#include <subgraph.hpp>

Inheritance diagram for vg::SubHandleGraph:

Public Member Functions
template<typename HandleIter >
	SubHandleGraph (const HandleGraph *super, HandleIter begin, HandleIter end)

	SubHandleGraph (const HandleGraph *super)
	Initialize as empty subgraph of a super graph. More...

void	add_handle (const handle_t &handle)

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

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. 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

virtual id_t	max_node_id () const

virtual 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 *	super = nullptr

unordered_set< id_t >	contents

id_t	min_id = numeric_limits<id_t>::max()

id_t	max_id = numeric_limits<id_t>::min()

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 implementation that acts as a subgraph of some other HandleGraph using a layer of indirection. Only subsets based on nodes; all edges between the nodes in the super graph are considered part of the subgraph. Subgraph handles can also be used by the super graph.

Constructor & Destructor Documentation

◆ SubHandleGraph() [1/2]

template<typename HandleIter >

vg::SubHandleGraph::SubHandleGraph	(	const HandleGraph *	super,
		HandleIter	begin,
		HandleIter	end
	)

Initialize with a super graph and nodes returned by iterators to handles from the super graph

◆ SubHandleGraph() [2/2]

vg::SubHandleGraph::SubHandleGraph ( const HandleGraph * super )

Initialize as empty subgraph of a super graph.

Member Function Documentation

◆ add_handle()

void vg::SubHandleGraph::add_handle ( const handle_t & handle )

Add a node from the super graph to the subgraph. Must be a handle to the super graph. No effect if the node is already included in the subgraph. Generally invalidates the results of any previous algorithms.

◆ flip()

handle_t vg::SubHandleGraph::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::SubHandleGraph::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::SubHandleGraph::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.

◆ get_handle()

handle_t vg::SubHandleGraph::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::SubHandleGraph::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::SubHandleGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::SubHandleGraph::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::SubHandleGraph::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::SubHandleGraph::has_node ( id_t node_id ) const

virtual

HandleGraph interface.

Implements handlegraph::HandleGraph.

◆ max_node_id()

id_t vg::SubHandleGraph::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::SubHandleGraph::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

◆ contents

unordered_set<id_t> vg::SubHandleGraph::contents

private

◆ max_id

id_t vg::SubHandleGraph::max_id = numeric_limits<id_t>::min()

private

◆ min_id

id_t vg::SubHandleGraph::min_id = numeric_limits<id_t>::max()

private

◆ super

const HandleGraph* vg::SubHandleGraph::super = nullptr

private

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

src/subgraph.hpp
src/subgraph.cpp

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SubHandleGraph() [1/2]

◆ SubHandleGraph() [2/2]

Member Function Documentation

◆ add_handle()

◆ 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

◆ contents

◆ max_id

◆ min_id

◆ super