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

Example 66 with CySubNetwork

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

the class CyGroupImpl method expand.

/**
 * @see org.cytoscape.group.CyGroup#expand()
 */
@Override
public void expand(CyNetwork net) {
    synchronized (lock) {
        if (!isCollapsed(net))
            // Already expanded
            return;
        if (!networkSet.contains(net))
            // We're not in that network
            return;
    }
    cyEventHelper.fireEvent(new GroupAboutToCollapseEvent(CyGroupImpl.this, net, false));
    expanding = true;
    CySubNetwork subnet = (CySubNetwork) net;
    List<CyNode> nodes;
    synchronized (lock) {
        // Get the list of nodes we collapsed in this net
        nodes = collapsedNodes.get(net.getSUID());
        // initialized.  Handle this special case here
        if (nodes == null) {
            nodes = getNodeList();
        }
    }
    boolean groupNodeShown = nodeShownSet.contains(net.getSUID());
    // Make sure the group node isn't selected
    if (!groupNodeShown && net.containsNode(groupNode)) {
        cyEventHelper.silenceEventSource(net.getDefaultNodeTable());
        net.getRow(groupNode).set(CyNetwork.SELECTED, Boolean.FALSE);
        cyEventHelper.unsilenceEventSource(net.getDefaultNodeTable());
    }
    // Expand it.
    final CyNetworkViewManager netViewMgr = mgr.getService(CyNetworkViewManager.class);
    final Collection<CyNetworkView> netViewList = netViewMgr.getNetworkViews(net);
    final Set<CyIdentifiable> addedElements = new HashSet<CyIdentifiable>();
    synchronized (lock) {
        // the group node did not go away.
        if (memberEdges.size() == 0 && !groupNodeShown) {
            // First, get all of the group node's edges
            List<CyEdge> groupEdges = subnet.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY);
            // Save group node's locked visual properties values before they are removed
            lvpMgr.saveLockedValues(groupNode, netViewList);
            saveLocalAttributes(net, groupNode);
            for (CyEdge e : groupEdges) {
                lvpMgr.saveLockedValues(e, netViewList);
                saveLocalAttributes(net, e);
            }
            groupNodeEdges = new HashSet<CyEdge>();
            // Now, see which of these groupEdges aren't meta-edges
            for (CyEdge edge : groupEdges) {
                if (!isMeta(edge))
                    groupNodeEdges.add(edge);
            }
            // Remove the group node, if we're supposed to
            if (!nodeShownSet.contains(subnet.getSUID())) {
                List<CyEdge> groupNodeEdges = subnet.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY);
                subnet.removeNodes(Collections.singletonList(groupNode));
                rootNetwork.restoreNode(groupNode);
                for (CyEdge e : groupNodeEdges) rootNetwork.restoreEdge(e);
            }
        }
        // Add all of the member nodes and edges in
        for (CyNode n : nodes) {
            subnet.addNode(n);
            addedElements.add(n);
        }
    }
    // Make sure everyone knows about all of our changes!
    cyEventHelper.flushPayloadEvents();
    synchronized (lock) {
        // Add all of the interior edges in
        for (CyEdge e : getInternalEdgeList()) {
            if (subnet.containsNode(e.getSource()) && subnet.containsNode(e.getTarget())) {
                subnet.addEdge(e);
                addedElements.add(e);
            }
        }
        // Add all of the exterior edges in
        for (CyEdge e : getExternalEdgeList()) {
            // collapsed group
            if (subnet.containsNode(e.getSource()) && subnet.containsNode(e.getTarget())) {
                subnet.addEdge(e);
                addedElements.add(e);
            }
        }
        // our nodes to collapsed groups.  Add those in
        for (CyEdge e : getMetaEdgeList()) {
            if (subnet.containsNode(e.getSource()) && subnet.containsNode(e.getTarget())) {
                subnet.addEdge(e);
                addedElements.add(e);
            }
        }
        // Add all of the member edges in
        for (CyEdge e : memberEdges) {
            subnet.addEdge(e);
            addedElements.add(e);
        }
    }
    // Make sure everyone knows about all of our changes!
    cyEventHelper.flushPayloadEvents();
    // Restore locked visual property values of added nodes/edges
    lvpMgr.setLockedValues(netViewList, addedElements);
    restoreLocalAttributes(net, addedElements);
    synchronized (lock) {
        collapseSet.remove(net.getSUID());
        collapsedNodes.remove(net.getSUID());
    }
    // Finish up
    expanding = false;
    cyEventHelper.fireEvent(new GroupCollapsedEvent(CyGroupImpl.this, net, false));
}

