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

#include <split_strand_graph.hpp>

Inheritance diagram for vg::StrandSplitGraph:
handlegraph::ExpandingOverlayGraph handlegraph::HandleGraph

Public Member Functions

 StrandSplitGraph (const HandleGraph *graph)
 
 StrandSplitGraph ()=default
 Default constructor – not actually functional. More...
 
 ~StrandSplitGraph ()=default
 Default destructor. More...
 
bool has_node (id_t node_id) const
 HandleGraph interface. More...
 
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...
 
id_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...
 
string get_sequence (const handle_t &handle) const
 
bool follow_edges_impl (const handle_t &handle, bool go_left, const function< bool(const handle_t &)> &iteratee) const
 
bool for_each_handle_impl (const function< bool(const handle_t &)> &iteratee, bool parallel=false) const
 
size_t get_node_count () const
 Return the number of nodes in the graph. More...
 
id_t min_node_id () const
 
id_t max_node_id () const
 
handle_t get_underlying_handle (const handle_t &handle) const
 ExpandingOverlayGraph interface. More...
 
bool has_overlay_node_for (const nid_t &underlying_id) const
 Extra methods. More...
 
handle_t get_overlay_handle (const handle_t &underlying_handle) const
 
- Public Member Functions inherited from handlegraph::ExpandingOverlayGraph
virtual ~ExpandingOverlayGraph ()=default
 
- 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
 

Private Attributes

const HandleGraphgraph = nullptr
 The underlying graph we're making splitting. 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

A HandleGraph implementation that overlays some other handle graph and splits the two strands of its nodes into separate nodes

Constructor & Destructor Documentation

◆ StrandSplitGraph() [1/2]

vg::StrandSplitGraph::StrandSplitGraph ( const HandleGraph graph)

Initialize as the reverse version of another graph, optionally also complementing

◆ StrandSplitGraph() [2/2]

vg::StrandSplitGraph::StrandSplitGraph ( )
default

Default constructor – not actually functional.

◆ ~StrandSplitGraph()

vg::StrandSplitGraph::~StrandSplitGraph ( )
default

Default destructor.

Member Function Documentation

◆ flip()

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

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_handle_impl()

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

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_handle()

handle_t vg::StrandSplitGraph::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_id()

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

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

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

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_overlay_handle()

handle_t vg::StrandSplitGraph::get_overlay_handle ( const handle_t underlying_handle) const

Returns the handle in the overlay graph that corresponds to a handle and orientation in the underlying graph. Reverse versions of underlying graph nodes become the locally-forward overlay node that represents them.

◆ get_sequence()

string vg::StrandSplitGraph::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.

◆ get_underlying_handle()

handle_t vg::StrandSplitGraph::get_underlying_handle ( const handle_t handle) const
virtual

ExpandingOverlayGraph interface.

Returns the handle in the underlying graph that corresponds to a handle in the overlay

Implements handlegraph::ExpandingOverlayGraph.

◆ has_node()

bool vg::StrandSplitGraph::has_node ( id_t  node_id) const
virtual

HandleGraph interface.

Implements handlegraph::HandleGraph.

◆ has_overlay_node_for()

bool vg::StrandSplitGraph::has_overlay_node_for ( const nid_t underlying_id) const

Extra methods.

Returns true if any nodes in the overlay correspond to the given node in the underlying graph.

◆ max_node_id()

id_t vg::StrandSplitGraph::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()

id_t vg::StrandSplitGraph::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.

Member Data Documentation

◆ graph

const HandleGraph* vg::StrandSplitGraph::graph = nullptr
private

The underlying graph we're making splitting.


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