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

Example 76 with CyNetwork

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

the class GetEdgePropertiesTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    edgePropertiesMap = new HashMap<CyEdge, Map<String, VisualPropertyObjectTuple>>();
    CyNetwork network = edgeTunable.getNetwork();
    if (propertyList == null || propertyList.length() == 0) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Property list must be specified");
        return;
    }
    // Get the list of properties
    String[] props = propertyList.split(",");
    for (CyEdge edge : edgeTunable.getEdgeList()) {
        taskMonitor.showMessage(TaskMonitor.Level.INFO, "   Edge property values for edge " + DataUtils.getEdgeName(network.getDefaultEdgeTable(), edge) + ":");
        Map<String, VisualPropertyObjectTuple> propertyMap = new HashMap<String, VisualPropertyObjectTuple>();
        for (String property : props) {
            try {
                VisualProperty vp = getProperty(network, edge, property.trim());
                Object value = getPropertyValue(network, edge, vp);
                if (value != null) {
                    taskMonitor.showMessage(TaskMonitor.Level.INFO, "        " + vp.getDisplayName() + "=" + value.toString());
                    propertyMap.put(vp.getIdString(), new VisualPropertyObjectTuple(vp, value));
                }
            } catch (Exception e) {
                taskMonitor.showMessage(TaskMonitor.Level.ERROR, e.getMessage());
                return;
            }
        }
        edgePropertiesMap.put(edge, propertyMap);
    }
}

Example 77 with CyNetwork

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

the class UnGroupNodesTaskFactoryImpl method isReady.

public boolean isReady(CyNetworkView netView) {
    if (netView == null) {
        return false;
    }
    // Get all of the selected nodes
    CyNetwork net = netView.getModel();
    final List<CyNode> selNodes = CyTableUtil.getNodesInState(net, CyNetwork.SELECTED, true);
    if (getGroups(net, selNodes).size() > 0)
        return true;
    return false;
}

Example 78 with CyNetwork

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

the class UnGroupNodesTaskFactoryImpl method createTaskIterator.

public TaskIterator createTaskIterator(CyNetworkView netView) {
    CyNetwork net = netView.getModel();
    final List<CyNode> selNodes = CyTableUtil.getNodesInState(net, CyNetwork.SELECTED, true);
    Set<CyGroup> groups = getGroups(net, selNodes);
    return new TaskIterator(new UnGroupNodesTask(undoSupport, netView.getModel(), factory, groups, mgr, netView));
}

Example 79 with CyNetwork

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

the class HideFromSelectionTask method run.

@Override
public void run(final TaskMonitor tm) {
    tm.setProgress(0.0);
    final CyNetwork network = view.getModel();
    final List<CyIdentifiable> elements = new ArrayList<>();
    List<CyNode> nodes = null;
    List<CyEdge> edges = null;
    if (hideNodes) {
        nodes = CyTableUtil.getNodesInState(network, CyNetwork.SELECTED, selectionValue);
        elements.addAll(nodes);
    }
    tm.setProgress(0.1);
    if (hideEdges) {
        edges = CyTableUtil.getEdgesInState(network, CyNetwork.SELECTED, selectionValue);
        elements.addAll(edges);
    }
    final UndoSupport undoSupport = serviceRegistrar.getService(UndoSupport.class);
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
    undoSupport.postEdit(new HideEdit(description, view, elements, false, eventHelper, vmMgr));
    tm.setProgress(0.4);
    if (nodes != null)
        HideUtils.setVisibleNodes(nodes, false, view);
    tm.setProgress(0.6);
    if (edges != null)
        HideUtils.setVisibleEdges(edges, false, view);
    tm.setProgress(0.8);
    VisualStyle style = vmMgr.getVisualStyle(view);
    for (CyIdentifiable e : elements) {
        View<? extends CyIdentifiable> ev = null;
        if (e instanceof CyNode)
            ev = view.getNodeView((CyNode) e);
        else if (e instanceof CyEdge)
            ev = view.getEdgeView((CyEdge) e);
        if (ev != null)
            style.apply(network.getRow(e), ev);
    }
    view.updateView();
    tm.setProgress(1.0);
}

Example 80 with CyNetwork

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

the class GroupNodesTaskFactoryImpl method isReady.

public boolean isReady(View<CyNode> nodeView, CyNetworkView netView) {
    if (nodeView == null || netView == null)
        return false;
    // Get all of the selected nodes
    CyNetwork net = netView.getModel();
    final List<CyNode> selNodes = CyTableUtil.getNodesInState(net, CyNetwork.SELECTED, true);
    return (selNodes.size() > 1);
}