#include <extra_node_graph.hpp>

Inheritance diagram for vg::ExtraNodeGraph:

Public Member Functions
	ExtraNodeGraph (const HandleGraph *backing, const string &sequence, const vector< handle_t > &edges_in, const vector< handle_t > &edges_out)

handle_t	get_created_handle () const
	Expose the handle to the new extra node. More...

virtual bool	has_node (id_t node_id) const
	Check if a node exists by ID. More...

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

virtual id_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 string	get_sequence (const handle_t &handle) const

virtual bool	follow_edges_impl (const handle_t &handle, bool go_left, const function< bool(const handle_t &)> &iteratee) const

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

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

virtual id_t	min_node_id () const
	Return the smallest ID in the graph. More...

virtual id_t	max_node_id () const
	Return the largest ID in the graph. More...

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

handle_t	from_backing (const handle_t &backing_handle) const
	Convert a backing graph handle to our handle to the same node. More...

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 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

Protected Member Functions
handle_t	to_backing (const handle_t &our_handle) const
	Convert our handle to a backing graph node into a backing graph handle to the same node. More...

bool	is_ours (const handle_t &our_handle) const
	Determine if a handle points to an overlay-added node or not. More...

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 Attributes
const HandleGraph *	backing
	What backing graph do we overlay? More...

unordered_set< handle_t >	in_from
	What are the handles in the backing graph that read into our new node forward? More...

unordered_set< handle_t >	out_to
	And where do we go after our new node forward? More...

id_t	added_id
	What is our projected node ID? More...

string	sequence

const handle_t	added_fwd = as_handle(0)

const handle_t	added_rev = as_handle(1)

Detailed Description

Present a HandleGraph that is a backing HandleGraph with an additional node and edges to/from it added.

Constructor & Destructor Documentation

◆ ExtraNodeGraph()

vg::ExtraNodeGraph::ExtraNodeGraph	(	const HandleGraph *	backing,
		const string &	sequence,
		const vector< handle_t > &	edges_in,
		const vector< handle_t > &	edges_out
	)

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

Creates a new handle with the given sequence, with edges from all the edges_in handles to it, and edges from it to all the edges_out handles.

Self loops on the new node are not supported.

Member Function Documentation

◆ flip()

handle_t vg::ExtraNodeGraph::flip ( const handle_t & handle ) const

virtual

Invert the orientation of a handle (potentially without getting its ID)

Implements handlegraph::HandleGraph.

◆ follow_edges_impl()

bool vg::ExtraNodeGraph::follow_edges_impl	(	const handle_t &	handle,
		bool	go_left,
		const function< bool(const handle_t &)> &	iteratee
	)		const

virtual

Loop over all the handles to next/previous (right/left) nodes. Passes them to a callback which returns false to stop iterating and true to continue. Returns true if we finished and false if we stopped early.

◆ for_each_handle_impl()

bool vg::ExtraNodeGraph::for_each_handle_impl	(	const function< bool(const handle_t &)> &	iteratee,
		bool	parallel = `false`
	)		const

virtual

Loop over all the nodes in the graph in their local forward orientations, in their internal stored order. Stop if the iteratee returns false.

◆ from_backing()

handle_t vg::ExtraNodeGraph::from_backing ( const handle_t & backing_handle ) const

inline

Convert a backing graph handle to our handle to the same node.

◆ get_created_handle()

handle_t vg::ExtraNodeGraph::get_created_handle ( ) const

Expose the handle to the new extra node.

◆ get_degree()

size_t vg::ExtraNodeGraph::get_degree	(	const handle_t &	handle,
		bool	go_left
	)		const

virtual

Compute the degree of one side of a handle in O(1) time, if the backing graph also provides this facility in O(1) time. Takes O(n) time otherwise in the returned degree.

Reimplemented from handlegraph::HandleGraph.

◆ get_handle()

handle_t vg::ExtraNodeGraph::get_handle	(	const id_t &	node_id,
		bool	is_reverse
	)		const

virtual

Look up the handle for the node with the given ID in the given orientation.

Implements handlegraph::HandleGraph.

◆ get_id()

id_t vg::ExtraNodeGraph::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

bool vg::ExtraNodeGraph::get_is_reverse ( const handle_t & handle ) const

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

size_t vg::ExtraNodeGraph::get_length ( const handle_t & handle ) const

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::ExtraNodeGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::ExtraNodeGraph::get_sequence ( const handle_t & handle ) const

virtual

Get the sequence of a node, presented in the handle's local forward orientation.

Implements handlegraph::HandleGraph.

◆ has_node()

bool vg::ExtraNodeGraph::has_node ( id_t node_id ) const

virtual

Check if a node exists by ID.

Implements handlegraph::HandleGraph.

◆ is_ours()

bool vg::ExtraNodeGraph::is_ours ( const handle_t & our_handle ) const

inlineprotected

Determine if a handle points to an overlay-added node or not.

◆ max_node_id()

id_t vg::ExtraNodeGraph::max_node_id ( ) const

virtual

Return the largest ID in the graph.

Implements handlegraph::HandleGraph.

◆ min_node_id()

id_t vg::ExtraNodeGraph::min_node_id ( ) const

virtual

Return the smallest ID in the graph.

Implements handlegraph::HandleGraph.

◆ to_backing()

handle_t vg::ExtraNodeGraph::to_backing ( const handle_t & our_handle ) const

inlineprotected

Convert our handle to a backing graph node into a backing graph handle to the same node.

Member Data Documentation

◆ added_fwd

const handle_t vg::ExtraNodeGraph::added_fwd = as_handle(0)

protected

◆ added_id

id_t vg::ExtraNodeGraph::added_id

protected

What is our projected node ID?

◆ added_rev

const handle_t vg::ExtraNodeGraph::added_rev = as_handle(1)

protected

◆ backing

const HandleGraph* vg::ExtraNodeGraph::backing

protected

What backing graph do we overlay?

◆ in_from

unordered_set<handle_t> vg::ExtraNodeGraph::in_from

protected

What are the handles in the backing graph that read into our new node forward?

◆ out_to

unordered_set<handle_t> vg::ExtraNodeGraph::out_to

protected

And where do we go after our new node forward?

◆ sequence

string vg::ExtraNodeGraph::sequence

protected

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

src/extra_node_graph.hpp
src/extra_node_graph.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ExtraNodeGraph()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ from_backing()

◆ get_created_handle()

◆ get_degree()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ has_node()

◆ is_ours()

◆ max_node_id()

◆ min_node_id()

◆ to_backing()

Member Data Documentation

◆ added_fwd

◆ added_id

◆ added_rev

◆ backing

◆ in_from

◆ out_to

◆ sequence