name: ADPfusionForest version: 0.0.0.1 author: Christian Hoener zu Siederdissen, Sarah Berkemer, 2016-2017 copyright: Christian Hoener zu Siederdissen, 2016-2017 homepage: https://github.com/choener/ADPfusionForest bug-reports: https://github.com/choener/ADPfusionForest/issues maintainer: choener@bioinf.uni-leipzig.de category: Formal Languages, Bioinformatics license: BSD3 license-file: LICENSE build-type: Simple stability: experimental cabal-version: >= 1.10.0 tested-with: GHC == 8.0.2 synopsis: Dynamic programming on tree and forest structures description: ADPfusion for formal languages on tree and forest structures. This library connects , a library which defines efficient, tree-like structures and . The result is the ability to easily write formal grammars which act on input trees (as compared to the more common input strings). . Build this library with GHC-8.0.2 Extra-Source-Files: changelog.md README.md stack.yaml examples/t1.nwk examples/t2.nwk flag examples description: build the examples default: False manual: True library build-depends: base >= 4.7 && < 5.0 , containers >= 0.5 , fgl >= 5.5 , strict >= 0.3 , text >= 1.2 , unordered-containers >= 0.2 , vector >= 0.10 -- >= 3.4 for Hashable (Vector a) , vector-instances >= 3.4 , vector-th-unbox >= 0.2 , vector-algorithms >= 0.7 -- , ADPfusion == 0.5.2.* , DPutils == 0.0.1.* , ForestStructures == 0.0.0.* , GrammarProducts == 0.1.* , PrimitiveArray == 0.8.0.* exposed-modules: ADP.Fusion.Forest.Align.PRL ADP.Fusion.Forest.Align.RL ADP.Fusion.Forest.Edit.LL -- done ADP.Fusion.Core.ForestEdit.LeftLinear ADP.Fusion.SynVar.Indices.ForestEdit.LeftLinear ADP.Fusion.Term.Deletion.ForestEdit.LeftLinear ADP.Fusion.Term.Epsilon.ForestEdit.LeftLinear ADP.Fusion.Term.Node.ForestEdit.LeftLinear ADP.Fusion.Term.Node.Type -- wip ADP.Fusion.Core.ForestAlign.PermuteRightLinear ADP.Fusion.Term.Epsilon.ForestAlign.PermuteRightLinear ADP.Fusion.Term.Node.ForestAlign.PermuteRightLinear -- current ADP.Fusion.Core.ForestAlign.RightLinear ADP.Fusion.Term.Epsilon.ForestAlign.RightLinear ADP.Fusion.Term.Deletion.ForestAlign.RightLinear ADP.Fusion.Term.Node.ForestAlign.RightLinear ADP.Fusion.SynVar.Indices.ForestAlign.RightLinear default-language: Haskell2010 default-extensions: AllowAmbiguousTypes , BangPatterns , DataKinds , FlexibleContexts , FlexibleInstances , GADTs , KindSignatures , MultiParamTypeClasses , OverloadedStrings , RankNTypes , ScopedTypeVariables , StandaloneDeriving , TypeFamilies , TypeOperators , UndecidableInstances ghc-options: -O2 -funbox-strict-fields executable AlignNewickTrees if flag(examples) buildable: True build-depends: base , cmdargs >= 0.10 , containers , filepath , log-domain >= 0.10 , text , vector -- , ADPfusion , ADPfusionForest , BiobaseNewick >= 0.0.0.1 , ForestStructures , FormalGrammars >= 0.3 , PrimitiveArray , PrimitiveArray-Pretty >= 0.0 else buildable: False hs-source-dirs: src main-is: AlignNewickTrees.hs default-language: Haskell2010 default-extensions: BangPatterns , DataKinds , DeriveDataTypeable , FlexibleContexts , GADTs , MultiParamTypeClasses , OverloadedStrings , QuasiQuotes , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields executable AffineAlignNewickTreesSmall if flag(examples) buildable: True build-depends: base , cmdargs >= 0.10 , containers , filepath , log-domain >= 0.10 , text , vector -- , ADPfusion , ADPfusionForest , BiobaseNewick >= 0.0.0.1 , ForestStructures , FormalGrammars >= 0.3 , PrimitiveArray , PrimitiveArray-Pretty >= 0.0 else buildable: False hs-source-dirs: src main-is: AffineAlignNewickTreesSmall.hs default-language: Haskell2010 default-extensions: BangPatterns , DataKinds , DeriveDataTypeable , FlexibleContexts , GADTs , MultiParamTypeClasses , OverloadedStrings , QuasiQuotes , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -- AffineAlignNewickTrees