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

Example 71 with CyNetwork

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

the class NewEmptyNetworkTask method run.

@Override
public void run(final TaskMonitor tm) {
    tm.setProgress(0.0);
    final String networkCollectionName = rootNetworkList.getSelectedValue();
    if (networkCollectionName == null || networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
        // This is a new network collection, create a root network and a subnetwork, which is a base subnetwork
        subNetwork = (CySubNetwork) netFactory.createNetwork();
    } else {
        // Add a new subNetwork to the given collection
        subNetwork = this.name2RootMap.get(networkCollectionName).addSubNetwork();
    }
    tm.setProgress(0.2);
    final String networkName = namingUtil.getSuggestedNetworkTitle(name);
    subNetwork.getRow(subNetwork).set(CyNetwork.NAME, networkName);
    if (networkCollectionName == null || networkCollectionName.equalsIgnoreCase(CRERATE_NEW_COLLECTION_STRING)) {
        // Set the name of new root network
        final CyNetwork rootNetwork = subNetwork.getRootNetwork();
        rootNetwork.getRow(rootNetwork).set(CyNetwork.NAME, networkName);
    }
    NetworkViewRenderer nvRenderer = null;
    try {
        nvRenderer = renderers.getSelectedValue();
    } catch (ClassCastException cce) {
        tm.showMessage(TaskMonitor.Level.WARN, "Unknown renderer: " + renderers.getSelectedValue() + " using default renderer.");
    }
    if (nvRenderer == null)
        nvRenderer = appMgr.getDefaultNetworkViewRenderer();
    final CyNetworkViewFactory netViewFactory = nvRenderer.getNetworkViewFactory();
    tm.setProgress(0.4);
    view = netViewFactory.createNetworkView(subNetwork);
    tm.setProgress(0.6);
    netMgr.addNetwork(subNetwork, false);
    appMgr.setCurrentNetwork(subNetwork);
    tm.setProgress(0.8);
    // get the current style before registering the view!
    final VisualStyle style = vmMgr.getCurrentVisualStyle();
    netViewMgr.addNetworkView(view);
    tm.setProgress(0.9);
    applyVisualStyle(style);
    tm.setProgress(1.0);
}

Example 72 with CyNetwork

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

the class RegisterNetworkTask method run.

@Override
public void run(TaskMonitor tm) throws Exception {
    tm.setProgress(0.0);
    for (CyNetwork network : networks) {
        if (!networkManager.networkExists(network.getSUID()))
            networkManager.addNetwork(network, false);
    }
    tm.setProgress(0.1);
    if (views != null) {
        for (CyNetworkView view : views) {
            if (view != null) {
                networkViewManager.addNetworkView(view, false);
                tm.setProgress(0.2);
                if (style != null) {
                    vmm.setVisualStyle(style, view);
                    tm.setProgress(0.8);
                }
                view.updateView();
            }
        }
    }
    if (views != null) {
        appMgr.setCurrentNetworkView(views.get(0));
        appMgr.setSelectedNetworkViews(views);
        tm.setProgress(0.9);
    } else {
        appMgr.setCurrentNetwork(networks.get(0));
    }
    tm.setProgress(1.0);
}

Example 73 with CyNetwork

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

the class ExportSelectedNetworkTaskFactoryImpl method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView view = applicationManager.getCurrentNetworkView();
    if (view != null)
        return getExportNetworkViewTaskFactory().createTaskIterator(view);
    CyNetwork network = applicationManager.getCurrentNetwork();
    if (network != null)
        return getExportNetworkTaskFactory().createTaskIterator(network);
    return null;
}

Example 74 with CyNetwork

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

the class ExportAsWebArchiveTaskFactory method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    final Set<CyNetwork> networks = networkManager.getNetworkSet();
    boolean showWarning = false;
    for (final CyNetwork network : networks) {
        final int nodeCount = network.getNodeCount();
        final int edgeCount = network.getEdgeCount();
        if (nodeCount > TH || edgeCount > TH) {
            showWarning = true;
            break;
        }
    }
    final ExportAsWebArchiveTask exportTask = new ExportAsWebArchiveTask(fullWriterFactory, simpleWriterFactory, zippedWriterFactory, applicationManager, sessionManager);
    if (showWarning) {
        return new TaskIterator(new ShowWarningTask(exportTask));
    } else {
        return new TaskIterator(exportTask);
    }
}

Example 75 with CyNetwork

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

the class AbstractPropertyTask method getPropertyValue.

public Object getPropertyValue(CyNetwork network, CyIdentifiable target, VisualProperty vp) {
    CyNetworkView networkView = getViewForNetwork(network);
    Class<? extends CyIdentifiable> vpTargetType = vp.getTargetDataType();
    if (target instanceof CyNetwork) {
        if (vpTargetType != CyNetwork.class)
            throw new RuntimeException("Property '" + vp.getDisplayName() + "' not available for networks");
        return networkView.getVisualProperty(vp);
    } else if (target instanceof CyNode) {
        if (vpTargetType != CyNode.class)
            throw new RuntimeException("Property '" + vp.getDisplayName() + "' not available for nodes");
        View<CyNode> nodeView = networkView.getNodeView((CyNode) target);
        return nodeView.getVisualProperty(vp);
    } else if (target instanceof CyEdge) {
        if (vpTargetType != CyEdge.class)
            throw new RuntimeException("Property '" + vp.getDisplayName() + "' not available for edges");
        View<CyEdge> edgeView = networkView.getEdgeView((CyEdge) target);
        return edgeView.getVisualProperty(vp);
    }
    return null;
}