vg
tools for working with variation graphs
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handlegraph::DeletableHandleGraph Class Referenceabstract

#include <deletable_handle_graph.hpp>

Inheritance diagram for handlegraph::DeletableHandleGraph:
handlegraph::MutableHandleGraph handlegraph::HandleGraph handlegraph::MutablePathDeletableHandleGraph vg::VG

Public Member Functions

virtual ~DeletableHandleGraph ()=default
 
virtual void destroy_handle (const handle_t &handle)=0
 
virtual void destroy_edge (const handle_t &left, const handle_t &right)=0
 
void destroy_edge (const edge_t &edge)
 Convenient wrapper for destroy_edge. More...
 
virtual void clear ()=0
 Remove all nodes and edges. More...
 
- Public Member Functions inherited from handlegraph::MutableHandleGraph
virtual ~MutableHandleGraph ()=default
 
virtual handle_t create_handle (const std::string &sequence)=0
 Create a new node with the given sequence and return the handle. More...
 
virtual handle_t create_handle (const std::string &sequence, const nid_t &id)=0
 Create a new node with the given id and sequence, then return the handle. More...
 
virtual void create_edge (const handle_t &left, const handle_t &right)=0
 
void create_edge (const edge_t &edge)
 Convenient wrapper for create_edge. More...
 
virtual handle_t apply_orientation (const handle_t &handle)=0
 
virtual std::vector< handle_tdivide_handle (const handle_t &handle, const std::vector< size_t > &offsets)=0
 
std::pair< handle_t, handle_tdivide_handle (const handle_t &handle, size_t offset)
 Specialization of divide_handle for a single division point. More...
 
virtual void optimize (bool allow_id_reassignment=true)=0
 
virtual void apply_ordering (const std::vector< handle_t > &order, bool compact_ids=false)=0
 
virtual void set_id_increment (const nid_t &min_id)=0
 
virtual void increment_node_ids (nid_t increment)=0
 Add the given value to all node IDs. 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 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

This is the interface for a handle graph that supports both addition of new nodes and edges as well as deletion of nodes and edges.

Constructor & Destructor Documentation

◆ ~DeletableHandleGraph()

virtual handlegraph::DeletableHandleGraph::~DeletableHandleGraph ( )
virtualdefault

Member Function Documentation

◆ clear()

virtual void handlegraph::DeletableHandleGraph::clear ( )
pure virtual

Remove all nodes and edges.

Implemented in vg::VG.

◆ destroy_edge() [1/2]

void handlegraph::DeletableHandleGraph::destroy_edge ( const edge_t edge)
inline

Convenient wrapper for destroy_edge.

◆ destroy_edge() [2/2]

virtual void handlegraph::DeletableHandleGraph::destroy_edge ( const handle_t left,
const handle_t right 
)
pure virtual

Remove the edge connecting the given handles in the given order and orientations. Ignores nonexistent edges. Does not update any stored paths.

Implemented in vg::VG.

◆ destroy_handle()

virtual void handlegraph::DeletableHandleGraph::destroy_handle ( const handle_t handle)
pure virtual

Remove the node belonging to the given handle and all of its edges. Does not update any stored paths. Invalidates the destroyed handle. May be called during serial for_each_handle iteration ONLY on the node being iterated. May NOT be called during parallel for_each_handle iteration. May NOT be called on the node from which edges are being followed during follow_edges.

Implemented in vg::VG.


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