170, 40, 170, 170, 170} + ,{ 230, 100, 230, 100, 230} + } + ,{{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 200, 280, 150, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 280, 200, 280, 150, 280} + } + ,{{ 250, 120, 230, 250, 230} + ,{ 180, 50, 180, 180, 180} + ,{ 230, 100, 230, 100, 230} + ,{ 250, 120, 120, 250, 120} + ,{ 230, 100, 230, 100, 230} + } + ,{{ 280, 170, 280, 190, 280} + ,{ 280, 140, 280, 150, 280} + ,{ 250, 170, 250, 120, 250} + ,{ 280, 140, 280, 150, 280} + ,{ 190, 60, 190, 190, 190} + } + } + ,{{{ 340, 280, 280, 280, 340} + ,{ 340, 280, 280, 280, 340} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + ,{ 280, 280, 280, 280, 280} + } + ,{{ 340, 280, 280, 280, 340} + ,{ 340, 280, 280, 280, 340} + ,{ 230, 230, 230, 230, 230} + ,{ 230, 170, 230, 170, 170} + ,{ 230, 230, 230, 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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} + } + } + } + ,{{{{ 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, 180, 190} + } + ,{{ 180, 170, 180, 170, 180} + ,{ 180, 170, 180, 170, 180} + ,{ 170, 170, 170, 170, 170} + ,{ 140, 80, 140, 80, 140} + ,{ 170, 170, 170, 170, 170} + } + ,{{ 220, 210, 220, 210, 220} + ,{ 220, 210, 220, 210, 220} + ,{ 200, 200, 200, 200, 200} + ,{ 220, 210, 220, 210, 220} + ,{ 190, 180, 190, 180, 190} + } + ,{{ 170, 170, 170, 170, 170} + ,{ 140, 80, 140, 80, 140} + ,{ 170, 170, 170, 170, 170} + ,{ 30, 20, 30, 20, 30} + ,{ 170, 170, 170, 170, 170} + } + ,{{ 220, 210, 220, 210, 220} + ,{ 220, 210, 220, 210, 220} + ,{ 190, 180, 190, 180, 190} + ,{ 220, 210, 220, 210, 220} + ,{ 100, 90, 100, 90, 100} + } + } + ,{{{ 220, 160, 220, 130, 220} + ,{ 220, 110, 220, 60, 220} + ,{ 210, 160, 210, 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} + 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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} + 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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, 290} + } + ,{{ 310, 310, 290, 310, 290} + ,{ 310, 310, 290, 250, 290} + ,{ 310, 310, 290, 310, 290} + ,{ 310, 310, 290, 250, 290} + ,{ 310, 310, 290, 310, 290} + } + ,{{ 310, 310, 290, 250, 290} + ,{ 270, 270, 250, 210, 250} + ,{ 310, 310, 290, 250, 290} + ,{ 250, 180, 160, 250, 160} + ,{ 310, 310, 290, 250, 290} + } + ,{{ 370, 370, 290, 310, 290} + ,{ 310, 310, 290, 250, 290} + ,{ 310, 310, 290, 310, 290} + ,{ 310, 310, 290, 250, 290} + ,{ 370, 370, 290, 250, 290} + } + } + ,{{{ 320, 320, 320, 320, 320} + ,{ 320, 320, 320, 320, 320} + ,{ 290, 280, 290, 280, 290} + ,{ 290, 280, 290, 280, 290} + ,{ 290, 280, 290, 280, 290} + } + ,{{ 320, 320, 320, 320, 320} + ,{ 320, 320, 320, 320, 320} + ,{ 290, 280, 290, 280, 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} 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260} + ,{ 280, 280, 260, 220, 260} + ,{ 280, 280, 260, 280, 260} + } + ,{{ 310, 310, 290, 250, 290} + ,{ 310, 310, 290, 250, 290} + ,{ 280, 280, 260, 220, 260} + ,{ 220, 150, 130, 220, 130} + ,{ 280, 280, 260, 220, 260} + } + ,{{ 340, 340, 260, 280, 260} + ,{ 280, 280, 260, 220, 260} + ,{ 280, 280, 260, 280, 260} + ,{ 280, 280, 260, 220, 260} + ,{ 340, 340, 260, 220, 260} + } + } + ,{{{ 350, 280, 350, 280, 350} + ,{ 350, 280, 350, 280, 350} + ,{ 260, 250, 260, 250, 260} + ,{ 260, 250, 260, 250, 260} + ,{ 260, 250, 260, 250, 260} + } + ,{{ 260, 250, 260, 250, 260} + ,{ 220, 220, 220, 220, 220} + ,{ 260, 250, 260, 250, 260} + ,{ 180, 120, 180, 120, 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} + } + ,{{ 350, 280, 350, 280, 350} + ,{ 350, 280, 350, 280, 350} + ,{ 260, 250, 260, 250, 260} + ,{ 130, 120, 130, 120, 130} + ,{ 260, 250, 260, 250, 260} 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200} + ,{ 260, 250, 260, 250, 170} + ,{ 260, 250, 260, 250, 170} + ,{ 260, 250, 260, 250, 170} + } + ,{{ 260, 250, 260, 250, 190} + ,{ 220, 220, 220, 220, 190} + ,{ 260, 250, 260, 250, 170} + ,{ 180, 120, 180, 120, 30} + ,{ 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} + ,{ 260, 250, 260, 250, 170} + } + ,{{ 350, 280, 350, 280, 200} + ,{ 350, 280, 350, 280, 200} + ,{ 260, 250, 260, 250, 170} + ,{ 170, 120, 130, 120, 170} + ,{ 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} + ,{ 260, 250, 260, 250, 170} + } + } + } + ,{{{{ 280, 280, 260, 260, 260} + ,{ 280, 280, 260, 250, 260} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 240, 250} + ,{ 260, 260, 240, 260, 240} + } + ,{{ 280, 280, 260, 250, 260} + ,{ 280, 280, 260, 250, 260} + ,{ 250, 250, 240, 230, 240} + ,{ 190, 150, 190, 130, 190} + ,{ 250, 250, 240, 230, 240} + } + ,{{ 260, 260, 250, 260, 250} + ,{ 260, 260, 250, 240, 250} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 240, 250} + ,{ 260, 260, 240, 260, 240} + } + ,{{ 260, 250, 260, 230, 260} + ,{ 260, 220, 260, 200, 260} + ,{ 250, 250, 240, 230, 240} + ,{ 190, 110, 90, 190, 120} + ,{ 250, 250, 240, 230, 240} + } + ,{{ 260, 260, 250, 260, 250} + ,{ 260, 260, 250, 240, 250} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 240, 250} + ,{ 230, 230, 150, 140, 150} + } + } + ,{{{ 280, 280, 260, 260, 260} + ,{ 280, 280, 260, 220, 260} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 210, 250} + ,{ 260, 260, 240, 260, 240} + } + ,{{ 280, 280, 260, 220, 260} + ,{ 280, 280, 260, 220, 260} + ,{ 250, 250, 240, 200, 240} + ,{ 150, 150, 140, 100, 140} + ,{ 250, 250, 240, 200, 240} + } + ,{{ 260, 260, 250, 260, 250} + ,{ 260, 260, 250, 210, 250} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 210, 250} + ,{ 260, 260, 240, 260, 240} + } + ,{{ 250, 250, 240, 200, 240} + ,{ 220, 220, 210, 170, 210} + ,{ 250, 250, 240, 200, 240} + ,{ 180, 100, 90, 180, 90} + ,{ 250, 250, 240, 200, 240} + } + ,{{ 260, 260, 250, 260, 250} + ,{ 260, 260, 250, 210, 250} + ,{ 260, 260, 240, 260, 240} + ,{ 260, 260, 250, 210, 250} + ,{ 230, 230, 150, 110, 150} + } + } + ,{{{ 260, 250, 260, 250, 260} + ,{ 260, 250, 260, 250, 260} + ,{ 240, 230, 240, 230, 240} + ,{ 240, 240, 240, 240, 240} + ,{ 240, 230, 240, 230, 240} + } + ,{{ 260, 250, 260, 250, 260} + ,{ 260, 250, 260, 250, 260} + ,{ 230, 230, 230, 230, 230} + ,{ 190, 130, 190, 130, 190} + ,{ 230, 230, 230, 230, 230} + } + ,{{ 240, 240, 240, 240, 240} + ,{ 240, 240, 240, 240, 240} + ,{ 240, 230, 240, 230, 240} + ,{ 240, 240, 240, 240, 240} + ,{ 240, 230, 240, 230, 240} + } + ,{{ 260, 230, 260, 230, 260} + ,{ 260, 200, 260, 200, 260} + ,{ 230, 230, 230, 230, 230} + ,{ 80, 80, 80, 80, 80} + ,{ 230, 230, 230, 230, 230} + } + ,{{ 240, 240, 240, 240, 240} + ,{ 240, 240, 240, 240, 240} + ,{ 240, 230, 240, 230, 240} + ,{ 240, 240, 240, 240, 240} + ,{ 150, 140, 150, 140, 150} + } + } + ,{{{ 260, 190, 260, 190, 260} + ,{ 260, 150, 260, 180, 260} + ,{ 240, 190, 240, 80, 240} + ,{ 250, 140, 250, 190, 250} + ,{ 240, 190, 240, 120, 240} + } + ,{{ 260, 150, 260, 110, 260} + ,{ 260, 150, 260, 100, 260} + ,{ 240, 130, 240, 80, 240} + ,{ 140, 30, 140, 110, 140} + ,{ 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} + } + ,{{ 280, 280, 260, 250, 260} + ,{ 280, 280, 260, 250, 260} + ,{ 230, 230, 220, 210, 220} + ,{ 210, 170, 210, 150, 210} + ,{ 230, 230, 220, 210, 220} + } + ,{{ 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} + } + ,{{ 230, 230, 220, 210, 220} + ,{ 220, 180, 220, 160, 220} + ,{ 230, 230, 220, 210, 220} + ,{ 210, 130, 110, 210, 140} + ,{ 230, 230, 220, 210, 220} + } + ,{{ 280, 280, 260, 250, 260} + ,{ 280, 280, 260, 250, 260} + ,{ 250, 250, 230, 250, 230} + ,{ 280, 280, 260, 250, 260} + ,{ 250, 250, 180, 170, 180} + } + } + ,{{{ 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} + } + ,{{ 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, 250, 260, 250, 170} + ,{ 260, 250, 260, 250, 170} + ,{ 230, 220, 230, 220, 140} + ,{ 260, 250, 260, 250, 170} + ,{ 170, 170, 170, 170, 80} + } + } + } + ,{{{{ 370, 370, 350, 320, 350} + ,{ 350, 340, 350, 320, 350} + ,{ 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} + } + ,{{ 350, 310, 350, 280, 350} + 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310, 310, 290, 250, 290} + ,{ 370, 370, 290, 250, 290} + } + } + ,{{{ 350, 320, 350, 320, 350} + ,{ 350, 320, 350, 320, 350} + ,{ 290, 280, 290, 280, 290} + ,{ 290, 280, 290, 280, 290} + ,{ 290, 280, 290, 280, 290} + } + ,{{ 320, 320, 320, 320, 320} + ,{ 320, 320, 320, 320, 320} + ,{ 290, 280, 290, 280, 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} + } + ,{{ 350, 280, 350, 280, 350} + ,{ 350, 280, 350, 280, 350} + ,{ 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, 260, 330} + ,{ 290, 240, 290, 130, 290} + ,{ 290, 180, 290, 260, 290} + ,{ 290, 240, 290, 260, 290} + } + 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210, 210, 210, 170, 210} + ,{ 240, 240, 240, 190, 240} + ,{ 180, 180, 120, 90, 120} + } + } + ,{{{ 240, 240, 240, 190, 240} + ,{ 240, 240, 240, 140, 240} + ,{ 220, 220, 220, 190, 220} + ,{ 240, 240, 240, 140, 240} + ,{ 210, 210, 210, 170, 210} + } + ,{{ 200, 200, 200, 100, 200} + ,{ 200, 200, 200, 100, 200} + ,{ 190, 190, 190, 100, 190} + ,{ 100, 100, 100, 10, 100} + ,{ 190, 190, 190, 100, 190} + } + ,{{ 240, 240, 240, 190, 240} + ,{ 240, 240, 240, 140, 240} + ,{ 220, 220, 220, 190, 220} + ,{ 240, 240, 240, 140, 240} + ,{ 210, 210, 210, 170, 210} + } + ,{{ 190, 190, 190, 100, 190} + ,{ 100, 100, 100, 10, 100} + ,{ 190, 190, 190, 100, 190} + ,{ 80, 50, 50, 80, 50} + ,{ 190, 190, 190, 100, 190} + } + ,{{ 240, 240, 240, 170, 240} + ,{ 240, 240, 240, 140, 240} + ,{ 210, 210, 210, 170, 210} + ,{ 240, 240, 240, 140, 240} + ,{ 180, 180, 120, 20, 120} + } + } + ,{{{ 240, 190, 240, 190, 210} + ,{ 240, 190, 240, 190, 210} + ,{ 220, 180, 220, 180, 190} + ,{ 240, 190, 240, 190, 210} + ,{ 210, 160, 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220, 70, 220} + ,{ 240, 130, 240, 80, 240} + ,{ 210, 160, 210, 50, 210} + } + ,{{ 190, 90, 190, 150, 190} + ,{ 100, 0, 100, 80, 100} + ,{ 190, 90, 190, 40, 190} + ,{ 150, 70, 50, 150, 50} + ,{ 190, 90, 190, 40, 190} + } + ,{{ 240, 160, 240, 90, 240} + ,{ 240, 130, 240, 80, 240} + ,{ 210, 160, 210, 50, 210} + ,{ 240, 130, 240, 80, 240} + ,{ 120, 10, 120, 90, 120} + } + } + ,{{{ 240, 190, 240, 190, 170} + ,{ 240, 190, 240, 190, 170} + ,{ 220, 180, 220, 180, 140} + ,{ 240, 190, 240, 190, 150} + ,{ 210, 160, 210, 160, 120} + } + ,{{ 200, 150, 200, 150, 170} + ,{ 200, 150, 200, 150, 170} + ,{ 190, 150, 190, 150, 110} + ,{ 160, 60, 160, 60, 20} + ,{ 190, 150, 190, 150, 110} + } + ,{{ 240, 190, 240, 190, 150} + ,{ 240, 190, 240, 190, 150} + ,{ 220, 180, 220, 180, 140} + ,{ 240, 190, 240, 190, 150} + ,{ 210, 160, 210, 160, 120} + } + ,{{ 190, 150, 190, 150, 110} + ,{ 160, 60, 160, 60, 20} + ,{ 190, 150, 190, 150, 110} + ,{ 90, 0, 50, 0, 90} + ,{ 190, 150, 190, 150, 110} + } + ,{{ 240, 190, 240, 190, 150} + ,{ 240, 190, 240, 190, 150} + ,{ 210, 160, 210, 160, 120} + ,{ 240, 190, 240, 190, 150} + ,{ 120, 70, 120, 70, 30} + } + } + } + ,{{{{ 210, 210, 210, 170, 210} + ,{ 210, 210, 210, 170, 210} + ,{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 150, 180} + ,{ 190, 190, 190, 150, 190} + } + ,{{ 210, 210, 210, 170, 210} + ,{ 210, 210, 210, 170, 210} + ,{ 190, 190, 190, 140, 190} + ,{ 70, 10, 70, -10, 40} + ,{ 190, 190, 190, 140, 190} + } + ,{{ 190, 190, 190, 150, 190} + ,{ 180, 180, 180, 140, 180} + ,{ 190, 190, 190, 150, 190} + ,{ 180, 180, 180, 140, 180} + ,{ 190, 190, 190, 150, 190} + } + ,{{ 190, 190, 190, 150, 190} + ,{ 130, 70, 130, 50, 100} + ,{ 190, 190, 190, 140, 190} + ,{ 150, 70, 50, 150, 90} + ,{ 190, 190, 190, 140, 190} + } + ,{{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 140, 180} + ,{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 140, 180} + ,{ 170, 170, 110, 90, 110} + } + } + ,{{{ 210, 210, 210, 160, 210} + ,{ 210, 210, 210, 120, 210} + ,{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 90, 180} + ,{ 190, 190, 190, 150, 190} + } + ,{{ 210, 210, 210, 120, 210} + ,{ 210, 210, 210, 120, 210} + ,{ 190, 190, 190, 90, 190} + ,{ 10, 10, 10, -80, 10} + ,{ 190, 190, 190, 90, 190} + } + ,{{ 190, 190, 190, 150, 190} + ,{ 180, 180, 180, 90, 180} + ,{ 190, 190, 190, 150, 190} + ,{ 180, 180, 180, 90, 180} + ,{ 190, 190, 190, 150, 190} + } + ,{{ 190, 190, 190, 90, 190} + ,{ 70, 70, 70, -20, 70} + ,{ 190, 190, 190, 90, 190} + ,{ 80, 50, 50, 80, 50} + ,{ 190, 190, 190, 90, 190} + } + ,{{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 90, 180} + ,{ 190, 190, 190, 160, 190} + ,{ 180, 180, 180, 90, 180} + ,{ 170, 170, 110, 20, 110} + } + } + ,{{{ 210, 170, 210, 170, 180} + ,{ 210, 170, 210, 170, 180} + ,{ 190, 150, 190, 150, 160} + ,{ 180, 140, 180, 140, 150} + ,{ 190, 140, 190, 140, 160} + } + ,{{ 210, 170, 210, 170, 180} + ,{ 210, 170, 210, 170, 180} + ,{ 190, 140, 190, 140, 160} + ,{ 70, -30, 70, -30, 40} + ,{ 190, 140, 190, 140, 160} + } + ,{{ 190, 140, 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340, 300, 340} + ,{ 310, 310, 310, 270, 310} + ,{ 310, 310, 310, 280, 310} + ,{ 370, 370, 310, 280, 310} + } + ,{{ 340, 340, 340, 300, 340} + ,{ 340, 340, 340, 300, 340} + ,{ 310, 310, 310, 260, 310} + ,{ 290, 230, 290, 200, 260} + ,{ 310, 310, 310, 260, 310} + } + ,{{ 310, 310, 310, 270, 310} + ,{ 310, 310, 310, 260, 310} + ,{ 310, 310, 310, 270, 310} + ,{ 310, 310, 310, 260, 310} + ,{ 310, 310, 310, 270, 310} + } + ,{{ 330, 310, 330, 280, 310} + ,{ 330, 270, 330, 240, 300} + ,{ 310, 310, 310, 260, 310} + ,{ 280, 200, 180, 280, 220} + ,{ 310, 310, 310, 260, 310} + } + ,{{ 370, 370, 310, 280, 310} + ,{ 310, 310, 310, 260, 310} + ,{ 310, 310, 310, 270, 310} + ,{ 310, 310, 310, 260, 310} + ,{ 370, 370, 310, 280, 310} + } + } + ,{{{ 370, 370, 340, 270, 340} + ,{ 340, 340, 340, 250, 340} + ,{ 310, 310, 310, 270, 310} + ,{ 310, 310, 310, 210, 310} + ,{ 370, 370, 310, 270, 310} + } + ,{{ 340, 340, 340, 250, 340} + ,{ 340, 340, 340, 250, 340} + ,{ 310, 310, 310, 210, 310} + ,{ 230, 230, 230, 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310} + ,{ 310, 200, 310, 150, 310} + ,{ 310, 200, 310, 280, 310} + } + } + ,{{{ 340, 300, 340, 300, 320} + ,{ 340, 300, 340, 300, 320} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + } + ,{{ 340, 300, 340, 300, 320} + ,{ 340, 300, 340, 300, 320} + ,{ 310, 260, 310, 260, 220} + ,{ 290, 180, 290, 180, 140} + ,{ 310, 260, 310, 260, 220} + } + ,{{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + } + ,{{ 330, 260, 330, 260, 220} + ,{ 330, 220, 330, 220, 180} + ,{ 310, 260, 310, 260, 220} + ,{ 220, 130, 180, 130, 220} + ,{ 310, 260, 310, 260, 220} + } + ,{{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + ,{ 310, 260, 310, 260, 220} + } + } + } + ,{{{{ 370, 340, 370, 280, 340} + ,{ 370, 310, 370, 280, 340} + ,{ 280, 280, 280, 240, 280} + ,{ 280, 280, 280, 250, 280} + ,{ 340, 340, 280, 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120} + ,{ 280, 230, 280, 230, 250} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + } + } + ,{{{ 310, 230, 310, 280, 310} + ,{ 310, 200, 310, 280, 310} + ,{ 280, 230, 280, 120, 280} + ,{ 280, 170, 280, 250, 280} + ,{ 280, 230, 280, 250, 280} + } + ,{{ 280, 170, 280, 120, 280} + ,{ 240, 140, 240, 90, 240} + ,{ 280, 170, 280, 120, 280} + ,{ 140, 40, 140, 120, 140} + ,{ 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, 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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} + ,{ 280, 230, 280, 230, 250} + ,{ 260, 210, 260, 210, 230} + ,{ 260, 220, 260, 220, 230} + ,{ 260, 210, 260, 210, 230} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 250, 210, 250, 210, 220} + ,{ 210, 110, 210, 110, 180} + ,{ 250, 210, 250, 210, 220} + } + ,{{ 260, 220, 260, 220, 230} + ,{ 260, 220, 260, 220, 230} + ,{ 260, 210, 260, 210, 230} + ,{ 260, 220, 260, 220, 230} + ,{ 260, 210, 260, 210, 230} + } + ,{{ 280, 210, 280, 210, 250} + ,{ 280, 180, 280, 180, 250} + ,{ 250, 210, 250, 210, 220} + ,{ 100, 60, 100, 60, 70} + ,{ 250, 210, 250, 210, 220} + } + ,{{ 260, 220, 260, 220, 230} + ,{ 260, 220, 260, 220, 230} 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120, 120, 160, 120} + ,{ 230, 230, 230, 140, 230} + } + ,{{ 280, 280, 280, 210, 280} + ,{ 280, 280, 280, 180, 280} + ,{ 250, 250, 250, 210, 250} + ,{ 280, 280, 280, 180, 280} + ,{ 250, 250, 190, 100, 190} + } + } + ,{{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 230, 190, 230, 190, 200} + ,{ 230, 130, 230, 130, 200} + ,{ 230, 190, 230, 190, 200} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + } + ,{{ 240, 190, 240, 190, 210} + ,{ 240, 140, 240, 140, 210} + ,{ 230, 190, 230, 190, 200} + ,{ 120, 80, 120, 80, 90} + ,{ 230, 190, 230, 190, 200} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 250, 200, 250, 200, 220} + ,{ 280, 230, 280, 230, 250} + ,{ 190, 150, 190, 150, 160} + } + } + ,{{{ 280, 230, 280, 230, 280} + ,{ 280, 170, 280, 160, 280} + ,{ 280, 230, 280, 120, 280} + ,{ 280, 170, 280, 230, 280} + ,{ 280, 230, 280, 170, 280} + } + ,{{ 280, 170, 280, 150, 280} + ,{ 280, 170, 280, 120, 280} + ,{ 230, 130, 230, 80, 230} + ,{ 170, 70, 170, 150, 170} + ,{ 230, 130, 230, 80, 230} + } + ,{{ 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} + } + ,{{ 230, 150, 230, 230, 230} + ,{ 180, 80, 180, 160, 180} + ,{ 230, 130, 230, 80, 230} + ,{ 230, 150, 120, 230, 120} + ,{ 230, 130, 230, 80, 230} + } + ,{{ 280, 200, 280, 170, 280} + ,{ 280, 170, 280, 120, 280} + ,{ 250, 200, 250, 90, 250} + ,{ 280, 170, 280, 120, 280} + ,{ 190, 90, 190, 170, 190} + } + } + ,{{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 190} + ,{ 280, 230, 280, 230, 190} + ,{ 280, 230, 280, 230, 190} + } + ,{{ 280, 230, 280, 230, 250} + ,{ 280, 230, 280, 230, 250} + ,{ 230, 190, 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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, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + } + ,{{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + ,{ INF, INF, INF, INF, INF} + } + ,{{ INF, 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, 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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} + 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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} + ,{ 220, 220, 220, 220, 220} + ,{ 210, 80, 80, 80, 210} + ,{ 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} + } + } + } + ,{{{{ 430, 430, 370, 400, 430} + ,{ 430, 410, 370, 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} + } + ,{{ 370, 370, 360, 340, 360} + ,{ 360, 360, 360, 300, 360} + ,{ 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} + ,{ 360, 360, 300, 300, 300} + ,{ 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} + } + } + ,{{{ 370, 370, 370, 370, 370} + ,{ 370, 370, 370, 370, 370} + ,{ 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} + } + ,{{ 360, 340, 360, 340, 360} + ,{ 360, 300, 360, 300, 360} + ,{ 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, 300, 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} + ,{ 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} + ,{ 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} + } + ,{{ 360, 340, 360, 340, 340} + ,{ 360, 300, 360, 300, 300} + ,{ 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} + } + } + } + ,{{{{ 400, 400, 400, 370, 400} + ,{ 400, 370, 400, 360, 400} + ,{ 370, 340, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 370, 310} + } + ,{{ 360, 360, 310, 360, 330} + ,{ 360, 360, 270, 360, 330} + ,{ 340, 340, 310, 310, 310} + ,{ 230, 220, 230, 170, 230} + ,{ 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} + ,{ 370, 340, 310, 370, 310} + } + ,{{ 400, 370, 400, 340, 400} + ,{ 400, 370, 400, 340, 400} + ,{ 340, 340, 310, 310, 310} + ,{ 310, 230, 180, 310, 310} + ,{ 340, 340, 310, 310, 310} + } + ,{{ 400, 400, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 370, 340, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 310, 310} + } + } + ,{{{ 400, 400, 340, 370, 340} + ,{ 370, 370, 340, 360, 340} + ,{ 370, 340, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 370, 310} + } + ,{{ 360, 360, 310, 360, 310} + ,{ 360, 360, 270, 360, 270} + ,{ 340, 340, 310, 310, 310} + ,{ 220, 220, 170, 170, 170} + ,{ 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} + ,{ 370, 340, 310, 370, 310} + } + ,{{ 370, 370, 340, 340, 340} + ,{ 370, 370, 340, 340, 340} + ,{ 340, 340, 310, 310, 310} + ,{ 310, 210, 180, 310, 180} + ,{ 340, 340, 310, 310, 310} + } + ,{{ 400, 400, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 370, 340, 310, 370, 310} + ,{ 340, 340, 310, 310, 310} + ,{ 400, 400, 310, 310, 310} + } + } + ,{{{ 400, 340, 400, 340, 400} + ,{ 400, 340, 400, 340, 400} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 310, 310, 310, 310, 310} + ,{ 270, 270, 270, 270, 270} + ,{ 310, 310, 310, 310, 310} + ,{ 230, 170, 230, 170, 230} + ,{ 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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290, 310, 310, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 290, 310, 180, 310} + ,{ 310, 230, 310, 180, 310} + ,{ 310, 230, 310, 310, 310} + } + } + ,{{{ 400, 340, 400, 340, 340} + ,{ 400, 340, 400, 340, 340} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 330, 310, 310, 310, 330} + ,{ 330, 270, 270, 270, 330} + ,{ 310, 310, 310, 310, 310} + ,{ 230, 170, 230, 170, 170} + ,{ 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} + ,{ 310, 310, 310, 310, 310} + } + ,{{ 400, 340, 400, 340, 340} + ,{ 400, 340, 400, 340, 340} + ,{ 310, 310, 310, 310, 310} + ,{ 310, 180, 180, 180, 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, 310} + ,{ 310, 310, 310, 310, 310} + } + } + } + ,{{{{ 370, 340, 310, 350, 370} + ,{ 370, 340, 310, 310, 370} + ,{ 350, 320, 290, 350, 290} + ,{ 330, 330, 290, 290, 290} + ,{ 350, 320, 290, 350, 290} + } + ,{{ 370, 340, 310, 310, 370} + ,{ 370, 340, 310, 310, 370} + ,{ 320, 320, 280, 280, 280} + ,{ 240, 220, 240, 180, 240} + ,{ 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, 310, 280, 310} + ,{ 310, 290, 310, 250, 310} + ,{ 320, 320, 280, 280, 280} + ,{ 260, 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, 290, 160, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 290, 270, 290, 160, 290} + } + ,{{ 280, 200, 280, 260, 280} + ,{ 250, 170, 250, 250, 250} + ,{ 280, 200, 280, 150, 280} + ,{ 260, 180, 130, 260, 130} + ,{ 280, 200, 280, 150, 280} + } + ,{{ 290, 270, 290, 200, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 290, 270, 290, 160, 290} + ,{ 290, 210, 290, 160, 290} + ,{ 200, 120, 200, 200, 200} + } + } + ,{{{ 370, 310, 310, 310, 370} + ,{ 370, 310, 310, 310, 370} + ,{ 290, 290, 290, 290, 290} + ,{ 290, 290, 290, 290, 290} + ,{ 290, 290, 290, 290, 290} + } + ,{{ 370, 310, 310, 310, 370} + ,{ 370, 310, 310, 310, 370} + ,{ 280, 280, 280, 280, 280} + ,{ 240, 180, 240, 180, 180} + ,{ 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, 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, 310, 310} + } + ,{{ 310, 310, 310, 310, 310} + ,{ 310, 310, 310, 310, 310} + ,{ 260, 260, 260, 260, 260} + ,{ 260, 200, 260, 200, 260} + ,{ 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} + } + ,{{ 270, 260, 270, 260, 270} + ,{ 270, 210, 270, 210, 270} + ,{ 260, 260, 260, 260, 260} + ,{ 150, 150, 150, 150, 150} + ,{ 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} + } + } + ,{{{ 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} + ,{ 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} + } + } + } + }}; diff --git a/C/ViennaRNA/intl22dH.h b/C/ViennaRNA/intl22dH.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/intl22dH.h @@ -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, 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,{ 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, 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-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, 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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, 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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} + } + } + } + ,{{{{ 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, 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-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, 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-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, 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-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, 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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, 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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} 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-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, 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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} + } + } + } + ,{{{{ 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, 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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} + } + } + } 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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} + } + } + } + ,{{{{ 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} + 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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} + } + 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-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, 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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} 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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} + } + } + } + }}; diff --git a/C/ViennaRNA/inverse.c b/C/ViennaRNA/inverse.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/inverse.c @@ -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 +#include +#include +#include +#include +#include +#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; i0) do { + cont=0; + + if (fold_type==0) { /* min free energy fold */ + make_ptable(structure, test_table); + for (j=w1=w2=flag=0; j0)) + if ((target_table[j-1]1) if (w2_list[w2-2]==w2_list[w2-1]) w2--; + + flag = 1; + } else { + if (flag==1) if ((tt0) 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; i0)&&(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 (j0) && 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 +#include +#include +#include + +#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; +} + diff --git a/C/ViennaRNA/ligand.h b/C/ViennaRNA/ligand.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ligand.h @@ -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 + + +/** + * @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 diff --git a/C/ViennaRNA/list.c b/C/ViennaRNA/list.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/list.c @@ -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 +#include +#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 diff --git a/C/ViennaRNA/list.h b/C/ViennaRNA/list.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/list.h @@ -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 diff --git a/C/ViennaRNA/loop_energies.h b/C/ViennaRNA/loop_energies.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/loop_energies.h @@ -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 + * + *

