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adpfusion efficient high level dynamic programming hackage package search browse what s new upload user accounts adpfusion efficient high level dynamic programming algorithms bioinformatics bsd3 data structures formal languages library propose tags report a vulnerability generalized algebraic dynamic programming adpfusion combines stream fusion using the stream interface provided by the vector library and type level programming to provide highly efficient dynamic programming combinators adpfusion allows writing dynamic programs for single and multi tape problems inputs can be sequences or sets new input types can be defined without having to rewrite this library thanks to the open world assumption of adpfusion the library provides the machinery for outside and ensemble algorithms as well ensemble algorithms combine inside and outside calculations starting with version 0 4 1 we support writing multiple context free grammars interleaved syntactic variables such grammars have applications in bioinformatics and linguistics the homepage provides a number of tutorial style examples with linear and context free grammars over sequence and set inputs the formal background for generalized algebraic dynamic programming and adpfusion is described in a number of papers these can be found on the gadp homepage and in the readme note the core adpfusion library only provides machinery for linear language over sequences the add ons adpfusionsubword adpfusionforest and others provide specialized machinery for other types of formal languages skip to readme modules index quick jump adp fusion adp fusion core adp fusion core apply adp fusion core classes adp fusion core multi synvar adp fusion core synvar array adp fusion core synvar array type adp fusion core synvar axiom adp fusion core synvar backtrack adp fusion core synvar fill adp fusion core synvar filltylvl adp fusion core synvar indices recursive adp fusion core synvar recursive type split adp fusion core synvar split type adp fusion core synvar tablewrap adp fusion core th adp fusion core th backtrack adp fusion core th common term adp fusion core term chr adp fusion core term deletion adp fusion core term edge adp fusion core term epsilon adp fusion core term multichr adp fusion core term peekindex adp fusion core term str adp fusion core term switch adp fusion core term test adp fusion core tylvlix adp fusion pointl adp fusion pointl core synvar adp fusion pointl synvar indices term adp fusion pointl term chr adp fusion pointl term deletion adp fusion pointl term epsilon adp fusion pointl term multichr adp fusion pointl term str adp fusion pointl term switch adp fusion pointr adp fusion pointr core synvar adp fusion pointr synvar indices term adp fusion pointr term chr adp fusion pointr term deletion adp fusion pointr term epsilon adp fusion pointr term multichr adp fusion unit adp fusion unit core synvar adp fusion unit synvar indices term adp fusion unit term deletion adp fusion unit term epsilon flags manual flags name description default 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 debugdump enable dumping intermediate core files disabled dump core dump html for the core generated by ghc during compilation disabled examples build the examples disabled spectest build the spec ctor test case disabled devel build additional tests disabled btstruc performance test for backtracking structures disabled llvm use llvm disabled use f flag to enable a flag or f flag to disable that flag more info downloads adpfusion 0 6 0 0 tar gz browse cabal source package package description as included in the package maintainer s corner package maintainers christianhoener for package maintainers and hackage trustees edit package information candidates no candidates versions rss 0 0 1 0 0 0 1 1 0 0 1 2 0 1 0 0 0 2 0 0 0 2 0 1 0 2 0 2 0 2 0 3 0 2 0 4 0 2 1 0 0 4 0 0 0 4 0 1 0 4 0 2 0 4 1 0 0 4 1 1 0 5 0 0 0 5 1 0 0 5 2 0 0 5 2 2 0 6 0 0 info change log changelog md dependencies base 4 7 5 0 bits 0 4 containers deepseq dputils 0 1 0 0 1 1 ghc prim mmorph 1 0 mtl 2 0 orderedbits 0 0 2 0 0 3 primitive 0 5 4 primitivearray 0 10 0 0 10 1 quickcheck 2 7 singletons 2 4 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 6 4 license bsd 3 clause copyright christian hoener zu siederdissen 2011 2019 author christian hoener zu siederdissen 2011 2019 maintainer choener bioinf uni leipzig de uploaded by christianhoener at 2019 10 01t18 22 22z category algorithms data structures bioinformatics formal languages home page https github com choener adpfusion bug tracker https github com choener adpfusion issues source repo head git clone git github com choener adpfusion distributions reverse dependencies 15 direct 1 indirect details executables spectest smithwaterman needlemanwunsch downloads 20531 total 82 in the last 30 days rating no votes yet estimated by bayesian average your rating λ λ λ status docs available build log last success reported on 2019 10 01 all 1 reports readme for adpfusion 0 6 0 0 back to package description adpfusion generalized algebraic dynamic programming homepage ideas implemented here are described in a couple of papers 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 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 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 christian höner zu siederdissen sonja j prohaska and peter f stadler algebraic dynamic programming over general data structures 2015 bmc bioinformatics preprint maik riechert christian höner zu siederdissen and peter f stadler algebraic dynamic programming for multiple context free languages 2016 theoretical computer science preprint introduction adpfusion combines stream fusion using the stream interface provided by the vector library and type level programming to provide highly efficient dynamic programming combinators from the programmers viewpoint adpfusion behaves very much like the original adp implementation http bibiserv techfak uni bielefeld de adp developed by robert giegerich and colleagues though both combinator semantics and backtracking are different the library internals however are designed not only to speed up adp by a large margin which this library does but also to provide further runtime improvements by allowing the programmer to switch over to other kinds of data structures with better time and space behaviour most importantly dynamic programming tables can be strict removing indirections present in lazy boxed tables as an example even rather complex adp code tends to be completely optimized to loops that use only unboxed variables int and others indexintarray and others completely novel compared to adp is the idea of allowing efficient monadic combinators this facilitates writing code that performs backtracking or samples structures stochastically among others things installation follow the gadp examples implementors notes if you want to extend adpfusion these have been moved to hacking md contact christian hoener zu siederdissen leipzig university leipzig germany choener bioinf uni leipzig de http www bioinf uni leipzig de choener produced by hackage and cabal 3 16 1 0
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