name: ADPfusion version: 0.5.1.0 author: Christian Hoener zu Siederdissen, 2011-2016 copyright: Christian Hoener zu Siederdissen, 2011-2016 homepage: https://github.com/choener/ADPfusion bug-reports: https://github.com/choener/ADPfusion/issues maintainer: choener@bioinf.uni-leipzig.de category: Algorithms, Data Structures, Bioinformatics, Formal Languages license: BSD3 license-file: LICENSE build-type: Simple stability: experimental cabal-version: >= 1.10.0 tested-with: GHC == 7.8.4, GHC == 7.10.3 synopsis: Efficient, high-level dynamic programming. description: . ADPfusion combines stream-fusion (using the stream interface provided by the vector library) and type-level programming to provide highly efficient dynamic programming combinators. . ADPfusion allows writing dynamic programs for single- and multi-tape problems. Inputs can be sequences, or sets. New input types can be defined, without having to rewrite this library thanks to the open-world assumption of ADPfusion. . The library provides the machinery for Outside and Ensemble algorithms as well. Ensemble algorithms combine Inside and Outside calculations. . Starting with version 0.4.1 we support writing multiple context-free grammars (interleaved syntactic variables). Such grammars have applications in bioinformatics and linguistics. . The homepage provides a number of tutorial-style examples, with linear and context-free grammars over sequence and set inputs. . The formal background for generalized algebraic dynamic progrmaming and ADPfusion is described in a number of papers. These can be found on the gADP homepage and in the README. . Extra-Source-Files: README.md changelog.md flag examples description: build the examples default: False manual: True flag debug description: dump intermediate Core files default: False manual: True flag spectest description: build the spec-ctor test case default: False manual: True library build-depends: base >= 4.7 && < 4.9 , bits >= 0.4 && < 0.5 , containers , mmorph >= 1.0 && < 1.1 , mtl >= 2.0 && < 2.3 , OrderedBits >= 0.0.1.0 && < 0.0.2.0 , primitive >= 0.5.4 && < 0.7 , PrimitiveArray >= 0.7.0 && < 0.7.1 , QuickCheck >= 2.7 && < 2.9 , strict >= 0.3 && < 0.4 , template-haskell >= 2.0 && < 3.0 , th-orphans >= 0.12 && < 0.14 , transformers >= 0.3 && < 0.5 , tuple >= 0.3 && < 0.4 , vector >= 0.11 && < 0.12 exposed-modules: ADP.Fusion ADP.Fusion.Apply ADP.Fusion.Base ADP.Fusion.Base.Classes ADP.Fusion.Base.Multi ADP.Fusion.Base.Point ADP.Fusion.Base.Set ADP.Fusion.Base.Subword ADP.Fusion.Base.Term ADP.Fusion.Base.TyLvlIx ADP.Fusion.Base.Unit ADP.Fusion.SynVar ADP.Fusion.SynVar.Array ADP.Fusion.SynVar.Array.TermSymbol ADP.Fusion.SynVar.Array.Type ADP.Fusion.SynVar.Axiom ADP.Fusion.SynVar.Backtrack ADP.Fusion.SynVar.Fill ADP.Fusion.SynVar.Indices ADP.Fusion.SynVar.Indices.Classes ADP.Fusion.SynVar.Indices.Point ADP.Fusion.SynVar.Indices.Set0 ADP.Fusion.SynVar.Indices.Subword ADP.Fusion.SynVar.Indices.Unit ADP.Fusion.SynVar.Recursive ADP.Fusion.SynVar.Recursive.Point ADP.Fusion.SynVar.Recursive.Subword ADP.Fusion.SynVar.Recursive.Type ADP.Fusion.SynVar.Split ADP.Fusion.SynVar.Split.Subword ADP.Fusion.SynVar.Split.Type ADP.Fusion.Term ADP.Fusion.Term.Chr ADP.Fusion.Term.Chr.Point ADP.Fusion.Term.Chr.Set0 ADP.Fusion.Term.Chr.Subword ADP.Fusion.Term.Chr.Type ADP.Fusion.Term.Deletion ADP.Fusion.Term.Deletion.Point ADP.Fusion.Term.Deletion.Subword ADP.Fusion.Term.Deletion.Type ADP.Fusion.Term.Deletion.Unit ADP.Fusion.Term.Edge ADP.Fusion.Term.Edge.Set ADP.Fusion.Term.Edge.Type ADP.Fusion.Term.Epsilon ADP.Fusion.Term.Epsilon.Point ADP.Fusion.Term.Epsilon.Set ADP.Fusion.Term.Epsilon.Subword ADP.Fusion.Term.Epsilon.Type ADP.Fusion.Term.Epsilon.Unit ADP.Fusion.Term.PeekIndex ADP.Fusion.Term.PeekIndex.Subword ADP.Fusion.Term.PeekIndex.Type ADP.Fusion.Term.Strng ADP.Fusion.Term.Strng.Point ADP.Fusion.Term.Strng.Subword