#include <subgraph_overlay.hpp>

Inheritance diagram for vg::PathSubgraphOverlay:

Public Member Functions
	PathSubgraphOverlay (const PathHandleGraph backing, const unordered_set< nid_t > node_subset)

virtual	~PathSubgraphOverlay ()

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

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

virtual std::string	get_path_name (const path_handle_t &path_handle) const
	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
	Look up whether a path is circular. More...

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

virtual handle_t	get_handle_of_step (const step_handle_t &step_handle) const
	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
	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

virtual step_handle_t	path_end (const path_handle_t &path_handle) const

virtual step_handle_t	path_back (const path_handle_t &path_handle) const

virtual step_handle_t	path_front_end (const path_handle_t &path_handle) const

virtual bool	has_next_step (const step_handle_t &step_handle) const
	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
	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

virtual step_handle_t	get_previous_step (const step_handle_t &step_handle) const

Public Member Functions inherited from vg::SubgraphOverlay
	SubgraphOverlay (const HandleGraph backing, const unordered_set< nid_t > node_subset)

virtual	~SubgraphOverlay ()

virtual bool	has_node (nid_t node_id) const
	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
	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
	Get the ID from a handle. More...

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

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

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

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

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

virtual nid_t	min_node_id () const

virtual nid_t	max_node_id () const

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

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::PathHandleGraph
virtual	~PathHandleGraph ()=default

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

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::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_sense (const std::unordered_set< PathSense > &senses, 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_of_sample (const std::unordered_set< std::string > &samples, 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

template<typename Iteratee >
bool	for_each_step_of_sense (const handle_t &visited, const std::unordered_set< PathSense > &senses, const Iteratee &iteratee) const

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

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

Protected Member Functions inherited from vg::SubgraphOverlay
virtual bool	follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const

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

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

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

Protected Attributes
const PathHandleGraph *	backing_path_graph
	the backing path graph, just to not have to bother with dynamic cast More...

unordered_set< path_handle_t >	path_subset
	the subset of paths from the backing graph that are entirely contained within our subgraph More...

Protected Attributes inherited from vg::SubgraphOverlay
const HandleGraph *	backing_graph
	the backing graph More...

const unordered_set< nid_t > *	node_subset

nid_t	min_node = 0
	keep min_node_id() and max_node_id() constant More...

nid_t	max_node = 0

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

Present a PathHandleGraph that is a backing HandleGraph but restricted to a subset of nodes.

Warning: we don't yet have a subgraph interface. So we only consider paths from the backing graph that are fully contained in the subgraph.

Constructor & Destructor Documentation

◆ PathSubgraphOverlay()

vg::PathSubgraphOverlay::PathSubgraphOverlay	(	const PathHandleGraph *	backing,
		const unordered_set< nid_t > *	node_subset
	)

Make a new PathSubgraphOverlay. The backing graph must not be modified while the overlay exists.

◆ ~PathSubgraphOverlay()

vg::PathSubgraphOverlay::~PathSubgraphOverlay ( )

virtual

Member Function Documentation

◆ for_each_path_handle_impl()

bool vg::PathSubgraphOverlay::for_each_path_handle_impl ( const std::function< bool(const path_handle_t &)> & iteratee ) const

protectedvirtual

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.

Implements handlegraph::PathHandleGraph.

◆ for_each_step_on_handle_impl()

bool vg::PathSubgraphOverlay::for_each_step_on_handle_impl	(	const handle_t &	handle,
		const std::function< bool(const step_handle_t &)> &	iteratee
	)		const

protectedvirtual

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.

Implements handlegraph::PathHandleGraph.

◆ get_handle_of_step()

handle_t vg::PathSubgraphOverlay::get_handle_of_step ( const step_handle_t & step_handle ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ get_is_circular()

bool vg::PathSubgraphOverlay::get_is_circular ( const path_handle_t & path_handle ) const

virtual

Look up whether a path is circular.

Implements handlegraph::PathHandleGraph.

◆ get_next_step()

step_handle_t vg::PathSubgraphOverlay::get_next_step ( const step_handle_t & step_handle ) const

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.

Implements handlegraph::PathHandleGraph.

◆ get_path_count()

size_t vg::PathSubgraphOverlay::get_path_count ( void ) const

virtual

Returns the number of paths stored in the graph.

Implements handlegraph::PathHandleGraph.

◆ get_path_handle()

path_handle_t vg::PathSubgraphOverlay::get_path_handle ( const std::string & path_name ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ get_path_handle_of_step()

path_handle_t vg::PathSubgraphOverlay::get_path_handle_of_step ( const step_handle_t & step_handle ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ get_path_name()

std::string vg::PathSubgraphOverlay::get_path_name ( const path_handle_t & path_handle ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ get_previous_step()

step_handle_t vg::PathSubgraphOverlay::get_previous_step ( const step_handle_t & step_handle ) const

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.

Implements handlegraph::PathHandleGraph.

◆ get_step_count()

size_t vg::PathSubgraphOverlay::get_step_count ( const path_handle_t & path_handle ) const

virtual

Returns the number of node steps in the path.

Implements handlegraph::PathHandleGraph.

◆ has_next_step()

bool vg::PathSubgraphOverlay::has_next_step ( const step_handle_t & step_handle ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ has_path()

bool vg::PathSubgraphOverlay::has_path ( const std::string & path_name ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ has_previous_step()

bool vg::PathSubgraphOverlay::has_previous_step ( const step_handle_t & step_handle ) const

virtual

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

Implements handlegraph::PathHandleGraph.

◆ path_back()

step_handle_t vg::PathSubgraphOverlay::path_back ( const path_handle_t & path_handle ) const

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().

Implements handlegraph::PathHandleGraph.

◆ path_begin()

step_handle_t vg::PathSubgraphOverlay::path_begin ( const path_handle_t & path_handle ) const

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().

Implements handlegraph::PathHandleGraph.

◆ path_end()

step_handle_t vg::PathSubgraphOverlay::path_end ( const path_handle_t & path_handle ) const

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.

Implements handlegraph::PathHandleGraph.

◆ path_front_end()

step_handle_t vg::PathSubgraphOverlay::path_front_end ( const path_handle_t & path_handle ) const

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.

Implements handlegraph::PathHandleGraph.

Member Data Documentation

◆ backing_path_graph

const PathHandleGraph* vg::PathSubgraphOverlay::backing_path_graph

protected

the backing path graph, just to not have to bother with dynamic cast

◆ path_subset

unordered_set<path_handle_t> vg::PathSubgraphOverlay::path_subset

protected

the subset of paths from the backing graph that are entirely contained within our subgraph

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

src/subgraph_overlay.hpp
src/subgraph_overlay.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ PathSubgraphOverlay()

◆ ~PathSubgraphOverlay()

Member Function Documentation

◆ for_each_path_handle_impl()

◆ 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()

◆ has_next_step()

◆ has_path()

◆ has_previous_step()

◆ path_back()

◆ path_begin()

◆ path_end()

◆ path_front_end()

Member Data Documentation

◆ backing_path_graph

◆ path_subset