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

Example 96 with Edge

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

the class PageRank method updateValueForNode.

private double updateValueForNode(Graph graph, Node s, double[] pagerankValues, double[] weights, HashMap<Node, Integer> indicies, boolean directed, boolean useWeights, double r, double prob) {
    double res = r;
    EdgeIterable eIter;
    if (directed) {
        eIter = ((DirectedGraph) graph).getInEdges(s);
    } else {
        eIter = graph.getEdges(s);
    }
    for (Edge edge : eIter) {
        Node neighbor = graph.getOpposite(s, edge);
        int neigh_index = indicies.get(neighbor);
        int normalize;
        if (directed) {
            normalize = ((DirectedGraph) graph).getOutDegree(neighbor);
        } else {
            normalize = graph.getDegree(neighbor);
        }
        if (useWeights) {
            double weight = edge.getWeight() / weights[neigh_index];
            res += prob * pagerankValues[neigh_index] * weight;
        } else {
            res += prob * (pagerankValues[neigh_index] / normalize);
        }
    }
    return res;
}

Example 97 with Edge

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

the class GraphDistanceNGTest method testDirectedStarOutGraphHarmonicCloseness.

@Test
public void testDirectedStarOutGraphHarmonicCloseness() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    DirectedGraph directedGraph = graphModel.getDirectedGraph();
    Node firstNode = graphModel.factory().newNode("0");
    directedGraph.addNode(firstNode);
    for (int i = 1; i <= 5; i++) {
        Node currentNode = graphModel.factory().newNode(((Integer) i).toString());
        directedGraph.addNode(currentNode);
        Edge currentEdge = graphModel.factory().newEdge(firstNode, currentNode);
        directedGraph.addEdge(currentEdge);
    }
    GraphDistance d = new GraphDistance();
    d.initializeStartValues();
    HashMap<Node, Integer> indicies = d.createIndiciesMap(graphModel.getGraph());
    HashMap<String, double[]> metricsMap = (HashMap) d.calculateDistanceMetrics(graphModel.getGraph(), indicies, true, false);
    double[] harmonic = metricsMap.get(GraphDistance.HARMONIC_CLOSENESS);
    Node n1 = directedGraph.getNode("0");
    Node n6 = directedGraph.getNode("5");
    int index1 = indicies.get(n1);
    int index6 = indicies.get(n6);
    assertEquals(harmonic[index1], 1.0, TOLERANCE);
    assertEquals(harmonic[index6], 0.0, TOLERANCE);
}

Example 98 with Edge

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

the class GraphDistanceNGTest method testSpecial1UndirectedGraphDiameter.

@Test
public void testSpecial1UndirectedGraphDiameter() {
    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);
    d.calculateDistanceMetrics(graphModel.getGraph(), indicies, false, false);
    double diameter = d.getDiameter();
    assertEquals(diameter, 5.0, TOLERANCE);
}

Example 99 with Edge

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

the class GraphDistanceNGTest method testSpecial1UndirectedGraphBetweenness.

@Test
public void testSpecial1UndirectedGraphBetweenness() {
    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");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    undirectedGraph.addNode(node7);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
    Edge edge14 = graphModel.factory().newEdge(node1, node4, false);
    Edge edge15 = graphModel.factory().newEdge(node1, node5, false);
    Edge edge16 = graphModel.factory().newEdge(node1, node6, false);
    Edge edge27 = graphModel.factory().newEdge(node2, node7, false);
    Edge edge37 = graphModel.factory().newEdge(node3, node7, false);
    Edge edge47 = graphModel.factory().newEdge(node4, node7, false);
    Edge edge57 = graphModel.factory().newEdge(node5, node7, false);
    Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge13);
    undirectedGraph.addEdge(edge14);
    undirectedGraph.addEdge(edge15);
    undirectedGraph.addEdge(edge16);
    undirectedGraph.addEdge(edge27);
    undirectedGraph.addEdge(edge37);
    undirectedGraph.addEdge(edge47);
    undirectedGraph.addEdge(edge57);
    undirectedGraph.addEdge(edge67);
    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[] betweenness = metricsMap.get(GraphDistance.BETWEENNESS);
    int index1 = indicies.get(node1);
    int index3 = indicies.get(node3);
    assertEquals(betweenness[index1], 5., TOLERANCE);
    assertEquals(betweenness[index3], 0.2, TOLERANCE);
}

Example 100 with Edge

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

the class GraphDistanceNGTest method testSpecial1UndirectedGraphHarmonicCloseness.

@Test
public void testSpecial1UndirectedGraphHarmonicCloseness() {
    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");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    undirectedGraph.addNode(node7);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge13 = graphModel.factory().newEdge(node1, node3, false);
    Edge edge14 = graphModel.factory().newEdge(node1, node4, false);
    Edge edge15 = graphModel.factory().newEdge(node1, node5, false);
    Edge edge16 = graphModel.factory().newEdge(node1, node6, false);
    Edge edge27 = graphModel.factory().newEdge(node2, node7, false);
    Edge edge37 = graphModel.factory().newEdge(node3, node7, false);
    Edge edge47 = graphModel.factory().newEdge(node4, node7, false);
    Edge edge57 = graphModel.factory().newEdge(node5, node7, false);
    Edge edge67 = graphModel.factory().newEdge(node6, node7, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge13);
    undirectedGraph.addEdge(edge14);
    undirectedGraph.addEdge(edge15);
    undirectedGraph.addEdge(edge16);
    undirectedGraph.addEdge(edge27);
    undirectedGraph.addEdge(edge37);
    undirectedGraph.addEdge(edge47);
    undirectedGraph.addEdge(edge57);
    undirectedGraph.addEdge(edge67);
    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[] harmonic = metricsMap.get(GraphDistance.HARMONIC_CLOSENESS);
    int index7 = indicies.get(node7);
    double res = (5.0 + 0.5) / 6.0;
    assertEquals(harmonic[index7], res, TOLERANCE);
}