vg
tools for working with variation graphs
Public Member Functions | Protected Attributes | List of all members
vg::PathTraversalFinder Class Reference

#include <traversal_finder.hpp>

Inheritance diagram for vg::PathTraversalFinder:
vg::TraversalFinder

Public Member Functions

 PathTraversalFinder (const PathHandleGraph &graph, SnarlManager &snarl_manager, const vector< string > &path_names={})
 
virtual vector< SnarlTraversalfind_traversals (const Snarl &site)
 
virtual pair< vector< SnarlTraversal >, vector< pair< step_handle_t, step_handle_t > > > find_path_traversals (const Snarl &site)
 
- Public Member Functions inherited from vg::TraversalFinder
virtual ~TraversalFinder ()=default
 

Protected Attributes

const PathHandleGraphgraph
 
SnarlManagersnarl_manager
 
unordered_set< path_handle_tpaths
 

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,
SnarlManager snarl_manager,
const vector< string > &  path_names = {} 
)

Member Function Documentation

◆ find_path_traversals()

pair< vector< SnarlTraversal >, vector< pair< step_handle_t, step_handle_t > > > vg::PathTraversalFinder::find_path_traversals ( const Snarl site)
virtual

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

◆ find_traversals()

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

◆ snarl_manager

SnarlManager& vg::PathTraversalFinder::snarl_manager
protected

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