Uses of Class
edu.claflin.finder.logic.Graph

Packages that use Graph

Package	Description
edu.claflin.finder	Subgraph Finder - Used to find and locate subgraphs within a network.
edu.claflin.finder.algo	Contains the Algorithm code for finding bipartite subgraphs.
edu.claflin.finder.algo.clustering
edu.claflin.finder.io.graph	Contains the specific graph formats supported by the SNBA program family.
edu.claflin.finder.io.graph.sub	Contains the general classes used to support extensibility of the IO classes.
edu.claflin.finder.logic	Contains the data structure and processing code-base.
edu.claflin.finder.logic.communities
edu.claflin.finder.logic.cond	Contains Condition implementations for identifying subgraph types.
edu.claflin.finder.logic.cygrouper

Uses of Graph in edu.claflin.finder

Method parameters in edu.claflin.finder with type arguments of type Graph

Modifier and Type	Method	Description
private static void	Main.writeGraphs(java.util.ArrayList<Graph> graphs, java.lang.String output, GraphWriter writer)	Writes Graph objects to memory.

Uses of Graph in edu.claflin.finder.algo

Methods in edu.claflin.finder.algo that return Graph

Modifier and Type	Method	Description
private Graph	MatrixPatternAnalyzer.checkSubGraphs(Graph inGraph, int transpositions)	Deprecated. Step 3: Repeat Step 2 for each "Cornered" Sub-matrix of the original Graph.
private Graph	ShortestPath.removePaths(Graph graph, Node from, Node to)	Private class for removing visited paths that not reach the destination node.
private Graph	BreadthFirstTraversalSearch.searchNode(Graph graph, Node node)	Helper method to search for the SubGraphs in Breadth First Search.
private Graph	DepthFirstTraversalSearch.searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited)	Helper method to search for the SubGraphs in Depth First search.

Methods in edu.claflin.finder.algo that return types with arguments of type Graph

Modifier and Type	Method	Description
static java.util.ArrayList<Graph>	BronKerbosch.bronKerboschBiclique(Graph graph)	Bipartite Bron Kerbosch algorithm that uses the above to find all complete bipartite graphs within a bipartite graph.
static java.util.ArrayList<Graph>	BronKerbosch.bronKerboschClique(Graph graph)	Given a graph, finds all complete subgraphs.
protected java.util.ArrayList<Graph>	Algorithm.cull(java.util.ArrayList<Graph> subGraphs)	Removes duplicate subGraphs from the provided ArrayList.
private java.util.ArrayList<Graph>	ConnectedComponentsDFS.getConnectedComponents(Graph graph)	Gets a list of this Graph's Connected Components.
static java.util.ArrayList<Graph>	BronKerbosch.maximumBicliques(Graph graph)	Gets the Maximum Complete Bipartite Graphs by Node count from the input Graph using Bron-Kersboch.
static java.util.ArrayList<Graph>	BronKerbosch.maximumCliques(Graph graph)	Given a graph, finds all complete subgraphs, and then returns the largest one.
java.util.ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	BronKerbosch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	Bundle.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	ConnectedComponentsDFS.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	DijkstraShortestPath.process(Graph graph)
java.util.ArrayList<Graph>	Kruskal.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph)	Deprecated. Processes data.
java.util.ArrayList<Graph>	Prim.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	ShortestPath.process(Graph graph)