Example 67 with CySubNetwork

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

the class GraphMLParser method createNode.

private void createNode(final Attributes atts) {
    // Parse node entry.
    String currentAttributeID = atts.getValue(ID.getTag());
    // If nested, add them to all parent networks.
    if (networkStack.size() > 1) {
        final CyNetwork rootNetwork = networkStack.get(0);
        currentObject = nodeid2CyNodeMap.get(currentAttributeID);
        if (currentObject == null) {
            currentObject = rootNetwork.addNode();
            rootNetwork.getRow(currentObject).set(CyNetwork.NAME, currentAttributeID);
            nodeid2CyNodeMap.put(currentAttributeID, currentObject);
        }
        for (CyNetwork network : networkStack) {
            if (network != rootNetwork) {
                ((CySubNetwork) network).addNode((CyNode) currentObject);
            }
        }
    } else {
        // Root
        currentObject = nodeid2CyNodeMap.get(currentAttributeID);
        if (currentObject == null) {
            currentObject = currentNetwork.addNode();
            currentNetwork.getRow(currentObject).set(CyNetwork.NAME, currentAttributeID);
            nodeid2CyNodeMap.put(currentAttributeID, currentObject);
        }
    }
    lastNode = (CyNode) currentObject;
}

Example 68 with CySubNetwork

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

the class GroupViewCollapseHandler method handleEvent.

@Override
public void handleEvent(GroupCollapsedEvent e) {
    getServices();
    CyNetwork network = e.getNetwork();
    CyGroup group = e.getSource();
    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;
    CyRootNetwork rootNetwork = group.getRootNetwork();
    GroupViewType groupViewType = cyGroupSettings.getGroupViewType(group);
    if (e.collapsed()) {
        // System.out.println("Got collapse event for "+group);
        // Get the location to move the group node to
        Dimension d = ViewUtils.getLocation(network, group);
        if (d != null) {
            // Move it.
            ViewUtils.moveNode(view, group.getGroupNode(), d);
        }
        View<CyNode> nView = view.getNodeView(group.getGroupNode());
        if (cyGroupSettings.getUseNestedNetworks(group)) {
            // Now, if we're displaying the nested network, create it....
            CyNetwork nn = group.getGroupNetwork();
            CyNetworkView nnView = null;
            // If we've already registered the network, don't do it again
            if (!cyNetworkManager.networkExists(nn.getSUID())) {
                cyNetworkManager.addNetwork(nn, false);
                nnView = cyNetworkViewFactory.createNetworkView(nn);
                cyNetworkViewManager.addNetworkView(nnView, false);
                // Apply our current style to the nested network
                VisualStyle style = cyStyleManager.getVisualStyle(view);
                cyStyleManager.setVisualStyle(style, nnView);
                style.apply(nnView);
            } else if (cyNetworkViewManager.viewExists(nn)) {
                nnView = cyNetworkViewManager.getNetworkViews(nn).iterator().next();
            }
            if (nnView != null) {
                ViewUtils.moveNodes(group, nnView, d);
                nnView.updateView();
                // Allow the nested network image to be displayed
                nView.clearValueLock(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE);
            }
        } else {
            // Make sure the nested network image is not displayed
            nView.setLockedValue(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE, Boolean.FALSE);
        }
