Uses of Interface
edu.ucla.sspace.graph.Graph

Packages that use Graph

Package	Description
edu.ucla.sspace.graph
edu.ucla.sspace.graph.io
edu.ucla.sspace.graph.isomorphism

Uses of Graph in edu.ucla.sspace.graph

Classes in edu.ucla.sspace.graph with type parameters of type Graph

Modifier and Type	Class and Description
class	SubgraphIterator<E extends Edge,G extends Graph<E>> An implementation of the EnumerateSubgraphs (ESU) method from Wernicke (2006), which enumerates all possible k-vertex subgraphs of a given graph.

Subinterfaces of Graph in edu.ucla.sspace.graph

Modifier and Type	Interface and Description
interface	DirectedGraph<E extends DirectedEdge> An interface specification for interacting with directed graph objects.
interface	DynamicGraph A stub interface for Graph instances that encode time on their vertices and edges.
interface	Multigraph<T,E extends TypedEdge<T>> An interface specification for interacting with MultiGraph objects.
interface	WeightedGraph<E extends WeightedEdge> An interface specification for interacting with weighted Graph objects.

Classes in edu.ucla.sspace.graph that implement Graph

Modifier and Type	Class and Description
class	AbstractGraph<T extends Edge,S extends EdgeSet<T>> A base class for many Graph implementations.
protected class	AbstractGraph.Subgraph A Graph implementation for representing the view of a subset of a graph's vertices while tracking changes to the graph on which this Subgraph is a view.
class	DirectedMultigraph<T> A directed multigraph implementation.
class	GenericGraph<T extends Edge> A graph that imposes no restriction on the types of edges that may connect its vertices.
class	GraphAdaptor<T extends Edge> An abstract adaptor class that wraps an existing Graph.
class	LabeledGraph<L,E extends Edge> A decorator around all graph types that allows vertices to take on arbitrary labels.
class	SparseDirectedGraph An implementation of DirectedGraph that uses a sparse backing representation.
class	SparseUndirectedGraph An undirected implementation of Graph that uses a sparse backing representation.
class	SparseWeightedGraph An implementation of DirectedGraph that uses a sparse backing representation.
class	UndirectedMultigraph<T> A directed multigraph implementation.
class	WeightedDirectedMultigraph<T> A weighted, directed Multigraph implementation.

Methods in edu.ucla.sspace.graph with type parameters of type Graph

Modifier and Type	Method and Description
static <E extends Edge,G extends Graph<E>> Graph<Edge>	Graphs.toLineGraph(G graph) Converts the provided graph into a line graph, where each edge is mapped to a vertex and edges that share vertices are connected by an edge in the line graph.
static <E extends Edge,G extends Graph<E>> Graph<Edge>	Graphs.toLineGraph(G graph, Indexer<E> edgeIndices) Converts the provided graph into a line graph, where each edge is mapped to a vertex and edges that share vertices are connected by an edge in the line graph, using edgeIndices to specify the mapping between edges in the input graph and their corresponding vertices in the line graph.

