#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 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

◆ 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

◆ clear()

◆ destroy_edge() [1/2]

◆ destroy_edge() [2/2]

◆ destroy_handle()

◆ truncate_handle()