vg::ReverseGraph Class Reference

#include <reverse_graph.hpp>

Inheritance diagram for vg::ReverseGraph:

Public Member Functions
	ReverseGraph (const HandleGraph *forward_graph, bool complement)
	ReverseGraph ()=default
	Default constructor – not actually functional.
	~ReverseGraph ()=default
	Default destructor.
virtual bool	has_node (id_t node_id) const
	HandleGraph interface.
virtual 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.
virtual id_t	get_id (const handle_t &handle) const
	Get the ID from a handle.
virtual bool	get_is_reverse (const handle_t &handle) const
	Get the orientation of a handle.
virtual handle_t	flip (const handle_t &handle) const
	Invert the orientation of a handle (potentially without getting its ID).
virtual size_t	get_length (const handle_t &handle) const
	Get the length of a node.
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.
virtual id_t	min_node_id () const
virtual id_t	max_node_id () const
handle_t	from_backing (const handle_t &backing_handle) const
	(Future) Overlay Interface

Protected Member Functions
virtual handle_t	get_underlying_handle (const handle_t &handle) const
	ExpandingOverlayGraph interface.

Protected Attributes
const HandleGraph *	forward_graph = nullptr
	The forward version of the graph we're making backwards.
bool	complement = false
	Complement the sequences?

Detailed Description

A HandleGraph implementation that wraps some other handle graph and reverses and optionally complements the sequences.

Constructor & Destructor Documentation

ReverseGraph() [1/2]

vg::ReverseGraph::ReverseGraph	(	const HandleGraph *	forward_graph,
		bool	complement )

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

ReverseGraph() [2/2]

vg::ReverseGraph::ReverseGraph ( )

default

Default constructor – not actually functional.

~ReverseGraph()

vg::ReverseGraph::~ReverseGraph ( )

default

Default destructor.

Member Function Documentation

flip()

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

virtual

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

follow_edges_impl()

bool vg::ReverseGraph::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::ReverseGraph::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. 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.

from_backing()

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

inline

(Future) Overlay Interface

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

get_handle()

handle_t vg::ReverseGraph::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.

get_id()

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

virtual

Get the ID from a handle.

get_is_reverse()

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

virtual

Get the orientation of a handle.

get_length()

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

virtual

Get the length of a node.

get_node_count()

size_t vg::ReverseGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

get_sequence()

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

virtual

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

get_underlying_handle()

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

protectedvirtual

ExpandingOverlayGraph interface.

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

has_node()

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

virtual

HandleGraph interface.

max_node_id()

id_t vg::ReverseGraph::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.

min_node_id()

id_t vg::ReverseGraph::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.

Member Data Documentation

complement

bool vg::ReverseGraph::complement = false

protected

Complement the sequences?

forward_graph

const HandleGraph* vg::ReverseGraph::forward_graph = nullptr

protected

The forward version of the graph we're making backwards.

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

• src/reverse_graph.hpp
• src/reverse_graph.cpp