AlignmentAlgorithms 0.0.2.0 → 0.0.2.1
raw patch · 3 files changed
+24/−6 lines, 3 filesdep ~ADPfusiondep ~PrimitiveArraydep ~vectorPVP: major bump suggested
API removals or changes: PVP suggests a major version bump
Dependency ranges changed: ADPfusion, PrimitiveArray, vector
API changes (from Hackage documentation)
- DP.Alignment.Global.Tapes2: align :: SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW -> s_abOT -> (:.) ((:.) Z t_l_abOV) t_u_abOW -> s_abOT
- DP.Alignment.Global.Tapes2: delin :: SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW -> s_abOT -> (:.) ((:.) Z t_l_abOV) () -> s_abOT
- DP.Alignment.Global.Tapes2: done :: SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW -> (:.) ((:.) Z ()) () -> s_abOT
- DP.Alignment.Global.Tapes2: h :: SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW -> Stream m_abOS s_abOT -> m_abOS r_abOU
- DP.Alignment.Global.Tapes2: indel :: SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW -> s_abOT -> (:.) ((:.) Z ()) t_u_abOW -> s_abOT
- DP.Alignment.Global.Tapes2: instance (Monad mL0, Monad mR0, Eq xL0, mL0 ~ mR0, xL0 ~ rL0) => ProductBacktracking (SigGlobal mL0 xL0 rL0 t_l0 t_u0) (SigGlobal mR0 xR0 rR0 t_l0 t_u0)
+ DP.Alignment.Global.Tapes2: [align] :: SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6 -> s_adl3 -> (:.) ((:.) Z t_l_adl5) t_u_adl6 -> s_adl3
+ DP.Alignment.Global.Tapes2: [delin] :: SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6 -> s_adl3 -> (:.) ((:.) Z t_l_adl5) () -> s_adl3
+ DP.Alignment.Global.Tapes2: [done] :: SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6 -> (:.) ((:.) Z ()) () -> s_adl3
+ DP.Alignment.Global.Tapes2: [h] :: SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6 -> Stream m_adl2 s_adl3 -> m_adl2 r_adl4
+ DP.Alignment.Global.Tapes2: [indel] :: SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6 -> s_adl3 -> (:.) ((:.) Z ()) t_u_adl6 -> s_adl3
+ DP.Alignment.Global.Tapes2: backtrackFun :: Monad m => (l -> u -> r) -> (l -> u -> r) -> u -> l -> SigGlobal m (FMList r) [FMList r] l u
+ DP.Alignment.Global.Tapes2: instance (GHC.Base.Monad mL0, GHC.Base.Monad mR0, GHC.Classes.Eq xL0, mL0 ~ mR0, xL0 ~ rL0) => ADP.Fusion.TH.Backtrack.ProductBacktracking (DP.Alignment.Global.Tapes2.SigGlobal mL0 xL0 rL0 t_l0 t_u0) (DP.Alignment.Global.Tapes2.SigGlobal mR0 xR0 rR0 t_l0 t_u0)
- DP.Alignment.Global.Tapes2: SigGlobal :: (s_abOT -> (:.) ((:.) Z t_l_abOV) t_u_abOW -> s_abOT) -> (s_abOT -> (:.) ((:.) Z t_l_abOV) () -> s_abOT) -> ((:.) ((:.) Z ()) () -> s_abOT) -> (s_abOT -> (:.) ((:.) Z ()) t_u_abOW -> s_abOT) -> (Stream m_abOS s_abOT -> m_abOS r_abOU) -> SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW
+ DP.Alignment.Global.Tapes2: SigGlobal :: (s_adl3 -> (:.) ((:.) Z t_l_adl5) t_u_adl6 -> s_adl3) -> (s_adl3 -> (:.) ((:.) Z t_l_adl5) () -> s_adl3) -> ((:.) ((:.) Z ()) () -> s_adl3) -> (s_adl3 -> (:.) ((:.) Z ()) t_u_adl6 -> s_adl3) -> (Stream m_adl2 s_adl3 -> m_adl2 r_adl4) -> SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6
- DP.Alignment.Global.Tapes2: data SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW
+ DP.Alignment.Global.Tapes2: data SigGlobal m_adl2 s_adl3 r_adl4 t_l_adl5 t_u_adl6
- DP.Alignment.Global.Tapes2: gGlobal :: (Build b2, MkStream m S t3, MkStream m (Stack b2) t3, Element (Stack b2) t3, RuleContext t3, TermStaticVar (TermSymbol (TermSymbol M Deletion) b1) t3, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) t3, TermStaticVar (TermSymbol (TermSymbol M b) Deletion) t3, TermStaticVar (TermSymbol (TermSymbol M b) b1) t3, TerminalStream m (TermSymbol (TermSymbol M Deletion) b1) t3, TerminalStream m (TermSymbol (TermSymbol M Epsilon) Epsilon) t3, TerminalStream m (TermSymbol (TermSymbol M b) Deletion) t3, TerminalStream m (TermSymbol (TermSymbol M b) b1) t3, Apply ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> a), Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> a), Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) b1)) -> a), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> a)) (a -> (:.) ((:.) Z t1) () -> a), (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> a)) (a -> (:.) ((:.) Z t1) t2 -> a), (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) b1)) -> a)) (a -> (:.) ((:.) Z ()) t2 -> a)) => SigGlobal m a t t1 t2 -> ((t3 -> t3 -> m t) -> b2) -> b -> b1 -> (:.) Z b2
