vg::PathOrientedDistanceMeasurer Class Reference

#include <cluster.hpp>

Inheritance diagram for vg::PathOrientedDistanceMeasurer:

Public Member Functions
	PathOrientedDistanceMeasurer (const PathPositionHandleGraph *graph, const PathComponentIndex *path_component_index=nullptr)
	~PathOrientedDistanceMeasurer ()=default
	Default desctructor.
int64_t	oriented_distance (const pos_t &pos_1, const pos_t &pos_2)
vector< vector< size_t > >	get_buckets (const function< pos_t(size_t)> &get_position, size_t num_items)
vector< pair< size_t, size_t > >	exclude_merges (vector< vector< size_t > > &current_groups, const function< pos_t(size_t)> &get_position)
Public Member Functions inherited from vg::OrientedDistanceMeasurer
virtual	~OrientedDistanceMeasurer ()=default

Public Attributes
size_t	max_walk = 50
	The maximum distance we will walk trying to find a shared path.

Private Attributes
const PathPositionHandleGraph *	graph = nullptr
const PathComponentIndex *	path_component_index = nullptr

Constructor & Destructor Documentation

PathOrientedDistanceMeasurer()

vg::PathOrientedDistanceMeasurer::PathOrientedDistanceMeasurer	(	const PathPositionHandleGraph *	graph,
		const PathComponentIndex *	path_component_index = nullptr )

Construct a distance service to measures distance along paths in this graph. Optionally measures all distances on the forward strand of the paths.

~PathOrientedDistanceMeasurer()

vg::PathOrientedDistanceMeasurer::~PathOrientedDistanceMeasurer ( )

default

Default desctructor.

Member Function Documentation

exclude_merges()

vector< pair< size_t, size_t > > vg::PathOrientedDistanceMeasurer::exclude_merges ( vector< vector< size_t > > & current_groups, const function< pos_t(size_t)> & get_position )

virtual

Return a vector of pairs of groups (referred to by indexes in the current_groups vector) that cannot have finite distances between them (typically because they are on separate components).

Implements vg::OrientedDistanceMeasurer.

get_buckets()

vector< vector< size_t > > vg::PathOrientedDistanceMeasurer::get_buckets ( const function< pos_t(size_t)> & get_position, size_t num_items )

virtual

Return a vector of groups that we believe will have finite distances under this metric, can be empty.

Implements vg::OrientedDistanceMeasurer.

oriented_distance()

int64_t vg::PathOrientedDistanceMeasurer::oriented_distance ( const pos_t & pos_1, const pos_t & pos_2 )

virtual

Returns a signed distance, where positive indicates that pos_2 is to the right of pos_1, and negative indicates to the left. If the distance is infinite or can't be determined, returns numeric_limits<int64_t>::max().

Implements vg::OrientedDistanceMeasurer.

Member Data Documentation

graph

const PathPositionHandleGraph* vg::PathOrientedDistanceMeasurer::graph = nullptr

private

max_walk

size_t vg::PathOrientedDistanceMeasurer::max_walk = 50

The maximum distance we will walk trying to find a shared path.

path_component_index

const PathComponentIndex* vg::PathOrientedDistanceMeasurer::path_component_index = nullptr

private

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

• src/cluster.hpp
• src/cluster.cpp