#include <handle_graph.hpp>
Inheritance diagram for handlegraph::VectorizableHandleGraph:
Public Member Functions | |
| virtual | ~VectorizableHandleGraph ()=default |
| virtual size_t | node_vector_offset (const nid_t &node_id) const =0 |
| virtual nid_t | node_at_vector_offset (const size_t &offset) const =0 |
| Return the node overlapping the given offset in the implicit node vector. More... | |
| virtual size_t | edge_index (const edge_t &edge) const =0 |
| Return a unique index among edges in the graph. More... | |
 Public Member Functions inherited from handlegraph::RankedHandleGraph | |
| 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 providing a vectorization of the graph nodes and edges, which can be co-inherited alongside HandleGraph.
Constructor & Destructor Documentation
◆ ~VectorizableHandleGraph()
|
virtualdefault |
Member Function Documentation
◆ edge_index()
|
pure virtual |
Return a unique index among edges in the graph.
Implemented in xg::XG.
◆ node_at_vector_offset()
|
pure virtual |
Return the node overlapping the given offset in the implicit node vector.
Implemented in xg::XG.
◆ node_vector_offset()
|
pure virtual |
Return the start position of the node in a (possibly implict) sorted array constructed from the concatenation of the node sequences
Implemented in xg::XG.
The documentation for this class was generated from the following file:
- deps/libhandlegraph/src/include/handlegraph/handle_graph.hpp
