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.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.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 and 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 and 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	DepthFirstTraversalSearch.searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited) Helper method to search for the SubGraphs.
private Graph	BreadthFirstTraversalSearch.searchNode(Graph graph, Node node) Helper method to search for the SubGraphs.

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

Modifier and Type	Method and Description
protected java.util.ArrayList<Graph>	Algorithm.cull(java.util.ArrayList<Graph> subGraphs) Removes duplicate subGraphs from the provided ArrayList.
java.util.ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	Bundle.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph) Deprecated. Processes data.

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

Modifier and Type	Method and Description
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 boolean	Algorithm.compare(Graph base, Graph match) Compares the two graphs based on edges.
java.util.ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	Bundle.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph) Processes data.
java.util.ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph) Deprecated. Processes data.
private boolean	Algorithm.reorder(Graph base, Graph match) Deprecated. No replacement. There is no longer a need to reorder graphs to test equality.
private Graph	DepthFirstTraversalSearch.searchNode(Graph graph, Graph subGraph, Node node, java.util.List<Node> visited) Helper method to search for the SubGraphs.
private Graph	BreadthFirstTraversalSearch.searchNode(Graph graph, Node node) Helper method to search for the SubGraphs.

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

Modifier and Type	Method and Description
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.io.graph

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

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

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

Modifier and Type	Method and Description
Graph	Graph.copy() Copies this Graph object using the getSubGraph() method.
Graph	Graph.getSubGraph(java.util.ArrayList<java.lang.String> subStringSet, java.lang.String nameQualifier) Deprecated. Outdated since v3. Replaced by getSubGraph(java.util.List, java.lang.String)
Graph	Graph.getSubGraph(int startNode, int stopNode, java.lang.String nameQualifier) Deprecated. Outdated since v3. Replaced by getSubGraph(java.util.List, java.lang.String)
Graph	Graph.getSubGraph(java.util.List<Node> nodes, java.lang.String nameQualifier) Returns a subGraph of this graph.
static Graph	BronKerboschHandler.maximumCompleteClique(Graph graph) Given a graph, finds all complete subgraphs, and then returns the largest one.
Graph	Graph.uniqueCopy() Copies this Graph producing a unique copy in which there is no entanglement between the two Graph objects.

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

Modifier and Type	Method and Description
static java.util.ArrayList<Graph>	BronKerboschHandler.bronKerbosch(Graph graph) Given a graph, finds all complete subgraphs.
static java.util.ArrayList<Graph>	BronKerboschHandler.bronKerboschBipartite(Graph graph) Bipartite Bron Kerbosch algorithm that usees the above to find all complete bipartite graphs within a bipartite graph.

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

Modifier and Type	Method and Description
static java.util.ArrayList<java.util.ArrayList<Node>>	BronKerboschBipartiteUtils.bipartiteDivision(Graph existingGraph) Divides the given graph into bipartite sets.
static void	BronKerboschHandler.bronKerbosch(java.util.ArrayList<Graph> results, Graph r, Graph p, Graph x) Recursive helper method to do the above.
static java.util.ArrayList<Graph>	BronKerboschHandler.bronKerbosch(Graph graph) Given a graph, finds all complete subgraphs.
static java.util.ArrayList<Graph>	BronKerboschHandler.bronKerboschBipartite(Graph graph) Bipartite Bron Kerbosch algorithm that usees the above to find all complete bipartite graphs within a bipartite graph.
private ConditionedGraph	ConditionedGraph.conditionOther(Graph graph) Private method used for copying the ConditionedGraph.
static Graph	BronKerboschHandler.maximumCompleteClique(Graph graph) Given a graph, finds all complete subgraphs, and then returns the largest one.
abstract boolean	Condition.satisfies(Graph existingGraph) Used to test if the supplied graph is within the bounds of the condition's implementation.
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.
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.

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

Modifier and Type	Method and Description
static void	BronKerboschHandler.bronKerbosch(java.util.ArrayList<Graph> results, Graph r, Graph p, Graph x) Recursive helper method to do the above.

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

Constructor and 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.cond

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

Modifier and Type	Method and Description
boolean	BipartiteCondition.satisfies(Graph existingGraph) Used to test if the supplied graph is within the bounds of the condition's implementation.
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.
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.

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

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

Modifier and Type	Method and 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 and 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 and Description
CytogrouperMain(java.util.List<Graph> subgraphs, CommunicationListener listener, int partiteNumber)