BiobaseXNA (empty) → 0.5.0.0

raw patch · 10 files changed

+1437/−0 lines, 10 filesdep +basedep +bytestringdep +primitivesetup-changed

Dependencies added: base, bytestring, primitive, text, tuple, vector, vector-read-instances

Files

Biobase/Primary.hs +150/−0
Biobase/Primary/Bounds.hs +52/−0
Biobase/Primary/Hashed.hs +44/−0
Biobase/Secondary.hs +168/−0
Biobase/Secondary/Constraint.hs +44/−0
Biobase/Secondary/Diagrams.hs +203/−0
Biobase/Secondary/PseudoKnots.hs +55/−0
BiobaseXNA.cabal +44/−0
LICENSE +675/−0
Setup.hs +2/−0

+ Biobase/Primary.hs view

@@ -0,0 +1,150 @@+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE TypeSynonymInstances #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE StandaloneDeriving #-}++-- | The primary structure: interface to efficient encoding of RNA and DNA+-- sequences. The design aims toward the 'vector' library and repa. In+-- particular, everything is strict; if you want to stream full genomes, use+-- 'text' or lazy 'bytestring's instead and cast to Biobase.Primary definitions+-- only at the last moment.+--+-- NOTE individual nucleotides are encoded is 'Int's internally without any+-- tagging. This means that we have no way of deciding if we are dealing with+-- RNA or DNA on this level.++module Biobase.Primary where++import Data.Char (toUpper)+import Data.Ix (Ix(..))+import Data.Primitive.Types+import Data.Tuple (swap)+import qualified Data.ByteString.Char8 as BS+import qualified Data.ByteString.Lazy.Char8 as BSL+import qualified Data.Text as T+import qualified Data.Vector.Generic as VG+import qualified Data.Vector.Generic.Mutable as VGM+import qualified Data.Vector.Unboxed as VU++import Biobase.Primary.Bounds++++-- * Convert different types of sequence representations to the internal+-- "Primary Structure" representation++-- | Given a sequence of nucleotides encoded in some "text-form", create a+-- 'Nuc'-based unboxed vector.++class MkPrimary a where+  mkPrimary :: a -> Primary++type Primary = VU.Vector Nuc++++-- * Efficient nucleotide encoding++-- A 'Nuc'leotide is simply an Int wrapped up.++newtype Nuc = Nuc {unNuc :: Int}+  deriving (Eq,Ord,Ix)++(nN : nA : nC : nG : nT : _) = map Nuc [0 .. ]+nU = nT++acgt = [nA..nT]+acgu = acgt+nacgt = [nN..nT]+nacgu = nacgt++-- | Translate between 'Char's and 'Nuc's.++mkNuc :: Char -> Nuc+mkNuc = f . toUpper where+  f k+    | Just v <- k `lookup` charNucList = v+    | otherwise = nN++fromNuc :: Nuc -> Char+fromNuc = f where+  f k+    | Just v <- k `lookup` nucCharList = v+    | otherwise = 'N'++charNucList =+  [ ('N',nN)+  , ('A',nA)+  , ('C',nC)+  , ('G',nG)+  , ('T',nT)+  , ('U',nU)+  ]++nucCharList = map swap charNucList++++-- * Instances of different type classes++-- ** instances for 'Nuc'++-- | Human-readable Show instance.++instance Show Nuc where+  show n = [fromNuc n]++-- | Human-readable Read instance.++instance Read Nuc where+  readsPrec p [] = []+  readsPrec p (x:xs)+    | x ==' ' = readsPrec p xs+    | Just n <- x `lookup` charNucList = [(n,xs)]+    | otherwise = []++-- for vectors++deriving instance Prim Nuc+deriving instance VGM.MVector VU.MVector Nuc+deriving instance VG.Vector VU.Vector Nuc+deriving instance VU.Unbox Nuc++-- | The bounded instance from GHC proper. Captures all defined symbols.++instance Bounded Nuc where+  minBound = nN+  maxBound = nT++-- | Special bounds for energy / score arrays++instance Bounds Nuc where+  minNormal = nA+  maxNormal = nT+  minExtended = nN+  maxExtended = nT++-- | Enum++instance Enum Nuc where+  toEnum = Nuc+  fromEnum = unNuc++-- ** Instances for 'MkPrimary'++instance MkPrimary String where+  mkPrimary = VU.fromList . map mkNuc++instance MkPrimary BS.ByteString where+  mkPrimary = mkPrimary . BS.unpack++instance MkPrimary BSL.ByteString where+  mkPrimary = mkPrimary . BSL.unpack++instance MkPrimary T.Text where+  mkPrimary = mkPrimary . T.unpack++instance MkPrimary [Nuc] where+  mkPrimary = VU.fromList+

