diff --git a/BioInf/ViennaRNA/Bindings.hs b/BioInf/ViennaRNA/Bindings.hs --- a/BioInf/ViennaRNA/Bindings.hs +++ b/BioInf/ViennaRNA/Bindings.hs @@ -13,8 +13,8 @@ import qualified Data.Array.IArray as A -import BioInf.ViennaRNA.Bindings.FFI.Fold as FFI -import BioInf.ViennaRNA.Bindings.FFI.CoFold as FFI +import BioInf.ViennaRNA.Bindings.FFI.CoFold as FFI +import BioInf.ViennaRNA.Bindings.FFI.Fold as FFI import BioInf.ViennaRNA.Bindings.FFI.PartFunc as FFI -- | Fold a sequence into an optimal secondary structure. Returns a pair of @@ -35,7 +35,10 @@ -- pair probability table. part :: String -> IO (Double,String,A.Array (Int,Int) Double) -part = ffiPartitionFunction +part = ffi_pf_fold + +partConstrained :: String -> String -> IO (Double, String, A.Array (Int,Int) Double) +partConstrained = ffi_pf_fold_constrained 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 @@ -8,28 +8,26 @@ , CofoldF (..) ) where -import Foreign.C.String -import Foreign.C.Types -import Foreign.Marshal.Alloc -import Foreign.Ptr -import Foreign.Storable -import GHC.Float -import Unsafe.Coerce +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 Foreign.Marshal.Array -import Control.Applicative -import Control.Monad - -import BioInf.ViennaRNA.Bindings.FFI.Utils +import Unsafe.Coerce -import Debug.Trace +import BioInf.ViennaRNA.Bindings.FFI.Utils -#include -#include -#include -#include +#include "cofold.h" +#include "data_structures.h" +#include "fold.h" +#include "part_func_co.h" {#pointer *cofoldF as CofoldFPtr -> CofoldF #} 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 @@ -17,8 +17,7 @@ - -#include +#include "fold.h" ffiFold :: String -> IO (Double,String) ffiFold inp = withCAString inp $ \cinp -> 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 @@ -1,34 +1,52 @@ {-# LANGUAGE ForeignFunctionInterface #-} module BioInf.ViennaRNA.Bindings.FFI.PartFunc - ( ffiPartitionFunction + ( ffi_pf_fold + , ffi_pf_fold_constrained ) where -import Foreign.C.String -import Foreign.C.Types -import Foreign.Marshal.Alloc -import Foreign.Marshal.Array -import Foreign.Ptr -import GHC.Float +import Foreign.C.String +import Foreign.C.Types +import Foreign.Marshal.Alloc +import Foreign.Marshal.Array +import Foreign.Ptr +import GHC.Float import qualified Data.Array.IArray as A -import Unsafe.Coerce +import Unsafe.Coerce import BioInf.ViennaRNA.Bindings.FFI.Utils -#include +#include "part_func.h" -ffiPartitionFunction :: String -> IO (Double,String,A.Array (Int,Int) Double) -ffiPartitionFunction i = +ffi_pf_fold :: String -> IO (Double,String,A.Array (Int,Int) Double) +ffi_pf_fold i = withCAString i $ \ci -> withCAString i $ \cs -> do let n = length i let z = n * (n+1) `div` 2 +1 - e <- {#call pf_fold #} ci cs + e <- {#call ffiwrap_pf_fold_constrained #} ci cs 0 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 -> + withCAString s $ \cs -> do + let n = length i + let z = n * (n+1) `div` 2 +1 + e <- {#call ffiwrap_pf_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); +#endc diff --git a/ViennaRNA-bindings.cabal b/ViennaRNA-bindings.cabal --- a/ViennaRNA-bindings.cabal +++ b/ViennaRNA-bindings.cabal @@ -1,10 +1,10 @@ name: ViennaRNA-bindings -version: 0.1.0.0 +version: 0.1.1.0 synopsis: ViennaRNA v2 bindings homepage: http://www.tbi.univie.ac.at/~choener/ license: OtherLicense license-file: LICENSE -author: Christian Hoener zu Siederdissen (bindings) 2013, The ViennaRNA Team (library) 1994-2013 +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 category: Bioinformatics, FFI @@ -22,8 +22,12 @@ 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 + . + @ + 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 @@ -55,6 +59,7 @@ include/PS_dot.h include/subopt.h include/utils.h + changelog library @@ -83,6 +88,7 @@ cbits/part_func.c cbits/part_func_co.c cbits/cofold.c + cbits/ffiwrap_part_func.c cc-options: include-dirs: include includes: config.h diff --git a/cbits/ffiwrap_part_func.c b/cbits/ffiwrap_part_func.c new file mode 100644 --- /dev/null +++ b/cbits/ffiwrap_part_func.c @@ -0,0 +1,8 @@ + +#include "part_func.h" + +float ffiwrap_pf_fold_constrained (const char *sequence, char *structure, int constrained) +{ + return pf_fold_par (sequence, structure, 0, 1, constrained, 0); +} + diff --git a/changelog b/changelog new file mode 100644 --- /dev/null +++ b/changelog @@ -0,0 +1,11 @@ +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