+ * 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()] .
+ * The unit of the free energy returned is @f$10^{-2} * \mathrm{kcal}/\mathrm{mol}@f$ + *

+ *

+ * 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() ]. + *

+ */ + + +/* below we include the loop type specific energy evaluation functions */ + +#include + +#include + +#include + +#include + +/** + * @} + */ + +#endif diff --git a/C/ViennaRNA/mfe.c b/C/ViennaRNA/mfe.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/mfe.c @@ -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 +#include +#include +#include +#include +#include + +#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= 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; spair[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]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]pair[S[s][1]][S[s][j]]; + if(tt==0) tt=7; + energy += E_ExtLoop(tt, -1, (jgquad){ + 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]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; sspair[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; sspair[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 (minqup_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; sspair[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;ssmismatchI[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 +#include + +/** + * @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 diff --git a/C/ViennaRNA/mm.c b/C/ViennaRNA/mm.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/mm.c @@ -0,0 +1,103 @@ +/* + Implementation of Nussinov Maximum Matching + Ronny Lorenz +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#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); i0; 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); i0; 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); i0; 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; +} + diff --git a/C/ViennaRNA/mm.h b/C/ViennaRNA/mm.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/mm.h @@ -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 diff --git a/C/ViennaRNA/model.c b/C/ViennaRNA/model.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/model.c @@ -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 +#include +#include +#include +#include +#include + +#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 + + diff --git a/C/ViennaRNA/model.h b/C/ViennaRNA/model.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/model.h @@ -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 °C @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 diff --git a/C/ViennaRNA/model_avg.inc b/C/ViennaRNA/model_avg.inc new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/model_avg.inc @@ -0,0 +1,1095 @@ +char* avg_model_string= +"svm_type nu_svr\n" +"kernel_type rbf\n" +"gamma 6\n" +"nr_class 2\n" +"total_sv 1087\n" +"rho 0.107628\n" +"SV\n" +"-0.2927223412287951 1:0.2 2:0.2 3:0.4 4:0 \n" +"-0.2726129259719185 1:0.2 2:0.2 3:0.5 4:0 \n" +"-0.4429394065483267 1:0.2 2:0.2 3:0.6 4:0 \n" +"0.3450198571957915 1:0.2 2:0.2 3:0.8 4:0 \n" +"1 1:0.2 2:0.25 3:0.2 4:0 \n" +"0.9846600387002246 1:0.2 2:0.25 3:0.5 4:0 \n" +"0.4361932664094919 1:0.2 2:0.3 3:0.6 4:0 \n" +"0.08551999173355709 1:0.2 2:0.35 3:0.8 4:0 \n" +"-0.459481107722125 1:0.2 2:0.45 3:0.5 4:0 \n" +"-0.1858952118588858 1:0.2 2:0.45 3:0.7 4:0 \n" +"-0.7957932783829218 1:0.2 2:0.55 3:0.2 4:0 \n" 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3:0.7516129 4:1 \n" +"-1 1:0.775 2:0.7 3:0.6516129 4:1 \n" +"0.01718174475549202 1:0.775 2:0.8 3:0.2516129 4:1 \n" +"-0.2052635276433671 1:0.8 2:0.25 3:0.25 4:1 \n" +"-1 1:0.8 2:0.25 3:0.6 4:1 \n" +"1 1:0.8 2:0.25 3:0.75 4:1 \n" +"-0.04518204611438701 1:0.8 2:0.25 3:0.8 4:1 \n" +"0.6768238613754204 1:0.8 2:0.3 3:0.45 4:1 \n" +"-0.5138797159875904 1:0.8 2:0.35 3:0.25 4:1 \n" +"0.0261438872042605 1:0.8 2:0.4 3:0.2 4:1 \n" +"-0.004793297131704656 1:0.8 2:0.4 3:0.65 4:1 \n" +"1 1:0.8 2:0.4 3:0.75 4:1 \n" +"1 1:0.8 2:0.5 3:0.45 4:1 \n" +"-0.3991872047745405 1:0.8 2:0.5 3:0.6 4:1 \n" +"-1 1:0.8 2:0.5 3:0.65 4:1 \n" +"0.2567252018577118 1:0.8 2:0.55 3:0.2 4:1 \n" +"-0.8822601344526142 1:0.8 2:0.55 3:0.35 4:1 \n" +"1 1:0.8 2:0.6 3:0.75 4:1 \n" +"0.223252672606951 1:0.8 2:0.65 3:0.75 4:1 \n" +"-0.3335795703441325 1:0.8 2:0.65 3:0.8 4:1 \n" +"-0.5098200396284942 1:0.8 2:0.75 3:0.65 4:1 \n" +"1 1:0.8 2:0.75 3:0.75 4:1 \n"; diff --git a/C/ViennaRNA/move_set.c b/C/ViennaRNA/move_set.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/move_set.c @@ -0,0 +1,1138 @@ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include +#include + +#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]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; ifirst[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; iend_unpr; i++) { + if (Enc->unprocessed[i]) { + free(Enc->unprocessed[i]); + Enc->unprocessed[i]=NULL; + } + } + for (i=Enc->begin_pr; iend_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; iend_pr; i++) { + if (equals(Enc->processed[i], str->structure)) { + found = 1; + break; + } + } + for (i=Enc->begin_unpr; !found && iend_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) { /*'('*/ + 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]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/*'('*/) { + 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; kk/*'('*/) { + 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]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; inum_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; inum_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]str[str[i]]) { /* '('*/ + if (i+1==str[0] || str[i+1]==0 || str[i+1]str[str[i+1]]) i++; + } + + if (str[i]str[str[i+1]]) { + return i; + } else while (i+1!=str[0] && str[i+1]!=0 && str[i+1]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; istructure); + 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]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 +#include +#include +#include +#include +#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[iup_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; +} diff --git a/C/ViennaRNA/multibranch_loops.h b/C/ViennaRNA/multibranch_loops.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/multibranch_loops.h @@ -0,0 +1,252 @@ +#ifndef VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H +#define VIENNA_RNA_PACKAGE_MULTIBRANCH_LOOPS_H + +#include +#include +#include + +#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) + *

Compute the Energy contribution of a Multiloop stem

+ * 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.
+ * 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 diff --git a/C/ViennaRNA/naview.c b/C/ViennaRNA/naview.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/naview.c @@ -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 +#include +#include +#include + +#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; ii) 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 = ®ions[nregion]; + for (i++,mate--; + inconnection = 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; inconnection > 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; idepth = 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; +} + diff --git a/C/ViennaRNA/naview.h b/C/ViennaRNA/naview.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/naview.h @@ -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 diff --git a/C/ViennaRNA/pair_mat.h b/C/ViennaRNA/pair_mat.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/pair_mat.h @@ -0,0 +1,153 @@ +#ifndef VIENNA_RNA_PACKAGE_PAIR_MAT_H +#define VIENNA_RNA_PACKAGE_PAIR_MAT_H + +#include +#include +#include + +#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 G */ + alias[i++] = 2; /* B <-> C */ + } + for (i=1; i GC */ + i++; + pair[i][i-1] = 1; /* BA <-> CG */ + } + } + else if (energy_set==2) { + for (i=1; i A*/ + alias[i++] = 4; /* B <-> U */ + } + for (i=1; i AU */ + i++; + pair[i][i-1] = 6; /* BA <-> UA */ + } + } + else if (energy_set==3) { + for (i=1; i G */ + alias[i++] = 2; /* B <-> C */ + alias[i++] = 1; /* C <-> A */ + alias[i++] = 4; /* D <-> U */ + } + for (i=1; i 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 */ diff --git a/C/ViennaRNA/params.c b/C/ViennaRNA/params.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/params.c @@ -0,0 +1,889 @@ +/* + + c Ivo Hofacker + + Vienna RNA package +*/ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include "ViennaRNA/energy_par.h" +#include "ViennaRNA/fold_vars.h" +#include "ViennaRNA/utils.h" +#include "ViennaRNA/params.h" +/** +*** \file params.c +***

+*** This file provides functions that return temperature scaled energy parameters and +*** Boltzmann weights packed in datastructures +***

