RNAFold 1.99.1.2 → 1.99.1.3

raw patch · 2 files changed

+29/−22 lines, 2 filesdep ~ADPfusiondep ~BiobaseViennadep ~BiobaseXNAPVP ok

version bump matches the API change (PVP)

Dependency ranges changed: ADPfusion, BiobaseVienna, BiobaseXNA, PrimitiveArray

API changes (from Hackage documentation)

Files

• BioInf/RNAfold.hs +15/−6
• RNAFold.cabal +14/−16

@@ -1,3 +1,4 @@+{-# LANGUAGE ScopedTypeVariables #-} {-# LANGUAGE BangPatterns #-} {-# LANGUAGE TypeOperators #-} {-# LANGUAGE TupleSections #-}@@ -90,15 +91,23 @@       hS = ScalarM . S.foldl' min (999999::Int)       {-# INLINE hS #-} -  weak   <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []-  block  <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []-  comps  <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []-  struct <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 0 []+  weak   :: MArr0 s DIM2 Int <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []+  block  :: MArr0 s DIM2 Int <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []+  comps  :: MArr0 s DIM2 Int <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 999999 []+  struct :: MArr0 s DIM2 Int <- fromAssocsM (Z:.0:.0) (Z:.n:.n) 0 [] +  let iif = iloopIF ener <<< primary #~~ weak ~~# primary ... hS+      {-# INLINE [0] iif #-}++  let mif = multiIF ener <<< block +~+ comps ... hS+      {-# INLINE [0] mif #-}+   fillTables     weak (-      multiOF   ener <<< baseLr -~+ (multiIF ener <<< block +~+ comps              ... hS) +~- baselR |||-      iloopOF   ener <<< baseLr -~+ (iloopIF ener <<< primary #~~ weak ~~# primary ... hS) +~- baselR |||+      -- multiOF   ener <<< baseLr -~+ (multiIF ener <<< block +~+ comps              ... hS) +~- baselR |||+      multiOF   ener <<< baseLr -~+ mif +~- baselR |||+      -- iloopOF   ener <<< baseLr -~+ (iloopIF ener <<< primary #~~ weak ~~# primary ... hS) +~- baselR |||+      iloopOF   ener <<< baseLr -~+ iif +~- baselR |||       iloop1NF  ener <<< primary ---~+ weak +~@   primary   |||       iloopN1F  ener <<< primary   @~+ weak +~--- primary   |||       bulgeRF   ener <<< baseLr    -~+ weak +~*   primary   |||

@@ -1,5 +1,5 @@ name:           RNAFold-version:        1.99.1.2+version:        1.99.1.3 author:         Christian Hoener zu Siederdissen (Haskell), Ivo L. Hofacker et al (ViennaRNA), 2010-2012 copyright:      Christian Hoener zu Siederdissen, 2010-2012 homepage:       http://www.tbi.univie.ac.at/~choener/adpfusion@@ -44,21 +44,24 @@     strict         >= 0.3.2,     primitive      == 0.4.*   ,     vector         == 0.9.*   ,-    PrimitiveArray == 0.2.1.1 ,-    BiobaseVienna  == 0.2.2.4 ,-    BiobaseXNA     == 0.6.2.4 ,-    ADPfusion      == 0.0.1.1+    PrimitiveArray == 0.2.2.0 ,+    BiobaseVienna  == 0.2.2.5 ,+    BiobaseXNA     == 0.6.2.5 ,+    ADPfusion      == 0.0.1.2   exposed-modules:     BioInf.RNAfold     BioInf.RNAfold.Combinators     BioInf.RNAfold.Energy     BioInf.RNAfold.Library   ghc-options:-    -Odph+    -O2     -funbox-strict-fields     -fspec-constr+    -fspec-constr-threshold=500+    -fspec-constr-count=10     -funfolding-use-threshold100     -funfolding-keeness-factor100+    -fsimplifier-phases10   if flag (llvm)     ghc-options:       -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts@@ -67,15 +70,7 @@  executable RNAFold   build-depends:---    base >= 4 && < 5,---    mtl,---    strict,---    primitive      == 0.4.*   ,---    vector         == 0.9.*   ,---    PrimitiveArray == 0.2.1.1 ,---    BiobaseVienna  == 0.2.2.3 ,---    BiobaseXNA     == 0.6.2.2 ,---    ADPfusion      == 0.0.1.0+--    we get all build depends from the library dependencies   main-is:     RNAFold.hs   other-modules:@@ -85,11 +80,14 @@     BioInf.RNAfold.Library   ghc-options:     -rtsopts-    -Odph+    -O2     -funbox-strict-fields     -fspec-constr+    -fspec-constr-threshold=500+    -fspec-constr-count=10     -funfolding-use-threshold100     -funfolding-keeness-factor100+    -fsimplifier-phases10   if flag (llvm)     ghc-options:       -fllvm -optlo-O3 -optlo-inline -optlo-std-compile-opts