+ DP.Alignment.Global.Tapes2: gGlobal :: (TermStream t (TermSymbol (TermSymbol M b) b1) r r, TermStream t (TermSymbol (TermSymbol M b) Deletion) r r, TermStream t (TermSymbol (TermSymbol M Epsilon) Epsilon) r r, TermStream t (TermSymbol (TermSymbol M Deletion) b1) r r, TermStaticVar (TermSymbol (TermSymbol M b) b1) r, TermStaticVar (TermSymbol (TermSymbol M b) Deletion) r, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) r, TermStaticVar (TermSymbol (TermSymbol M Deletion) b1) r, RuleContext r, MkStream t (Stack b2) r, MkStream t S r, Element (Stack b2) r, Build b2, Apply ((:.) (Arg (Stack b2)) ((:.) ((:.) Z (TermArg b)) (TermArg b1)) -> t1), Apply ((:.) (Arg (Stack b2)) ((:.) ((:.) Z (TermArg b)) ()) -> t1), Apply ((:.) (Arg (Stack b2)) ((:.) ((:.) Z ()) (TermArg b1)) -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) ((:.) Z (TermArg b)) (TermArg b1)) -> t1)) (t1 -> (:.) ((:.) Z t3) t4 -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) ((:.) Z (TermArg b)) ()) -> t1)) (t1 -> (:.) ((:.) Z t3) () -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) ((:.) Z ()) (TermArg b1)) -> t1)) (t1 -> (:.) ((:.) Z ()) t4 -> t1)) => SigGlobal t t1 t2 t3 t4 -> ((r -> r -> t t2) -> b2) -> b -> b1 -> (:.) Z b2
- DP.Alignment.Global.Tapes2: runBacktrack :: FMList (u, l) -> [(u, l)]
+ DP.Alignment.Global.Tapes2: runBacktrack :: FMList r -> [r]
Files
- AlignmentAlgorithms.cabal +5/−5
- DP/Alignment/Global/Tapes2.hs +13/−1
- changelog.md +6/−0
AlignmentAlgorithms.cabal view
@@ -1,5 +1,5 @@ name: AlignmentAlgorithms-version: 0.0.2.0+version: 0.0.2.1 author: Christian Hoener zu Siederdissen, 2013-2015 copyright: Christian Hoener zu Siederdissen, 2013-2015 homepage: https://github.com/choener/AlignmentAlgorithms@@ -11,7 +11,7 @@ build-type: Simple stability: experimental cabal-version: >= 1.10.0-tested-with: GHC == 7.8.4, GHC == 7.10.1+tested-with: GHC == 7.8.4, GHC == 7.10.2 synopsis: Collection of alignment algorithms description: <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>@@ -40,13 +40,13 @@ library build-depends: base >= 4.7 && < 4.9- , ADPfusion >= 0.4.0.2 && < 0.4.2+ , ADPfusion >= 0.4.0.2 && < 0.5.1 , containers >= 0.5 && < 0.6 , fmlist >= 0.9 && < 0.10 , FormalGrammars >= 0.2.1 && < 0.2.2 , GrammarProducts >= 0.1.1 && < 0.1.2- , PrimitiveArray >= 0.6.0 && < 0.6.2- , vector >= 0.10 && < 0.11+ , PrimitiveArray >= 0.6.0 && < 0.7.1+ , vector >= 0.10 && < 0.12 exposed-modules: DP.Alignment.Global.Tapes2 default-language:
DP/Alignment/Global/Tapes2.hs view
@@ -52,10 +52,22 @@ } {-# Inline backtrack #-} +-- | Backtracking with more options++backtrackFun :: Monad m => (l -> u -> r) -> (l -> u -> r) -> u -> l -> SigGlobal m (FMList r) [FMList r] l u+backtrackFun f g ud ld = SigGlobal+ { done = \ _ -> F.empty+ , align = \ x (Z:.l:.u) -> x `F.snoc` f l u+ , indel = \ x (Z:._:.u) -> x `F.snoc` g ld u+ , delin = \ x (Z:.l:._) -> x `F.snoc` g l ud+ , h = toList+ }+{-# Inline backtrackFun #-}+ -- | Turn a single @FMList@ backtracking result into the corresponding -- list. -runBacktrack :: FMList (u,l) -> [(u,l)]+runBacktrack :: FMList r -> [r] runBacktrack = F.toList {-# Inline runBacktrack #-}
changelog.md view
@@ -1,3 +1,9 @@+0.0.2.1+-------++- addded and updated stack files+- updated travis.yml+ 0.0.1.0 -------