Template base class for all graphs used in the indigoX library. More...

#include <indigox/graph/base_graph.hpp>

Inheritance diagram for BaseGraph< V, E, S, D, VP, EP >:

Collaboration diagram for BaseGraph< V, E, S, D, VP, EP >:

Public Types
using	ComponentContain = std::vector< VertContain >
	Type for storing components. More...

using	CycleEdgeContain = std::vector< EdgeContain >
	Type for storing edge cycles. More...

using	CycleVertContain = std::vector< VertContain >
	Type for storing vertex cycles. More...

using	EdgeContain = std::vector< E >
	Type for storing edges. More...

using	EdgeIter = typename graph_type::edge_iterator
	Type for iterator over edges. More...

using	EdgeMap = indigox::utils::SimpleBiMap< E, EdgeType >
	Type for bidirectional mapping of E to edge descriptor type. More...

using	EdgeType = typename graph_type::edge_descriptor
	Type of the graph edge descriptor. More...

using	graph_type = boost::adjacency_list< boost::setS, boost::listS, typename D::is_directed_t, VP, EP >
	Type of the underlying boost graph. More...

using	NbrsContain = std::map< V, VertContain >
	Type for storing neighbours. More...

using	NbrsIter = typename graph_type::adjacency_iterator
	Type for iterator over neighbours of vertex descriptor. More...

using	PredIter = typename graph_type::inv_adjacency_iterator
	Type for iterator over predecessors of a vertex descriptor. More...

using	SubgraphType = S

using	VertContain = std::vector< V >
	Type for storing vertices. More...

using	VertIter = typename graph_type::vertex_iterator
	Type for iterator over graph vertex descriptors. More...

using	VertMap = indigox::utils::SimpleBiMap< V, VertType >
	Type for bidirectional mapping of V to vertex descriptor type. More...

using	VertType = typename graph_type::vertex_descriptor
	Type of the graph vertex descriptor. More...

Public Member Functions
	BaseGraph ()
	Default constructor. More...

virtual	~BaseGraph ()

int64_t	Degree (const V &v) const
	Degree of a vertex. More...

const ComponentContain &	GetConnectedComponents ()
	Get the connected components of the graph. More...

const CycleEdgeContain &	GetCycles ()
	Get the cycles of the graph. More...

E	GetEdge (const V &u, const V &v) const
	Get the edge between two vertices. More...

const EdgeContain &	GetEdges () const
	Get the edges of the graph. More...

const VertContain &	GetNeighbours (const V &v)
	Get the neighbouring vertices of a vertex. More...

const VertContain &	GetPredecessors (const V &v)
	Get the predecessor vertices of a vertex. More...

V	GetSourceVertex (const E &e) const
	Get the source vertex of an edge. More...

const VertContain &	GetSuccessors (const V &v)

V	GetTargetVertex (const E &e) const
	Get the target vertex of an edge. More...

std::pair< V, V >	GetVertices (const E &e) const
	Get the two vertices that make up an edge. More...

const VertContain &	GetVertices () const
	Get the vertices of the graph. More...

bool	HasEdge (const E &e) const
	Is the edge in the graph. More...

bool	HasEdge (const V &u, const V &v) const
	Does an edge exist between two vertices. More...

bool	HasVertex (const V &v) const
	Is the vertex in the graph. More...

int64_t	InDegree (const V &v) const
	Indegree of a vertex. More...

bool	IsConnected ()
	Determine if the graph is connected. More...

bool	IsCyclic (const V &v)
	Determine if a vertex of this graph is cyclic. More...

bool	IsCyclic (const V &v, uint32_t sz)

bool	IsCyclic (const E &e)
	Determine if an edge of this graph is cycle. More...

bool	IsCyclic (const E &e, uint32_t sz)

int64_t	NumConnectedComponents ()
	Get the number of connected components of the graph. More...

int64_t	NumCycles ()

int64_t	NumEdges () const
	Number of edges in the graph. More...

int64_t	NumVertices () const
	Number of vertices in the graph. More...

virtual S	Subgraph (std::vector< V > &verts)=0

virtual S	Subgraph (std::vector< V > &verts, std::vector< E > &edges)=0

Protected Member Functions
void	AddEdge (const V &u, const V &v, const E &e)
	Add a new edge to the graph. More...

void	AddVertex (const V &v)
	Add a new vertex to the graph. More...

void	RemoveEdge (const E &e)
	Remove an edge from the graph. More...

void	RemoveEdge (const V &u, const V &v)
	Remove an edge from the graph. More...

void	RemoveVertex (const V &v)
	Remove a vertex from the graph. More...

