#include <snarl_manager_decomposition.hpp>

Inheritance diagram for vg::SnarlManagerDecomposition:

Classes
struct	ChainPosition
	The place of a chain node in its chain. More...

class	NodeDirectory

class	TraversalSet

class	TraversalSurvey

Public Member Functions
	SnarlManagerDecomposition (const SnarlManager &manager, const HandleGraph &graph)

	~SnarlManagerDecomposition () override=default

net_handle_t	get_snarl_net (const Snarl *snarl) const
	Get the start-to-end traversal of a snarl. More...

const Snarl *	get_snarl (const net_handle_t &net) const

net_handle_t	get_root () const override

bool	is_root (const net_handle_t &net) const override

bool	is_snarl (const net_handle_t &net) const override

bool	is_chain (const net_handle_t &net) const override

bool	is_node (const net_handle_t &net) const override

bool	is_sentinel (const net_handle_t &net) const override

net_handle_t	get_net (const handle_t &handle, const HandleGraph *handle_graph) const override

handle_t	get_handle (const net_handle_t &net, const HandleGraph *handle_graph) const override

net_handle_t	get_parent (const net_handle_t &child) const override

net_handle_t	get_bound (const net_handle_t &snarl, bool get_end, bool face_in) const override

net_handle_t	flip (const net_handle_t &net) const override
	Flip a traversal, or turn a sentinel to face the other way. More...

net_handle_t	canonical (const net_handle_t &net) const override

endpoint_t	starts_at (const net_handle_t &traversal) const override

endpoint_t	ends_at (const net_handle_t &traversal) const override

net_handle_t	get_parent_traversal (const net_handle_t &traversal_start, const net_handle_t &traversal_end) const override

Public Member Functions inherited from handlegraph::SnarlDecomposition
virtual	~SnarlDecomposition ()=default

template<typename Iteratee >
bool	for_each_child (const net_handle_t &parent, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_traversal (const net_handle_t &item, const Iteratee &iteratee) const

template<typename Iteratee >
bool	follow_net_edges (const net_handle_t &here, const HandleGraph *graph, bool go_left, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_tippy_child (const net_handle_t &parent, const Iteratee &iteratee) const

template<typename Iteratee >
bool	for_each_traversal_start (const net_handle_t &traversal, const Iteratee &) const

template<typename Iteratee >
bool	for_each_traversal_end (const net_handle_t &traversal, const Iteratee &) const

net_handle_t	get_start_bound (const net_handle_t &parent) const

net_handle_t	get_end_bound (const net_handle_t &parent) const

bool	starts_at_start (const net_handle_t &net) const

bool	starts_at_end (const net_handle_t &net) const

bool	starts_at_tip (const net_handle_t &net) const

bool	ends_at_start (const net_handle_t &net) const

bool	ends_at_end (const net_handle_t &net) const

bool	ends_at_tip (const net_handle_t &net) const

Protected Member Functions
bool	for_each_child_impl (const net_handle_t &traversal, const std::function< bool(const net_handle_t &)> &iteratee) const override

bool	for_each_traversal_impl (const net_handle_t &item, const std::function< bool(const net_handle_t &)> &iteratee) const override

bool	follow_net_edges_impl (const net_handle_t &here, const HandleGraph *handle_graph, bool go_left, const std::function< bool(const net_handle_t &)> &iteratee) const override

Protected Member Functions inherited from handlegraph::SnarlDecomposition
virtual bool	for_each_tippy_child_impl (const net_handle_t &parent, const std::function< bool(const net_handle_t &)> &iteratee) const

virtual bool	for_each_traversal_start_impl (const net_handle_t &traversal, const std::function< bool(const net_handle_t &)> &iteratee) const

virtual bool	for_each_traversal_end_impl (const net_handle_t &traversal, const std::function< bool(const net_handle_t &)> &iteratee) const

Private Member Functions
Visit	snarl_bound (const Snarl *snarl, bool get_end) const

const Snarl *	snarl_of_number (uint64_t number) const
	Get the manager's Snarl for a snarl number. More...

net_handle_t	snarl_net (const Snarl *snarl, bool forward) const

net_handle_t	chain_net (const Chain &chain) const
	Get a chain's start-to-end net handle. More...

