Examples with Edge org.gephi.graph.api.Edge used on opensource projects

Example 11 with Edge

use of org.gephi.graph.api.Edge in project gephi by gephi.

the class ConnectedComponents method computeWeeklyConnectedComponents.

public LinkedList<LinkedList<Node>> computeWeeklyConnectedComponents(Graph graph, HashMap<Node, Integer> indicies) {
    int N = graph.getNodeCount();
    //Keep track of which nodes have been seen
    int[] color = new int[N];
    Progress.start(progress, N);
    int seenCount = 0;
    LinkedList<LinkedList<Node>> components = new LinkedList<>();
    while (seenCount < N) {
        //The search Q
        LinkedList<Node> Q = new LinkedList<>();
        //The component-list
        LinkedList<Node> component = new LinkedList<>();
        //Seed the seach Q
        NodeIterable iter = graph.getNodes();
        for (Node first : iter) {
            if (color[indicies.get(first)] == 0) {
                Q.add(first);
                iter.doBreak();
                break;
            }
        }
        //While there are more nodes to search
        while (!Q.isEmpty()) {
            if (isCanceled) {
                return new LinkedList<>();
            }
            //Get the next Node and add it to the component list
            Node u = Q.removeFirst();
            component.add(u);
            //Iterate over all of u's neighbors
            EdgeIterable edgeIter = graph.getEdges(u);
            //For each neighbor
            for (Edge edge : edgeIter) {
                Node reachable = graph.getOpposite(u, edge);
                int id = indicies.get(reachable);
                //If this neighbor is unvisited
                if (color[id] == 0) {
                    color[id] = 1;
                    //Add it to the search Q
                    Q.addLast(reachable);
                    //Mark it as used 
                    Progress.progress(progress, seenCount);
                }
            }
            color[indicies.get(u)] = 2;
            seenCount++;
        }
        components.add(component);
    }
    return components;
}

Example 12 with Edge

use of org.gephi.graph.api.Edge in project gephi by gephi.

the class EigenvectorCentrality method computeMaxValueAndTempValues.

private double computeMaxValueAndTempValues(Graph graph, HashMap<Integer, Node> indicies, HashMap<Node, Integer> invIndicies, double[] tempValues, double[] centralityValues, boolean directed) {
    double max = 0.;
    int N = graph.getNodeCount();
    for (int i = 0; i < N; i++) {
        Node u = indicies.get(i);
        EdgeIterable iter;
        if (directed) {
            iter = ((DirectedGraph) graph).getInEdges(u);
        } else {
            iter = graph.getEdges(u);
        }
        for (Edge e : iter) {
            Node v = graph.getOpposite(u, e);
            Integer id = invIndicies.get(v);
            tempValues[i] += centralityValues[id];
        }
        max = Math.max(max, tempValues[i]);
        if (isCanceled) {
            return max;
        }
    }
    return max;
}

Example 13 with Edge

use of org.gephi.graph.api.Edge in project gephi by gephi.

the class ClusteringCoefficientNGTest method testSpecial2DirectedGraphClusteringCoefficient.

@Test
public void testSpecial2DirectedGraphClusteringCoefficient() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    DirectedGraph directedGraph = graphModel.getDirectedGraph();
    Node node1 = graphModel.factory().newNode("0");
    Node node2 = graphModel.factory().newNode("1");
    Node node3 = graphModel.factory().newNode("2");
    Node node4 = graphModel.factory().newNode("3");
    directedGraph.addNode(node1);
    directedGraph.addNode(node2);
    directedGraph.addNode(node3);
    directedGraph.addNode(node4);
    Edge edge21 = graphModel.factory().newEdge(node2, node1);
    Edge edge24 = graphModel.factory().newEdge(node2, node4);
    Edge edge31 = graphModel.factory().newEdge(node3, node1);
    Edge edge32 = graphModel.factory().newEdge(node3, node2);
    Edge edge43 = graphModel.factory().newEdge(node4, node3);
    directedGraph.addEdge(edge21);
    directedGraph.addEdge(edge24);
    directedGraph.addEdge(edge31);
    directedGraph.addEdge(edge32);
    directedGraph.addEdge(edge43);
    DirectedGraph graph = graphModel.getDirectedGraph();
    ClusteringCoefficient cc = new ClusteringCoefficient();
    ArrayWrapper[] network = new ArrayWrapper[4];
    int[] triangles = new int[4];
    double[] nodeClustering = new double[4];
    HashMap<String, Double> results = cc.computeClusteringCoefficient(graph, network, triangles, nodeClustering, true);
    double avClusteringCoefficient = results.get("clusteringCoefficient");
    double res = 0.4167;
    double diff = 0.01;
    assertTrue(Math.abs(avClusteringCoefficient - res) < diff);
}

Example 14 with Edge

use of org.gephi.graph.api.Edge in project gephi by gephi.

the class GraphDistanceNGTest method testSpecial2UndirectedGraphCloseness.

