BiobaseXNA 0.5.6.0 → 0.6.0.0

raw patch · 5 files changed

+180/−43 lines, 5 filesdep +repadep ~PrimitiveArrayPVP ok

version bump matches the API change (PVP)

Dependencies added: repa

Dependency ranges changed: PrimitiveArray

API changes (from Hackage documentation)

Files

• Biobase/Primary.hs +43/−1
• Biobase/Secondary.hs +74/−6
• Biobase/Secondary/Constraint.hs +13/−11
• Biobase/Secondary/Vienna.hs +38/−2
• BiobaseXNA.cabal +12/−23

@@ -1,3 +1,4 @@+{-# LANGUAGE TypeOperators #-} {-# LANGUAGE PatternGuards #-} {-# LANGUAGE OverlappingInstances #-} {-# LANGUAGE FlexibleInstances #-}@@ -18,10 +19,13 @@  module Biobase.Primary where +import Data.Array.Repa.Index+import Data.Array.Repa.Shape import Data.Char (toUpper) import Data.Ix (Ix(..)) import Data.Primitive.Types import Data.Tuple (swap)+import GHC.Base (remInt,quotInt) import qualified Data.ByteString.Char8 as BS import qualified Data.ByteString.Lazy.Char8 as BSL import qualified Data.Text as T@@ -55,7 +59,7 @@ newtype Nuc = Nuc {unNuc :: Int}   deriving (Eq,Ord,Ix) -(nN : nA : nC : nG : nT : nIMI : _) = map Nuc [0 .. ]+(nN : nA : nC : nG : nT : nIMI : nUndefined : _) = map Nuc [0 .. ] nU = nT  acgt = [nA..nT]@@ -114,6 +118,44 @@ deriving instance VGM.MVector VU.MVector Nuc deriving instance VG.Vector VU.Vector Nuc deriving instance VU.Unbox Nuc++-- Shape-based indexing. Nucleotide representations go from nN (0) to nU (4),+-- with additional symbols being available for specialized problems. This is a+-- bit of a problem for shape-based indexing. In particular, we need to be+-- careful with size operations. To include, say, all of nN to nU one needs a+-- size of (z:.nIMI), as nIMI is the first element not in the size anymore.++instance (Shape sh,Show sh) => Shape (sh :. Nuc) where+  rank (sh:._) = rank sh + 1+  zeroDim = zeroDim:.Nuc 0+  unitDim = unitDim:.Nuc 1 -- TODO does this one make sense?+  intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2+  addDim (sh1:.Nuc n1) (sh2:.Nuc n2) = addDim sh1 sh2 :. Nuc (n1+n2) -- TODO will not necessarily yield a valid Nuc+  size (sh1:.Nuc n) = size sh1 * n+  sizeIsValid (sh1:.Nuc n) = sizeIsValid (sh1:.n)+  toIndex (sh1:.Nuc sh2) (sh1':.Nuc sh2') = toIndex (sh1:.sh2) (sh1':.sh2')+  fromIndex (ds:.Nuc d) n = fromIndex ds (n `quotInt` d) :. Nuc r where+                              r | rank ds == 0 = n+                                | otherwise    = n `remInt` d+  inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx+  listOfShape (sh:.Nuc n) = n : listOfShape sh+  shapeOfList xx = case xx of+    []   -> error "empty list in shapeOfList/Primary"+    x:xs -> shapeOfList xs :. Nuc x+  deepSeq (sh:.n) x = deepSeq sh (n `seq` x)+  {-# INLINE rank #-}+  {-# INLINE zeroDim #-}+  {-# INLINE unitDim #-}+  {-# INLINE intersectDim #-}+  {-# INLINE addDim #-}+  {-# INLINE size #-}+  {-# INLINE sizeIsValid #-}+  {-# INLINE toIndex #-}+  {-# INLINE fromIndex #-}+  {-# INLINE inShapeRange #-}+  {-# INLINE listOfShape #-}+  {-# INLINE shapeOfList #-}+  {-# INLINE deepSeq #-}  -- | The bounded instance from GHC proper. Captures all defined symbols. 