Protected Attributes
std::shared_ptr< BaseImpl >	m_basedata

Friends
struct	algorithm::access
	Friendship allows graph algorithm access to internals. More...

class	cereal::access
	Friendship allows serialisation. More...

Detailed Description

template<class V, class E, class S, class D = Undirected, class VP = GraphLabel, class EP = GraphLabel>
class indigox::graph::BaseGraph< V, E, S, D, VP, EP >

Template base class for all graphs used in the indigoX library.

Template Parameters

V	type of the graph vertices.
E	type of the graph edges.
D	type indicating the directed nature of the graph. Defaults to Undirected.
VertProp	type of the label for a vertex. Defaults to GraphLabel.
EdgeProp	type of the label for an edge. Defaults to GraphLabel.

Graph classes should contain an IXGraphBase member, not inherit from it. Vertex and Edge types are purely interacted with though the use of raw pointers. The IXGraphBase class will never deallocate any memory passed to it.

Member Typedef Documentation

◆ ComponentContain

using ComponentContain = std::vector<VertContain>

Type for storing components.

◆ CycleEdgeContain

using CycleEdgeContain = std::vector<EdgeContain>

Type for storing edge cycles.

◆ CycleVertContain

using CycleVertContain = std::vector<VertContain>

Type for storing vertex cycles.

◆ EdgeContain

using EdgeContain = std::vector<E>

Type for storing edges.

◆ EdgeIter

using EdgeIter = typename graph_type::edge_iterator

Type for iterator over edges.

◆ EdgeMap

using EdgeMap = indigox::utils::SimpleBiMap<E, EdgeType>

Type for bidirectional mapping of E to edge descriptor type.

◆ EdgeType

using EdgeType = typename graph_type::edge_descriptor

Type of the graph edge descriptor.

◆ graph_type

using graph_type = boost::adjacency_list<boost::setS, boost::listS, typename D::is_directed_t, VP, EP>

Type of the underlying boost graph.

◆ NbrsContain

using NbrsContain = std::map<V, VertContain>

Type for storing neighbours.

◆ NbrsIter

using NbrsIter = typename graph_type::adjacency_iterator

Type for iterator over neighbours of vertex descriptor.

◆ PredIter

using PredIter = typename graph_type::inv_adjacency_iterator

Type for iterator over predecessors of a vertex descriptor.

◆ SubgraphType

using SubgraphType = S

◆ VertContain

using VertContain = std::vector<V>

Type for storing vertices.

◆ VertIter

using VertIter = typename graph_type::vertex_iterator

Type for iterator over graph vertex descriptors.

◆ VertMap

using VertMap = indigox::utils::SimpleBiMap<V, VertType>

Type for bidirectional mapping of V to vertex descriptor type.

◆ VertType

using VertType = typename graph_type::vertex_descriptor

Type of the graph vertex descriptor.

Constructor & Destructor Documentation

◆ BaseGraph()

BaseGraph ( )

inline

Default constructor.

◆ ~BaseGraph()

virtual ~BaseGraph ( )

inlinevirtual

Member Function Documentation

◆ AddEdge()

void AddEdge	(	const V &	u,
		const V &	v,
		const E &	e
	)

protected

Add a new edge to the graph.

Vertex u is used as the source and vertex v as the target. If u and/or v are not already part of the graph, they are added. It is the callers responsibility to ensure that the edge is not part of the graph.

Parameters

u,v	vertices the edge is between.
e	the edge.

◆ AddVertex()

void AddVertex ( const V & v )

protected

Add a new vertex to the graph.

It is the callers responsability to ensure that the vertex added is not already part of the graph. If it is, a mismatch between the vertices in the graph and the what the _verts member thinks are in the graph may arise.

Parameters

v	the vertex to add.

◆ Degree()

int64_t Degree ( const V & v ) const

Degree of a vertex.

In the case of a directed graph, the degree of a vertex is the number of edges leaving the vertex.

Parameters

v	the vertex to get the degree of.

Returns: pair of the degree of the vertex and if it is valid.

◆ GetConnectedComponents()

const BaseGraph< V, E, S, D, VP, EP >::ComponentContain & GetConnectedComponents ( )

Get the connected components of the graph.

Returns: reference to the connected components of the graph.

◆ GetCycles()

const BaseGraph< V, E, S, D, VP, EP >::CycleEdgeContain & GetCycles ( )

Get the cycles of the graph.

Returns: the cycles of the graph.

