gatb.core-API-1.4.2
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

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