vg::FlowSort Class Reference

#include <flow_sort.hpp>

Classes
struct	Growth
struct	WeightedGraph

Public Member Functions
	FlowSort (VG &vg)
std::unique_ptr< list< NodeTraversal > >	max_flow_sort (const string &ref_name, bool isGrooming=true)
void	fast_linear_sort (const string &ref_name, bool isGrooming=true)
void	flow_sort_nodes (list< NodeTraversal > &sorted_nodes, const string &ref_name, bool isGrooming)
int	get_node_degree (WeightedGraph &wg, id_t node_id)
void	update_in_out_edges (EdgeMapping &edges_in, EdgeMapping &edges_out, Edge *e)
void	erase_in_out_edges (EdgeMapping &edges_in, EdgeMapping &edges_out, Edge *e)
void	reverse_edge (Edge *&e)
void	reverse_from_start_to_end_edge (Edge *&e)
id_t	from_simple_reverse (Edge *&e)
id_t	from_simple_reverse_orientation (Edge *&e)
id_t	to_simple_reverse (Edge *&e)
id_t	to_simple_reverse_orientation (Edge *&e)
vector< set< id_t > >	get_cc_in_wg (EdgeMapping &edges_in, EdgeMapping &edges_out, const set< id_t > &all_nodes, id_t start_ref_node)
void	groom_components (EdgeMapping &edges_in, EdgeMapping &edges_out, set< id_t > &isolated_nodes, set< id_t > &main_nodes, map< id_t, set< Edge * >> &minus_start, map< id_t, set< Edge * >> &minus_end)
id_t	get_next_node_recalc_degrees (WeightedGraph &wg, std::vector< std::set< id_t >> &degrees, std::set< id_t > &sources, id_t node)
id_t	find_max_node (std::vector< std::set< id_t >> nodes_degree)
bool	bfs (set< id_t > &nodes, map< id_t, map< id_t, int >> &edge_weight, id_t s, id_t t, map< id_t, id_t > &parent)
void	dfs (set< id_t > &nodes, id_t s, set< id_t > &visited, map< id_t, map< id_t, int >> &edge_weight)
void	find_in_out_web (list< NodeTraversal > &sorted_nodes, Growth &in_out_growth, WeightedGraph &weighted_graph, set< id_t > &unsorted_nodes, id_t start_node, bool in_out, int count)
void	process_in_out_growth (EdgeMapping &edges_out_nodes, id_t current_id, Growth &in_out_growth, WeightedGraph &weighted_graph, set< id_t > &visited, list< NodeTraversal > &sorted_nodes, bool reverse, set< id_t > &unsorted_nodes, bool in_out, int count)
void	mark_dfs (EdgeMapping &graph_matrix, id_t s, set< id_t > &new_nodes, set< id_t > &visited, bool reverse, set< id_t > &nodes, set< id_t > &backbone)
vector< pair< id_t, id_t > >	min_cut (map< id_t, map< id_t, int >> &graph_weight, set< id_t > &nodes, id_t s, id_t t, EdgeMapping &edges_out_nodes, set< Edge * > &in_joins)
void	remove_edge (EdgeMapping &nodes_to_edges, id_t node, id_t to, bool reverse)

Static Public Attributes
static const size_t	DEFAULT_PATH_WEIGHT = 5

Private Attributes
VG &	vg

Constructor & Destructor Documentation

FlowSort()

vg::FlowSort::FlowSort

(

VG &

vg

)

Member Function Documentation

bfs()

bool vg::FlowSort::bfs	(	set< id_t > &	nodes,
		map< id_t, map< id_t, int >> &	edge_weight,
		id_t	s,
		id_t	t,
		map< id_t, id_t > &	parent
	)

dfs()

void vg::FlowSort::dfs	(	set< id_t > &	nodes,
		id_t	s,
		set< id_t > &	visited,
		map< id_t, map< id_t, int >> &	edge_weight
	)

erase_in_out_edges()

void vg::FlowSort::erase_in_out_edges	(	EdgeMapping &	edges_in,
		EdgeMapping &	edges_out,
		Edge *	e
	)

fast_linear_sort()

void vg::FlowSort::fast_linear_sort	(	const string &	ref_name,
		bool	isGrooming = true
	)