+***/ + +/*------------------------------------------------------------------------*/ +#define SCALE 10 +/** +*** dangling ends should never be destabilizing, i.e. expdangle>=1
+*** specific heat needs smooth function (2nd derivative)
+*** we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2, +*** in the interval b0.8660254)?(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)Tetraloop_E[i] = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*tempf; + for (i=0; (i*5)Triloop_E[i] = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*tempf; + for (i=0; (i*9)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)exptetra[i] = exp( -GT*10./kT); + } + for (i=0; (i*5)exptri[i] = exp( -GT*10./kT); + } + for (i=0; (i*9)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)exptetra[i] = exp( -GT*10./kTn); + } + for (i=0; (i*5)exptri[i] = exp( -GT*10./kTn); + } + for (i=0; (i*9)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 + diff --git a/C/ViennaRNA/params.h b/C/ViennaRNA/params.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/params.h @@ -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 +#include +#include + +#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.
+ * 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 diff --git a/C/ViennaRNA/part_func.c b/C/ViennaRNA/part_func.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func.c @@ -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 +#include +#include +#include +#include /* #defines FLT_MAX ... */ +#include + +#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 +#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; kMAXLOOP) break; + lstart = ln1+p-1+n-MAXLOOP; + if(lstart 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; kqo = 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; kpair[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; sexp_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 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; spair[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; kup_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 */ + /* = \sum_{a,b} p_a p_b d(S_a,S_b) + this can be computed from the pair probs p_ij as + = \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 */ + /* = \sum_{a,b} p_a p_b d(S_a,S_b) + this can be computed from the pair probs p_ij as + = \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 diff --git a/C/ViennaRNA/part_func.h b/C/ViennaRNA/part_func.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func.h @@ -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 +#include +#include +#include +#include + +#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 RNAlib 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 OpenMP notice:
+ * 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 QB matrix + * @param[out] qm_p A pointer to the QM 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$ = \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$ = \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 diff --git a/C/ViennaRNA/part_func_co.c b/C/ViennaRNA/part_func_co.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func_co.c @@ -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 +#include +#include +#include +#include /* #defines FLT_MAX ... */ +#include + +#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 +#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, (jexp_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; kexp_f(i, j, k, k+1, VRNA_DECOMP_EXT_EXT_EXT, sc->data); + temp += q_temp; + } + } else { + for (k=i; kQmax) { + 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 (ll; t--) { + for (k=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; t1) ? S1[k-1] : -1, (l<(cp-1)) ? S1[l+1] : -1, pf_params); + if (l+1 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, iexp_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 r) break; + } + if (qbt1 > r) break; + } + if (l=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) break; + } + if (k>j) vrna_message_error("backtrack failed in qm"); + + backtrack_qm1(vc, k,j, pstruc); + + if (k= 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??*/ + 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; + } +} + diff --git a/C/ViennaRNA/part_func_co.h b/C/ViennaRNA/part_func_co.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func_co.h @@ -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 +#include + +/** + * @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 diff --git a/C/ViennaRNA/part_func_up.c b/C/ViennaRNA/part_func_up.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func_up.c @@ -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 +#include +#include +#include +#include /* #defines FLT_MAX ... */ +#include +#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 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); l1) ? S1[p-1] : -1, (oexpMLclosing; + 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, (pexpMLclosing * 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; jE[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 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, (j1) ? SS2[j-1] : -1, (i 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)=1 && (b+ib)=1) { + qint_4[i][j][a+iaa][b+ib] += qint_4[k][l][iaa][ib]*E; + ++iaa; + } + + ibb=ib+1; + while( (b+ibb) 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 && kPi[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 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)&&(jptype[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; lptype[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 iptype[con->indx[k]-l] = 0; + /* don't allow pairs kptype[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]; + } +} diff --git a/C/ViennaRNA/part_func_up.h b/C/ViennaRNA/part_func_up.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/part_func_up.h @@ -0,0 +1,149 @@ +#ifndef VIENNA_RNA_PACKAGE_PART_FUNC_UP_H +#define VIENNA_RNA_PACKAGE_PART_FUNC_UP_H + +#include + +#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 +#include +#include +#include +#include + +#ifdef WITH_GSL +#include +#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*)¶meters; + + 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); +} + diff --git a/C/ViennaRNA/perturbation_fold.h b/C/ViennaRNA/perturbation_fold.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/perturbation_fold.h @@ -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 diff --git a/C/ViennaRNA/plex.c b/C/ViennaRNA/plex.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plex.c @@ -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 +#include +#include +#include +#include +#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= 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 (ldangle3[type2][SS2[l+1]]; + *** Replaced by the line below + **/ + E+=E_ExtLoop(type2, (k>1) ? SS1[k-1] : -1, (l 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 (idangle3[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 (i1) 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; istack[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_min11 ) 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 (jdangle3[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, (jDuplexInit+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 (jtemperature - 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 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 (jdangle3[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, (j0 && 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 (idangle3[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, (i1 ) 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, (j1) E -= P->dangle5[type][SS1[i-1]]+extension_cost; + *** if (jdangle3[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 (jtemperature - 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; iDuplexInit + 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_min11 ) 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 (jdangle3[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, (jDuplexInit+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 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 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\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); +} diff --git a/C/ViennaRNA/plex.h b/C/ViennaRNA/plex.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plex.h @@ -0,0 +1,80 @@ +#ifndef VIENNA_RNA_PACKAGE_PLEX_H +#define VIENNA_RNA_PACKAGE_PLEX_H + +#include + + +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 diff --git a/C/ViennaRNA/plex_functions.c b/C/ViennaRNA/plex_functions.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plex_functions.c @@ -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 +#include +#include +#include +#include +#include + +#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 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;kDuplexInit; + 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; ji_pos_begin; k--) { + for (l=j+1; li_pos_begin+1)? SS1[k-1]:-1),((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, ((kj-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; kn) continue; + type = pair[S1[i]][S1[j]]; + while ((i>=1)&&(j<=n)) { + if ((i>1)&&(j +#include +#include +#include +#include +#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 (lengthi) { + /* 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') 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 (lengthi) { + /* 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 +#include +#include +#include "ViennaRNA/utils.h" +#include "ViennaRNA/plot_layouts.h" + +#ifdef _OPENMP +#include +#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; +} diff --git a/C/ViennaRNA/plot_layouts.h b/C/ViennaRNA/plot_layouts.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plot_layouts.h @@ -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 +#include + +#ifndef PI +#define PI 3.141592654 +#endif +#define PIHALF PI/2. + + +/** + * @brief Definition of Plot type simple + * + * This is the plot type definition for several RNA structure plotting functions telling + * them to use Simple 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 Naview + * + * This is the plot type definition for several RNA structure plotting functions telling + * them to use Naview 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 Circular + * + * This is the plot type definition for several RNA structure plotting functions telling + * them to produce a Circular plot + * + * @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 Simple way + * + * @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 Circular Plot + * + * 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 R2 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 diff --git a/C/ViennaRNA/plot_structure.c b/C/ViennaRNA/plot_structure.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plot_structure.c @@ -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 +#include +#include +#include +#include +#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 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 (ii) + 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; ki) + 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;ipair_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 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 (ii) + 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;i0) { + 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, + "\n" + "\n"); + fprintf(xyplot, + "\n"); + fprintf(xyplot, + " \n" + " \n", + SIZE/size, SIZE/size, (size-xmin-xmax)/2, (size-ymin-ymax)/2); + + fprintf(xyplot, + " \n"); + + fprintf(xyplot," \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, + " \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, + " \n", + i,j, X[i-1], Y[i-1], X[j-1], Y[j-1]); + } + } + fprintf(xyplot, " \n"); + fprintf(xyplot, " \n"); + for (i = 0; i < length; i++) + fprintf(xyplot, " %c\n", X[i], Y[i], string[i]); + fprintf(xyplot, " \n"); + fprintf(xyplot, " \n"); + fprintf(xyplot, "\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 + diff --git a/C/ViennaRNA/plot_structure.h b/C/ViennaRNA/plot_structure.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/plot_structure.h @@ -0,0 +1,168 @@ +#ifndef VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H +#define VIENNA_RNA_PACKAGE_PLOT_STRUCTURE_H + +#include +#include + +#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 diff --git a/C/ViennaRNA/profiledist.h b/C/ViennaRNA/profiledist.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/profiledist.h @@ -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 + +/** \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 diff --git a/C/ViennaRNA/read_epars.c b/C/ViennaRNA/read_epars.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/read_epars.c @@ -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 +#include +#include +#include +#include +#include +#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 +#include +#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; jmaximum) 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; +} + diff --git a/C/ViennaRNA/ribo.h b/C/ViennaRNA/ribo.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/ribo.h @@ -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 diff --git a/C/ViennaRNA/snofold.c b/C/ViennaRNA/snofold.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/snofold.c @@ -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 +#include +#include +#include +#include +#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) = 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; in_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=1)&&(j<=n)) { + if ((i>1)&&(j0) ? 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; sTURN?(j-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=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 max_asymm) continue; + for (energy = s=0; s> 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; ssstack[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= minq; q--) { + for (ss=energy=0; ssMLclosing+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 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> 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= 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)||(qMLclosing+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; sn) continue; + type = pair[S[i]][S[j]]; + while ((i>=1)&&(j<=n)) { + if ((i>1)&&(j + +/* 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 diff --git a/C/ViennaRNA/snoop.c b/C/ViennaRNA/snoop.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/snoop.c @@ -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 +#include +#include +#include +#include +#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; smin_d1; j--) { + int type4, k,l,psc,psc2,psc3; + for (s=0; s=MINPSCORE) ? (n_seq*P->DuplexInit) : INF; + if (psc 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 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; s0 && (i-k)2*MAXLOOP_L-2) break; + if (abs(i-k-l+j) >= ASS ) continue; + for (E=s=0; sdangle3[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 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; s6 ) 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 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; s1; i--){ + for (j=1; j<=n2; j++) { + int ii,jj, Ed,psc,skip; + for (s=0; sdangle3[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] 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; s1) ? Sali2[s][j-1] : -1, (idangle3[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; s0 && (i-k)2*MAXLOOP_L-2) break; + if (abs(i-k-l+j) >= ASS) continue; + for (s=LE=0; s 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; sMINPSCORE /*&& 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; s2*MAXLOOP_L-2) break; + if (abs(i-k-l+j) >= ASS) continue; + for (s=LE=0; s1) ? Sali1[s][i-1] : -1, (j1) {E -= P->dangle5[type[s]][Sali1[s][i-1]]; *Duplex_El +=P->dangle5[type[s]][Sali1[s][i-1]];} + *** if (jdangle3[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=j0 && k<=j){ */ + /* struct_const[k-1]='x'; */ + /* } */ + /* else{ */ + /* if(kj) {struct_const[k-1]='>';} */ + /* } */ + } + + /* char duplexseq_1[j0+1]; */ + /* char duplexseq_2[n2-j+3]; */ + if(jtemperature - 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, (j1) lc[idx][j] += P->dangle5[type][SS1[i-1]]; + *** if (jdangle3[type][SS2[j+1]]; + *** if (type>2) lc[idx][j] += P->TerminalAU; + **/ + + if(j1){ + 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(j2){ + 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(j3){ + 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=min_colonne){ + max=min_colonne; + max_pos=i; + } + min_colonne=INF; + } + + free(S1); free(S2); free(SS1); free(SS2); + if(maxtemperature - 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(j1){ */ + /* 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(j2){ */ + /* 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(j3){ */ + /* 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(maxdistance;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)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 (idangle3[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 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_min1 ) 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)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 (idangle3[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 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 (idangle3[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, (ithresh) 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] 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 (idangle3[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, (ithresh) 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] 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 (idangle3[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, (i0 && 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)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)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, (j1) {E -= P->dangle5[type][SS1[i-1]]; *Duplex_El +=P->dangle5[type][SS1[i-1]];} + *** if (jdangle3[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=j0 && k<=j){ */ + /* struct_const[k-1]='x'; */ + /* } */ + /* else{ */ + /* if(kj) {struct_const[k-1]='>';} */ + /* } */ + } + char duplexseq_1[j0]; + char duplexseq_2[n2-j+2]; + if(jtemperature - 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(j1){ */ + /* 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(maxdistance;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 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 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)=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)=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 (jdangle3[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(kj) {struct_const[k-1]='>';} */ + /* } */ + } + char duplexseq_1[j]; + char duplexseq_2[n2-j0+2]; + if(j00 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; sn_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; +} + + + diff --git a/C/ViennaRNA/snoop.h b/C/ViennaRNA/snoop.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/snoop.h @@ -0,0 +1,284 @@ +#ifndef VIENNA_RNA_PACKAGE_SNOOP_H +#define VIENNA_RNA_PACKAGE_SNOOP_H + +#include +/** +*** 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 diff --git a/C/ViennaRNA/string_utils.c b/C/ViennaRNA/string_utils.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/string_utils.c @@ -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 +#include +#include +#include +#include +#include +#include +#include +#include + +#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 diff --git a/C/ViennaRNA/string_utils.h b/C/ViennaRNA/string_utils.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/string_utils.h @@ -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 +#include + +/** + * @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 +#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 T and t with U and u, 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 diff --git a/C/ViennaRNA/stringdist.c b/C/ViennaRNA/stringdist.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/stringdist.c @@ -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 +#include +#include +#include +#include +#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; i0) { + 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=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 + + +/** + * \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 diff --git a/C/ViennaRNA/structure_utils.c b/C/ViennaRNA/structure_utils.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/structure_utils.c @@ -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 +#include +#include +#include + +#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=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]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= 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 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; ii != 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; ii != 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 diff --git a/C/ViennaRNA/structure_utils.h b/C/ViennaRNA/structure_utils.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/structure_utils.h @@ -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 + +#include + +/** + * @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 +#include +#include +#include +#include +#include +#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 +#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; istructure[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; kup_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= 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= 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; kMLclosing; + 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; lMLclosing <= 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 = (jnopush){ + 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 (minqup_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)||(qenergy_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!----------------------------------------------------*/ +/*---------------------------------------------------------------------------*/ diff --git a/C/ViennaRNA/subopt.h b/C/ViennaRNA/subopt.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/subopt.h @@ -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 +#include + + +/** + * @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 all 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 all 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 diff --git a/C/ViennaRNA/svm_utils.c b/C/ViennaRNA/svm_utils.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/svm_utils.c @@ -0,0 +1,478 @@ + +#ifdef HAVE_CONFIG_H +#include "config.h" +#endif + +#include +#include +#include +#include +#include + +#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;jrho[j]); + } + } else + + if (strcmp(key,"nr_sv")==0){ + int n = model->nr_class; + model->nSV = (int*)vrna_alloc(sizeof(int)*n); + for(j=0;jnSV[j]); + } + } else + + if (strcmp(key,"label")==0){ + int n = model->nr_class; + model->label = (int*)vrna_alloc(sizeof(int)*n); + for(j=0;jlabel[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;jprobA[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;jprobB[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;isv_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;iSV[i] = &x_space[j]; + k=0; + while ((field=fields[k])!=NULL){ + if (ksv_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 +#include +#include +#include +#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; k8*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); +} + +/*---------------------------------------------------------------------------*/ diff --git a/C/ViennaRNA/treedist.h b/C/ViennaRNA/treedist.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/treedist.h @@ -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 + +/** + * \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 diff --git a/C/ViennaRNA/unstructured_domains.c b/C/ViennaRNA/unstructured_domains.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/unstructured_domains.c @@ -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 +#include +#include +#include +#include +#include + +#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; +} diff --git a/C/ViennaRNA/unstructured_domains.h b/C/ViennaRNA/unstructured_domains.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/unstructured_domains.h @@ -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 + +/** + * @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 diff --git a/C/ViennaRNA/utils.c b/C/ViennaRNA/utils.c new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/utils.c @@ -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 +#include +#include +#include +#include +#include +#include +#include +#include +#include + +/* for getpid() we need some distinction between UNIX and Win systems */ +#ifdef _WIN32 +#include +#define getpid() GetCurrentProcessId() /* rename windows specific getpid function */ +#else +#include +#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 */ + +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 diff --git a/C/ViennaRNA/utils.h b/C/ViennaRNA/utils.h new file mode 100644 --- /dev/null +++ b/C/ViennaRNA/utils.h @@ -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 +#include + +#include +#include +#include +#include +#include + +/* 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 ERROR: 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 ERROR: 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 WARNING: 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 WARNING: 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 diff --git a/C/ffiwrap_centroid.c b/C/ffiwrap_centroid.c new file mode 100644 --- /dev/null +++ b/C/ffiwrap_centroid.c @@ -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 +#include +#include + +#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; +} + diff --git a/C/ffiwrap_fold.c b/C/ffiwrap_fold.c new file mode 100644 --- /dev/null +++ b/C/ffiwrap_fold.c @@ -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 + +#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; +} + + diff --git a/C/ffiwrap_part_func.c b/C/ffiwrap_part_func.c new file mode 100644 --- /dev/null +++ b/C/ffiwrap_part_func.c @@ -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 + +#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; +} + diff --git a/README.md b/README.md new file mode 100644 --- /dev/null +++ b/README.md @@ -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/ + diff --git a/ViennaRNA-bindings.cabal b/ViennaRNA-bindings.cabal --- a/ViennaRNA-bindings.cabal +++ b/ViennaRNA-bindings.cabal @@ -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 + @ + . + -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 - @ - . - + 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 diff --git a/cbits/circfold.inc b/cbits/circfold.inc deleted file mode 100644 --- a/cbits/circfold.inc +++ /dev/null @@ -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 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_cMAXLOOP) break; - qmin = u1+i-1+length-MAXLOOP; - if (qminMAXLOOP) 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_cMLclosing; - if (fmMLclosing; - if (fmMLclosing; - if (fmMLclosing; - if (fmMLclosing; - if (fm0)?Md5i:-Md5i; - sector[(*bt)].ml = 2; - i = (Md5i>0)?Md5i+1 : -Md5i+2; /* let's backtrack fm_d5[Md5i+1] */ - for (u=i+TURN; u0)?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 */ -/* - minimum free energy - RNA secondary structure prediction - - c Ivo Hofacker, Chrisoph Flamm - original implementation by - Walter Fontana - - Vienna RNA package -*/ - -#include -#include -#include -#include -#include -#include -#include - -#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 -#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) */ -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 = 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 (minqi+1)||(q= 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, (jMLbase); - } - } - 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; k0)? (cut_point):(j-2-TURN); - /* additional ML decomposition as two coaxially stacked helices */ - for (decomp = INF, k = i+1+TURN; kstack[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 (i0) { - 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=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[i1 && 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(kMLbase == 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, (jMLbase + 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= 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)||(qMLclosing; - 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> 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 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; kn) continue; - type = pair[S[i]][S[j]]; - while ((i>=1)&&(j<=n)) { - if ((i>1)&&(jj]+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 (exj]+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=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; plength) 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 - -#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; -} - diff --git a/cbits/fold.c b/cbits/fold.c deleted file mode 100644 --- a/cbits/fold.c +++ /dev/null @@ -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 -#include -#include -#include -#include -#include -#include - -#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 -#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) = 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= 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 (minqi+1)||(qMLbase); - 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 = ((jMLbase); - 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; j1; 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=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= 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)||(qMLclosing - 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 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 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 (d3dangle3[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 (d50) - 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 (pq)) 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 (p0) - 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)) && (q1) && !pair_table[p-1]) ? S1[p-1] : -1; - mm3 = ((SAME_STRAND(q,q+1)) && (qmodel_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]]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+dang5MLclosing; - /* 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=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 ij) 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; kn) continue; - type = pair[S[i]][S[j]]; - while ((i>=1)&&(j<=n)) { - if ((i>1)&&(ji){ - (*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]]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+dang56) ) - 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); -} - diff --git a/cbits/fold_vars.c b/cbits/fold_vars.c deleted file mode 100644 --- a/cbits/fold_vars.c +++ /dev/null @@ -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
-*** Also there are some functions that make the live easier when -*** using functions of the Vienna RNA package -**/ -#include -#include -#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; - } -} diff --git a/cbits/gquad.c b/cbits/gquad.c deleted file mode 100644 --- a/cbits/gquad.c +++ /dev/null @@ -1,1043 +0,0 @@ -/* - gquad.c - - Ronny Lorenz 2012 - - Vienna RNA package -*/ - -#include -#include -#include -#include - -#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;in-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;i0.) { - 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= (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); - } - } - } - } -} - diff --git a/cbits/params.c b/cbits/params.c deleted file mode 100644 --- a/cbits/params.c +++ /dev/null @@ -1,751 +0,0 @@ -/* - - c Ivo Hofacker - - Vienna RNA package -*/ -#include -#include -#include -#include -#include -#include "energy_par.h" -#include "fold_vars.h" -#include "utils.h" -#include "params.h" -/** -*** \file params.c -***

-*** This file provides functions that return temperature scaled energy parameters and -*** Boltzmann weights packed in datastructures -***

