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

Example 11 with CyEdge

use of org.cytoscape.model.CyEdge in project EnrichmentMapApp by BaderLab.

the class TestUtils method getSignatureEdges.

public static Map<String, CyEdge> getSignatureEdges(CyNetwork network, String prefix, String sigSetName) {
    Map<String, CyEdge> edges = new HashMap<>();
    for (CyEdge edge : network.getEdgeList()) {
        CyRow row = network.getRow(edge);
        String sigName = Columns.EDGE_SIG_DATASET.get(row, prefix);
        if (sigName != null && sigName.equals(sigSetName)) {
            edges.put(row.get(CyNetwork.NAME, String.class), edge);
        }
    }
    return edges;
}

Example 12 with CyEdge

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

the class CloneNetworkTask method cloneEdge.

private CyEdge cloneEdge(final CyNetwork origNet, final CyNetwork newNet, final CyEdge origEdge) {
    if (orig2NewEdgeMap.containsKey(origEdge))
        return orig2NewEdgeMap.get(origEdge);
    final CyNode newSource = orig2NewNodeMap.get(origEdge.getSource());
    final CyNode newTarget = orig2NewNodeMap.get(origEdge.getTarget());
    final boolean newDirected = origEdge.isDirected();
    final CyEdge newEdge = newNet.addEdge(newSource, newTarget, newDirected);
    new2OrigEdgeMap.put(newEdge, origEdge);
    orig2NewEdgeMap.put(origEdge, newEdge);
    cloneRow(newNet, CyEdge.class, origNet.getRow(origEdge, CyNetwork.LOCAL_ATTRS), newNet.getRow(newEdge, CyNetwork.LOCAL_ATTRS));
    cloneRow(newNet, CyEdge.class, origNet.getRow(origEdge, CyNetwork.HIDDEN_ATTRS), newNet.getRow(newEdge, CyNetwork.HIDDEN_ATTRS));
    return newEdge;
}

Example 13 with CyEdge

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

the class GroupUtils method addGroupToNetwork.

public static void addGroupToNetwork(CyGroup group, CyNetwork origNet, CyNetwork newNet) {
    CyNetwork groupNetwork = group.getGroupNetwork();
    Dimension d = getPosition(origNet, group, groupNetwork.getSUID(), CyNetwork.class);
    updatePosition(newNet, group, groupNetwork.getSUID(), CyNetwork.class, d);
    for (CyNode node : group.getNodeList()) {
        Long nodeSUID = node.getSUID();
        d = getPosition(origNet, group, nodeSUID, CyNode.class);
        updatePosition(newNet, group, nodeSUID, CyNode.class, d);
        // This helps out collapse
        ((CySubNetwork) newNet).addNode(node);
    }
    for (CyEdge edge : group.getInternalEdgeList()) {
        // This helps out collapse
        ((CySubNetwork) newNet).addEdge(edge);
    }
    for (CyEdge edge : group.getExternalEdgeList()) {
        // This helps out collapse
        ((CySubNetwork) newNet).addEdge(edge);
    }
    group.addGroupToNetwork(newNet);
    group.collapse(newNet);
}

Example 14 with CyEdge

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

the class AddEdgeTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    if (network == null) {
        network = serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetwork();
        if (network == null) {
            taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Network must be specified for add command");
            return;
        }
    }
    if (sourceName == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Source node name must be specified for add command");
        return;
    }
    if (targetName == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Target node name must be specified for add command");
        return;
    }
    // Find the source and target nodes
    CyNode source = null;
    CyNode target = null;
    for (CyNode node : network.getNodeList()) {
        String nodeName = network.getRow(node).get(CyNetwork.NAME, String.class);
        if (sourceName.equals(nodeName))
            source = node;
        else if (targetName.equals(nodeName))
            target = node;
        if (source != null && target != null)
            break;
    }
    if (source == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Can't find source node named '" + sourceName + "'");
        return;
    }
    if (target == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Can't find target node named '" + targetName + "'");
        return;
    }
    newEdge = network.addEdge(source, target, isDirected);
    if (name != null) {
        network.getRow(newEdge).set(CyNetwork.NAME, name);
        network.getRow(newEdge).set(CyRootNetwork.SHARED_NAME, name);
    }
    cyEventHelper.flushPayloadEvents();
    if (networkViewManager.viewExists(network)) {
        for (CyNetworkView view : networkViewManager.getNetworkViews(network)) {
            View<CyEdge> edgeView = view.getEdgeView(newEdge);
            VisualStyle style = visualMappingManager.getVisualStyle(view);
            if (style != null) {
                style.apply(network.getRow(newEdge), edgeView);
            }
            // Not sure why we need to refresh the view for edges and not nodes, but apparently we do
            view.updateView();
        }
    }
    cyEventHelper.flushPayloadEvents();
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Added edge " + newEdge.toString() + " to network");
}

Example 15 with CyEdge

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

the class AddTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    network = nodesAndEdges.getNetwork();
    if (network == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Network must be specified for add command");
        return;
    }
    nodeList = nodesAndEdges.getNodeList(false);
    edgeList = nodesAndEdges.getEdgeList(false);
    if ((nodeList == null || nodeList.size() == 0) && (edgeList == null || edgeList.size() == 0)) {
        taskMonitor.showMessage(TaskMonitor.Level.WARN, "Nothing to add");
        return;
    }
    int nodeCount = nodeList.size();
    int edgeCount = 0;
    for (CyNode node : nodeList) ((CySubNetwork) network).addNode(node);
    // nodes and "all" edges
    for (CyEdge edge : edgeList) {
        if (network.containsNode(edge.getSource()) && network.containsNode(edge.getTarget())) {
            ((CySubNetwork) network).addEdge(edge);
            edgeCount++;
        }
    }
    eventHelper.flushPayloadEvents();
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Added " + nodeCount + " nodes and " + edgeCount + " edges to network " + network.toString());
}