        // If we were showing this as a compound node, we need to restyle
        if (groupViewType.equals(GroupViewType.COMPOUND)) {
            deActivateCompoundNode(group, view);
        }
        styleGroupNode(group, view, views);
    } else {
        // System.out.println("Got expand event for "+group);
        CyNode groupNode = group.getGroupNode();
        // Get the location of the group node before it went away
        Dimension center = ViewUtils.getLocation(network, group);
        if (center != null)
            ViewUtils.moveNodes(group, view, center);
        // If we're asked to, show the group node
        if (!groupViewType.equals(GroupViewType.NONE)) {
            CySubNetwork subnet = (CySubNetwork) network;
            // Add the node back
            subnet.addNode(group.getGroupNode());
            // Add the group nodes's edges back
            List<CyEdge> groupNodeEdges = rootNetwork.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY);
            for (CyEdge edge : groupNodeEdges) {
                CyRow row = rootNetwork.getRow(edge, CyNetwork.HIDDEN_ATTRS);
                // Only add non-meta edges
                if (row != null && (!row.isSet(CyGroupImpl.ISMETA_EDGE_ATTR) || !row.get(CyGroupImpl.ISMETA_EDGE_ATTR, Boolean.class))) {
                    subnet.addEdge(edge);
                } else if (subnet.containsEdge(edge) && row != null && row.isSet(CyGroupImpl.ISMETA_EDGE_ATTR) && row.get(CyGroupImpl.ISMETA_EDGE_ATTR, Boolean.class)) {
                    // Edge is a meta edge, but is still in the network.  Remove it
                    subnet.removeEdges(Collections.singletonList(edge));
                }
            }
            if (groupViewType.equals(GroupViewType.SHOWGROUPNODE)) {
                // If this is the first time, we need to add our member
                // edges in.
                addMemberEdges(group, network);
                // Style our member edges
                styleGroupNode(group, view, views);
            }
            // Flush events so that the view hears about it
            final CyEventHelper cyEventHelper = cyGroupManager.getService(CyEventHelper.class);
            cyEventHelper.flushPayloadEvents();
            // Now, call ourselves as if we had been collapsed
            handleEvent(new GroupCollapsedEvent(group, network, true));
            if (groupViewType.equals(GroupViewType.COMPOUND) || groupViewType.equals(GroupViewType.SINGLENODE)) {
                // May be redundant, but just to make sure
                ((CyGroupImpl) group).setGroupNodeShown(network, true);
                activateCompoundNode(group, view);
            }
            cyEventHelper.flushPayloadEvents();
            view.updateView();
            return;
        }
        final List<CyNode> nodeList = group.getNodeList();
        // TODO: turn off stupid nested network thing
        for (CyNode node : nodeList) {
            if (!network.containsNode(node))
                continue;
            View<CyNode> nView = view.getNodeView(node);
            if (node.getNetworkPointer() != null && cyGroupManager.isGroup(node, network)) {
                if (!cyGroupSettings.getUseNestedNetworks(cyGroupManager.getGroup(node, network))) {
                    nView.setLockedValue(BasicVisualLexicon.NODE_NESTED_NETWORK_IMAGE_VISIBLE, Boolean.FALSE);
                }
            }
        }
        // Apply visual property to added graph elements
        ViewUtils.applyStyle(nodeList, views, cyStyleManager);
        ViewUtils.applyStyle(group.getInternalEdgeList(), views, cyStyleManager);
        ViewUtils.applyStyle(group.getExternalEdgeList(), views, cyStyleManager);
    }
    view.updateView();
}

