#include <identity_overlay.hpp>

Inheritance diagram for vg::IdentityOverlay:

Public Member Functions
	IdentityOverlay (const HandleGraph *graph)

	IdentityOverlay ()=default
	Default constructor – not actually functional. More...

	~IdentityOverlay ()=default
	Default destructor. More...

bool	has_node (id_t node_id) const
	HandleGraph interface. More...

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. More...

id_t	get_id (const handle_t &handle) const
	Get the ID from a handle. More...

bool	get_is_reverse (const handle_t &handle) const
	Get the orientation of a handle. More...

handle_t	flip (const handle_t &handle) const
	Invert the orientation of a handle (potentially without getting its ID) More...

size_t	get_length (const handle_t &handle) const
	Get the length of a node. More...

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. More...

id_t	min_node_id () const

id_t	max_node_id () const

handle_t	get_underlying_handle (const handle_t &handle) const
	ExpandingOverlayGraph interface. More...

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 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

Private Attributes
const HandleGraph *	graph = nullptr
	The underlying graph. More...

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

A HandleGraph overlay that does not modify the underlying graph but is still useful for providing a uniform interface when choosing between overlays.

Constructor & Destructor Documentation

◆ IdentityOverlay() [1/2]

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

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

◆ IdentityOverlay() [2/2]

vg::IdentityOverlay::IdentityOverlay ( )

default

Default constructor – not actually functional.

◆ ~IdentityOverlay()

vg::IdentityOverlay::~IdentityOverlay ( )

default

Default destructor.

Member Function Documentation

◆ flip()

handle_t vg::IdentityOverlay::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::IdentityOverlay::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::IdentityOverlay::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::IdentityOverlay::get_handle	(	const id_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()

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

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::IdentityOverlay::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::IdentityOverlay::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_underlying_handle()

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

virtual

ExpandingOverlayGraph interface.

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

Implements handlegraph::ExpandingOverlayGraph.

◆ has_node()

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

virtual

HandleGraph interface.

Implements handlegraph::HandleGraph.

◆ max_node_id()

id_t vg::IdentityOverlay::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()

id_t vg::IdentityOverlay::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

◆ graph

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

private

The underlying graph.

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

src/identity_overlay.hpp
src/identity_overlay.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ IdentityOverlay() [1/2]

◆ IdentityOverlay() [2/2]

◆ ~IdentityOverlay()

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()

◆ get_underlying_handle()

◆ has_node()

◆ max_node_id()

◆ min_node_id()

Member Data Documentation

◆ graph