find_in_out_web()

void vg::FlowSort::find_in_out_web	(	list< NodeTraversal > &	sorted_nodes,
		Growth &	in_out_growth,
		WeightedGraph &	weighted_graph,
		set< id_t > &	unsorted_nodes,
		id_t	start_node,
		bool	in_out,
		int	count
	)

find_max_node()

id_t vg::FlowSort::find_max_node

(

std::vector< std::set< id_t >>

nodes_degree

)

flow_sort_nodes()

void vg::FlowSort::flow_sort_nodes	(	list< NodeTraversal > &	sorted_nodes,
		const string &	ref_name,
		bool	isGrooming
	)

from_simple_reverse()

id_t vg::FlowSort::from_simple_reverse

(

Edge *&

e

)

from_simple_reverse_orientation()

id_t vg::FlowSort::from_simple_reverse_orientation

(

Edge *&

e

)

get_cc_in_wg()

vector< set< id_t > > vg::FlowSort::get_cc_in_wg	(	EdgeMapping &	edges_in,
		EdgeMapping &	edges_out,
		const set< id_t > &	all_nodes,
		id_t	start_ref_node
	)

get_next_node_recalc_degrees()

id_t vg::FlowSort::get_next_node_recalc_degrees	(	WeightedGraph &	wg,
		std::vector< std::set< id_t >> &	degrees,
		std::set< id_t > &	sources,
		id_t	node
	)

get_node_degree()

int vg::FlowSort::get_node_degree	(	FlowSort::WeightedGraph &	wg,
		id_t	node_id
	)

groom_components()

void vg::FlowSort::groom_components	(	EdgeMapping &	edges_in,
		EdgeMapping &	edges_out,
		set< id_t > &	isolated_nodes,
		set< id_t > &	main_nodes,
		map< id_t, set< Edge * >> &	minus_start,
		map< id_t, set< Edge * >> &	minus_end
	)

mark_dfs()

void vg::FlowSort::mark_dfs	(	EdgeMapping &	graph_matrix,
		id_t	s,
		set< id_t > &	new_nodes,
		set< id_t > &	visited,
		bool	reverse,
		set< id_t > &	nodes,
		set< id_t > &	backbone
	)

max_flow_sort()

std::unique_ptr< list< NodeTraversal > > vg::FlowSort::max_flow_sort	(	const string &	ref_name,
		bool	isGrooming = true
	)

min_cut()

vector< pair< id_t, id_t > > vg::FlowSort::min_cut	(	map< id_t, map< id_t, int >> &	graph_weight,
		set< id_t > &	nodes,
		id_t	s,
		id_t	t,
		EdgeMapping &	edges_out_nodes,
		set< Edge * > &	in_joins
	)

process_in_out_growth()

void vg::FlowSort::process_in_out_growth	(	EdgeMapping &	edges_out_nodes,
		id_t	current_id,
		Growth &	in_out_growth,
		WeightedGraph &	weighted_graph,
		set< id_t > &	visited,
		list< NodeTraversal > &	sorted_nodes,
		bool	reverse,
		set< id_t > &	unsorted_nodes,
		bool	in_out,
		int	count
	)

remove_edge()

void vg::FlowSort::remove_edge	(	EdgeMapping &	nodes_to_edges,
		id_t	node,
		id_t	to,
		bool	reverse
	)

reverse_edge()

void vg::FlowSort::reverse_edge

(

Edge *&

e

)

reverse_from_start_to_end_edge()

void vg::FlowSort::reverse_from_start_to_end_edge

(

Edge *&

e

)

to_simple_reverse()

id_t vg::FlowSort::to_simple_reverse

(

Edge *&

e

)

to_simple_reverse_orientation()

id_t vg::FlowSort::to_simple_reverse_orientation

(

Edge *&

e

)

update_in_out_edges()

void vg::FlowSort::update_in_out_edges	(	EdgeMapping &	edges_in,
		EdgeMapping &	edges_out,
		Edge *	e
	)

Member Data Documentation

DEFAULT_PATH_WEIGHT

const size_t vg::FlowSort::DEFAULT_PATH_WEIGHT = 5

static

vg

VG& vg::FlowSort::vg

private

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

• src/flow_sort.hpp
• src/flow_sort.cpp