Examples with CyEdge org.cytoscape.model.CyEdge used on opensource projects

Example 86 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class GroupViewCollapseHandler method addMemberEdges.

private void addMemberEdges(CyGroup group, CyNetwork network) {
    CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
    CyNode groupNode = group.getGroupNode();
    List<CyEdge> newEdges = new ArrayList<CyEdge>();
    for (CyNode node : group.getNodeList()) {
        if (!network.containsEdge(groupNode, node)) {
            CyEdge edge = network.addEdge(groupNode, node, true);
            CyRow edgeRow = network.getRow(edge);
            CyRow edgeRootRow = rootNetwork.getRow(edge, CyRootNetwork.SHARED_ATTRS);
            // Add a name
            String name = getNodeName(groupNode, network) + " (member) " + getNodeName(node, network);
            edgeRow.set(CyNetwork.NAME, name);
            edgeRootRow.set(CyRootNetwork.SHARED_NAME, name);
            // Set the interaction
            edgeRow.set(CyEdge.INTERACTION, "member");
            edgeRootRow.set(CyRootNetwork.SHARED_INTERACTION, "member");
            newEdges.add(edge);
        }
    }
    if (newEdges.size() > 0)
        group.addEdges(newEdges);
}

Example 87 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class GraphMLWriter method writeEdges.

private void writeEdges(Document doc, Element parent) {
    final List<CyEdge> edges = network.getEdgeList();
    final CyTable table = network.getDefaultEdgeTable();
    final Collection<CyColumn> edgeColumns = table.getColumns();
    for (final CyEdge edge : edges) {
        final Element edgeElm = doc.createElement(EDGE);
        edgeElm.setAttribute(SOURCE, edge.getSource().getSUID().toString());
        edgeElm.setAttribute(TARGET, edge.getTarget().getSUID().toString());
        final CyRow row = network.getRow(edge);
        appendData(row, edgeColumns, doc, edgeElm, edge);
        parent.appendChild(edgeElm);
    }
}

Example 88 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class TestCyGroupFactory method testMetaEdges.

// Test maintenance of meta-edges
// Create two groups that share edges
// Collapse both and expand them in the opposite order
@Test
public void testMetaEdges() throws Exception {
    // Set up our data structures
    final CyGroupFactory factory = TestCyGroupFactory.getFactory();
    final NetworkTestSupport support = new NetworkTestSupport();
    final CyNetwork net = support.getNetwork();
    final CyNode nodeA = net.addNode();
    final CyNode nodeB = net.addNode();
    final CyNode nodeC = net.addNode();
    final CyNode nodeD = net.addNode();
    final CyNode nodeE = net.addNode();
    final CyEdge edge1 = net.addEdge(nodeA, nodeE, false);
    final CyEdge edge2 = net.addEdge(nodeE, nodeB, false);
    final CyEdge edge3 = net.addEdge(nodeE, nodeC, false);
    final CyEdge edge4 = net.addEdge(nodeE, nodeD, false);
    final CyEdge edge5 = net.addEdge(nodeC, nodeB, false);
    final CyEdge edge6 = net.addEdge(nodeC, nodeD, false);
    final CyGroup group1 = factory.createGroup(net, null, Arrays.asList(nodeA, nodeB, nodeC), null, true);
    assertNotNull(group1);
    assertEqualWithoutOrder(group1.getNodeList(), Arrays.asList(nodeA, nodeB, nodeC));
    assertEqualWithoutOrder(group1.getInternalEdgeList(), Arrays.asList(edge5));
    assertEqualWithoutOrder(group1.getExternalEdgeList(), Arrays.asList(edge1, edge2, edge3, edge6));
    final CyGroup group2 = factory.createGroup(net, null, Arrays.asList(nodeD, nodeE), null, true);
    assertNotNull(group2);
    assertEqualWithoutOrder(group2.getNodeList(), Arrays.asList(nodeD, nodeE));
    assertEqualWithoutOrder(group2.getInternalEdgeList(), Arrays.asList(edge4));
    // 4 external edges, we create meta-edges when we collapse
    assertTrue(group2.getExternalEdgeList().size() == 4);
    // Collapse both groups
    group1.collapse(net);
    assertTrue(group1.isCollapsed(net));
    group2.collapse(net);
    assertTrue(group2.isCollapsed(net));
    assertEqualWithoutOrder(net.getNodeList(), Arrays.asList(group1.getGroupNode(), group2.getGroupNode()));
    // Expand in opposite order
    group1.expand(net);
    assertEqualWithoutOrder(net.getNodeList(), Arrays.asList(nodeA, nodeB, nodeC, group2.getGroupNode()));
    // 1 internal edge + 3 meta-edges
    assertTrue(net.getEdgeList().size() == 4);
    group2.expand(net);
    assertEqualWithoutOrder(net.getNodeList(), Arrays.asList(nodeA, nodeB, nodeC, nodeD, nodeE));
    assertEqualWithoutOrder(net.getEdgeList(), Arrays.asList(edge1, edge2, edge3, edge4, edge5, edge6));
}

Example 89 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class FilterWorker method doWork.

