#include <subgraph_overlay.hpp>

Inheritance diagram for vg::SubgraphOverlay:

Public Member Functions
	SubgraphOverlay (const HandleGraph backing, const unordered_set< nid_t > node_subset)

virtual	~SubgraphOverlay ()

virtual bool	has_node (nid_t node_id) const
	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
	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
	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 std::string	get_sequence (const handle_t &handle) const

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

virtual nid_t	min_node_id () const

virtual nid_t	max_node_id () const

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 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

Protected Member Functions
virtual bool	follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const

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

Protected Attributes
const HandleGraph *	backing_graph
	the backing graph More...

const unordered_set< nid_t > *	node_subset

nid_t	min_node = 0
	keep min_node_id() and max_node_id() constant More...

nid_t	max_node = 0

Detailed Description

Present a HandleGraph that is a backing HandleGraph but restricted to a subset of nodes. It won't give handles to nodes not in the subset, but it's not bulletproof: handles from outside the subset won't undergo any special checks.

Constructor & Destructor Documentation

◆ SubgraphOverlay()

vg::SubgraphOverlay::SubgraphOverlay	(	const HandleGraph *	backing,
		const unordered_set< nid_t > *	node_subset
	)

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

◆ ~SubgraphOverlay()

vg::SubgraphOverlay::~SubgraphOverlay ( )

virtual

Member Function Documentation

◆ flip()

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

protectedvirtual

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.

Implements handlegraph::HandleGraph.

◆ for_each_handle_impl()

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

protectedvirtual

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. Returns true if we finished and false if we stopped early.

Implements handlegraph::HandleGraph.

◆ get_handle()

handle_t vg::SubgraphOverlay::get_handle	(	const nid_t &	node_id,
		bool	is_reverse = `false`
	)		const

virtual

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

Implements handlegraph::HandleGraph.

◆ get_id()

nid_t vg::SubgraphOverlay::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::SubgraphOverlay::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

std::string vg::SubgraphOverlay::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::SubgraphOverlay::has_node ( nid_t node_id ) const

virtual

Method to check if a node exists by ID.

Implements handlegraph::HandleGraph.

◆ max_node_id()

nid_t vg::SubgraphOverlay::max_node_id ( ) const

virtual

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.

Implements handlegraph::HandleGraph.

◆ min_node_id()

nid_t vg::SubgraphOverlay::min_node_id ( ) const

virtual

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.

Implements handlegraph::HandleGraph.

Member Data Documentation

◆ backing_graph

const HandleGraph* vg::SubgraphOverlay::backing_graph

protected

the backing graph

◆ max_node

nid_t vg::SubgraphOverlay::max_node = 0

protected

◆ min_node

nid_t vg::SubgraphOverlay::min_node = 0

protected

keep min_node_id() and max_node_id() constant

◆ node_subset

const unordered_set<nid_t>* vg::SubgraphOverlay::node_subset

protected

the node subset. note, we don't own this so its up to client to keep in scope, just like the backing graph

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

src/subgraph_overlay.hpp
src/subgraph_overlay.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SubgraphOverlay()

◆ ~SubgraphOverlay()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ has_node()

◆ max_node_id()

◆ min_node_id()

Member Data Documentation

◆ backing_graph

◆ max_node

◆ min_node

◆ node_subset