cabal-version: 2.2 name: BiobaseXNA version: 0.11.0.0 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 - 2019 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 == 8.4.4 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) @ . 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 == 0.2.0.* , ForestStructures == 0.0.1.* , PrimitiveArray == 0.9.1.* 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