◆ GetEdge()

E GetEdge	(	const V &	u,
		const V &	v
	)		const

Get the edge between two vertices.

It is the callers responsibilty to ensure that the vertices are a part of the graph.

Parameters

u,v	vertices to get the edge between.

Returns: a pair of the edge between the two vertces and if it is valid.

◆ GetEdges()

const BaseGraph< V, E, S, D, VP, EP >::EdgeContain & GetEdges ( ) const

Get the edges of the graph.

Parameters

[out] edges the vector where the list of edges will be set. The vector is cleared before any edges are added to it.

Returns: the number of edges added to the vector.

◆ GetNeighbours()

const BaseGraph< V, E, S, D, VP, EP >::VertContain & GetNeighbours ( const V & v )

Get the neighbouring vertices of a vertex.

The neighbours of a vertex are those for which the edge v -> u exists within the graph. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

	v	the vertex to get the neighbours of.
[out]	nbrs	the vector where the list of neighbours will be set. The vector is cleared before any neighbouring vertices are added to it.

Returns: if the vector has been populated or not.

◆ GetPredecessors()

const BaseGraph< V, E, S, D, VP, EP >::VertContain & GetPredecessors ( const V & v )

Get the predecessor vertices of a vertex.

The predecessors of a vertex are those for which the edge u -> v exists within the graph. For an undirected graph, this is equivalent to the neighbours. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

[in]	v	the vertex to get the predecessors of.
[out]	pres	the vector where the list of predecessors will be set. The vector is cleared before any predecessing vertices are added to it.

Returns: if the vector has been populated or not.

◆ GetSourceVertex()

V GetSourceVertex ( const E & e ) const

Get the source vertex of an edge.

It is the callers responsibilty to ensure that the edge is a part of the graph.

Parameters

e	the edge to get the source of.

Returns: a pair of the source vertex of the edge and if it is valid.

◆ GetSuccessors()

const BaseGraph< V, E, S, D, VP, EP >::VertContain & GetSuccessors ( const V & v )

◆ GetTargetVertex()

V GetTargetVertex ( const E & e ) const

Get the target vertex of an edge.

It is the callers responsibilty to ensure that the edge is a part of the graph.

Parameters

e	the edge to get the target of.

Returns: the target vertex of the edge.

◆ GetVertices() [1/2]

std::pair< V, V > GetVertices ( const E & e ) const

Get the two vertices that make up an edge.

It is the callers responsibility to ensure that the edge is a part of the graph.

Parameters

e	the edge to get vertices of.

Returns: a pair of a pair of the two vertices making up the edge and if they are valid.

◆ GetVertices() [2/2]

const BaseGraph< V, E, S, D, VP, EP >::VertContain & GetVertices ( ) const

Get the vertices of the graph.

Parameters

[out] verts the vector where the list of vertices will be set. The vector is cleared before any vertices are added to it.

Returns: the number of vertices added to the vector.

◆ HasEdge() [1/2]

bool HasEdge ( const E & e ) const

Is the edge in the graph.

Parameters

e	edge to search for.

Returns: if the requested edge is contained in the graph or not.

◆ HasEdge() [2/2]

bool HasEdge	(	const V &	u,
		const V &	v
	)		const

Does an edge exist between two vertices.

Parameters

u,v	vertices to check between.

Returns: if there is an edge between the two vertices.

◆ HasVertex()

bool HasVertex ( const V & v ) const

Is the vertex in the graph.

Parameters

v	vertex to search for.

Returns: if the requested vertex is contained in the graph or not.

◆ InDegree()

int64_t InDegree ( const V & v ) const

Indegree of a vertex.

The indegree of a vertex is the number of edges entering the vertex. For an undirected graph, this is equivalent to Degree(V) const. It is the callers responsibilty to ensure that the vertex is a part of the graph.

Parameters

v	the vertex to get indegree of.

Returns: pair of the indegree of the vertex and if it is valid.

◆ IsConnected()

bool IsConnected ( )

Determine if the graph is connected.

Returns: if the graph is connected or not.

◆ IsCyclic() [1/4]

bool IsCyclic ( const V & v )

Determine if a vertex of this graph is cyclic.

Parameters

v	the vertex to check if in a cycle

Returns: if the vertex is in a cycle or not.

◆ IsCyclic() [2/4]

bool IsCyclic	(	const V &	v,
		uint32_t	sz
	)

◆ IsCyclic() [3/4]

bool IsCyclic ( const E & e )

Determine if an edge of this graph is cycle.

Parameters

e	the edge to check if in a cycle.

Returns: if the edge is in a cycle or not.

