align 0.1.1.1 → 0.1.1.2

raw patch · 2 files changed

+26/−13 lines, 2 filesdep +containersdep +transformersdep −uglymemoPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependencies added: containers, transformers

Dependencies removed: uglymemo

API changes (from Hackage documentation)

Files

• align.cabal +3/−2
• src/Data/Align.hs +23/−11

@@ -1,5 +1,5 @@ name:                align-version:             0.1.1.1+version:             0.1.1.2 synopsis:            Sequence alignment algorithms. description:         Global or local sequence alignment, not exclusively for text. license:             BSD3@@ -17,7 +17,8 @@   exposed-modules:     Data.Align,                        Data.Align.Demo   build-depends:       base >=4.6 && <5,-                       uglymemo >= 0.1,+                       containers,+                       transformers,                        vector >=0.10   hs-source-dirs:      src   default-language:    Haskell98

@@ -19,10 +19,11 @@   , debugMultiAlign   ) where +import Control.Monad.Trans.State.Strict import Data.Function (fix, on) import qualified Data.List as L+import qualified Data.Map.Strict as M import Data.Maybe (fromMaybe)-import Data.MemoUgly import Data.Ord import qualified Data.Vector as V import qualified Data.Vector.Generic as G@@ -77,7 +78,8 @@ instance (Show a, Show s) => Show (Trace a s) where   show (Trace s t) = "Trace(score = " ++ show s ++ ", steps = " ++ show t ++ ")" -(Trace s ts) `tappend` (Trace z (t:_)) = Trace (s+z) (t:ts)+mt `tappend` (Trace z (t:_)) =+    fmap (\(Trace s ts) -> Trace (s+z) (t:ts)) mt  -- | Utility for displaying a Char-based alignment. debugAlign :: [Step Char] -> String@@ -110,24 +112,34 @@   -> v a  -- ^ Right sequence.   -> Trace a s align AlignConfig{..} as bs =-  revTrace . fix (memo . go) $ (lastIndex as, lastIndex bs)+  let p = (lastIndex as, lastIndex bs)+  in revTrace $ evalState (go p) M.empty   where   revTrace (Trace s t) = Trace s (reverse t)   lastIndex v = G.length v - 1   ---  go k (i,j)-    | i == (-1) || j == (-1) =+  go p = do+    res <- gets $ M.lookup p+    case res of+        Just r -> return r+        Nothing -> do+            newRes <- pgo p+            modify (M.insert p newRes)+            return newRes+  --+  pgo (i,j)+    | i == (-1) || j == (-1) = return $       if i == j then Trace 0 []       else if i == (-1)            then skipInit j stepRight bs            else skipInit i stepLeft as-    | otherwise =+    | otherwise = do       let a = as G.! i           b = bs G.! j-          diag  = k (i-1,j-1) `tappend` Trace (acPairScore a b) [stepBoth a b]-          a_gap = k (i-1,  j) `tappend` Trace ac_gap_penalty [stepLeft a]-          b_gap = k (  i,j-1) `tappend` Trace ac_gap_penalty [stepRight b]-      in L.maximumBy (comparing traceScore) [diag, a_gap, b_gap]+      diag  <- go (i-1,j-1) `tappend` Trace (acPairScore a b) [stepBoth a b]+      a_gap <- go (i-1,  j) `tappend` Trace ac_gap_penalty [stepLeft a]+      b_gap <- go (  i,j-1) `tappend` Trace ac_gap_penalty [stepRight b]+      return $ L.maximumBy (comparing traceScore) [diag, a_gap, b_gap]   --   skipInit idx stepFun xs =     let score = ac_initial_gap_penalty * fromIntegral (idx+1)@@ -201,7 +213,7 @@ -- | Align multiple sequences using the Center Star heuristic method by -- Chin, Ho, Lam, Wong and Chan (2003). -- <http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.90.7448&rep=rep1&type=pdf>. --- Assumes the list of sequences to be non-empty, and the indices to be unique.+-- Assumes the list of sequences to have length > 1, and the indices to be unique. centerStar :: (G.Vector v a, Num s, Ord s, Ord i)   => AlignConfig a s   -> [(i, v a)]  -- TODO use internal indices rather to make uniqueness sure