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

Example 66 with CyNetwork

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

the class DestroyNetworkViewsAction method updateEnableState.

@Override
public void updateEnableState() {
    final List<CyNetwork> networks = serviceRegistrar.getService(CyApplicationManager.class).getSelectedNetworks();
    final CyNetworkViewManager netViewManager = serviceRegistrar.getService(CyNetworkViewManager.class);
    int count = 0;
    for (CyNetwork n : networks) count += netViewManager.getNetworkViews(n).size();
    if (count > 0)
        setName("Destroy " + count + " View" + (count == 1 ? "" : "s"));
    else
        setName("Destroy Views");
    setEnabled(count > 0);
}

Example 67 with CyNetwork

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

the class SessionHandler method postLoading.

private final void postLoading(final CySession sess) {
    NetworkList netList = null;
    final Map<String, List<File>> filesMap = sess.getAppFileListMap();
    if (filesMap != null) {
        final List<File> files = filesMap.get(APP_NAME);
        if (files != null) {
            SessionState sessState = null;
            for (File f : files) {
                if (f.getName().endsWith(SESSION_STATE_FILENAME))
                    sessState = sessionIO.read(f, SessionState.class);
                else if (f.getName().endsWith(NETWORK_LIST_FILENAME))
                    netList = sessionIO.read(f, NetworkList.class);
            }
            if (sessState != null)
                setCytoPanelStates(sessState.getCytopanels());
        }
    }
    if (netList == null) {
        // Probably a Cy2 session file, which does not provide a separate "network_list" file
        // so let's get the orders from the networks in the CySession file
        // (we just assume the Session Reader sent the networks in the correct order in a LinkedHashSet)
        final Set<CyNetwork> netSet = sess.getNetworks();
        final Map<Long, Integer> netOrder = new HashMap<>();
        int count = 0;
        for (CyNetwork n : netSet) netOrder.put(n.getSUID(), count++);
        setSessionNetworks(netOrder);
    } else {
        setSessionNetworks(netList.getNetwork(), sess);
    }
}

Example 68 with CyNetwork

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

the class SessionHandler method setSessionNetworks.

private void setSessionNetworks(final List<Network> netInfoList, final CySession sess) {
    final Map<Long, Integer> netOrder = new HashMap<>();
    for (final Network n : netInfoList) {
        // in order to retrieve the new SUID
        final CyNetwork net = sess.getObject(n.getId(), CyNetwork.class);
        if (net != null)
            netOrder.put(net.getSUID(), n.getOrder());
    }
    setSessionNetworks(netOrder);
}

Example 69 with CyNetwork

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

the class SelectFirstNeighborsNodeViewTask method run.

public void run(TaskMonitor tm) throws Exception {
    tm.setProgress(0.0);
    if (nodeView == null)
        throw new NullPointerException("node view is null");
    if (netView == null)
        throw new NullPointerException("network view is null");
    final Set<CyNode> selNodes = new HashSet<CyNode>();
    final CyNode node = nodeView.getModel();
    final CyNetwork net = netView.getModel();
    tm.setProgress(0.1d);
    selNodes.add(node);
    tm.setProgress(0.4d);
    selNodes.addAll(net.getNeighborList(node, direction));
    tm.setProgress(0.6d);
    selectUtils.setSelectedNodes(net, selNodes, true);
    tm.setProgress(0.8d);
    netView.updateView();
    tm.setProgress(1.0d);
}

Example 70 with CyNetwork

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

the class AbstractOpenSessionTask method disposeCancelledSession.

protected void disposeCancelledSession(Exception e, CySessionManager sessionManager) {
    if (reader == null)
        return;
    final CySession newSession = reader.getSession();
    if (newSession != null) {
        // Destroy any new views and networks
        for (CyNetworkView view : newSession.getNetworkViews()) view.dispose();
        CyRootNetworkManager rootNetManager = serviceRegistrar.getService(CyRootNetworkManager.class);
        final Set<CyRootNetwork> rootNetworks = new HashSet<>();
        for (CyNetwork net : newSession.getNetworks()) rootNetworks.add(rootNetManager.getRootNetwork(net));
        for (CyRootNetwork rootNet : rootNetworks) rootNet.dispose();
    }
    // Reset the Group Manager, because groups can be registered by the reader
    // TODO Remove this after groups no longer registered inside the IO bundle.
    serviceRegistrar.getService(CyGroupManager.class).reset();
    // Destroy any global tables registered by the reader
    serviceRegistrar.getService(CyTableManager.class).reset();
    // Set a new, empty session
    sessionManager.setCurrentSession(null, null);
}