#include <tree_subgraph.hpp>

Inheritance diagram for vg::TreeSubgraph:

Public Member Functions
	TreeSubgraph (const HandleGraph *super, vector< pair< int64_t, handle_t >> &&tree, size_t root_trim=0)

vector< handle_t >	get_topological_order () const
	Get a topological order very easily, since the tree defines one. More...

handle_t	get_root () const

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 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 handle_t	get_underlying_handle (const handle_t &handle) const
	ExpandingOverlayGraph interface. More...

Path	translate_down (const Path &path_against_subgraph) const
	Additional Interface. More...

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

Protected Member Functions
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

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

Protected Attributes
const HandleGraph *	super
	What graph are we based on? More...

vector< pair< int64_t, handle_t > >	tree

size_t	root_trim
	How much of the root do we trim off? More...

vector< vector< size_t > >	children
	For each node, what child indexes does it have? More...

Detailed Description

A HandleGraph implementation that represents a subgraph of another HandleGraph, defined by an internal tree whose nodes and edges are embedded in the nodes and edges of the backing graph.

Useful for describing the haplotype tree embedded in a graph, radiating from a certain point.

The tree is always exposed as rooted at the left, with child nodes radiating out on the right. The user has to re-orient the handles fed in to match that topology.

The root handle can be trimmed on its left side.

Supports translation of other Paths from this graph into the base graph.

Constructor & Destructor Documentation

◆ TreeSubgraph()

vg::TreeSubgraph::TreeSubgraph	(	const HandleGraph *	super,
		vector< pair< int64_t, handle_t >> &&	tree,
		size_t	root_trim = `0`
	)

Create a TreeSubgraph describing the subgraph of the given graph defined by the given tree. The tree is stored as a vector of pairs of (previous item number, base graph handle).

The tree handles must be given reading from the root end of the tree towards the branches.

The tree must be topologically sorted, with the root at 0. The root must point to -1.

If given, root_trim specifies a number of bases to cut off of the left side of the root handle.

Member Function Documentation

◆ flip()

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

protectedvirtual

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

protectedvirtual

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::TreeSubgraph::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::TreeSubgraph::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

bool vg::TreeSubgraph::get_is_reverse ( const handle_t & handle ) const

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

size_t vg::TreeSubgraph::get_length ( const handle_t & handle ) const

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::TreeSubgraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_root()

handle_t vg::TreeSubgraph::get_root ( ) const

Get a handle to the root of the tree, oriented towards the side with edges, if any.

Throws an exception if the tree is empty and there is no root.

◆ get_sequence()

string vg::TreeSubgraph::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_topological_order()

vector< handle_t > vg::TreeSubgraph::get_topological_order ( ) const

Get a topological order very easily, since the tree defines one.

◆ get_underlying_handle()

handle_t vg::TreeSubgraph::get_underlying_handle ( const handle_t & handle ) const

virtual

ExpandingOverlayGraph interface.

Get the handle in the backing graph that the given handle in this graph represents.

Implements handlegraph::ExpandingOverlayGraph.

◆ has_node()

bool vg::TreeSubgraph::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::TreeSubgraph::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::TreeSubgraph::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.

◆ translate_down()

Path vg::TreeSubgraph::translate_down ( const Path & path_against_subgraph ) const

Additional Interface.

Translate a Path against us to a Path against the base graph

Member Data Documentation

◆ children

vector<vector<size_t> > vg::TreeSubgraph::children

protected

For each node, what child indexes does it have?

◆ root_trim

size_t vg::TreeSubgraph::root_trim

protected

How much of the root do we trim off?

◆ super

const HandleGraph* vg::TreeSubgraph::super

protected

What graph are we based on?

◆ tree

vector<pair<int64_t, handle_t> > vg::TreeSubgraph::tree

protected

What tree are we using in the backing graph? Index in this vector corresponds to node ID in the projected graph.

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

src/tree_subgraph.hpp
src/tree_subgraph.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TreeSubgraph()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_root()

◆ get_sequence()

◆ get_topological_order()

◆ get_underlying_handle()

◆ has_node()

◆ max_node_id()

◆ min_node_id()

◆ translate_down()

Member Data Documentation

◆ children

◆ root_trim

◆ super

◆ tree