#include <path_handle_graph.hpp>

Inheritance diagram for handlegraph::PathHandleGraph:

Public Member Functions
virtual	~PathHandleGraph ()=default

virtual size_t	get_path_count () const =0
	Returns the number of paths stored in the graph. More...

virtual bool	has_path (const std::string &path_name) const =0
	Determine if a path name exists and is legal to get a path handle for. More...

virtual path_handle_t	get_path_handle (const std::string &path_name) const =0

virtual std::string	get_path_name (const path_handle_t &path_handle) const =0
	Look up the name of a path from a handle to it. More...

virtual bool	get_is_circular (const path_handle_t &path_handle) const =0
	Look up whether a path is circular. More...

virtual size_t	get_step_count (const path_handle_t &path_handle) const =0
	Returns the number of node steps in the path. More...

virtual size_t	get_step_count (const handle_t &handle) const
	Returns the number of node steps on a handle. More...

virtual handle_t	get_handle_of_step (const step_handle_t &step_handle) const =0
	Get a node handle (node ID and orientation) from a handle to an step on a path. More...

virtual path_handle_t	get_path_handle_of_step (const step_handle_t &step_handle) const =0
	Returns a handle to the path that an step is on. More...

virtual step_handle_t	path_begin (const path_handle_t &path_handle) const =0

virtual step_handle_t	path_end (const path_handle_t &path_handle) const =0

virtual step_handle_t	path_back (const path_handle_t &path_handle) const =0

virtual step_handle_t	path_front_end (const path_handle_t &path_handle) const =0

virtual bool	has_next_step (const step_handle_t &step_handle) const =0
	Returns true if the step is not the last step in a non-circular path. More...

virtual bool	has_previous_step (const step_handle_t &step_handle) const =0
	Returns true if the step is not the first step in a non-circular path. More...

virtual step_handle_t	get_next_step (const step_handle_t &step_handle) const =0

virtual step_handle_t	get_previous_step (const step_handle_t &step_handle) const =0

template<typename Iteratee >
bool	for_each_path_handle (const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_step_on_handle (const handle_t &handle, const Iteratee &iteratee) const

virtual std::vector< step_handle_t >	steps_of_handle (const handle_t &handle, bool match_orientation=false) const

virtual bool	is_empty (const path_handle_t &path_handle) const
	Returns true if the given path is empty, and false otherwise. More...

PathForEachSocket	scan_path (const path_handle_t &path) const

template<typename Iteratee >
bool	for_each_step_in_path (const path_handle_t &path, const Iteratee &iteratee) const

Public Member Functions inherited from handlegraph::HandleGraph
virtual	~HandleGraph ()=default

virtual bool	has_node (nid_t node_id) const =0
	Method to check if a node exists by ID. More...

virtual handle_t	get_handle (const nid_t &node_id, bool is_reverse=false) const =0
	Look up the handle for the node with the given ID in the given orientation. More...

virtual nid_t	get_id (const handle_t &handle) const =0
	Get the ID from a handle. More...

virtual bool	get_is_reverse (const handle_t &handle) const =0
	Get the orientation of a handle. More...

virtual handle_t	flip (const handle_t &handle) const =0
	Invert the orientation of a handle (potentially without getting its ID) More...

virtual size_t	get_length (const handle_t &handle) const =0
	Get the length of a node. More...

virtual std::string	get_sequence (const handle_t &handle) const =0

virtual size_t	get_node_count () const =0
	Return the number of nodes in the graph. More...

virtual nid_t	min_node_id () const =0

virtual nid_t	max_node_id () const =0

template<typename Iteratee >
bool	follow_edges (const handle_t &handle, bool go_left, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_handle (const Iteratee &iteratee, bool parallel=false) const

virtual size_t	get_degree (const handle_t &handle, bool go_left) const

virtual bool	has_edge (const handle_t &left, const handle_t &right) const

bool	has_edge (const edge_t &edge) const
	Convenient wrapper of has_edge for edge_t argument. More...

virtual size_t	get_edge_count () const

virtual size_t	get_total_length () const

virtual char	get_base (const handle_t &handle, size_t index) const

virtual std::string	get_subsequence (const handle_t &handle, size_t index, size_t size) const

handle_t	forward (const handle_t &handle) const
	Get the locally forward version of a handle. More...

