vg::SnarlState Class Reference

#include <genome_state.hpp>

Public Member Functions
	SnarlState (const NetGraph *graph)
	Create a SnarlState that uses the given net graph. More...
void	dump () const
	Dump internal state to cerr. More...
size_t	size () const
	How many haplotypes traverse this snarl? More...
void	trace (size_t overall_lane, bool backward, const function< void(const handle_t &, size_t)> &iteratee) const
void	insert (const vector< pair< handle_t, size_t >> &haplotype)
const vector< pair< handle_t, size_t > > &	append (const vector< handle_t > &haplotype, bool backward=false)
const vector< pair< handle_t, size_t > > &	insert (size_t overall_lane, const vector< handle_t > &haplotype, bool backward=false)
vector< pair< handle_t, size_t > >	erase (size_t overall_lane)
void	swap (size_t lane1, size_t lane2)

Protected Attributes
vector< vector< pair< handle_t, size_t > > >	haplotypes
unordered_map< handle_t, vector< decltype(haplotypes)::value_type::iterator > >	net_node_lanes
const NetGraph *	graph

Detailed Description

Represents the state of a snarl: zero or more haplotypes traversing its NetGraph.

Only admits full-length traversals of a snarl from start to end.

Every traversing haplotype is assigned a "lane" number at which it traverses the snarl. Lane is the same looking backward or forward through the snarl. Within each child snarl or child node, the traversal is also assigned a lane. The lane assignments at the start and end nodes are the same, and define the lane assignments for the overall snarl. Traversals can be inserted at any lane number in any internal node.

Constructor & Destructor Documentation

SnarlState()

vg::SnarlState::SnarlState

(

const NetGraph *

graph

)

Create a SnarlState that uses the given net graph.

Member Function Documentation

append()

const vector< pair< handle_t, size_t > > & vg::SnarlState::append	(	const vector< handle_t > &	haplotype,
		bool	backward = false
	)

Insert the given traversal of this snarl from start to end or end to start (as determined by the backward flag), assigning each visit to a handle to the next available lane. Returns the haplotype annotated with lane assignments. If handles to the same node or child snarl appear more than once, their lane numbers will be strictly increasing.

dump()

void vg::SnarlState::dump

(

)

const

Dump internal state to cerr.

erase()

vector< pair< handle_t, size_t > > vg::SnarlState::erase

(

size_t

overall_lane

)

Erase the traversal of this haplotype in the given overall lane. Shifts everything in a higher lane 1 rank down. Returns the erased haplotype and its old lane assignments.

insert() [1/2]

void vg::SnarlState::insert

(

const vector< pair< handle_t, size_t >> &

haplotype

)

Insert the given traversal of this snarl from start to end, with the given lane assignments for each oriented handle. If handles to the same node or child snarl appear more than once, their lane numbers must be strictly increasing.

insert() [2/2]

const vector< pair< handle_t, size_t > > & vg::SnarlState::insert	(	size_t	overall_lane,
		const vector< handle_t > &	haplotype,
		bool	backward = false
	)

Insert the given traversal of this snarl from start to end or end to start (as determined by the backward flag), assigning it to the given overall lane. Returns the haplotype annotated with lane assignments for all the internal handles. If the internal handles represent child snarls, this can be used to recurse down and insert traversals of them at the right lanes. If handles to the same node or child snarl appear more than once, their assigned lane numbers will be strictly increasing. Returns the haplotype annotated with lane assignments.

size()

size_t vg::SnarlState::size

(

)

const

How many haplotypes traverse this snarl?

swap()

void vg::SnarlState::swap	(	size_t	lane1,
		size_t	lane2
	)

Swap the traversals of this haplotype in the two given overall lanes. Internal lane assignments (as are used by child snarls) are not affected.

trace()

void vg::SnarlState::trace	(	size_t	overall_lane,
		bool	backward,
		const function< void(const handle_t &, size_t)> &	iteratee
	)		const

Trace the haplotype int eh given overall lane in the given orientation. Yields the oriented handles visited and the per-forward-handle lane assignments.

Member Data Documentation

graph

const NetGraph* vg::SnarlState::graph

protected

We need to keep track of the net graph, because we may need to traverse haplotypes forward or reverse and we need to flip things.

haplotypes

vector<vector<pair<handle_t, size_t> > > vg::SnarlState::haplotypes

protected

net_node_lanes

unordered_map<handle_t, vector<decltype(haplotypes)::value_type::iterator> > vg::SnarlState::net_node_lanes

protected

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

• src/genome_state.hpp
• src/genome_state.cpp