BiobaseXNA 0.5.3.0 → 0.5.4.0

raw patch · 2 files changed

+65/−1 lines, 2 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• Biobase/Secondary.hs +60/−0
• BiobaseXNA.cabal +5/−1

@@ -1,3 +1,4 @@+{-# LANGUAGE FunctionalDependencies #-} {-# LANGUAGE PatternGuards #-} {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE GeneralizedNewtypeDeriving #-}@@ -36,6 +37,7 @@   , Just x' <- L.lookup (toUpper x) charEdgeList   , Just y' <- L.lookup (toUpper y) charEdgeList   = (c',x',y')+  | map toLower s == "bif" = (unknownCT,unknownEdge,unknownEdge)   | otherwise = error $ "can't convert string: " ++ s  -- | Each nucleotide in a pair may be paired using one of three edges:@@ -83,7 +85,9 @@ charCTList =   [ ('c',cis)   , ('t',trans)+  , ('?',unknownCT)   -- TODO antiCT, paraCT+  -- TODO '?' type (??? could denote bifurcation)   ]  ctCharList = map swap charCTList@@ -178,6 +182,28 @@   +-- * little helpers++cWW = (cis,wc,wc)+cWS = (cis,wc,sugar)+cWH = (cis,wc,hoogsteen)+cSW = (cis,sugar,wc)+cSS = (cis,sugar,sugar)+cSH = (cis,sugar,hoogsteen)+cHW = (cis,hoogsteen,wc)+cHS = (cis,hoogsteen,sugar)+cHH = (cis,hoogsteen,hoogsteen)+tWW = (trans,wc,wc)+tWS = (trans,wc,sugar)+tWH = (trans,wc,hoogsteen)+tSW = (trans,sugar,wc)+tSS = (trans,sugar,sugar)+tSH = (trans,sugar,hoogsteen)+tHW = (trans,hoogsteen,wc)+tHS = (trans,hoogsteen,sugar)+tHH = (trans,hoogsteen,hoogsteen)++ -- * special show instances  -- | This one requires ghc head@@ -187,3 +213,37 @@ --instance Show (CTisomerism,Edge,Edge) where --  show (ct,eI,eJ) = concat [show ct, show eI, show eJ] +++-- * tuple-like selection++-- | Selection of nucleotides and/or type classes independent of which type we+-- are looking at.++class BaseSelect a b | a -> b where+  -- |  select first index or nucleotide+  baseL :: a -> b+  -- | select second index or nucleotide+  baseR :: a -> b+  -- | select basepair type if existing or return default cWW+  baseT :: a -> ExtPairAnnotation++-- | extended pairtype annotation given++instance BaseSelect ((a,a),ExtPairAnnotation) a where+  baseL ((a,_),_) = a+  baseR ((_,b),_) = b+  baseT (_,t) = t+  {-# INLINE baseL #-}+  {-# INLINE baseR #-}+  {-# INLINE baseT #-}++-- | simple cis/wc-wc basepairs++instance BaseSelect (a,a) a where+  baseL (a,_) = a+  baseR (_,a) = a+  baseT _ = cWW+  {-# INLINE baseL #-}+  {-# INLINE baseR #-}+  {-# INLINE baseT #-}

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.5.3.0+version:        0.5.4.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/@@ -17,6 +17,10 @@                 efficient encodings for short sequences, as required by RNA                 folding tools. Extended RNA secondary structures can be                 represented as well.+                .+                Changes since 0.5.3.0+                .+                * tuple-like (selN) selection of basepairing elements (baseL,baseR,baseT)                 .                 Changes since 0.5.1.0                 .