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

Example 66 with CyEdge

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

the class CySubNetworkTest method testAddNewEdgeEventBeforeNetworkAdd.

@Test
public void testAddNewEdgeEventBeforeNetworkAdd() {
    CySubNetwork sub = root.addSubNetwork();
    CyNode nx1 = sub.addNode();
    CyNode nx2 = sub.addNode();
    CyEdge ex1 = sub.addEdge(nx1, nx2, false);
    Object payload = deh.getLastPayload();
    assertNull(payload);
}

Example 67 with CyEdge

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

the class VizMapperMediator method createPreviewNetworkView.

private void createPreviewNetworkView() {
    // Create dummy view first
    final CyNetwork net = servicesUtil.get(CyNetworkFactory.class).createNetworkWithPrivateTables(SavePolicy.DO_NOT_SAVE);
    final CyNode source = net.addNode();
    final CyNode target = net.addNode();
    net.getRow(source).set(CyNetwork.NAME, "Source");
    net.getRow(target).set(CyNetwork.NAME, "Target");
    final CyEdge edge = net.addEdge(source, target, true);
    net.getRow(edge).set(CyNetwork.NAME, "Source (interaction) Target");
    net.getRow(net).set(CyNetwork.NAME, "Default Appearance");
    final CyNetworkView view = servicesUtil.get(CyNetworkViewFactory.class).createNetworkView(net);
    // Set node locations
    view.getNodeView(source).setVisualProperty(NODE_X_LOCATION, 0d);
    view.getNodeView(source).setVisualProperty(NODE_Y_LOCATION, 0d);
    view.getNodeView(target).setVisualProperty(NODE_X_LOCATION, 150d);
    view.getNodeView(target).setVisualProperty(NODE_Y_LOCATION, 20d);
    previewNetView = view;
}

Example 68 with CyEdge

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

the class GetGroupTask method groupJSON.

public String groupJSON(CyNetwork network, CyGroup group) {
    this.jsonUtil = serviceRegistrar.getService(CyJSONUtil.class);
    long suid = group.getGroupNode().getSUID();
    List<CyNode> nodes = group.getNodeList();
    List<CyEdge> internalEdges = group.getInternalEdgeList();
    Set<CyEdge> externalEdges = group.getExternalEdgeList();
    CyRow groupRow = ((CySubNetwork) net).getRootNetwork().getRow(group.getGroupNode(), CyRootNetwork.SHARED_ATTRS);
    String name = groupRow.get(CyRootNetwork.SHARED_NAME, String.class);
    String result = "{\"group\":" + suid + "," + "\"name\":\"" + name + "\",";
    result += "\"nodes\":" + jsonUtil.cyIdentifiablesToJson(nodes) + ",";
    result += "\"internalEdges\":" + jsonUtil.cyIdentifiablesToJson(internalEdges) + ",";
    result += "\"externalEdges\":" + jsonUtil.cyIdentifiablesToJson(externalEdges) + ",";
    result += "\"collapsed\":";
    if (group.isCollapsed(network))
        result += "true";
    else
        result += "false";
    result += "}";
    return result;
}

Example 69 with CyEdge

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

the class GroupEdit method createShadowGroup.

private void createShadowGroup(CyGroup group) {
    // Get the nodes, edges, and external edges
    nodeMap.put(group, group.getNodeList());
    List<CyEdge> edgesList = new ArrayList<CyEdge>(group.getInternalEdgeList());
    edgesList.addAll(group.getExternalEdgeList());
    edgesMap.put(group, edgesList);
    // Get the networks
    networkMap.put(group, new ArrayList<CyNetwork>(group.getNetworkSet()));
    // Get the collapse set
    List<CyNetwork> collapseList = new ArrayList<CyNetwork>();
    for (CyNetwork net : group.getNetworkSet()) {
        if (group.isCollapsed(net)) {
            collapseList.add(net);
        }
    }
    collapseMap.put(group, collapseList);
}

Example 70 with CyEdge

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

the class RemoveFromGroupTask method run.

@Override
public void run(TaskMonitor tm) throws Exception {
    net = nodesAndEdges.getNetwork();
    if (groupName == null) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Group must be specified");
        return;
    }
    CyGroup grp = getGroup(groupName);
    if (grp == null) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Can't find group '" + groupName + "' in network: " + net.toString());
        return;
    }
    List<CyEdge> edgeList = nodesAndEdges.getEdgeList(false);
    List<CyNode> nodeList = nodesAndEdges.getNodeList(false);
    if (edgeList == null && nodeList == null) {
        tm.showMessage(TaskMonitor.Level.ERROR, "Nothing to remove");
        return;
    }
    int edges = 0;
    if (edgeList != null)
        edges = edgeList.size();
    int nodes = 0;
    if (nodeList != null)
        nodes = nodeList.size();
    tm.showMessage(TaskMonitor.Level.INFO, "Removing " + nodes + " nodes and " + edges + " edges from group " + getGroupDesc(grp));
    if (edgeList != null && edgeList.size() > 0) {
        grp.removeEdges(edgeList);
    }
    if (nodeList != null && nodeList.size() > 0) {
        grp.removeNodes(nodeList);
    }
    tm.showMessage(TaskMonitor.Level.INFO, "Removed " + nodes + " nodes and " + edges + " edges from group " + getGroupDesc(grp));
}