vg::SnarlGraph Class Reference

#include <snarl_graph.hpp>

Inheritance diagram for vg::SnarlGraph:

Public Member Functions
	SnarlGraph (const HandleGraph *backing_graph, SnarlManager &snarl_manager, vector< const Snarl * > snarls)
pair< bool, handle_t >	node_to_snarl (handle_t handle) const
tuple< bool, handle_t, edge_t >	edge_to_snarl_edge (edge_t edge) const
void	embed_snarl (Visit &visit)
void	embed_snarls (SnarlTraversal &traversal)
void	embed_ref_path_snarls (SnarlTraversal &traversal)
bool	has_node (nid_t node_id) const
handle_t	get_handle (const nid_t &node_id, bool is_reverse=false) const
nid_t	get_id (const handle_t &handle) const
bool	get_is_reverse (const handle_t &handle) const
handle_t	flip (const handle_t &handle) const
size_t	get_length (const handle_t &handle) const
std::string	get_sequence (const handle_t &handle) const
size_t	get_node_count () const
nid_t	min_node_id () const
nid_t	max_node_id () const

Protected Member Functions
bool	for_each_handle_impl (const std::function< bool(const handle_t &)> &iteratee, bool parallel=false) const
bool	follow_edges_impl (const handle_t &handle, bool go_left, const std::function< bool(const handle_t &)> &iteratee) const

Protected Attributes
const HandleGraph *	backing_graph
	the backing graph
SnarlManager &	snarl_manager
	the snarl manager
unordered_map< handle_t, pair< handle_t, bool > >	snarls
	the snarls (indexed both ways). flag is true for original orientation

Detailed Description

Simplification of a NetGraph that ignores chains. It is designed only for traversal finding. Todo: generalize NestedFlowCaller to the point where we can remove this and use NetGraph instead

Constructor & Destructor Documentation

SnarlGraph()

vg::SnarlGraph::SnarlGraph	(	const HandleGraph *	backing_graph,
		SnarlManager &	snarl_manager,
		vector< const Snarl * >	snarls )

Member Function Documentation

edge_to_snarl_edge()

tuple< bool, handle_t, edge_t > vg::SnarlGraph::edge_to_snarl_edge

(

edge_t

edge

)

const

embed_ref_path_snarls()

void vg::SnarlGraph::embed_ref_path_snarls

(

SnarlTraversal &

traversal

)

embed_snarl()

void vg::SnarlGraph::embed_snarl

(

Visit &

visit

)

embed_snarls()

void vg::SnarlGraph::embed_snarls

(

SnarlTraversal &

traversal

)

flip()

handle_t vg::SnarlGraph::flip

(

const handle_t &

handle

)

const

follow_edges_impl()

bool vg::SnarlGraph::follow_edges_impl ( const handle_t & handle, bool go_left, const std::function< bool(const handle_t &)> & iteratee ) const

protected

this is the only function that's changed to do anything different from the backing graph: it is changed to "pass through" snarls by pretending there are edges from into snarl starts out of ends and vice versa.

for_each_handle_impl()

bool vg::SnarlGraph::for_each_handle_impl ( const std::function< bool(const handle_t &)> & iteratee, bool parallel = false ) const

protected

get_handle()

handle_t vg::SnarlGraph::get_handle	(	const nid_t &	node_id,
		bool	is_reverse = false ) const

get_id()

nid_t vg::SnarlGraph::get_id

(

const handle_t &

handle

)

const

get_is_reverse()

bool vg::SnarlGraph::get_is_reverse

(

const handle_t &

handle

)

const

get_length()

size_t vg::SnarlGraph::get_length

(

const handle_t &

handle

)

const

get_node_count()

size_t vg::SnarlGraph::get_node_count

(

)

const

get_sequence()

std::string vg::SnarlGraph::get_sequence

(

const handle_t &

handle

)

const

has_node()

bool vg::SnarlGraph::has_node

(

nid_t

node_id

)

const

max_node_id()

nid_t vg::SnarlGraph::max_node_id

(

)

const

min_node_id()

nid_t vg::SnarlGraph::min_node_id

(

)

const

node_to_snarl()

pair< bool, handle_t > vg::SnarlGraph::node_to_snarl

(

handle_t

handle

)

const

Member Data Documentation

backing_graph

const HandleGraph* vg::SnarlGraph::backing_graph

protected

the backing graph

snarl_manager

SnarlManager& vg::SnarlGraph::snarl_manager

protected

the snarl manager

snarls

unordered_map<handle_t, pair<handle_t, bool> > vg::SnarlGraph::snarls

protected

the snarls (indexed both ways). flag is true for original orientation

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

• src/snarl_graph.hpp
• src/snarl_graph.cpp