-***/ - -/*@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)Tetraloop_E[i] = TetraloopdH[i] - (TetraloopdH[i]-Tetraloop37[i])*tempf; - for (i=0; (i*5)Triloop_E[i] = TriloopdH[i] - (TriloopdH[i]-Triloop37[i])*tempf; - for (i=0; (i*9)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
-*** specific heat needs smooth function (2nd derivative)
-*** we use a*(sin(x+b)+1)^2, with a=2/(3*sqrt(3)), b=Pi/6-sqrt(3)/2, -*** in the interval b0.8660254)?(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)exptetra[i] = exp( -GT*10./kT); - } - for (i=0; (i*5)exptri[i] = exp( -GT*10./kT); - } - for (i=0; (i*9)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)exptetra[i] = exp( -GT*10./kTn); - } - for (i=0; (i*5)exptri[i] = exp( -GT*10./kTn); - } - for (i=0; (i*9)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)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 -} diff --git a/cbits/part_func.c b/cbits/part_func.c deleted file mode 100644 --- a/cbits/part_func.c +++ /dev/null @@ -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 -#include -#include -#include -#include -#include /* #defines FLT_MAX ... */ -#include - -#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 -#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); l1) || circular) ? S1[i-1] : -1, ((ji; 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, ((jQmax) { - 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; kMAXLOOP) break; - lstart = ln1+p-1+n-MAXLOOP; - if(lstart 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; kexpMLclosing; - 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(lstartMAXLOOP) 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(lstartMAXLOOP) 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) && (j0.)) { - probs[ij] = q1k[i-1]*qln[j+1]/q1k[n]; - probs[ij] *= exp_E_ExtLoop(type, (i>1) ? S1[i-1] : -1, (jTURN+1; l--) { - - /* 2. bonding k,l as substem of 2:loop enclosed by i,j */ - for (k=1; k0.)) { - /* 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 (ll+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, (l1) ? S1[k-1] : -1, (lQmax) { - 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; imodel_details.noLP; - - n=S[0]; - for (k=1; kn) continue; - type = pair[S[i]][S[j]]; - while ((i>=1)&&(j<=n)) { - if ((i>1)&&(j 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 (j1) ? S1[i-1] : -1, (j 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 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 (ur){ 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 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; kr){ 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) break; - } - if(k>j) nrerror("backtrack failed in qm"); - - backtrack_qm1(k,j); - - if(k= r) break; /* no more pairs */ - j = k-1; - } -} - -PRIVATE void backtrack_qm1(int i,int j){ - /* i is paired to l, i=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 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 r) break; - } - if (qbt1 > r) break; - } - if (l=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; ii != 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 - = \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; i0.5) { - /* 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 = \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; i0; 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 - = \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; i0.5) { - 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; icutoff) { - 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 */ - /* = \sum_{a,b} p_a p_b d(S_a,S_b) - this can be computed from the pair probs p_ij as - = \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 - = \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; i0.5) { - 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 */ - /* = \sum_{a,b} p_a p_b d(S_a,S_b) - this can be computed from the pair probs p_ij as - = \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 */ -} - - diff --git a/cbits/part_func_co.c b/cbits/part_func_co.c deleted file mode 100644 --- a/cbits/part_func_co.c +++ /dev/null @@ -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 -#include -#include -#include -#include -#include /* #defines FLT_MAX ... */ -#include - -#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 -#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_point2)||(((I)>=cut_point)&&((J)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); lcut_point) temp*=scale[1]; - if (i1) ? S1[i-1] : -1, (j1)&&(SAME_STRAND(i-1,i))) ? S1[i-1] : -1, ((jQmax) { - 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, ((jTURN+1; l--) { - - /* 2. bonding k,l as substem of 2:loop enclosed by i,j */ - for (k=1; k0)) { - 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 ((l1)&&SAME_STRAND(k-1,k)) ? S1[k-1] : -1, - ((lQmax) { - 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 (ll; t--) { - for (k=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; t1) ? S1[k-1] : -1, (l<(cut_point-1)) ? S1[l+1] : -1, pf_params); - if (l+10) 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=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 r) break; - } - if (qbt1 > r) break; - } - if (l=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) break; - } - if (k>j) nrerror("backtrack failed in qm"); - - backtrack_qm1(k,j); - - if (k= 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??*/ - 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 */ } diff --git a/cbits/utils.c b/cbits/utils.c deleted file mode 100644 --- a/cbits/utils.c +++ /dev/null @@ -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 -#include -#include -#include -#include -#include -#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=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]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 : 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>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': /* 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': /* 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= 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; -} diff --git a/changelog b/changelog deleted file mode 100644 --- a/changelog +++ /dev/null @@ -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 diff --git a/changelog.md b/changelog.md new file mode 100644 --- /dev/null +++ b/changelog.md @@ -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 + diff --git a/include/1.8.4_epars.h b/include/1.8.4_epars.h deleted file mode 100644 --- a/include/1.8.4_epars.h +++ /dev/null @@ -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 diff --git a/include/1.8.4_intloops.h b/include/1.8.4_intloops.h deleted file mode 100644 --- a/include/1.8.4_intloops.h +++ /dev/null @@ -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, -958,-1278},{ -479, -948,-1308, -988,-1308},{ -429, -898,-1258, -938,-1258},{ -329, -798,-1158, -838,-1158}}, -/* GC.C..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.G..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.U..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.. @ */ -{{ -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.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.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}} -} -}, -{ /* 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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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}}, -/* GU.G..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},{ -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 */ -{{ 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.C..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.G..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.U..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.. @ */ -{{ -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.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.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}} -} -}, -{ /* 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 */ -{{ 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, -978,-1048,-1218,-1068},{ -389,-1058,-1128,-1298,-1148},{ -379,-1048,-1118,-1288,-1138}}, -/* UG.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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.U..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.. @ */ -{{ -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.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.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}} -} -}, -{ /* 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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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}}, -/* AU.U..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 */ -{{ 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.C..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},{ -649, -938,-1288,-1288,-1288},{ -289, -578, -928, -928, -928},{ -739,-1028,-1378,-1378,-1378},{ -379, -668,-1018,-1018,-1018}}, -/* AU.U..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}} -}, -{ -/* AU.@..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}}, -/* AU.A..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}}, -/* AU.C..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}}, -/* AU.G..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}}, -/* AU.U..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.. @ */ -{{ -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.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.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}} -} -}, -{ /* 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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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.U..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 */ -{{ 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.C..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},{ -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},{ -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 */ -{{ 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.C..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.G..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.U..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.. @ */ -{{ -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, 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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}}, -{{ 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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, 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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, 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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, 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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, 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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}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}} -}, -{ -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340},{ 340, 340, 340, 340, 340}}, -{{ 340, 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, -668}, -{ -309, -518, -498, -498, -498}, -{ -389, -598, -578, -578, -578}, -{ -379, -588, -568, -568, -568}}, -/* GU.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}}, -/* GU.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}}, -/* GU.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}}}, -/* GU.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}}, -/* GU.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}}, -/* 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, -818,-1168,-1168,-1168}, -{ -859,-1148,-1498,-1498,-1498}, -{ -489, -778,-1128,-1128,-1128}}, -/* AU.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}}, -/* AU.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}}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* 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}, -{ -739,-1028,-1378,-1378,-1378}, -{ -379, -668,-1018,-1018,-1018}}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}}}, -/* AU.@@..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}}, -/* 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, -479, -649, -649, -649}, -{ -100, -479, -649, -649, -649}, -{ -100, -479, -649, -649, -649}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}, -/* AU.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}}}, -/* AU.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}}, -/* AU.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}}, -/* 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}}}}}}; - - diff --git a/include/PS_dot.h b/include/PS_dot.h deleted file mode 100644 --- a/include/PS_dot.h +++ /dev/null @@ -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 diff --git a/include/aln_util.h b/include/aln_util.h deleted file mode 100644 --- a/include/aln_util.h +++ /dev/null @@ -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 diff --git a/include/cofold.h b/include/cofold.h deleted file mode 100644 --- a/include/cofold.h +++ /dev/null @@ -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 RNAcofold 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 RNAlib 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 diff --git a/include/config.h b/include/config.h deleted file mode 100644 --- a/include/config.h +++ /dev/null @@ -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 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 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 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 header file. */ -#define HAVE_MALLOC_H 1 - -/* Define to 1 if you have the 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 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 header file. */ -#define HAVE_STDINT_H 1 - -/* Define to 1 if you have the 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 header file. */ -#define HAVE_STRINGS_H 1 - -/* Define to 1 if you have the 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 header file. */ -#define HAVE_SYS_STAT_H 1 - -/* Define to 1 if you have the header file. */ -#define HAVE_SYS_TYPES_H 1 - -/* Define to 1 if you have the 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 does not define. */ -/* #undef size_t */ diff --git a/include/data_structures.h b/include/data_structures.h deleted file mode 100644 --- a/include/data_structures.h +++ /dev/null @@ -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 (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 diff --git a/include/energy_const.h b/include/energy_const.h deleted file mode 100644 --- a/include/energy_const.h +++ /dev/null @@ -1,33 +0,0 @@ -#ifndef __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__ -#define __VIENNA_RNA_PACKAGE_ENERGY_CONST_H__ - -#include - -/** - * \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 diff --git a/include/energy_par.h b/include/energy_par.h deleted file mode 100644 --- a/include/energy_par.h +++ /dev/null @@ -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 diff --git a/include/fold.h b/include/fold.h deleted file mode 100644 --- a/include/fold.h +++ /dev/null @@ -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 diff --git a/include/fold_vars.h b/include/fold_vars.h deleted file mode 100644 --- a/include/fold_vars.h +++ /dev/null @@ -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 diff --git a/include/gquad.h b/include/gquad.h deleted file mode 100644 --- a/include/gquad.h +++ /dev/null @@ -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 diff --git a/include/intl11.h b/include/intl11.h deleted file mode 100644 --- a/include/intl11.h +++ /dev/null @@ -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} - } - }}; diff --git a/include/intl11dH.h b/include/intl11dH.h deleted file mode 100644 --- a/include/intl11dH.h +++ /dev/null @@ -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} - } - }}; diff --git a/include/intl21.h b/include/intl21.h deleted file mode 100644 --- a/include/intl21.h +++ /dev/null @@ -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} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - } -,{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 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, 110, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - } - ,{{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 150, 150, 150, 150, 150} - } - } - ,{{{ 250, 250, 250, 230, 230} - ,{ 250, 250, 230, 230, 230} - ,{ 250, 230, 250, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 250, 250, 230, 230, 230} - } - ,{{ 250, 250, 230, 110, 230} - ,{ 250, 250, 230, 110, 230} - ,{ 230, 230, 170, 110, 230} - ,{ 110, 80, 110, 110, 110} - ,{ 230, 230, 230, 110, 230} - } - ,{{ 250, 250, 250, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 250, 230, 250, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 250, 250, 230, 230, 230} - } - ,{{ 230, 170, 230, 110, 230} - ,{ 230, 170, 230, 80, 230} - ,{ 230, 110, 230, 110, 230} - ,{ 120, 120, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - } - ,{{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 220, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 170, 150, 170, 150, 140} - } - } - ,{{{ 300, 300, 300, 300, 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} - } - } - ,{{{ 300, 300, 300, 300, 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} - } - } - ,{{{ 300, 300, 300, 300, 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} - } - } - } -,{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ 250, 250, 230, 230, 230} - ,{ 250, 250, 230, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 230, 230, 230, 230, 230} - } - ,{{ 250, 250, 230, 230, 230} - ,{ 250, 250, 230, 210, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 120, 120, 110, 110, 110} - ,{ 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, 190, 230, 230} - } - ,{{ 230, 110, 230, 110, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - } - ,{{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 150, 150, 150, 150, 150} - } - } - ,{{{ 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, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 230, 230, 230, 230, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 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, 230, 230} - } - ,{{ 230, 110, 230, 110, 230} - ,{ 230, 110, 230, 110, 230} - ,{ 230, 110, 230, 110, 230} - ,{ 110, 110, 110, 110, 110} - ,{ 230, 110, 230, 110, 230} - } - ,{{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 230, 150} - ,{ 230, 230, 230, 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, 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, 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} - } - } - ,{{{ 300, 300, 300, 300, 300} - ,{ 300, 300, 300, 300, 300} - ,{ 300, 300, 300, 300, 300} - ,{ 300, 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} - } - } - }}; diff --git a/include/intl21dH.h b/include/intl21dH.h deleted file mode 100644 --- a/include/intl21dH.h +++ /dev/null @@ -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} - 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} - ,{{ 850, 850, 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} - 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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, 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} - 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} - } - ,{{{ 850, 850, 850, 850, 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} - 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,{ 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} - } - } - }}; diff --git a/include/intl22.h b/include/intl22.h deleted file mode 100644 --- a/include/intl22.h +++ /dev/null @@ -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} - 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,{ 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} - ,{ 150, 20, 150, -40, 150} - } - ,{{ 200, 90, 200, 20, 200} - ,{ 200, 60, 200, 10, 200} - ,{ 170, 90, 170, -20, 170} - ,{ 200, 60, 200, 10, 200} - ,{ 80, -50, 80, 20, 80} - } - } - ,{{{ 170, 150, 170, 150, 100} - ,{ 170, 150, 170, 150, 100} - ,{ 150, 140, 150, 140, 60} - ,{ 170, 150, 170, 150, 80} - ,{ 140, 120, 140, 120, 50} - } - ,{{ 130, 110, 130, 110, 100} - ,{ 130, 110, 130, 110, 100} - ,{ 120, 110, 120, 110, 30} - ,{ 90, 20, 90, 20, -50} - ,{ 120, 110, 120, 110, 30} - } - ,{{ 170, 150, 170, 150, 80} - ,{ 170, 150, 170, 150, 80} - ,{ 150, 140, 150, 140, 60} - ,{ 170, 150, 170, 150, 80} - ,{ 140, 120, 140, 120, 50} - } - ,{{ 120, 110, 120, 110, 30} - ,{ 90, 20, 90, 20, -50} - ,{ 120, 110, 120, 110, 30} - ,{ 20, -40, -20, -40, 20} - ,{ 120, 110, 120, 110, 30} - } - ,{{ 170, 150, 170, 150, 80} - ,{ 170, 150, 170, 150, 80} - ,{ 140, 120, 140, 120, 50} - ,{ 170, 150, 170, 150, 80} - ,{ 50, 30, 50, 30, -40} - } - } - } - ,{{{{ 220, 150, 220, 140, 170} - ,{ 220, 130, 220, 130, 170} - ,{ 150, 110, 150, 110, 150} - ,{ 140, 100, 140, 100, 140} - ,{ 170, 150, 150, 140, 170} - } - ,{{ 220, 130, 220, 130, 170} - ,{ 220, 130, 220, 130, 170} - ,{ 150, 110, 150, 100, 150} - ,{ 70, -30, 70, -70, 50} - ,{ 150, 110, 150, 100, 150} - } - ,{{ 190, 110, 190, 100, 170} - ,{ 190, 110, 190, 100, 140} - ,{ 150, 110, 150, 100, 150} - ,{ 140, 100, 140, 100, 140} - ,{ 170, 110, 150, 100, 170} - } - ,{{ 150, 110, 150, 100, 150} - ,{ 140, 70, 70, -10, 140} - ,{ 150, 110, 150, 100, 150} - ,{ 80, -30, 10, 80, 70} - ,{ 150, 110, 150, 100, 150} - } - ,{{ 150, 150, 150, 140, 150} - ,{ 140, 100, 140, 100, 140} - ,{ 150, 110, 150, 110, 150} - ,{ 140, 100, 140, 100, 140} - ,{ 150, 150, 70, 140, 70} - } - } - ,{{{ 170, 150, 150, 90, 170} - ,{ 170, 130, 140, 10, 170} - ,{ 150, 110, 150, 80, 150} - ,{ 140, 100, 140, 10, 140} - ,{ 150, 150, 150, 90, 150} - } - ,{{ 170, 130, 150, 10, 170} - ,{ 170, 130, 60, 0, 170} - ,{ 150, 110, 150, -70, 150} - ,{ 10, -30, 10, -160, -30} - ,{ 150, 110, 150, 10, 150} - } - ,{{ 150, 110, 150, 70, 150} - ,{ 140, 100, 50, -100, 140} - ,{ 150, 110, 150, -60, 150} - ,{ 140, 100, 140, 10, 140} - ,{ 150, 110, 150, 70, 150} - } - ,{{ 150, 110, 150, 10, 150} - ,{ 40, 40, 30, -70, 30} - ,{ 150, 110, 150, 10, 150} - ,{ 10, -30, -30, 0, 10} - ,{ 150, 110, 150, 10, 150} - } - ,{{ 150, 150, 150, 90, 150} - ,{ 140, 100, 140, 10, 140} - ,{ 150, 110, 150, 80, 150} - ,{ 140, 100, 140, 10, 140} - ,{ 150, 150, 0, 90, 70} - } - } - ,{{{ 220, 130, 220, 130, 170} - ,{ 220, 130, 220, 130, 140} - ,{ 140, 110, 140, 110, 120} - ,{ 130, 100, 130, 100, 110} - ,{ 170, 100, 130, 100, 170} - } - ,{{ 220, 130, 220, 130, 140} - ,{ 220, 130, 220, 130, 140} - ,{ 130, 100, 130, 100, 120} - ,{ 70, -70, 70, -70, 0} - ,{ 130, 100, 130, 100, 120} - } - ,{{ 190, 110, 190, 100, 170} - ,{ 190, 110, 190, 100, 110} - ,{ 130, 100, 130, 100, 120} - ,{ 130, 100, 130, 100, 110} - ,{ 170, 100, 130, 100, 170} - } - ,{{ 130, 100, 130, 100, 120} - ,{ 70, 70, 70, -10, 60} - ,{ 130, 100, 130, 100, 120} - ,{ 20, -40, -10, -40, 20} - ,{ 130, 100, 130, 100, 120} - } - ,{{ 140, 110, 140, 110, 120} - ,{ 130, 100, 130, 100, 110} - ,{ 140, 110, 140, 110, 120} - ,{ 130, 100, 130, 100, 110} - ,{ 30, -20, -10, 30, 20} - } - } - ,{{{ 170, 90, 170, 140, 170} - ,{ 170, 70, 170, -10, 170} - ,{ 150, 80, 150, -40, 150} - ,{ 140, 10, 140, 80, 140} - ,{ 150, 90, 150, 140, 150} - } - ,{{ 170, 10, 170, -10, 170} - ,{ 170, -20, 170, -10, 170} - ,{ 150, -40, 150, -40, 150} - ,{ -30, -170, -30, -90, -30} - ,{ 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, 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} - ,{ 270, 230, 270, 130, 270} - ,{ 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} - } - } - ,{{{ 310, 260, 310, 260, 300} - ,{ 310, 260, 310, 260, 300} - ,{ 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} - } - ,{{ 310, 220, 310, 220, 300} - ,{ 310, 220, 310, 220, 300} - ,{ 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, 210, 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} - ,{ 270, 130, 270, 210, 270} - ,{ 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} - } - } - ,{{{ 300, 260, 300, 260, 240} - ,{ 300, 260, 300, 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} - } - ,{{ 300, 220, 300, 220, 150} - ,{ 300, 220, 300, 220, 150} - ,{ 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} - } - } - } - } -,{{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 190, 150, 150} - ,{ 170, 170, 150, 150, 150} - ,{ 220, 220, 190, 130, 140} - ,{ 170, 170, 150, 150, 150} - ,{ 140, 140, 120, 140, 120} - } - ,{{ 150, 130, 110, 110, 150} - ,{ 150, 130, 110, 110, 150} - ,{ 130, 130, 110, 100, 110} - ,{ 90, 10, 70, 10, 90} - ,{ 130, 130, 100, 100, 110} - } - ,{{ 220, 220, 190, 150, 150} - ,{ 150, 150, 150, 150, 150} - ,{ 220, 220, 190, 130, 140} - ,{ 170, 170, 150, 150, 150} - ,{ 140, 140, 120, 120, 120} - } - ,{{ 140, 130, 100, 100, 140} - ,{ 90, 10, 70, 10, 90} - ,{ 130, 130, 100, 100, 110} - ,{ 140, -10, 20, 80, 140} - ,{ 130, 130, 100, 100, 110} - } - ,{{ 170, 170, 170, 150, 150} - ,{ 170, 170, 150, 150, 150} - ,{ 170, 140, 170, 120, 120} - ,{ 170, 170, 150, 150, 150} - ,{ 140, 140, 30, 140, 30} - } - } - ,{{{ 220, 220, 190, 140, 140} - ,{ 170, 170, 140, 40, 140} - ,{ 220, 220, 190, 70, 130} - ,{ 170, 170, 140, 30, 140} - ,{ 140, 140, 110, 140, 110} - } - ,{{ 130, 130, 110, 70, 100} - ,{ 130, 130, 100, 40, 100} - ,{ 130, 130, 110, 70, 100} - ,{ 70, -20, 70, -50, 10} - ,{ 130, 130, 100, -10, 100} - } - ,{{ 220, 220, 190, 70, 140} - ,{ 140, 60, 50, 30, 140} - ,{ 220, 220, 190, 70, 130} - ,{ 170, 170, 140, 30, 140} - ,{ 140, 140, 110, 50, 110} - } - ,{{ 130, 130, 100, -10, 100} - ,{ 10, 0, -100, -70, 10} - ,{ 130, 130, 100, -10, 100} - ,{ -10, -10, -50, -30, -50} - ,{ 130, 130, 100, -10, 100} - } - ,{{ 170, 170, 140, 140, 140} - ,{ 170, 170, 140, 30, 140} - ,{ 140, 140, 110, 60, 110} - ,{ 170, 170, 140, 30, 140} - ,{ 140, 140, 30, 140, 20} - } - } - ,{{{ 150, 150, 150, 150, 150} - ,{ 150, 150, 150, 150, 150} - ,{ 140, 130, 130, 130, 140} - ,{ 150, 150, 