◆ IsCyclic() [4/4]

bool IsCyclic	(	const E &	e,
		uint32_t	sz
	)

◆ NumConnectedComponents()

int64_t NumConnectedComponents ( )

Get the number of connected components of the graph.

Returns: the number of cnnected components of the graph.

◆ NumCycles()

int64_t NumCycles ( )

◆ NumEdges()

int64_t NumEdges ( ) const

Number of edges in the graph.

Returns: the number of edges in the graph.

◆ NumVertices()

int64_t NumVertices ( ) const

Number of vertices in the graph.

Returns: the number of vertices in the graph.

◆ RemoveEdge() [1/2]

void RemoveEdge ( const E & e )

protected

Remove an edge from the graph.

It is the callers responsibility to ensure that the edge is a part of the graph.

Parameters

e	the edge to remove.

◆ RemoveEdge() [2/2]

void RemoveEdge	(	const V &	u,
		const V &	v
	)

protected

Remove an edge from the graph.

It is the callers responsibility to ensure that there is an edge between u and v to remove.

Parameters

u,v	vertices to remove an edge from between.

Referenced by BaseGraph< CMGVertex, CMGEdge, CondensedMolecularGraph >::RemoveEdge().

◆ RemoveVertex()

void RemoveVertex ( const V & v )

protected

Remove a vertex from the graph.

Removing a vertex also removes all edges incident on it. It is the callers responsibility to ensure that the vertex removed is within the graph.

Parameters

v	the vertex to remove.

◆ Subgraph() [1/2]

virtual S Subgraph ( std::vector< V > & verts )

pure virtual

Implemented in CondensedMolecularGraph, and MolecularGraph.

◆ Subgraph() [2/2]

virtual S Subgraph	(	std::vector< V > &	verts,
		std::vector< E > &	edges
	)

pure virtual

Implemented in CondensedMolecularGraph, and MolecularGraph.

Friends And Related Function Documentation

◆ algorithm::access

friend struct algorithm::access

friend

Friendship allows graph algorithm access to internals.

◆ cereal::access

friend class cereal::access

friend

Friendship allows serialisation.

Member Data Documentation

◆ m_basedata

std::shared_ptr<BaseImpl> m_basedata

protected

Referenced by access::GetEdgeMap(), access::GetGraph(), and access::GetVertexMap().

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

include/indigox/graph/base_graph.hpp
include/indigox/graph/base_graph_impl.hpp

Public Types

Public Member Functions

Protected Member Functions

Protected Attributes

Friends

Detailed Description

template<class V, class E, class S, class D = Undirected, class VP = GraphLabel, class EP = GraphLabel> class indigox::graph::BaseGraph< V, E, S, D, VP, EP >

Member Typedef Documentation

◆ ComponentContain

◆ CycleEdgeContain

◆ CycleVertContain

◆ EdgeContain

◆ EdgeIter

◆ EdgeMap

◆ EdgeType

◆ graph_type

◆ NbrsContain

◆ NbrsIter

◆ PredIter

◆ SubgraphType

◆ VertContain

◆ VertIter

◆ VertMap

◆ VertType

Constructor & Destructor Documentation

◆ BaseGraph()

◆ ~BaseGraph()

Member Function Documentation

◆ AddEdge()

◆ AddVertex()

◆ Degree()

◆ GetConnectedComponents()

◆ GetCycles()

◆ GetEdge()

◆ GetEdges()

◆ GetNeighbours()

◆ GetPredecessors()

◆ GetSourceVertex()

◆ GetSuccessors()

◆ GetTargetVertex()

◆ GetVertices() [1/2]

◆ GetVertices() [2/2]

◆ HasEdge() [1/2]

◆ HasEdge() [2/2]

◆ HasVertex()

◆ InDegree()

◆ IsConnected()

◆ IsCyclic() [1/4]

◆ IsCyclic() [2/4]

◆ IsCyclic() [3/4]

◆ IsCyclic() [4/4]

◆ NumConnectedComponents()

◆ NumCycles()

◆ NumEdges()

◆ NumVertices()

◆ RemoveEdge() [1/2]

◆ RemoveEdge() [2/2]

◆ RemoveVertex()

◆ Subgraph() [1/2]

◆ Subgraph() [2/2]

Friends And Related Function Documentation

◆ algorithm::access

◆ cereal::access

Member Data Documentation

◆ m_basedata

template<class V, class E, class S, class D = Undirected, class VP = GraphLabel, class EP = GraphLabel>
class indigox::graph::BaseGraph< V, E, S, D, VP, EP >