#include <quetzal/coalescence/graph/network.hpp>

Detailed Description

template<class VertexProperty>
requires (!std::is_same_v<VertexProperty, no_property>)
class quetzal::coalescence::network< VertexProperty, no_property >

A network class with information attached to vertices.

Template Parameters

VertexProperty The type of information to store at each vertex.

This class can be used as a simple way to describe the kind of topology and mutational process that emerge from evolutionary relationships between a sample of sequences for a non-recombining locus. Vertices embed a user-defined type of information. Edges embed no additional information. This graph structure is bidirected and allows to model a forest of disconnected networks and isolated vertices.

Invariant: Guarantees that each vertex \(v\) has exactly \(0\) or \(n \geq 2\) successors, never \(1\).; Guarantees that each vertex \(v\) has exactly \(0\) or \(1\) predecessor.; Guarantees that if \((u,v)\) is an edge of the graph, then \((v,u)\) is also an edge.

Remarks: As it would be too costly to enforce non-cyclicity, it is left to the user responsability not to introduce any cycle.

Example

Output

Public Types
using	edge_descriptor = typename base::edge_descriptor
	Edge descriptor.

using	vertex_descriptor = typename base::vertex_descriptor
	Vertex descriptor.

using	vertex_property = VertexProperty
	Vertex information.

using	edge_property = no_property
	Edge information.

using	degree_size_type = typename base::degree_size_type
	Degree size type.

using	traversal_category = typename base::traversal_category
	The ways in which the vertices in the graph can be traversed.

using	directed_category = typename base::directed_category
	The graph is bidirected.

using	in_edge_iterator = typename base::in_edge_iterator
	Iterate through the in-edges.

using	out_edge_iterator = typename base::out_edge_iterator
	Iterate through the out-edges.

using	edge_parallel_category = typename base::edge_parallel_category

Public Member Functions
Constructors
	network ()
	Default constructor. Initializes a graph with 0 vertices.

	network (size_t n)
	Construct graph with \(n\) vertices.

Topology Modifiers
auto	add_vertex (const VertexProperty &p)
	Add a vertex and its properties to the graph.

std::vector< edge_descriptor >	add_edges (vertex_descriptor parent, std::vector< vertex_descriptor > children)
	Add edges from the parent vertex (source) to the children (target)

Property Lookup
const VertexProperty &	operator[] (vertex_descriptor v) const
	Read only access to the vertex property.

VertexProperty &	operator[] (vertex_descriptor v)
	Read and write access to the vertex property.

Topology Lookup
bool	is_isomorphic (network_common const &other) const
	Detects if there is a 1-to-1 mapping of the vertices in one graph to the vertices of another graph such that adjacency is preserved.

vertex_descriptor	find_root_from (vertex_descriptor u) const
	Finds the root of the network graph starting from a vertex \(u\).

degree_size_type	degree (vertex_descriptor u) const
	Returns the number of in-edges plus out-edges.

degree_size_type	in_degree (vertex_descriptor u) const
	Returns the number of in-edges of vertex \(u\).

degree_size_type	out_degree (vertex_descriptor v) const
	Returns the number of out-edges of vertex \(v\).

bool	has_predecessor (vertex_descriptor u) const
	Evaluates if vertex \(u\) has a predecessor.

vertex_descriptor	predecessor (vertex_descriptor u) const
	The predecessor of vertex \(u\).

bool	has_successors (vertex_descriptor u) const
	Evaluates if vertex \(u\) has successors.

auto	successors (vertex_descriptor u) const
	The successors of vertex \(u\).

std::optional< edge_descriptor >	edge (vertex_descriptor u, vertex_descriptor v) const
	Returns the edge between two vertices of the graph if the edge exists.

vertex_descriptor	source (edge_descriptor e) const
	Returns the source vertex of a directed edge.

vertex_descriptor	target (edge_descriptor e) const
	Returns the target vertex of a directed edge.

