vg
tools for working with variation graphs
Public Member Functions | Private Attributes | List of all members
vg::ProtoHandleGraph Class Reference

#include <proto_handle_graph.hpp>

Inheritance diagram for vg::ProtoHandleGraph:
handlegraph::HandleGraph

Public Member Functions

 ProtoHandleGraph (const Graph *graph)
 Initialize as a wrapper for a Protobuf graph. More...
 
 ProtoHandleGraph ()=default
 Default constructor – not actually functional. More...
 
 ~ProtoHandleGraph ()=default
 Default destructor. More...
 
handle_t get_handle_by_index (const size_t &i) const
 Non-HandleGraph methods from Protobuf. More...
 
size_t edge_size () const
 Returns the number of edges in the graph. More...
 
edge_t get_edge_by_index (const size_t &i) const
 Get a handle to the i-th edge. More...
 
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 bool for_each_edge (const function< bool(const edge_t &)> &iteratee, bool parallel=false) 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 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 Graphgraph = nullptr
 The Protobuf graph we're wrapping. More...
 

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 NOT AN EFFICIENT GRAPH IMPLMENTATION. It is a HandleGraph wrapper for an unindexed Protobuf graph, which is primarily intended to provide a shim that eases the transition away from using Protobuf. In particular, it does not maintain adjacency lists, so edge and node lookup are O(N). However, it does provide the ability to look up nodes and edges by ordinal index in addition to the standard HandleGraph interface.

Constructor & Destructor Documentation

◆ ProtoHandleGraph() [1/2]

vg::ProtoHandleGraph::ProtoHandleGraph ( const Graph graph)

Initialize as a wrapper for a Protobuf graph.

◆ ProtoHandleGraph() [2/2]

vg::ProtoHandleGraph::ProtoHandleGraph ( )
default

Default constructor – not actually functional.

◆ ~ProtoHandleGraph()

vg::ProtoHandleGraph::~ProtoHandleGraph ( )
default

Default destructor.

Member Function Documentation

◆ edge_size()

size_t vg::ProtoHandleGraph::edge_size ( ) const

Returns the number of edges in the graph.

◆ flip()

handle_t vg::ProtoHandleGraph::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::ProtoHandleGraph::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_edge()

bool vg::ProtoHandleGraph::for_each_edge ( const function< bool(const edge_t &)> &  iteratee,
bool  parallel = false 
) const
virtual

Loop over all edges in their canonical orientation (as returned by edge_handle) and execute an iteratee on each one. Can stop early by returning false from the iteratee. Early stopping may not be immediate if executing in parallel. TODO: Promote to HandleGraph interface with a default implementation.

◆ for_each_handle_impl()

bool vg::ProtoHandleGraph::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_edge_by_index()

edge_t vg::ProtoHandleGraph::get_edge_by_index ( const size_t &  i) const

Get a handle to the i-th edge.

◆ get_handle()

handle_t vg::ProtoHandleGraph::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_handle_by_index()

handle_t vg::ProtoHandleGraph::get_handle_by_index ( const size_t &  i) const

Non-HandleGraph methods from Protobuf.

Get a handle to the i-th node

◆ get_id()

id_t vg::ProtoHandleGraph::get_id ( const handle_t handle) const
virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

bool vg::ProtoHandleGraph::get_is_reverse ( const handle_t handle) const
virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

size_t vg::ProtoHandleGraph::get_length ( const handle_t handle) const
virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::ProtoHandleGraph::get_node_count ( ) const
virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::ProtoHandleGraph::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::ProtoHandleGraph::has_node ( id_t  node_id) const
virtual

HandleGraph interface.

Method to check if a node exists by ID

Implements handlegraph::HandleGraph.

◆ max_node_id()

id_t vg::ProtoHandleGraph::max_node_id ( void  ) 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::ProtoHandleGraph::min_node_id ( void  ) 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

◆ graph

const Graph* vg::ProtoHandleGraph::graph = nullptr
private

The Protobuf graph we're wrapping.


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