Example 69 with CySubNetwork

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

the class NNFParser method parse.

/**
 * Parse an entry/line in an NNF file.
 *
 * @param line
 */
public boolean parse(final String line) {
    // Split with white space chars
    parts = splitLine(line);
    length = parts.length;
    final String originalName = parts[0];
    CyNetwork network = getNetworkByName(originalName);
    if (network == null) {
        // Create network without view.  View will be created later.
        network = rootNetwork.addSubNetwork();
        final String actualName = namingUtil.getSuggestedNetworkTitle(originalName);
        network.getRow(network).set(CyNetwork.NAME, actualName);
        networksByName.put(originalName, network);
        networks.add(network);
        // Attempt to nest network within the node with the same name
        CyNode parent = getNodeByName(originalName);
        if (parent != null)
            setNestedNetwork(network, parent, network);
        // is the node exist in the overview network
        parent = getNodefromOverview(originalName);
        if (parent != null)
            setNestedNetwork(network, parent, network);
    }
    if (length == 2) {
        CyNode node;
        if (this.nMap.get(parts[1]) == null) {
            node = network.addNode();
            this.nMap.put(parts[1], this.rootNetwork.getNode(node.getSUID()));
        } else {
            node = this.nMap.get(parts[1]);
            CySubNetwork subnet = (CySubNetwork) network;
            subnet.addNode(node);
        }
        network.getRow(node).set(CyNetwork.NAME, parts[1]);
        final CyNetwork nestedNetwork = getNetworkByName(parts[1]);
        if (nestedNetwork != null) {
            setNestedNetwork(network, node, nestedNetwork);
        }
    } else if (length == 4) {
        CyNode source = null;
        // Check if the source node already existed in the network
        Collection<CyRow> matchingRows = network.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, parts[1]);
        if (!matchingRows.isEmpty()) {
            // source node already existed, get it
            CyRow row = matchingRows.iterator().next();
            Long suid = row.get("SUID", Long.class);
            if (suid != null) {
                source = network.getNode(suid);
            }
        } else {
            // source node does not existed yet, create one
            if (this.nMap.get(parts[1]) == null) {
                // Cytoscape.getCyNode(parts[1], true);
                source = network.addNode();
                CyNode newNode = this.rootNetwork.getNode(source.getSUID());
                this.nMap.put(parts[1], newNode);
            } else {
                CyNode newNode = this.nMap.get(parts[1]);
                CySubNetwork subNet = (CySubNetwork) network;
                subNet.addNode(newNode);
                source = network.getNode(newNode.getSUID());
            }
            network.getRow(source).set(CyNetwork.NAME, parts[1]);
        }
        CyNetwork nestedNetwork = networksByName.get(parts[1]);
        if (nestedNetwork != null) {
            setNestedNetwork(network, source, nestedNetwork);
        }
        CyNode target = null;
        // Check if the target already existed in the network
        Collection<CyRow> matchingRows2 = network.getDefaultNodeTable().getMatchingRows(CyNetwork.NAME, parts[3]);
        if (!matchingRows2.isEmpty()) {
            // source node already existed, get it
            CyRow row = matchingRows2.iterator().next();
            Long suid = row.get("SUID", Long.class);
            if (suid != null) {
                target = network.getNode(suid);
            }
        } else {
            if (this.nMap.get(parts[3]) == null) {
                target = network.addNode();
                CyNode newNode = this.rootNetwork.getNode(target.getSUID());
                this.nMap.put(parts[3], newNode);
            } else {
                CyNode newNode = this.nMap.get(parts[3]);
                CySubNetwork subNet = (CySubNetwork) network;
                subNet.addNode(newNode);
                target = network.getNode(newNode.getSUID());
            }
            // target = network.addNode();
            network.getRow(target).set(CyNetwork.NAME, parts[3]);
        }
        // 
        nestedNetwork = networksByName.get(parts[3]);
        if (nestedNetwork != null) {
            setNestedNetwork(network, target, nestedNetwork);
        }
        CyEdge newEdge = network.addEdge(source, target, true);
        network.getRow(newEdge).set(CyEdge.INTERACTION, parts[2]);
        network.getRow(newEdge).set(CyNetwork.NAME, parts[1] + " (" + parts[2] + ") " + parts[3]);
    } else {
        // Invalid number of columns.
        return false;
    }
    return true;
}

Example 70 with CySubNetwork

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

the class SIFNetworkReader method readInput.

private void readInput(TaskMonitor tm) throws IOException {
    this.parentTaskMonitor = tm;
    tm.setProgress(0.0);
    String line;
    final BufferedReader br = new BufferedReader(new InputStreamReader(inputStream, Charset.forName("UTF-8").newDecoder()), 128 * 1024);
    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();
    Map<Object, CyNode> nMap = getNodeMap();
    tm.setProgress(0.1);
    final String firstLine = br.readLine();
    if (firstLine.contains(TAB))
        delimiter = TAB;
    createEdge(new Interaction(firstLine.trim(), delimiter), newNetwork, nMap);
    tm.setProgress(0.15);
    tm.setStatusMessage("Processing the interactions...");
    int numInteractionsRead = 0;
    while ((line = br.readLine()) != null) {
        if (cancelled) {
            // Cancel called. Clean up the garbage.
            nMap.clear();
            br.close();
            return;
        }
        if (line.trim().length() <= 0)
            continue;
        try {
            final Interaction itr = new Interaction(line, delimiter);
            createEdge(itr, newNetwork, nMap);
        } catch (Exception e) {
            // Simply ignore invalid lines.
            continue;
        }
        if ((++numInteractionsRead % 1000) == 0)
            tm.setStatusMessage("Processed " + numInteractionsRead + " interactions so far.");
    }
    br.close();
    tm.setStatusMessage("Processed " + numInteractionsRead + " interactions in total.");
    nMap.clear();
    nMap = null;
    this.networks = new CyNetwork[] { newNetwork };
    tm.setProgress(1.0);
}