The FormalGrammars package

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generalized Algebraic Dynamic Programming

Context-free grammars in formal language theory are sets of production rules, non-terminal and terminal symbols. This library provides basic data types and functions to manipulate such grammars.

Grammars can be defined in a small domain-specific language that is very close to typical CFG notation. The DSL parser can easily be extended. Grammar products, for example, are implemented as a single additional sub-parser.

This library also provides the machinery that transforms an Inside grammar into the corresponding Outside grammar.

Starting with version 0.2.1 it is possible to write multiple context-free grammars within this framework.

In addition, TemplateHaskell and QuasiQuoting functionality allow embedding thusly defined grammars in Haskell programs. ADPfusion then turns such a grammar into an efficient dynamic program. It is also possible to generate Haskell modules that contain the resulting grammar, signature and algebra product.

Alternatives are ansi- or LaTeX-based pretty-printing for users that want to implement their CFG in another language than Haskell.

Formal background can be found in a number of papers which are given in the README.

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DependenciesADPfusion (==0.5.2.*), ansi-wl-pprint (>=0.6.7), base (>=4.7 && <5.0), bytestring (>=0.10), cmdargs (>=0.10), containers, data-default (>=0.5), FormalGrammars, HaTeX (>=3.16), lens (>=4.0), mtl (>=2.0), parsers (>=0.12), PrimitiveArray (==0.8.0.*), semigroups (>=0.16), template-haskell, text (>=1.0), transformers (>=0.3), trifecta (>=1.6), unordered-containers (>=0.2), vector (>=0.10) [details]
CopyrightChristian Hoener zu Siederdissen, 2013-2017
AuthorChristian Hoener zu Siederdissen, 2013-2017
CategoryFormal Languages, Bioinformatics
Home page
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Source repositoryhead: git clone git://
ExecutablesTriNeedleFG, NeedlemanWunschFG, NussinovFG, GrammarPP
UploadedThu Aug 31 14:11:23 UTC 2017 by ChristianHoener





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FormalGrammars: A DSL for formal languages in Haskell

generalized Algebraic Dynamic Programming Homepage

The gADP homepage has a tutorial and example on how to write algorithms / grammars.

Ideas implemented here are described in a couple of papers:

  1. Christian Hoener zu Siederdissen
    Sneaking Around ConcatMap: Efficient Combinators for Dynamic Programming
    2012, Proceedings of the 17th ACM SIGPLAN international conference on Functional programming
    paper preprint
  2. Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill.
    The HERMIT in the stream: fusing stream fusion’s concatMap
    2014, Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation.
  3. Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler.
    Product Grammars for Alignment and Folding
    2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics. 99
  4. Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
    Algebraic Dynamic Programming over General Data Structures
    2015, BMC Bioinformatics
  5. Maik Riechert, Christian Höner zu Siederdissen, and Peter F. Stadler
    Algebraic dynamic programming for multiple context-free languages
    2015, submitted


Christian Hoener zu Siederdissen
Leipzig University, Leipzig, Germany