BiobaseXNA.cabal

cabal-version:  2.2
name:           BiobaseXNA
version:        0.11.1.1
author:         Christian Hoener zu Siederdissen
maintainer:     choener@bioinf.uni-leipzig.de
homepage:       https://github.com/choener/BiobaseXNA
bug-reports:    https://github.com/choener/BiobaseXNA/issues
copyright:      Christian Hoener zu Siederdissen, 2011 - 2021
category:       Bioinformatics
synopsis:       Efficient RNA/DNA/Protein Primary/Secondary Structure
license:        BSD-3-Clause
license-file:   LICENSE
build-type:     Simple
stability:      experimental
tested-with:    GHC == 8.8, GHC == 8.10, GHC == 9.0
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 (limited by the
                amount of RAM) 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
  README.md

data-files:
  sources/iupac-nucleotides


common deps
  build-depends: base                     >= 4.7      &&  < 5.0
               , aeson                    >= 1.0
               , attoparsec               >= 0.13
               , binary                   >= 0.7
               , bytes                    >= 0.15
               , bytestring               >= 0.10
               , cereal                   >= 0.4
               , cereal-vector            >= 0.2
               , containers               >= 0.5
               , csv                      >= 0.1
               , data-default             >= 0.7
               , deepseq                  >= 1.3
               , file-embed               >= 0.0.8
               , hashable                 >= 1.2
               , lens                     >= 4.0
               , mtl                      >= 2.0
               , primitive                >= 0.5
               , QuickCheck               >= 2.7
               , split                    >= 0.2
               , text                     >= 1.0
               , tuple                    >= 0.3
               , vector                   >= 0.11
               , vector-binary-instances  >= 0.2
               , vector-th-unbox          >= 0.2
               --
               , bimaps                   == 0.1.0.*
               , BiobaseENA               == 0.0.0.*
               , BiobaseTypes             == 0.2.1.*
               , DPutils                  == 0.1.1.*
               , ForestStructures         == 0.0.1.*
               , PrimitiveArray           == 0.10.2.*
  default-extensions: BangPatterns
                    , DataKinds
                    , DeriveDataTypeable
                    , DeriveFunctor
                    , DeriveGeneric
                    , DeriveGeneric
                    , DeriveTraversable
                    , EmptyDataDecls
                    , FlexibleContexts
                    , FlexibleInstances
                    , GeneralizedNewtypeDeriving
                    , LambdaCase
                    , MultiParamTypeClasses
                    , PatternSynonyms
                    , PolyKinds
                    , RankNTypes
                    , RecordWildCards
                    , ScopedTypeVariables
                    , StandaloneDeriving
                    , TemplateHaskell
                    , TypeApplications
                    , TypeFamilies
                    , TypeOperators
                    , UndecidableInstances
                    , UnicodeSyntax
                    , ViewPatterns
  default-language:
    Haskell2010
  ghc-options:
    -O2 -funbox-strict-fields


library
  import:
    deps
  exposed-modules:
    -- new
    Biobase.Primary.AA
    Biobase.Primary.Letter
    Biobase.Primary.Nuc.RNA
    Biobase.Primary.Unknown
    -- old
    Biobase.Primary
    Biobase.Primary.Bounds
    Biobase.Primary.Hashed
    Biobase.Primary.IUPAC
    Biobase.Primary.Nuc
    Biobase.Primary.Nuc.Conversion
    Biobase.Primary.Nuc.DNA
    Biobase.Primary.Nuc.XNA
    Biobase.Primary.Pretty
    Biobase.Primary.Trans
    Biobase.Secondary
    Biobase.Secondary.New
    Biobase.Secondary.Basepair
--    Biobase.Secondary.Constraint
    Biobase.Secondary.Convert
    Biobase.Secondary.Diagrams
    Biobase.Secondary.Isostericity
    Biobase.Secondary.Pseudoknots
    Biobase.Secondary.Structure
    Biobase.Secondary.Vienna



executable SubOptDistance
  import:
    deps
  build-depends: base
               , BiobaseXNA
               , cmdargs      >= 0.10
  main-is:
    SubOptDistance.hs
  hs-source-dirs:
    src



test-suite properties
  import:
    deps
  type:
    exitcode-stdio-1.0
  main-is:
    properties.hs
  ghc-options:
    -threaded -rtsopts -with-rtsopts=-N
  hs-source-dirs:
    tests
  default-language:
    Haskell2010
  default-extensions: TemplateHaskell
                    , ScopedTypeVariables
  build-depends: base
               , QuickCheck         >= 2.7
               , tasty              >= 0.11
               , tasty-quickcheck   >= 0.8
               , tasty-th           >= 0.1
               --
               , BiobaseXNA



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