#include <deletable_handle_graph.hpp>

Inheritance diagram for handlegraph::DeletableHandleGraph:

Public Member Functions
virtual	~DeletableHandleGraph ()=default

virtual void	destroy_handle (const handle_t &handle)=0

virtual handle_t	change_sequence (const handle_t &handle, const std::string &sequence)

virtual void	destroy_edge (const handle_t &left, const handle_t &right)=0

virtual handle_t	truncate_handle (const handle_t &handle, bool trunc_left, size_t offset)

void	destroy_edge (const edge_t &edge)
	Convenient wrapper for destroy_edge. More...

virtual void	clear ()=0
	Remove all nodes and edges. May also remove all paths, if applicable. More...

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

virtual handle_t	create_handle (const std::string &sequence)=0

virtual handle_t	create_handle (const std::string &sequence, const nid_t &id)=0

virtual void	create_edge (const handle_t &left, const handle_t &right)=0

void	create_edge (const edge_t &edge)
	Convenient wrapper for create_edge. More...

virtual handle_t	apply_orientation (const handle_t &handle)=0

virtual std::vector< handle_t >	divide_handle (const handle_t &handle, const std::vector< size_t > &offsets)=0

std::pair< handle_t, handle_t >	divide_handle (const handle_t &handle, size_t offset)
	Specialization of divide_handle for a single division point. More...

virtual void	optimize (bool allow_id_reassignment=true)=0

virtual bool	apply_ordering (const std::vector< handle_t > &order, bool compact_ids=false)=0

virtual void	set_id_increment (const nid_t &min_id)=0

virtual void	increment_node_ids (nid_t increment)

virtual void	increment_node_ids (long increment)
	This specialization for long appears to be needed to avoid confusion about nid_t. More...

virtual void	reassign_node_ids (const std::function< nid_t(const nid_t &)> &get_new_id)=0

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

Additional Inherited Members
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

Detailed Description

This is the interface for a handle graph that supports both addition of new nodes and edges as well as deletion of nodes and edges.

Constructor & Destructor Documentation

◆ ~DeletableHandleGraph()

virtual handlegraph::DeletableHandleGraph::~DeletableHandleGraph ( )

virtualdefault

Member Function Documentation

◆ change_sequence()

handle_t handlegraph::DeletableHandleGraph::change_sequence	(	const handle_t &	handle,
		const std::string &	sequence
	)

virtual

Change the sequence of handle's forward orientation to a new sequence. Returns a (possibly altered) handle to the node with the new sequence. The returned handle has the same orientation as the handle provided as an argument. May invalidate existing handles to the node. Updates paths to follow the new node if called through a class inheriting a MutablePathHandleGraph interface.

Reimplemented in handlegraph::MutablePathDeletableHandleGraph.

◆ clear()

virtual void handlegraph::DeletableHandleGraph::clear ( )

pure virtual

Remove all nodes and edges. May also remove all paths, if applicable.

Implemented in vg::VG.

◆ destroy_edge() [1/2]

void handlegraph::DeletableHandleGraph::destroy_edge ( const edge_t & edge )

inline

Convenient wrapper for destroy_edge.

◆ destroy_edge() [2/2]

virtual void handlegraph::DeletableHandleGraph::destroy_edge	(	const handle_t &	left,
		const handle_t &	right
	)

pure virtual

Remove the edge connecting the given handles in the given order and orientations. Ignores nonexistent edges. Does not update any stored paths.

Implemented in vg::VG.

◆ destroy_handle()

virtual void handlegraph::DeletableHandleGraph::destroy_handle ( const handle_t & handle )

pure virtual

Remove the node belonging to the given handle and all of its edges. Either destroys any paths in which the node participates, or leaves a "hidden", un-iterateable handle in the path to represent the sequence of the removed node. Invalidates the destroyed handle. May be called during serial for_each_handle iteration ONLY on the node being iterated. May NOT be called during parallel for_each_handle iteration. May NOT be called on the node from which edges are being followed during follow_edges. May NOT be called during iteration over paths, if it could destroy a path. May NOT be called during iteration along a path, if it could destroy that path.

Implemented in vg::VG.

◆ truncate_handle()

handle_t handlegraph::DeletableHandleGraph::truncate_handle	(	const handle_t &	handle,
		bool	trunc_left,
		size_t	offset
	)

virtual

Shorten a node by truncating either the left or right side of the node, relative to the orientation of the handle, starting from a given offset along the nodes sequence. Any edges on the truncated end of the node are deleted. Returns a (possibly altered) handle to the truncated node. May invalid stored paths.

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

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

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ~DeletableHandleGraph()

Member Function Documentation

◆ change_sequence()

◆ clear()

◆ destroy_edge() [1/2]

◆ destroy_edge() [2/2]

◆ destroy_handle()

◆ truncate_handle()