const Chain &	chain_of_net (const net_handle_t &net) const
	Get the chain that a chain's net handle is for. More...

net_handle_t	chain_node_net (const Chain &chain, size_t position, bool is_reverse) const

bool	for_each_snarl_child (const Snarl *parent, const std::function< bool(const net_handle_t &)> &iteratee) const
	Call a function on each child of a snarl, or of the root if given null. More...

bool	for_each_chain_child (const net_handle_t &traversal, const std::function< bool(const net_handle_t &)> &iteratee) const
	Call a function on each chain node and snarl of a chain. More...

std::optional< net_handle_t >	next_in_chain (const net_handle_t &here) const

net_handle_t	sibling_entered_by (const HandleGraph &graph, const handle_t &handle, const Snarl *parent) const

bool	for_each_sibling_ahead (const HandleGraph &graph, const net_handle_t &here, const std::function< bool(const net_handle_t &)> &iteratee) const

bool	for_each_traversal_from (const net_handle_t &element, endpoint_t start, const std::function< bool(const net_handle_t &)> &iteratee) const

bool	follow_right (const HandleGraph &graph, const net_handle_t &here, const std::function< bool(const net_handle_t &)> &iteratee) const

std::pair< net_handle_t, endpoint_t >	parent_endpoint (const net_handle_t &net, bool is_start) const

TraversalSet	traversals_of (const net_handle_t &item) const

Private Attributes
const SnarlManager &	manager
	The manager whose snarls the view presents. More...

NodeDirectory	directory

TraversalSurvey	survey

Additional Inherited Members
Public Types inherited from handlegraph::SnarlDecomposition
enum	endpoint_t { START , END , TIP }

Detailed Description

A view of the snarls and chains in a SnarlManager, through the SnarlDecomposition interface.

A chain alternates chain nodes and snarls, starting and ending with a chain node. Each chain node has a position, counting from 0 at the start bound of the chain. The snarl of rank i lies between the chain nodes at positions i and i + 1.

Each snarl is oriented forward along its chain. So a Snarl that is reversed in parent starts at its end() flipped and ends at its start() flipped.

In a looping chain, the last snarl leads back into the first chain node. That node is both bounds of the chain, and one child at position 0.

Each node that is not a chain node is a free node. It is a trivial chain whose start-to-end traversal visits the node forward.

The view keeps a reference to the manager, which must outlive it and must not change. It does not keep the graph. A graph passed to a method must have the same nodes and edges as the graph the view was made with.

Note: Unlike a SnarlDistanceIndex, the view puts top-level chains directly in the root, and shows snarls that have no children.

Constructor & Destructor Documentation

◆ SnarlManagerDecomposition()

vg::SnarlManagerDecomposition::SnarlManagerDecomposition	(	const SnarlManager &	manager,
		const HandleGraph &	graph
	)

Make a view of the snarls in a SnarlManager.

Walk the graph to find which traversals of each snarl and chain are realizable.

Precondition: finish() has been called on the manager.

Exceptions

std::invalid_argument If the manager holds a unary snarl.

◆ ~SnarlManagerDecomposition()

vg::SnarlManagerDecomposition::~SnarlManagerDecomposition ( )

overridedefault

Member Function Documentation

◆ canonical()

net_handle_t vg::SnarlManagerDecomposition::canonical ( const net_handle_t & net ) const

overridevirtual

Get the canonical traversal of a net graph element.

For a snarl, chain or node, pick the first realizable traversal among start-to-end, start-to-tip, end-to-tip, start-to-start, end-to-end and tip-to-tip. For a sentinel, pick its bound facing in.

TODO: An element with no realizable traversal gets start-to-end, but the interface requires the canonical traversal to be realizable. Such elements exist: IntegratedSnarlFinder makes a snarl around a cycle that walks from both of its bounds fall into and never leave.

Implements handlegraph::SnarlDecomposition.

◆ chain_net()

net_handle_t vg::SnarlManagerDecomposition::chain_net ( const Chain & chain ) const

private

Get a chain's start-to-end net handle.

