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.algo.clustering.struct.girvan_newman_struct
edu.claflin.finder.algo.clustering.struct.infomap_struct
edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct
edu.claflin.finder.algo.clustering.struct.louvain_struct
edu.claflin.finder.algo.shortestpath
edu.claflin.finder.algo.spanningtree
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.comp	Contains Comparator implementations for expansion ordering.
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(ArrayList<Graph> graphs, 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	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, 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
private List<Graph>	BronKerbosch.bronKerboschBiclique(Graph graph)	Finds all bicliques within a bipartite graph.
private List<Graph>	BronKerbosch.bronKerboschClique(Graph graph)	Given a graph, finds all complete subgraphs.
protected final ArrayList<Graph>	Algorithm.cull(ArrayList<Graph> subGraphs)	Removes duplicate subGraphs from the provided ArrayList.
private ArrayList<Graph>	ConnectedComponentsDFS.getConnectedComponents(Graph graph)	Gets a list of this Graph's Connected Components.
private List<Graph>	BronKerbosch.maximalBicliques(Graph graph)	Gets the Maximal Complete Bipartite Graphs from the input Graph using Bron-Kersboch.
private List<Graph>	BronKerbosch.maximalCliques(Graph graph)	Given a graph, finds all complete subgraphs, and then returns the largest one.
private List<Graph>	BronKerbosch.nameGraphs(List<Graph> graphs, String originalName, boolean bipartite)
ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph)	Processes data.
ArrayList<Graph>	BronKerbosch.process(Graph graph)	Processes data.
ArrayList<Graph>	Bundle.process(Graph graph)	Processes data.
ArrayList<Graph>	ConnectedComponentsDFS.process(Graph graph)	Processes data.
ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph)	Processes data.
ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph)	Deprecated. Processes data.

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

Modifier and Type	Method	Description
private void	BronKerbosch.addEdgesInParititeSet(Graph graph, List<Node> list)	Adds edges to a Graph between all Nodes in a partite set.
private List<Graph>	BronKerbosch.bronKerboschBiclique(Graph graph)	Finds all bicliques within a bipartite graph.
private List<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 boolean	Algorithm.compare(Graph base, Graph match)	Compares the two graphs based on edges.
private ArrayList<Graph>	ConnectedComponentsDFS.getConnectedComponents(Graph graph)	Gets a list of this Graph's Connected Components.
private List<Graph>	BronKerbosch.maximalBicliques(Graph graph)	Gets the Maximal Complete Bipartite Graphs from the input Graph using Bron-Kersboch.
private List<Graph>	BronKerbosch.maximalCliques(Graph graph)	Given a graph, finds all complete subgraphs, and then returns the largest one.
ArrayList<Graph>	BreadthFirstTraversalSearch.process(Graph graph)	Processes data.
ArrayList<Graph>	BronKerbosch.process(Graph graph)	Processes data.
ArrayList<Graph>	Bundle.process(Graph graph)	Processes data.
ArrayList<Graph>	ConnectedComponentsDFS.process(Graph graph)	Processes data.
ArrayList<Graph>	DepthFirstTraversalSearch.process(Graph graph)	Processes data.
ArrayList<Graph>	MatrixPatternAnalyzer.process(Graph graph)	Deprecated. Processes data.
private void	BronKerbosch.removeEdgesInPartiteSet(Graph graph, List<Node> list)	Removes edges in a Graph between all Nodes in a partite set.
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, 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
protected final ArrayList<Graph>	Algorithm.cull(ArrayList<Graph> subGraphs)	Removes duplicate subGraphs from the provided ArrayList.
private List<Graph>	BronKerbosch.nameGraphs(List<Graph> graphs, String originalName, boolean bipartite)

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

Fields in edu.claflin.finder.algo.clustering declared as Graph

Modifier and Type	Field	Description
private Graph	Communities.g

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

Modifier and Type	Method	Description
protected ArrayList<Graph>	ClusteringAlgorithm.buildCommunityGraphs(List<List<Node>> cs, Graph graph, String algo_name)
ArrayList<Graph>	FastGreedy.process(Graph graph)	Performs FastGreedy community detection on a given Graph, returning the clustering with the maximum modularity.
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.
ArrayList<Graph>	Infomap.process(Graph graph)	Performs community detection using the InfoMap algorithm
ArrayList<Graph>	LabelPropagation.process(Graph graph)	Performs Label Propagation (LPA) community detection on a given Graph, returning the significant communities present within a network.
ArrayList<Graph>	LeadingEigenvector.process(Graph graph)	Performs community detection using Mark Newman's Leading Eigenvector algorithm on a given Graph object, returning the clustering the highest approximated modularity.
ArrayList<Graph>	Louvain.process(Graph graph)	Performs community detection using the Louvain algorithm
ArrayList<Graph>	Walktrap.process(Graph graph)

