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

Example 21 with Edge

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

the class AttributeTableCSVExporter method writeCSVFile.

/**
     * <p>Export a AttributeTable to the specified file.</p>
     *
     * @param graph Graph containing the table and rows
     * @param table Table to export. Cannot be null
     * @param out Ouput stream to write. Cannot be null.
     * @param separator Separator to use for separating values of a row in the CSV file. If null ',' will be used.
     * @param charset Charset encoding for the file. If null, UTF-8 will be used
     * @param columnIndexesToExport Indicates the indexes of the columns to export. All columns will be exported if null. For special columns in edges table, use {@code FAKE_COLUMN_EDGE_} values in this class.
     * @param rows Elements (table rows: nodes/edges) to include in the exported file. Cannot be null. If null, all nodes/edges will be exported.
     * @throws IOException When an error happens while writing the file
     */
public static void writeCSVFile(Graph graph, Table table, OutputStream out, Character separator, Charset charset, Integer[] columnIndexesToExport, Element[] rows) throws IOException {
    if (out == null) {
        throw new IllegalArgumentException("out cannot be null");
    }
    if (separator == null) {
        separator = DEFAULT_SEPARATOR;
    }
    if (charset == null) {
        charset = Charset.forName("UTF-8");
    }
    AttributeColumnsController ac = Lookup.getDefault().lookup(AttributeColumnsController.class);
    boolean isEdgeTable = ac.isEdgeTable(table);
    if (rows == null) {
        if (isEdgeTable) {
            rows = graph.getEdges().toArray();
        } else {
            rows = graph.getNodes().toArray();
        }
    }
    TimeFormat timeFormat = graph.getModel().getTimeFormat();
    DateTimeZone timeZone = graph.getModel().getTimeZone();
    if (columnIndexesToExport == null) {
        List<Integer> columnIndexesToExportList = new ArrayList<>();
        //Add special columns for edges table:
        if (isEdgeTable) {
            columnIndexesToExportList.add(FAKE_COLUMN_EDGE_SOURCE);
            columnIndexesToExportList.add(FAKE_COLUMN_EDGE_TARGET);
            columnIndexesToExportList.add(FAKE_COLUMN_EDGE_TYPE);
        }
        for (Column column : table) {
            columnIndexesToExportList.add(column.getIndex());
        }
        columnIndexesToExport = columnIndexesToExportList.toArray(new Integer[0]);
    }
    CsvWriter writer = new CsvWriter(out, separator, charset);
    //Write column headers:
    for (int column = 0; column < columnIndexesToExport.length; column++) {
        int columnIndex = columnIndexesToExport[column];
        if (columnIndex == FAKE_COLUMN_EDGE_SOURCE) {
            writer.write("Source");
        } else if (columnIndex == FAKE_COLUMN_EDGE_TARGET) {
            writer.write("Target");
        } else if (columnIndex == FAKE_COLUMN_EDGE_TYPE) {
            writer.write("Type");
        } else {
            //Use the title only if it's the same as the id (case insensitive):
            String columnId = table.getColumn(columnIndex).getId();
            String columnTitle = table.getColumn(columnIndex).getId();
            String columnHeader = columnId.equalsIgnoreCase(columnTitle) ? columnTitle : columnId;
            writer.write(columnHeader, true);
        }
    }
    writer.endRecord();
    //Write rows:
    Object value;
    String text;
    for (int row = 0; row < rows.length; row++) {
        for (int i = 0; i < columnIndexesToExport.length; i++) {
            int columnIndex = columnIndexesToExport[i];
            if (columnIndex == FAKE_COLUMN_EDGE_SOURCE) {
                value = ((Edge) rows[row]).getSource().getId();
            } else if (columnIndex == FAKE_COLUMN_EDGE_TARGET) {
                value = ((Edge) rows[row]).getTarget().getId();
            } else if (columnIndex == FAKE_COLUMN_EDGE_TYPE) {
                value = ((Edge) rows[row]).isDirected() ? "Directed" : "Undirected";
            } else {
                value = rows[row].getAttribute(table.getColumn(columnIndex));
            }
            if (value != null) {
                text = AttributeUtils.print(value, timeFormat, timeZone);
            } else {
                text = "";
            }
            writer.write(text, true);
        }
        writer.endRecord();
    }
    writer.close();
}

Example 22 with Edge

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

the class PageRankNGTest method testUndirectedWeightedGraphPageRank.

