#include <graph_caller.hpp>

Inheritance diagram for vg::SnarlGraph:

Public Member Functions
	SnarlGraph (const HandleGraph backing_graph, SnarlManager &snarl_manager, vector< const Snarl > snarls)

pair< bool, handle_t >	node_to_snarl (handle_t handle) const

tuple< bool, handle_t, edge_t >	edge_to_snarl_edge (edge_t edge) const

void	embed_snarl (Visit &visit)

void	embed_snarls (SnarlTraversal &traversal)

void	embed_ref_path_snarls (SnarlTraversal &traversal)

bool	has_node (nid_t node_id) const
	Method to check if a node exists by ID. More...

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...

nid_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...

std::string	get_sequence (const handle_t &handle) const

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

nid_t	min_node_id () const

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

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

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

SnarlManager &	snarl_manager
	the snarl manager More...

unordered_map< handle_t, pair< handle_t, bool > >	snarls
	the snarls (indexed both ways). flag is true for original orientation More...

Detailed Description

Simplification of a NetGraph that ignores chains. It is designed only for traversal finding. Todo: generalize NestedFlowCaller to the point where we can remove this and use NetGraph instead

Constructor & Destructor Documentation

◆ SnarlGraph()

vg::SnarlGraph::SnarlGraph	(	const HandleGraph *	backing_graph,
		SnarlManager &	snarl_manager,
		vector< const Snarl * >	snarls
	)

Member Function Documentation

◆ edge_to_snarl_edge()

tuple< bool, handle_t, edge_t > vg::SnarlGraph::edge_to_snarl_edge ( edge_t edge ) const

◆ embed_ref_path_snarls()

void vg::SnarlGraph::embed_ref_path_snarls ( SnarlTraversal & traversal )

◆ embed_snarl()

void vg::SnarlGraph::embed_snarl ( Visit & visit )

◆ embed_snarls()

void vg::SnarlGraph::embed_snarls ( SnarlTraversal & traversal )

◆ flip()

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

protectedvirtual

this is the only function that's changed to do anything different from the backing graph: it is changed to "pass through" snarls by pretending there are edges from into snarl starts out of ends and vice versa.

Implements handlegraph::HandleGraph.

◆ for_each_handle_impl()

bool vg::SnarlGraph::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::SnarlGraph::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::SnarlGraph::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::SnarlGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

std::string vg::SnarlGraph::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::SnarlGraph::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::SnarlGraph::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::SnarlGraph::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.

◆ node_to_snarl()

pair< bool, handle_t > vg::SnarlGraph::node_to_snarl ( handle_t handle ) const

Member Data Documentation

◆ backing_graph

const HandleGraph* vg::SnarlGraph::backing_graph

protected

the backing graph

◆ snarl_manager

SnarlManager& vg::SnarlGraph::snarl_manager

protected

the snarl manager

◆ snarls

unordered_map<handle_t, pair<handle_t, bool> > vg::SnarlGraph::snarls

protected

the snarls (indexed both ways). flag is true for original orientation

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

src/graph_caller.hpp
src/graph_caller.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ SnarlGraph()

Member Function Documentation

◆ edge_to_snarl_edge()

◆ embed_ref_path_snarls()

◆ embed_snarl()

◆ embed_snarls()

◆ 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()

◆ node_to_snarl()

Member Data Documentation

◆ backing_graph

◆ snarl_manager

◆ snarls