#include <dagified_graph.hpp>

Inheritance diagram for vg::DagifiedGraph:

Public Member Functions
	DagifiedGraph (const HandleGraph *graph, size_t min_preserved_path_length, size_t max_num_duplications=std::numeric_limits< size_t >::max())

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

	~DagifiedGraph ()=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...

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
uint64_t	scc_copy_of_handle (const handle_t &handle) const

uint64_t	scc_copy_of_node_id (const id_t &node_id) const

size_t	layout_order_of_handle (const handle_t &handle) const
	Helper function that returns the layout order of a handle from the underlying graph. More...

id_t	get_underlying_id (const id_t &node_id) const

handle_t	nth_copy_of_handle (const handle_t &handle, const uint64_t &n) const
	Helper function, returns the n-th copy in the dagified graph of a handle in the underlying graph. More...

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 *	graph = nullptr
	The underlying graph we're dagifiying. More...

unordered_map< handle_t, size_t >	layout_order

vector< uint64_t >	scc_of_handle

vector< uint64_t >	scc_copy_count

uint64_t	min_handle = std::numeric_limits<uint64_t>::max()
	The minimum value of a handle in the underlying graph, interpreted as an integer. More...

uint64_t	handle_val_range = 0
	The width of the range of values that handles in the underlying graph take. More...

size_t	node_count = 0
	The number of nodes including duplicated nodes, computed during construction. More...

id_t	max_id = std::numeric_limits<uint64_t>::min()
	The maximum ID of the graph, computed during construction. More...

Detailed Description

A HandleGraph implementation that wraps some other handle graph and converts it into a DAG, preserving all paths up a a minimum length.

Constructor & Destructor Documentation

◆ DagifiedGraph() [1/2]

vg::DagifiedGraph::DagifiedGraph	(	const HandleGraph *	graph,
		size_t	min_preserved_path_length,
		size_t	max_num_duplications = `std::numeric_limits<size_t>::max()`
	)

Expand a single-stranded graph into a DAG, preserving all walks up to the minimum length. If max duplications is provided, limits the number of times any node is copied.

◆ DagifiedGraph() [2/2]

vg::DagifiedGraph::DagifiedGraph ( )

default

Default constructor – not actually functional.

◆ ~DagifiedGraph()

vg::DagifiedGraph::~DagifiedGraph ( )

default

Default destructor.

Member Function Documentation

◆ flip()

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

virtual

Get the ID from a handle.

Implements handlegraph::HandleGraph.

◆ get_is_reverse()

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

virtual

Get the orientation of a handle.

Implements handlegraph::HandleGraph.

◆ get_length()

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

virtual

Get the length of a node.

Implements handlegraph::HandleGraph.

◆ get_node_count()

size_t vg::DagifiedGraph::get_node_count ( ) const

virtual

Return the number of nodes in the graph.

Implements handlegraph::HandleGraph.

◆ get_sequence()

string vg::DagifiedGraph::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::DagifiedGraph::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::DagifiedGraph::get_underlying_id ( const id_t & node_id ) const

protected

Helper function to identify the node ID in the original graph that corresponds to a node in the dagified graph

◆ has_node()

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

virtual

HandleGraph interface.

Implements handlegraph::HandleGraph.

◆ layout_order_of_handle()

size_t vg::DagifiedGraph::layout_order_of_handle ( const handle_t & handle ) const

protected

Helper function that returns the layout order of a handle from the underlying graph.

◆ max_node_id()

id_t vg::DagifiedGraph::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::DagifiedGraph::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.

◆ nth_copy_of_handle()

handle_t vg::DagifiedGraph::nth_copy_of_handle	(	const handle_t &	handle,
		const uint64_t &	n
	)		const

protected

Helper function, returns the n-th copy in the dagified graph of a handle in the underlying graph.

◆ scc_copy_of_handle()

uint64_t vg::DagifiedGraph::scc_copy_of_handle ( const handle_t & handle ) const

protected

Helper function to identify which ordinal copy of a strongly connected component in the underlying graph the handle belongs to

◆ scc_copy_of_node_id()

uint64_t vg::DagifiedGraph::scc_copy_of_node_id ( const id_t & node_id ) const

protected

Helper function to identify which ordinal copy of a strongly connected component in the underlying graph the node ID belongs to

Member Data Documentation

◆ graph

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

protected

The underlying graph we're dagifiying.

◆ handle_val_range

uint64_t vg::DagifiedGraph::handle_val_range = 0

protected

The width of the range of values that handles in the underlying graph take.

◆ layout_order

unordered_map<handle_t, size_t> vg::DagifiedGraph::layout_order

protected

Map from a canonical orientation of underlying handles (not necessarily forward!) to the ordinal position of the node in a low-FAS layout

◆ max_id

id_t vg::DagifiedGraph::max_id = std::numeric_limits<uint64_t>::min()

protected

The maximum ID of the graph, computed during construction.

◆ min_handle

uint64_t vg::DagifiedGraph::min_handle = std::numeric_limits<uint64_t>::max()

protected

The minimum value of a handle in the underlying graph, interpreted as an integer.

◆ node_count

size_t vg::DagifiedGraph::node_count = 0

protected

The number of nodes including duplicated nodes, computed during construction.

◆ scc_copy_count

vector<uint64_t> vg::DagifiedGraph::scc_copy_count

protected

The number of times each strongly connected component is duplicated in the dagified graph

◆ scc_of_handle

vector<uint64_t> vg::DagifiedGraph::scc_of_handle

protected

The ID of the strongly connected component that the handle at each layout position belongs to

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

src/dagified_graph.hpp
src/dagified_graph.cpp

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ DagifiedGraph() [1/2]

◆ DagifiedGraph() [2/2]

◆ ~DagifiedGraph()

Member Function Documentation

◆ flip()

◆ follow_edges_impl()

◆ for_each_handle_impl()

◆ get_handle()

◆ get_id()

◆ get_is_reverse()

◆ get_length()

◆ get_node_count()

◆ get_sequence()

◆ get_underlying_handle()

◆ get_underlying_id()

◆ has_node()

◆ layout_order_of_handle()

◆ max_node_id()

◆ min_node_id()

◆ nth_copy_of_handle()

◆ scc_copy_of_handle()

◆ scc_copy_of_node_id()

Member Data Documentation

◆ graph

◆ handle_val_range

◆ layout_order

◆ max_id

◆ min_handle

◆ node_count

◆ scc_copy_count

◆ scc_of_handle