IterativeExtensions< span, Node, Edge, Graph_t > Class Template Reference

Class providing helpers for graph traversal. More...

#include <IterativeExtensions.hpp>

Public Types
typedef kmer::impl::Kmer< span >::ModelCanonical	Model

Public Member Functions
	IterativeExtensions (const Graph_t &graph, TerminatorTemplate< Node, Edge, Graph_t > &terminator, tools::misc::TraversalKind traversalKind, tools::misc::ExtendStopMode_e whenToStop, tools::misc::SearchMode_e searchMode, bool dontOutputFirstNucl, int max_depth, int max_nodes)
void	construct_linear_seqs (const std::string &L, const std::string &R, bank::IBank *outputBank, bool swf=false)
void	construct_linear_seqs (const std::string &L, const std::string &R, const std::string &output_file, bool swf=false)

Detailed Description

template<size_t span = KMER_DEFAULT_SPAN, typename Node = Node_t<>, typename Edge = Edge_t<Node_t<> >, typename Graph_t = Graph>
class gatb::core::debruijn::impl::IterativeExtensions< span, Node, Edge, Graph_t >

Class providing helpers for graph traversal.

The implementation relies on the Graph class of GATB-CORE, which provides the API to traverse a de Bruijn graph.

Member Typedef Documentation

typedef kmer::impl::Kmer<span>::ModelCanonical Model

ShortcutS.

Constructor & Destructor Documentation

IterativeExtensions	(	const Graph_t &	graph,
		TerminatorTemplate< Node, Edge, Graph_t > &	terminator,
		tools::misc::TraversalKind	traversalKind,
		tools::misc::ExtendStopMode_e	whenToStop,
		tools::misc::SearchMode_e	searchMode,
		bool	dontOutputFirstNucl,
		int	max_depth,
		int	max_nodes
	)

Constructor.

Parameters

[in]	graph	: de Bruijn graph of the reads
[in]	terminator	: object used to mark nodes during graph traversal.
[in]	traversalKind	: kind of graph traversal (unitig,contig)
[in]	whenToStop	: tells when to stop the extension
[in]	searchMode	: mode of graph traversal
[in]	dontOutputFirstNucl	: tells whether the first nucleotide of an extension has to be output
[in]	max_depth	: max depth of the graph traversal
[in]	max_nodes	: max nodes

Member Function Documentation

void construct_linear_seqs	(	const std::string &	L,
		const std::string &	R,
		bank::IBank *	outputBank,
		bool	swf = false
	)

Return the unitig/contig which starts with L, as well as all ths contigs that follow him, up to max_depth. Results go to a fasta file (output_file)

Parameters

[in]	L	: starter string for the unitig/contig
[in]	R	:
[in]	outputBank	: bank where the unitig/contig have to be dumped
[in]	swf	: to be detailed

void construct_linear_seqs	(	const std::string &	L,
		const std::string &	R,
		const std::string &	output_file,
		bool	swf = false
	)

Return the unitig/contig which starts with L, as well as all ths contigs that follow him, up to max_depth. Results go to a fasta file (output_file)

Parameters

[in]	L	: starter string for the unitig/contig
[in]	R	:
[in]	output_file	: uri of the file where the unitig/contig have to be dumped
[in]	swf	: to be detailed

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The documentation for this class was generated from the following files:

• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.hpp
• /builds/workspace/publish-doc-api-gitlab/gatb-core/src/gatb/debruijn/impl/IterativeExtensions.cpp