◆ chain_node_net()

net_handle_t vg::SnarlManagerDecomposition::chain_node_net	(	const Chain &	chain,
		size_t	position,
		bool	is_reverse
	)		const

private

Get the net handle for the chain node at a position, oriented in reverse along the chain if is_reverse, and forward along it otherwise.

◆ chain_of_net()

const Chain & vg::SnarlManagerDecomposition::chain_of_net ( const net_handle_t & net ) const

private

Get the chain that a chain's net handle is for.

◆ ends_at()

handlegraph::SnarlDecomposition::endpoint_t vg::SnarlManagerDecomposition::ends_at ( const net_handle_t & traversal ) const

overridevirtual

Return the kind of location at which the given traversal ends.

Implements handlegraph::SnarlDecomposition.

◆ flip()

net_handle_t vg::SnarlManagerDecomposition::flip ( const net_handle_t & net ) const

overridevirtual

Flip a traversal, or turn a sentinel to face the other way.

Implements handlegraph::SnarlDecomposition.

◆ follow_net_edges_impl()

bool vg::SnarlManagerDecomposition::follow_net_edges_impl	(	const net_handle_t &	here,
		const HandleGraph *	handle_graph,
		bool	go_left,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

overrideprotectedvirtual

Call a function on each realizable traversal that comes just after or just before a traversal in its parent.

In a looping chain, going right from the last snarl gives the first chain node.

Implements handlegraph::SnarlDecomposition.

◆ follow_right()

bool vg::SnarlManagerDecomposition::follow_right	(	const HandleGraph &	graph,
		const net_handle_t &	here,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

private

Do follow_net_edges() going right.

Find the net graph elements that edges from the end of here lead into, and give each realizable traversal of them that starts at the endpoint the edge leads into.

◆ for_each_chain_child()

bool vg::SnarlManagerDecomposition::for_each_chain_child	(	const net_handle_t &	traversal,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

private

Call a function on each chain node and snarl of a chain.

◆ for_each_child_impl()

bool vg::SnarlManagerDecomposition::for_each_child_impl	(	const net_handle_t &	traversal,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

overrideprotectedvirtual

Call a function on each child of the root, a snarl, a chain or a trivial chain.

The root or a snarl gives its chains in the manager's order, then its free nodes in ID order. A chain traversal other than start-to-end and end-to-start gives the children in chain order, each start-to-end.

Implements handlegraph::SnarlDecomposition.

◆ for_each_sibling_ahead()

bool vg::SnarlManagerDecomposition::for_each_sibling_ahead	(	const HandleGraph &	graph,
		const net_handle_t &	here,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

private

Call a function on each sibling that an edge from the end of a traversal leads into.

A sibling is a chain or trivial chain in the same parent, or a sentinel of the parent facing out. A looping chain, a sentinel facing out, and a traversal that ends at a tip have no siblings ahead.

◆ for_each_snarl_child()

bool vg::SnarlManagerDecomposition::for_each_snarl_child	(	const Snarl *	parent,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

private

Call a function on each child of a snarl, or of the root if given null.

◆ for_each_traversal_from()

bool vg::SnarlManagerDecomposition::for_each_traversal_from	(	const net_handle_t &	element,
		endpoint_t	start,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

private

Call a function on each realizable traversal of a net graph element that starts at the given endpoint.

◆ for_each_traversal_impl()

bool vg::SnarlManagerDecomposition::for_each_traversal_impl	(	const net_handle_t &	item,
		const std::function< bool(const net_handle_t &)> &	iteratee
	)		const

overrideprotectedvirtual

Call a function on each realizable traversal of a net graph element.

Give them ordered by start endpoint, then end endpoint, each in the order START, END, TIP. A sentinel is its own only traversal.

Implements handlegraph::SnarlDecomposition.

◆ get_bound()

net_handle_t vg::SnarlManagerDecomposition::get_bound	(	const net_handle_t &	snarl,
		bool	get_end,
		bool	face_in
	)		const

overridevirtual

Get a sentinel of a snarl, or a boundary node of a chain.

A looping chain gives its first chain node as both bounds.

Implements handlegraph::SnarlDecomposition.

