Biobase 0.0.2.0 → 0.0.2.1

raw patch · 2 files changed

+19/−6 lines, 2 filesdep ~vectorPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: vector

API changes (from Hackage documentation)

- Biobase.Structure: instance (Eq a) => Eq (SSTree a)

- Biobase.Structure: instance (Read a) => Read (SSTree a)

- Biobase.Structure: instance (Show a) => Show (SSTree a)

+ Biobase.RNA: instance Prim ViennaPair

+ Biobase.Structure: instance Eq a => Eq (SSTree a)

+ Biobase.Structure: instance Read a => Read (SSTree a)

+ Biobase.Structure: instance Show a => Show (SSTree a)

- Biobase.RNA: mkPrimary :: (MkPrimary a) => a -> Primary

+ Biobase.RNA: mkPrimary :: MkPrimary a => a -> Primary

- Biobase.RNA: unPrimary :: (MkPrimary a) => Primary -> a

+ Biobase.RNA: unPrimary :: MkPrimary a => Primary -> a

Files

Biobase.cabal +5/−5
Biobase/RNA.hs +14/−1

Biobase.cabal view

@@ -1,5 +1,5 @@ name:           Biobase-version:        0.0.2.0+version:        0.0.2.1 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/Haskell/@@ -23,10 +23,10 @@ library   build-depends:     array,-    base >= 4 && < 5,-    vector >= 0.6 && < 7,-    primitive >= 0.3 && < 0.4,-    PrimitiveArray >= 0.0.2.1 && < 0.0.3+    base >=4 && <5,+    vector >=0.7 && <8,+    primitive >=0.3 && <0.4,+    PrimitiveArray >=0.0.2.1 && <0.0.3    exposed-modules:     Biobase.Constants

Biobase/RNA.hs view

@@ -119,6 +119,7 @@ deriving instance VGM.MVector VU.MVector ViennaPair deriving instance VG.Vector VU.Vector ViennaPair deriving instance VU.Unbox ViennaPair+deriving instance Prim ViennaPair  instance Enum ViennaPair where   toEnum x@@ -160,8 +161,19 @@  -- * Transformations between Nucleotide and ViennaPair +pairTable = fromAssocs (nucE,nucE) (nucU,nucU) vpNP+  [ ((nucC,nucG),vpCG)+  , ((nucG,nucC),vpGC)+  , ((nucG,nucU),vpGU)+  , ((nucU,nucG),vpUG)+  , ((nucA,nucU),vpAU)+  , ((nucU,nucA),vpUA)+  ]+{- NOINLINE pairTable #-}+ toPair :: Nucleotide -> Nucleotide -> ViennaPair-toPair x y+toPair x y = pairTable ! (x,y)+{-   | x==nucC&&y==nucG = vpCG   | x==nucG&&y==nucC = vpGC   | x==nucG&&y==nucU = vpGU@@ -169,6 +181,7 @@   | x==nucA&&y==nucU = vpAU   | x==nucU&&y==nucA = vpUA   | otherwise        = vpNP+-} {-# INLINE toPair #-}  pairs :: Nucleotide -> Nucleotide -> Bool