AlignmentAlgorithms 0.0.1.0 → 0.0.1.2

raw patch · 3 files changed

+13/−11 lines, 3 filesdep ~ADPfusionPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: ADPfusion

API changes (from Hackage documentation)

- DP.Alignment.Global.Tapes2: [align] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z t_l_acje) t_u_acjf -> s_acjc

- DP.Alignment.Global.Tapes2: [delin] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z t_l_acje) () -> s_acjc

- DP.Alignment.Global.Tapes2: [done] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> (:.) ((:.) Z ()) () -> s_acjc

- DP.Alignment.Global.Tapes2: [h] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> Stream m_acjb s_acjc -> m_acjb r_acjd

- DP.Alignment.Global.Tapes2: [indel] :: SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf -> s_acjc -> (:.) ((:.) Z ()) t_u_acjf -> s_acjc

- DP.Alignment.Global.Tapes2: instance (GHC.Base.Monad mL0, GHC.Base.Monad mR0, GHC.Classes.Eq xL0, mL0 ~ mR0) => ADP.Fusion.TH.Backtrack.BacktrackingProduct (DP.Alignment.Global.Tapes2.SigGlobal mL0 xL0 xL0 t_l0 t_u0) (DP.Alignment.Global.Tapes2.SigGlobal mR0 xR0 rR0 t_l0 t_u0)

+ DP.Alignment.Global.Tapes2: align :: SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> s_aakP -> (:.) ((:.) Z t_l_aakR) t_u_aakS -> s_aakP

+ DP.Alignment.Global.Tapes2: delin :: SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> s_aakP -> (:.) ((:.) Z t_l_aakR) () -> s_aakP

+ DP.Alignment.Global.Tapes2: done :: SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> (:.) ((:.) Z ()) () -> s_aakP

+ DP.Alignment.Global.Tapes2: h :: SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> Stream m_aakO s_aakP -> m_aakO r_aakQ

+ DP.Alignment.Global.Tapes2: indel :: SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> s_aakP -> (:.) ((:.) Z ()) t_u_aakS -> s_aakP

+ DP.Alignment.Global.Tapes2: instance (Monad mL0, Monad mR0, Eq xL0, mL0 ~ mR0) => BacktrackingProduct (SigGlobal mL0 xL0 xL0 t_l0 t_u0) (SigGlobal mR0 xR0 rR0 t_l0 t_u0)

- DP.Alignment.Global.Tapes2: SigGlobal :: (s_acjc -> (:.) ((:.) Z t_l_acje) t_u_acjf -> s_acjc) -> (s_acjc -> (:.) ((:.) Z t_l_acje) () -> s_acjc) -> ((:.) ((:.) Z ()) () -> s_acjc) -> (s_acjc -> (:.) ((:.) Z ()) t_u_acjf -> s_acjc) -> (Stream m_acjb s_acjc -> m_acjb r_acjd) -> SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf

+ DP.Alignment.Global.Tapes2: SigGlobal :: (s_aakP -> (:.) ((:.) Z t_l_aakR) t_u_aakS -> s_aakP) -> (s_aakP -> (:.) ((:.) Z t_l_aakR) () -> s_aakP) -> ((:.) ((:.) Z ()) () -> s_aakP) -> (s_aakP -> (:.) ((:.) Z ()) t_u_aakS -> s_aakP) -> (Stream m_aakO s_aakP -> m_aakO r_aakQ) -> SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS

- DP.Alignment.Global.Tapes2: data SigGlobal m_acjb s_acjc r_acjd t_l_acje t_u_acjf

+ DP.Alignment.Global.Tapes2: data SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS

- DP.Alignment.Global.Tapes2: gGlobal :: (Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> t1), Apply ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) b1)) -> t1), Apply ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> t1), TerminalStream t (TermSymbol (TermSymbol M b) b1) r, TerminalStream t (TermSymbol (TermSymbol M b) Deletion) r, TerminalStream t (TermSymbol (TermSymbol M Deletion) b1) r, TerminalStream t (TermSymbol (TermSymbol M Epsilon) Epsilon) r, TermStaticVar (TermSymbol (TermSymbol M b) b1) r, TermStaticVar (TermSymbol (TermSymbol M b) Deletion) r, TermStaticVar (TermSymbol (TermSymbol M Deletion) b1) r, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) r, RuleContext r, Element (Stack b2) r, MkStream t (Stack b2) r, MkStream t S r, Build b2, (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M b) b1)) -> t1)) (t1 -> (:.) ((:.) Z t3) t4 -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) ((:.) (TermArg (TermSymbol M b)) ()) -> t1)) (t1 -> (:.) ((:.) Z t3) () -> t1), (~) * (Fun ((:.) (Arg (Stack b2)) (TermArg (TermSymbol (TermSymbol M Deletion) 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: gGlobal :: (Build b2, MkStream m S t3, MkStream m (Stack b2) t3, Element (Stack b2) t3, RuleContext t3, TermStaticVar (TermSymbol (TermSymbol M Epsilon) Epsilon) t3, TermStaticVar (TermSymbol (TermSymbol M Deletion) b1) t3, TermStaticVar (TermSymbol (TermSymbol M b) Deletion) t3, TermStaticVar (TermSymbol (TermSymbol M b) b1) t3, TerminalStream m (TermSymbol (TermSymbol M Epsilon) Epsilon) t3, TerminalStream m (TermSymbol (TermSymbol M Deletion) b1) 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

Files

AlignmentAlgorithms.cabal +3/−3
README.md +1/−1
changelog.md +9/−7

AlignmentAlgorithms.cabal view

@@ -1,5 +1,5 @@ name:           AlignmentAlgorithms-version:        0.0.1.0+version:        0.0.1.2 author:         Christian Hoener zu Siederdissen, 2013-2015 copyright:      Christian Hoener zu Siederdissen, 2013-2015 homepage:       http://www.bioinf.uni-leipzig.de/Software/gADP/@@ -19,7 +19,7 @@                 the grammar here, but bind the required data type for alignment                 in user code.                 .-                <https://github.com/choener/AlignmentAlgorithms/README.md>+                <https://github.com/choener/AlignmentAlgorithms/blob/master/README.md>                 .                 That being said, these algorithms are mostly aimed towards                 sequence alignment problems.@@ -66,7 +66,7 @@  library   build-depends: base             >= 4.7      && < 4.9-               , ADPfusion        == 0.4.0.*+               , ADPfusion        >= 0.4.0.2  && < 0.4.1                , containers       == 0.5.*                , fmlist           >= 0.9      && < 0.10                , FormalGrammars   == 0.2.0.*

README.md view

@@ -1,6 +1,6 @@ # AlignmentAlgorithms -[![Build Status](https://travis-ci.org/choener/ADPfusion.svg?branch=master)](https://travis-ci.org/choener/ADPfusion)+[![Build Status](https://travis-ci.org/choener/AlignmentAlgorithms.svg?branch=master)](https://travis-ci.org/choener/AlignmentAlgorithms)  [*generalized ADPfusion Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)

changelog.md view

@@ -1,11 +1,13 @@ 0.0.1.0-=======-	- restructured into DP.Alignment schemes-	- added FMList dependency for better snoc-backtracking-	- single global-alignment example+-------++  - restructured into DP.Alignment schemes+  - added FMList dependency for better snoc-backtracking+  - single global-alignment example   - travis-ci integration  0.0.0.1-=======-	- initial checkin-	- just provide the grammar descriptions+-------++  - initial checkin+  - just provide the grammar descriptions