◆ get_handle()

handle_t vg::SnarlManagerDecomposition::get_handle	(	const net_handle_t &	net,
		const HandleGraph *	handle_graph
	)		const

overridevirtual

Get the graph handle for a node, a trivial chain, or a sentinel.

A sentinel gives its boundary node, oriented the way the sentinel faces.

Exceptions

std::invalid_argument If the net handle is for a snarl, the root, or a chain that holds a snarl.

Implements handlegraph::SnarlDecomposition.

◆ get_net()

net_handle_t vg::SnarlManagerDecomposition::get_net	(	const handle_t &	handle,
		const HandleGraph *	graph
	)		const

overridevirtual

Turn a handle to an oriented node into a net handle for a start-to-end or end-to-start traversal of the node, as appropriate.

Implements handlegraph::SnarlDecomposition.

◆ get_parent()

net_handle_t vg::SnarlManagerDecomposition::get_parent ( const net_handle_t & child ) const

overridevirtual

Get the parent snarl of a chain, or the parent chain of a snarl or node. If the child is start-to-end or end-to-start, and the parent is a chain, the chain comes out facing the same way, accounting for the relative orientation of the child snarl or node in the chain. Otherwise, everything is produced as start-to-end, even if that is not actually a realizable traversal of a snarl or chain. May not be called on the root snarl.

Also works on snarl boundary sentinels.

Implements handlegraph::SnarlDecomposition.

◆ get_parent_traversal()

net_handle_t vg::SnarlManagerDecomposition::get_parent_traversal	(	const net_handle_t &	traversal_start,
		const net_handle_t &	traversal_end
	)		const

overridevirtual

Get the traversal of a snarl or chain from one of its children or bounds to another.

Exceptions

std::invalid_argument If the two arguments are in different snarls or chains, or if the traversal between them is not realizable.

Implements handlegraph::SnarlDecomposition.

◆ get_root()

net_handle_t vg::SnarlManagerDecomposition::get_root ( ) const

overridevirtual

Get a net handle referring to a tip-to-tip traversal of the contents of the root snarl. TODO: Special handling for circular things in the root snarl? Circular traversal type?

Implements handlegraph::SnarlDecomposition.

◆ get_snarl()

const Snarl * vg::SnarlManagerDecomposition::get_snarl ( const net_handle_t & net ) const

Get the manager's Snarl for a traversal of a snarl.

Exceptions

std::invalid_argument If the net handle is not for a snarl.

◆ get_snarl_net()

net_handle_t vg::SnarlManagerDecomposition::get_snarl_net ( const Snarl * snarl ) const

Get the start-to-end traversal of a snarl.

◆ is_chain()

bool vg::SnarlManagerDecomposition::is_chain ( const net_handle_t & net ) const

overridevirtual

Returns true if the given net handle refers to (a traversal of) a chain.

Implements handlegraph::SnarlDecomposition.

◆ is_node()

bool vg::SnarlManagerDecomposition::is_node ( const net_handle_t & net ) const

overridevirtual

Returns true if the given net handle refers to (a traversal of) a single node, and thus has a corresponding handle_t.

Implements handlegraph::SnarlDecomposition.

◆ is_root()

bool vg::SnarlManagerDecomposition::is_root ( const net_handle_t & net ) const

overridevirtual

Return true if the given handle refers to (a traversal of) the root snarl, and false otherwise.

Implements handlegraph::SnarlDecomposition.

◆ is_sentinel()

bool vg::SnarlManagerDecomposition::is_sentinel ( const net_handle_t & net ) const

overridevirtual

Return true if the given net handle is a snarl bound sentinel (in either inward or outward orientation), and false otherwise.

Implements handlegraph::SnarlDecomposition.

◆ is_snarl()

bool vg::SnarlManagerDecomposition::is_snarl ( const net_handle_t & net ) const

overridevirtual

Returns true if the given net handle refers to (a traversal of) a snarl.

Implements handlegraph::SnarlDecomposition.

◆ next_in_chain()

optional< net_handle_t > vg::SnarlManagerDecomposition::next_in_chain ( const net_handle_t & here ) const

private

Get the next child in a chain after a chain node or snarl.

Return nullopt when here ends at a tip, leaves its chain at a bound, or is a free node.

