Examples with CySubNetwork org.cytoscape.model.subnetwork.CySubNetwork used on opensource projects

Example 16 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class AbstractGroupTask method getGroup.

protected CyGroup getGroup(String groupName) {
    CyRootNetwork rootNet = ((CySubNetwork) net).getRootNetwork();
    Set<CyGroup> allGroups = groupMgr.getGroupSet(net);
    for (CyGroup group : allGroups) {
        CyRow groupRow = rootNet.getRow(group.getGroupNode(), CyRootNetwork.SHARED_ATTRS);
        if (groupName.length() > 5 && groupName.substring(0, 5).equalsIgnoreCase("suid:")) {
            String suidString = groupRow.get(CyNetwork.SUID, Long.class).toString();
            if (suidString != null && groupName.substring(5).equals(suidString))
                return group;
        } else if (groupName.equals(groupRow.get(CyRootNetwork.SHARED_NAME, String.class)))
            return group;
    }
    return null;
}

Example 17 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class NetworkMainPanel method getNetworkListOrder.

public Map<Long, Integer> getNetworkListOrder() {
    final Map<Long, Integer> order = new HashMap<>();
    final List<SubNetworkPanel> items = getAllSubNetworkItems();
    int count = 0;
    for (SubNetworkPanel snp : items) {
        final CySubNetwork net = snp.getModel().getNetwork();
        order.put(net.getSUID(), count++);
    }
    return order;
}

Example 18 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class NetworkMainPanel method getSubNetworkPanel.

SubNetworkPanel getSubNetworkPanel(final CyNetwork net) {
    if (net instanceof CySubNetwork) {
        final CySubNetwork subNet = (CySubNetwork) net;
        final CyRootNetwork rootNet = subNet.getRootNetwork();
        final RootNetworkPanel rootNetPanel = getRootNetworkPanel(rootNet);
        if (rootNetPanel != null)
            return rootNetPanel.getItem(subNet);
    }
    return null;
}

Example 19 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class ViewUtil method getParent.

public static CySubNetwork getParent(final CySubNetwork net, final CyServiceRegistrar serviceRegistrar) {
    final CyTable hiddenTable = net.getTable(CyNetwork.class, CyNetwork.HIDDEN_ATTRS);
    final CyRow row = hiddenTable != null ? hiddenTable.getRow(net.getSUID()) : null;
    final Long suid = row != null ? row.get(PARENT_NETWORK_COLUMN, Long.class) : null;
    if (suid != null) {
        final CyNetwork parent = serviceRegistrar.getService(CyNetworkManager.class).getNetwork(suid);
        if (parent instanceof CySubNetwork)
            return (CySubNetwork) parent;
    }
    return null;
}

Example 20 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project cytoscape-impl by cytoscape.

the class GraphMLReader method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    this.taskMonitor = taskMonitor;
    try {
        final SAXParserFactory spf = SAXParserFactory.newInstance();
        spf.setNamespaceAware(true);
        final SAXParser sp = spf.newSAXParser();
        final XMLReader xmlReader = sp.getXMLReader();
        CyRootNetwork root = getRootNetwork();
        final CySubNetwork newNetwork;
        if (root != null) {
            newNetwork = root.addSubNetwork();
        } else {
            // Need to create new network with new root.
            newNetwork = (CySubNetwork) cyNetworkFactory.createNetwork();
            root = newNetwork.getRootNetwork();
        }
        parser = new GraphMLParser(taskMonitor, cyNetworkFactory, cyRootNetworkManager, root, newNetwork);
        xmlReader.setContentHandler(parser);
        final InputSource inputSource = new InputSource(inputStream);
        inputSource.setEncoding("UTF-8");
        xmlReader.parse(inputSource);
    } finally {
        if (inputStream != null) {
            inputStream.close();
            inputStream = null;
        }
    }
}