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ADPfusionForest: Dynamic programming on tree and forest structures

[ bioinformatics, bsd3, formal-languages, library ] [ Propose Tags ]

ADPfusion for formal languages on tree and forest structures. This library connects @ForestStructures@, a library which defines efficient, tree-like structures and @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

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Modules

  • ADP
    • Fusion
      • Core
        • ForestAlign
          • ADP.Fusion.Core.ForestAlign.PermuteRightLinear
          • ADP.Fusion.Core.ForestAlign.RightLinear
        • ForestEdit
          • ADP.Fusion.Core.ForestEdit.LeftLinear
      • Forest
        • Align
          • ADP.Fusion.Forest.Align.PRL
          • ADP.Fusion.Forest.Align.RL
        • Edit
          • ADP.Fusion.Forest.Edit.LL
      • SynVar
        • Indices
          • ForestAlign
            • ADP.Fusion.SynVar.Indices.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.SynVar.Indices.ForestEdit.LeftLinear
      • Term
        • Deletion
          • ForestAlign
            • ADP.Fusion.Term.Deletion.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Deletion.ForestEdit.LeftLinear
        • Epsilon
          • ForestAlign
            • ADP.Fusion.Term.Epsilon.ForestAlign.PermuteRightLinear
            • ADP.Fusion.Term.Epsilon.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Epsilon.ForestEdit.LeftLinear
        • Node
          • ForestAlign
            • ADP.Fusion.Term.Node.ForestAlign.PermuteRightLinear
            • ADP.Fusion.Term.Node.ForestAlign.RightLinear
          • ForestEdit
            • ADP.Fusion.Term.Node.ForestEdit.LeftLinear
          • ADP.Fusion.Term.Node.Type

Flags

Manual Flags

NameDescriptionDefault
examples

build the examples

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Versions [RSS] 0.0.0.1
Change log changelog.md
Dependencies ADPfusion (>=0.5.2 && <0.5.3), base (>=4.7 && <5.0), containers (>=0.5), DPutils (>=0.0.1 && <0.0.2), fgl (>=5.5), ForestStructures (>=0.0.0 && <0.0.1), GrammarProducts (>=0.1 && <0.2), PrimitiveArray (>=0.8.0 && <0.8.1), strict (>=0.3), text (>=1.2), unordered-containers (>=0.2), vector (>=0.10), vector-algorithms (>=0.7), vector-instances (>=3.4), vector-th-unbox (>=0.2) [details]
License BSD-3-Clause
Copyright Christian Hoener zu Siederdissen, 2016-2017
Author Christian Hoener zu Siederdissen, Sarah Berkemer, 2016-2017
Maintainer choener@bioinf.uni-leipzig.de
Category Formal Languages, Bioinformatics
Home page https://github.com/choener/ADPfusionForest
Bug tracker https://github.com/choener/ADPfusionForest/issues
Source repo head: git clone git://github.com/choener/ADPfusionForest
Uploaded by ChristianHoener at 2017-11-23T22:15:26Z
Distributions
Reverse Dependencies 1 direct, 1 indirect [details]
Executables AffineAlignNewickTreesSmall, AlignNewickTrees
Downloads 1088 total (4 in the last 30 days)
Rating (no votes yet) [estimated by Bayesian average]
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Status Docs not available [build log]
Last success reported on 2017-11-24 [all 3 reports]

Readme for ADPfusionForest-0.0.0.1

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Build Status

ADPfusionForest: Dynamic and static tree and forest structures

This library extents ADPfusion to accept input in the form of trees and forests.

WARNING: Building with examples will leading to somewhat long compilation times.

Contact

Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany
choener@bioinf.uni-leipzig.de
http://www.bioinf.uni-leipzig.de/~choener/