#include <splicing.hpp>

Inheritance diagram for vg::JoinedSpliceGraph:

Public Member Functions
	JoinedSpliceGraph (const HandleGraph &parent_graph, const IncrementalSubgraph &left_subgraph, handle_t left_splice_node, size_t left_splice_offset, const IncrementalSubgraph &right_subgraph, handle_t right_splice_node, size_t right_splice_offset)

	JoinedSpliceGraph ()=default

	~JoinedSpliceGraph ()=default

pair< size_t, size_t >	translate_node_ids (Path &path) const
	Specialized interface. More...

handle_t	left_seed_node () const
	Get the handle corresponding to the seed node of the left subgraph. More...

handle_t	right_seed_node () const
	Get the handle corresponding to the seed node of the right subgraph. More...

handle_t	left_splice_node () const
	Get the handle corresponding to the left side of the splice join. More...

handle_t	right_splice_node () const
	Get the handle corresponding to the right side of the splice join. More...

int64_t	min_link_length () const
	Get the minimum length of a walk from the left seed to the right seed. More...

int64_t	max_link_length () const
	Get the maximum length of a walk from the left seed to the right seed. 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

char	get_base (const handle_t &handle, size_t index) const
	Optional HandleGraph interface. More...

string	get_subsequence (const handle_t &handle, size_t index, size_t size) 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 size_t	get_edge_count () const

virtual size_t	get_total_length () 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 Member Functions
pair< size_t, size_t >	underlying_interval (const handle_t &handle) const

Private Attributes
const HandleGraph *	parent_graph

const IncrementalSubgraph *	left_subgraph

const IncrementalSubgraph *	right_subgraph

vector< int64_t >	left_handle_trans

vector< int64_t >	right_handle_trans

size_t	left_splice_offset

size_t	right_splice_offset

vector< size_t >	handle_idxs

size_t	num_left_handles

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

Constructor & Destructor Documentation

◆ JoinedSpliceGraph() [1/2]

vg::JoinedSpliceGraph::JoinedSpliceGraph	(	const HandleGraph &	parent_graph,
		const IncrementalSubgraph &	left_subgraph,
		handle_t	left_splice_node,
		size_t	left_splice_offset,
		const IncrementalSubgraph &	right_subgraph,
		handle_t	right_splice_node,
		size_t	right_splice_offset
	)

◆ JoinedSpliceGraph() [2/2]

vg::JoinedSpliceGraph::JoinedSpliceGraph ( )

default

◆ ~JoinedSpliceGraph()

vg::JoinedSpliceGraph::~JoinedSpliceGraph ( )

default

Member Function Documentation

◆ flip()

handle_t vg::JoinedSpliceGraph::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::JoinedSpliceGraph::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::JoinedSpliceGraph::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_base()

char vg::JoinedSpliceGraph::get_base	(	const handle_t &	handle,
		size_t	index
	)		const

virtual

Optional HandleGraph interface.

Returns one base of a handle's sequence, in the orientation of the handle.

Reimplemented from handlegraph::HandleGraph.

◆ get_handle()

handle_t vg::JoinedSpliceGraph::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::JoinedSpliceGraph::get_id ( const handle_t & handle ) const

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::JoinedSpliceGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::JoinedSpliceGraph::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_subsequence()

string vg::JoinedSpliceGraph::get_subsequence	(	const handle_t &	handle,
		size_t	index,
		size_t	size
	)		const

virtual

Returns a substring of a handle's sequence, in the orientation of the handle. If the indicated substring would extend beyond the end of the handle's sequence, the return value is truncated to the sequence's end.

Reimplemented from handlegraph::HandleGraph.

◆ has_node()

bool vg::JoinedSpliceGraph::has_node ( id_t node_id ) const

virtual

HandleGraph interface.

Method to check if a node exists by ID

Implements handlegraph::HandleGraph.

◆ left_seed_node()

handle_t vg::JoinedSpliceGraph::left_seed_node ( ) const

Get the handle corresponding to the seed node of the left subgraph.

◆ left_splice_node()

handle_t vg::JoinedSpliceGraph::left_splice_node ( ) const

Get the handle corresponding to the left side of the splice join.

◆ max_link_length()

int64_t vg::JoinedSpliceGraph::max_link_length ( ) const

Get the maximum length of a walk from the left seed to the right seed.

◆ max_node_id()

id_t vg::JoinedSpliceGraph::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_link_length()

int64_t vg::JoinedSpliceGraph::min_link_length ( ) const

Get the minimum length of a walk from the left seed to the right seed.

◆ min_node_id()

id_t vg::JoinedSpliceGraph::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.

◆ right_seed_node()

handle_t vg::JoinedSpliceGraph::right_seed_node ( ) const

Get the handle corresponding to the seed node of the right subgraph.

◆ right_splice_node()

handle_t vg::JoinedSpliceGraph::right_splice_node ( ) const

Get the handle corresponding to the right side of the splice join.

◆ translate_node_ids()

pair< size_t, size_t > vg::JoinedSpliceGraph::translate_node_ids ( Path & path ) const

Specialized interface.

Translates an aligned path to the underlying graph of the two incremental subgraphs Also returns the indexes of the left and right splice points. If either is not present, the corresponding index is set to numeric_limits<size_t>::max()

◆ underlying_interval()

pair< size_t, size_t > vg::JoinedSpliceGraph::underlying_interval ( const handle_t & handle ) const

private

Member Data Documentation

◆ handle_idxs

vector<size_t> vg::JoinedSpliceGraph::handle_idxs

private

◆ left_handle_trans

vector<int64_t> vg::JoinedSpliceGraph::left_handle_trans

private

◆ left_splice_offset

size_t vg::JoinedSpliceGraph::left_splice_offset

private

◆ left_subgraph

const IncrementalSubgraph* vg::JoinedSpliceGraph::left_subgraph

private

◆ num_left_handles

size_t vg::JoinedSpliceGraph::num_left_handles

private

◆ parent_graph

const HandleGraph* vg::JoinedSpliceGraph::parent_graph

private

◆ right_handle_trans

vector<int64_t> vg::JoinedSpliceGraph::right_handle_trans

private

◆ right_splice_offset

size_t vg::JoinedSpliceGraph::right_splice_offset

private

◆ right_subgraph

const IncrementalSubgraph* vg::JoinedSpliceGraph::right_subgraph

private

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

src/splicing.hpp
src/splicing.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ JoinedSpliceGraph() [1/2]

◆ JoinedSpliceGraph() [2/2]

◆ ~JoinedSpliceGraph()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ get_base()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ get_subsequence()

◆ has_node()

◆ left_seed_node()

◆ left_splice_node()

◆ max_link_length()

◆ max_node_id()

◆ min_link_length()

◆ min_node_id()

◆ right_seed_node()

◆ right_splice_node()

◆ translate_node_ids()

◆ underlying_interval()

Member Data Documentation

◆ handle_idxs

◆ left_handle_trans

◆ left_splice_offset

◆ left_subgraph

◆ num_left_handles

◆ parent_graph

◆ right_handle_trans

◆ right_splice_offset

◆ right_subgraph