GrammarProducts 0.1.1.1 → 0.1.1.2
raw patch · 5 files changed
+18/−13 lines, 5 filesdep ~ADPfusiondep ~FormalGrammarsdep ~semigroupsPVP ok
version bump matches the API change (PVP)
Dependency ranges changed: ADPfusion, FormalGrammars, semigroups
API changes (from Hackage documentation)
Files
- FormalLanguage/GrammarProduct/Parser.hs +1/−1
- GrammarProducts.cabal +7/−7
- README.md +1/−1
- changelog.md +6/−0
- src/AlignGlobal.hs +3/−4
FormalLanguage/GrammarProduct/Parser.hs view
@@ -30,7 +30,7 @@ import Text.Trifecta import Text.Trifecta.Delta import Text.Trifecta.Result-import Data.Semigroup ((<>),times1p)+import Data.Semigroup ((<>)) import qualified Control.Newtype as T --import Numeric.Natural.Internal import Prelude hiding (subtract)
GrammarProducts.cabal view
@@ -1,7 +1,7 @@ name: GrammarProducts-version: 0.1.1.1-author: Christian Hoener zu Siederdissen, 2013-2015-copyright: Christian Hoener zu Siederdissen, 2013-2015+version: 0.1.1.2+author: Christian Hoener zu Siederdissen, 2013-2016+copyright: Christian Hoener zu Siederdissen, 2013-2016 homepage: https://github.com/choener/GrammarProducts bug-reports: https://github.com/choener/GrammarProducts/issues maintainer: choener@bioinf.uni-leipzig.de@@ -60,17 +60,17 @@ library build-depends: base >= 4.7 && < 4.9- , ADPfusion >= 0.4.1 && < 0.5.1+ , ADPfusion >= 0.5.1 && < 0.5.2 , ansi-wl-pprint >= 0.6 && < 0.7 , bytestring >= 0.10 && < 0.11 , containers >= 0.5 && < 0.6 , data-default >= 0.5 && < 0.6- , FormalGrammars >= 0.2.1 && < 0.2.2+ , FormalGrammars >= 0.2.1 && < 0.3.1 , lens >= 4 && < 5 , newtype >= 0.2 && < 0.3 , parsers >= 0.12 && < 0.13 , PrimitiveArray >= 0.6.0.1 && < 0.7.1- , semigroups >= 0.15 && < 0.17+ , semigroups >= 0.15 && < 0.19 , template-haskell >= 2 && < 3 , transformers >= 0.4 && < 0.5 , trifecta >= 1.5 && < 1.6@@ -139,7 +139,7 @@ build-depends: base >= 4.7 && < 4.9 , ADPfusion , containers- , FormalGrammars+ , FormalGrammars >= 0.3 , GrammarProducts , PrimitiveArray , template-haskell
README.md view
@@ -4,7 +4,7 @@ [*generalized Algebraic Dynamic Programming Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/) -An algebra of liner and context-free grammars.+An abstract algebra for linear and context-free grammars. 1. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler. *Product Grammars for Alignment and Folding*
changelog.md view
@@ -1,3 +1,9 @@+0.1.1.2+-------++- This new version builds with both FormalGrammars 0.2 and 0.3. However, the+ example requires 0.3+ 0.1.1.1 -------
src/AlignGlobal.hs view
@@ -16,7 +16,6 @@ import Data.Vector.Unboxed (Vector) import Text.Printf import Data.Sequence ((|>),Seq,empty)-import qualified Data.Vector.Fusion.Stream as S import Data.Foldable (toList) import ADP.Fusion@@ -55,7 +54,7 @@ -score :: Monad m => SigGlobal m Int Int Char+score :: Monad m => SigGlobal m Int Int Char Char score = SigGlobal { donDon = \ (Z:.():.()) -> 0 , stpStp = \ x (Z:.a :.b ) -> if a==b then x+1 else -999999@@ -69,7 +68,7 @@ -- -- TODO use fmlist to make this more efficient. -pretty :: Monad m => SigGlobal m (String,String) [(String,String)] Char+pretty :: Monad m => SigGlobal m (String,String) [(String,String)] Char Char pretty = SigGlobal { donDon = \ (Z:.():.()) -> ("","") , stpStp = \ (x,y) (Z:.a :.b ) -> (x ++ [a],y ++ [b])@@ -89,7 +88,7 @@ -- | Decoupling the forward phase for CORE observation. -runNeedlemanWunschForward :: Vector Char -> Vector Char -> Z:.(ITbl Id Unboxed (Z:.PointL:.PointL) Int)+runNeedlemanWunschForward :: Vector Char -> Vector Char -> Z:.(ITbl Id Unboxed (Z:.PointL I:.PointL I) Int) runNeedlemanWunschForward i1 i2 = let n1 = VU.length i1; n2 = VU.length i2 in mutateTablesDefault $ gGlobal score (ITbl 0 0 (Z:.EmptyOk:.EmptyOk) (PA.fromAssocs (Z:.PointL 0:.PointL 0) (Z:.PointL n1:.PointL n2) (-999999) []))