vg::SubpathOverlay Class Reference

#include <subpath_overlay.hpp>

Inheritance diagram for vg::SubpathOverlay:

Public Member Functions
	SubpathOverlay (const PathHandleGraph *backing, const step_handle_t &begin, const step_handle_t &end)
	SubpathOverlay ()=default
	~SubpathOverlay ()=default
bool	has_node (nid_t node_id) const
	Method to check if a node exists by ID.
handle_t	get_handle (const nid_t &node_id, bool is_reverse=false) const
	Look up the handle for the node with the given ID in the given orientation.
nid_t	get_id (const handle_t &handle) const
	Get the ID from a handle.
bool	get_is_reverse (const handle_t &handle) const
	Get the orientation of a handle.
handle_t	flip (const handle_t &handle) const
	Invert the orientation of a handle (potentially without getting its ID).
size_t	get_length (const handle_t &handle) const
	Get the length of a node.
std::string	get_sequence (const handle_t &handle) const
size_t	get_node_count () const
	Return the number of nodes in the graph.
nid_t	min_node_id () const
nid_t	max_node_id () const
handle_t	get_underlying_handle (const handle_t &handle) const
	ExpandingOverlayGraph interface.

Protected Member Functions
bool	follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const
bool	for_each_handle_impl (const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const

Protected Attributes
const HandleGraph *	backing_graph = nullptr
	the backing graph
std::vector< handle_t >	subpath_handles

Detailed Description

Overlay that presents a linear graph corresponding to a subinterval of a path

Constructor & Destructor Documentation

SubpathOverlay() [1/2]

vg::SubpathOverlay::SubpathOverlay	(	const PathHandleGraph *	backing,
		const step_handle_t &	begin,
		const step_handle_t &	end )

Construct new SubpathOverlay between two steps. The 'end' step is past-the-last.

SubpathOverlay() [2/2]

vg::SubpathOverlay::SubpathOverlay ( )

default

~SubpathOverlay()

vg::SubpathOverlay::~SubpathOverlay ( )

default

Member Function Documentation

flip()

handle_t vg::SubpathOverlay::flip

(

const handle_t &

handle

)

const

Invert the orientation of a handle (potentially without getting its ID).

follow_edges_impl()

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

protected

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

protected

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. Returns true if we finished and false if we stopped early.

get_handle()

handle_t vg::SubpathOverlay::get_handle	(	const nid_t &	node_id,
		bool	is_reverse = false ) const

Look up the handle for the node with the given ID in the given orientation.

get_id()

nid_t vg::SubpathOverlay::get_id

(

const handle_t &

handle

)

const

Get the ID from a handle.

get_is_reverse()

bool vg::SubpathOverlay::get_is_reverse

(

const handle_t &

handle

)

const

Get the orientation of a handle.

get_length()

size_t vg::SubpathOverlay::get_length

(

const handle_t &

handle

)

const

Get the length of a node.

get_node_count()

size_t vg::SubpathOverlay::get_node_count

(

)

const

Return the number of nodes in the graph.

get_sequence()

std::string vg::SubpathOverlay::get_sequence

(

const handle_t &

handle

)

const

Get the sequence of a node, presented in the handle's local forward orientation.

get_underlying_handle()

handle_t vg::SubpathOverlay::get_underlying_handle

(

const handle_t &

handle

)

const

ExpandingOverlayGraph interface.

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

has_node()

bool vg::SubpathOverlay::has_node

(

nid_t

node_id

)

const

Method to check if a node exists by ID.

max_node_id()

nid_t vg::SubpathOverlay::max_node_id

(

)

const

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.

min_node_id()

nid_t vg::SubpathOverlay::min_node_id

(

)

const

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.

Member Data Documentation

backing_graph

const HandleGraph* vg::SubpathOverlay::backing_graph = nullptr

protected

the backing graph

subpath_handles

std::vector<handle_t> vg::SubpathOverlay::subpath_handles

protected

---

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

• src/subpath_overlay.hpp
• src/subpath_overlay.cpp