Precondition: here is a start-to-end or end-to-start traversal of a node, or any traversal of a snarl.

◆ parent_endpoint()

pair< net_handle_t, endpoint_t > vg::SnarlManagerDecomposition::parent_endpoint	(	const net_handle_t &	net,
		bool	is_start
	)		const

private

Find the snarl or chain, and its endpoint, where a traversal of it can start or end at a net graph element or sentinel.

Parameters

net

One of:

A sentinel facing into its snarl, if is_start, or out of it otherwise. This gives the snarl and the bound of the sentinel.
A node traversal that enters its chain or trivial chain at a bound, if is_start, or leaves it at a bound otherwise. This gives the chain and that bound.
A snarl, chain or trivial chain, which gives its parent and TIP.

Returns: The snarl or chain, start-to-end, and the endpoint.

Exceptions

std::invalid_argument If net is the root, a child of the root, a sentinel facing the wrong way, or a node traversal that does not enter or leave its chain at a bound.

◆ sibling_entered_by()

net_handle_t vg::SnarlManagerDecomposition::sibling_entered_by	(	const HandleGraph &	graph,
		const handle_t &	handle,
		const Snarl *	parent
	)		const

private

Get the child of a snarl or the root that a handle enters.

If the handle leaves the parent, return the sentinel of the parent for that bound, facing out.

Exceptions

std::logic_error If the handle enters a chain between its bounds.

◆ snarl_bound()

Visit vg::SnarlManagerDecomposition::snarl_bound	(	const Snarl *	snarl,
		bool	get_end
	)		const

private

Get a snarl's start bound oriented into the snarl, or its end bound oriented out of it.

◆ snarl_net()

net_handle_t vg::SnarlManagerDecomposition::snarl_net	(	const Snarl *	snarl,
		bool	forward
	)		const

private

Get a snarl's net handle, start-to-end if forward and end-to-start otherwise.

◆ snarl_of_number()

const Snarl * vg::SnarlManagerDecomposition::snarl_of_number ( uint64_t number ) const

private

Get the manager's Snarl for a snarl number.

◆ starts_at()

handlegraph::SnarlDecomposition::endpoint_t vg::SnarlManagerDecomposition::starts_at ( const net_handle_t & traversal ) const

overridevirtual

Return the kind of location at which the given traversal starts.

Implements handlegraph::SnarlDecomposition.

◆ traversals_of()

SnarlManagerDecomposition::TraversalSet vg::SnarlManagerDecomposition::traversals_of ( const net_handle_t & item ) const

private

Get the realizable traversals of a net graph element. A sentinel's only traversal is itself.

Member Data Documentation

◆ directory

NodeDirectory vg::SnarlManagerDecomposition::directory

private

Tells the view each node's place in its chain, and the snarl that contains it.

◆ manager

const SnarlManager& vg::SnarlManagerDecomposition::manager

private

The manager whose snarls the view presents.

◆ survey

TraversalSurvey vg::SnarlManagerDecomposition::survey

private

Tells the view which traversals of each snarl and chain are realizable.

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

Classes

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ SnarlManagerDecomposition()

◆ ~SnarlManagerDecomposition()

Member Function Documentation

◆ canonical()

◆ chain_net()

◆ chain_node_net()

◆ chain_of_net()

◆ ends_at()

◆ flip()

◆ follow_net_edges_impl()

◆ follow_right()

◆ for_each_chain_child()

◆ for_each_child_impl()

◆ for_each_sibling_ahead()

◆ for_each_snarl_child()

◆ for_each_traversal_from()

◆ for_each_traversal_impl()

◆ get_bound()

◆ get_handle()

◆ get_net()

◆ get_parent()

◆ get_parent_traversal()

◆ get_root()

◆ get_snarl()

◆ get_snarl_net()

◆ is_chain()

◆ is_node()

◆ is_root()

◆ is_sentinel()

◆ is_snarl()

◆ next_in_chain()

◆ parent_endpoint()

◆ sibling_entered_by()

◆ snarl_bound()

◆ snarl_net()

◆ snarl_of_number()

◆ starts_at()

◆ traversals_of()

Member Data Documentation

◆ directory

◆ manager

◆ survey