+ Biobase/Primary/Bounds.hs view

@@ -0,0 +1,52 @@++-- | A special class of bounds for RNA/pair encodings that are used to index+-- into tables. We typically encode more in the alphabets than we want to use+-- to index, so in order to keep things simple, we have specialized bounds.++module Biobase.Primary.Bounds where++++-- | 'minNormal' and 'maxNormal' encode for, say, ACGU; while 'minExtended' and+-- 'maxExtended' would allow 'N' as well. See Biobase.RNA and+-- Biobase.RNA.ViennaPair for instances.++class Bounded a => Bounds a where+  minNormal :: a+  maxNormal :: a+  minExtended :: a+  maxExtended :: a++++-- * Instances for tuples of size 2-6++instance (Bounds a, Bounds b) => Bounds (a,b) where+  minNormal = (minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal)+  minExtended = (minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c) => Bounds (a,b,c) where+  minNormal = (minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d) => Bounds (a,b,c,d) where+  minNormal = (minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d, Bounds e) => Bounds (a,b,c,d,e) where+  minNormal = (minNormal, minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended, maxExtended)++instance (Bounds a, Bounds b, Bounds c, Bounds d, Bounds e, Bounds f) => Bounds (a,b,c,d,e,f) where+  minNormal = (minNormal, minNormal, minNormal, minNormal, minNormal, minNormal)+  maxNormal = (maxNormal, maxNormal, maxNormal, maxNormal, maxNormal, maxNormal)+  minExtended = (minExtended, minExtended, minExtended, minExtended, minExtended, minExtended)+  maxExtended = (maxExtended, maxExtended, maxExtended, maxExtended, maxExtended, maxExtended)

+ Biobase/Primary/Hashed.hs view

@@ -0,0 +1,44 @@+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE StandaloneDeriving #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}++-- | Fast hash functions for 'Primary' sequences. A hash is just an 'Int', so+-- use these only for short sequences.++module Biobase.Primary.Hashed where++import Control.Exception.Base (assert)+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 Biobase.Primary++++newtype HashedPrimary = HashedPrimary Int+  deriving (Eq,Ord,Ix,Read,Show,Enum,Bounded)++deriving instance Prim HashedPrimary+deriving instance VGM.MVector VU.MVector HashedPrimary+deriving instance VG.Vector VU.Vector HashedPrimary+deriving instance VU.Unbox HashedPrimary++-- | Given a piece of primary sequence information, reduce it to an index.+--+-- Will throw an assertion in debug code if 'ps' are not within bounds. Note+-- that "mkPrimary [minBound]" and "mkPrimary [minBound,minBound]" map to the+-- same index. Meaning that indices are only unique within the same length+-- group. Furthermore, indices with different (l,u)-bounds are not compatible+-- with each other. All indices start at 0.+--+-- The empty input produces an index of 0.++mkHashedPrimary :: (Nuc,Nuc) -> Primary -> HashedPrimary+mkHashedPrimary (l,u) ps = assert (VU.all (\p -> l<=p && p<=u) ps) $ HashedPrimary idx where+  idx   = VU.sum $ VU.zipWith f ps (VU.enumFromStepN (VU.length ps -1) (-1) (VU.length ps))+  f p c = (unNuc p - unNuc l) * (cnst^c)+  cnst = unNuc u - unNuc l + 1+{-# INLINE mkHashedPrimary #-}

