ViennaRNA-bindings 0.1.1.1 → 0.1.2.0

raw patch · 5 files changed

+67/−12 lines, 5 files

Files

• BioInf/ViennaRNA/Bindings.hs +4/−0
• BioInf/ViennaRNA/Bindings/FFI/CoFold.chs +29/−7
• ViennaRNA-bindings.cabal +2/−5
• cbits/ffiwrap_part_func.c +28/−0
• changelog +4/−0

@@ -55,3 +55,7 @@ copart :: String -> Int -> IO (CofoldF,String,A.Array (Int,Int) Double) copart s c = ffiCoPartitionFunction  c s +copartConstrained :: String -> String -> Int -> IO (CofoldF,String,A.Array (Int,Int) Double)+copartConstrained sq str c = ffiCoPartitionConstrained c sq str++

@@ -5,6 +5,7 @@   ( ffiCoFold   , ffiCoEnergyOfStructure   , ffiCoPartitionFunction+  , ffiCoPartitionConstrained   , CofoldF (..)   ) where @@ -78,18 +79,39 @@   setCutPoint cutpoint   let n = length i   let z = n * (n+1) `div` 2 +1-  eF <- co_pf_fold_p ci cs >>= peek -- {#call co_pf_fold #} ci cs+  eF <- co_pf_fold_p ci cs >>= peek   s  <- peekCAString cs   bp <- {#call export_co_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 (eF, s, ar) -foreign import ccall "co_pf_fold" co_pf_fold_p :: CString -> CString -> IO CofoldFPtr+-- | Constrained partition function+--+-- NOTE the wrapped C function we @foreign import@ use very dirty+-- return-pointer-from-stack stuff. We should fix that. On the other hand, it just+-- works, because we immediately peek into the structure and marshall to Haskell. -#c-cofoldF * co_pf_fold_p (char * inp, char * str)-{ return & co_pf_fold (inp, str);-}-#endc+ffiCoPartitionConstrained :: Int -> String -> String -> IO (CofoldF,String,A.Array (Int,Int) Double)+ffiCoPartitionConstrained cutpoint sq st =+  withCAString sq $ \csq ->+  withCAString st $ \cst -> do+  print sq+  print st+  print cutpoint+  setCutPoint cutpoint+  let n = length sq+  let z = n * (n+1) `div` 2 +1+  eF <- co_pf_fold_constrained_p csq cst 1 >>= peek+  s  <- peekCAString cst+  bp <- {#call export_co_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 (eF, s, ar)++++foreign import ccall "ffiwrap_co_pf_fold" co_pf_fold_p :: CString -> CString -> IO CofoldFPtr++foreign import ccall "ffiwrap_co_pf_fold_constrained" co_pf_fold_constrained_p :: CString -> CString -> Int -> IO CofoldFPtr 

@@ -1,12 +1,12 @@ name:                ViennaRNA-bindings-version:             0.1.1.1+version:             0.1.2.0 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 1994-2013+copyright:           The ViennaRNA Team 1994-2014 category:            Bioinformatics, FFI build-type:          Simple cabal-version:       >=1.8@@ -73,7 +73,6 @@     BioInf.ViennaRNA.Bindings.FFI.Fold     BioInf.ViennaRNA.Bindings.FFI.PartFunc     BioInf.ViennaRNA.Bindings.FFI.Utils-  -- other-modules:   build-depends:     base == 4.* ,     array@@ -94,6 +93,4 @@   cc-options:   include-dirs: include   includes: config.h---    RNA---    gomp 

@@ -1,8 +1,36 @@ +// functions wrapped in here need a C-wrapper because they do "more work"+// before they can be called from C.++#include <stdio.h>+ #include "part_func.h"+#include "part_func_co.h" +// wrap the RNAfold constrained partition function+ float ffiwrap_pf_fold_constrained (const char *sequence, char *structure, int constrained) {   return pf_fold_par (sequence, structure, 0, 1, constrained, 0);+}++// wrap the RNAcofold constrained partition function.+//+// TODO the current implementation makes me cry.++cofoldF * ffiwrap_co_pf_fold_constrained (char *sequence, char *structure, int constrained)+{+  cofoldF x = co_pf_fold_par (sequence, structure, 0, 1, constrained);+  return &x;+}++// wrap RNAcofold partition function+//+// TODO the current implementation makes me cry.++cofoldF * ffiwrap_co_pf_fold (char * inp, char * str)+{+  cofoldF x = co_pf_fold (inp, str);+  return &x; } 

@@ -1,3 +1,7 @@+0.1.2.0++- constrained cofold partition function added+ 0.1.1.1  - export everything in the bindings