vg::PathTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::PathTraversalFinder:

Public Member Functions
	PathTraversalFinder (const PathHandleGraph &graph, const vector< string > &path_names={})
virtual vector< SnarlTraversal >	find_traversals (const Snarl &site)
virtual vector< Traversal >	find_traversals (const handle_t &snarl_start, const handle_t &snarl_end)
virtual pair< vector< SnarlTraversal >, vector< PathInterval > >	find_path_traversals (const Snarl &site)
virtual pair< vector< Traversal >, vector< PathInterval > >	find_path_traversals (const handle_t &snarl_start, const handle_t &snarl_end)
Public Member Functions inherited from vg::TraversalFinder
virtual	~TraversalFinder ()=default

Protected Attributes
const PathHandleGraph &	graph
unordered_set< path_handle_t >	paths

Detailed Description

This is a Handle Graph replacement for PathRestrictedTraversalFinder that uses the PathHandleGraph interface instead of the VG-based path index. It returns all traversals through a snarl that are contained within paths in the graph. It can also return a mapping from the traversals to their paths

Constructor & Destructor Documentation

PathTraversalFinder()

vg::PathTraversalFinder::PathTraversalFinder	(	const PathHandleGraph &	graph,
		const vector< string > &	path_names = {}
	)

Member Function Documentation

find_path_traversals() [1/2]

pair< vector< Traversal >, vector< PathInterval > > vg::PathTraversalFinder::find_path_traversals ( const handle_t &  snarl_start, const handle_t &  snarl_end  )

virtual

find_path_traversals() [2/2]

pair< vector< SnarlTraversal >, vector< PathInterval > > vg::PathTraversalFinder::find_path_traversals ( const Snarl &  site )

virtual

Like above, but return the path steps for the for the traversal endpoints

find_traversals() [1/2]

vector< Traversal > vg::PathTraversalFinder::find_traversals ( const handle_t &  snarl_start, const handle_t &  snarl_end  )

virtual

Reimplemented from vg::TraversalFinder.

find_traversals() [2/2]

vector< SnarlTraversal > vg::PathTraversalFinder::find_traversals ( const Snarl &  site )

virtual

Return all traversals through the site that are sub-paths of embedded paths in the graph

Implements vg::TraversalFinder.

Member Data Documentation

graph

const PathHandleGraph& vg::PathTraversalFinder::graph

protected

paths

unordered_set<path_handle_t> vg::PathTraversalFinder::paths

protected

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

• src/traversal_finder.hpp
• src/traversal_finder.cpp