edge_t	edge_handle (const handle_t &left, const handle_t &right) const

handle_t	traverse_edge_handle (const edge_t &edge, const handle_t &left) const

template<typename Iteratee >
bool	for_each_edge (const Iteratee &iteratee, bool parallel=false) const

Public Member Functions inherited from handlegraph::PathMetadata
virtual	~PathMetadata ()=default

virtual PathSense	get_sense (const path_handle_t &handle) const
	What is the given path meant to be representing? More...

virtual std::string	get_sample_name (const path_handle_t &handle) const

virtual std::string	get_locus_name (const path_handle_t &handle) const

virtual size_t	get_haplotype (const path_handle_t &handle) const

virtual size_t	get_phase_block (const path_handle_t &handle) const

virtual subrange_t	get_subrange (const path_handle_t &handle) const

template<typename Iteratee >
bool	for_each_path_of_sense (const PathSense &sense, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_of_sample (const std::string &sample, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > senses, const std::unordered_set< std::string > samples, const std::unordered_set< std::string > *loci, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_path_matching (const std::unordered_set< PathSense > &senses, const std::unordered_set< std::string > &samples, const std::unordered_set< std::string > &loci, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_step_of_sense (const handle_t &visited, const PathSense &sense, const Iteratee &iteratee) const

Protected Member Functions
virtual bool	for_each_path_handle_impl (const std::function< bool(const path_handle_t &)> &iteratee) const =0

virtual bool	for_each_step_on_handle_impl (const handle_t &handle, const std::function< bool(const step_handle_t &)> &iteratee) const =0

Protected Member Functions inherited from handlegraph::HandleGraph
virtual bool	follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const =0

virtual bool	for_each_handle_impl (const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const =0

Protected Member Functions inherited from handlegraph::PathMetadata
virtual bool	for_each_path_matching_impl (const std::unordered_set< PathSense > senses, const std::unordered_set< std::string > samples, const std::unordered_set< std::string > *loci, const std::function< bool(const path_handle_t &)> &iteratee) const

virtual bool	for_each_step_of_sense_impl (const handle_t &visited, const PathSense &sense, const std::function< bool(const step_handle_t &)> &iteratee) const

Additional Inherited Members
Static Public Member Functions inherited from handlegraph::PathMetadata
static PathSense	parse_sense (const std::string &path_name)

static std::string	parse_sample_name (const std::string &path_name)

static std::string	parse_locus_name (const std::string &path_name)

static size_t	parse_haplotype (const std::string &path_name)

static size_t	parse_phase_block (const std::string &path_name)

static subrange_t	parse_subrange (const std::string &path_name)

static void	parse_path_name (const std::string &path_name, PathSense &sense, std::string &sample, std::string &locus, size_t &haplotype, size_t &phase_block, subrange_t &subrange)
	Decompose a formatted path name into metadata. More...

static std::string	create_path_name (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange)

Static Public Attributes inherited from handlegraph::PathMetadata
static const std::string	NO_SAMPLE_NAME = ""

static const std::string	NO_LOCUS_NAME = ""

static const size_t	NO_HAPLOTYPE = std::numeric_limits<size_t>::max()

static const size_t	NO_PHASE_BLOCK = std::numeric_limits<size_t>::max()

static const subrange_t	NO_SUBRANGE {PathMetadata::NO_END_POSITION, PathMetadata::NO_END_POSITION}

static const offset_t	NO_END_POSITION = std::numeric_limits<offset_t>::max()

Detailed Description

This is the interface for a handle graph that stores embedded paths.

Constructor & Destructor Documentation

◆ ~PathHandleGraph()

virtual handlegraph::PathHandleGraph::~PathHandleGraph ( )

virtualdefault

Member Function Documentation

◆ for_each_path_handle()

template<typename Iteratee >

bool handlegraph::PathHandleGraph::for_each_path_handle ( const Iteratee & iteratee ) const

Execute a function on each path_handle_t in the graph. If it returns bool, and it returns false, stop iteration. Returns true if we finished and false if we stopped early.

