# 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)`