150, 150, 150} - ,{ 120, 120, 120, 120, 120} - } - ,{{ 110, 110, 110, 110, 110} - ,{ 110, 110, 110, 110, 110} - ,{ 110, 100, 100, 100, 110} - ,{ 80, -40, 70, 10, 80} - ,{ 110, 100, 100, 100, 110} - } - ,{{ 150, 150, 150, 150, 150} - ,{ 150, 150, 150, 150, 150} - ,{ 140, 130, 130, 130, 140} - ,{ 150, 150, 150, 150, 150} - ,{ 120, 120, 120, 120, 120} - } - ,{{ 110, 100, 100, 100, 110} - ,{ 80, -70, -60, 10, 80} - ,{ 110, 100, 100, 100, 110} - ,{ -40, -40, -40, -40, -50} - ,{ 110, 100, 100, 100, 110} - } - ,{{ 150, 150, 150, 150, 150} - ,{ 150, 150, 150, 150, 150} - ,{ 120, 120, 120, 120, 120} - ,{ 150, 150, 150, 150, 150} - ,{ 30, 30, 30, 30, 30} - } - } - ,{{{ 140, 70, 140, 80, 140} - ,{ 140, 10, 140, 10, 140} - ,{ 130, 70, 130, 20, 130} - ,{ 140, -30, 140, 80, 140} - ,{ 110, 50, 110, 70, 110} - } - ,{{ 100, -30, 100, -30, 100} - ,{ 100, -30, 100, -30, 100} - ,{ 100, -70, 100, -40, 100} - ,{ 10, -170, 10, -30, 10} - ,{ 100, -70, 100, -40, 100} - } - ,{{ 140, 70, 140, 10, 140} - ,{ 140, 10, 140, -30, 140} - ,{ 130, 70, 130, -10, 130} - ,{ 140, -30, 140, 10, 140} - ,{ 110, 0, 110, -60, 110} - } - ,{{ 100, -70, 100, 80, 100} - ,{ 10, -160, 10, 0, 10} - ,{ 100, -70, 100, -40, 100} - ,{ 80, -90, -50, 80, -50} - ,{ 100, -70, 100, -40, 100} - } - ,{{ 140, 50, 140, 70, 140} - ,{ 140, -30, 140, 10, 140} - ,{ 110, 0, 110, 20, 110} - ,{ 140, -30, 140, 10, 140} - ,{ 70, 50, 20, 70, 20} - } - } - ,{{{ 170, 150, 170, 150, 150} - ,{ 150, 150, 150, 150, 150} - ,{ 170, 130, 170, 130, 30} - ,{ 150, 150, 150, 150, 140} - ,{ 120, 120, 120, 120, 40} - } - ,{{ 150, 110, 110, 110, 150} - ,{ 150, 110, 110, 110, 150} - ,{ 100, 100, 100, 100, -20} - ,{ 90, 10, 70, 10, 90} - ,{ 100, 100, 100, 100, 30} - } - ,{{ 150, 150, 150, 150, 70} - ,{ 150, 150, 150, 150, 0} - ,{ 130, 130, 130, 130, -10} - ,{ 150, 150, 150, 150, 70} - ,{ 120, 120, 120, 120, 40} - } - ,{{ 140, 100, 100, 100, 140} - ,{ 90, 10, 70, 10, 90} - ,{ 100, 100, 100, 100, 30} - ,{ 140, -40, 20, -40, 140} - ,{ 100, 100, 100, 100, 30} - } - ,{{ 170, 150, 170, 150, 70} - ,{ 150, 150, 150, 150, 70} - ,{ 170, 120, 170, 120, 20} - ,{ 150, 150, 150, 150, 70} - ,{ 30, 30, 30, 30, -60} - } - } - } - ,{{{{ 150, 150, 120, 120, 130} - ,{ 150, 150, 120, 120, 130} - ,{ 130, 130, 100, 100, 110} - ,{ 120, 120, 90, 90, 100} - ,{ 120, 120, 100, 100, 100} - } - ,{{ 150, 150, 120, 120, 130} - ,{ 150, 150, 120, 120, 130} - ,{ 120, 120, 100, 100, 100} - ,{ -10, -50, -20, -80, -10} - ,{ 120, 120, 100, 100, 100} - } - ,{{ 120, 120, 100, 100, 100} - ,{ 120, 120, 90, 90, 100} - ,{ 120, 120, 100, 100, 100} - ,{ 120, 120, 90, 90, 100} - ,{ 120, 120, 100, 100, 100} - } - ,{{ 120, 120, 100, 100, 100} - ,{ 50, 10, 50, -10, 50} - ,{ 120, 120, 100, 100, 100} - ,{ 80, -20, -40, 80, 10} - ,{ 120, 120, 100, 100, 100} - } - ,{{ 130, 130, 100, 100, 110} - ,{ 120, 120, 90, 90, 100} - ,{ 130, 130, 100, 100, 110} - ,{ 120, 120, 90, 90, 100} - ,{ 110, 110, 20, 20, 30} - } - } - ,{{{ 150, 150, 120, 50, 120} - ,{ 150, 150, 120, 10, 120} - ,{ 130, 130, 100, 50, 100} - ,{ 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, 170} - ,{ 20, 10, 10, 10, 20} - ,{ 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} - ,{ 80, 80, 80, 80, 80} - } - } - ,{{{ 180, 50, 180, 130, 180} - ,{ 180, 10, 180, 120, 180} - ,{ 160, 50, 160, 30, 160} - ,{ 170, 0, 170, 130, 170} - ,{ 160, 50, 160, 70, 160} - } - ,{{ 180, 10, 180, 50, 180} - ,{ 180, 10, 180, 50, 180} - ,{ 160, -10, 160, 20, 160} - ,{ 60, -110, 60, 50, 60} - ,{ 160, -10, 160, 20, 160} - } - ,{{ 170, 50, 170, 30, 170} - ,{ 170, 0, 170, 30, 170} - ,{ 160, 50, 160, 30, 160} - ,{ 170, 0, 170, 30, 170} - ,{ 160, 50, 160, 30, 160} - } - ,{{ 160, -10, 160, 130, 160} - ,{ 130, -40, 130, 120, 130} - ,{ 160, -10, 160, 20, 160} - ,{ 130, -30, 10, 130, 10} - ,{ 160, -10, 160, 20, 160} - } - ,{{ 170, 50, 170, 70, 170} - ,{ 170, 0, 170, 30, 170} - ,{ 160, 50, 160, 30, 160} - ,{ 170, 0, 170, 30, 170} - ,{ 70, -100, 70, 70, 70} - } - } - ,{{{ 190, 190, 190, 190, 170} - ,{ 190, 190, 190, 190, 170} - ,{ 170, 170, 170, 170, 90} - ,{ 170, 170, 170, 170, 100} - ,{ 170, 170, 170, 170, 90} - } - ,{{ 190, 190, 190, 190, 170} - ,{ 190, 190, 190, 190, 170} - ,{ 160, 160, 160, 160, 90} - ,{ 120, 60, 120, 60, -10} - ,{ 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} - ,{ 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, 140} - } - ,{{ 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} - } - ,{{ 170, 170, 140, 50, 140} - ,{ 120, 120, 90, -20, 90} - ,{ 170, 170, 140, 30, 140} - ,{ 60, 60, 30, 50, 30} - ,{ 170, 170, 140, 30, 140} - } - ,{{ 210, 210, 180, 100, 180} - ,{ 210, 210, 180, 70, 180} - ,{ 180, 180, 150, 100, 150} - ,{ 210, 210, 180, 70, 180} - ,{ 190, 190, 100, -10, 100} - } - } - ,{{{ 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} - ,{ 190, 190, 190, 190, 190} - ,{ 150, 140, 140, 140, 150} - ,{ 150, 80, 140, 80, 150} - ,{ 150, 140, 140, 140, 150} - } - ,{{ 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} - } - ,{{ 160, 140, 150, 140, 160} - ,{ 160, 90, 150, 90, 160} - ,{ 150, 140, 140, 140, 150} - ,{ 40, 30, 30, 30, 40} - ,{ 150, 140, 140, 140, 150} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 190, 190, 190, 190, 190} - ,{ 160, 160, 160, 160, 160} - ,{ 190, 190, 190, 190, 190} - ,{ 110, 100, 100, 100, 110} - } - } - ,{{{ 180, 70, 180, 150, 180} - ,{ 180, 10, 180, 80, 180} - ,{ 180, 70, 180, 50, 180} - ,{ 180, 10, 180, 150, 180} - ,{ 180, 70, 180, 90, 180} - } - ,{{ 180, 10, 180, 70, 180} - ,{ 180, 10, 180, 50, 180} - ,{ 140, -30, 140, 0, 140} - ,{ 80, -90, 80, 70, 80} - ,{ 140, -30, 140, 0, 140} - } - ,{{ 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} - } - ,{{ 150, -10, 140, 150, 140} - ,{ 90, -80, 90, 80, 90} - ,{ 140, -30, 140, 0, 140} - ,{ 150, -10, 30, 150, 30} - ,{ 140, -30, 140, 0, 140} - } - ,{{ 180, 40, 180, 90, 180} - ,{ 180, 10, 180, 50, 180} - ,{ 150, 40, 150, 20, 150} - ,{ 180, 10, 180, 50, 180} - ,{ 100, -70, 100, 90, 100} - } - } - ,{{{ 190, 190, 190, 190, 170} - ,{ 190, 190, 190, 190, 170} - ,{ 190, 190, 190, 190, 110} - ,{ 190, 190, 190, 190, 110} - ,{ 190, 190, 190, 190, 110} - } - ,{{ 190, 190, 190, 190, 170} - ,{ 190, 190, 190, 190, 170} - ,{ 140, 140, 140, 140, 70} - ,{ 140, 80, 140, 80, 10} - ,{ 140, 140, 140, 140, 70} - } - ,{{ 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} - } - ,{{ 150, 140, 150, 140, 90} - ,{ 150, 90, 150, 90, 20} - ,{ 140, 140, 140, 140, 70} - ,{ 90, 30, 30, 30, 90} - ,{ 140, 140, 140, 140, 70} - } - ,{{ 190, 190, 190, 190, 110} - ,{ 190, 190, 190, 190, 110} - ,{ 160, 160, 160, 160, 80} - ,{ 190, 190, 190, 190, 110} - ,{ 100, 100, 100, 100, 30} - } - } - } - ,{{{{ 300, 300, 280, 250, 280} - ,{ 280, 280, 280, 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, 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} - ,{ 240, 240, 210, 100, 210} - ,{ 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, 140, 210} - } - } - ,{{{ 280, 250, 280, 250, 280} - ,{ 280, 250, 280, 250, 280} - ,{ 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} - } - ,{{ 280, 220, 280, 220, 280} - ,{ 280, 220, 280, 220, 280} - ,{ 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, 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} - ,{ 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, 50, 210, 210, 210} - } - } - ,{{{ 280, 250, 280, 250, 240} - ,{ 280, 250, 280, 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, 90} - ,{ 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, 220, 280, 220, 140} - ,{ 280, 220, 280, 220, 140} - ,{ 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} - } - } - } - } -,{{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 270, 270, 290} - ,{ 300, 300, 270, 270, 290} - ,{ 290, 290, 250, 270, 250} - ,{ 300, 300, 270, 270, 270} - ,{ 270, 270, 240, 260, 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} - } - ,{{ 300, 300, 270, 270, 270} - ,{ 300, 300, 270, 270, 270} - ,{ 290, 290, 250, 270, 250} - ,{ 300, 300, 270, 270, 270} - ,{ 270, 270, 240, 260, 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, 270, 270} - ,{ 300, 300, 270, 270, 270} - ,{ 270, 270, 240, 260, 240} - ,{ 300, 300, 270, 270, 270} - ,{ 240, 240, 150, 150, 150} - } - } - ,{{{ 300, 300, 270, 270, 270} - ,{ 300, 300, 270, 230, 270} - ,{ 290, 290, 250, 270, 250} - ,{ 300, 300, 270, 230, 270} - ,{ 270, 270, 240, 260, 240} - } - ,{{ 270, 270, 230, 190, 230} - ,{ 270, 270, 230, 190, 230} - ,{ 260, 260, 220, 180, 220} - ,{ 170, 170, 130, 90, 130} - ,{ 260, 260, 220, 180, 220} - } - ,{{ 300, 300, 270, 270, 270} - ,{ 300, 300, 270, 230, 270} - ,{ 290, 290, 250, 270, 250} - ,{ 300, 300, 270, 230, 270} - ,{ 270, 270, 240, 260, 240} - } - ,{{ 260, 260, 220, 180, 220} - ,{ 170, 170, 130, 90, 130} - ,{ 260, 260, 220, 180, 220} - ,{ 170, 110, 80, 170, 80} - ,{ 260, 260, 220, 180, 220} - } - ,{{ 300, 300, 270, 260, 270} - ,{ 300, 300, 270, 230, 270} - ,{ 270, 270, 240, 260, 240} - ,{ 300, 300, 270, 230, 270} - ,{ 240, 240, 150, 110, 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, 240, 300} - ,{ 300, 280, 240, 240, 300} - ,{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 210, 210} - ,{ 250, 250, 220, 240, 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} - } - ,{{ 250, 250, 220, 240, 220} - ,{ 250, 250, 210, 210, 210} - ,{ 250, 250, 220, 240, 220} - ,{ 250, 250, 210, 210, 210} - ,{ 250, 250, 220, 240, 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} - } - ,{{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 210, 210} - ,{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 210, 210} - ,{ 240, 240, 140, 140, 140} - } - } - ,{{{ 280, 280, 240, 240, 240} - ,{ 280, 280, 240, 200, 240} - ,{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 170, 210} - ,{ 250, 250, 220, 240, 220} - } - ,{{ 280, 280, 240, 200, 240} - ,{ 280, 280, 240, 200, 240} - ,{ 250, 250, 220, 180, 220} - ,{ 70, 70, 40, 0, 40} - ,{ 250, 250, 220, 180, 220} - } - ,{{ 250, 250, 220, 240, 220} - ,{ 250, 250, 210, 170, 210} - ,{ 250, 250, 220, 240, 220} - ,{ 250, 250, 210, 170, 210} - ,{ 250, 250, 220, 240, 220} - } - ,{{ 250, 250, 220, 180, 220} - ,{ 140, 140, 100, 60, 100} - ,{ 250, 250, 220, 180, 220} - ,{ 170, 110, 80, 170, 80} - ,{ 250, 250, 220, 180, 220} - } - ,{{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 170, 210} - ,{ 260, 260, 220, 240, 220} - ,{ 250, 250, 210, 170, 210} - ,{ 240, 240, 140, 100, 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, 60, 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, 40} - ,{ 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, 100} - ,{ 220, 220, 220, 220, 220} - ,{ 210, 80, 80, 80, 210} - ,{ 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} - } - } - } - ,{{{{ 430, 430, 370, 370, 430} - ,{ 430, 410, 370, 370, 430} - ,{ 370, 370, 340, 360, 340} - ,{ 370, 370, 340, 340, 340} - ,{ 430, 430, 340, 360, 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} - } - ,{{ 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, 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} - } - ,{{ 360, 340, 360, 340, 360} - ,{ 360, 300, 360, 300, 360} - ,{ 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, 300, 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} - ,{ 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} - ,{ 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} - } - ,{{ 360, 340, 360, 340, 340} - ,{ 360, 300, 360, 300, 300} - ,{ 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} - } - } - } - ,{{{{ 400, 400, 400, 360, 400} - ,{ 400, 370, 400, 360, 400} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 330, 310} - } - ,{{ 360, 360, 310, 360, 330} - ,{ 360, 360, 270, 360, 330} - ,{ 340, 340, 310, 310, 310} - ,{ 230, 220, 230, 170, 230} - ,{ 340, 340, 310, 310, 310} - } - ,{{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 310} - } - ,{{ 400, 370, 400, 340, 400} - ,{ 400, 370, 400, 340, 400} - ,{ 340, 340, 310, 310, 310} - ,{ 310, 230, 180, 310, 310} - ,{ 340, 340, 310, 310, 310} - } - ,{{ 400, 400, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 310, 310} - } - } - ,{{{ 400, 400, 340, 360, 340} - ,{ 370, 370, 340, 360, 340} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 400, 400, 310, 330, 310} - } - ,{{ 360, 360, 310, 360, 310} - ,{ 360, 360, 270, 360, 270} - ,{ 340, 340, 310, 270, 310} - ,{ 220, 220, 170, 130, 170} - ,{ 340, 340, 310, 270, 310} - } - ,{{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - } - ,{{ 370, 370, 340, 300, 340} - ,{ 370, 370, 340, 300, 340} - ,{ 340, 340, 310, 270, 310} - ,{ 270, 210, 180, 270, 180} - ,{ 340, 340, 310, 270, 310} - } - ,{{ 400, 400, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 400, 400, 310, 270, 310} - } - } - ,{{{ 400, 340, 400, 340, 400} - ,{ 400, 340, 400, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 310, 310, 310, 310, 310} - ,{ 270, 270, 270, 270, 270} - ,{ 310, 310, 310, 310, 310} - ,{ 230, 170, 230, 170, 230} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 400, 340, 400} - ,{ 400, 340, 400, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 180, 180, 180, 180, 180} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - } - ,{{{ 340, 290, 340, 340, 340} - ,{ 340, 260, 340, 340, 340} - ,{ 310, 290, 310, 180, 310} - ,{ 310, 230, 310, 310, 310} - ,{ 310, 290, 310, 310, 310} - } - ,{{ 310, 230, 310, 180, 310} - ,{ 270, 190, 270, 140, 270} - ,{ 310, 230, 310, 180, 310} - ,{ 170, 20, 170, 170, 170} - ,{ 310, 230, 310, 180, 310} - } - ,{{ 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} - } - ,{{ 340, 260, 340, 340, 340} - ,{ 340, 260, 340, 340, 340} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 230, 180, 310, 180} - ,{ 310, 230, 310, 180, 310} - } - ,{{ 310, 290, 310, 310, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 290, 310, 180, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 230, 310, 310, 310} - } - } - ,{{{ 400, 340, 400, 340, 340} - ,{ 400, 340, 400, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 330, 310, 310, 310, 330} - ,{ 330, 270, 270, 270, 330} - ,{ 310, 310, 310, 310, 310} - ,{ 230, 170, 230, 170, 170} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 400, 340, 340} - ,{ 400, 340, 400, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 180, 180, 180, 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, 310} - ,{ 310, 310, 310, 310, 310} - } - } - } - ,{{{{ 370, 340, 310, 310, 370} - ,{ 370, 340, 310, 310, 370} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 320, 320, 290, 310, 290} - } - ,{{ 370, 340, 310, 310, 370} - ,{ 370, 340, 310, 310, 370} - ,{ 320, 320, 280, 280, 280} - ,{ 240, 220, 240, 180, 240} - ,{ 320, 320, 280, 280, 280} - } - ,{{ 330, 330, 290, 310, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 320, 320, 290, 310, 290} - } - ,{{ 320, 320, 310, 280, 310} - ,{ 310, 290, 310, 250, 310} - ,{ 320, 320, 280, 280, 280} - ,{ 260, 180, 130, 260, 260} - ,{ 320, 320, 280, 280, 280} - } - ,{{ 330, 330, 290, 310, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 290, 290, 200, 200, 200} - } - } - ,{{{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 250, 290} - ,{ 320, 320, 290, 310, 290} - } - ,{{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 320, 320, 280, 240, 280} - ,{ 220, 220, 180, 140, 180} - ,{ 320, 320, 280, 240, 280} - } - ,{{ 330, 330, 290, 310, 290} - ,{ 330, 330, 290, 250, 290} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 250, 290} - ,{ 320, 320, 290, 310, 290} - } - ,{{ 320, 320, 280, 240, 280} - ,{ 290, 290, 250, 210, 250} - ,{ 320, 320, 280, 240, 280} - ,{ 220, 170, 130, 220, 130} - ,{ 320, 320, 280, 240, 280} - } - ,{{ 330, 330, 290, 310, 290} - ,{ 330, 330, 290, 250, 290} - ,{ 320, 320, 290, 310, 290} - ,{ 330, 330, 290, 250, 290} - ,{ 290, 290, 200, 160, 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, 290, 160, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 290, 270, 290, 160, 290} - } - ,{{ 280, 200, 280, 260, 280} - ,{ 250, 170, 250, 250, 250} - ,{ 280, 200, 280, 150, 280} - ,{ 260, 180, 130, 260, 130} - ,{ 280, 200, 280, 150, 280} - } - ,{{ 290, 270, 290, 200, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 290, 270, 290, 160, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 200, 120, 200, 200, 200} - } - } - ,{{{ 370, 310, 310, 310, 370} - ,{ 370, 310, 310, 310, 370} - ,{ 290, 290, 290, 290, 290} - ,{ 290, 290, 290, 290, 290} - ,{ 290, 290, 290, 290, 290} - } - ,{{ 370, 310, 310, 310, 370} - ,{ 370, 310, 310, 310, 370} - ,{ 280, 280, 280, 280, 280} - ,{ 240, 180, 240, 180, 180} - ,{ 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, 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, 330, 370} - ,{ 370, 340, 310, 310, 370} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 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} - } - ,{{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 340, 340, 310, 330, 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, 310, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 310, 310, 280, 300, 280} - ,{ 340, 340, 310, 310, 310} - ,{ 320, 320, 220, 220, 220} - } - } - ,{{{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - } - ,{{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 300, 300, 260, 220, 260} - ,{ 240, 240, 200, 160, 200} - ,{ 300, 300, 260, 220, 260} - } - ,{{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 340, 340, 310, 330, 310} - } - ,{{ 300, 300, 260, 240, 260} - ,{ 250, 250, 210, 170, 210} - ,{ 300, 300, 260, 220, 260} - ,{ 240, 190, 150, 240, 150} - ,{ 300, 300, 260, 220, 260} - } - ,{{ 340, 340, 310, 300, 310} - ,{ 340, 340, 310, 270, 310} - ,{ 310, 310, 280, 300, 280} - ,{ 340, 340, 310, 270, 310} - ,{ 320, 320, 220, 180, 220} - } - } - ,{{{ 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} - } - ,{{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 200, 260, 200, 260} - ,{ 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} - } - ,{{ 270, 260, 270, 260, 270} - ,{ 270, 210, 270, 210, 270} - ,{ 260, 260, 260, 260, 260} - ,{ 150, 150, 150, 150, 150} - ,{ 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} - } - } - ,{{{ 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} - ,{ 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, 370, 430} - ,{ 430, 410, 400, 370, 430} - ,{ 370, 370, 340, 360, 340} - ,{ 370, 370, 340, 340, 340} - ,{ 430, 430, 340, 360, 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} - } - ,{{ 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} - } - ,{{ 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, 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, 360, 370} - ,{ 370, 370, 340, 360, 340} - ,{ 370, 370, 340, 300, 340} - ,{ 430, 430, 340, 360, 340} - } - ,{{ 410, 410, 370, 360, 370} - ,{ 410, 410, 370, 360, 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} - ,{ 370, 370, 340, 300, 340} - ,{ 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} - } - } - ,{{{ 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} - } - } - } - } -,{{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 240, 240, 310, 260} - ,{ 270, 240, 240, 270, 260} - ,{ 310, 220, 220, 310, 220} - ,{ 270, 240, 240, 270, 240} - ,{ 300, 210, 210, 300, 210} - } - ,{{ 260, 200, 200, 230, 260} - ,{ 260, 200, 200, 230, 260} - ,{ 220, 190, 190, 220, 190} - ,{ 160, 100, 160, 130, 160} - ,{ 220, 190, 190, 220, 190} - } - ,{{ 310, 240, 240, 310, 240} - ,{ 270, 240, 240, 270, 240} - ,{ 310, 220, 220, 310, 220} - ,{ 270, 240, 240, 270, 240} - ,{ 300, 210, 210, 300, 210} - } - ,{{ 220, 190, 190, 220, 190} - ,{ 160, 100, 160, 130, 160} - ,{ 220, 190, 190, 220, 190} - ,{ 210, 50, 50, 210, 180} - ,{ 220, 190, 190, 220, 190} - } - ,{{ 300, 240, 240, 300, 240} - ,{ 270, 240, 240, 270, 240} - ,{ 300, 210, 210, 300, 210} - ,{ 270, 240, 240, 270, 240} - ,{ 150, 140, 120, 150, 120} - } - } - ,{{{ 310, 200, 240, 310, 240} - ,{ 270, 200, 240, 270, 240} - ,{ 310, 190, 220, 310, 220} - ,{ 270, 200, 240, 270, 240} - ,{ 300, 170, 210, 300, 210} - } - ,{{ 230, 160, 200, 230, 200} - ,{ 230, 160, 200, 230, 200} - ,{ 220, 160, 190, 220, 190} - ,{ 130, 70, 100, 130, 100} - ,{ 220, 160, 190, 220, 190} - } - ,{{ 310, 200, 240, 310, 240} - ,{ 270, 200, 240, 270, 240} - ,{ 310, 190, 220, 310, 220} - ,{ 270, 200, 240, 270, 240} - ,{ 300, 170, 210, 300, 210} - } - ,{{ 220, 160, 190, 220, 190} - ,{ 130, 70, 100, 130, 100} - ,{ 220, 160, 190, 220, 190} - ,{ 210, 10, 50, 210, 50} - ,{ 220, 160, 190, 220, 190} - } - ,{{ 300, 200, 240, 300, 240} - ,{ 270, 200, 240, 270, 240} - ,{ 300, 170, 210, 300, 210} - ,{ 270, 200, 240, 270, 240} - ,{ 150, 140, 120, 150, 120} - } - } - ,{{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 220, 220, 220, 220, 220} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - } - ,{{ 200, 200, 200, 200, 200} - ,{ 200, 200, 200, 200, 200} - ,{ 190, 190, 190, 190, 190} - ,{ 160, 100, 160, 100, 160} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 220, 220, 220, 220, 220} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 160, 100, 160, 100, 160} - ,{ 190, 190, 190, 190, 190} - ,{ 50, 50, 50, 50, 50} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - ,{ 240, 240, 240, 240, 240} - ,{ 120, 120, 120, 120, 120} - } - } - ,{{{ 240, 150, 240, 180, 240} - ,{ 240, 100, 240, 110, 240} - ,{ 220, 150, 220, 90, 220} - ,{ 240, 100, 240, 180, 240} - ,{ 210, 130, 210, 120, 210} - } - ,{{ 200, 60, 200, 100, 200} - ,{ 200, 60, 200, 70, 200} - ,{ 190, 60, 190, 60, 190} - ,{ 100, -30, 100, 100, 100} - ,{ 190, 60, 190, 60, 190} - } - ,{{ 240, 150, 240, 110, 240} - ,{ 240, 100, 240, 110, 240} - ,{ 220, 150, 220, 90, 220} - ,{ 240, 100, 240, 110, 240} - ,{ 210, 130, 210, 80, 210} - } - ,{{ 190, 60, 190, 180, 190} - ,{ 100, -30, 100, 100, 100} - ,{ 190, 60, 190, 60, 190} - ,{ 180, 40, 50, 180, 50} - ,{ 190, 60, 190, 60, 190} - } - ,{{ 240, 130, 240, 120, 240} - ,{ 240, 100, 240, 110, 240} - ,{ 210, 130, 210, 80, 210} - ,{ 240, 100, 240, 110, 240} - ,{ 120, -10, 120, 120, 120} - } - } - ,{{{ 260, 240, 240, 240, 260} - ,{ 260, 240, 240, 240, 260} - ,{ 220, 220, 220, 220, 220} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - } - ,{{ 260, 200, 200, 200, 260} - ,{ 260, 200, 200, 200, 260} - ,{ 190, 190, 190, 190, 190} - ,{ 160, 100, 160, 100, 100} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 220, 220, 220, 220, 220} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 160, 100, 160, 100, 100} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 50, 50, 50, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 210, 210, 210, 210, 210} - ,{ 240, 240, 240, 240, 240} - ,{ 120, 120, 120, 120, 120} - } - } - } - ,{{{{ 280, 210, 210, 280, 270} - ,{ 270, 210, 210, 240, 270} - ,{ 280, 190, 190, 280, 190} - ,{ 210, 180, 180, 210, 180} - ,{ 280, 190, 190, 280, 190} - } - ,{{ 270, 210, 210, 240, 270} - ,{ 270, 210, 210, 240, 270} - ,{ 220, 190, 190, 220, 190} - ,{ 70, 10, 70, 40, 70} - ,{ 220, 190, 190, 220, 190} - } - ,{{ 280, 190, 190, 280, 190} - ,{ 210, 180, 180, 210, 180} - ,{ 280, 190, 190, 280, 190} - ,{ 210, 180, 180, 210, 180} - ,{ 280, 190, 190, 280, 190} - } - ,{{ 220, 190, 190, 220, 190} - ,{ 130, 70, 130, 100, 130} - ,{ 220, 190, 190, 220, 190} - ,{ 210, 50, 50, 210, 180} - ,{ 220, 190, 190, 220, 190} - } - ,{{ 280, 190, 190, 280, 190} - ,{ 210, 180, 180, 210, 180} - ,{ 280, 190, 190, 280, 190} - ,{ 210, 180, 180, 210, 180} - ,{ 140, 140, 110, 140, 110} - } - } - ,{{{ 280, 190, 210, 280, 210} - ,{ 240, 190, 210, 240, 210} - ,{ 280, 160, 190, 280, 190} - ,{ 210, 150, 180, 210, 180} - ,{ 280, 150, 190, 280, 190} - } - ,{{ 240, 190, 210, 240, 210} - ,{ 240, 190, 210, 240, 210} - ,{ 220, 150, 190, 220, 190} - ,{ 40, -20, 10, 40, 10} - ,{ 220, 150, 190, 220, 190} - } - ,{{ 280, 150, 190, 280, 190} - ,{ 210, 150, 180, 210, 180} - ,{ 280, 150, 190, 280, 190} - ,{ 210, 150, 180, 210, 180} - ,{ 280, 150, 190, 280, 190} - } - ,{{ 220, 150, 190, 220, 190} - ,{ 100, 40, 70, 100, 70} - ,{ 220, 150, 190, 220, 190} - ,{ 210, 10, 50, 210, 50} - ,{ 220, 150, 190, 220, 190} - } - ,{{ 280, 160, 190, 280, 190} - ,{ 210, 150, 180, 210, 180} - ,{ 280, 160, 190, 280, 190} - ,{ 210, 150, 180, 210, 180} - ,{ 140, 140, 110, 140, 110} - } - } - ,{{{ 210, 210, 210, 210, 210} - ,{ 210, 210, 210, 210, 210} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 210, 210, 210, 210, 210} - ,{ 210, 210, 210, 210, 210} - ,{ 190, 190, 190, 190, 190} - ,{ 70, 10, 70, 10, 70} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 130, 70, 130, 70, 130} - ,{ 190, 190, 190, 190, 190} - ,{ 50, 50, 50, 50, 50} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 110, 110, 110, 110, 110} - } - } - ,{{{ 210, 120, 210, 180, 210} - ,{ 210, 80, 210, 80, 210} - ,{ 190, 120, 190, 60, 190} - ,{ 180, 50, 180, 180, 180} - ,{ 190, 110, 190, 110, 190} - } - ,{{ 210, 80, 210, 80, 210} - ,{ 210, 80, 210, 80, 210} - ,{ 190, 50, 190, 60, 190} - ,{ 10, -120, 10, 10, 10} - ,{ 190, 50, 190, 60, 190} - } - ,{{ 190, 110, 190, 60, 190} - ,{ 180, 50, 180, 50, 180} - ,{ 190, 110, 190, 60, 190} - ,{ 180, 50, 180, 50, 180} - ,{ 190, 110, 190, 60, 190} - } - ,{{ 190, 50, 190, 180, 190} - ,{ 70, -60, 70, 70, 70} - ,{ 190, 50, 190, 60, 190} - ,{ 180, 40, 50, 180, 50} - ,{ 190, 50, 190, 60, 190} - } - ,{{ 190, 120, 190, 110, 190} - ,{ 180, 50, 180, 50, 180} - ,{ 190, 120, 190, 60, 190} - ,{ 180, 50, 180, 50, 180} - ,{ 110, -20, 110, 110, 110} - } - } - ,{{{ 270, 210, 210, 210, 270} - ,{ 270, 210, 210, 210, 270} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 270, 210, 210, 210, 270} - ,{ 270, 210, 210, 210, 270} - ,{ 190, 190, 190, 190, 190} - ,{ 70, 10, 70, 10, 10} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 130, 70, 130, 70, 70} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 50, 50, 50, 180} - ,{ 190, 190, 190, 190, 190} - } - ,{{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 190, 190, 190, 190, 190} - ,{ 180, 180, 180, 180, 180} - ,{ 110, 110, 110, 110, 110} - } - } - } - ,{{{{ 400, 360, 340, 400, 400} - ,{ 400, 360, 340, 370, 400} - ,{ 400, 310, 310, 400, 310} - ,{ 340, 310, 310, 340, 310} - ,{ 400, 330, 310, 400, 310} - } - ,{{ 400, 360, 340, 370, 400} - ,{ 400, 360, 340, 370, 400} - ,{ 340, 310, 310, 340, 310} - ,{ 290, 230, 290, 260, 290} - ,{ 340, 310, 310, 340, 310} - } - ,{{ 400, 310, 310, 400, 310} - ,{ 340, 310, 310, 340, 