vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor Class Reference

Classes
struct	WalkEnds
	The places in a snarl or chain where a walk can end. More...

Public Member Functions
	Surveyor (const SnarlManager &manager, const HandleGraph &graph, const NodeDirectory &directory, const TraversalSurvey &survey)
TraversalSet	survey_snarl (const Snarl *snarl) const
TraversalSet	survey_chain (const Chain &chain) const

Private Member Functions
WalkEnds	walk_snarl (const Snarl *snarl, const std::vector< handle_t > &starts) const
WalkEnds	walk_chain (const Chain &chain, const std::vector< std::pair< size_t, bool >> &starts) const
bool	enter_child (const handle_t &entering, std::vector< handle_t > &exits) const

Static Private Member Functions
static void	add_walks_from_bounds (TraversalSet &traversals, const WalkEnds &from_start, const WalkEnds &from_end)

Private Attributes
const SnarlManager &	manager
	The manager whose snarls and chains are surveyed. More...
const HandleGraph &	graph
	The graph the snarls were found in. More...
const NodeDirectory &	directory
const TraversalSurvey &	survey

Detailed Description

A surveyor that finds the realizable traversals of one snarl or chain at a time, by walking the graph.

A walk crosses each child as the survey says the traversals of that child allow. So the surveyor must survey each child before its parent.

Constructor & Destructor Documentation

Surveyor()

vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::Surveyor	(	const SnarlManager &	manager,
		const HandleGraph &	graph,
		const NodeDirectory &	directory,
		const TraversalSurvey &	survey
	)

Make a surveyor for one survey.

The surveyor keeps references to its arguments, which must outlive it.

Member Function Documentation

add_walks_from_bounds()

void vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::add_walks_from_bounds ( TraversalSet &  traversals, const WalkEnds &  from_start, const WalkEnds &  from_end  )

staticprivate

Add the traversals made by walks from the start and end bounds.

Also add each of those traversals taken backward that starts at a tip.

enter_child()

bool vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::enter_child ( const handle_t &  entering, std::vector< handle_t > &  exits  ) const

private

Find where a walk that enters a child chain or free node can leave it.

Add each exit to exits. A walk leaves the child through the right side of an exit. The one exit of a free node is the entering handle.

Returns

True if a walk entering the chain can end at a tip in it.

Precondition

The chain has been surveyed.

Exceptions

std::logic_error

If the handle enters a chain between its bounds.

survey_chain()

SnarlManagerDecomposition::TraversalSet vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::survey_chain

(

const Chain &

chain

)

const

Find the realizable traversals of a chain.

Precondition

Each snarl in the chain has been surveyed.

survey_snarl()

SnarlManagerDecomposition::TraversalSet vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::survey_snarl

(

const Snarl *

snarl

)

const

Find the realizable traversals of a snarl.

Precondition

Each chain in the snarl has been surveyed.

walk_chain()

SnarlManagerDecomposition::TraversalSurvey::Surveyor::WalkEnds vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::walk_chain ( const Chain &  chain, const std::vector< std::pair< size_t, bool >> &  starts  ) const

private

Find where walks along a chain from some chain nodes can end.

Each start is the position of a chain node, and true to leave it going in reverse along the chain. Here the end bound has position chain.size() even in a looping chain. A walk that comes to a bound of a looping chain can leave there, and can also go on around the loop, since its boundary node is both bounds.

Precondition

Each snarl in the chain has been surveyed.

walk_snarl()

SnarlManagerDecomposition::TraversalSurvey::Surveyor::WalkEnds vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::walk_snarl ( const Snarl *  snarl, const std::vector< handle_t > &  starts  ) const

private

Find where walks through a snarl from some handles can end.

A walk leaves each start through its right side. Each start is on a node in the snarl, or on a bound oriented into the snarl.

Precondition

Each chain in the snarl has been surveyed.

Member Data Documentation

directory

const NodeDirectory& vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::directory

private

Tells the surveyor which chain, if any, each node is a chain node of.

graph

const HandleGraph& vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::graph

private

The graph the snarls were found in.

manager

const SnarlManager& vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::manager

private

The manager whose snarls and chains are surveyed.

survey

const TraversalSurvey& vg::SnarlManagerDecomposition::TraversalSurvey::Surveyor::survey

private

Tells the surveyor the traversals of each child already surveyed.

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

• src/snarl_manager_decomposition.hpp
• src/snarl_manager_decomposition.cpp