#include <dozeu_pinning_overlay.hpp>

Inheritance diagram for vg::DozeuPinningOverlay:

Public Member Functions
	DozeuPinningOverlay (const HandleGraph *graph, bool preserve_sinks)

	DozeuPinningOverlay ()=default
	Default constructor – not actually functional. More...

	~DozeuPinningOverlay ()=default
	Default destructor. More...

bool	performed_duplications () const

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...

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 Member Functions
bool	is_a_duplicate_handle (const handle_t &handle) const

bool	is_a_duplicate_id (const id_t &node_id) const

id_t	get_underlying_id (const id_t &node_id) const

handle_t	get_duplicate_handle (const handle_t &handle) const

Private Attributes
const HandleGraph *	graph = nullptr
	The graph we're masking empty nodes in. More...

bool	preserve_sinks
	Are we duplicating to preserve sources or sinks? More...

size_t	num_null_nodes = 0
	The total number of null nodes. More...

uint64_t	max_handle = numeric_limits<uint64_t>::min()
	The minimum numeric value of a handle. More...

uint64_t	handle_val_range = 0
	The length of the interval between the max and min numeric values of handles. More...

unordered_set< handle_t >	duplicated_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

◆ DozeuPinningOverlay() [1/2]

vg::DozeuPinningOverlay::DozeuPinningOverlay	(	const HandleGraph *	graph,
		bool	preserve_sinks
	)

Initialize with the graph we want to do pinned alignment to. Boolean flag indicates whether sources or sinks should be preserved (for pinning right or left respectively).

◆ DozeuPinningOverlay() [2/2]

vg::DozeuPinningOverlay::DozeuPinningOverlay ( )

default

Default constructor – not actually functional.

◆ ~DozeuPinningOverlay()

vg::DozeuPinningOverlay::~DozeuPinningOverlay ( )

default

Default destructor.

Member Function Documentation

◆ flip()

handle_t vg::DozeuPinningOverlay::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::DozeuPinningOverlay::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::DozeuPinningOverlay::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_duplicate_handle()

handle_t vg::DozeuPinningOverlay::get_duplicate_handle ( const handle_t & handle ) const

private

◆ get_handle()

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

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::DozeuPinningOverlay::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::DozeuPinningOverlay::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::DozeuPinningOverlay::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.

◆ get_underlying_id()

id_t vg::DozeuPinningOverlay::get_underlying_id ( const id_t & node_id ) const

private

◆ has_node()

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

virtual

HandleGraph interface.

Implements handlegraph::HandleGraph.

◆ is_a_duplicate_handle()

bool vg::DozeuPinningOverlay::is_a_duplicate_handle ( const handle_t & handle ) const

private

◆ is_a_duplicate_id()

bool vg::DozeuPinningOverlay::is_a_duplicate_id ( const id_t & node_id ) const

private

◆ max_node_id()

id_t vg::DozeuPinningOverlay::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::DozeuPinningOverlay::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.

◆ performed_duplications()

bool vg::DozeuPinningOverlay::performed_duplications ( ) const

Returns true if any node has been duplicated in the overlay, in which case it may be necessary to translate between the IDs of this overlay and the underlying graph.

Member Data Documentation

◆ duplicated_handles

unordered_set<handle_t> vg::DozeuPinningOverlay::duplicated_handles

private

◆ graph

const HandleGraph* vg::DozeuPinningOverlay::graph = nullptr

private

The graph we're masking empty nodes in.

◆ handle_val_range

uint64_t vg::DozeuPinningOverlay::handle_val_range = 0

private

The length of the interval between the max and min numeric values of handles.

◆ max_handle

uint64_t vg::DozeuPinningOverlay::max_handle = numeric_limits<uint64_t>::min()

private

The minimum numeric value of a handle.

◆ num_null_nodes

size_t vg::DozeuPinningOverlay::num_null_nodes = 0

private

The total number of null nodes.

◆ preserve_sinks

bool vg::DozeuPinningOverlay::preserve_sinks

private

Are we duplicating to preserve sources or sinks?

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

src/dozeu_pinning_overlay.hpp
src/dozeu_pinning_overlay.cpp

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DozeuPinningOverlay() [1/2]

◆ DozeuPinningOverlay() [2/2]

◆ ~DozeuPinningOverlay()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ get_duplicate_handle()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ get_underlying_handle()

◆ get_underlying_id()

◆ has_node()

◆ is_a_duplicate_handle()

◆ is_a_duplicate_id()

◆ max_node_id()

◆ min_node_id()

◆ performed_duplications()

Member Data Documentation

◆ duplicated_handles

◆ graph

◆ handle_val_range

◆ max_handle

◆ num_null_nodes

◆ preserve_sinks