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

Computation of the branching nodes of a Graph. More...

#include <BranchingAlgorithm.hpp>

Inheritance diagram for BranchingAlgorithm< span, Node, Edge, Graph_t >:

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

Public Member Functions
	BranchingAlgorithm (const Graph_t &graph, tools::storage::impl::Storage &storage, tools::misc::BranchingKind kind, size_t nb_cores=0, tools::misc::IProperties *options=0)
	BranchingAlgorithm (tools::storage::impl::Storage &storage)
	~BranchingAlgorithm ()
void	execute ()
tools::collections::Collection< Count > *	getBranchingCollection ()
Public Member Functions inherited from Algorithm
	Algorithm (const std::string &name, int nbCores=-1, gatb::core::tools::misc::IProperties *input=0)
virtual	~Algorithm ()
std::string	getName () const
void	run ()
virtual IProperties *	getInput ()
virtual IProperties *	getOutput ()
virtual IProperties *	getInfo ()
virtual dp::IDispatcher *	getDispatcher ()
virtual TimeInfo &	getTimeInfo ()
virtual IProperties *	getSystemInfo ()
template<typename Item >
dp::Iterator< Item > *	createIterator (dp::Iterator< Item > *iter, size_t nbIterations=0, const char *message=0, dp::IteratorListener *listener=0)
virtual dp::IteratorListener *	createIteratorListener (size_t nbIterations, const char *message)
Public Member Functions inherited from SmartPointer
void	use ()
void	forget ()
Public Member Functions inherited from ISmartPointer
virtual	~ISmartPointer ()

Static Public Member Functions
static tools::misc::IOptionsParser *	getOptionsParser ()
Static Public Member Functions inherited from Algorithm
template<template< size_t > class Functor>
static int	mainloop (tools::misc::IOptionsParser *parser, int argc, char *argv[])

Additional Inherited Members
Protected Member Functions inherited from Algorithm
std::string	getUriByKey (const std::string &key)
std::string	getUri (const std::string &str)
void	setInput (IProperties *input)
Protected Member Functions inherited from SmartPointer
	SmartPointer ()
virtual	~SmartPointer ()

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::BranchingAlgorithm< span, Node, Edge, Graph_t >

Computation of the branching nodes of a Graph.

This class implements an algorithm that looks for branching nodes in the provided graph.

A node N is branching <=> successors(N).size()!=1 || predecessors(N).size()!=1

All found branching nodes are put into a storage object.

Actually, this class is mainly used in the debruijn::impl::Graph class as a fourth step for the de Bruijn graph creation.

Member Typedef Documentation

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

Shortcuts.

Constructor & Destructor Documentation

BranchingAlgorithm	(	const Graph_t &	graph,
		tools::storage::impl::Storage &	storage,
		tools::misc::BranchingKind	kind,
		size_t	nb_cores = 0,
		tools::misc::IProperties *	options = 0
	)

Constructor.

Parameters

[in]	graph	: graph from which we look for branching nodes
[in]	storage	: storage where the found branching nodes will be put
[in]	kind	: kind of branching algorithm
[in]	nb_cores	: number of cores to be used; 0 means all available cores
[in]	options	: extra options

BranchingAlgorithm

(

tools::storage::impl::Storage &

storage

)

Constructor.

Parameters

[in]

storage

: retrieve the branching nodes from this storage.

~BranchingAlgorithm

(

)

Destructor.

Member Function Documentation

void execute ( )

virtual

Execution of the algorithm. Abstract method, must be refined in subclasses.

Implements Algorithm.

tools::collections::Collection<Count>* getBranchingCollection ( )

inline

Get the branching nodes as a collection of Count objects, ie couples of [kmer,abundance]

Returns

the collection of Count object.

IOptionsParser * getOptionsParser ( )

static

Get an option parser for branching parameters. Dynamic allocation, so must be released when no more used.

Returns

an instance of IOptionsParser.

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