#include <path_index.hpp>

Public Types
using	iterator = map< size_t, vg::NodeSide >::const_iterator
	We keep iterators to node occurrences along the ref path. More...

Public Member Functions
	PathIndex (const Path &path)
	Index just a path. More...

	PathIndex (const list< mapping_t > &mappings)
	Index just a list of mappings. More...

	PathIndex (const list< mapping_t > &mappings, VG &vg)

	PathIndex (const Path &path, const HandleGraph &graph)
	Index a path and pull sequence from a graph. More...

	PathIndex (VG &vg, const string &path_name, bool extract_sequence=false)
	Make a PathIndex from a path in a graph. More...

	PathIndex (const PathHandleGraph &graph, const string &path_name, bool extract_sequence=false)
	Make a PathIndex from a path in an indexed graph. More...

void	update_mapping_positions (VG &vg, const string &path_name)

NodeSide	at_position (size_t position) const

bool	path_contains_node (int64_t node_id) const
	Check whether a node is on the reference path. More...

bool	path_contains_node_in_orientation (int64_t node_id, bool is_reverse) const
	Check whether a node is on the reference path in a given path-relative orientation. More...

pair< bool, bool >	get_contained_orientations (int64_t node_id) const

iterator	find_in_orientation (int64_t node_id, bool is_reverse) const
	Find the first occurrence of the given node in the given orientation. More...

iterator	begin () const
	Get the iterator to the first node occurrence on the indexed path. More...

iterator	end () const
	Get the iterator to the last node occurrence on the indexed path. More...

iterator	find_position (size_t position) const

size_t	node_length (const iterator &here) const

pair< size_t, size_t >	round_outward (size_t start, size_t past_end) const

void	apply_translation (const Translation &translation)

void	apply_translations (const vector< Translation > &translations)

Public Attributes
map< int64_t, pair< size_t, bool > >	by_id

map< size_t, NodeSide >	by_start

std::string	sequence
	The actual sequence of the path, if desired. More...

map< const mapping_t *, size_t >	mapping_positions

Protected Member Functions
map< id_t, vector< Mapping > >	parse_translation (const Translation &translation)

void	replace_occurrence (iterator to_replace, const vector< Mapping > &replacements)

Protected Attributes
size_t	last_node_length

map< id_t, vector< iterator > >	node_occurrences

Detailed Description

Holds indexes of the reference in a graph: position to node, node to position and orientation, and the full reference string. Also knows about the lengths of nodes on the path, and lets you iterate back and forth over it.

Member Typedef Documentation

◆ iterator

using vg::PathIndex::iterator = map<size_t, vg::NodeSide>::const_iterator

We keep iterators to node occurrences along the ref path.

Constructor & Destructor Documentation

◆ PathIndex() [1/6]

vg::PathIndex::PathIndex ( const Path & path )

Index just a path.

◆ PathIndex() [2/6]

vg::PathIndex::PathIndex ( const list< mapping_t > & mappings )

Index just a list of mappings.

◆ PathIndex() [3/6]

vg::PathIndex::PathIndex	(	const list< mapping_t > &	mappings,
		VG &	vg
	)

Index a list of mappings embedded in the given vg's Paths object, and pull sequence from the given vg.

◆ PathIndex() [4/6]

vg::PathIndex::PathIndex	(	const Path &	path,
		const HandleGraph &	graph
	)

Index a path and pull sequence from a graph.

◆ PathIndex() [5/6]

vg::PathIndex::PathIndex	(	VG &	vg,
		const string &	path_name,
		bool	extract_sequence = `false`
	)

Make a PathIndex from a path in a graph.

◆ PathIndex() [6/6]

vg::PathIndex::PathIndex	(	const PathHandleGraph &	graph,
		const string &	path_name,
		bool	extract_sequence = `false`
	)

Make a PathIndex from a path in an indexed graph.

Member Function Documentation

◆ apply_translation()

void vg::PathIndex::apply_translation ( const Translation & translation )

Update the index to reflect the changes described by a Translation. References to nodes along the "from" path are changed to references to nodes along the "to" path. The translation must contain two paths of equal length, containing only matches. The translation must only divide nodes; it may not join nodes together. The translation must fully account for each old node that it touches (it can't translate only part of a node). The translation may not re-use the ID from one original node for a piece of a different original node. All the Mappings in the Translation must have Edits.

◆ apply_translations()

void vg::PathIndex::apply_translations ( const vector< Translation > & translations )

Update the index to reflect the changes described by the given collection of Translations. These translations are expected to be in the format produced by VG::edit() which is one to Mapping per translation. The vector may include both forward and reverse versions of each to node, and may also include translations mapping nodes that did not change to themselves.