Methods in edu.ucla.sspace.graph that return Graph

Modifier and Type	Method and Description
Graph<Edge>	SparseUndirectedGraph.copy(Set<Integer> vertices) Creates a copy of this graph containing only the specified number of vertices and all edges between those vertices.
abstract Graph<T>	AbstractGraph.copy(Set<Integer> vertices) Creates a copy of this graph containing only the specified number of vertices and all edges between those vertices.
Graph<T>	AbstractGraph.Subgraph.copy(Set<Integer> vertices)
Graph<E>	Graph.copy(Set<Integer> vertices) Creates a copy of this graph containing only the specified number of vertices and all edges between those vertices.
Graph<T>	GraphAdaptor.copy(Set<Integer> vertices) Creates a copy of this graph containing only the specified number of vertices and all edges between those vertices.
Graph<T>	GenericGraph.copy(Set<Integer> vertices) Creates a copy of this graph containing only the specified number of vertices and all edges between those vertices.
Graph<T>	SamplingSubgraphIterator.next() Returns the next subgraph from the backing graph.
static <E extends Edge> Graph<E>	Graphs.pack(Graph<E> g) Creates a copy of the provided graph where all vertices are remapped to a contiguous range from 0 to g.order()-1.
static Graph<? extends Edge>	GraphIO.read(File f, GraphIO.GraphType type)
static Graph<Edge>	GraphIO.readUndirected(File f)
static Graph<Edge>	GraphIO.readUndirected(File f, Indexer<String> vertexIndexer)
static Graph<Edge>	GraphIO.readUndirectedFromWeighted(File f, Indexer<String> vertexIndexer, double minWeight) Reads in an undirected network from a file containing weighted edges, only keeping those undirected edges whose weight was above the specified threshold
Graph	DynamicGraph.subgraph(IntSet vertices) Returns a view of this graph containing only the specified vertices.
Graph	DynamicGraph.subgraph(IntSet vertices, Calendar atTime)
Graph	DynamicGraph.subgraph(IntSet vertices, Calendar startTime, Calendar endTime)
Graph	DynamicGraph.subgraph(IntSet vertices, Date atTime)
Graph	DynamicGraph.subgraph(IntSet vertices, Date startTime, Date endTime)
Graph	DynamicGraph.subgraph(IntSet vertices, long atTime)
Graph	DynamicGraph.subgraph(IntSet vertices, long startTime, long endTime)
Graph<T>	AbstractGraph.subgraph(Set<Integer> vertices) Returns a view of this graph containing only the specified vertices where the returned graph's vertinces are renamed (0, ..., n).
Graph<T>	AbstractGraph.Subgraph.subgraph(Set<Integer> vertices) Returns a view of this graph containing only the specified vertices where the returned graph's vertinces are renamed (0, ..., n).
Graph<E>	Graph.subgraph(Set<Integer> vertices) Returns a view of this graph containing only the specified vertices where the returned graph's vertinces are renamed (0, ..., n).
Graph<T>	GraphAdaptor.subgraph(Set<Integer> vertices) Returns a view of this graph containing only the specified vertices where the returned graph's vertinces are renamed (0, ..., n).
static <T extends Edge> Graph<T>	Graphs.synchronizedGraph(Graph<T> g) To-do
static <E extends Edge,G extends Graph<E>> Graph<Edge>	Graphs.toLineGraph(G graph) Converts the provided graph into a line graph, where each edge is mapped to a vertex and edges that share vertices are connected by an edge in the line graph.
static <E extends Edge,G extends Graph<E>> Graph<Edge>	Graphs.toLineGraph(G graph, Indexer<E> edgeIndices) Converts the provided graph into a line graph, where each edge is mapped to a vertex and edges that share vertices are connected by an edge in the line graph, using edgeIndices to specify the mapping between edges in the input graph and their corresponding vertices in the line graph.
static <T extends Edge> Graph<T>	Graphs.unmodifiable(Graph<T> g) To-do

Methods in edu.ucla.sspace.graph that return types with arguments of type Graph

Modifier and Type	Method and Description
<E extends Edge> Map<Graph<E>,Fanmod.Result>	Fanmod.findMotifs(Graph<E> g, int motifSize, int numRandomGraphs, Fanmod.MotifFilter filter) Finds motifs in the input graph according to the specified parameters.