@@ -1,3 +1,4 @@+{-# LANGUAGE TypeOperators #-} {-# LANGUAGE FunctionalDependencies #-} {-# LANGUAGE PatternGuards #-} {-# LANGUAGE FlexibleInstances #-}@@ -15,14 +16,17 @@  module Biobase.Secondary where +import Data.Array.Repa.Index+import Data.Array.Repa.Shape+import Data.Char (toLower, toUpper)+import Data.Ix (Ix(..))+import Data.List as L import Data.Primitive.Types+import Data.Tuple (swap)+import GHC.Base (remInt,quotInt) import qualified Data.Vector.Generic as VG import qualified Data.Vector.Generic.Mutable as VGM import qualified Data.Vector.Unboxed as VU-import Data.Ix (Ix(..))-import Data.Tuple (swap)-import Data.List as L-import Data.Char (toLower, toUpper)  import Biobase.Primary import Biobase.Primary.Bounds@@ -46,8 +50,40 @@ newtype Edge = Edge {unEdge :: Int}   deriving (Eq,Ord,Ix) -(wc : sugar : hoogsteen : unknownEdge : _) = map Edge [0..]+instance (Shape sh,Show sh) => Shape (sh :. Edge) where+  rank (sh:._) = rank sh + 1+  zeroDim = zeroDim:.Edge 0+  unitDim = unitDim:.Edge 1 -- TODO does this one make sense?+  intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2+  addDim (sh1:.Edge n1) (sh2:.Edge n2) = addDim sh1 sh2 :. Edge (n1+n2) -- TODO will not necessarily yield a valid Edge+  size (sh1:.Edge n) = size sh1 * n+  sizeIsValid (sh1:.Edge n) = sizeIsValid (sh1:.n)+  toIndex (sh1:.Edge sh2) (sh1':.Edge sh2') = toIndex (sh1:.sh2) (sh1':.sh2')+  fromIndex (ds:.Edge d) n = fromIndex ds (n `quotInt` d) :. Edge r where+                              r | rank ds == 0 = n+                                | otherwise    = n `remInt` d+  inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx+  listOfShape (sh:.Edge n) = n : listOfShape sh+  shapeOfList xx = case xx of+    []   -> error "empty list in shapeOfList/Primary"+    x:xs -> shapeOfList xs :. Edge x+  deepSeq (sh:.n) x = deepSeq sh (n `seq` x)+  {-# INLINE rank #-}+  {-# INLINE zeroDim #-}+  {-# INLINE unitDim #-}+  {-# INLINE intersectDim #-}+  {-# INLINE addDim #-}+  {-# INLINE size #-}+  {-# INLINE sizeIsValid #-}+  {-# INLINE toIndex #-}+  {-# INLINE fromIndex #-}+  {-# INLINE inShapeRange #-}+  {-# INLINE listOfShape #-}+  {-# INLINE shapeOfList #-}+  {-# INLINE deepSeq #-} +(wc : sugar : hoogsteen : unknownEdge : edgeUndefined : _) = map Edge [0..]+ charEdgeList =   [ ('W',wc)   , ('S',sugar)@@ -78,7 +114,39 @@ newtype CTisomerism = CT {unCT :: Int}   deriving (Eq,Ord,Ix) -(cis : trans : unknownCT : _) = map CT [0..]+instance (Shape sh,Show sh) => Shape (sh :. CTisomerism) where+  rank (sh:._) = rank sh + 1+  zeroDim = zeroDim:.CT 0+  unitDim = unitDim:.CT 1 -- TODO does this one make sense?+  intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2+  addDim (sh1:.CT n1) (sh2:.CT n2) = addDim sh1 sh2 :. CT (n1+n2) -- TODO will not necessarily yield a valid CT+  size (sh1:.CT n) = size sh1 * n+  sizeIsValid (sh1:.CT n) = sizeIsValid (sh1:.n)+  toIndex (sh1:.CT sh2) (sh1':.CT sh2') = toIndex (sh1:.sh2) (sh1':.sh2')+  fromIndex (ds:.CT d) n = fromIndex ds (n `quotInt` d) :. CT r where+                              r | rank ds == 0 = n+                                | otherwise    = n `remInt` d+  inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx+  listOfShape (sh:.CT n) = n : listOfShape sh+  shapeOfList xx = case xx of+    []   -> error "empty list in shapeOfList/Primary"+    x:xs -> shapeOfList xs :. CT x+  deepSeq (sh:.n) x = deepSeq sh (n `seq` x)+  {-# INLINE rank #-}+  {-# INLINE zeroDim #-}+  {-# INLINE unitDim #-}+  {-# INLINE intersectDim #-}+  {-# INLINE addDim #-}+  {-# INLINE size #-}+  {-# INLINE sizeIsValid #-}+  {-# INLINE toIndex #-}+  {-# INLINE fromIndex #-}+  {-# INLINE inShapeRange #-}+  {-# INLINE listOfShape #-}+  {-# INLINE shapeOfList #-}+  {-# INLINE deepSeq #-}++(cis : trans : unknownCT : undefinedCT : _) = map CT [0..] antiCT = undefined paraCT = undefined 