+ Biobase/Secondary.hs view

@@ -0,0 +1,168 @@+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE StandaloneDeriving #-}++-- | Secondary structure: define basepairs as Int-tuples, the three edges, a+-- nucleotide can use for pairing and the cis/trans isomerism. Both edges and+-- cis/trans come with a tag for "unknown".+--+-- TODO set ext-annotations to be (isomerism,edge,edge) and have a asString+-- instance to read "cWW" "tSH" and other notation.++module Biobase.Secondary where++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.Ix (Ix(..))+import Data.Tuple (swap)++import Biobase.Primary+import Biobase.Primary.Bounds++++-- | 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.++newtype Edge = Edge {unEdge :: Int}+  deriving (Eq,Ord,Ix)++(wc : sugar : hoogsteen : unknownEdge : _) = map Edge [0..]++charEdgeList =+  [ ('W',wc)+  , ('S',sugar)+  , ('H',hoogsteen)+  , ('?',unknownEdge)+  ]++edgeCharList = map swap charEdgeList++-- | Human-readable Show instance.++instance Show Edge where+  show k+    | Just v <- k `lookup` edgeCharList = [v]+    | otherwise = "?"++-- | Human-readable Read instance.++instance Read Edge where+  readsPrec p [] = []+  readsPrec p (x:xs)+    | x ==' ' = readsPrec p xs+    | Just n <- x `lookup` charEdgeList = [(n,xs)]+    | otherwise = []++-- | Nucleotides in a pairing may be in the cis(==?) or trans(==?) state.++newtype CTisomerism = CT {unCT :: Int}+  deriving (Eq,Ord,Ix)++(cis : trans : unknownCT : _) = map CT [0..]+antiCT = undefined+paraCT = undefined++charCTList =+  [ ('C',cis)+  , ('T',trans)+  -- TODO antiCT, paraCT+  ]++ctCharList = map swap charCTList++-- | Human-readable Show instance.++instance Show CTisomerism where+  show k+    | Just v <- k `lookup` ctCharList = [v]+    | otherwise = "?"++-- | Human-readable Read instance.++instance Read CTisomerism where+  readsPrec p [] = []+  readsPrec p (x:xs)+    | x ==' ' = readsPrec p xs+    | Just n <- x `lookup` charCTList = [(n,xs)]+    | otherwise = []++++-- * Instances++-- ** Instances for 'Edge'++deriving instance Prim Edge+deriving instance VGM.MVector VU.MVector Edge+deriving instance VG.Vector VU.Vector Edge+deriving instance VU.Unbox Edge++instance Bounded Edge where+  minBound = wc+  maxBound = unknownEdge++instance Bounds Edge where+  minNormal = wc+  maxNormal = wc+  minExtended = wc+  maxExtended = hoogsteen++instance Enum Edge where+  toEnum   = Edge+  fromEnum = unEdge++-- ** Instances for 'CTisomerism'++deriving instance Prim CTisomerism+deriving instance VGM.MVector VU.MVector CTisomerism+deriving instance VG.Vector VU.Vector CTisomerism+deriving instance VU.Unbox CTisomerism++instance Bounded CTisomerism where+  minBound = cis+  maxBound = unknownCT++instance Bounds CTisomerism where+  minNormal = cis+  maxNormal = cis+  minExtended = cis+  maxExtended = trans++instance Enum CTisomerism where+  toEnum   = CT+  fromEnum = unCT++-- ** 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]

+ Biobase/Secondary/Constraint.hs view

@@ -0,0 +1,44 @@+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE TypeSynonymInstances #-}+{-# LANGUAGE GeneralizedNewtypeDeriving #-}+{-# LANGUAGE MultiParamTypeClasses #-}+{-# LANGUAGE StandaloneDeriving #-}++module Biobase.Secondary.Constraint where++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 Biobase.Secondary.Diagrams++++-- | We can create a constraint from different sources++class MkConstraint a where+  mkConstraint :: a -> Constraint++-- | A constraint is nothing more than a vector of constraint characters+-- together with a possible pairing for each character.++newtype Constraint = Constraint {unConstraint :: VU.Vector (Char,Int)}+  deriving (Show,Read,Eq)++bonusCC = VU.fromList "()<>|"+{-# NOINLINE bonusCC #-}++nobonusCC = VU.fromList ".x"+{-# NOINLINE nobonusCC #-}++++-- * Instances++instance MkConstraint String where+  mkConstraint xs = mkConstraint . VU.fromList $ xs++instance MkConstraint (VU.Vector Char) where+  mkConstraint cs = Constraint $ VU.zip cs ks where+    (D1S ks) = mkD1S cs

