#include <handle_graph.hpp>

Inheritance diagram for handlegraph::RankedHandleGraph:

Public Member Functions
virtual size_t	id_to_rank (const nid_t &node_id) const =0
	Return the rank of a node (ranks start at 1 and are dense). More...

virtual nid_t	rank_to_id (const size_t &rank) const =0
	Return the node with a given rank. More...

virtual size_t	handle_to_rank (const handle_t &handle) const

virtual handle_t	rank_to_handle (const size_t &rank) const
	Return the handle with a given rank. More...

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

virtual bool	has_node (nid_t node_id) const =0
	Method to check if a node exists by ID. More...

virtual handle_t	get_handle (const nid_t &node_id, bool is_reverse=false) const =0
	Look up the handle for the node with the given ID in the given orientation. More...

virtual nid_t	get_id (const handle_t &handle) const =0
	Get the ID from a handle. More...

virtual bool	get_is_reverse (const handle_t &handle) const =0
	Get the orientation of a handle. More...

virtual handle_t	flip (const handle_t &handle) const =0
	Invert the orientation of a handle (potentially without getting its ID) More...

virtual size_t	get_length (const handle_t &handle) const =0
	Get the length of a node. More...

virtual std::string	get_sequence (const handle_t &handle) const =0

virtual size_t	get_node_count () const =0
	Return the number of nodes in the graph. More...

virtual nid_t	min_node_id () const =0

virtual nid_t	max_node_id () const =0

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

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

Defines an interface for a handle graph that can rank its nodes and handles.

Doesn't actually require an efficient node lookup by sequence position as in VectorizableHandleGraph.

Member Function Documentation

◆ handle_to_rank()

size_t handlegraph::RankedHandleGraph::handle_to_rank ( const handle_t & handle ) const

virtual

Return the rank of a handle (ranks start at 1 and are dense, and each orientation has its own rank). Handle ranks may not have anything to do with node ranks.

◆ id_to_rank()

virtual size_t handlegraph::RankedHandleGraph::id_to_rank ( const nid_t & node_id ) const

pure virtual

Return the rank of a node (ranks start at 1 and are dense).

Implemented in xg::XG.

◆ rank_to_handle()

handle_t handlegraph::RankedHandleGraph::rank_to_handle ( const size_t & rank ) const

virtual

Return the handle with a given rank.

◆ rank_to_id()

virtual nid_t handlegraph::RankedHandleGraph::rank_to_id ( const size_t & rank ) const

pure virtual

Return the node with a given rank.