#include <source_sink_overlay.hpp>

Inheritance diagram for vg::SourceSinkOverlay:

Public Member Functions
	SourceSinkOverlay (const HandleGraph *backing, size_t length=1024, id_t source_id=0, id_t sink_id=0, bool break_disconnected=true)

handle_t	get_source_handle () const
	Expose the handle to the synthetic source. More...

handle_t	get_sink_handle () const
	Expose the handle to the synthetic sink. 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

virtual handle_t	get_underlying_handle (const handle_t &handle) const

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

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

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
size_t	node_length
	How long are the projected nodes? More...

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

id_t	source_id
	What is our projected source node ID? More...

id_t	sink_id
	What is our projected sink node ID? More...

unordered_set< handle_t >	backing_heads

unordered_set< handle_t >	backing_tails
	And similarly for the tails. These handles read out of their components. More...

const handle_t	source_fwd = as_handle(0)

const handle_t	source_rev = as_handle(1)

const handle_t	sink_fwd = as_handle(2)

const handle_t	sink_rev = as_handle(3)

Detailed Description

Present a HandleGraph that is a backing HandleGraph with all its head nodes connected to a single source node, and all its tail nodes connected to a single sink node.

Constructor & Destructor Documentation

◆ SourceSinkOverlay()

vg::SourceSinkOverlay::SourceSinkOverlay	(	const HandleGraph *	backing,
		size_t	length = `1024`,
		id_t	source_id = `0`,
		id_t	sink_id = `0`,
		bool	break_disconnected = `true`
	)

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

The overlay will project a source node consisting of '#' characters, and a sink node consisting of '$' characters. The lengths of the nodes may be specified, and default to 1024, the max length that GCSA2 supports. The IDs of the nodes will be autodetected from the backing graph's max ID if not specified (or given as 0). If either is specified, both must be specified.

Also breaks into disconnected components with no tips, unless break_disconnected is false. When breaking into such a component, we choose an arbitrary node, link the source node to its start, and link everything that also went to its start to the sink node.

Member Function Documentation

◆ flip()

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

inlineprotected

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

◆ get_degree()

size_t vg::SourceSinkOverlay::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::SourceSinkOverlay::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::SourceSinkOverlay::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::SourceSinkOverlay::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::SourceSinkOverlay::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.

◆ get_sink_handle()

handle_t vg::SourceSinkOverlay::get_sink_handle ( ) const

Expose the handle to the synthetic sink.

◆ get_source_handle()

handle_t vg::SourceSinkOverlay::get_source_handle ( ) const

Expose the handle to the synthetic source.

◆ get_underlying_handle()

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

virtual

Get the handle in the underlying graph that corresponds to the handle in the overlay. Throws an error if called on either the source or sink node

Implements handlegraph::ExpandingOverlayGraph.

◆ has_node()

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

virtual

Check if a node exists by ID.

Implements handlegraph::HandleGraph.

◆ is_ours()

bool vg::SourceSinkOverlay::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::SourceSinkOverlay::max_node_id ( ) const

virtual

Return the largest ID in the graph.

Implements handlegraph::HandleGraph.

◆ min_node_id()

id_t vg::SourceSinkOverlay::min_node_id ( ) const

virtual

Return the smallest ID in the graph.

Implements handlegraph::HandleGraph.

◆ to_backing()

handle_t vg::SourceSinkOverlay::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

◆ backing

const HandleGraph* vg::SourceSinkOverlay::backing

protected

What backing graph do we overlay?

◆ backing_heads

unordered_set<handle_t> vg::SourceSinkOverlay::backing_heads

protected

We keep a set of backing graph head handles, in backing graph handle space. This also includes anything else we need to hook up to our source node to break into tipless components.

◆ backing_tails

unordered_set<handle_t> vg::SourceSinkOverlay::backing_tails

protected

And similarly for the tails. These handles read out of their components.

◆ node_length

size_t vg::SourceSinkOverlay::node_length

protected

How long are the projected nodes?

◆ sink_fwd

const handle_t vg::SourceSinkOverlay::sink_fwd = as_handle(2)

protected

◆ sink_id

id_t vg::SourceSinkOverlay::sink_id

protected

What is our projected sink node ID?

◆ sink_rev

const handle_t vg::SourceSinkOverlay::sink_rev = as_handle(3)

protected

◆ source_fwd

const handle_t vg::SourceSinkOverlay::source_fwd = as_handle(0)

protected

◆ source_id

id_t vg::SourceSinkOverlay::source_id

protected

What is our projected source node ID?

◆ source_rev

const handle_t vg::SourceSinkOverlay::source_rev = as_handle(1)

protected

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

src/source_sink_overlay.hpp
src/source_sink_overlay.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SourceSinkOverlay()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ from_backing()

◆ get_degree()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ get_sink_handle()

◆ get_source_handle()

◆ get_underlying_handle()

◆ has_node()

◆ is_ours()

◆ max_node_id()

◆ min_node_id()

◆ to_backing()

Member Data Documentation

◆ backing

◆ backing_heads

◆ backing_tails

◆ node_length

◆ sink_fwd

◆ sink_id

◆ sink_rev

◆ source_fwd

◆ source_id

◆ source_rev