310} - ,{ 400, 310, 310, 400, 310} - ,{ 340, 310, 310, 340, 310} - ,{ 400, 310, 310, 400, 310} - } - ,{{ 360, 360, 330, 340, 330} - ,{ 360, 360, 330, 300, 330} - ,{ 340, 310, 310, 340, 310} - ,{ 340, 180, 180, 340, 310} - ,{ 340, 310, 310, 340, 310} - } - ,{{ 400, 330, 310, 400, 310} - ,{ 340, 310, 310, 340, 310} - ,{ 400, 310, 310, 400, 310} - ,{ 340, 310, 310, 340, 310} - ,{ 340, 330, 310, 340, 310} - } - } - ,{{{ 400, 360, 340, 400, 340} - ,{ 370, 360, 340, 370, 340} - ,{ 400, 270, 310, 400, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 400, 330, 310, 400, 310} - } - ,{{ 370, 360, 340, 370, 340} - ,{ 370, 360, 340, 370, 340} - ,{ 340, 270, 310, 340, 310} - ,{ 260, 190, 230, 260, 230} - ,{ 340, 270, 310, 340, 310} - } - ,{{ 400, 270, 310, 400, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 400, 270, 310, 400, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 400, 270, 310, 400, 310} - } - ,{{ 360, 360, 310, 340, 310} - ,{ 360, 360, 270, 300, 270} - ,{ 340, 270, 310, 340, 310} - ,{ 340, 140, 180, 340, 180} - ,{ 340, 270, 310, 340, 310} - } - ,{{ 400, 330, 310, 400, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 400, 270, 310, 400, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 340, 330, 310, 340, 310} - } - } - ,{{{ 340, 340, 340, 340, 340} - ,{ 340, 340, 340, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 340, 340, 340, 340, 340} - ,{ 340, 340, 340, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 290, 230, 290, 230, 290} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 330, 310, 330, 310, 330} - ,{ 330, 270, 330, 270, 330} - ,{ 310, 310, 310, 310, 310} - ,{ 180, 180, 180, 180, 180} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - } - ,{{{ 340, 230, 340, 310, 340} - ,{ 340, 220, 340, 270, 340} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 170, 310, 310, 310} - ,{ 310, 230, 310, 310, 310} - } - ,{{ 340, 220, 340, 230, 340} - ,{ 340, 220, 340, 210, 340} - ,{ 310, 170, 310, 180, 310} - ,{ 230, 20, 230, 230, 230} - ,{ 310, 170, 310, 180, 310} - } - ,{{ 310, 230, 310, 180, 310} - ,{ 310, 170, 310, 180, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 170, 310, 180, 310} - ,{ 310, 230, 310, 180, 310} - } - ,{{ 310, 170, 310, 310, 310} - ,{ 270, 130, 270, 270, 270} - ,{ 310, 170, 310, 180, 310} - ,{ 310, 170, 180, 310, 180} - ,{ 310, 170, 310, 180, 310} - } - ,{{ 310, 230, 310, 310, 310} - ,{ 310, 170, 310, 180, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 170, 310, 180, 310} - ,{ 310, 170, 310, 310, 310} - } - } - ,{{{ 400, 340, 340, 340, 400} - ,{ 400, 340, 340, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 340, 340, 400} - ,{ 400, 340, 340, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 290, 230, 290, 230, 230} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 330, 310, 330, 310, 310} - ,{ 330, 270, 330, 270, 270} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 180, 180, 180, 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, 310} - ,{ 310, 310, 310, 310, 310} - } - } - } - ,{{{{ 370, 310, 370, 370, 370} - ,{ 370, 310, 370, 340, 370} - ,{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 300, 280, 370, 280} - } - ,{{ 310, 280, 280, 310, 300} - ,{ 300, 240, 240, 270, 300} - ,{ 310, 280, 280, 310, 280} - ,{ 200, 140, 200, 170, 200} - ,{ 310, 280, 280, 310, 280} - } - ,{{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - } - ,{{ 370, 310, 370, 340, 370} - ,{ 370, 310, 370, 340, 370} - ,{ 310, 280, 280, 310, 280} - ,{ 310, 150, 150, 310, 280} - ,{ 310, 280, 280, 310, 280} - } - ,{{ 370, 300, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 310, 300, 280, 310, 280} - } - } - ,{{{ 370, 300, 310, 370, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 300, 280, 370, 280} - } - ,{{ 310, 240, 280, 310, 280} - ,{ 270, 210, 240, 270, 240} - ,{ 310, 240, 280, 310, 280} - ,{ 170, 110, 140, 170, 140} - ,{ 310, 240, 280, 310, 280} - } - ,{{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - } - ,{{ 340, 270, 310, 340, 310} - ,{ 340, 270, 310, 340, 310} - ,{ 310, 240, 280, 310, 280} - ,{ 310, 110, 150, 310, 150} - ,{ 310, 240, 280, 310, 280} - } - ,{{ 370, 300, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 310, 300, 280, 310, 280} - } - } - ,{{{ 370, 310, 370, 310, 370} - ,{ 370, 310, 370, 310, 370} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 240, 240, 240, 240, 240} - ,{ 280, 280, 280, 280, 280} - ,{ 200, 140, 200, 140, 200} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 370, 310, 370, 310, 370} - ,{ 370, 310, 370, 310, 370} - ,{ 280, 280, 280, 280, 280} - ,{ 150, 150, 150, 150, 150} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - } - ,{{{ 310, 200, 310, 310, 310} - ,{ 310, 170, 310, 310, 310} - ,{ 280, 200, 280, 150, 280} - ,{ 280, 140, 280, 280, 280} - ,{ 280, 200, 280, 280, 280} - } - ,{{ 280, 140, 280, 150, 280} - ,{ 240, 110, 240, 110, 240} - ,{ 280, 140, 280, 150, 280} - ,{ 140, 10, 140, 140, 140} - ,{ 280, 140, 280, 150, 280} - } - ,{{ 280, 200, 280, 150, 280} - ,{ 280, 140, 280, 150, 280} - ,{ 280, 200, 280, 150, 280} - ,{ 280, 140, 280, 150, 280} - ,{ 280, 200, 280, 150, 280} - } - ,{{ 310, 170, 310, 310, 310} - ,{ 310, 170, 310, 310, 310} - ,{ 280, 140, 280, 150, 280} - ,{ 280, 140, 150, 280, 150} - ,{ 280, 140, 280, 150, 280} - } - ,{{ 280, 200, 280, 280, 280} - ,{ 280, 140, 280, 150, 280} - ,{ 280, 200, 280, 150, 280} - ,{ 280, 140, 280, 150, 280} - ,{ 280, 140, 280, 280, 280} - } - } - ,{{{ 370, 310, 370, 310, 310} - ,{ 370, 310, 370, 310, 310} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 300, 280, 280, 280, 300} - ,{ 300, 240, 240, 240, 300} - ,{ 280, 280, 280, 280, 280} - ,{ 200, 140, 200, 140, 140} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 370, 310, 370, 310, 310} - ,{ 370, 310, 370, 310, 310} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 150, 150, 150, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - } - } - ,{{{{ 350, 280, 280, 350, 340} - ,{ 340, 280, 280, 310, 340} - ,{ 350, 260, 260, 350, 260} - ,{ 290, 260, 260, 290, 260} - ,{ 350, 260, 260, 350, 260} - } - ,{{ 340, 280, 280, 310, 340} - ,{ 340, 280, 280, 310, 340} - ,{ 280, 250, 250, 280, 250} - ,{ 210, 150, 210, 180, 210} - ,{ 280, 250, 250, 280, 250} - } - ,{{ 350, 260, 260, 350, 260} - ,{ 290, 260, 260, 290, 260} - ,{ 350, 260, 260, 350, 260} - ,{ 290, 260, 260, 290, 260} - ,{ 350, 260, 260, 350, 260} - } - ,{{ 280, 250, 280, 280, 280} - ,{ 280, 220, 280, 250, 280} - ,{ 280, 250, 250, 280, 250} - ,{ 260, 100, 100, 260, 230} - ,{ 280, 250, 250, 280, 250} - } - ,{{ 350, 260, 260, 350, 260} - ,{ 290, 260, 260, 290, 260} - ,{ 350, 260, 260, 350, 260} - ,{ 290, 260, 260, 290, 260} - ,{ 200, 190, 170, 200, 170} - } - } - ,{{{ 350, 240, 280, 350, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 350, 220, 260, 350, 260} - ,{ 290, 230, 260, 290, 260} - ,{ 350, 220, 260, 350, 260} - } - ,{{ 310, 240, 280, 310, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 280, 220, 250, 280, 250} - ,{ 180, 120, 150, 180, 150} - ,{ 280, 220, 250, 280, 250} - } - ,{{ 350, 230, 260, 350, 260} - ,{ 290, 230, 260, 290, 260} - ,{ 350, 220, 260, 350, 260} - ,{ 290, 230, 260, 290, 260} - ,{ 350, 220, 260, 350, 260} - } - ,{{ 280, 220, 250, 280, 250} - ,{ 250, 190, 220, 250, 220} - ,{ 280, 220, 250, 280, 250} - ,{ 260, 70, 100, 260, 100} - ,{ 280, 220, 250, 280, 250} - } - ,{{ 350, 230, 260, 350, 260} - ,{ 290, 230, 260, 290, 260} - ,{ 350, 220, 260, 350, 260} - ,{ 290, 230, 260, 290, 260} - ,{ 200, 190, 170, 200, 170} - } - } - ,{{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 250, 250, 250, 250, 250} - ,{ 210, 150, 210, 150, 210} - ,{ 250, 250, 250, 250, 250} - } - ,{{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - } - ,{{ 280, 250, 280, 250, 280} - ,{ 280, 220, 280, 220, 280} - ,{ 250, 250, 250, 250, 250} - ,{ 100, 100, 100, 100, 100} - ,{ 250, 250, 250, 250, 250} - } - ,{{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 170, 170, 170, 170, 170} - } - } - ,{{{ 280, 180, 280, 230, 280} - ,{ 280, 140, 280, 220, 280} - ,{ 260, 180, 260, 130, 260} - ,{ 260, 130, 260, 230, 260} - ,{ 260, 180, 260, 170, 260} - } - ,{{ 280, 140, 280, 150, 280} - ,{ 280, 140, 280, 150, 280} - ,{ 250, 120, 250, 120, 250} - ,{ 150, 20, 150, 150, 150} - ,{ 250, 120, 250, 120, 250} - } - ,{{ 260, 180, 260, 130, 260} - ,{ 260, 130, 260, 130, 260} - ,{ 260, 180, 260, 130, 260} - ,{ 260, 130, 260, 130, 260} - ,{ 260, 180, 260, 130, 260} - } - ,{{ 250, 120, 250, 230, 250} - ,{ 220, 90, 220, 220, 220} - ,{ 250, 120, 250, 120, 250} - ,{ 230, 100, 100, 230, 100} - ,{ 250, 120, 250, 120, 250} - } - ,{{ 260, 180, 260, 170, 260} - ,{ 260, 130, 260, 130, 260} - ,{ 260, 180, 260, 130, 260} - ,{ 260, 130, 260, 130, 260} - ,{ 170, 30, 170, 170, 170} - } - } - ,{{{ 340, 280, 280, 280, 340} - ,{ 340, 280, 280, 280, 340} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - } - ,{{ 340, 280, 280, 280, 340} - ,{ 340, 280, 280, 280, 340} - ,{ 250, 250, 250, 250, 250} - ,{ 210, 150, 210, 150, 150} - ,{ 250, 250, 250, 250, 250} - } - ,{{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - } - ,{{ 280, 250, 280, 250, 250} - ,{ 280, 220, 280, 220, 220} - ,{ 250, 250, 250, 250, 250} - ,{ 230, 100, 100, 100, 230} - ,{ 250, 250, 250, 250, 250} - } - ,{{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 260, 260, 260, 260} - ,{ 170, 170, 170, 170, 170} - } - } - } - ,{{{{ 370, 280, 280, 370, 340} - ,{ 340, 280, 280, 310, 340} - ,{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - } - ,{{ 340, 280, 280, 310, 340} - ,{ 340, 280, 280, 310, 340} - ,{ 260, 230, 230, 260, 230} - ,{ 230, 170, 230, 200, 230} - ,{ 260, 230, 230, 260, 230} - } - ,{{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 370, 280, 280, 370, 280} - } - ,{{ 280, 230, 240, 280, 250} - ,{ 240, 180, 240, 210, 240} - ,{ 260, 230, 230, 260, 230} - ,{ 280, 120, 120, 280, 250} - ,{ 260, 230, 230, 260, 230} - } - ,{{ 340, 280, 280, 340, 280} - ,{ 310, 280, 280, 310, 280} - ,{ 340, 250, 250, 340, 250} - ,{ 310, 280, 280, 310, 280} - ,{ 220, 220, 190, 220, 190} - } - } - ,{{{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - } - ,{{ 310, 240, 280, 310, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 260, 200, 230, 260, 230} - ,{ 200, 140, 170, 200, 170} - ,{ 260, 200, 230, 260, 230} - } - ,{{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 370, 240, 280, 370, 280} - } - ,{{ 280, 200, 230, 280, 230} - ,{ 210, 150, 180, 210, 180} - ,{ 260, 200, 230, 260, 230} - ,{ 280, 90, 120, 280, 120} - ,{ 260, 200, 230, 260, 230} - } - ,{{ 340, 240, 280, 340, 280} - ,{ 310, 240, 280, 310, 280} - ,{ 340, 210, 250, 340, 250} - ,{ 310, 240, 280, 310, 280} - ,{ 220, 220, 190, 220, 190} - } - } - ,{{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - } - ,{{ 280, 280, 280, 280, 280} - ,{ 280, 280, 280, 280, 280} - ,{ 230, 230, 230, 230, 230} - ,{ 230, 170, 230, 170, 230} - ,{ 230, 230, 230, 230, 230} - } - ,{{ 280, 280, 280, 280, 280} - 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,{ 310, 170, 310, 310, 310} - } - } - ,{{{ 400, 340, 370, 340, 400} - ,{ 400, 340, 370, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 340, 340, 400} - ,{ 400, 340, 340, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 290, 230, 290, 230, 230} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 370, 310, 370, 310, 310} - ,{ 370, 310, 370, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 180, 180, 180, 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, 310} - ,{ 310, 310, 310, 310, 310} - } - } - } - } -,{{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 180, 190} - } - ,{{ 180, 170, 180, 170, 180} - ,{ 180, 170, 180, 170, 180} - ,{ 170, 170, 170, 170, 170} - ,{ 140, 80, 140, 80, 140} - ,{ 170, 170, 170, 170, 170} - } - ,{{ 220, 210, 220, 210, 220} - ,{ 220, 210, 220, 210, 220} - ,{ 200, 200, 200, 200, 200} - ,{ 220, 210, 220, 210, 220} - ,{ 190, 180, 190, 180, 190} - } - ,{{ 170, 170, 170, 170, 170} - ,{ 140, 80, 140, 80, 140} - ,{ 170, 170, 170, 170, 170} - ,{ 30, 20, 30, 20, 30} - ,{ 170, 170, 170, 170, 170} - } - ,{{ 220, 210, 220, 210, 220} - ,{ 220, 210, 220, 210, 220} - ,{ 190, 180, 190, 180, 190} - ,{ 220, 210, 220, 210, 220} - ,{ 100, 90, 100, 90, 100} - } - } - ,{{{ 220, 160, 220, 130, 220} - ,{ 220, 110, 220, 60, 220} - ,{ 210, 160, 210, 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, 170} - ,{ 30, 20, 30, 20, 30} - ,{ 170, 160, 170, 160, 170} - } - ,{{ 170, 170, 170, 170, 170} - ,{ 160, 160, 160, 160, 160} - ,{ 170, 170, 170, 170, 170} - ,{ 160, 160, 160, 160, 160} - ,{ 90, 90, 90, 90, 90} - } - } - ,{{{ 200, 130, 200, 130, 200} - ,{ 200, 90, 200, 40, 200} - ,{ 180, 130, 180, 20, 180} - ,{ 170, 60, 170, 130, 170} - ,{ 170, 120, 170, 70, 170} - } - ,{{ 200, 90, 200, 40, 200} - ,{ 200, 90, 200, 40, 200} - ,{ 170, 60, 170, 10, 170} - ,{ 0, -110, 0, -30, 0} - ,{ 170, 60, 170, 10, 170} - } - ,{{ 170, 120, 170, 10, 170} - ,{ 170, 60, 170, 10, 170} - ,{ 170, 120, 170, 10, 170} - ,{ 170, 60, 170, 10, 170} - ,{ 170, 120, 170, 10, 170} - } - ,{{ 170, 60, 170, 130, 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, 290} - } - ,{{ 310, 310, 290, 310, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 310, 310, 290, 310, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 310, 310, 290, 310, 290} - } - ,{{ 310, 310, 290, 250, 290} - ,{ 270, 270, 250, 210, 250} - ,{ 310, 310, 290, 250, 290} - ,{ 250, 180, 160, 250, 160} - ,{ 310, 310, 290, 250, 290} - } - ,{{ 370, 370, 290, 310, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 310, 310, 290, 310, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 370, 370, 290, 250, 290} - } - } - ,{{{ 320, 320, 320, 320, 320} - ,{ 320, 320, 320, 320, 320} - ,{ 290, 280, 290, 280, 290} - ,{ 290, 280, 290, 280, 290} - ,{ 290, 280, 290, 280, 290} - } - ,{{ 320, 320, 320, 320, 320} - ,{ 320, 320, 320, 320, 320} - ,{ 290, 280, 290, 280, 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, 280, 350} - ,{ 280, 280, 260, 280, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 340, 340, 260, 280, 260} - } - ,{{ 280, 280, 260, 250, 260} - ,{ 240, 240, 230, 220, 230} - ,{ 280, 280, 260, 250, 260} - ,{ 180, 140, 180, 120, 180} - ,{ 280, 280, 260, 250, 260} - } - ,{{ 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} - } - ,{{ 350, 310, 350, 280, 350} - ,{ 350, 310, 350, 280, 350} - ,{ 280, 280, 260, 250, 260} - ,{ 230, 150, 130, 230, 170} - ,{ 280, 280, 260, 250, 260} - } - ,{{ 340, 340, 260, 280, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 280, 280, 260, 280, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 340, 340, 260, 250, 260} - } - } - ,{{{ 340, 340, 290, 280, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 280, 280, 260, 280, 260} - ,{ 280, 280, 260, 220, 260} - ,{ 340, 340, 260, 280, 260} - } - ,{{ 280, 280, 260, 220, 260} - ,{ 240, 240, 230, 190, 230} - ,{ 280, 280, 260, 220, 260} - ,{ 140, 140, 130, 90, 130} - ,{ 280, 280, 260, 220, 260} - } - ,{{ 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} - } - ,{{ 310, 310, 290, 250, 290} - ,{ 310, 310, 290, 250, 290} - ,{ 280, 280, 260, 220, 260} - ,{ 220, 150, 130, 220, 130} - ,{ 280, 280, 260, 220, 260} - } - ,{{ 340, 340, 260, 280, 260} - ,{ 280, 280, 260, 220, 260} - ,{ 280, 280, 260, 280, 260} - ,{ 280, 280, 260, 220, 260} - ,{ 340, 340, 260, 220, 260} - } - } - ,{{{ 350, 280, 350, 280, 350} - ,{ 350, 280, 350, 280, 350} - ,{ 260, 250, 260, 250, 260} - ,{ 260, 250, 260, 250, 260} - ,{ 260, 250, 260, 250, 260} - } - ,{{ 260, 250, 260, 250, 260} - ,{ 220, 220, 220, 220, 220} - ,{ 260, 250, 260, 250, 260} - ,{ 180, 120, 180, 120, 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} - } - ,{{ 350, 280, 350, 280, 350} - ,{ 350, 280, 350, 280, 350} - ,{ 260, 250, 260, 250, 260} - ,{ 130, 120, 130, 120, 130} - ,{ 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} - } - } - ,{{{ 290, 210, 290, 260, 290} - ,{ 290, 180, 290, 260, 290} - ,{ 260, 210, 260, 100, 260} - ,{ 260, 150, 260, 230, 260} - ,{ 260, 210, 260, 230, 260} - } - ,{{ 260, 150, 260, 100, 260} - ,{ 230, 120, 230, 70, 230} - ,{ 260, 150, 260, 100, 260} - ,{ 130, 20, 130, 100, 130} - ,{ 260, 150, 260, 100, 260} - } - ,{{ 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} - } - ,{{ 290, 180, 290, 260, 290} - ,{ 290, 180, 290, 260, 290} - ,{ 260, 150, 260, 100, 260} - ,{ 230, 150, 130, 230, 130} - ,{ 260, 150, 260, 100, 260} - } - ,{{ 260, 210, 260, 230, 260} - ,{ 260, 150, 260, 100, 260} - ,{ 260, 210, 260, 100, 260} - ,{ 260, 150, 260, 100, 260} - ,{ 260, 150, 260, 230, 260} - } - } - ,{{{ 350, 280, 350, 280, 200} - ,{ 350, 280, 350, 280, 200} - ,{ 260, 250, 260, 250, 170} - ,{ 260, 250, 260, 250, 170} - ,{ 260, 250, 260, 250, 170} - } - ,{{ 260, 250, 260, 250, 190} - ,{ 220, 220, 220, 220, 190} - ,{ 260, 250, 260, 250, 170} - ,{ 180, 120, 180, 120, 30} - ,{ 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} - ,{ 260, 250, 260, 250, 170} - } - ,{{ 350, 280, 350, 280, 200} - ,{ 350, 280, 350, 280, 200} - ,{ 260, 250, 260, 250, 170} - ,{ 170, 120, 130, 120, 170} - ,{ 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} - ,{ 260, 250, 260, 250, 170} - } - } - } - ,{{{{ 280, 280, 260, 260, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 240, 250} - ,{ 260, 260, 240, 260, 240} - } - ,{{ 280, 280, 260, 250, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 250, 250, 240, 230, 240} - ,{ 190, 150, 190, 130, 190} - ,{ 250, 250, 240, 230, 240} - } - ,{{ 260, 260, 250, 260, 250} - ,{ 260, 260, 250, 240, 250} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 240, 250} - ,{ 260, 260, 240, 260, 240} - } - ,{{ 260, 250, 260, 230, 260} - ,{ 260, 220, 260, 200, 260} - ,{ 250, 250, 240, 230, 240} - ,{ 190, 110, 90, 190, 120} - ,{ 250, 250, 240, 230, 240} - } - ,{{ 260, 260, 250, 260, 250} - ,{ 260, 260, 250, 240, 250} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 240, 250} - ,{ 230, 230, 150, 140, 150} - } - } - ,{{{ 280, 280, 260, 260, 260} - ,{ 280, 280, 260, 220, 260} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 210, 250} - ,{ 260, 260, 240, 260, 240} - } - ,{{ 280, 280, 260, 220, 260} - ,{ 280, 280, 260, 220, 260} - ,{ 250, 250, 240, 200, 240} - ,{ 150, 150, 140, 100, 140} - ,{ 250, 250, 240, 200, 240} - } - ,{{ 260, 260, 250, 260, 250} - ,{ 260, 260, 250, 210, 250} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 210, 250} - ,{ 260, 260, 240, 260, 240} - } - ,{{ 250, 250, 240, 200, 240} - ,{ 220, 220, 210, 170, 210} - ,{ 250, 250, 240, 200, 240} - ,{ 180, 100, 90, 180, 90} - ,{ 250, 250, 240, 200, 240} - } - ,{{ 260, 260, 250, 260, 250} - ,{ 260, 260, 250, 210, 250} - ,{ 260, 260, 240, 260, 240} - ,{ 260, 260, 250, 210, 250} - ,{ 230, 230, 150, 110, 150} - } - } - ,{{{ 260, 250, 260, 250, 260} - ,{ 260, 250, 260, 250, 260} - ,{ 240, 230, 240, 230, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 240, 230, 240, 230, 240} - } - ,{{ 260, 250, 260, 250, 260} - ,{ 260, 250, 260, 250, 260} - ,{ 230, 230, 230, 230, 230} - ,{ 190, 130, 190, 130, 190} - ,{ 230, 230, 230, 230, 230} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 240, 230, 240, 230, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 240, 230, 240, 230, 240} - } - ,{{ 260, 230, 260, 230, 260} - ,{ 260, 200, 260, 200, 260} - ,{ 230, 230, 230, 230, 230} - ,{ 80, 80, 80, 80, 80} - ,{ 230, 230, 230, 230, 230} - } - ,{{ 240, 240, 240, 240, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 240, 230, 240, 230, 240} - ,{ 240, 240, 240, 240, 240} - ,{ 150, 140, 150, 140, 150} - } - } - ,{{{ 260, 190, 260, 190, 260} - ,{ 260, 150, 260, 180, 260} - ,{ 240, 190, 240, 80, 240} - ,{ 250, 140, 250, 190, 250} - ,{ 240, 190, 240, 120, 240} - } - ,{{ 260, 150, 260, 110, 260} - ,{ 260, 150, 260, 100, 260} - ,{ 240, 130, 240, 80, 240} - ,{ 140, 30, 140, 110, 140} - ,{ 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} - } - ,{{ 280, 280, 260, 250, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 230, 230, 220, 210, 220} - ,{ 210, 170, 210, 150, 210} - ,{ 230, 230, 220, 210, 220} - } - ,{{ 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} - } - ,{{ 230, 230, 220, 210, 220} - ,{ 220, 180, 220, 160, 220} - ,{ 230, 230, 220, 210, 220} - ,{ 210, 130, 110, 210, 140} - ,{ 230, 230, 220, 210, 220} - } - ,{{ 280, 280, 260, 250, 260} - ,{ 280, 280, 260, 250, 260} - ,{ 250, 250, 230, 250, 230} - ,{ 280, 280, 260, 250, 260} - ,{ 250, 250, 180, 170, 180} - } - } - ,{{{ 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} - } - ,{{ 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, 250, 260, 250, 170} - ,{ 260, 250, 260, 250, 170} - ,{ 230, 220, 230, 220, 140} - ,{ 260, 250, 260, 250, 170} - ,{ 170, 170, 170, 170, 80} - } - } - } - ,{{{{ 370, 370, 350, 320, 350} - ,{ 350, 340, 350, 320, 350} - ,{ 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} - } - ,{{ 350, 310, 350, 280, 350} - 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,{ 370, 370, 290, 250, 290} - } - } - ,{{{ 350, 320, 350, 320, 350} - ,{ 350, 320, 350, 320, 350} - ,{ 290, 280, 290, 280, 290} - ,{ 290, 280, 290, 280, 290} - ,{ 290, 280, 290, 280, 290} - } - ,{{ 320, 320, 320, 320, 320} - ,{ 320, 320, 320, 320, 320} - ,{ 290, 280, 290, 280, 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} - } - ,{{ 350, 280, 350, 280, 350} - ,{ 350, 280, 350, 280, 350} - ,{ 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, 260, 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} - ,{ 290, 180, 290, 260, 290} - ,{ 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} - } - } - ,{{{ 350, 320, 350, 320, 290} - ,{ 350, 320, 350, 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} - } - ,{{ 350, 280, 350, 280, 200} - ,{ 350, 280, 350, 280, 200} - ,{ 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} - } - } - } - } -,{{{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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, 240, 190, 240} - ,{ 240, 240, 240, 190, 240} - ,{ 220, 220, 220, 190, 220} - ,{ 240, 240, 240, 190, 240} - ,{ 210, 210, 210, 170, 210} - } - ,{{ 200, 200, 200, 150, 200} - ,{ 200, 200, 200, 150, 200} - ,{ 190, 190, 190, 150, 190} - ,{ 160, 100, 160, 80, 130} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 240, 240, 240, 190, 240} - ,{ 240, 240, 240, 190, 240} - ,{ 220, 220, 220, 190, 220} - ,{ 240, 240, 240, 190, 240} - ,{ 210, 210, 210, 170, 210} - } - ,{{ 190, 190, 190, 150, 190} - ,{ 160, 100, 160, 80, 130} - ,{ 190, 190, 190, 150, 190} - ,{ 150, 70, 50, 150, 90} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 240, 240, 240, 190, 240} - ,{ 240, 240, 240, 190, 240} - ,{ 210, 210, 210, 170, 210} - ,{ 240, 240, 240, 190, 240} - ,{ 180, 180, 120, 90, 120} - } - } - ,{{{ 240, 240, 240, 190, 240} - ,{ 240, 240, 240, 140, 240} - ,{ 220, 220, 220, 190, 220} - ,{ 240, 240, 240, 140, 240} - ,{ 210, 210, 210, 170, 210} - } - ,{{ 200, 200, 200, 100, 200} - ,{ 200, 200, 200, 100, 200} - ,{ 190, 190, 190, 100, 190} - ,{ 100, 100, 100, 10, 100} - ,{ 190, 190, 190, 100, 190} - } - ,{{ 240, 240, 240, 190, 240} - ,{ 240, 240, 240, 140, 240} - ,{ 220, 220, 220, 190, 220} - ,{ 240, 240, 240, 140, 240} - ,{ 210, 210, 210, 170, 210} - } - ,{{ 190, 190, 190, 100, 190} - ,{ 100, 100, 100, 10, 100} - ,{ 190, 190, 190, 100, 190} - ,{ 80, 50, 50, 80, 50} - ,{ 190, 190, 190, 100, 190} - } - ,{{ 240, 240, 240, 170, 240} - ,{ 240, 240, 240, 140, 240} - ,{ 210, 210, 210, 170, 210} - ,{ 240, 240, 240, 140, 240} - ,{ 180, 180, 120, 20, 120} - } - } - ,{{{ 240, 190, 240, 190, 210} - ,{ 240, 190, 240, 190, 210} - ,{ 220, 180, 220, 180, 190} - ,{ 240, 190, 240, 190, 210} - ,{ 210, 160, 210, 160, 180} - } - ,{{ 200, 150, 200, 150, 170} - ,{ 200, 150, 200, 150, 170} - ,{ 190, 150, 190, 150, 160} - ,{ 160, 60, 160, 60, 130} - ,{ 190, 150, 190, 150, 160} - } - ,{{ 240, 190, 240, 190, 210} - ,{ 240, 190, 240, 190, 210} - ,{ 220, 180, 220, 180, 190} - ,{ 240, 190, 240, 190, 210} - ,{ 210, 160, 210, 160, 180} - } - ,{{ 190, 150, 190, 150, 160} - ,{ 160, 60, 160, 60, 130} - ,{ 190, 150, 190, 150, 160} - ,{ 50, 0, 50, 0, 20} - ,{ 190, 150, 190, 150, 160} - } - ,{{ 240, 190, 240, 190, 210} - ,{ 240, 190, 240, 190, 210} - ,{ 210, 160, 210, 160, 180} - ,{ 240, 190, 240, 190, 210} - ,{ 120, 70, 120, 70, 90} - } - } - ,{{{ 240, 180, 240, 150, 240} - ,{ 240, 130, 240, 80, 240} - ,{ 220, 180, 220, 70, 220} - ,{ 240, 130, 240, 150, 240} - ,{ 210, 160, 210, 90, 210} - } - ,{{ 200, 90, 200, 80, 200} - ,{ 200, 90, 200, 40, 200} - ,{ 190, 90, 190, 40, 190} - ,{ 100, 0, 100, 80, 100} - ,{ 190, 90, 190, 40, 190} - } - ,{{ 240, 180, 240, 80, 240} - ,{ 240, 130, 240, 80, 240} - ,{ 220, 180, 220, 70, 220} - ,{ 240, 130, 240, 80, 240} - ,{ 210, 160, 210, 50, 210} - } - ,{{ 190, 90, 190, 150, 190} - ,{ 100, 0, 100, 80, 100} - ,{ 190, 90, 190, 40, 190} - ,{ 150, 70, 50, 150, 50} - ,{ 190, 90, 190, 40, 190} - } - ,{{ 240, 160, 240, 90, 240} - ,{ 240, 130, 240, 80, 240} - ,{ 210, 160, 210, 50, 210} - ,{ 240, 130, 240, 80, 240} - ,{ 120, 10, 120, 90, 120} - } - } - ,{{{ 240, 190, 240, 190, 170} - ,{ 240, 190, 240, 190, 170} - ,{ 220, 180, 220, 180, 140} - ,{ 240, 190, 240, 190, 150} - ,{ 210, 160, 210, 160, 120} - } - ,{{ 200, 150, 200, 150, 170} - ,{ 200, 150, 200, 150, 170} - ,{ 190, 150, 190, 150, 110} - ,{ 160, 60, 160, 60, 20} - ,{ 190, 150, 190, 150, 110} - } - ,{{ 240, 190, 240, 190, 150} - ,{ 240, 190, 240, 190, 150} - ,{ 220, 180, 220, 180, 140} - ,{ 240, 190, 240, 190, 150} - ,{ 210, 160, 210, 160, 120} - } - ,{{ 190, 150, 190, 150, 110} - ,{ 160, 60, 160, 60, 20} - ,{ 190, 150, 190, 150, 110} - ,{ 90, 0, 50, 0, 90} - ,{ 190, 150, 190, 150, 110} - } - ,{{ 240, 190, 240, 190, 150} - ,{ 240, 190, 240, 190, 150} - ,{ 210, 160, 210, 160, 120} - ,{ 240, 190, 240, 190, 150} - ,{ 120, 70, 120, 70, 30} - } - } - } - ,{{{{ 210, 210, 210, 170, 210} - ,{ 210, 210, 210, 170, 210} - ,{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 150, 180} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 210, 210, 210, 170, 210} - ,{ 210, 210, 210, 170, 210} - ,{ 190, 190, 190, 140, 190} - ,{ 70, 10, 70, -10, 40} - ,{ 190, 190, 190, 140, 190} - } - ,{{ 190, 190, 190, 150, 190} - ,{ 180, 180, 180, 140, 180} - ,{ 190, 190, 190, 150, 190} - ,{ 180, 180, 180, 140, 180} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 190, 190, 190, 