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

Modifier and Type	Method	Description
protected ArrayList<Graph>	ClusteringAlgorithm.buildCommunityGraphs(List<List<Node>> cs, Graph graph, String algo_name)
private HashMap<Node,Double>	Walktrap.cprobs(List<Node> C, Graph graph, List<Node> nList)	Get a probability vector for a community.
private List<Node>	LabelPropagation.generateCommunityFromLabel(int target, int[] labels, Graph graph)	Performs FastGreedy community detection on a given Graph, returning the clustering with the maximum modularity.
ArrayList<Graph>	FastGreedy.process(Graph graph)	Performs FastGreedy community detection on a given Graph, returning the clustering with the maximum modularity.
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.
ArrayList<Graph>	Infomap.process(Graph graph)	Performs community detection using the InfoMap algorithm
ArrayList<Graph>	LabelPropagation.process(Graph graph)	Performs Label Propagation (LPA) community detection on a given Graph, returning the significant communities present within a network.
ArrayList<Graph>	LeadingEigenvector.process(Graph graph)	Performs community detection using Mark Newman's Leading Eigenvector algorithm on a given Graph object, returning the clustering the highest approximated modularity.
ArrayList<Graph>	Louvain.process(Graph graph)	Performs community detection using the Louvain algorithm
ArrayList<Graph>	Walktrap.process(Graph graph)

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

Modifier	Constructor	Description
	Communities(Graph g, boolean weighted)	Constructor to initialize 1-Node Communities from a Graph.
	Communities(Map<Integer,List<Node>> list, Graph g, boolean weighted)	Constructor to create Communities from existing Community group.
private	Communities(Map<Integer,List<Node>> list, Graph g, boolean weighted, double m2)	Constructor called by copy().

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

Fields in edu.claflin.finder.algo.clustering.struct.girvan_newman_struct declared as Graph

Modifier and Type	Field	Description
protected Graph	BetweennessCentrality.graph

Constructors in edu.claflin.finder.algo.clustering.struct.girvan_newman_struct with parameters of type Graph

Modifier	Constructor	Description
	BetweennessCentrality(Graph graph, boolean weighted)	Calculates betweenness scores based on the all-pairs unweighted shortest paths in the graph.

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

Fields in edu.claflin.finder.algo.clustering.struct.infomap_struct declared as Graph

Modifier and Type	Field	Description
private Graph	RelativeUndirectedBitLength.g
private Graph	AvgBitLength.graph
private Graph	InfomapAlgorithm.graph
private final Graph	InfomapImplementation.originalGraph

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

Modifier and Type	Method	Description
private void	InfomapImplementation.fine_tuning(Graph g)
static RelativeUndirectedBitLength	RelativeUndirectedBitLength.fromNodeToModule(Graph graph, Map<Node,Integer> nodeToModule)
private void	InfomapImplementation.oneModulePerNode(Graph g)	Puts each node in its own module
private void	InfomapImplementation.optimize(Graph g, Map<Node,Integer> nodeToModule)
private static ArrayList<Node>	AvgBitLength.randomWalker(Graph g)	Generates a path taken by random walker.
void	AvgBitLength.setGraph(Graph graph)
private static ArrayList<Node>	AvgBitLength.testRandomWalker(Graph g)

Constructors in edu.claflin.finder.algo.clustering.struct.infomap_struct with parameters of type Graph

Modifier	Constructor	Description
	AvgBitLength(Graph graph, Map<Integer,List<Node>> modules)
	InfomapAlgorithm(Graph g)
	InfomapImplementation(Graph graph)
	RelativeUndirectedBitLength(Graph graph, Map<Node,Integer> nodeToModule)

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

Fields in edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct declared as Graph

Modifier and Type	Field	Description
private Graph	LeadingEigenvectorAlgorithm.graph
private Graph	LeadingEigenvectorCaller.graph
private static Graph	Tester.graph

Fields in edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct with type parameters of type Graph

Modifier and Type	Field	Description
private ArrayList<Graph>	LeadingEigenvectorCaller.components

Methods in edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct that return Graph

Modifier and Type	Method	Description
Graph	LeadingEigenvectorAlgorithm.getGraph()

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

Modifier and Type	Method	Description
private ArrayList<Graph>	LeadingEigenvectorCaller.getComponents(Graph g)
private ArrayList<Graph>	LeadingEigenvectorCaller.getGraphList(int[] groupVector, Graph g)

