ADPfusionForest-0.0.0.1: ADPfusionForest.cabal
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
<http://hackage.haskell.org/package/ForestStructures @ForestStructures@>,
a library which defines efficient, tree-like structures and
<http://hackage.haskell.org/package/ADPfusion @ADPfusion@>.
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