name:           Biobase
version:        0.3.1.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@tbi.univie.ac.at
homepage:       http://www.tbi.univie.ac.at/~choener/
copyright:      Christian Hoener zu Siederdissen, 2010,2011
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 sequences and energy files:
                .
                * efficient format for RNA sequences, based on the vector package
                .
                * internal conversion from strings and bytestrings
                .
                * secondary structure manipulation functions, im- and export of Vienna-dotbracket notation
                .
                .
                .
                Utility classes:
                .
                * algebraic ring class
                .
                * instances for Gibbs free energy, partition function probabilities, and scores
                .
                * conversion between different entities
                .
                .
                .
                Bioinformatics data sources:
                .
                * mostly just imports, some export functions are provided
                .
                * Fasta (please use the "bio" library by Ketil Malde)
                .
                * Mafft
                .
                * RNA secondary structure: Dot-Bracket, CT
                .
                * ViennaRNA energy files (with default parameters)
                .
                * Turner energy files: cf. <http://rna.urmc.rochester.edu/NNDB/index.html>
                .
                * RNAstrand database: dot-parenthesis (one file, many entries)
                .
                * FR3D: basepairs
                .
                * Infernal: covariance models (text-based)
                .
                * MC-Fold: NCM database
                .
                .
                .
                Important notes:
                .
                * In general, this library is not unicode safe (and could somebody tell me the reason for encoding DNA/RNA sequences in unicode?)



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

library
  build-depends:
    array,
    base >=4 && <5,
    ghc-prim,
    bytestring,
    containers,
    deepseq,
    directory >=1,
    file-embed >=0.0.3,
    filemanip >=0.3.3 && <0.4,
    filepath,
    mtl,
    parsec >=3 && <4,
    primitive >=0.3 && <0.4,
    split >=0.1.2.3,
    tuple >=0.2.0.1,
    utility-ht,
    vector >=0.7 && <0.8,
    zlib,
    either-unwrap,

    HsTools >=0.0.1.1 && <0.0.2,
    ParsecTools >=0.0.2 && <0.0.3,
    PrimitiveArray >=0.0.3.1 && <0.0.4,
    vector-read-instances

  exposed-modules:
    Biobase.Constants
    Biobase.DataSource.CT
    Biobase.DataSource.CT.Import
    Biobase.DataSource.DotParen
    Biobase.DataSource.DotParen.Import
    Biobase.DataSource.FR3D
    Biobase.DataSource.FR3D.Import
    Biobase.DataSource.InfernalCM
    Biobase.DataSource.InfernalCM.Export
    Biobase.DataSource.InfernalCM.Import
    Biobase.DataSource.Mafft
    Biobase.DataSource.Mafft.Import
    Biobase.DataSource.MCFold
    Biobase.DataSource.MCFold.Conversions
    Biobase.DataSource.MCFold.Import
    Biobase.DataSource.Turner
    Biobase.DataSource.Turner.Import
    Biobase.DataSource.Turner.Tables
    Biobase.DataSource.Vienna
    Biobase.DataSource.Vienna.Default
    Biobase.DataSource.Vienna.Export.ViennaC
    Biobase.DataSource.Vienna.Export.ViennaPar
    Biobase.DataSource.Vienna.Import.Turner
    Biobase.DataSource.Vienna.Import.ViennaPar
    Biobase.DataSource.Vienna.Modification.NonStandard
    Biobase.DataSource.Vienna.Modification.Partition
    Biobase.DataSource.Vienna.Modification.Temperature
    Biobase.RNA
    Biobase.RNA.Complex
    Biobase.RNA.Hashes
    Biobase.RNA.NucBounds
    Biobase.RNA.Pairs
    Biobase.RNA.ViennaPair
    Biobase.ScoreTypes
    Biobase.Structure
    Biobase.Structure.Constraint
    Biobase.Structure.Shapes
    Biobase.Types.Convert
    Biobase.Types.Energy
    Biobase.Types.Partition
    Biobase.Types.Ring
    Biobase.Types.Score

  ghc-options:
    -Odph

  if impl(ghc > 6.13)
    ghc-options:
      -fllvm