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

Example 36 with CySubNetwork

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

the class GroupUtil method prepareGroupsForSerialization.

public void prepareGroupsForSerialization(final Collection<CyNetwork> networks) {
    if (networks == null)
        return;
    addedNodes = new HashMap<>();
    for (CyNetwork net : networks) {
        if (!(net instanceof CySubNetwork))
            continue;
        // Get all of our groups
        final CyGroupManager groupMgr = serviceRegistrar.getService(CyGroupManager.class);
        Set<CyGroup> groupSet = groupMgr.getGroupSet(net);
        // For each group, save the list of external edges
        for (CyGroup group : groupSet) {
            updateExternalEdgeAttribute(group);
            updateCollapsedGroupsAttribute(group);
            updateGroupAttribute(net, group);
        }
    }
}

Example 37 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project clusterMaker2 by RBVI.

the class ClusterManagerImpl method createGroup.

public CyGroup createGroup(CyNetwork network, String name, List<CyNode> nodeList, List<CyEdge> edgeList, boolean registerGroup) {
    CyGroup group = groupFactory.createGroup(network, nodeList, edgeList, registerGroup);
    if (group != null) {
        CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
        // The name of the group node is the name of the group
        rootNetwork.getRow(group.getGroupNode()).set(CyNetwork.NAME, name);
        rootNetwork.getRow(group.getGroupNode(), CyRootNetwork.SHARED_ATTRS).set(CyRootNetwork.SHARED_NAME, name);
    }
    return group;
}

Example 38 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project clusterMaker2 by RBVI.

the class ClusterManagerImpl method unlinkNetworkSelection.

public void unlinkNetworkSelection(CyNetwork network) {
    if (!isLinked(network))
        return;
    CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
    unregisterService(linkedNetworks.get(rootNetwork), RowsSetListener.class);
    linkedNetworks.remove(rootNetwork);
}

Example 39 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project clusterMaker2 by RBVI.

the class ClusterManagerImpl method linkNetworkSelection.

public void linkNetworkSelection(CyNetwork network) {
    if (isLinked(network))
        return;
    CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
    CyEventHelper helper = serviceRegistrar.getService(CyEventHelper.class);
    NetworkSelectionLinker linker = new NetworkSelectionLinker(rootNetwork, helper, this);
    registerService(linker, RowsSetListener.class, new Properties());
    linkedNetworks.put(rootNetwork, linker);
}

Example 40 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project clusterMaker2 by RBVI.

the class NetworkSelectionLinker method handleEvent.

public void handleEvent(RowsSetEvent e) {
    if (!e.containsColumn(CyNetwork.SELECTED) || ignoreSelection)
        return;
    // System.out.println("Select");
    CyNetworkView currentNetworkView = clusterManager.getNetworkView();
    ignoreSelection = true;
    Map<CyNetwork, Boolean> stateMap = new HashMap<CyNetwork, Boolean>();
    for (CySubNetwork subNetwork : rootNetwork.getSubNetworkList()) {
        if (e.getSource().equals(subNetwork.getTable(CyNode.class, CyNetwork.LOCAL_ATTRS))) {
            for (RowSetRecord record : e.getColumnRecords(CyNetwork.SELECTED)) {
                Long suid = record.getRow().get(CyIdentifiable.SUID, Long.class);
                Boolean value = (Boolean) record.getValue();
                for (CySubNetwork sub2 : rootNetwork.getSubNetworkList()) {
                    if (subNetwork.equals(sub2) || sub2.getDefaultNodeTable().getRow(suid) == null)
                        continue;
                    // System.out.println("Selecting row "+suid);
                    sub2.getDefaultNodeTable().getRow(suid).set(CyNetwork.SELECTED, value);
                }
            }
        }
        if (viewManager.viewExists(subNetwork)) {
            for (CyNetworkView view : viewManager.getNetworkViews(subNetwork)) {
                if (!view.equals(currentNetworkView)) {
                    view.updateView();
                }
            }
        }
    }
    eventHelper.flushPayloadEvents();
    ignoreSelection = false;
}