ADP.Fusion.Term.Strng.Type ADP.Fusion.TH ADP.Fusion.TH.Backtrack ADP.Fusion.TH.Common default-extensions: BangPatterns , ConstraintKinds , CPP , DataKinds , DefaultSignatures , FlexibleContexts , FlexibleInstances , GADTs , KindSignatures , MultiParamTypeClasses , RankNTypes , RecordWildCards , ScopedTypeVariables , StandaloneDeriving , TemplateHaskell , TupleSections , TypeFamilies , TypeOperators , TypeSynonymInstances , UndecidableInstances default-language: Haskell2010 ghc-options: -O2 -funbox-strict-fields -- Very simple two-sequence alignment. executable NeedlemanWunsch if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: NeedlemanWunsch.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all -- Basic RNA secondary structure folding executable Nussinov if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: Nussinov.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators , UndecidableInstances ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all -- Basic RNA secondary structure folding with partition function calculations executable PartNussinov if flag(examples) buildable: True build-depends: base , ADPfusion , log-domain == 0.10.* , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: PartNussinov.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all executable Durbin if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: Durbin.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -fcpr-off -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all executable Pseudoknot if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: Pseudoknot.hs default-language: Haskell2010 default-extensions: BangPatterns , DataKinds , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all executable OverlappingPalindromes if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: OverlappingPalindromes.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all executable SplitTests if flag(examples) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: SplitTests.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all test-suite properties type: exitcode-stdio-1.0 main-is: properties.hs other-modules: QuickCheck.Common QuickCheck.Point QuickCheck.Set QuickCheck.Subword ghc-options: -threaded -rtsopts -with-rtsopts=-N hs-source-dirs: tests default-language: Haskell2010 default-extensions: BangPatterns , CPP , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , TemplateHaskell , TypeFamilies , TypeOperators , TypeSynonymInstances cpp-options: -DADPFUSION_TEST_SUITE_PROPERTIES build-depends: base , ADPfusion , bits , OrderedBits , PrimitiveArray , QuickCheck , strict , test-framework >= 0.8 && < 0.9 , test-framework-quickcheck2 >= 0.3 && < 0.4 , test-framework-th >= 0.2 && < 0.3 , vector benchmark performance type: exitcode-stdio-1.0 main-is: performance.hs ghc-options: -rtsopts -with-rtsopts=-N -with-rtsopts=-T -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all hs-source-dirs: tests default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , TemplateHaskell , RecordWildCards , TypeFamilies , TypeOperators , StandaloneDeriving , DeriveGeneric build-depends: base , ADPfusion , BenchmarkHistory >= 0.0.0 && < 0.0.1 , PrimitiveArray , vector -- Very simple two-sequence alignment. executable spectest if flag(spectest) buildable: True build-depends: base , ADPfusion , PrimitiveArray , template-haskell , vector else buildable: False hs-source-dirs: src main-is: SpecTest.hs default-language: Haskell2010 default-extensions: BangPatterns , FlexibleContexts , FlexibleInstances , MultiParamTypeClasses , RecordWildCards , TemplateHaskell , TypeFamilies , TypeOperators ghc-options: -O2 -funbox-strict-fields -funfolding-use-threshold1000 -funfolding-keeness-factor1000 if flag(debug) ghc-options: -ddump-to-file -ddump-simpl -dsuppress-all source-repository head type: git location: git://github.com/choener/ADPfusion