Methods in edu.claflin.finder.algo with parameters of type Graph

Modifier and Type	Method	Description
static void	BronKerbosch.bronKerbosch(java.util.ArrayList<Graph> results, Graph r, Graph p, Graph x, Graph orig)	Recursive helper method to do the above.
static java.util.ArrayList<Graph>	BronKerbosch.bronKerboschBiclique(Graph graph)	Bipartite Bron Kerbosch algorithm that uses the above to find all complete bipartite graphs within a bipartite graph.
static java.util.ArrayList<Graph>	BronKerbosch.bronKerboschClique(Graph graph)	Given a graph, finds all complete subgraphs.
private boolean	MatrixPatternAnalyzer.checkNodeGroupings(Graph inGraph)	Deprecated. Step 2: Iterate on Step 1 through all contiguous node groupings.
private Graph	MatrixPatternAnalyzer.checkSubGraphs(Graph inGraph, int transpositions)	Deprecated. Step 3: Repeat Step 2 for each "Cornered" Sub-matrix of the original Graph.
private boolean	MatrixPatternAnalyzer.checkZeroMatrices(Graph inGraph, int nodeCap)	Deprecated. Step 1: Check for valid 0 Sub-matrices.
private Node	DijkstraShortestPath.closestReachableUnvisited(java.util.HashMap<Node,java.lang.Double> shortestPathMap, Graph graph, java.util.Set<java.lang.String> visited)
private boolean	Algorithm.compare(Graph base, Graph match)	Compares the two graphs based on edges.
private void	ConnectedComponentsDFS.dfs(Node n, java.util.List<Node> inodes, java.util.List<Node> onodes, Graph orig)	Recursive dfs that stores the nodes of a connected component.
private java.util.ArrayList<Graph>	ConnectedComponentsDFS.getConnectedComponents(Graph graph)	Gets a list of this Graph's Connected Components.
static java.util.ArrayList<Graph>	BronKerbosch.maximumBicliques(Graph graph)	Gets the Maximum Complete Bipartite Graphs by Node count from the input Graph using Bron-Kersboch.
static java.util.ArrayList<Graph>	BronKerbosch.maximumCliques(Graph graph)	Given a graph, finds all complete subgraphs, and then returns the largest one.
java.util.ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	BronKerbosch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	Bundle.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	ConnectedComponentsDFS.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	DijkstraShortestPath.process(Graph graph)
java.util.ArrayList<Graph>	Kruskal.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph)	Deprecated. Processes data.
java.util.ArrayList<Graph>	Prim.process(Graph graph)	Processes data.
java.util.ArrayList<Graph>	ShortestPath.process(Graph graph)
private Graph	ShortestPath.removePaths(Graph graph, Node from, Node to)	Private class for removing visited paths that not reach the destination node.
private boolean	Algorithm.reorder(Graph base, Graph match)	Deprecated. No replacement.
private Graph	BreadthFirstTraversalSearch.searchNode(Graph graph, Node node)	Helper method to search for the SubGraphs in Breadth First Search.
private Graph	DepthFirstTraversalSearch.searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited)	Helper method to search for the SubGraphs in Depth First search.

Method parameters in edu.claflin.finder.algo with type arguments of type Graph

Modifier and Type	Method	Description
static void	BronKerbosch.bronKerbosch(java.util.ArrayList<Graph> results, Graph r, Graph p, Graph x, Graph orig)	Recursive helper method to do the above.
protected java.util.ArrayList<Graph>	Algorithm.cull(java.util.ArrayList<Graph> subGraphs)	Removes duplicate subGraphs from the provided ArrayList.

Uses of Graph in edu.claflin.finder.algo.clustering

Methods in edu.claflin.finder.algo.clustering that return types with arguments of type Graph

Modifier and Type	Method	Description
protected java.util.ArrayList<Graph>	ClusteringAlgorithm.buildCommunityGraphs(java.util.List<java.util.List<Node>> cs, Graph graph)
java.util.ArrayList<Graph>	FastGreedy.process(Graph graph)	Performs FastGreedy community detection on a given Graph, returning the clustering with the maximum modularity.
java.util.ArrayList<Graph>	GirvanNewman.process(Graph graph)	Performs Edge Betweenness community detection with Girvan-Newman algorithm a given Graph, returning the clustering with the maximum modularity.
java.util.ArrayList<Graph>	Walktrap.process(Graph graph)

Methods in edu.claflin.finder.algo.clustering with parameters of type Graph

Modifier and Type	Method	Description
protected java.util.ArrayList<Graph>	ClusteringAlgorithm.buildCommunityGraphs(java.util.List<java.util.List<Node>> cs, Graph graph)
private java.util.HashMap<Node,java.lang.Double>	Walktrap.cprobs(java.util.List<Node> C, Graph graph, java.util.List<Node> graphNodes)	Get a probability vector for a community.
java.util.ArrayList<Graph>	FastGreedy.process(Graph graph)	Performs FastGreedy community detection on a given Graph, returning the clustering with the maximum modularity.
java.util.ArrayList<Graph>	GirvanNewman.process(Graph graph)	Performs Edge Betweenness community detection with Girvan-Newman algorithm a given Graph, returning the clustering with the maximum modularity.
java.util.ArrayList<Graph>	Walktrap.process(Graph graph)

Uses of Graph in edu.claflin.finder.io.graph

Methods in edu.claflin.finder.io.graph that return Graph

Modifier and Type	Method	Description
Graph	SIFGraphIO.parseGraph(java.io.File source, boolean undirected)	Reads a graph from memory.
Graph	SimpleGraphIO.parseGraph(java.io.File source, boolean undirected)	Reads a graph from memory.

Methods in edu.claflin.finder.io.graph with parameters of type Graph

Modifier and Type	Method	Description
void	NOABatchIO.writeGraph(Graph toWrite)	Writes graphs to memory.
void	SIFGraphIO.writeGraph(Graph toWrite)	Writes graphs to memory.
void	SimpleGraphIO.writeGraph(Graph toWrite)	Writes graphs to memory.

Uses of Graph in edu.claflin.finder.io.graph.sub

Methods in edu.claflin.finder.io.graph.sub that return Graph

Modifier and Type	Method	Description
Graph	GraphReader.parseGraph(java.io.File source, boolean undirected)	Reads a graph from memory.