Methods in edu.ucla.sspace.graph with parameters of type Graph

Modifier and Type	Method and Description
static <E extends DirectedEdge> DirectedGraph<E>	Graphs.asDirectedGraph(Graph<E> g)
static <T,E extends TypedEdge<T>> Multigraph<T,E>	Graphs.asMultigraph(Graph<E> g)
static <E extends WeightedEdge> WeightedGraph<E>	Graphs.asWeightedGraph(Graph<E> g)
<E extends Edge> MultiMap<Integer,Integer>	ChineseWhispersClustering.cluster(Graph<E> graph)
<E extends Edge> MultiMap<Integer,Integer>	ChineseWhispersClustering.cluster(Graph<E> graph, int maxIterations)
<E extends Edge> MultiMap<Integer,Integer>	ChineseWhispersClustering.cluster(Graph<E> graph, int maxIterations, double randomAssignmentProb)
<E extends Edge> MultiMap<Integer,Integer>	LinkClustering.cluster(Graph<E> graph, int numClusters, Properties props) Computes the similarity of the graph's edges and merges them until the specified number of clusters has been reached.
<E extends Edge> MultiMap<Integer,Integer>	LinkClustering.cluster(Graph<E> graph, Properties props) Computes the similarity of the graph's edges and merges them to select the final partitioning that maximizes the overall cluster density.
<E extends Edge> double[]	BetweennessCentrality.compute(Graph<E> g) Returns a mapping from each vertex to its betweenness centrality measure.
<E extends Edge> Map<Graph<E>,Fanmod.Result>	Fanmod.findMotifs(Graph<E> g, int motifSize, int numRandomGraphs, Fanmod.MotifFilter filter) Finds motifs in the input graph according to the specified parameters.
protected <E extends Edge> double	WeightedLinkClustering.getConnectionSimilarity(Graph<E> graph, int keystone, int impost1, int impost2)
protected <E extends Edge> double	LinkClustering.getConnectionSimilarity(Graph<E> graph, int keystone, int impost1, int impost2) Computes the similarity of the two edges as the Jaccard index of the neighbors of two impost nodes.
static <E extends Edge> Graph<E>	Graphs.pack(Graph<E> g) Creates a copy of the provided graph where all vertices are remapped to a contiguous range from 0 to g.order()-1.
static <E extends Edge> int	Graphs.shufflePreserve(Graph<E> g, int shufflesPerEdge) Shuffles the edges of g while still preserving the degree sequence of the graph.
static <E extends Edge> int	Graphs.shufflePreserve(Graph<E> g, int shufflesPerEdge, Random rnd) Shuffles the edges of g while still preserving the degree sequence of the graph.
static <T extends Edge> Graph<T>	Graphs.synchronizedGraph(Graph<T> g) To-do
static String	Graphs.toAdjacencyMatrixString(Graph<?> g) Returns a pretty-print string version of the graph as an adjacency matrix where a 1 indicates an edge and a 0 indicates no edge.
static <T extends Edge> Graph<T>	Graphs.unmodifiable(Graph<T> g) To-do
static void	GraphIO.writeUndirected(File f, Graph<? extends Edge> g, Indexer<String> vertexLabels)

Constructors in edu.ucla.sspace.graph with parameters of type Graph

Constructor and Description
DirectedMultigraph(Graph<? extends DirectedTypedEdge<T>> g) Creates a directed multigraph with a copy of all the vertices and edges in g.
GenericGraph(Graph<? extends T> g) Creates a new GenericGraph with a copy of all the edges and vertices contained within g
GraphAdaptor(Graph<T> g)
LabeledGraph(Graph<E> graph)
LabeledGraph(Graph<E> graph, Indexer<L> vertexLabels)
SamplingSubgraphIterator(Graph<T> g, int subgraphSize, double[] traversalProbabilitiesAtDepth) Constructs an iterator over all the subgraphs of g with the specified subgraph size, where the list of probabilities is used to decide probabilistically whether the next level of expansion should be taken.
SparseDirectedGraph(Graph<? extends DirectedEdge> g) Creates a directed graph with a copy of all the vertices and edges in g.
SparseUndirectedGraph(Graph<? extends Edge> g) Creates an undirected graph with a copy of all the vertices and edges in g.
SparseWeightedGraph(Graph<? extends WeightedEdge> g) Creates a directed graph with a copy of all the vertices and edges in g.
UndirectedMultigraph(Graph<? extends TypedEdge<T>> g) Creates a directed multigraph with a copy of all the vertices and edges in g.
WeightedDirectedMultigraph(Graph<? extends WeightedDirectedTypedEdge<T>> g) Creates a directed multigraph with a copy of all the vertices and edges in g.

Uses of Graph in edu.ucla.sspace.graph.io

Methods in edu.ucla.sspace.graph.io that return Graph

Modifier and Type	Method and Description
Graph	DotIO.readGraph(File dotFile)
static Graph<DirectedEdge>	PajekIO.readPajek(File f)
Graph<Edge>	GraphReaderAdapter.readUndirected(File f) Reads in the graph from the provided file
Graph<Edge>	GraphReader.readUndirected(File f) Reads in the graph from the provided file
Graph<Edge>	EdgeListReader.readUndirected(File f)
Graph<Edge>	GraphReaderAdapter.readUndirected(File f, Indexer<String> vertexLabels) Reads in the graph from the provided file, using the specified Indexer to decide how vertex labels in the file are mapped to numeric vertices.
Graph<Edge>	GraphReader.readUndirected(File f, Indexer<String> vertexLabels) Reads in the graph from the provided file, using the specified Indexer to decide how vertex labels in the file are mapped to numeric vertices.
Graph<Edge>	EdgeListReader.readUndirected(File f, Indexer<String> vertexIndexer)
Graph<Edge>	GraphReaderAdapter.readUndirectedFromWeighted(File f, Indexer<String> vertexLabels, double minWeight) Reads in an undirected network from a file containing weighted edges, only keeping those undirected edges whose weight was above the specified threshold
Graph<Edge>	GraphReader.readUndirectedFromWeighted(File f, Indexer<String> vertexLabels, double minWeight) Reads in an undirected network from a file containing weighted edges, only keeping those undirected edges whose weight was above the specified threshold
Graph<Edge>	EdgeListReader.readUndirectedFromWeighted(File f, Indexer<String> vertexIndexer, double minWeight) Reads in an undirected network from a file containing weighted edges, only keeping those undirected edges whose weight was above the specified threshold