+ Biobase/Secondary/Diagrams.hs view

@@ -0,0 +1,203 @@+{-# LANGUAGE ScopedTypeVariables #-}+{-# LANGUAGE TypeSynonymInstances #-}+{-# LANGUAGE FlexibleInstances #-}++-- | Types for RNA secondary structure. Types vary from the simplest array+-- (D1Secondary) to rather complex ones.+--+-- TODO The complex ones are still coming in from other libraries.+--+-- TODO can we use Char8 instead of Char?+--+-- TODO prepare for extended RNA secondary structures!++{-# LANGUAGE RecordWildCards #-}++module Biobase.Secondary.Diagrams where++import qualified Data.Vector.Unboxed as VU+import Data.Vector.Unboxed.Read+import Data.List (sort,groupBy,sortBy)+import Data.Tuple.Select (sel1,sel2)+import Data.Tuple (swap)+import Control.Arrow++import Biobase.Primary+import Biobase.Secondary++++-- | RNA secondary structure with 1-diagrams. Each nucleotide is paired with at+-- most one other nucleotide. A nucleotide with index k \in [0..len-1] is+-- paired if unD1S VU.! k > 0.++newtype D1Secondary = D1S {unD1S :: VU.Vector Int}+  deriving (Read,Show,Eq)++-- RNA secondary structure with 2-diagrams. Each nucleotide is paired with up+-- to two other nucleotides.++newtype D2Secondary = D2S {unD2S :: VU.Vector ( (Int,Edge,CTisomerism), (Int,Edge,CTisomerism) )}+  deriving (Read,Show,Eq)++-- |++class MkD1Secondary a where+  mkD1S :: a -> D1Secondary+  fromD1S :: D1Secondary -> a++-- |++class MkD2Secondary a where+  mkD2S :: a -> D2Secondary+  fromD2S :: D2Secondary -> a++++-- * Tree-based representation+--+-- Tree -> d1/2Secondary ?++-- | A secondary-structure tree. Has no notion of pseudoknots.++data SSTree idx a = SSTree idx a [SSTree idx a]+                  | SSExt  Int a [SSTree idx a]+  deriving (Read,Show,Eq)++-- | Create a tree from (pseudoknot-free [not checked]) 1-diagrams.++d1sTree :: D1Secondary -> SSTree PairIdx ()+d1sTree s = ext $ sort ps where+  (len,ps) = fromD1S s+  ext [] = SSExt len () []+  ext xs = SSExt len () . map tree $ groupBy (\l r -> snd l > fst r) xs -- ">=" would be partial allowance for 2-diagrams+  tree [ij]    = SSTree ij () []+  tree (ij:xs) = SSTree ij () . map tree $ groupBy (\l r -> snd l > fst r) xs++-- | Create a tree from (pseudoknot-free [not checked]) 2-diagrams.++d2sTree :: D2Secondary -> SSTree ExtPairIdx ()+d2sTree s = ext $ sortBy d2Compare ps where+  (len,ps) = fromD2S s+  ext [] = SSExt len () []+  ext xs = SSExt len () . map tree . groupBy d2Grouping $ xs+  tree [ij]    = SSTree ij () []+  tree (ij:xs) = SSTree ij () . map tree . groupBy d2Grouping $ xs++d2Compare ((i,j),_) ((k,l),_)+  | i==k = compare l j+  | j==l = compare i k+  | otherwise = compare (i,j) (k,l)++d2Grouping ((i,j),_) ((k,l),_) = i<=k && j>=l++test :: (Int,[ExtPairIdx])+test = (20,test')++test' =+  [ ((2,15),(cis,wc,wc))+  , ((3,14),(cis,wc,wc))+  , ((4,13),(cis,wc,wc))+  , ((5,12),(cis,wc,wc))+  , ((6,10),(trans,wc,hoogsteen))+  , ((2,18),(trans,sugar,sugar))+  , ((15,18),(cis,sugar,sugar))+  ]+++-- * Instances for D1S++-- | Conversion between D1S and D2S is lossy in D2S -> D1S++instance MkD1Secondary D2Secondary where+  mkD1S = fromD2S+  fromD1S = mkD2S++-- | (Length,List of Pairs)++instance MkD1Secondary (Int,[PairIdx]) where+  mkD1S (len,ps) = let xs = concatMap (\ij -> [ij,swap ij]) ps+                   in D1S $ VU.replicate len (-1) VU.