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ADPfusionSet: Dynamic programming for Set data structures.

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generalized Algebraic Dynamic Programming

Extensions of ADPfusion for set-(like) data structures.

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Flags

Manual Flags

NameDescriptionDefault
examples

build the examples

Disabled
debug

Enable bounds checking and various other debug operations at the cost of a significant performance penalty.

Disabled
debugoutput

Enable debug output, which spams the screen full of index information

Disabled

Use -f <flag> to enable a flag, or -f -<flag> to disable that flag. More info

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Versions [RSS] 0.0.0.1, 0.0.0.2
Change log changelog.md
Dependencies ADPfusion (>=0.5.2 && <0.5.3), base (>=4.7 && <5.0), bits (>=0.4), containers, DPutils (>=0.0.1 && <0.0.2), mmorph (>=1.0), mtl (>=2.0), OrderedBits (>=0.0.1 && <0.0.2), primitive (>=0.5.4), PrimitiveArray (>=0.8.0 && <0.8.1), QuickCheck (>=2.7), strict (>=0.3), template-haskell (>=2.0), th-orphans (>=0.12), transformers (>=0.3), tuple (>=0.3), vector (>=0.11) [details]
Tested with ghc ==8.0.2, ghc ==8.2.1
License BSD-3-Clause
Copyright Christian Hoener zu Siederdissen, 2016-2017
Author Christian Hoener zu Siederdissen, 2016-2017
Maintainer choener@bioinf.uni-leipzig.de
Category Algorithms, Data Structures, Bioinformatics, Formal Languages
Home page https://github.com/choener/ADPfusionSet
Bug tracker https://github.com/choener/ADPfusionSet/issues
Source repo head: git clone git://github.com/choener/ADPfusionSet
Uploaded by ChristianHoener at 2017-10-19T14:36:27Z
Distributions
Reverse Dependencies 3 direct, 0 indirect [details]
Downloads 2060 total (2 in the last 30 days)
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Status Docs available [build log]
Last success reported on 2017-10-19 [all 1 reports]

Readme for ADPfusionSet-0.0.0.2

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Build Status

ADPfusionSet

generalized Algebraic Dynamic Programming Homepage

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.
    paper
  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
    paper
  4. Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
    Algebraic Dynamic Programming over General Data Structures
    2015, BMC Bioinformatics
    preprint
  5. Maik Riechert, Christian Höner zu Siederdissen, and Peter F. Stadler
    Algebraic dynamic programming for multiple context-free languages
    2015, submitted
    preprint

Introduction

ADPfusionSet extends ADPfusion with index structures suitable for sets. Included are sets, and sets with one and two boundaries. The classical example for DP on sets with a single boundary is the travelling salesman problem. Here, the set denotes the set of cities already visited, while the boundary is the last city that was visited.

Installation

Follow the gADP examples.

Contact

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