too big, use AffineAlignNewickTreesSmall -- executable EditNewickTrees -- if flag(examples) -- buildable: -- True -- build-depends: base -- , cmdargs >= 0.10 -- , containers -- , filepath -- , log-domain >= 0.10 -- , text -- , vector -- -- -- , ADPfusion -- , ADPfusionForest -- , BiobaseNewick >= 0.0.0.1 -- , ForestStructures -- , FormalGrammars >= 0.3 -- , PrimitiveArray -- , PrimitiveArray-Pretty >= 0.0 -- else -- buildable: -- False -- hs-source-dirs: -- src -- main-is: -- EditNewickTrees.hs -- default-language: -- Haskell2010 -- default-extensions: BangPatterns -- , DataKinds -- , DeriveDataTypeable -- , FlexibleContexts -- , GADTs -- , MultiParamTypeClasses -- , OverloadedStrings -- , QuasiQuotes -- , RecordWildCards -- , TemplateHaskell -- , TypeFamilies -- , TypeOperators -- ghc-options: -- -O2 -- -funbox-strict-fields -- executable AffineEditNewickTrees -- if flag(examples) -- buildable: -- True -- build-depends: base -- , cmdargs >= 0.10 -- , containers -- , filepath -- , log-domain >= 0.10 -- , text -- , vector -- -- -- , ADPfusion -- , ADPfusionForest -- , BiobaseNewick >= 0.0.0.1 -- , ForestStructures -- , FormalGrammars >= 0.3 -- , PrimitiveArray -- , PrimitiveArray-Pretty >= 0.0 -- else -- buildable: -- False -- hs-source-dirs: -- src -- main-is: -- AffineEditNewickTrees.hs -- default-language: -- Haskell2010 -- default-extensions: BangPatterns -- , DataKinds -- , DeriveDataTypeable -- , FlexibleContexts -- , GADTs -- , MultiParamTypeClasses -- , OverloadedStrings -- , QuasiQuotes -- , RecordWildCards -- , TemplateHaskell -- , TypeFamilies -- , TypeOperators -- ghc-options: -- -O2 -- -funbox-strict-fields -- executable EditNew -- if flag(examples) -- buildable: -- True -- build-depends: base -- , cmdargs >= 0.10 -- , containers -- , filepath -- , log-domain >= 0.10 -- , text -- , vector -- -- -- , ADPfusion -- , ADPfusionForest -- , BiobaseNewick >= 0.0.0.1 -- , ForestStructures -- , FormalGrammars >= 0.3 -- , PrimitiveArray -- , PrimitiveArray-Pretty >= 0.0 -- else -- buildable: -- False -- hs-source-dirs: -- src -- main-is: -- EditNew.hs -- default-language: -- Haskell2010 -- default-extensions: BangPatterns -- , DataKinds -- , DeriveDataTypeable -- , FlexibleContexts -- , GADTs -- , MultiParamTypeClasses -- , OverloadedStrings -- , QuasiQuotes -- , RecordWildCards -- , TemplateHaskell -- , TypeFamilies -- , TypeOperators -- ghc-options: -- -O2 -- -funbox-strict-fields -- executable SingleEdit -- if flag(examples) -- buildable: -- True -- build-depends: base -- , cmdargs >= 0.10 -- , containers -- , filepath -- , log-domain >= 0.10 -- , text -- , vector -- -- -- , ADPfusion -- , ADPfusionForest -- , BiobaseNewick >= 0.0.0.1 -- , ForestStructures -- , FormalGrammars >= 0.3 -- , PrimitiveArray -- , PrimitiveArray-Pretty >= 0.0 -- else -- buildable: -- False -- hs-source-dirs: -- src -- main-is: -- SingleEdit.hs -- default-language: -- Haskell2010 -- default-extensions: BangPatterns -- , DataKinds -- , DeriveDataTypeable -- , FlexibleContexts -- , GADTs -- , MultiParamTypeClasses -- , OverloadedStrings -- , QuasiQuotes -- , RecordWildCards -- , TemplateHaskell -- , TypeFamilies -- , TypeOperators -- ghc-options: -- -O2 -- -funbox-strict-fields test-suite properties type: exitcode-stdio-1.0 main-is: properties.hs ghc-options: -threaded -rtsopts -with-rtsopts=-N -O2 -funbox-strict-fields hs-source-dirs: tests default-language: Haskell2010 default-extensions: BangPatterns build-depends: base , QuickCheck , tasty >= 0.11 , tasty-quickcheck >= 0.8 , tasty-th >= 0.1 -- , ADPfusionForest benchmark benchmark build-depends: base , criterion >= 1.0.2 , ForestStructures default-language: Haskell2010 hs-source-dirs: tests main-is: benchmark.hs type: exitcode-stdio-1.0 ghc-options: -O2 source-repository head type: git location: git://github.com/choener/ADPfusionForest