// xs+  fromD1S (D1S s) = (VU.length s, filter (\(i,j) -> i<j && j>=0) . zip [0..] . VU.toList $ s)++-- * Instances for D2S++-- | Conversion between D1S and D2S is lossy in D2S -> D1S+--+-- TODO 'fromD2S' makes me wanna rewrite everything...++instance MkD2Secondary D1Secondary where+  mkD2S (D1S xs) = D2S . VU.map (\k -> ((k,wc,cis),(-1,unknownEdge,unknownCT))) $ xs+  fromD2S (D2S xs) = D1S . VU.map (sel1 . sel1) $ xs++instance MkD2Secondary (Int,[ExtPairIdx]) where+  mkD2S (len,ps) = let xs = concatMap (\((i,j),(ct,e1,e2)) ->+                                          [ (i, (j,e1,ct))+                                          , (j, (i,e2,ct))+                                          ]) ps+                       f (x,y) z = if sel1 x == -1 then (z,y) else (x,z)+                   in D2S $ VU.accum f (VU.replicate len ((-1,unknownEdge,unknownCT),(-1,unknownEdge,unknownCT))) xs+  fromD2S (D2S s) = ( VU.length s+                    , let (xs,ys) = unzip . VU.toList $ s+                          g i j = let z = s VU.! i in if sel1 (sel1 z) == j then sel2 (sel1 z) else sel2 (sel2 z)+                          f (i,(j,eI,ct)) = ((i,j),(ct,eI,g j i))+                      in+                      map f . filter (\(i,(j,_,_)) -> i<j && j>=0) $ zip [0..] xs ++ zip [0..] ys+                    )++++-- * Older instances (should still work)++-- | A second primitive generator, requiring dictionary and String. This one+-- generates pairs that are then used by the above instance. The dict is a list+-- of possible brackets: ["()"] being the minimal set.+--+-- NOTE no dictionary is returned by "fromD1S".+--+-- TODO return dictionary that is actually seen?++instance MkD1Secondary ([String],String) where+  mkD1S (dict,xs) = mkD1S (length xs,ps) where+    ps :: [(Int,Int)]+    ps = dotBracket dict xs+  fromD1S (D1S s) = ([], zipWith f [0..] $ VU.toList s) where+    f k (-1) = '.'+    f k p+      | k>p = ')'+      | otherwise = '('++-- | Generate Secondary given that we have an unboxed vector of characters++instance MkD1Secondary ([String],VU.Vector Char) where+  mkD1S (dict,xs) = mkD1S (dict, VU.toList xs)+  fromD1S s = let (dict,res) = fromD1S s in (dict,VU.fromList res)++-- | A "fast" instance for getting the pair list of vienna-structures.++instance MkD1Secondary String where+  mkD1S xs = mkD1S (["()"],xs)+  fromD1S s = let (_::[String],res) = fromD1S s in res++instance MkD1Secondary (VU.Vector Char) where+  mkD1S xs = mkD1S (["()"],xs)+  fromD1S s = let (_::[String],res::VU.Vector Char) = fromD1S s in res++++-- * Helper functions++-- | Secondary structure parser which allows pseudoknots, if they use different+-- kinds of brackets.++dotBracket :: [String] -> String -> [(Int,Int)]+dotBracket dict xs = sort . concatMap (f xs) $ dict where+  f xs [l,r] = g 0 [] . map (\x -> if x `elem` [l,r] then x else '.') $ xs where+    g :: Int -> [Int] -> String -> [(Int,Int)]+    g _ st [] = []+    g k st ('.':xs) = g (k+1) st xs+    g k sst (x:xs)+      | l==x = g (k+1) (k:sst) xs+    g k (s:st) (x:xs)+      | r==x = (s,k) : g (k+1) st xs+    g a b c = error $ show (a,b,c)

