GrammarProducts: Grammar products and higher-dimensional grammars

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

An algebra of liner and context-free grammars.

This library provides the implementation of our theory of algebraic operations over linear and context-free grammars. Using algebraic operations, it is possible to construct complex dynamic programming algorithms from simpler "atomic" grammars.

Our most important contribution is the definition of a product of grammars which naturally leads to alignment-like algorithms on multiple tapes.

An efficient implementation of the resulting grammars is possible via the ADPfusion framework. The FormalGrammars library provides the required "Template Haskell" machinary.

Alternatively, the resulting grammars can also be pretty-printed in various ways (LaTeX, ANSI, Haskell module with signature and grammar).

Formal background can be found in two papers:

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
Product Grammars for Alignment and Folding
submitted

and

Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler
How to Multiply Dynamic Programming Algorithms
Brazilian Symposium on Bioinformatics (BSB 2013)
Lecture Notes in Bioinformatics 8213, Springer, Heidelberg
Versions 0.0.0.2, 0.0.0.3, 0.0.0.4, 0.1.0.0, 0.1.1.0, 0.1.1.1, 0.1.1.2, 0.1.1.3
Change log changelog
Dependencies ADPfusion (>=0.2.0), ansi-wl-pprint, base (==4.*), bytestring, cmdargs (==0.10.*), containers, data-default, FormalGrammars (>=0.0.0.1), HaTeX, lens, newtype, parsers, PrimitiveArray (>=0.5.1.0), semigroups, transformers, trifecta [details]
License GPL-3.0-only
Copyright Christian Hoener zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler, 2013
Author Christian Hoener zu Siederdissen, 2013
Maintainer choener@tbi.univie.ac.at
Category Formal Languages, Bioinformatics
Home page http://www.tbi.univie.ac.at/~choener/
Source repo head: git clone git://github.com/choener/GrammarProducts
Uploaded by ChristianHoener at Wed Dec 18 00:21:59 UTC 2013
Distributions NixOS:0.1.1.3
Executables GrammarProductPP
Downloads 2569 total (24 in the last 30 days)
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Status Docs not available [build log]
Successful builds reported [all 8 reports]
Hackage Matrix CI

Modules

  • FormalLanguage
    • FormalLanguage.GrammarProduct
      • Op
        • FormalLanguage.GrammarProduct.Op.Add
        • FormalLanguage.GrammarProduct.Op.Chomsky
          • FormalLanguage.GrammarProduct.Op.Chomsky.Proof
        • FormalLanguage.GrammarProduct.Op.Common
        • FormalLanguage.GrammarProduct.Op.Greibach
          • FormalLanguage.GrammarProduct.Op.Greibach.Proof
        • FormalLanguage.GrammarProduct.Op.Linear
        • FormalLanguage.GrammarProduct.Op.Power
        • FormalLanguage.GrammarProduct.Op.Subtract
      • FormalLanguage.GrammarProduct.Parser

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