@Test
public void testSpecial2UndirectedGraphCloseness() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
    Node node1 = graphModel.factory().newNode("0");
    Node node2 = graphModel.factory().newNode("1");
    Node node3 = graphModel.factory().newNode("2");
    Node node4 = graphModel.factory().newNode("3");
    Node node5 = graphModel.factory().newNode("4");
    Node node6 = graphModel.factory().newNode("5");
    Node node7 = graphModel.factory().newNode("6");
    Node node8 = graphModel.factory().newNode("7");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    undirectedGraph.addNode(node7);
    undirectedGraph.addNode(node8);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
    Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
    Edge edge24 = graphModel.factory().newEdge(node2, node4, false);
    Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
    Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
    Edge edge78 = graphModel.factory().newEdge(node7, node8, false);
    Edge edge85 = graphModel.factory().newEdge(node8, node5, false);
    Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge13);
    undirectedGraph.addEdge(edge34);
    undirectedGraph.addEdge(edge24);
    undirectedGraph.addEdge(edge56);
    undirectedGraph.addEdge(edge67);
    undirectedGraph.addEdge(edge78);
    undirectedGraph.addEdge(edge85);
    undirectedGraph.addEdge(edge45);
    GraphDistance d = new GraphDistance();
    d.initializeStartValues();
    UndirectedGraph hierarchicalUndirectedGraph = graphModel.getUndirectedGraph();
    HashMap<Node, Integer> indicies = d.createIndiciesMap(hierarchicalUndirectedGraph);
    HashMap<String, double[]> metricsMap = (HashMap) d.calculateDistanceMetrics(graphModel.getGraph(), indicies, false, false);
    double[] closeness = metricsMap.get(GraphDistance.CLOSENESS);
    int index2 = indicies.get(node2);
    double res = 1.0 / 2.2857;
    assertEquals(closeness[index2], res, TOLERANCE);
}

Example 15 with Edge

use of org.gephi.graph.api.Edge in project gephi by gephi.

the class GraphDistanceNGTest method testSpecial2UndirectedGraphDiameter.

@Test
public void testSpecial2UndirectedGraphDiameter() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
    Node node1 = graphModel.factory().newNode("0");
    Node node2 = graphModel.factory().newNode("1");
    Node node3 = graphModel.factory().newNode("2");
    Node node4 = graphModel.factory().newNode("3");
    Node node5 = graphModel.factory().newNode("4");
    Node node6 = graphModel.factory().newNode("5");
    Node node7 = graphModel.factory().newNode("6");
    Node node8 = graphModel.factory().newNode("7");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    undirectedGraph.addNode(node7);
    undirectedGraph.addNode(node8);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge23 = graphModel.factory().newEdge(node2, node3, false);
    Edge edge34 = graphModel.factory().newEdge(node3, node4, false);
    Edge edge45 = graphModel.factory().newEdge(node4, node5, false);
    Edge edge56 = graphModel.factory().newEdge(node5, node6, false);
    Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
    Edge edge78 = graphModel.factory().newEdge(node7, node8, false);
    Edge edge81 = graphModel.factory().newEdge(node8, node1, false);
    Edge edge14 = graphModel.factory().newEdge(node1, node4, false);
    Edge edge85 = graphModel.factory().newEdge(node8, node5, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge23);
    undirectedGraph.addEdge(edge34);
    undirectedGraph.addEdge(edge45);
    undirectedGraph.addEdge(edge56);
    undirectedGraph.addEdge(edge67);
    undirectedGraph.addEdge(edge78);
    undirectedGraph.addEdge(edge81);
    undirectedGraph.addEdge(edge14);
    undirectedGraph.addEdge(edge85);
    GraphDistance d = new GraphDistance();
    d.initializeStartValues();
    UndirectedGraph hierarchicalUndirectedGraph = graphModel.getUndirectedGraph();
    HashMap<Node, Integer> indicies = d.createIndiciesMap(hierarchicalUndirectedGraph);
    d.calculateDistanceMetrics(graphModel.getGraph(), indicies, false, false);
    double diameter = d.getDiameter();
    assertEquals(diameter, 4.0, TOLERANCE);
}