BiobaseXNA 0.5.1.0 → 0.5.2.0

raw patch · 2 files changed

+77/−3 lines, 2 filesdep +PrimitiveArrayPVP ok

version bump matches the API change (PVP)

Dependencies added: PrimitiveArray

API changes (from Hackage documentation)

Files

• Biobase/Secondary/Constraint.hs +70/−1
• BiobaseXNA.cabal +7/−2

@@ -6,11 +6,15 @@  module Biobase.Secondary.Constraint where +import Data.Char (toLower) 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.PrimitiveArray+import Data.PrimitiveArray.Ix+ import Biobase.Secondary.Diagrams  @@ -32,12 +36,77 @@ nobonusCC = VU.fromList ".x" {-# NOINLINE nobonusCC #-} +-- | Given a 'Constraint', create an NxN matrix with bonus energies. These+-- energies can be included in all pair-creating functions and will disallow or+-- strongly favor certain pairings, while others will receive neither bonus nor+-- malus.+--+-- In case, a pair (i,j) is annotated as both, bonus- and malus-receiving, it+-- will be set to receive a malus. This can happen, if something like "<" would+-- give a bonus, but "x" gives a malus (and other cases).+--+-- TODO and again, we should parametrize over "Energy", "Score", etc (that is,+-- Prim a) +bonusTable :: Double -> Double -> Constraint -> PrimArray (Int,Int) Double+bonusTable bonus malus (Constraint constraint) = arr where+  arr = fromAssocs (0,0) (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)+            | (i,('(',j)) <- zip [0..] $ VU.toList constraint+            ]+  malusBr = [ ((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)+            | i<-[0..n]+            , fst (constraint VU.! i) == '<'+            , j<-[i+1..n]+            ] +++            [ ((i,j),bonus)+            | j<-[0..n]+            , fst (constraint VU.! j) == '>'+            , i<-[0..j-1]+            ]+  malusAn = [ ((i,j),malus)+            | i<-[0..n]+            , j<-[i+1..n]+            , fst (constraint VU.! j) == '<'+            ] +++            [ ((i,j),malus)+            | i<-[0..n]+            , j<-[i+1..n]+            , fst (constraint VU.! i) == '>'+            ]+  bonusBa = [ ((i,j),bonus)+            | i<-[0..n]+            , j<-[i+1..n]+            , fst (constraint VU.! i) == '|' || fst (constraint VU.! j) == '|'+            ]+  malusX  = [ ((i,j),malus)+            | i<-[0..n]+            , j<-[i+1..n]+            , fst (constraint VU.! i) == 'x' || fst (constraint VU.! j) == 'x'+            ] +{-+testC = putStrLn $ f as where+  f [] = ""+  f xs = show (take 9 xs) ++ "\n" ++ f (drop 9 xs)+  as = toList $ bonusTable (1) 2 (mkConstraint "(<<..x|>)")+-}+ -- * Instances  instance MkConstraint String where-  mkConstraint xs = mkConstraint . VU.fromList $ xs+  mkConstraint xs = mkConstraint . VU.fromList . map toLower $ xs  instance MkConstraint (VU.Vector Char) where   mkConstraint cs = Constraint $ VU.zip cs ks where

@@ -1,5 +1,5 @@ name:           BiobaseXNA-version:        0.5.1.0+version:        0.5.2.0 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 0.5.1.0+                .+                * bonusTable for constrained folding  extra-source-files: @@ -28,7 +32,8 @@     text,     tuple,     vector >=0.7 && <0.8,-    vector-read-instances+    vector-read-instances,+    PrimitiveArray    exposed-modules:     Biobase.Primary