@Override
public void doWork(ProgressMonitor monitor) {
    if (controller == null) {
        return;
    }
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView networkView = applicationManager.getCurrentNetworkView();
    CyNetwork network;
    if (networkView != null) {
        network = networkView.getModel();
    } else {
        network = applicationManager.getCurrentNetwork();
    }
    if (network == null) {
        return;
    }
    monitor.setProgress(0);
    monitor.setStatusMessage(null);
    int nodeCount = 0;
    int edgeCount = 0;
    int counter = 0;
    long startTime = System.currentTimeMillis();
    try {
        Filter<CyNetwork, CyIdentifiable> filter = controller.getFilter();
        if (filter instanceof CompositeFilter) {
            // If we have an empty CompositeFilter, bail out.
            CompositeFilter<CyNetwork, CyIdentifiable> composite = (CompositeFilter<CyNetwork, CyIdentifiable>) filter;
            if (composite.getLength() == 0) {
                return;
            }
        }
        if (filter instanceof MemoizableTransformer) {
            ((MemoizableTransformer) filter).startCaching();
        }
        try {
            List<CyNode> nodeList = network.getNodeList();
            List<CyEdge> edgeList = network.getEdgeList();
            double total = nodeList.size() + edgeList.size();
            List<CyIdentifiable> selected = new ArrayList<>();
            List<CyIdentifiable> unselected = new ArrayList<>();
            for (CyNode node : nodeList) {
                if (monitor.isCancelled()) {
                    return;
                }
                boolean accepted = filter.accepts(network, node);
                if (accepted) {
                    selected.add(node);
                    nodeCount++;
                } else {
                    unselected.add(node);
                }
                monitor.setProgress(++counter / total);
            }
            for (CyEdge edge : edgeList) {
                if (monitor.isCancelled()) {
                    return;
                }
                boolean accepted = filter.accepts(network, edge);
                if (accepted) {
                    selected.add(edge);
                    edgeCount++;
                } else {
                    unselected.add(edge);
                }
                monitor.setProgress(++counter / total);
            }
            // now do the selection
            for (CyIdentifiable element : unselected) {
                CyRow row = network.getRow(element);
                if (row.get(CyNetwork.SELECTED, Boolean.class)) {
                    row.set(CyNetwork.SELECTED, Boolean.FALSE);
                }
            }
            for (CyIdentifiable element : selected) {
                CyRow row = network.getRow(element);
                if (!row.get(CyNetwork.SELECTED, Boolean.class)) {
                    row.set(CyNetwork.SELECTED, Boolean.TRUE);
                }
            }
        } finally {
            if (filter instanceof MemoizableTransformer) {
                ((MemoizableTransformer) filter).clearCache();
            }
        }
        if (networkView != null) {
            networkView.updateView();
        }
    } finally {
        long duration = System.currentTimeMillis() - startTime;
        monitor.setProgress(1.0);
        monitor.setStatusMessage(String.format("Selected %d %s and %d %s in %dms", nodeCount, nodeCount == 1 ? "node" : "nodes", edgeCount, edgeCount == 1 ? "edge" : "edges", duration));
    }
}

Example 90 with CyEdge

use of org.cytoscape.model.CyEdge in project cytoscape-impl by cytoscape.

the class GetEdgeAttributeTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    CyNetwork network = edgeTunable.getNetwork();
    edgeTable = getNetworkTable(network, CyEdge.class, columnTunable.getNamespace());
    edgeDataMap = new HashMap<CyIdentifiable, Map<String, Object>>();
    for (CyEdge edge : edgeTunable.getEdgeList()) {
        Map<String, Object> edgeData = getCyIdentifierData(edgeTable, edge, columnTunable.getColumnNames(edgeTable));
        if (edgeData == null || edgeData.size() == 0)
            continue;
        edgeDataMap.put(edge, edgeData);
        taskMonitor.showMessage(TaskMonitor.Level.INFO, "   Edge table values for edge " + DataUtils.getEdgeName(edgeTable, edge) + ":");
        for (String column : edgeData.keySet()) {
            if (edgeData.get(column) != null)
                taskMonitor.showMessage(TaskMonitor.Level.INFO, "        " + column + "=" + DataUtils.convertData(edgeData.get(column)));
        }
    }
}