If the graph contains compressed haplotype paths and properly implements for_each_path_of_sense to retrieve them, they should not be visible here. Only reference or generic named paths should be visible.

◆ for_each_path_handle_impl()

virtual bool handlegraph::PathHandleGraph::for_each_path_handle_impl ( const std::function< bool(const path_handle_t &)> & iteratee ) const

protectedpure virtual

Execute a function on each path in the graph. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.

If the graph contains compressed haplotype paths and properly implements for_each_path_of_sense to retrieve them, they should not be visible here. Only reference or generic named paths should be visible.

Implements handlegraph::PathMetadata.

Implemented in xg::XG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ for_each_step_in_path()

template<typename Iteratee >

bool handlegraph::PathHandleGraph::for_each_step_in_path	(	const path_handle_t &	path,
		const Iteratee &	iteratee
	)		const

Loop over all the steps (step_handle_t) along a path. In a non-circular path, iterates from first through last step. In a circular path, iterates from the step returned by path_begin forward around to the step immediately before it. If the iteratee returns bool, and it returns false, stop. Returns true if we finished and false if we stopped early.

◆ for_each_step_on_handle()

template<typename Iteratee >

bool handlegraph::PathHandleGraph::for_each_step_on_handle	(	const handle_t &	handle,
		const Iteratee &	iteratee
	)		const

Execute a function on each step (step_handle_t) of a handle in any path. If it returns bool and returns false, stop iteration. Returns true if we finished and false if we stopped early.

If the graph contains compressed haplotype paths and properly implements for_each_step_of_sense to find them, they should not be visible here. Only reference or generic named paths should be visible.

◆ for_each_step_on_handle_impl()

virtual bool handlegraph::PathHandleGraph::for_each_step_on_handle_impl	(	const handle_t &	handle,
		const std::function< bool(const step_handle_t &)> &	iteratee
	)		const

protectedpure virtual

Execute a function on each step of a handle in any path. If it returns false, stop iteration. Returns true if we finished and false if we stopped early.

If the graph contains compressed haplotype paths and properly implements for_each_step_of_sense to find them, they should not be visible here. Only reference or generic named paths should be visible.

Implements handlegraph::PathMetadata.

Implemented in xg::XG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_handle_of_step()

virtual handle_t handlegraph::PathHandleGraph::get_handle_of_step ( const step_handle_t & step_handle ) const

pure virtual

Get a node handle (node ID and orientation) from a handle to an step on a path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_is_circular()

virtual bool handlegraph::PathHandleGraph::get_is_circular ( const path_handle_t & path_handle ) const

pure virtual

Look up whether a path is circular.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_next_step()

virtual step_handle_t handlegraph::PathHandleGraph::get_next_step ( const step_handle_t & step_handle ) const

pure virtual

Returns a handle to the next step on the path. If the given step is the final step of a non-circular path, this method has undefined behavior. In a circular path, the "last" step will loop around to the "first" step.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_path_count()

virtual size_t handlegraph::PathHandleGraph::get_path_count ( ) const

pure virtual

Returns the number of paths stored in the graph.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_path_handle()

virtual path_handle_t handlegraph::PathHandleGraph::get_path_handle ( const std::string & path_name ) const

pure virtual

Look up the path handle for the given path name. The path with that name must exist.

Implemented in xg::XG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_path_handle_of_step()

virtual path_handle_t handlegraph::PathHandleGraph::get_path_handle_of_step ( const step_handle_t & step_handle ) const

pure virtual

Returns a handle to the path that an step is on.

Implements handlegraph::PathMetadata.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_path_name()

virtual std::string handlegraph::PathHandleGraph::get_path_name ( const path_handle_t & path_handle ) const

pure virtual

Look up the name of a path from a handle to it.

Implements handlegraph::PathMetadata.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_previous_step()

virtual step_handle_t handlegraph::PathHandleGraph::get_previous_step ( const step_handle_t & step_handle ) const

pure virtual

Returns a handle to the previous step on the path. If the given step is the first step of a non-circular path, this method has undefined behavior. In a circular path, it will loop around from the "first" step (i.e. the one returned by path_begin) to the "last" step.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ get_step_count() [1/2]

size_t handlegraph::PathHandleGraph::get_step_count ( const handle_t & handle ) const

virtual

Returns the number of node steps on a handle.

