gatb.core-API-0.0.0
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Implementation of Traversal that produces unitigs. More...
#include <Traversal.hpp>
Public Member Functions | |
SimplePathsTraversalTemplate (const Graph &graph, TerminatorTemplate< Node, Edge, Graph > &terminator, int maxlen=SimplePathsTraversalTemplate::defaultMaxLen, int max_depth=SimplePathsTraversalTemplate::defaultMaxDepth, int max_breadth=SimplePathsTraversalTemplate::defaultMaxBreadth) | |
std::string | getName () const |
Public Member Functions inherited from TraversalTemplate< Node, Edge, Graph > | |
int | traverse (Node &node, Direction dir, Path_t< Node > &resulting_sequence) |
int | traverse (Node &startingNode, Node &endingNode, Direction dir, Path_t< Node > &resulting_sequence) |
unsigned int | getMaxDepth () const |
unsigned int | getMaxBreadth () const |
const std::vector< std::pair< int, int > > & | getBubbles () const |
Public Member Functions inherited from SmartPointer | |
void | use () |
void | forget () |
Public Member Functions inherited from ISmartPointer | |
virtual | ~ISmartPointer () |
Additional Inherited Members | |
Static Public Member Functions inherited from TraversalTemplate< Node, Edge, Graph > | |
static TraversalTemplate< Node, Edge, Graph > * | create (tools::misc::TraversalKind type, const Graph &graph, TerminatorTemplate< Node, Edge, Graph > &terminator, int max_len=defaultMaxLen, int max_depth=defaultMaxDepth, int max_breadth=defaultMaxBreadth) |
static TraversalTemplate< Node, Edge, Graph > * | create (const std::string &type, const Graph &graph, TerminatorTemplate< Node, Edge, Graph > &terminator, int max_len=defaultMaxLen, int max_depth=defaultMaxDepth, int max_breadth=defaultMaxBreadth) |
static float | needleman_wunch (const Path_t< Node > &a, const Path_t< Node > &b) |
Protected Member Functions inherited from SmartPointer | |
SmartPointer () | |
virtual | ~SmartPointer () |
Implementation of Traversal that produces unitigs.
SimplePathsTraversalTemplate | ( | const Graph & | graph, |
TerminatorTemplate< Node, Edge, Graph > & | terminator, | ||
int | maxlen = SimplePathsTraversalTemplate< Node, Edge, Graph >::defaultMaxLen , |
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int | max_depth = SimplePathsTraversalTemplate< Node, Edge, Graph >::defaultMaxDepth , |
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int | max_breadth = SimplePathsTraversalTemplate< Node, Edge, Graph >::defaultMaxBreadth |
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Factory method that creates an instance of SimplePathsTraversal
[in] | graph | : graph object to be traversed |
[in] | terminator | : object used to tag traversed nodes |
[in] | maxlen | : maximum length of the traversal |
[in] | max_depth | : maximum depth of the traversal |
[in] | max_breadth | : maximum depth of the traversal |
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inlinevirtual |