◆ at_position()

NodeSide vg::PathIndex::at_position ( size_t position ) const

Find what node and orientation covers a position. The position must not be greater than the path length.

◆ begin()

PathIndex::iterator vg::PathIndex::begin ( ) const

Get the iterator to the first node occurrence on the indexed path.

◆ end()

PathIndex::iterator vg::PathIndex::end ( ) const

Get the iterator to the last node occurrence on the indexed path.

◆ find_in_orientation()

PathIndex::iterator vg::PathIndex::find_in_orientation	(	int64_t	node_id,
		bool	is_reverse
	)		const

Find the first occurrence of the given node in the given orientation.

◆ find_position()

PathIndex::iterator vg::PathIndex::find_position ( size_t position ) const

Find the iterator at the given position along the ref path. The position must not be greater than the path length.

◆ get_contained_orientations()

pair< bool, bool > vg::PathIndex::get_contained_orientations ( int64_t node_id ) const

Return two flags for if the path contains the given node in forward and reverse orientation.

◆ node_length()

size_t vg::PathIndex::node_length ( const iterator & here ) const

Get the length of the node occurrence on the path represented by this iterator.

◆ parse_translation()

map< id_t, vector< Mapping > > vg::PathIndex::parse_translation ( const Translation & translation )

protected

Convert a Translation that partitions old nodes into a map from old node ID to the Mappings that replace it in its forward orientation.

◆ path_contains_node()

bool vg::PathIndex::path_contains_node ( int64_t node_id ) const

Check whether a node is on the reference path.

◆ path_contains_node_in_orientation()

bool vg::PathIndex::path_contains_node_in_orientation	(	int64_t	node_id,
		bool	is_reverse
	)		const

Check whether a node is on the reference path in a given path-relative orientation.

◆ replace_occurrence()

void vg::PathIndex::replace_occurrence	(	iterator	to_replace,
		const vector< Mapping > &	replacements
	)

protected

Given an iterator into by_start, replace the occurrence of the node there with occurrences of the nodes given in the vector of mappings, which partition the forward strand of the node being replaced.

◆ round_outward()

pair< size_t, size_t > vg::PathIndex::round_outward	(	size_t	start,
		size_t	past_end
	)		const

Given an end-exclusive range on the path, round outward to the nearest node boundary positions.

◆ update_mapping_positions()

void vg::PathIndex::update_mapping_positions	(	VG &	vg,
		const string &	path_name
	)

Rebuild the mapping positions map by tracing all the paths in the given graph. TODO: We ought to move this functionality to the Paths object and make it use a good datastructure instead of brute force.

Member Data Documentation

◆ by_id

map<int64_t, pair<size_t, bool> > vg::PathIndex::by_id

Index from node ID to first position on the reference string and orientation it occurs there.

◆ by_start

map<size_t, NodeSide> vg::PathIndex::by_start

Index from start position on the reference to the side of the node that begins there. If it is a right side, the node occurs on the path in a reverse orientation.

◆ last_node_length

size_t vg::PathIndex::last_node_length

protected

This, combined with by_start, gets us the length of every node on the indexed path.

◆ mapping_positions

map<const mapping_t*, size_t> vg::PathIndex::mapping_positions

Index from Mapping pointers in a VG Paths object to their actual positions along their paths. Pointers may dangle if the vg graph changes the path.

◆ node_occurrences

map<id_t, vector<iterator> > vg::PathIndex::node_occurrences

protected

This holds all the places that a particular node occurs, in order. TODO: use this to replace by_id

◆ sequence

std::string vg::PathIndex::sequence

The actual sequence of the path, if desired.

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

src/path_index.hpp
src/path_index.cpp

Public Types

Public Member Functions

Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ iterator

Constructor & Destructor Documentation

◆ PathIndex() [1/6]

◆ PathIndex() [2/6]

◆ PathIndex() [3/6]

◆ PathIndex() [4/6]

◆ PathIndex() [5/6]

◆ PathIndex() [6/6]

Member Function Documentation

◆ apply_translation()

◆ apply_translations()

◆ at_position()

◆ begin()

◆ end()

◆ find_in_orientation()

◆ find_position()

◆ get_contained_orientations()

◆ node_length()

◆ parse_translation()

◆ path_contains_node()

◆ path_contains_node_in_orientation()

◆ replace_occurrence()

◆ round_outward()

◆ update_mapping_positions()

Member Data Documentation

◆ by_id

◆ by_start

◆ last_node_length

◆ mapping_positions

◆ node_occurrences

◆ sequence