gatb.core-API-1.4.2
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.