Methods in edu.ucla.sspace.graph.io with parameters of type Graph

Modifier and Type	Method and Description
void	DotWriter.write(Graph<? extends Edge> g, File f)
<E extends Edge> void	PajekIO.writeUndirectedGraph(Graph<E> g, File f)
<E extends Edge> void	DotIO.writeUndirectedGraph(Graph<E> g, File f)
<E extends Edge> void	DotIO.writeUndirectedGraph(Graph<E> g, File f, Indexer<String> vertexLabels)

Uses of Graph in edu.ucla.sspace.graph.isomorphism

Classes in edu.ucla.sspace.graph.isomorphism with type parameters of type Graph

Modifier and Type	Class and Description
class	IsomorphicGraphCounter<G extends Graph<? extends Edge>> A special-purpose Counter that counts graphs based on isomorphism, rather than object equivalence (which may take into account vertex labeling, etc.).
class	IsomorphicSet<G extends Graph<? extends Edge>> A Set of Graph instances that maintains the invariant that all graphs in the set are non-isomorphisms of each other.

Methods in edu.ucla.sspace.graph.isomorphism that return Graph

Modifier and Type	Method and Description
Graph<? extends Edge>	VF2State.getGraph1() Returns the first graph being matched
Graph<? extends Edge>	State.getGraph1() Returns the first graph being matched
Graph<? extends Edge>	TypedVF2State.getGraph1() Returns the first graph being matched
Graph<? extends Edge>	VF2State.getGraph2() Returns the first graph being matched
Graph<? extends Edge>	State.getGraph2() Returns the first graph being matched
Graph<? extends Edge>	TypedVF2State.getGraph2() Returns the first graph being matched

Methods in edu.ucla.sspace.graph.isomorphism with parameters of type Graph

Modifier and Type	Method and Description
boolean	IsomorphismTester.areIsomorphic(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns true if the graphs are isomorphism of each other.
boolean	IsomorphismTester.areIsomorphic(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns true if the graphs are isomorphism of each other.
boolean	AbstractIsomorphismTester.areIsomorphic(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns true if the graphs are isomorphism of each other.
boolean	AbstractIsomorphismTester.areIsomorphic(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns true if the graphs are isomorphism of each other.
Map<Integer,Integer>	IsomorphismTester.findIsomorphism(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns an isomorphic mapping from the vertices in g1 to the vertices in g2, or an empty Map if no such mapping exists.
Map<Integer,Integer>	IsomorphismTester.findIsomorphism(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns an isomorphic mapping from the vertices in g1 to the vertices in g2, or an empty Map if no such mapping exists.
Map<Integer,Integer>	AbstractIsomorphismTester.findIsomorphism(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns an isomorphic mapping from the vertices in g1 to the vertices in g2, or an empty Map if no such mapping exists.
Map<Integer,Integer>	AbstractIsomorphismTester.findIsomorphism(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns an isomorphic mapping from the vertices in g1 to the vertices in g2, or an empty Map if no such mapping exists.
protected State	VF2IsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns a new State for running the VF2 algorithm.
protected State	VF2IsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns a new State for running the VF2 algorithm.
protected abstract State	AbstractIsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates an empty State for mapping the vertices of g1 to g2.
protected abstract State	AbstractIsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates an empty State for mapping the vertices of g1 to g2.
protected State	TypedVF2IsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns a new State for running the VF2 algorithm.
protected State	TypedVF2IsomorphismTester.makeInitialState(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Returns a new State for running the VF2 algorithm.

Constructors in edu.ucla.sspace.graph.isomorphism with parameters of type Graph

Constructor and Description
TypedVF2State(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates a new TypedVF2State with an empty mapping between the two graphs.
TypedVF2State(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates a new TypedVF2State with an empty mapping between the two graphs.
VF2State(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates a new VF2State with an empty mapping between the two graphs.
VF2State(Graph<? extends Edge> g1, Graph<? extends Edge> g2) Creates a new VF2State with an empty mapping between the two graphs.