name:           BiobaseXNA
version:        0.9.1.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       http://www.bioinf.uni-leipzig.de/~choener/
copyright:      Christian Hoener zu Siederdissen, 2011 - 2015
category:       Bioinformatics
synopsis:       Efficient RNA/DNA representations
license:        GPL-3
license-file:   LICENSE
build-type:     Simple
stability:      experimental
cabal-version:  >= 1.10.0
description:
                This is a base library for bioinformatics with emphasis on RNA
                and DNA primary structure as well as amino acid sequences.
                .
                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)
                @
                .
                <http://dx.crossref.org/10.1093%2Fnar%2Fgkp011>



extra-source-files:
  sources/isostericity-matrices.csv
  sources/isostericity-detailed.csv
  sources/iupac-nucleotides
  sources/codontable
  changelog.md

library
  build-depends: base                    >= 4.7       && < 4.9
               , aeson                   == 0.8.*
               , bimaps                  == 0.0.0.*
               , binary                  == 0.7.*
               , bytes                   == 0.15.*
               , bytestring              == 0.10.*
               , cereal                  == 0.4.*
               , cereal-vector           == 0.2.*
               , containers              == 0.5.*
               , csv                     == 0.1.*
               , file-embed              == 0.0.8.*
               , hashable                == 1.2.*
               , lens                    == 4.*
               , primitive               >= 0.5       && < 0.7
               , PrimitiveArray          == 0.6.*
               , split                   == 0.2.*
               , text                    == 1.*
               , tuple                   == 0.3.*
               , vector                  == 0.10.*
               , vector-binary-instances == 0.2.*
               , vector-th-unbox         == 0.2.*

  exposed-modules:
    Biobase.Primary
    Biobase.Primary.AA
    Biobase.Primary.Bounds
    Biobase.Primary.Hashed
    Biobase.Primary.IUPAC
    Biobase.Primary.Letter
    Biobase.Primary.Nuc
    Biobase.Primary.Nuc.Conversion
    Biobase.Primary.Nuc.DNA
    Biobase.Primary.Nuc.RNA
    Biobase.Primary.Nuc.XNA
    Biobase.Primary.Trans
    Biobase.Secondary
    Biobase.Secondary.Basepair
    Biobase.Secondary.Constraint
    Biobase.Secondary.Diagrams
    Biobase.Secondary.Isostericity
    Biobase.Secondary.Pseudoknots
    Biobase.Secondary.Structure
    Biobase.Secondary.Vienna

  default-extensions: BangPatterns
                    , DeriveGeneric
                    , EmptyDataDecls
                    , FlexibleContexts
                    , FlexibleInstances
                    , GeneralizedNewtypeDeriving
                    , LambdaCase
                    , MultiParamTypeClasses
                    , PatternSynonyms
                    , ScopedTypeVariables
                    , TemplateHaskell
                    , TypeFamilies
                    , TypeOperators
                    , UndecidableInstances
                    , ViewPatterns

  default-language: Haskell2010

  ghc-options:
    -O2 -funbox-strict-fields

executable SubOptDistance
  build-depends:  base
               ,  cmdargs == 0.10.*
               ,  BiobaseXNA
  main-is:
    SubOptDistance.hs
  hs-source-dirs:
    src
  default-language:
    Haskell2010
  default-extensions: DeriveDataTypeable
                    , NoMonomorphismRestriction
                    , RecordWildCards
                    , ScopedTypeVariables
  ghc-options:
    -O2

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