BiobaseXNA 0.5.0.1 → 0.5.1.0

raw patch · 3 files changed

+140/−24 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Biobase/Secondary.hs +30/−23
• Biobase/Secondary/Vienna.hs +108/−0
• BiobaseXNA.cabal +2/−1

@@ -38,28 +38,6 @@   = (c',x',y')   | otherwise = error $ "can't convert string: " ++ s --- | A basepair is simply a pair of Ints which are 0-indexing a sequence.------ TODO storable vector, newtype, peek/poke?--type PairIdx = (Int,Int)---- | A pair as a tuple containing 'Nuc's.--type Pair = (Nuc,Nuc)---- | Annotation for a basepair.--type ExtPairAnnotation = (CTisomerism,Edge,Edge)---- | An extended basepair is a basepair, annotated with edge and CTisomerism.--type ExtPairIdx = (PairIdx,ExtPairAnnotation)---- | An extended basepair, with nucleotides an annotation.--type ExtPair = (Pair,ExtPairAnnotation)- -- | Each nucleotide in a pair may be paired using one of three edges: -- watson-crik, sugar, or hoogsteen. @@ -172,11 +150,40 @@   toEnum   = CT   fromEnum = unCT --- ** special show instances ++-- * Types++-- | A basepair is simply a pair of Ints which are 0-indexing a sequence.+--+-- TODO storable vector, newtype, peek/poke?++type PairIdx = (Int,Int)++-- | A pair as a tuple containing 'Nuc's.++type Pair = (Nuc,Nuc)++-- | Annotation for a basepair.++type ExtPairAnnotation = (CTisomerism,Edge,Edge)++-- | An extended basepair is a basepair, annotated with edge and CTisomerism.++type ExtPairIdx = (PairIdx,ExtPairAnnotation)++-- | An extended basepair, with nucleotides an annotation.++type ExtPair = (Pair,ExtPairAnnotation)++++-- * special show instances+ -- | This one requires ghc head -- -- TODO maybe newtype this triple?  --instance Show (CTisomerism,Edge,Edge) where --  show (ct,eI,eJ) = concat [show ct, show eI, show eJ]+

@@ -0,0 +1,108 @@+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE StandaloneDeriving #-}++-- | Encoding of Watson-Crick and Wobble Pairs in the Vienna RNA package style.++module Biobase.Secondary.Vienna where++import Data.Ix+import Data.Primitive.Types+import qualified Data.Vector.Generic as VG+import qualified Data.Vector.Generic.Mutable as VGM+import qualified Data.Vector.Unboxed as VU+import Data.Tuple (swap)++import Biobase.Primary+import Biobase.Primary.Bounds++++-- | Use machine Ints internally++newtype ViennaPair = ViennaPair Int+  deriving (Eq,Ord,Ix)++(vpNP:vpCG:vpGC:vpGU:vpUG:vpAU:vpUA:vpNS:_) = map ViennaPair [0..]++class MkViennaPair a where+  mkViennaPair :: a -> ViennaPair+  fromViennaPair :: ViennaPair -> a++instance MkViennaPair (Nuc,Nuc) where+  mkViennaPair (b1,b2)+    | b1==nC&&b2==nG = vpCG+    | b1==nG&&b2==nC = vpGC+    | b1==nG&&b2==nU = vpGU+    | b1==nU&&b2==nG = vpUG+    | b1==nA&&b2==nU = vpAU+    | b1==nU&&b2==nA = vpUA+    | otherwise = vpNS+  fromViennaPair p+    | p==vpCG = (nC,nG)+    | p==vpGC = (nG,nC)+    | p==vpGU = (nG,nU)+    | p==vpUG = (nU,nG)+    | p==vpAU = (nA,nU)+    | p==vpUA = (nU,nA)+    | otherwise = error "non-standard pairs can't be backcasted"++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+    | x>=0 && x<=7 = ViennaPair x+    | otherwise    = error $ "can't make to enum" ++ show x+  fromEnum (ViennaPair x) = x+  {-# INLINE toEnum #-}+  {-# INLINE fromEnum #-}++instance Bounded ViennaPair where+  minBound = vpNP+  maxBound = vpNS++instance Bounds ViennaPair where+  minNormal = vpCG+  maxNormal = vpUA+  minExtended = vpNP+  maxExtended = vpNS++instance Show ViennaPair where+  show x+    | Just s <- x `lookup` pairToString = s++instance Read ViennaPair where+  readsPrec p [] = []+  readsPrec p [x] = []+  readsPrec p (x:y:xs)+    | x ==' ' = readsPrec p (y:xs)+    | Just n <- (x:y:[]) `lookup` s2p = [(n,xs)]+    | otherwise = []+    where s2p = (map swap pairToString)++++-- | reverse a vienna pair++revPair :: ViennaPair -> ViennaPair+revPair p+  | p==vpCG = vpGC+  | p==vpGC = vpCG+  | p==vpGU = vpUG+  | p==vpUG = vpGU+  | p==vpAU = vpUA+  | p==vpUA = vpAU+  | p==vpNP = vpNP+  | p==vpNS = vpNS++++-- * Convenience structures++cguaP = [vpCG..vpUA]+cgnsP = [vpCG..vpNS]+pairToString = [(vpCG,"CG"),(vpGC,"GC"),(vpUA,"UA"),(vpAU,"AU"),(vpGU,"GU"),(vpUG,"UG"),(vpNS,"NS"),(vpNP,"NP")]

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.5.0.1+version:        0.5.1.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -38,6 +38,7 @@     Biobase.Secondary.Constraint     Biobase.Secondary.Diagrams     Biobase.Secondary.PseudoKnots+    Biobase.Secondary.Vienna    ghc-options:     -O2