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

Example 36 with CyEdge

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

the class NewNetworkCommandTask method getNodes.

/**
 * Returns the selected nodes plus all nodes that connect the selected edges
 */
@Override
Set<CyNode> getNodes(final CyNetwork net) {
    if (nodes == null) {
        nodes = new HashSet<CyNode>(nodeList.getValue());
        if (edgeList != null && edgeList.getValue() != null) {
            final Collection<CyEdge> selectedEdges = edgeList.getValue();
            for (final CyEdge e : selectedEdges) {
                nodes.add(e.getSource());
                nodes.add(e.getTarget());
            }
        }
    }
    return nodes;
}

Example 37 with CyEdge

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

the class NewNetworkSelectedNodesEdgesTask method getNodes.

/**
 * Returns the selected nodes plus all nodes that connect the selected edges
 */
@Override
Set<CyNode> getNodes(final CyNetwork net) {
    if (nodes == null) {
        nodes = new HashSet<>(CyTableUtil.getNodesInState(net, CyNetwork.SELECTED, true));
        final Collection<CyEdge> selectedEdges = getEdges(net);
        for (final CyEdge e : selectedEdges) {
            nodes.add(e.getSource());
            nodes.add(e.getTarget());
        }
    }
    return nodes;
}

Example 38 with CyEdge

use of org.cytoscape.model.CyEdge 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;
}

Example 39 with CyEdge

use of org.cytoscape.model.CyEdge 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 40 with CyEdge

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

the class InvertSelectedEdgesTask method run.

@Override
public void run(final TaskMonitor tm) {
    tm.setTitle("Invert Edge Selection");
    tm.setProgress(0.0);
    final Collection<CyNetworkView> views = networkViewManager.getNetworkViews(network);
    CyNetworkView view = null;
    if (views.size() != 0)
        view = views.iterator().next();
    undoSupport.postEdit(new SelectionEdit(eventHelper, "Invert Selected Edges", network, view, SelectionEdit.SelectionFilter.EDGES_ONLY));
    tm.setStatusMessage("Inverting Edge Selection...");
    tm.setProgress(0.2);
    for (final CyEdge e : network.getEdgeList()) {
        if (network.getRow(e).get(CyNetwork.SELECTED, Boolean.class))
            network.getRow(e).set(CyNetwork.SELECTED, false);
        else
            network.getRow(e).set(CyNetwork.SELECTED, true);
    }
    tm.setStatusMessage("Updating View...");
    tm.setProgress(0.6);
    eventHelper.flushPayloadEvents();
    tm.setProgress(0.8);
    updateView();
    tm.setProgress(1.0);
}