name:           AlignmentAlgorithms
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/
maintainer:     choener@bioinf.uni-leipzig.de
category:       Algorithms, Data Structures, Bioinformatics, Linguistics
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.10.0
tested-with:    GHC == 7.8.4, GHC == 7.10.1
synopsis:       Collection of alignment algorithms
description:
                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>
                @
                .
                @
                Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler.
                Algebraic Dynamic Programming over General Data Structures.
                2015. submitted.
                @
                .



Extra-Source-Files:
  README.md
  changelog.md



library
  build-depends: base             >= 4.7      && < 4.9
               , ADPfusion        >= 0.4.0.2  && < 0.4.1
               , containers       == 0.5.*
               , fmlist           >= 0.9      && < 0.10
               , FormalGrammars   == 0.2.0.*
               , GrammarProducts  == 0.1.0.*
               , PrimitiveArray   == 0.6.0.*
               , vector           == 0.10.*
  exposed-modules:
    DP.Alignment.Global.Tapes2
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , FlexibleContexts
                    , FlexibleInstances
                    , MultiParamTypeClasses
                    , QuasiQuotes
                    , TemplateHaskell
                    , TypeFamilies
  ghc-options:
    -O2 -funbox-strict-fields

source-repository head
  type: git
  location: git://github.com/choener/AlignmentAlgorithms