◆ get_step_count() [2/2]

virtual size_t handlegraph::PathHandleGraph::get_step_count ( const path_handle_t & path_handle ) const

pure virtual

Returns the number of node steps in the path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ has_next_step()

virtual bool handlegraph::PathHandleGraph::has_next_step ( const step_handle_t & step_handle ) const

pure virtual

Returns true if the step is not the last step in a non-circular path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ has_path()

virtual bool handlegraph::PathHandleGraph::has_path ( const std::string & path_name ) const

pure virtual

Determine if a path name exists and is legal to get a path handle for.

Implemented in xg::XG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ has_previous_step()

virtual bool handlegraph::PathHandleGraph::has_previous_step ( const step_handle_t & step_handle ) const

pure virtual

Returns true if the step is not the first step in a non-circular path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ is_empty()

bool handlegraph::PathHandleGraph::is_empty ( const path_handle_t & path_handle ) const

virtual

Returns true if the given path is empty, and false otherwise.

Reimplemented in vg::MemoizingGraph.

◆ path_back()

virtual step_handle_t handlegraph::PathHandleGraph::path_back ( const path_handle_t & path_handle ) const

pure virtual

Get a handle to the last step, which will be an arbitrary step in a circular path that we consider "last" based on our construction of the path. If the path is empty then the implementation must return the same value as path_front_end().

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ path_begin()

virtual step_handle_t handlegraph::PathHandleGraph::path_begin ( const path_handle_t & path_handle ) const

pure virtual

Get a handle to the first step, which will be an arbitrary step in a circular path that we consider "first" based on our construction of the path. If the path is empty, then the implementation must return the same value as path_end().

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ path_end()

virtual step_handle_t handlegraph::PathHandleGraph::path_end ( const path_handle_t & path_handle ) const

pure virtual

Get a handle to a fictitious position past the end of a path. This position is returned by get_next_step for the final step in a path in a non-circular path. Note: get_next_step will NEVER return this value for a circular path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ path_front_end()

virtual step_handle_t handlegraph::PathHandleGraph::path_front_end ( const path_handle_t & path_handle ) const

pure virtual

Get a handle to a fictitious position before the beginning of a path. This position is return by get_previous_step for the first step in a path in a non-circular path. Note: get_previous_step will NEVER return this value for a circular path.

Implemented in xg::XG, vg::VG, vg::PathSubgraphOverlay, and vg::MemoizingGraph.

◆ scan_path()

PathForEachSocket handlegraph::PathHandleGraph::scan_path ( const path_handle_t & path ) const

Returns a class with an STL-style iterator interface that can be used directly in a for each loop like: for (handle_t handle : graph->scan_path(path)) { }

◆ steps_of_handle()

std::vector< step_handle_t > handlegraph::PathHandleGraph::steps_of_handle	(	const handle_t &	handle,
		bool	match_orientation = `false`
	)		const

virtual

Returns a vector of all steps of a node on paths. Optionally restricts to steps that match the handle in orientation.

Reimplemented in vg::MemoizingGraph.

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

deps/libhandlegraph/src/include/handlegraph/path_handle_graph.hpp
deps/libhandlegraph/src/path_handle_graph.cpp

Public Member Functions

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~PathHandleGraph()

Member Function Documentation

◆ for_each_path_handle()

◆ for_each_path_handle_impl()

◆ for_each_step_in_path()

◆ for_each_step_on_handle()

◆ for_each_step_on_handle_impl()

◆ get_handle_of_step()

◆ get_is_circular()

◆ get_next_step()

◆ get_path_count()

◆ get_path_handle()

◆ get_path_handle_of_step()

◆ get_path_name()

◆ get_previous_step()

◆ get_step_count() [1/2]

◆ get_step_count() [2/2]

◆ has_next_step()

◆ has_path()

◆ has_previous_step()

◆ is_empty()

◆ path_back()

◆ path_begin()

◆ path_end()

◆ path_front_end()

◆ scan_path()

◆ steps_of_handle()