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

Modifier and Type	Method	Description
private ArrayList<Graph>	LeadingEigenvectorCaller.getComponents(Graph g)
private ArrayList<Graph>	LeadingEigenvectorCaller.getGraphList(int[] groupVector, Graph g)

Constructors in edu.claflin.finder.algo.clustering.struct.leading_eigenvector_struct with parameters of type Graph

Modifier	Constructor	Description
	LeadingEigenvectorAlgorithm(Graph g)
	LeadingEigenvectorCaller(Graph g)

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

Fields in edu.claflin.finder.algo.clustering.struct.louvain_struct declared as Graph

Modifier and Type	Field	Description
private Graph	LouvainAlgorithm.graph

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

Modifier and Type	Method	Description
static String	Tester.communitiesToString(HashMap<Integer,List<Node>> communities, Graph graph)
static String	Tester.groupMapToString(HashMap<Integer,ArrayList<Integer>> groupMap, Graph graph)
static String	Tester.groupToString(int[] groupVector, int groupLabel, Graph graph)
static String	Tester.groupToString(HashMap<Integer,ArrayList<Integer>> groupMap, int groupLabel, Graph graph)
static String	Tester.labelToGroupArray(int groupLabel, int[] groupVector, Graph graph)

Constructors in edu.claflin.finder.algo.clustering.struct.louvain_struct with parameters of type Graph

Modifier	Constructor	Description
	LouvainAlgorithm(Graph g)

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

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

Modifier and Type	Method	Description
private Graph	ShortestPath.removePaths(Graph graph, Node from, Node to)	Private class for removing visited paths that not reach the destination node.

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

Modifier and Type	Method	Description
ArrayList<Graph>	DijkstraShortestPath.process(Graph graph)
ArrayList<Graph>	ShortestPath.process(Graph graph)

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

Modifier and Type	Method	Description
private Node	DijkstraShortestPath.closestReachableUnvisited(HashMap<Node,Double> shortestPathMap, Graph graph, Set<String> visited)
ArrayList<Graph>	DijkstraShortestPath.process(Graph graph)
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.

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

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

Modifier and Type	Method	Description
ArrayList<Graph>	Kruskal.process(Graph graph)	Processes data.
ArrayList<Graph>	Prim.process(Graph graph)	Processes data.

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

Modifier and Type	Method	Description
protected String	ExtremumSpanningTree.getName(Graph g, String algo, List<Edge> edges)
ArrayList<Graph>	Kruskal.process(Graph graph)	Processes data.
ArrayList<Graph>	Prim.process(Graph graph)	Processes data.
private void	Prim.startSearch(PrioritySet<Prim.DistanceRecord> ps, List<Node> treeList, List<Node> remainingNodes, 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(File source, boolean undirected)	Reads a graph from memory.
Graph	SimpleGraphIO.parseGraph(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(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.crosstalk(Graph subgraph1, Graph subgraph2)	Crosstalk of 2 subgraphs of this Graph.
Graph	Graph.difference(Graph that)	Difference of this Graph with a provided Graph.
Graph	Graph.getSubGraph(int startNode, int stopNode, String nameQualifier)	Deprecated. Outdated since v3.
Graph	Graph.getSubGraph(ArrayList<String> subStringSet, String nameQualifier)	Deprecated. Outdated since v3.
Graph	Graph.getSubGraph(List<Node> nodes, String nameQualifier)	Returns a subGraph of this graph.
Graph	Graph.intersect(Graph that)	Intersects this Graph with a provided Graph.
Graph	Graph.union(Graph that)	Union this Graph with a provided 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(String gName)

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

Modifier and Type	Method	Description
private ConditionedGraph	ConditionedGraph.conditionOther(Graph graph)	Private method used for copying the ConditionedGraph.
Graph	Graph.crosstalk(Graph subgraph1, Graph subgraph2)	Crosstalk of 2 subgraphs of this Graph.
Graph	Graph.difference(Graph that)	Difference of this Graph with a provided Graph.
Graph	Graph.intersect(Graph that)	Intersects this Graph with a provided Graph.
abstract boolean	Condition.satisfies(Graph existingGraph)	Used to test if the supplied graph is within the bounds of the condition's implementation.
Graph	Graph.union(Graph that)	Union this Graph with a provided Graph.

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

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

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

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

Modifier and Type	Method	Description
int	GraphAverageWeightComparator.compare(Graph g1, Graph g2)
int	GraphSizeComparator.compare(Graph g1, Graph g2)

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.
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 ArrayList<Graph>	Communicator.uniqueSubgraphs

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

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

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

Modifier	Constructor	Description
	CytogrouperMain(List<Graph> subgraphs, CommunicationListener listener, int partiteNumber)