Topology Modification
vertex_descriptor	add_vertex ()

void	clear_vertex (vertex_descriptor u)
	Remove all edges to and from vertex \(u\) from the graph.

void	remove_vertex (vertex_descriptor u)
	Remove vertex u from the graph, also removing all edges to and from vertex \(u\).

edge_descriptor	add_edge (vertex_descriptor u, vertex_descriptor v)
	Inserts the edge \((u,v)\) into the graph if it does not exist, and returns an edge descriptor pointing to the new edge.

void	remove_edge (vertex_descriptor u, vertex_descriptor v)
	Remove the edge \((u,v)\) from the graph.

void	remove_edge (edge_descriptor e)
	Remove the edge \(e\) from the graph.

Iterators
auto	in_edges (vertex_descriptor u) const
	Provides a range to iterate over the in-going edges of vertex \(u\).

auto	out_edges (vertex_descriptor u) const
	Provides a range to iterate over the out-going edges of vertex \(u\).

auto	vertices () const
	Provides a range to iterate over the vertices of the graph.

Algorithms
void	depth_first_search (vertex_descriptor start, DFSVisitor &vis)
	Performs a read-and-write depth-first traversal of the vertices starting at vertex \(s\).

void	depth_first_search (vertex_descriptor start, DFSVisitor &vis) const
	Performs a read-only depth-first traversal of the vertices starting at vertex \(s\).

Input/Output
void	to_graphviz (std::ostream &out) const
	Print the graph to the graphviz format.

Static Public Member Functions
static constexpr vertex_descriptor	null_vertex ()
	Null vertex identifier.

Protected Attributes
base	_graph

Member Function Documentation

◆ add_edge()

edge_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::add_edge	(	vertex_descriptor	u,
		vertex_descriptor	v
	)

inlineinherited

Inserts the edge \((u,v)\) into the graph if it does not exist, and returns an edge descriptor pointing to the new edge.

Parameters

u	Source vertex
u	Target vertex

◆ clear_vertex()

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::clear_vertex ( vertex_descriptor u )

inlineinherited

Remove all edges to and from vertex \(u\) from the graph.

Parameters

u	The vertex

◆ degree()

degree_size_type quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::degree ( vertex_descriptor u ) const

inlineinherited

Returns the number of in-edges plus out-edges.

Parameters

u	The vertex \(u\)

Returns: Returns the number of in-edges plus out-edges.

◆ depth_first_search() [1/2]

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::depth_first_search	(	vertex_descriptor	start,
		DFSVisitor &	vis
	)

inlineinherited

Performs a read-and-write depth-first traversal of the vertices starting at vertex \(s\).

Template Parameters

DFSVisitor

Parameters

start	The vertex to start from.
vis	The visitor to apply.

◆ depth_first_search() [2/2]

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::depth_first_search	(	vertex_descriptor	start,
		DFSVisitor &	vis
	)		const

inlineinherited

Performs a read-only depth-first traversal of the vertices starting at vertex \(s\).

Template Parameters

DFSVisitor

Parameters

start	The vertex to start from.
vis	The visitor to apply.

◆ edge()

std::optional< edge_descriptor > quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::edge	(	vertex_descriptor	u,
		vertex_descriptor	v
	)		const

inlineinherited

Returns the edge between two vertices of the graph if the edge exists.

Parameters

u	The first vertex
u	The second vertex

Returns: An optional edge descriptor \(e\).

◆ find_root_from()

vertex_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::find_root_from ( vertex_descriptor u ) const

inlineinherited

Finds the root of the network graph starting from a vertex \(u\).

Parameters

u	The vertex to start from.

Remarks: This function will be an infinite loop if called on a recurrent network

◆ has_predecessor()

bool quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::has_predecessor ( vertex_descriptor u ) const

inlineinherited

Evaluates if vertex \(u\) has a predecessor.

Parameters

u	The vertex to evaluate

Returns: True if u has a predecessor, false otherwise

◆ has_successors()

bool quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::has_successors ( vertex_descriptor u ) const

inlineinherited

Evaluates if vertex \(u\) has successors.

