Examples with CyGroup org.cytoscape.group.CyGroup used on opensource projects

Example 11 with CyGroup

use of org.cytoscape.group.CyGroup in project cytoscape-impl by cytoscape.

the class CyGroupImpl method updateMetaEdges.

/**
 * This method is the central method for the creation and maintenance of a
 * meta-node.  Essentially, it is responsible for creating all of the meta-edges
 * that connect this meta-node to external nodes.
 *
 * Basic approach:
 *  for each external edge:
 *	add a meta-edge to the parter
 *	if the partner is a group and the group is in our network:
 *	  add ourselves to the group's outer edges list (recursively)
 *	  add ourselves to the partner's meta edge list
 *	if the partner is in a group:
 *	  add ourselves to the group's meta edge list
 */
private void updateMetaEdges(boolean ignoreMetaEdges) {
    synchronized (lock) {
        metaEdges = new HashMap<CyEdge, CyEdge>();
        Set<CyGroup> partnersSeen = new HashSet<CyGroup>();
        // System.out.println("Updating metaEdges: ignoreMetaEdges = "+ignoreMetaEdges);
        // long simpleMeta = 0L;
        // long recursiveMeta1 = 0L;
        // long recursiveMeta2 = 0L;
        // System.out.println(this.toString()+" updating meta edges");
        // We need to use a list iterator because we might need to add new
        // edges to our outer edge list and we want to add them to the
        // iterator to re-examine them
        ListIterator<CyEdge> iterator = (new ArrayList<CyEdge>(externalEdges)).listIterator();
        while (iterator.hasNext()) {
            // long timeStamp = System.currentTimeMillis();
            CyEdge edge = iterator.next();
            CyNode node = getPartner(edge);
            if (ignoreMetaEdges && isMeta(edge)) {
                this.addMetaEdge(edge, edge);
                continue;
            }
            // If the edge is already on our group node, don't create a metaedge for it
            if (edge.getSource() == groupNode || edge.getTarget() == groupNode)
                continue;
            // but there you have it...
            if (rootNetwork.containsEdge(edge.getSource(), groupNode) && metaAlreadyExists(edge.getSource(), groupNode)) {
                this.addMetaEdge(edge, getMetaEdge(edge.getSource(), groupNode));
                continue;
            }
            if (rootNetwork.containsEdge(groupNode, edge.getTarget()) && metaAlreadyExists(groupNode, edge.getTarget())) {
                this.addMetaEdge(edge, getMetaEdge(groupNode, edge.getTarget()));
                continue;
            }
            // Create the meta-edge to the external node, but maintain the directionality
            // of the original edge
            CyEdge metaEdge = createMetaEdge(edge, node, groupNode);
            if (metaEdge == null)
                continue;
            // System.out.println("MetaEdge: "+metaEdge);
            this.addMetaEdge(edge, metaEdge);
            for (CyNetwork net : networkSet) {
                // timeStamp = System.currentTimeMillis();
                if (net.equals(rootNetwork))
                    continue;
                // Is the partner a group?
                CyGroup metaPartner = mgr.getGroup(node, net);
                if (metaPartner != null && !partnersSeen.contains(metaPartner)) {
                    // Recursively add links to the appropriate children
                    // System.out.println("Adding partner edges for "+metaPartner);
                    addPartnerEdges(metaPartner, net, partnersSeen);
                    ((CyGroupImpl) metaPartner).addMetaEdge(edge, metaEdge);
                }
            // recursiveMeta1 += System.currentTimeMillis()-timeStamp;
            // timeStamp = System.currentTimeMillis();
            /*
					// Now, handle the case where the partner is a member of one or more groups
					List<CyGroup> nodeGroups = mgr.getGroupsForNode(node);
					if (nodeGroups != null && nodeGroups.size() > 0) {
						// TODO: Should we skip this and handle this at collapse/expand time?
						addPartnerMetaEdges(net, edge, nodeGroups, metaEdge);
					}
					*/
            // recursiveMeta2 += System.currentTimeMillis()-timeStamp;
            }
        }
    // System.out.println("Simple Meta processing took: "+simpleMeta+"ms");
    // System.out.println("Recursive (partner edge) processing took: "+recursiveMeta1+"ms");
    // System.out.println("Recursive (partner meta edge) processing took: "+recursiveMeta2+"ms");
    }
}

Example 12 with CyGroup

use of org.cytoscape.group.CyGroup in project cytoscape-impl by cytoscape.

the class GroupViewDoubleClickListener method isReady.

public boolean isReady(View<CyNode> nodeView, CyNetworkView networkView) {
    CyNode node = nodeView.getModel();
    CyNetwork net = networkView.getModel();
    // Do we care about this double-click?
    if (cyGroupManager.isGroup(node, net)) {
        return true;
    } else {
        List<CyGroup> groups = cyGroupManager.getGroupsForNode(node);
        for (CyGroup g : groups) {
            // Make sure we're in the right network
            if (cyGroupManager.isGroup(g.getGroupNode(), net)) {
                return true;
            }
        }
    }
    return false;
}

Example 13 with CyGroup

use of org.cytoscape.group.CyGroup in project cytoscape-impl by cytoscape.

the class GroupViewDoubleClickListener method createTaskIterator.

