#include <split_strand_graph.hpp>

Inheritance diagram for vg::StrandSplitGraph:

Public Member Functions
	StrandSplitGraph (const HandleGraph *graph)
	StrandSplitGraph ()=default
	Default constructor – not actually functional.
	~StrandSplitGraph ()=default
	Default destructor.
bool	has_node (id_t node_id) const
	HandleGraph interface.
handle_t	get_handle (const id_t &node_id, bool is_reverse=false) const
	Look up the handle for the node with the given ID in the given orientation.
id_t	get_id (const handle_t &handle) const
	Get the ID from a handle.
bool	get_is_reverse (const handle_t &handle) const
	Get the orientation of a handle.
handle_t	flip (const handle_t &handle) const
	Invert the orientation of a handle (potentially without getting its ID).
size_t	get_length (const handle_t &handle) const
	Get the length of a node.
string	get_sequence (const handle_t &handle) const
bool	follow_edges_impl (const handle_t &handle, bool go_left, const function< bool(const handle_t &)> &iteratee) const
bool	for_each_handle_impl (const function< bool(const handle_t &)> &iteratee, bool parallel=false) const
size_t	get_node_count () const
	Return the number of nodes in the graph.
id_t	min_node_id () const
id_t	max_node_id () const
handle_t	get_underlying_handle (const handle_t &handle) const
	ExpandingOverlayGraph interface.
bool	has_overlay_node_for (const nid_t &underlying_id) const
	Extra methods.
handle_t	get_overlay_handle (const handle_t &underlying_handle) const

Private Attributes
const HandleGraph *	graph = nullptr
	The underlying graph we're making splitting.

Detailed Description

A HandleGraph implementation that overlays some other handle graph and splits the two strands of its nodes into separate nodes

Constructor & Destructor Documentation

◆ StrandSplitGraph() [1/2]

vg::StrandSplitGraph::StrandSplitGraph ( const HandleGraph * graph )

Initialize as the reverse version of another graph, optionally also complementing

◆ StrandSplitGraph() [2/2]

vg::StrandSplitGraph::StrandSplitGraph ( )

default

Default constructor – not actually functional.

◆ ~StrandSplitGraph()

vg::StrandSplitGraph::~StrandSplitGraph ( )

default

Default destructor.

Member Function Documentation

◆ flip()

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

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

◆ follow_edges_impl()

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

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

Loop over all the nodes in the graph in their local forward orientations, in their internal stored order. Stop if the iteratee returns false. Can be told to run in parallel, in which case stopping after a false return value is on a best-effort basis and iteration order is not defined.

◆ get_handle()

handle_t vg::StrandSplitGraph::get_handle	(	const id_t &	node_id,
		bool	is_reverse = false ) const

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

◆ get_id()

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

Get the ID from a handle.

◆ get_is_reverse()

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

Get the orientation of a handle.

◆ get_length()

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

Get the length of a node.

◆ get_node_count()

size_t vg::StrandSplitGraph::get_node_count ( ) const

Return the number of nodes in the graph.

◆ get_overlay_handle()

handle_t vg::StrandSplitGraph::get_overlay_handle ( const handle_t & underlying_handle ) const

Returns the handle in the overlay graph that corresponds to a handle and orientation in the underlying graph. Reverse versions of underlying graph nodes become the locally-forward overlay node that represents them.

◆ get_sequence()

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

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

◆ get_underlying_handle()

handle_t vg::StrandSplitGraph::get_underlying_handle ( const handle_t & handle ) const

ExpandingOverlayGraph interface.

Returns the handle in the underlying graph that corresponds to a handle in the overlay

◆ has_node()

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

HandleGraph interface.

◆ has_overlay_node_for()

bool vg::StrandSplitGraph::has_overlay_node_for ( const nid_t & underlying_id ) const

Extra methods.

Returns true if any nodes in the overlay correspond to the given node in the underlying graph.

◆ max_node_id()

id_t vg::StrandSplitGraph::max_node_id ( ) const

Return the largest ID in the graph, or some larger number if the largest ID is unavailable. Return value is unspecified if the graph is empty.

◆ min_node_id()

id_t vg::StrandSplitGraph::min_node_id ( ) const

Return the smallest ID in the graph, or some smaller number if the smallest ID is unavailable. Return value is unspecified if the graph is empty.

Member Data Documentation

◆ graph

const HandleGraph* vg::StrandSplitGraph::graph = nullptr

private

The underlying graph we're making splitting.

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

src/split_strand_graph.hpp
src/split_strand_graph.cpp

Public Member Functions

Private Attributes