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AlignmentAlgorithms 0.0.1.2 → 0.0.2.0

raw patch · 2 files changed

+19/−44 lines, 2 filesdep ~ADPfusiondep ~FormalGrammarsdep ~GrammarProductsPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: ADPfusion, FormalGrammars, GrammarProducts, PrimitiveArray

API changes (from Hackage documentation)

- 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: 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: 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: 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: 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: 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: data SigGlobal m_aakO s_aakP r_aakQ t_l_aakR t_u_aakS
+ DP.Alignment.Global.Tapes2: data SigGlobal m_abOS s_abOT r_abOU t_l_abOV t_u_abOW
- 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: 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_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> (:.) ((:.) Z ()) () -> s_aakP
+ 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: 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
+ 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: 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: 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_aakO s_aakP r_aakQ t_l_aakR t_u_aakS -> s_aakP -> (:.) ((:.) Z ()) t_u_aakS -> s_aakP
+ 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

Files

AlignmentAlgorithms.cabal view
@@ -1,8 +1,9 @@ name:           AlignmentAlgorithms-version:        0.0.1.2+version:        0.0.2.0 author:         Christian Hoener zu Siederdissen, 2013-2015 copyright:      Christian Hoener zu Siederdissen, 2013-2015-homepage:       http://www.bioinf.uni-leipzig.de/Software/gADP/+homepage:       https://github.com/choener/AlignmentAlgorithms+bug-reports:    https://github.com/choener/AlignmentAlgorithms/issues maintainer:     choener@bioinf.uni-leipzig.de category:       Algorithms, Data Structures, Bioinformatics, Linguistics license:        GPL-3@@ -13,47 +14,20 @@ tested-with:    GHC == 7.8.4, GHC == 7.10.1 synopsis:       Collection of alignment algorithms description:+                <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>+                .                 A selection of (sequence) alignment algorithms. Both terminal,                 and syntactic variables, as well as the index type is not fixed                 here. This makes it possible to select the correct structure of                 the grammar here, but bind the required data type for alignment                 in user code.                 .-                <https://github.com/choener/AlignmentAlgorithms/blob/master/README.md>-                .                 That being said, these algorithms are mostly aimed towards                 sequence alignment problems.                 .-                * global alignment (Needleman-Wunsch style)-                .-                .-                .-                @-                Christian Hoener zu Siederdissen-                Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming-                2012. Proceedings of the 17th ACM SIGPLAN international conference on Functional programming-                <http://doi.acm.org/10.1145/2364527.2364559> preprint: <http://www.tbi.univie.ac.at/newpapers/pdfs/TBI-p-2012-2.pdf>-                @-                .-                @-                Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.-                The HERMIT in the stream: fusing stream fusion’s concatMap.-                2014. Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.-                <http://dl.acm.org/citation.cfm?doid=2543728.2543736>-                @-                .-                @-                Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.-                Product Grammars for Alignment and Folding.-                2014. IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99.-                <http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6819790>-                @+                List of grammars:                 .-                @-                Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler.-                Algebraic Dynamic Programming over General Data Structures.-                2015. submitted.-                @+                * global alignment (Needleman-Wunsch style)                 .  @@ -66,13 +40,13 @@  library   build-depends: base             >= 4.7      && < 4.9-               , ADPfusion        >= 0.4.0.2  && < 0.4.1-               , containers       == 0.5.*+               , ADPfusion        >= 0.4.0.2  && < 0.4.2+               , containers       >= 0.5      && < 0.6                , fmlist           >= 0.9      && < 0.10-               , FormalGrammars   == 0.2.0.*-               , GrammarProducts  == 0.1.0.*-               , PrimitiveArray   == 0.6.0.*-               , vector           == 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   exposed-modules:     DP.Alignment.Global.Tapes2   default-language:
README.md view
@@ -1,7 +1,7 @@-# AlignmentAlgorithms- [![Build Status](https://travis-ci.org/choener/AlignmentAlgorithms.svg?branch=master)](https://travis-ci.org/choener/AlignmentAlgorithms) +# AlignmentAlgorithms+ [*generalized ADPfusion Homepage*](http://www.bioinf.uni-leipzig.de/Software/gADP/)  A selection of (sequence) alignment algorithms. Both terminal, and syntactic@@ -13,7 +13,8 @@  #### Contact -Christian Hoener zu Siederdissen-choener@bioinf.uni-leipzig.de-Leipzig University, Leipzig, Germany+Christian Hoener zu Siederdissen  +Leipzig University, Leipzig, Germany  +choener@bioinf.uni-leipzig.de  +http://www.bioinf.uni-leipzig.de/~choener/