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

Example 16 with Edge

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

the class GraphDensityNGTest method testSelfLoopNodeDensity.

@Test
public void testSelfLoopNodeDensity() {
    GraphModel graphModel = Lookup.getDefault().lookup(GraphController.class).getGraphModel();
    UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
    Node currentNode = graphModel.factory().newNode("0");
    undirectedGraph.addNode(currentNode);
    Edge currentEdge = graphModel.factory().newEdge(currentNode, currentNode, false);
    undirectedGraph.addEdge(currentEdge);
    Graph graph = graphModel.getGraph();
    GraphDensity d = new GraphDensity();
    double density = d.calculateDensity(graph, false);
    assertEquals(density, Double.POSITIVE_INFINITY);
}

Example 17 with Edge

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

the class GraphDistanceNGTest method testSpecial1UndirectedGraphCloseness.

@Test
public void testSpecial1UndirectedGraphCloseness() {
    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[] closeness = metricsMap.get(GraphDistance.CLOSENESS);
    int index7 = indicies.get(node7);
    double res = 1.0 / 1.1667;
    double diff = 0.01;
    assertEquals(closeness[index7], res, TOLERANCE);
}

Example 18 with Edge

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

the class GraphDistanceNGTest method testDirectedStarOutGraphCloseness.

@Test
public void testDirectedStarOutGraphCloseness() {
    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[] closeness = metricsMap.get(GraphDistance.CLOSENESS);
    Node n1 = directedGraph.getNode("0");
    Node n6 = directedGraph.getNode("5");
    int index1 = indicies.get(n1);
    int index6 = indicies.get(n6);
    assertEquals(closeness[index1], 1.0, TOLERANCE);
    assertEquals(closeness[index6], 0.0, TOLERANCE);
}

Example 19 with Edge

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

the class Hits method updateAutorithy.

void updateAutorithy(Graph graph, double[] newValues, double[] hubValues, boolean isDirected, Map<Node, Integer> indices) {
    double norm = 0;
    for (Node q : indices.keySet()) {
        double auth = 0;
        EdgeIterable edge_iter;
        if (isDirected) {
            edge_iter = ((DirectedGraph) graph).getInEdges(q);
        } else {
            edge_iter = graph.getEdges(q);
        }
        for (Edge edge : edge_iter) {
            if (!edge.isSelfLoop()) {
                Node p = graph.getOpposite(q, edge);
                auth += hubValues[indices.get(p)];
            }
        }
        newValues[indices.get(q)] = auth;
        norm += auth * auth;
        if (isCanceled) {
            return;
        }
    }
    norm = Math.sqrt(norm);
    if (norm > 0) {
        for (int i = 0; i < newValues.length; i++) {
            newValues[i] = newValues[i] / norm;
        }
    }
}

Example 20 with Edge

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

the class GraphDistanceNGTest method testSpecial1DirectedGraphHarmonicCloseness.

@Test
public void testSpecial1DirectedGraphHarmonicCloseness() {
    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");
    Node node5 = graphModel.factory().newNode("4");
    directedGraph.addNode(node1);
    directedGraph.addNode(node2);
    directedGraph.addNode(node3);
    directedGraph.addNode(node4);
    directedGraph.addNode(node5);
    Edge edge13 = graphModel.factory().newEdge(node1, node3);
    Edge edge32 = graphModel.factory().newEdge(node3, node2);
    Edge edge21 = graphModel.factory().newEdge(node2, node1);
    Edge edge34 = graphModel.factory().newEdge(node3, node4);
    Edge edge45 = graphModel.factory().newEdge(node4, node5);
    Edge edge53 = graphModel.factory().newEdge(node5, node3);
    directedGraph.addEdge(edge13);
    directedGraph.addEdge(edge32);
    directedGraph.addEdge(edge21);
    directedGraph.addEdge(edge34);
    directedGraph.addEdge(edge45);
    directedGraph.addEdge(edge53);
    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);
    int index2 = indicies.get(node2);
    int index3 = indicies.get(node3);
    assertEquals(harmonic[index2], (1.0 + 1.0 / 2.0 + 1.0 / 3.0 + 1.0 / 4.0) / 4.0, TOLERANCE);
    assertEquals(harmonic[index3], (1.0 / 2.0 + 1.0 + 1.0 + 1.0 / 2.0) / 4.0, TOLERANCE);
}