name:           Biobase
version:        0.1.0.0
author:         Christian Hoener zu Siederdissen
maintainer:     choener@tbi.univie.ac.at
homepage:       http://www.tbi.univie.ac.at/~choener/Haskell/
copyright:      Christian Hoener zu Siederdissen, 2010
category:       Bioinformatics
synopsis:       Base library for bioinformatics
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.4.0
description:
                Base library for bioinformatics providing the following features:
                .
                - RNA primary and secondary structure
                - Infernal covariance models
                - Turner and Vienna energy files
                .
                - efficient format for RNA sequences, based on the vector package
                - import from strings, bytestrings, fasta files (using the bio library)
                - secondary structure manipulation functions, im- and export of Vienna-dotbracket notation
                - import Turner energy files
                - cf. http://rna.urmc.rochester.edu/NNDB/index.html
                - im- and export of Vienna 2.0 energy files
                .
                - import covariance models
                - basic manipulation of covariance models
                - Stockholm file format manipulation
                .
                - algebraic ring class
                - instances for Gibbs free energy, partition function probabilities, and scores
                - conversion between different entities
                - ready for the vector library



extra-source-files:
  parfiles/Turner2004GH.par,
  templates/cheader

library
  build-depends:
    array,
    base >=4 && <5,
    bytestring,
    containers,
    directory >=1,
    file-embed >=0.0.3,
    filemanip >=0.3.3 && <0.4,
    parsec >=3 && <4,
    primitive >=0.3 && <0.4,
    tuple >=0.2.0.1,
    vector >=0.7 && <0.8,
    split >=0.1.2.3,

    HsTools >=0.0.1.1 && <0.0.2,
    ParsecTools >=0.0.2 && <0.0.3,
    PrimitiveArray >=0.0.2.1 && <0.0.3

  exposed-modules:
    Biobase.Constants
    Biobase.Infernal.CM
    Biobase.Infernal.CM.Export
    Biobase.Infernal.CM.Import
    Biobase.Infernal.Stockholm
    Biobase.Infernal.Stockholm.Import
    Biobase.RNA
    Biobase.Structure
    Biobase.Structure.DotBracket
    Biobase.Structure.Shapes
    Biobase.Turner
    Biobase.Turner.Import
    Biobase.Turner.Tables
    Biobase.Types.Convert
    Biobase.Types.Energy
    Biobase.Types.Partition
    Biobase.Types.Ring
    Biobase.Types.Score
    Biobase.Vienna
    Biobase.Vienna.Default
    Biobase.Vienna.Export.ViennaC
    Biobase.Vienna.Export.ViennaPar
    Biobase.Vienna.Import.Turner
    Biobase.Vienna.Import.ViennaPar
    Biobase.Vienna.Modification.NonStandard
    Biobase.Vienna.Modification.Partition
    Biobase.Vienna.Modification.Temperature

  ghc-options:
    -O2