#include <mutable_path_handle_graph.hpp>

Inheritance diagram for handlegraph::MutablePathHandleGraph:

Public Member Functions
virtual	~MutablePathHandleGraph ()=default

virtual void	destroy_path (const path_handle_t &path_handle)=0

virtual void	destroy_paths (const std::vector< path_handle_t > &paths)

virtual path_handle_t	create_path_handle (const std::string &name, bool is_circular=false)=0

virtual path_handle_t	rename_path (const path_handle_t &path_handle, const std::string &new_name)

virtual step_handle_t	append_step (const path_handle_t &path, const handle_t &to_append)=0

virtual step_handle_t	prepend_step (const path_handle_t &path, const handle_t &to_prepend)=0

virtual void	pop_front_step (const path_handle_t &path_handle)

virtual void	pop_back_step (const path_handle_t &path_handle)

virtual std::pair< step_handle_t, step_handle_t >	rewrite_segment (const step_handle_t &segment_begin, const step_handle_t &segment_end, const std::vector< handle_t > &new_segment)=0

virtual void	set_circularity (const path_handle_t &path, bool circular)=0

Public Member Functions inherited from handlegraph::PathHandleGraph
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

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

virtual path_handle_t	create_path (const PathSense &sense, const std::string &sample, const std::string &locus, const size_t &haplotype, const size_t &phase_block, const subrange_t &subrange, bool is_circular=false)

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()

Protected Member Functions inherited from handlegraph::PathHandleGraph
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

Detailed Description

This is the interface for a handle graph with embedded paths where the paths can be modified. Note that if the graph can also be modified, the implementation will also need to inherit from MutableHandleGraph, via the combination MutablePathMutableHandleGraph interface. TODO: This is a very limited interface at the moment. It will probably need to be extended.

Constructor & Destructor Documentation

◆ ~MutablePathHandleGraph()

virtual handlegraph::MutablePathHandleGraph::~MutablePathHandleGraph ( )

virtualdefault

Member Function Documentation

◆ append_step()

virtual step_handle_t handlegraph::MutablePathHandleGraph::append_step	(	const path_handle_t &	path,
		const handle_t &	to_append
	)

pure virtual

Append a visit to a node to the given path. Returns a handle to the new final step on the path which is appended. If the path is cirular, the new step is placed between the steps considered "last" and "first" by the method path_begin. Handles to prior steps on the path, and to other paths, must remain valid.

Implemented in vg::VG.

◆ create_path_handle()

virtual path_handle_t handlegraph::MutablePathHandleGraph::create_path_handle	(	const std::string &	name,
		bool	is_circular = `false`
	)

pure virtual

Create a path with the given name. The caller must ensure that no path with the given name exists already, or the behavior is undefined. Returns a handle to the created empty path. Handles to other paths must remain valid.

Implements handlegraph::MutablePathMetadata.

◆ destroy_path()

virtual void handlegraph::MutablePathHandleGraph::destroy_path ( const path_handle_t & path_handle )

pure virtual

Destroy the given path. Invalidates handles to the path and its steps.

Implemented in vg::VG.

◆ destroy_paths()

void handlegraph::MutablePathHandleGraph::destroy_paths ( const std::vector< path_handle_t > & paths )

virtual

Destroy the given set of paths. Invalidates handles to all the paths and their steps.

◆ pop_back_step()

void handlegraph::MutablePathHandleGraph::pop_back_step ( const path_handle_t & path_handle )

virtual

Remove the last step in a path. Undefined behavior if path is empty.

◆ pop_front_step()

void handlegraph::MutablePathHandleGraph::pop_front_step ( const path_handle_t & path_handle )

virtual

Remove the first step in a path. Undefined behavior if path is empty.

◆ prepend_step()

virtual step_handle_t handlegraph::MutablePathHandleGraph::prepend_step	(	const path_handle_t &	path,
		const handle_t &	to_prepend
	)

pure virtual

Prepend a visit to a node to the given path. Returns a handle to the new first step on the path which is appended. If the path is cirular, the new step is placed between the steps considered "last" and "first" by the method path_begin. Handles to later steps on the path, and to other paths, must remain valid.

Implemented in vg::VG.

◆ rename_path()

path_handle_t handlegraph::MutablePathHandleGraph::rename_path	(	const path_handle_t &	path_handle,
		const std::string &	new_name
	)

virtual

Renames a path. Existing path_handle_t's may become invalidated..

◆ rewrite_segment()

virtual std::pair<step_handle_t, step_handle_t> handlegraph::MutablePathHandleGraph::rewrite_segment	(	const step_handle_t &	segment_begin,
		const step_handle_t &	segment_end,
		const std::vector< handle_t > &	new_segment
	)

pure virtual

Delete a segment of a path and rewrite it as some other sequence of steps. Returns a pair of step_handle_t's that indicate the range of the new segment in the path. The segment to delete should be designated by the first (begin) and past-last (end) step handles. If the step that is returned by path_begin is deleted, path_begin will now return the first step from the new segment or, in the case that the new segment is empty, the step used as segment_end. Empty ranges consist of two copies of the same step handle. Empty ranges in empty paths consist of two copies of the end sentinel handle for the path. Rewriting an empty range inserts before the provided end handle.

◆ set_circularity()

virtual void handlegraph::MutablePathHandleGraph::set_circularity	(	const path_handle_t &	path,
		bool	circular
	)

pure virtual

Make a path circular or non-circular. If the path is becoming circular, the last step is joined to the first step. If the path is becoming linear, the step considered "last" is unjoined from the step considered "first" according to the method path_begin.

Implemented in vg::VG.

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~MutablePathHandleGraph()

Member Function Documentation

◆ append_step()

◆ create_path_handle()

◆ destroy_path()

◆ destroy_paths()

◆ pop_back_step()

◆ pop_front_step()

◆ prepend_step()

◆ rename_path()

◆ rewrite_segment()

◆ set_circularity()