Parameters

u	The vertex to evaluate

Returns: True if u has successors, false otherwise

◆ in_degree()

degree_size_type quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::in_degree ( vertex_descriptor u ) const

inlineinherited

Returns the number of in-edges of vertex \(u\).

Parameters

u	The vertex \(u\)

Returns: The number of in-edges.

◆ in_edges()

auto quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::in_edges ( vertex_descriptor u ) const

inlineinherited

Provides a range to iterate over the in-going edges of vertex \(u\).

Parameters

u	The vertex \(u\).

Returns: A range

◆ is_isomorphic()

bool quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::is_isomorphic ( network_common< VertexProperty, no_property, network< VertexProperty, no_property > > const & other ) const

inlineinherited

Detects if there is a 1-to-1 mapping of the vertices in one graph to the vertices of another graph such that adjacency is preserved.

Parameters

other A network graph.

Returns: true if there exists an isomorphism between the two graphs and false otherwise

◆ null_vertex()

static constexpr vertex_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::null_vertex ( )

inlinestaticconstexprinherited

Null vertex identifier.

Returns: A null vertex

◆ out_edges()

auto quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::out_edges ( vertex_descriptor u ) const

inlineinherited

Provides a range to iterate over the out-going edges of vertex \(u\).

Parameters

u	The vertex \(u\).

Returns: A range

◆ predecessor()

vertex_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::predecessor ( vertex_descriptor u ) const

inlineinherited

The predecessor of vertex \(u\).

Parameters

u	The vertex

Returns: The vertex that is the predecessor of \(u\).

◆ remove_edge() [1/2]

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::remove_edge ( edge_descriptor e )

inlineinherited

Remove the edge \(e\) from the graph.

Parameters

e	The edge to remove

◆ remove_edge() [2/2]

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::remove_edge	(	vertex_descriptor	u,
		vertex_descriptor	v
	)

inlineinherited

Remove the edge \((u,v)\) from the graph.

Parameters

u	Source vertex
u	Target vertex

◆ remove_vertex()

void quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::remove_vertex ( vertex_descriptor u )

inlineinherited

Remove vertex u from the graph, also removing all edges to and from vertex \(u\).

Parameters

u	The vertex to remove.

◆ source()

vertex_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::source ( edge_descriptor e ) const

inlineinherited

Returns the source vertex of a directed edge.

Parameters

e The edge

Returns: The source vertex of the edge \(e\).

◆ successors()

auto quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::successors ( vertex_descriptor u ) const

inlineinherited

The successors of vertex \(u\).

Parameters

u	The vertex

Returns: A pair of iterators on the vertices that are the successors of \(u\).

◆ target()

vertex_descriptor quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::target ( edge_descriptor e ) const

inlineinherited

Returns the target vertex of a directed edge.

Parameters

e The edge

Returns: The target vertex of the edge \(e\).

◆ vertices()

auto quetzal::coalescence::detail::network_common< VertexProperty, no_property , network< VertexProperty, no_property > >::vertices ( ) const

inlineinherited

Provides a range to iterate over the vertices of the graph.

Returns: A range

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

/home/runner/work/quetzal-CoaTL/quetzal-CoaTL/src/include/quetzal/coalescence/graph/network.hpp

Detailed Description

Example

Output

Public Types

Public Member Functions

Static Public Member Functions

Protected Attributes

Member Function Documentation

◆ add_edge()

◆ clear_vertex()

◆ degree()

◆ depth_first_search() [1/2]

◆ depth_first_search() [2/2]

◆ edge()

◆ find_root_from()

◆ has_predecessor()

◆ has_successors()

◆ in_degree()

◆ in_edges()

◆ is_isomorphic()

◆ null_vertex()

◆ out_edges()

◆ predecessor()

◆ remove_edge() [1/2]

◆ remove_edge() [2/2]

◆ remove_vertex()

◆ source()

◆ successors()

◆ target()

◆ vertices()