name:           GenussFold
version:        0.0.0.2
author:         Christian Hoener zu Siederdissen, 2015
copyright:      Christian Hoener zu Siederdissen, 2015
homepage:       https://github.com/choener/GenussFold
bug-reports:    https://github.com/choener/GenussFold/issues
maintainer:     choener@bioinf.uni-leipzig.de
category:       Formal Languages, Bioinformatics
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:       MCFGs for Genus-1 RNA Pseudoknots
description:
                <http://www.bioinf.uni-leipzig.de/Software/gADP/ generalized Algebraic Dynamic Programming>
                .
                Genus-1 RNA pseudoknot grammars implemented with a multiple
                context-free language. Compared to the usual implementations
                that are based on explicit recursions, an implementation based
                on a formal grammar is much more pleasing to write.
                .
                Consult the README for details.
                .
                * @BioInf.GenussFold.PKN@: Recursive pseudoknots with a simple
                  basepair maximization scoring scheme.
                .



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



flag debug
  description:  dump intermediate Core files
  default:      False
  manual:       True



library
  build-depends: base                   >= 4.7      && < 4.9
               , ADPfusion              >= 0.4.1.1  && < 0.4.2
               , ansi-wl-pprint         >= 0.6.7    && < 0.6.8
--               , BiobaseTurner          >= 0.3.2    && < 0.3.3
--               , BiobaseTypes           >= 0.1.1    && < 0.1.2
               , bytestring             >= 0.10     && < 0.11
               , containers
               , data-default           >= 0.5      && < 0.6
               , FormalGrammars         >= 0.2.1    && < 0.2.2
               , lens                   >= 4.0      && < 5.0
               , mtl                    >= 2.0      && < 3.0
               , PrimitiveArray         >= 0.6.0    && < 0.6.2
               , semigroups             >= 0.16     && < 0.17
               , template-haskell
               , text                   >= 1.0      && < 1.3
               , transformers           >= 0.3      && < 0.5
               , unordered-containers   >= 0.2      && < 0.3
               , vector                 >= 0.10     && < 0.11
  exposed-modules:
    BioInf.GenussFold
    BioInf.GenussFold.PKN
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , DataKinds
                    , DeriveDataTypeable
                    , FlexibleContexts
                    , KindSignatures
                    , MultiParamTypeClasses
                    , QuasiQuotes
                    , TemplateHaskell
                    , TypeFamilies
                    , TypeOperators
  ghc-options:
    -O2
    -funbox-strict-fields
    -fcpr-off
    -fno-liberate-case
  if flag(debug)
    ghc-options:
      -ddump-to-file
      -ddump-simpl
      -ddump-stg
      -dsuppress-all



-- Wrapper for the library

executable GenussFold
  build-depends: base
               , cmdargs          >= 0.10   && < 0.11
               , FormalGrammars
               , GenussFold
  hs-source-dirs:
    src
  default-language:
    Haskell2010
  default-extensions: DeriveDataTypeable
                    , RecordWildCards
  main-is:
    GenussFold.hs
  ghc-options:
    -O2
    -funbox-strict-fields



test-suite properties-fast
  type:
    exitcode-stdio-1.0
  main-is:
    properties-fast.hs
  ghc-options:
    -threaded -rtsopts -with-rtsopts=-N -O2 -funbox-strict-fields
  hs-source-dirs:
    tests
  default-language:
    Haskell2010
  default-extensions: BangPatterns
                    , CPP
                    , ForeignFunctionInterface
                    , TemplateHaskell
  build-depends: base
               , GenussFold
               , QuickCheck
               , test-framework               >= 0.8  && < 0.9
               , test-framework-quickcheck2   >= 0.3  && < 0.4
               , test-framework-th            >= 0.2  && < 0.3
  c-sources: C/genussfold.c
  cc-options: -fPIC



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