Methods in edu.claflin.finder.io.graph.sub with parameters of type Graph

Modifier and Type	Method	Description
void	GraphWriter.writeGraph(Graph toWrite)	Writes graphs to memory.

Uses of Graph in edu.claflin.finder.logic

Subclasses of Graph in edu.claflin.finder.logic

Modifier and Type	Class	Description
class	ConditionedGraph	Represents a "conditioned" graph.

Methods in edu.claflin.finder.logic that return Graph

Modifier and Type	Method	Description
Graph	Graph.copy()	Copies this Graph object using the getSubGraph() method.
Graph	Graph.getSubGraph(int startNode, int stopNode, java.lang.String nameQualifier)	Deprecated. Outdated since v3.
Graph	Graph.getSubGraph(java.util.ArrayList<java.lang.String> subStringSet, java.lang.String nameQualifier)	Deprecated. Outdated since v3.
Graph	Graph.getSubGraph(java.util.List<Node> nodes, java.lang.String nameQualifier)	Returns a subGraph of this graph.
Graph	Graph.uniqueCopy()	Copies this Graph producing a unique copy in which there is no entanglement between the two Graph objects.
Graph	Graph.uniqueCopy(java.lang.String gName)

Methods in edu.claflin.finder.logic with parameters of type Graph

Modifier and Type	Method	Description
static java.util.ArrayList<java.util.ArrayList<Node>>	BronKerboschBipartiteUtils.bipartiteDivision(Graph existingGraph)	Divides the given graph into bipartite sets.
private ConditionedGraph	ConditionedGraph.conditionOther(Graph graph)	Private method used for copying the ConditionedGraph.
private static boolean	BronKerboschBipartiteUtils.satisfies(Graph existingGraph, java.util.Set<Node> addSet, java.util.Set<Node> compareSet, Node current)	Private method for stepping through the adjacency lists and determining if the graph is bipartite.
abstract boolean	Condition.satisfies(Graph existingGraph)	Used to test if the supplied graph is within the bounds of the condition's implementation.
void	Graph.transferEdgesContainingNodeFromGraph(Graph graph, Node node)	Adds all edges containing the input node from the input graph to this graph, provided that the other vertex is already within this graph.

Constructors in edu.claflin.finder.logic with parameters of type Graph

Constructor	Description
ConditionedGraph(Graph graph, java.util.Collection<Condition> conditions)	Private constructor used to create copies of ConditionedGraph objects.

Uses of Graph in edu.claflin.finder.logic.communities

Fields in edu.claflin.finder.logic.communities declared as Graph

Modifier and Type	Field	Description
private Graph	Communities.g

Constructors in edu.claflin.finder.logic.communities with parameters of type Graph

Constructor	Description
Communities(java.util.HashMap<java.lang.Integer,java.util.List<Node>> list, Graph g)

Uses of Graph in edu.claflin.finder.logic.cond

Methods in edu.claflin.finder.logic.cond with parameters of type Graph

Modifier and Type	Method	Description
boolean	BipartiteCondition.satisfies(Graph existingGraph)	Used to test if the supplied graph is within the bounds of the condition's implementation.
private boolean	BipartiteCondition.satisfies(Graph existingGraph, java.util.Set<Node> addSet, java.util.Set<Node> compareSet, Node current)	Private method for stepping through the adjacency lists and determining if the graph is bipartite.
boolean	CliqueCondition.satisfies(Graph existingGraph)	Used to test if the supplied graph is within the bounds of the condition's implementation.
boolean	DirectedCliqueCondition.satisfies(Graph existingGraph)	Used to test if the supplied graph is within the bounds of the condition's implementation.

Uses of Graph in edu.claflin.finder.logic.cygrouper

Fields in edu.claflin.finder.logic.cygrouper with type parameters of type Graph

Modifier and Type	Field	Description
static java.util.ArrayList<Graph>	Communicator.uniqueSubgraphs

Methods in edu.claflin.finder.logic.cygrouper with parameters of type Graph

Modifier and Type	Method	Description
int	GraphAverageWeightComparator.compare(Graph g1, Graph g2)
int	GraphSizeComparator.compare(Graph g1, Graph g2)
static double	GraphAverageWeight.getAverageWeight(Graph g)

Method parameters in edu.claflin.finder.logic.cygrouper with type arguments of type Graph

Modifier and Type	Method	Description
void	CommunicationListener.setUniqueSubGraphs(java.util.ArrayList<Graph> subgraphs)
void	Communicator.setUniqueSubGraphs(java.util.ArrayList<Graph> subgraphs)

Constructor parameters in edu.claflin.finder.logic.cygrouper with type arguments of type Graph

Constructor	Description
CytogrouperMain(java.util.List<Graph> subgraphs, CommunicationListener listener, int partiteNumber)