gatb::core::debruijn::impl Namespace Reference

Implementation package for De Bruijn graph management. More...

Classes
class	BranchingAlgorithm
	Computation of the branching nodes of a Graph. More...
struct	BranchingEdge_t
	Specific Edge structure representing a transition between two branching nodes. More...
struct	BranchingNode_t
	Specific Node structure representing a branching node in the De Bruijn graph. More...
class	BranchingTerminatorTemplate
	Implementation of Terminator that marks branching nodes. More...
class	ContainerNode
	IContainerNode implementation with a Bloom filter and a cFP set. More...
class	ContainerNodeCascading
	IContainerNode implementation with cascading Bloom filters. More...
class	ContainerNodeNoCFP
	IContainerNode implementation with a Bloom filter. More...
struct	Edge_t
	Definition of an Edge, ie a transition between two nodes in the De Bruijn graph. More...
struct	FunctorSetVariant
class	GraphTemplate
	Class representing a De Bruijn graph. More...
class	GraphUnitigsTemplate
	Class representing a De Bruijn graph based on unitigs. More...
class	IterativeExtensions
	Class providing helpers for graph traversal. More...
class	MonumentTraversalTemplate
	Implementation of Traversal that produces contigs. More...
class	MPHFTerminatorTemplate
	MPHF implementation of Terminator. More...
struct	Node_t
	Node structure representing a node in the De Bruijn graph. More...
class	NullTerminatorTemplate
	Null implementation of Terminator. More...
class	NullTraversalTemplate
	Null implementation of Traversal. More...
struct	Path_t
	Structure representing a path in the De Bruijn graph. More...
struct	SimpleNode
	Specific Node structure representing a simple node in the De Bruijn graph. More...
class	SimplePathsTraversalTemplate
	Implementation of Traversal that produces unitigs. More...
class	TerminatorTemplate
	Interface that allows to mark certain nodes in a graph. Note: It is on the verge of becoming deprecated. More...
class	TraversalTemplate
	Class that traverse nodes of a Graph. More...
class	UnitigsConstructionAlgorithm
	Computation of the unitigs of a Graph, using BCALM 2. More...

Functions
template<typename T >
bool	operator< (const Path_t< T > &a, const Path_t< T > &b)
template<typename T >
std::ostream &	operator<< (std::ostream &s, const Path_t< T > &p)

Detailed Description

Implementation package for De Bruijn graph management.

Function Documentation

bool gatb::core::debruijn::impl::operator< ( const Path_t< T > &  a, const Path_t< T > &  b  )

inline

Define a comparator for two path. The comparison is a lexicographic comparison on the ascii representation of the path.

Parameters

[in]	a	: path a
[in]	b	: path b

Returns

true if path a is less than path b.

std::ostream& gatb::core::debruijn::impl::operator<< ( std::ostream &  s, const Path_t< T > &  p  )

inline

Output stream operator for dumping a Path object as an ascii string holding the nucleotides of the path.

Parameters

[in]	s	: the output stream
[in]	p	: the path to be output

Returns

the output stream.