@Override
public TaskIterator createTaskIterator(View<CyNode> nodeView, CyNetworkView networkView) {
    CyNode node = nodeView.getModel();
    CyNetwork net = networkView.getModel();
    CyGroup group = null;
    // Get the double click action for this group
    if (cyGroupManager.isGroup(node, net))
        group = cyGroupManager.getGroup(node, net);
    else {
        List<CyGroup> groups = cyGroupManager.getGroupsForNode(node);
        for (CyGroup g : groups) {
            // Make sure we're in the right network
            if (cyGroupManager.isGroup(g.getGroupNode(), net)) {
                group = g;
                break;
            }
        }
    }
    DoubleClickAction action = cyGroupSettings.getDoubleClickAction(group);
    if (action == DoubleClickAction.EXPANDCONTRACT) {
        // that group.
        return new TaskIterator(new CollapseGroupTask(nodeView, networkView));
    } else if (action == DoubleClickAction.SELECT) {
        // If all members of the group are selected, deselect that group
        return new TaskIterator(new SelectGroupTask(nodeView, networkView));
    } else {
        return new TaskIterator(new NullTask());
    }
}

Example 14 with CyGroup

use of org.cytoscape.group.CyGroup in project cytoscape-impl by cytoscape.

the class GroupViewCollapseHandler method handleEvent.

/**
 * We need to do some fixup after we load the session for compound nodes.
 * When the session gets loaded, we don't (yet) have a view.  We need to
 * go through and kick update things to work properly if we have a view
 * after the session gets loaded.
 */
@Override
public void handleEvent(SessionLoadedEvent e) {
    getServices();
    // System.out.println("SessionLoadedEvent");
    try {
        // For each network
        for (CyNetworkView networkView : e.getLoadedSession().getNetworkViews()) {
            CyNetwork network = networkView.getModel();
            // For each group
            for (CyGroup group : cyGroupManager.getGroupSet(network)) {
                GroupViewType groupViewType = cyGroupSettings.getGroupViewType(group);
                // If the group is a compound node and if it is expanded,
                if (groupViewType.equals(GroupViewType.COMPOUND) || groupViewType.equals(GroupViewType.SINGLENODE)) {
                    // If it's really collapsed, all of our children will
                    // be absent from the network.  Check that first
                    boolean haveChildren = true;
                    for (CyNode node : group.getNodeList()) {
                        if (!network.containsNode(node)) {
                            haveChildren = false;
                            break;
                        }
                    }
                    if (haveChildren && network.containsNode(group.getGroupNode())) {
                        // At this point, because of the way we create the
                        // group, it will think it's collapsed.  Change
                        // that.
                        ((CyGroupImpl) group).setCollapsed(network, false);
                        ((CyGroupImpl) group).setGroupNodeShown(network, true);
                        try {
                            // OK, now activate the group
                            activateCompoundNode(group, networkView);
                        } catch (Exception rtree) {
                            // We may get an RTree exception under rare
                            // circumstances.
                            rtree.printStackTrace();
                        }
                    }
                }
            }
        }
    } catch (Exception ex) {
        ex.printStackTrace();
    }
}

Example 15 with CyGroup

use of org.cytoscape.group.CyGroup in project cytoscape-impl by cytoscape.

the class GroupViewCollapseHandler method handleEvent.

@Override
public void handleEvent(GroupAboutToCollapseEvent e) {
    getServices();
    CyNetwork network = e.getNetwork();
    CyGroup group = e.getSource();
    CyRootNetwork rootNetwork = group.getRootNetwork();
    final Collection<CyNetworkView> views = cyNetworkViewManager.getNetworkViews(network);
    CyNetworkView view = null;
    if (views.size() == 0)
        return;
    for (CyNetworkView v : views) {
        if (v.getRendererId().equals("org.cytoscape.ding")) {
            view = v;
        }
    }
    if (view == null)
        return;
    GroupViewType groupViewType = cyGroupSettings.getGroupViewType(group);
    if (e.collapsing()) {
        // Calculate the center position of all of the
        // member nodes
        Dimension center = ViewUtils.calculateCenter(view, group.getNodeList());
        if (center != null) {
            // Save it in the groupNode attribute
            ViewUtils.updateGroupLocation(network, group, center);
            // save it in the node's attribute
            for (CyNode node : group.getNodeList()) {
                if (!network.containsNode(node))
                    continue;
                Dimension offset = ViewUtils.calculateOffset(center, view, node);
                ViewUtils.updateNodeOffset(network, group, node, offset);
            }
        }
    } else {
        // Get the current position of the groupNode
        View<CyNode> nView = view.getNodeView(group.getGroupNode());
        if (nView == null)
            return;
        double x = nView.getVisualProperty(xLoc);
        double y = nView.getVisualProperty(yLoc);
        // Save it in the groupNode attribute
        ViewUtils.updateGroupLocation(network, group, x, y);
    }
}