@@ -6,6 +6,8 @@  module Biobase.Secondary.Constraint where +import Data.Array.Repa.Index+import Data.Array.Repa.Shape import Data.Char (toLower) import Data.Primitive.Types import qualified Data.Vector.Generic as VG@@ -13,7 +15,7 @@ import qualified Data.Vector.Unboxed as VU  import Data.PrimitiveArray-import Data.PrimitiveArray.Ix+import Data.PrimitiveArray.Unboxed  import Biobase.Secondary.Diagrams @@ -48,49 +50,49 @@ -- TODO and again, we should parametrize over "Energy", "Score", etc (that is, -- Prim a) -bonusTable :: Double -> Double -> Constraint -> PrimArray (Int,Int) Double+bonusTable :: Double -> Double -> Constraint -> PrimArray DIM2 Double bonusTable bonus malus (Constraint constraint) = arr where-  arr = fromAssocs (0,0) (n,n) 0 $ bonusBr ++ bonusAn ++ bonusBa ++ malusBr ++ malusAn ++ malusX+  arr = fromAssocs zeroDim (Z:.n:.n) 0 $ bonusBr ++ bonusAn ++ bonusBa ++ malusBr ++ malusAn ++ malusX   n = VU.length constraint -1   infixl 1 `xor`   xor a b = a && not b || not a && b   -- "()" bonus energies-  bonusBr = [ ((i,j),bonus)+  bonusBr = [ (Z:.i:.j,bonus)             | (i,('(',j)) <- zip [0..] $ VU.toList constraint             ]-  malusBr = [ ((i,j),malus)+  malusBr = [ (Z:.i:.j,malus)             | i <- [0..n]             , j <- [i..n]             , let bi = constraint VU.! i             , let bj = constraint VU.! j             , fst bi == '(' && snd bi /= j || fst bj == ')' && snd bj /= i             ]-  bonusAn = [ ((i,j),bonus)+  bonusAn = [ (Z:.i:.j,bonus)             | i<-[0..n]             , fst (constraint VU.! i) == '<'             , j<-[i+1..n]             ] ++-            [ ((i,j),bonus)+            [ (Z:.i:.j,bonus)             | j<-[0..n]             , fst (constraint VU.! j) == '>'             , i<-[0..j-1]             ]-  malusAn = [ ((i,j),malus)+  malusAn = [ (Z:.i:.j,malus)             | i<-[0..n]             , j<-[i+1..n]             , fst (constraint VU.! j) == '<'             ] ++-            [ ((i,j),malus)+            [ (Z:.i:.j,malus)             | i<-[0..n]             , j<-[i+1..n]             , fst (constraint VU.! i) == '>'             ]-  bonusBa = [ ((i,j),bonus)+  bonusBa = [ (Z:.i:.j,bonus)             | i<-[0..n]             , j<-[i+1..n]             , fst (constraint VU.! i) == '|' || fst (constraint VU.! j) == '|'             ]-  malusX  = [ ((i,j),malus)+  malusX  = [ (Z:.i:.j,malus)             | i<-[0..n]             , j<-[i+1..n]             , fst (constraint VU.! i) == 'x' || fst (constraint VU.! j) == 'x'