+ Biobase/Secondary/PseudoKnots.hs view

@@ -0,0 +1,55 @@+{-# LANGUAGE FlexibleInstances #-}+{-# LANGUAGE BangPatterns #-}++-- | Methods to transform a secondary structure containing pseudoknots into a+-- structure which is pseudoknot-free.+--+-- TODO Until a better name is found, this module is home to functions for+-- "de-pseudoknotting" structures.+--+-- TODO Check if there are corner-cases remaining when considering 2-diagrams.++module Biobase.Secondary.PseudoKnots where++import qualified Data.Vector.Unboxed as VU+import Data.List++import Biobase.Secondary++++-- | Try to removed pseudoknots from the "pairlist". This works by counting for+-- each pair, how many pairs are incompatible with it. Then those with most+-- incompatibilities are successively removed. This function might well remove+-- more than necessary!++class RemovePseudoKnots a where+  removeByCounting :: a -> a++-- | Remove pseudoknotted pairs from RNA secondary structures.++instance RemovePseudoKnots (VU.Vector PairIdx) where+  removeByCounting = VU.force . wrapRemove where+    wrapRemove !ps+      | VU.null cnts = ps -- there are no pairs+      | mmx == 0     = ps -- there are no incompatibilities+      | otherwise    = wrapRemove $ VU.take pos ps VU.++ VU.drop (pos+1) ps+      where+        cnts = VU.map incomp ps+        mmx = VU.maximum cnts+        Just pos = VU.elemIndex mmx cnts+        incomp (i,j) = VU.length $ VU.filter (\(k,l) -> i<k&&k<j&&j<l || k<i&&i<l&&l<j) ps++-- | Remove pseudoknotted pairs from extended RNA secondary structures.++instance RemovePseudoKnots (VU.Vector ExtPairIdx) where+  removeByCounting = VU.force . wrapRemove where+    wrapRemove !ps+      | VU.null cnts = ps -- there are no pairs+      | mmx == 0     = ps -- there are no incompatibilities+      | otherwise    = wrapRemove $ VU.take pos ps VU.++ VU.drop (pos+1) ps+      where+        cnts = VU.map incomp ps+        mmx = VU.maximum cnts+        Just pos = VU.elemIndex mmx cnts+        incomp ((i,j),_) = VU.length $ VU.filter (\((k,l),_) -> i<k&&k<j&&j<l || k<i&&i<l&&l<j) ps

+ BiobaseXNA.cabal view

@@ -0,0 +1,44 @@+name:           BiobaseXNA+version:        0.5.0.0+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+category:       Bioinformatics+synopsis:       Efficient RNA/DNA representations+license:        GPL-3+license-file:   LICENSE+build-type:     Simple+stability:      experimental+cabal-version:  >= 1.4.0+description:+                This is a base library for bioinformatics with emphasis on RNA+                and DNA primary structure and related tools. Provided are+                efficient encodings for short sequences, as required by RNA+                folding tools. Extended RNA secondary structures can be+                represented as well.++extra-source-files:++library+  build-depends:+    base >3 && <5,+    text,+    bytestring,+    primitive,+    tuple,+    vector-read-instances,+    vector >=0.7 && <0.8++  exposed-modules:+    Biobase.Primary+    Biobase.Primary.Bounds+    Biobase.Primary.Hashed+    Biobase.Secondary+    Biobase.Secondary.Constraint+    Biobase.Secondary.Diagrams+    Biobase.Secondary.PseudoKnots++  ghc-options:+    -O2+

+ LICENSE view

@@ -0,0 +1,675 @@+              GNU GENERAL PUBLIC LICENSE+                Version 3, 29 June 2007++ Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/>+ Everyone is permitted to copy and distribute verbatim copies+ of this license document, but changing it is not allowed.++                     Preamble++  The GNU General Public License is a free, copyleft license for+software and other kinds of works.++  The licenses for most software and other practical works are designed+to take away your freedom to share and change the works.  By contrast,+the GNU General Public License is intended to guarantee your freedom to+share and change all versions of a program--to make sure it remains free+software for all its users.  We, the Free Software Foundation, use the+GNU General Public License for most of our software; it applies also to+any other work released this way by its authors.  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+ Setup.hs view

@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain