MC-Fold-DP 0.1.0.1 → 0.1.1.0

raw patch · 3 files changed

+29/−23 lines, 3 filesdep ~cmdargs

Dependency ranges changed: cmdargs

Files

• BioInf/MCFoldDP.hs +7/−7
• MC-Fold-DP.cabal +21/−16
• MCFoldDP.hs +1/−0

@@ -238,7 +238,7 @@  fncmSingle :: MotifDB -> Primary -> Constraint -> Int -> Int -> Double fncmSingle MotifDB{..} inp cns@(Constraint constr) i j-  | (fst $ constr VU.! i) == 'x' || (fst $ constr VU.! j) == 'x' = eInf+  | (fst $ constr `VU.unsafeIndex` i) == 'x' || (fst $ constr `VU.unsafeIndex` j) == 'x' = eInf   | l<4 = eInf   | otherwise = bonus + (maybe 0 ((!ci) . snd) $ find ((l==).fst) $ sCycles)   where@@ -256,7 +256,7 @@  fncmDS :: MotifDB -> Primary -> Constraint -> Int -> Int -> Int -> Int -> Table2 -> Double fncmDS MotifDB{..} inp cns@(Constraint constr) i j k l sncm-  | (fst $ constr VU.! i) == 'x' || (fst $ constr VU.! j) == 'x' = eInf+  | (fst $ constr `VU.unsafeIndex` i) == 'x' || (fst $ constr `VU.unsafeIndex` j) == 'x' = eInf   | k>=l = eInf   -- in case we have one of the three known single NCMs   | Just hinge <- ((di,dj),len) `lookup` dsConnect@@ -282,7 +282,7 @@  fncmDD :: MotifDB -> Primary -> Constraint -> Int -> Int -> Int -> Int -> [Table2] -> VU.Vector (Int,Double) fncmDD MotifDB{..} inp cns@(Constraint constr) i j k l dncms-  | (fst $ constr VU.! i) == 'x' || (fst $ constr VU.! j) == 'x' = VU.empty+  | (fst $ constr `VU.unsafeIndex` i) == 'x' || (fst $ constr `VU.unsafeIndex` j) == 'x' = VU.empty   | otherwise = VU.fromList $ zipWith3 f (map fst $ VU.toList knownDoubleNCM) [0..] dncms   where     bonus = giveBonus cns i j@@ -326,7 +326,7 @@  fMulti :: MotifDB -> Primary -> Constraint -> Int -> Int -> Table2 -> Table2 -> VU.Vector (Int,Double) fMulti db inp cns@(Constraint constr) i j mbr mbr1-  | (fst $ constr VU.! i) == 'x' || (fst $ constr VU.! j) == 'x' = VU.empty+  | (fst $ constr `VU.unsafeIndex` i) == 'x' || (fst $ constr `VU.unsafeIndex` j) == 'x' = VU.empty   | otherwise = xs   where     xs = VU.map (\k -> (k, mbr!(i+1,k) + mbr1!(k+1,j-1) + bonus)) $ (VU.enumFromN (i+1) (j-i-1))@@ -352,7 +352,7 @@  fInterior :: MotifDB -> Primary -> Constraint -> Int -> Int -> Table2 -> VU.Vector ((Int,Int),Double) fInterior MotifDB{..} inp cns@(Constraint constr) i j dncm-  | (fst $ constr VU.! i) == 'x' || (fst $ constr VU.! j) == 'x' = VU.empty+  | (fst $ constr `VU.unsafeIndex` i) == 'x' || (fst $ constr `VU.unsafeIndex` j) == 'x' = VU.empty   | otherwise = res   where     bonus = giveBonus cns i j@@ -422,5 +422,5 @@   | any (`VU.elem` bonusCC) [c,d] = bonusScore   | otherwise = 0   where-    (c,k) = constr VU.! i-    (d,l) = constr VU.! j+    (c,k) = constr `VU.unsafeIndex` i+    (d,l) = constr `VU.unsafeIndex` j

@@ -1,5 +1,5 @@ name:           MC-Fold-DP-version:        0.1.0.1+version:        0.1.1.0 author:         Christian Hoener zu Siederdissen, Stephan H Bernhart, Peter F Stadler, Ivo L Hofacker copyright:      Christian Hoener zu Siederdissen, 2010-2011 homepage:       http://www.tbi.univie.ac.at/software/mcfolddp/@@ -9,7 +9,7 @@ license-file:   LICENSE build-type:     Simple stability:      experimental-cabal-version:  >= 1.4.0+cabal-version:  >= 1.6.0 synopsis:                 Folding algorithm based on nucleotide cyclic motifs. description:@@ -17,17 +17,28 @@                 idea of combining small motifs, called nucleotide cyclic motifs                 (NCMs). The algorithm implemented here and described in                 .+                .                 Hoener zu Siederdissen C, Bernhart SH, Stadler PF, Hofacker IL,+                .                 "A Folding Algorithm for Extended RNA Secondary Structures",-                2011, submitted                 .+                Bioinformatics (2011) 27 (13), i129-136+                .+                <http://www.tbi.univie.ac.at/software/rnawolf/>+                .+                .                 has polynomial runtime in O(n^3) and uses a (pseudo-energy)                 scoring scheme based on                 .-                Parisien M, Major F. "The MC-Fold and MC-Sym pipeline infers-                RNA structure from sequence data",  Nature 2008,-                452(7183):51-55. <http://www.major.iric.ca/MC-Fold/>                 .+                Parisien M, Major F.+                .+                "The MC-Fold and MC-Sym pipeline infers RNA structure from+                sequence data",+                .+                Nature 2008, 452(7183):51-55. <http://www.major.iric.ca/MC-Fold/>+                .+                .                 This program uses the same database as MC-Fold (which has                 exponential run-time) and aims to be able to produce the same                 results.@@ -40,7 +51,7 @@                 .                 Current status:                 .-                * comparable prediction accuracy on sequences+                * comparable prediction accuracy on sequences (compared with MC-Fold)                 .                 * possibility to use sparse data correction                 .@@ -74,14 +85,11 @@       -O0   else     ghc-options:-      -Odph-    if impl(ghc > 6.13)-      ghc-options:-        -fllvm+      -O2  executable MCFoldDP   build-depends:-    cmdargs == 0.6.8,+    cmdargs == 0.10.* ,     split   main-is:     MCFoldDP.hs@@ -90,7 +98,4 @@       -O0   else     ghc-options:-      -Odph-    if impl(ghc > 6.13)-      ghc-options:-        -fllvm+      -O2

@@ -107,6 +107,7 @@        common . mkConstraint $ c   | otherwise = error $ "doFold: " ++ show (inp,cnstr)   where+    common :: Constraint -> IO ()     common c = do       let pri = mkPrimary inp       let ts = fold db pri c