@@ -1,3 +1,4 @@+{-# LANGUAGE TypeOperators #-} {-# LANGUAGE PatternGuards #-} {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE GeneralizedNewtypeDeriving #-}@@ -8,12 +9,15 @@  module Biobase.Secondary.Vienna where +import Data.Array.Repa.Index+import Data.Array.Repa.Shape import Data.Ix import Data.Primitive.Types+import Data.Tuple (swap)+import GHC.Base (remInt,quotInt) 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@@ -25,7 +29,39 @@ newtype ViennaPair = ViennaPair Int   deriving (Eq,Ord,Ix) -(vpNP:vpCG:vpGC:vpGU:vpUG:vpAU:vpUA:vpNS:_) = map ViennaPair [0..]+instance (Shape sh,Show sh) => Shape (sh :. ViennaPair) where+  rank (sh:._) = rank sh + 1+  zeroDim = zeroDim:.ViennaPair 0+  unitDim = unitDim:.ViennaPair 1 -- TODO does this one make sense?+  intersectDim (sh1:.n1) (sh2:.n2) = intersectDim sh1 sh2 :. min n1 n2+  addDim (sh1:.ViennaPair n1) (sh2:.ViennaPair n2) = addDim sh1 sh2 :. ViennaPair (n1+n2) -- TODO will not necessarily yield a valid ViennaPair+  size (sh1:.ViennaPair n) = size sh1 * n+  sizeIsValid (sh1:.ViennaPair n) = sizeIsValid (sh1:.n)+  toIndex (sh1:.ViennaPair sh2) (sh1':.ViennaPair sh2') = toIndex (sh1:.sh2) (sh1':.sh2')+  fromIndex (ds:.ViennaPair d) n = fromIndex ds (n `quotInt` d) :. ViennaPair r where+                              r | rank ds == 0 = n+                                | otherwise    = n `remInt` d+  inShapeRange (sh1:.n1) (sh2:.n2) (idx:.i) = i>=n1 && i<n2 && inShapeRange sh1 sh2 idx+  listOfShape (sh:.ViennaPair n) = n : listOfShape sh+  shapeOfList xx = case xx of+    []   -> error "empty list in shapeOfList/Primary"+    x:xs -> shapeOfList xs :. ViennaPair x+  deepSeq (sh:.n) x = deepSeq sh (n `seq` x)+  {-# INLINE rank #-}+  {-# INLINE zeroDim #-}+  {-# INLINE unitDim #-}+  {-# INLINE intersectDim #-}+  {-# INLINE addDim #-}+  {-# INLINE size #-}+  {-# INLINE sizeIsValid #-}+  {-# INLINE toIndex #-}+  {-# INLINE fromIndex #-}+  {-# INLINE inShapeRange #-}+  {-# INLINE listOfShape #-}+  {-# INLINE shapeOfList #-}+  {-# INLINE deepSeq #-}++(vpNP:vpCG:vpGC:vpGU:vpUG:vpAU:vpUA:vpNS:vpUndefined:_) = map ViennaPair [0..]  class MkViennaPair a where   mkViennaPair :: a -> ViennaPair

@@ -1,16 +1,16 @@ name:           BiobaseXNA-version:        0.5.6.0+version:        0.6.0.0 author:         Christian Hoener zu Siederdissen maintainer:     choener@tbi.univie.ac.at homepage:       http://www.tbi.univie.ac.at/~choener/-copyright:      Christian Hoener zu Siederdissen, 2011+copyright:      Christian Hoener zu Siederdissen, 2011-2012 category:       Bioinformatics synopsis:       Efficient RNA/DNA representations license:        GPL-3 license-file:   LICENSE build-type:     Simple stability:      experimental-cabal-version:  >= 1.4.0+cabal-version:  >= 1.6.0 description:                 This is a base library for bioinformatics with emphasis on RNA                 and DNA primary structure and related tools. Provided are@@ -30,25 +30,9 @@                 .                 .                 .-                Changes since 0.5.5.0-                .-                * isostericity for the 6 "missing" classes-                .-                Changes since 0.5.4.0-                .-                * tuple-like updating (updL, updR, updP, updT)-                .-                * baseP pair selection-                .-                * isostericity data, loaded from csv files-                .-                Changes since 0.5.3.0-                .-                * tuple-like (selN) selection of basepairing elements (baseL,baseR,baseT)-                .-                Changes since 0.5.1.0+                New in 0.6.0.0                 .-                * bonusTable for constrained folding+                * Updated to PrimitiveArrays >= 0.1  extra-source-files:   sources/isostericity-matrices.csv@@ -65,7 +49,8 @@     text,     tuple,     vector >=0.9 && <0.10,-    PrimitiveArray+    repa >= 2,+    PrimitiveArray >= 0.1.1.2    exposed-modules:     Biobase.Primary@@ -79,5 +64,9 @@     Biobase.Secondary.Vienna    ghc-options:-    -O2+    -Odph -funbox-strict-fields++source-repository head+  type: git+  location: git://github.com/choener/BiobaseXNA