@Test
public void testUndirectedWeightedGraphPageRank() {
    pc.newProject();
    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");
    undirectedGraph.addNode(node1);
    undirectedGraph.addNode(node2);
    undirectedGraph.addNode(node3);
    undirectedGraph.addNode(node4);
    undirectedGraph.addNode(node5);
    undirectedGraph.addNode(node6);
    Edge edge12 = graphModel.factory().newEdge(node1, node2, false);
    Edge edge23 = graphModel.factory().newEdge(node2, node3, 0, 10, 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 edge61 = graphModel.factory().newEdge(node6, node1, false);
    undirectedGraph.addEdge(edge12);
    undirectedGraph.addEdge(edge23);
    undirectedGraph.addEdge(edge34);
    undirectedGraph.addEdge(edge45);
    undirectedGraph.addEdge(edge56);
    undirectedGraph.addEdge(edge61);
    UndirectedGraph graph = graphModel.getUndirectedGraph();
    PageRank pr = new PageRank();
    double[] pageRank;
    HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
    pageRank = pr.calculatePagerank(graph, indicies, false, true, 0.001, 0.85);
    int index1 = indicies.get(node1);
    int index2 = indicies.get(node2);
    int index3 = indicies.get(node3);
    int index6 = indicies.get(node6);
    double diff = 0.01;
    double pr1 = pageRank[index1];
    double pr2 = pageRank[index2];
    double pr3 = pageRank[index3];
    double pr6 = pageRank[index6];
    assertTrue(Math.abs(pr2 - pr3) < diff);
    assertTrue(pr1 < pr2);
    assertTrue(pr1 < pr6);
}

Example 23 with Edge

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

the class WeightedDegreeNGTest method testDirectedStarOutGraphDegree.

@Test
public void testDirectedStarOutGraphDegree() {
    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);
    }
    DirectedGraph graph = graphModel.getDirectedGraph();
    Node n1 = graph.getNode("0");
    Node n3 = graph.getNode("2");
    WeightedDegree d = new WeightedDegree();
    d.execute(graph);
    double inDegree1 = (Double) n1.getAttribute(WeightedDegree.WINDEGREE);
    double outDegree1 = (Double) n1.getAttribute(WeightedDegree.WOUTDEGREE);
    double degree3 = (Double) n3.getAttribute(WeightedDegree.WDEGREE);
    assertEquals(inDegree1, 0.0);
    assertEquals(outDegree1, 5.0);
    assertEquals(degree3, 1.0);
}

Example 24 with Edge

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

the class ModularityNGTest method testComputeBarbellGraphModularityHasHighWeight.

@Test
public void testComputeBarbellGraphModularityHasHighWeight() {
    GraphModel graphModel = GraphGenerator.generateCompleteUndirectedGraph(4);
    UndirectedGraph undirectedGraph = graphModel.getUndirectedGraph();
    Node[] nodes = new Node[4];
    for (int i = 0; i < 4; i++) {
        Node currentNode = graphModel.factory().newNode(((Integer) (i + 4)).toString());
        nodes[i] = currentNode;
        undirectedGraph.addNode(currentNode);
    }
    for (int i = 0; i < 3; i++) {
        for (int j = i + 1; j < 4; j++) {
            Edge currentEdge = graphModel.factory().newEdge(nodes[i], nodes[j], false);
            undirectedGraph.addEdge(currentEdge);
        }
    }
    Edge currentEdge = graphModel.factory().newEdge(undirectedGraph.getNode("0"), undirectedGraph.getNode("5"), 0, 100.f, false);
    undirectedGraph.addEdge(currentEdge);
    UndirectedGraph graph = graphModel.getUndirectedGraph();
    Modularity mod = new Modularity();
    Modularity.CommunityStructure theStructure = mod.new CommunityStructure(graph);
    int[] comStructure = new int[graph.getNodeCount()];
    HashMap<String, Double> modularityValues = mod.computeModularity(graph, theStructure, comStructure, 1., true, true);
    int class4 = comStructure[0];
    int class5 = comStructure[5];
    assertEquals(class4, class5);
}

Example 25 with Edge

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

the class PageRankNGTest method testDirectedStarOutGraphPageRank.

@Test
public void testDirectedStarOutGraphPageRank() {
    pc.newProject();
    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);
    }
    DirectedGraph graph = graphModel.getDirectedGraph();
    PageRank pr = new PageRank();
    double[] pageRank;
    HashMap<Node, Integer> indicies = pr.createIndiciesMap(graph);
    pageRank = pr.calculatePagerank(graph, indicies, true, false, 0.001, 0.85);
    Node n1 = graph.getNode("0");
    Node n2 = graph.getNode("1");
    Node n3 = graph.getNode("2");
    Node n5 = graph.getNode("4");
    int index1 = indicies.get(n1);
    int index2 = indicies.get(n2);
    int index3 = indicies.get(n3);
    int index5 = indicies.get(n5);
    double pr1 = pageRank[index1];
    double pr2 = pageRank[index2];
    double pr3 = pageRank[index3];
    double pr5 = pageRank[index5];
    double res = 0.146;
    double diff = 0.01;
    assertTrue(pr1 < pr3);
    assertEquals(pr2, pr5);
    assertTrue(Math.abs(pr1 - res) < diff);
}