name:           BiobaseXNA
version:        0.5.5.0
author:         Christian Hoener zu Siederdissen
maintainer:     choener@tbi.univie.ac.at
homepage:       http://www.tbi.univie.ac.at/~choener/
copyright:      Christian Hoener zu Siederdissen, 2011
category:       Bioinformatics
synopsis:       Efficient RNA/DNA representations
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.4.0
description:
                This is a base library for bioinformatics with emphasis on RNA
                and DNA primary structure and related tools. Provided are
                efficient encodings for short sequences, as required by RNA
                folding tools. Extended RNA secondary structures can be
                represented as well.
                .
                Contains data from:
                .
                Frequency and isostericity of RNA base pairs
                .
                Jesse Stombaugh, Craig L. Zirbel, Eric Westhof, and Neocles B. Leontis
                .
                Nucl. Acids Res. (2009)
                .
                doi:10.1093/nar/gkp011
                .
                .
                .
                Changes since 0.5.4.0
                .
                * tuple-like updating (updL, updR, updP, updT)
                .
                * baseP pair selection
                .
                * isostericity data, loaded from csv files
                .
                Changes since 0.5.3.0
                .
                * tuple-like (selN) selection of basepairing elements (baseL,baseR,baseT)
                .
                Changes since 0.5.1.0
                .
                * bonusTable for constrained folding

extra-source-files:
  sources/isostericity-matrices.csv
  sources/isostericity-detailed.csv

library
  build-depends:
    base >3 && <5,
    containers,
    bytestring,
    csv,
    file-embed,
    primitive,
    text,
    tuple,
    vector >=0.9 && <0.10,
    PrimitiveArray

  exposed-modules:
    Biobase.Primary
    Biobase.Primary.Bounds
    Biobase.Primary.Hashed
    Biobase.Secondary
    Biobase.Secondary.Constraint
    Biobase.Secondary.Diagrams
    Biobase.Secondary.Isostericity
    Biobase.Secondary.PseudoKnots
    Biobase.Secondary.Vienna

  ghc-options:
    -O2