RNAdesign 0.0.2.1 → 0.1.0.0

raw patch · 4 files changed

+10/−6 lines, 4 filesdep ~ViennaRNA-bindings

Dependency ranges changed: ViennaRNA-bindings

Files

• BioInf/RNAdesign.hs +1/−1
• RNAdesign.cabal +4/−4
• RNAdesign.hs +1/−1
• changelog +4/−0

@@ -163,7 +163,7 @@         }   gs = independentGraphs xs   as = map (allCandidates asnLimit sv) gs-  ss = M.map fixup . M.unionsWith (++) $ map (M.fromList . zip [0..] . (map ((:[]). mkNuc))) scs+  ss = M.map fixup . M.unionsWith ((nub .) . (++)) $ map (M.fromList . zip [0..] . (map ((:[]). mkNuc))) scs   sv = V.fromList $ map (\k -> M.findWithDefault acgu k ss) [0 .. length (head xs) - 1]   fixup zs = filter (/=nN) $ if (all (==nN) zs) then acgu else zs 

@@ -1,5 +1,5 @@ name:           RNAdesign-version:        0.0.2.1+version:        0.1.0.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at category:       Bioinformatics@@ -29,7 +29,7 @@                 .                 Christian Hoener zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler                 .-                @A Graph Coloring Approach to Designing Multi-Stable Nucleic Acid Sequences@+                @Computational design of RNAs with complex energy landscapes@                 .                 Biopolymers, 99, 12, 1124-1136, 2013, Wiley @@ -62,7 +62,7 @@     ParsecTools               >= 0.0.2 && < 0.0.3 ,     PrimitiveArray            >= 0.5              ,     RNAFold                   >= 1.99.3.3         ,-    ViennaRNA-bindings        >= 0.0.2.3+    ViennaRNA-bindings        >= 0.1.0.0   exposed-modules:     BioInf.RNAdesign     BioInf.RNAdesign.Assignment@@ -96,7 +96,7 @@     ParsecTools               >= 0.0.2 && < 0.0.3 ,     PrimitiveArray            >= 0.5              ,     RNAFold                   >= 1.99.3.3         ,-    ViennaRNA-bindings        >= 0.0.2.3+    ViennaRNA-bindings        >= 0.1.0.0   main-is:     RNAdesign.hs   ghc-options:

@@ -113,7 +113,7 @@   cmds@Config{..} <- cmdArgs config   turner <- fmap turnerToVienna $ TI.fromDir turner "" ".dat"    strs' <- fmap lines $ getContents-  let (scs,strs) = first (filter ((">"/=) . take 1)) . partition (any isAlpha) $ strs'+  let (scs,strs) = partition (any isAlpha) . filter ((">"/=) . take 1) $ strs'   unless (length strs > 0) $ error "no structures given!"   let l = length $ head strs   unless (all ((l==) . length) strs) $ error "structures of different size detected"

@@ -1,3 +1,7 @@+0.1.0.0+    * uses new ViennaRNA bindings+    * added correct name+ 0.0.2.1     * post-publication version     * allows continuous Markovian walk for special applications