150, 190} - ,{ 130, 70, 130, 50, 100} - ,{ 190, 190, 190, 140, 190} - ,{ 150, 70, 50, 150, 90} - ,{ 190, 190, 190, 140, 190} - } - ,{{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 140, 180} - ,{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 140, 180} - ,{ 170, 170, 110, 90, 110} - } - } - ,{{{ 210, 210, 210, 160, 210} - ,{ 210, 210, 210, 120, 210} - ,{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 90, 180} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 210, 210, 210, 120, 210} - ,{ 210, 210, 210, 120, 210} - ,{ 190, 190, 190, 90, 190} - ,{ 10, 10, 10, -80, 10} - ,{ 190, 190, 190, 90, 190} - } - ,{{ 190, 190, 190, 150, 190} - ,{ 180, 180, 180, 90, 180} - ,{ 190, 190, 190, 150, 190} - ,{ 180, 180, 180, 90, 180} - ,{ 190, 190, 190, 150, 190} - } - ,{{ 190, 190, 190, 90, 190} - ,{ 70, 70, 70, -20, 70} - ,{ 190, 190, 190, 90, 190} - ,{ 80, 50, 50, 80, 50} - ,{ 190, 190, 190, 90, 190} - } - ,{{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 90, 180} - ,{ 190, 190, 190, 160, 190} - ,{ 180, 180, 180, 90, 180} - ,{ 170, 170, 110, 20, 110} - } - } - ,{{{ 210, 170, 210, 170, 180} - ,{ 210, 170, 210, 170, 180} - ,{ 190, 150, 190, 150, 160} - ,{ 180, 140, 180, 140, 150} - ,{ 190, 140, 190, 140, 160} - } - ,{{ 210, 170, 210, 170, 180} - ,{ 210, 170, 210, 170, 180} - ,{ 190, 140, 190, 140, 160} - ,{ 70, -30, 70, -30, 40} - ,{ 190, 140, 190, 140, 160} - } - ,{{ 190, 140, 190, 140, 160} - ,{ 180, 140, 180, 140, 150} - ,{ 190, 140, 190, 140, 160} - ,{ 180, 140, 180, 140, 150} - ,{ 190, 140, 190, 140, 160} - } - ,{{ 190, 140, 190, 140, 160} - ,{ 130, 30, 130, 30, 100} - ,{ 190, 140, 190, 140, 160} - ,{ 50, 0, 50, 0, 20} - ,{ 190, 140, 190, 140, 160} - } - ,{{ 190, 150, 190, 150, 160} - ,{ 180, 140, 180, 140, 150} - ,{ 190, 150, 190, 150, 160} - ,{ 180, 140, 180, 140, 150} - ,{ 110, 70, 110, 70, 80} - } - } - ,{{{ 210, 150, 210, 150, 210} - ,{ 210, 110, 210, 60, 210} - ,{ 190, 150, 190, 40, 190} - ,{ 180, 80, 180, 150, 180} - ,{ 190, 140, 190, 90, 190} - } - ,{{ 210, 110, 210, 60, 210} - ,{ 210, 110, 210, 60, 210} - ,{ 190, 80, 190, 30, 190} - ,{ 10, -90, 10, -10, 10} - ,{ 190, 80, 190, 30, 190} - } - ,{{ 190, 140, 190, 30, 190} - ,{ 180, 80, 180, 30, 180} - ,{ 190, 140, 190, 30, 190} - ,{ 180, 80, 180, 30, 180} - ,{ 190, 140, 190, 30, 190} - } - ,{{ 190, 80, 190, 150, 190} - ,{ 70, -30, 70, 50, 70} - ,{ 190, 80, 190, 30, 190} - ,{ 150, 70, 50, 150, 50} - ,{ 190, 80, 190, 30, 190} - } - ,{{ 190, 150, 190, 90, 190} - ,{ 180, 80, 180, 30, 180} - ,{ 190, 150, 190, 40, 190} - ,{ 180, 80, 180, 30, 180} - ,{ 110, 10, 110, 90, 110} - } - } - ,{{{ 210, 170, 210, 170, 190} - ,{ 210, 170, 210, 170, 190} - ,{ 190, 150, 190, 150, 110} - ,{ 180, 140, 180, 140, 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, 300, 340} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 280, 310} - ,{ 370, 370, 310, 280, 310} - } - ,{{ 340, 340, 340, 300, 340} - ,{ 340, 340, 340, 300, 340} - ,{ 310, 310, 310, 260, 310} - ,{ 290, 230, 290, 200, 260} - ,{ 310, 310, 310, 260, 310} - } - ,{{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - } - ,{{ 330, 310, 330, 280, 310} - ,{ 330, 270, 330, 240, 300} - ,{ 310, 310, 310, 260, 310} - ,{ 280, 200, 180, 280, 220} - ,{ 310, 310, 310, 260, 310} - } - ,{{ 370, 370, 310, 280, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 370, 370, 310, 280, 310} - } - } - ,{{{ 370, 370, 340, 270, 340} - ,{ 340, 340, 340, 250, 340} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 370, 370, 310, 270, 310} - } - ,{{ 340, 340, 340, 250, 340} - ,{ 340, 340, 340, 250, 340} - ,{ 310, 310, 310, 210, 310} - ,{ 230, 230, 230, 130, 230} - ,{ 310, 310, 310, 210, 310} - } - ,{{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - } - ,{{ 310, 310, 310, 210, 310} - ,{ 270, 270, 270, 170, 270} - ,{ 310, 310, 310, 210, 310} - ,{ 210, 180, 180, 210, 180} - ,{ 310, 310, 310, 210, 310} - } - ,{{ 370, 370, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 370, 370, 310, 210, 310} - } - } - ,{{{ 340, 300, 340, 300, 310} - ,{ 340, 300, 340, 300, 310} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 340, 300, 340, 300, 310} - ,{ 340, 300, 340, 300, 310} - ,{ 310, 260, 310, 260, 280} - ,{ 290, 180, 290, 180, 260} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 330, 260, 330, 260, 300} - ,{ 330, 220, 330, 220, 300} - ,{ 310, 260, 310, 260, 280} - ,{ 180, 130, 180, 130, 150} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - } - ,{{{ 340, 260, 340, 280, 340} - ,{ 340, 240, 340, 240, 340} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 280, 310} - ,{ 310, 260, 310, 280, 310} - } - ,{{ 340, 240, 340, 200, 340} - ,{ 340, 240, 340, 190, 340} - ,{ 310, 200, 310, 150, 310} - ,{ 230, 120, 230, 200, 230} - ,{ 310, 200, 310, 150, 310} - } - ,{{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - } - ,{{ 310, 200, 310, 280, 310} - ,{ 270, 160, 270, 240, 270} - ,{ 310, 200, 310, 150, 310} - ,{ 280, 200, 180, 280, 180} - ,{ 310, 200, 310, 150, 310} - } - ,{{ 310, 260, 310, 280, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 200, 310, 280, 310} - } - } - ,{{{ 340, 300, 340, 300, 320} - ,{ 340, 300, 340, 300, 320} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 340, 300, 340, 300, 320} - ,{ 340, 300, 340, 300, 320} - ,{ 310, 260, 310, 260, 220} - ,{ 290, 180, 290, 180, 140} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 330, 260, 330, 260, 220} - ,{ 330, 220, 330, 220, 180} - ,{ 310, 260, 310, 260, 220} - ,{ 220, 130, 180, 130, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - } - } - } - ,{{{{ 370, 340, 370, 280, 340} - ,{ 370, 310, 370, 280, 340} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 250, 280} - ,{ 340, 340, 280, 250, 280} - } - ,{{ 280, 280, 280, 230, 280} - ,{ 240, 240, 240, 200, 240} - ,{ 280, 280, 280, 230, 280} - ,{ 200, 140, 200, 120, 170} - ,{ 280, 280, 280, 230, 280} - } - ,{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 370, 310, 370, 280, 340} - ,{ 370, 310, 370, 280, 340} - ,{ 280, 280, 280, 230, 280} - ,{ 250, 170, 150, 250, 190} - ,{ 280, 280, 280, 230, 280} - } - ,{{ 340, 340, 280, 250, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 340, 340, 280, 250, 280} - } - } - ,{{{ 340, 340, 310, 240, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 340, 340, 280, 240, 280} - } - ,{{ 280, 280, 280, 180, 280} - ,{ 240, 240, 240, 150, 240} - ,{ 280, 280, 280, 180, 280} - ,{ 140, 140, 140, 50, 140} - ,{ 280, 280, 280, 180, 280} - } - ,{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 280, 280, 280, 180, 280} - ,{ 180, 150, 150, 180, 150} - ,{ 280, 280, 280, 180, 280} - } - ,{{ 340, 340, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 340, 340, 280, 180, 280} - } - } - ,{{{ 370, 260, 370, 260, 340} - ,{ 370, 260, 370, 260, 340} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 240, 200, 240, 200, 210} - ,{ 280, 230, 280, 230, 250} - ,{ 200, 100, 200, 100, 170} - ,{ 280, 230, 280, 230, 250} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - } - ,{{ 370, 260, 370, 260, 340} - ,{ 370, 260, 370, 260, 340} - ,{ 280, 230, 280, 230, 250} - ,{ 150, 100, 150, 100, 120} - ,{ 280, 230, 280, 230, 250} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - } - } - ,{{{ 310, 230, 310, 280, 310} - ,{ 310, 200, 310, 280, 310} - ,{ 280, 230, 280, 120, 280} - ,{ 280, 170, 280, 250, 280} - ,{ 280, 230, 280, 250, 280} - } - ,{{ 280, 170, 280, 120, 280} - ,{ 240, 140, 240, 90, 240} - ,{ 280, 170, 280, 120, 280} - ,{ 140, 40, 140, 120, 140} - ,{ 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} - } - ,{{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 250, 250, 250, 210, 250} - ,{ 210, 150, 210, 130, 180} - ,{ 250, 250, 250, 210, 250} - } - ,{{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - } - ,{{ 280, 250, 280, 210, 250} - ,{ 280, 220, 280, 200, 250} - ,{ 250, 250, 250, 210, 250} - ,{ 210, 130, 100, 210, 150} - ,{ 250, 250, 250, 210, 250} - } - ,{{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 260, 260, 260, 220, 260} - ,{ 230, 230, 170, 140, 170} - } - } - ,{{{ 280, 280, 280, 220, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 260, 260, 260, 220, 260} - ,{ 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} - ,{ 280, 230, 280, 230, 250} - ,{ 260, 210, 260, 210, 230} - ,{ 260, 220, 260, 220, 230} - ,{ 260, 210, 260, 210, 230} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 250, 210, 250, 210, 220} - ,{ 210, 110, 210, 110, 180} - ,{ 250, 210, 250, 210, 220} - } - ,{{ 260, 220, 260, 220, 230} - ,{ 260, 220, 260, 220, 230} - ,{ 260, 210, 260, 210, 230} - ,{ 260, 220, 260, 220, 230} - ,{ 260, 210, 260, 210, 230} - } - ,{{ 280, 210, 280, 210, 250} - ,{ 280, 180, 280, 180, 250} - ,{ 250, 210, 250, 210, 220} - ,{ 100, 60, 100, 60, 70} - ,{ 250, 210, 250, 210, 220} - } - ,{{ 260, 220, 260, 220, 230} - ,{ 260, 220, 260, 220, 230} - ,{ 260, 210, 260, 210, 230} - ,{ 260, 220, 260, 220, 230} - ,{ 170, 120, 170, 120, 140} - } - } - ,{{{ 280, 210, 280, 210, 280} - ,{ 280, 170, 280, 200, 280} - ,{ 260, 210, 260, 100, 260} - ,{ 260, 160, 260, 210, 260} - ,{ 260, 210, 260, 140, 260} - } - ,{{ 280, 170, 280, 130, 280} - ,{ 280, 170, 280, 120, 280} - ,{ 250, 150, 250, 100, 250} - ,{ 150, 50, 150, 130, 150} - ,{ 250, 150, 250, 100, 250} - } - ,{{ 260, 210, 260, 110, 260} - ,{ 260, 160, 260, 110, 260} - ,{ 260, 210, 260, 100, 260} - ,{ 260, 160, 260, 110, 260} - ,{ 260, 210, 260, 100, 260} - } - ,{{ 250, 150, 250, 210, 250} - ,{ 220, 120, 220, 200, 220} - ,{ 250, 150, 250, 100, 250} - ,{ 210, 130, 100, 210, 100} - ,{ 250, 150, 250, 100, 250} - } - ,{{ 260, 210, 260, 140, 260} - ,{ 260, 160, 260, 110, 260} - ,{ 260, 210, 260, 100, 260} - ,{ 260, 160, 260, 110, 260} - ,{ 170, 60, 170, 140, 170} - } - } - ,{{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 260, 210, 260, 210, 170} - ,{ 260, 220, 260, 220, 180} - ,{ 260, 210, 260, 210, 170} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 250, 210, 250, 210, 170} - ,{ 210, 110, 210, 110, 70} - ,{ 250, 210, 250, 210, 170} - } - ,{{ 260, 220, 260, 220, 180} - ,{ 260, 220, 260, 220, 180} - ,{ 260, 210, 260, 210, 170} - ,{ 260, 220, 260, 220, 180} - ,{ 260, 210, 260, 210, 170} - } - ,{{ 280, 210, 280, 210, 170} - ,{ 280, 180, 280, 180, 140} - ,{ 250, 210, 250, 210, 170} - ,{ 150, 60, 100, 60, 150} - ,{ 250, 210, 250, 210, 170} - } - ,{{ 260, 220, 260, 220, 180} - ,{ 260, 220, 260, 220, 180} - ,{ 260, 210, 260, 210, 170} - ,{ 260, 220, 260, 220, 180} - ,{ 170, 120, 170, 120, 80} - } - } - } - ,{{{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 230, 230, 230, 190, 230} - ,{ 230, 170, 230, 150, 200} - ,{ 230, 230, 230, 190, 230} - } - ,{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 240, 230, 240, 230, 230} - ,{ 240, 180, 240, 160, 210} - ,{ 230, 230, 230, 190, 230} - ,{ 230, 150, 120, 230, 170} - ,{ 230, 230, 230, 190, 230} - } - ,{{ 280, 280, 280, 230, 280} - ,{ 280, 280, 280, 230, 280} - ,{ 250, 250, 250, 210, 250} - ,{ 280, 280, 280, 230, 280} - ,{ 250, 250, 190, 170, 190} - } - } - ,{{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 230, 230, 230, 140, 230} - ,{ 170, 170, 170, 80, 170} - ,{ 230, 230, 230, 140, 230} - } - ,{{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 280, 280, 280, 240, 280} - } - ,{{ 230, 230, 230, 160, 230} - ,{ 180, 180, 180, 90, 180} - ,{ 230, 230, 230, 140, 230} - ,{ 160, 120, 120, 160, 120} - ,{ 230, 230, 230, 140, 230} - } - ,{{ 280, 280, 280, 210, 280} - ,{ 280, 280, 280, 180, 280} - ,{ 250, 250, 250, 210, 250} - ,{ 280, 280, 280, 180, 280} - ,{ 250, 250, 190, 100, 190} - } - } - ,{{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - } - ,{{ 280, 230, 280, 230, 250} - 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,{ 280, 230, 280, 120, 280} - } - ,{{ 230, 150, 230, 230, 230} - ,{ 180, 80, 180, 160, 180} - ,{ 230, 130, 230, 80, 230} - ,{ 230, 150, 120, 230, 120} - ,{ 230, 130, 230, 80, 230} - } - ,{{ 280, 200, 280, 170, 280} - ,{ 280, 170, 280, 120, 280} - ,{ 250, 200, 250, 90, 250} - ,{ 280, 170, 280, 120, 280} - ,{ 190, 90, 190, 170, 190} - } - } - ,{{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 190} - ,{ 280, 230, 280, 230, 190} - ,{ 280, 230, 280, 230, 190} - } - ,{{ 280, 230, 280, 230, 250} - ,{ 280, 230, 280, 230, 250} - ,{ 230, 190, 230, 190, 150} - ,{ 230, 130, 230, 130, 90} - ,{ 230, 190, 230, 190, 150} - } - ,{{ 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} - } - ,{{ 240, 190, 240, 190, 170} - ,{ 240, 140, 240, 140, 100} - ,{ 230, 190, 230, 190, 150} - ,{ 170, 80, 120, 80, 170} - ,{ 230, 190, 230, 190, 150} - } - ,{{ 280, 230, 280, 230, 190} - ,{ 280, 230, 280, 230, 190} - ,{ 250, 200, 250, 200, 160} - ,{ 280, 230, 280, 230, 190} - ,{ 190, 150, 190, 150, 110} - } - } - } - ,{{{{ 370, 370, 370, 300, 340} - ,{ 370, 340, 370, 300, 340} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 280, 310} - ,{ 370, 370, 310, 280, 310} - } - ,{{ 340, 340, 340, 300, 340} - ,{ 340, 340, 340, 300, 340} - ,{ 310, 310, 310, 260, 310} - ,{ 290, 230, 290, 200, 260} - ,{ 310, 310, 310, 260, 310} - } - ,{{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - } - ,{{ 370, 310, 370, 280, 340} - ,{ 370, 310, 370, 280, 340} - ,{ 310, 310, 310, 260, 310} - ,{ 280, 200, 180, 280, 220} - ,{ 310, 310, 310, 260, 310} - } - ,{{ 370, 370, 310, 280, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 260, 310} - ,{ 370, 370, 310, 280, 310} - } - } - ,{{{ 370, 370, 340, 270, 340} - ,{ 340, 340, 340, 250, 340} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 370, 370, 310, 270, 310} - } - ,{{ 340, 340, 340, 250, 340} - ,{ 340, 340, 340, 250, 340} - ,{ 310, 310, 310, 210, 310} - ,{ 230, 230, 230, 130, 230} - ,{ 310, 310, 310, 210, 310} - } - ,{{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - } - ,{{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 210, 180, 180, 210, 180} - ,{ 310, 310, 310, 210, 310} - } - ,{{ 370, 370, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 310, 310, 310, 270, 310} - ,{ 310, 310, 310, 210, 310} - ,{ 370, 370, 310, 210, 310} - } - } - ,{{{ 370, 300, 370, 300, 340} - ,{ 370, 300, 370, 300, 340} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 340, 300, 340, 300, 310} - ,{ 340, 300, 340, 300, 310} - ,{ 310, 260, 310, 260, 280} - ,{ 290, 180, 290, 180, 260} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 370, 260, 370, 260, 340} - ,{ 370, 260, 370, 260, 340} - ,{ 310, 260, 310, 260, 280} - ,{ 180, 130, 180, 130, 150} - ,{ 310, 260, 310, 260, 280} - } - ,{{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - ,{ 310, 260, 310, 260, 280} - } - } - ,{{{ 340, 260, 340, 280, 340} - ,{ 340, 240, 340, 280, 340} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 280, 310} - ,{ 310, 260, 310, 280, 310} - } - ,{{ 340, 240, 340, 200, 340} - ,{ 340, 240, 340, 190, 340} - ,{ 310, 200, 310, 150, 310} - ,{ 230, 120, 230, 200, 230} - ,{ 310, 200, 310, 150, 310} - } - ,{{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - } - ,{{ 310, 200, 310, 280, 310} - ,{ 310, 200, 310, 280, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 280, 200, 180, 280, 180} - ,{ 310, 200, 310, 150, 310} - } - ,{{ 310, 260, 310, 280, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 260, 310, 150, 310} - ,{ 310, 200, 310, 150, 310} - ,{ 310, 200, 310, 280, 310} - } - } - ,{{{ 370, 300, 370, 300, 320} - ,{ 370, 300, 370, 300, 320} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 340, 300, 340, 300, 320} - ,{ 340, 300, 340, 300, 320} - ,{ 310, 260, 310, 260, 220} - ,{ 290, 180, 290, 180, 140} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 370, 260, 370, 260, 220} - ,{ 370, 260, 370, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 220, 130, 180, 130, 220} - ,{ 310, 260, 310, 260, 220} - } - ,{{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 220} - ,{ 310, 260, 310, 260, 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} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - } - ,{{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - ,{ INF, INF, INF, INF, INF} - } - ,{{ INF, 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} - ,{ 220, 220, 220, 220, 220} - ,{ 210, 80, 80, 80, 210} - ,{ 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} - } - } - } - ,{{{{ 430, 430, 370, 400, 430} - ,{ 430, 410, 370, 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} - } - ,{{ 370, 370, 360, 340, 360} - ,{ 360, 360, 360, 300, 360} - ,{ 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} - ,{ 360, 360, 300, 300, 300} - ,{ 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} - } - } - ,{{{ 370, 370, 370, 370, 370} - ,{ 370, 370, 370, 370, 370} - ,{ 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} - } - ,{{ 360, 340, 360, 340, 360} - ,{ 360, 300, 360, 300, 360} - ,{ 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, 300, 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} - ,{ 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} - ,{ 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} - } - ,{{ 360, 340, 360, 340, 340} - ,{ 360, 300, 360, 300, 300} - ,{ 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} - } - } - } - ,{{{{ 400, 400, 400, 370, 400} - ,{ 400, 370, 400, 360, 400} - ,{ 370, 340, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 370, 310} - } - ,{{ 360, 360, 310, 360, 330} - ,{ 360, 360, 270, 360, 330} - ,{ 340, 340, 310, 310, 310} - ,{ 230, 220, 230, 170, 230} - ,{ 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} - ,{ 370, 340, 310, 370, 310} - } - ,{{ 400, 370, 400, 340, 400} - ,{ 400, 370, 400, 340, 400} - ,{ 340, 340, 310, 310, 310} - ,{ 310, 230, 180, 310, 310} - ,{ 340, 340, 310, 310, 310} - } - ,{{ 400, 400, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 370, 340, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 310, 310} - } - } - ,{{{ 400, 400, 340, 370, 340} - ,{ 370, 370, 340, 360, 340} - ,{ 370, 340, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 370, 310} - } - ,{{ 360, 360, 310, 360, 310} - ,{ 360, 360, 270, 360, 270} - ,{ 340, 340, 310, 310, 310} - ,{ 220, 220, 170, 170, 170} - ,{ 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} - ,{ 370, 340, 310, 370, 310} - } - ,{{ 370, 370, 340, 340, 340} - ,{ 370, 370, 340, 340, 340} - ,{ 340, 340, 310, 310, 310} - ,{ 310, 210, 180, 310, 180} - ,{ 340, 340, 310, 310, 310} - } - ,{{ 400, 400, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 370, 340, 310, 370, 310} - ,{ 340, 340, 310, 310, 310} - ,{ 400, 400, 310, 310, 310} - } - } - ,{{{ 400, 340, 400, 340, 400} - ,{ 400, 340, 400, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 310, 310, 310, 310, 310} - ,{ 270, 270, 270, 270, 270} - ,{ 310, 310, 310, 310, 310} - ,{ 230, 170, 230, 170, 230} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 400, 340, 400} - ,{ 400, 340, 400, 340, 400} - ,{ 310, 310, 310, 310, 310} - ,{ 180, 180, 180, 180, 180} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - } - ,{{{ 340, 290, 340, 340, 340} - ,{ 340, 260, 340, 340, 340} - ,{ 310, 290, 310, 180, 310} - ,{ 310, 230, 310, 310, 310} - ,{ 310, 290, 310, 310, 310} - } - ,{{ 310, 230, 310, 180, 310} - ,{ 270, 190, 270, 140, 270} - ,{ 310, 230, 310, 180, 310} - ,{ 170, 40, 170, 170, 170} - ,{ 310, 230, 310, 180, 310} - } - ,{{ 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} - } - ,{{ 340, 260, 340, 340, 340} - ,{ 340, 260, 340, 340, 340} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 230, 180, 310, 180} - ,{ 310, 230, 310, 180, 310} - } - ,{{ 310, 290, 310, 310, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 290, 310, 180, 310} - ,{ 310, 230, 310, 180, 310} - ,{ 310, 230, 310, 310, 310} - } - } - ,{{{ 400, 340, 400, 340, 340} - ,{ 400, 340, 400, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 330, 310, 310, 310, 330} - ,{ 330, 270, 270, 270, 330} - ,{ 310, 310, 310, 310, 310} - ,{ 230, 170, 230, 170, 170} - ,{ 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} - ,{ 310, 310, 310, 310, 310} - } - ,{{ 400, 340, 400, 340, 340} - ,{ 400, 340, 400, 340, 340} - ,{ 310, 310, 310, 310, 310} - ,{ 310, 180, 180, 180, 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, 310} - ,{ 310, 310, 310, 310, 310} - } - } - } - ,{{{{ 370, 340, 310, 350, 370} - ,{ 370, 340, 310, 310, 370} - ,{ 350, 320, 290, 350, 290} - ,{ 330, 330, 290, 290, 290} - ,{ 350, 320, 290, 350, 290} - } - ,{{ 370, 340, 310, 310, 370} - ,{ 370, 340, 310, 310, 370} - ,{ 320, 320, 280, 280, 280} - ,{ 240, 220, 240, 180, 240} - ,{ 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, 310, 280, 310} - ,{ 310, 290, 310, 250, 310} - ,{ 320, 320, 280, 280, 280} - ,{ 260, 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, 290, 160, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 290, 270, 290, 160, 290} - } - ,{{ 280, 200, 280, 260, 280} - ,{ 250, 170, 250, 250, 250} - ,{ 280, 200, 280, 150, 280} - ,{ 260, 180, 130, 260, 130} - ,{ 280, 200, 280, 150, 280} - } - ,{{ 290, 270, 290, 200, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 290, 270, 290, 160, 290} - ,{ 290, 210, 290, 160, 290} - ,{ 200, 120, 200, 200, 200} - } - } - ,{{{ 370, 310, 310, 310, 370} - ,{ 370, 310, 310, 310, 370} - ,{ 290, 290, 290, 290, 290} - ,{ 290, 290, 290, 290, 290} - ,{ 290, 290, 290, 290, 290} - } - ,{{ 370, 310, 310, 310, 370} - ,{ 370, 310, 310, 310, 370} - ,{ 280, 280, 280, 280, 280} - ,{ 240, 180, 240, 180, 180} - ,{ 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, 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, 310, 310} - } - ,{{ 310, 310, 310, 310, 310} - ,{ 310, 310, 310, 310, 310} - ,{ 260, 260, 260, 260, 260} - ,{ 260, 200, 260, 200, 260} - ,{ 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} - } - ,{{ 270, 260, 270, 260, 270} - ,{ 270, 210, 270, 210, 270} - ,{ 260, 260, 260, 260, 260} - ,{ 150, 150, 150, 150, 150} - ,{ 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} - } - } - ,{{{ 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} - ,{ 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} - } - } - } - }}; diff --git a/include/intl22dH.h b/include/intl22dH.h deleted file mode 100644 --- a/include/intl22dH.h +++ /dev/null @@ -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} - 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,{ -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} - 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,{ -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} - 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} - ,{{ 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} - 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} - ,{{ 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} - 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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} - } - } - } - ,{{{{ 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} - 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} - } - ,{{{ 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} - 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} - ,{{ 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} - 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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} - 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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} - } - } - } - ,{{{{ 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} - 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} - ,{{ -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} - 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} - ,{{ -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} - 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} - ,{{ -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} - 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,{ -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} - 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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} - } - } - } - ,{{{{ 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} - } - } - 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,{ 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} - 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,{ 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} - } - 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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} - } - } - } - ,{{{{ 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} - 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} - ,{{ 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} - 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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} - } - } - } - ,{{{{ 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} - 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,{ 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} - 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} - ,{{ 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} - 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} - ,{{ 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} - 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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} - 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} - ,{{ 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} - 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} - } - ,{{{ 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} - 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} - ,{{ 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} - 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,{ 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} - } - } - } - }}; diff --git a/include/list.h b/include/list.h deleted file mode 100644 --- a/include/list.h +++ /dev/null @@ -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 diff --git a/include/loop_energies.h b/include/loop_energies.h deleted file mode 100644 --- a/include/loop_energies.h +++ /dev/null @@ -1,660 +0,0 @@ -#ifndef __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__ -#define __VIENNA_RNA_PACKAGE_LOOP_ENERGIES_H__ - -#include -#include -#include -#include -#include -#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 - * - *

