ViennaRNA-bindings (empty) → 0.0.2.3

raw patch · 7 files changed

+180/−0 lines, 7 filesdep +arraydep +basesetup-changed

Dependencies added: array, base

Files

• BioInf/ViennaRNA/Bindings.hs +30/−0
• BioInf/ViennaRNA/Bindings/FFI/Fold.chs +33/−0
• BioInf/ViennaRNA/Bindings/FFI/PartFunc.chs +34/−0
• BioInf/ViennaRNA/Bindings/FFI/Utils.hs +12/−0
• LICENSE +19/−0
• Setup.hs +2/−0
• ViennaRNA-bindings.cabal +50/−0

@@ -0,0 +1,30 @@++-- | Bindings to important functions in the ViennaRNA library.++module BioInf.ViennaRNA.Bindings where++import qualified Data.Array.IArray as A++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+-- energy and structure.++mfe :: String -> IO (Double,String)+mfe = ffiFold++-- | 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++-- | 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+-- pair probability table.++part :: String -> IO (Double,String,A.Array (Int,Int) Double)+part = ffiPartitionFunction+

@@ -0,0 +1,33 @@+{-# LANGUAGE ForeignFunctionInterface #-}++module BioInf.ViennaRNA.Bindings.FFI.Fold+  ( ffiFold+  , ffiEnergyOfStructure+  ) 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>++ffiFold :: String -> IO (Double,String)+ffiFold inp = withCAString inp $ \cinp ->+              withCAString inp $ \struc -> do+  e <- {#call fold #} cinp struc+  s <- peekCAString struc+  return (cf2d e, s)++ffiEnergyOfStructure :: String -> String -> Int -> IO Double+ffiEnergyOfStructure inp struc verb =+  withCAString inp   $ \i ->+  withCAString struc $ \s ->+  {#call energy_of_structure #} i s (fromIntegral verb :: CInt) >>= (return . cf2d)+

@@ -0,0 +1,34 @@+{-# LANGUAGE ForeignFunctionInterface #-}++module BioInf.ViennaRNA.Bindings.FFI.PartFunc+  ( ffiPartitionFunction+  ) where++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 BioInf.ViennaRNA.Bindings.FFI.Utils++++#include <ViennaRNA/part_func.h>++ffiPartitionFunction :: String -> IO (Double,String,A.Array (Int,Int) Double)+ffiPartitionFunction 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+  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)+

@@ -0,0 +1,12 @@++module BioInf.ViennaRNA.Bindings.FFI.Utils where++import Foreign.C.Types+import GHC.Float+import Unsafe.Coerce++++cf2d :: CFloat -> Double+cf2d = float2Double . unsafeCoerce+

@@ -0,0 +1,19 @@+			 Disclaimer and Copyright++The programs, library and source code of the Vienna RNA Package are free+software. They are distributed in the hope that they will be useful+but WITHOUT ANY WARRANTY; without even the implied warranty of+MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  ++Permission is granted for research, educational, and commercial use+and modification so long as 1) the package and any derived works are not+redistributed for any fee, other than media costs, 2) proper credit is+given to the authors and the Institute for Theoretical Chemistry of the +University of Vienna.++If you want to include this software in a commercial product, please contact +the authors. ++Note that the file ./lib/naview.c has its own copyright attached. +The ./Readseq/ directory contains a modified version of Don Gilbert's+public domain readseq program.

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain

@@ -0,0 +1,50 @@+name:                ViennaRNA-bindings+version:             0.0.2.3+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+maintainer:          choener@tbi.univie.ac.at+copyright:           The ViennaRNA Team 1994-2013+category:            Bioinformatics, FFI+build-type:          Simple+cabal-version:       >=1.8++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 package needs to be installed. In addition, you should create a+  shared object from libRNA.a:+  .+  @mkdir tmp; ar -x /usr/lib/libRNA.a; rm svm.o; gcc -shared *.o -o libRNA.so@+  .+  Then, copy the resulting .so file into your library path or set+  @LD_LIBRARY_PATH@ appropriately. This is only necessary, if you want ghci+  support.+  .+  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++library+  exposed-modules:+    -- public interfaces+    BioInf.ViennaRNA.Bindings+    -- the FFI+    BioInf.ViennaRNA.Bindings.FFI.Fold+    BioInf.ViennaRNA.Bindings.FFI.PartFunc+    BioInf.ViennaRNA.Bindings.FFI.Utils+  -- other-modules:+  build-depends:+    base == 4.* ,+    array+  build-tools:+    c2hs+  extra-libraries:+    RNA+    gomp+