- * 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()] .
- * The unit of the free energy returned is \f$10^{-2} * \mathrm{kcal}/\mathrm{mol}\f$ - *

- *

- * 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() ]. - *

- */ - -/** - * \def E_MLstem(A,B,C,D) - *

Compute the Energy contribution of a Multiloop stem

- * 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.
- * 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) - *

Compute the Energy contribution of an Exterior loop stem

- * 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.
- * 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); - -/** - *

Compute the Energy of an interior-loop

- * This function computes the free energy \f$\Delta G\f$ of an interior-loop with the - * following structure:
- * 
- *        3'  5'
- *        |   |
- *        U - V
- *    a_n       b_1
- *     .        .
- *     .        .
- *     .        .
- *    a_1       b_m
- *        X - Y
- *        |   |
- *        5'  3'
- *
- * 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:
- * 5'-mismatch: a_1
- * 3'-mismatch: b_m
- * and for the enclosed base pair (V,U):
- * 5'-mismatch: b_1
- * 3'-mismatch: a_n
- * \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); - - -/** - *

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:
- * 
- *        a3 a4
- *      a2     a5
- *      a1     a6
- *        X - Y
- *        |   |
- *        5'  3'
- *
- * where X-Y marks the closing pair [e.g. a (G,C) 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 "a1.a2.a3.a4.a5.a6"
- * \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); - -/** - *

Compute the energy contribution of a stem branching off a loop-region

- * 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 immediately interior base pairs - * 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: - * 
- *        3'  5'
- *        |   |
- *        X - Y
- *  5'-si1     sj1-3'
- *
- * - * 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 internal-loop-penalty 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); - -/** - *

Compute the Boltzmann weighted energy contribution of a stem branching off a loop-region

- * 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); - -/** - *

Compute Boltzmann weight \f$e^{-\Delta G/kT} \f$ of a hairpin loop

- * 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); - -/** - *

Compute Boltzmann weight \f$e^{-\Delta G/kT} \f$ of interior loop

- * 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)||(j=cutpoint)||(p=cutpoint)||((q+1)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 diff --git a/include/naview.h b/include/naview.h deleted file mode 100644 --- a/include/naview.h +++ /dev/null @@ -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 diff --git a/include/pair_mat.h b/include/pair_mat.h deleted file mode 100644 --- a/include/pair_mat.h +++ /dev/null @@ -1,148 +0,0 @@ -#include -#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 G */ - alias[i++] = 2; /* B <-> C */ - } - for (i=1; i GC */ - i++; - pair[i][i-1] = 1; /* BA <-> CG */ - } - } - else if (energy_set==2) { - for (i=1; i A*/ - alias[i++] = 4; /* B <-> U */ - } - for (i=1; i AU */ - i++; - pair[i][i-1] = 6; /* BA <-> UA */ - } - } - else if (energy_set==3) { - for (i=1; i G */ - alias[i++] = 2; /* B <-> C */ - alias[i++] = 1; /* C <-> A */ - alias[i++] = 4; /* D <-> U */ - } - for (i=1; i 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; -} diff --git a/include/params.h b/include/params.h deleted file mode 100644 --- a/include/params.h +++ /dev/null @@ -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.
- * 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 diff --git a/include/part_func.h b/include/part_func.h deleted file mode 100644 --- a/include/part_func.h +++ /dev/null @@ -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 RNAlib 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 OpenMP notice:
- * 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 QB matrix - * \param[out] qm_p A pointer to the QM 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$ = \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$ = \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$ = \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$ = \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 diff --git a/include/part_func_co.h b/include/part_func_co.h deleted file mode 100644 --- a/include/part_func_co.h +++ /dev/null @@ -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 diff --git a/include/plot_layouts.h b/include/plot_layouts.h deleted file mode 100644 --- a/include/plot_layouts.h +++ /dev/null @@ -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 simple - * - * This is the plot type definition for several RNA structure plotting functions telling - * them to use Simple 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 Naview - * - * This is the plot type definition for several RNA structure plotting functions telling - * them to use Naview 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 Circular - * - * This is the plot type definition for several RNA structure plotting functions telling - * them to produce a Circular plot - * - * \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 Simple way - * - * \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 Circular Plot - * - * 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 R2 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 diff --git a/include/subopt.h b/include/subopt.h deleted file mode 100644 --- a/include/subopt.h +++ /dev/null @@ -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 all 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 diff --git a/include/utils.h b/include/utils.h deleted file mode 100644 --- a/include/utils.h +++ /dev/null @@ -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 -#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 T and t with U and u, 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 diff --git a/tests/properties.hs b/tests/properties.hs new file mode 100644 --- /dev/null +++ b/tests/properties.hs @@ -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) +