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

Example 1 with CySubNetwork

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

the class DestroyNetworkTask method destroyNetwork.

private void destroyNetwork(final CyNetwork net, CyNetworkManager netManager) {
    CyRootNetwork rootNet = null;
    CySubNetwork parentNet = null;
    if (net instanceof CySubNetwork) {
        rootNet = ((CySubNetwork) net).getRootNetwork();
        final Long suid = DataUtils.getParentNetworkSUID((CySubNetwork) net);
        if (suid != null && netManager.getNetwork(suid) instanceof CySubNetwork)
            parentNet = (CySubNetwork) netManager.getNetwork(suid);
    }
    netManager.destroyNetwork(net);
    if (net instanceof CySubNetwork)
        updateParentNetworkData(net.getSUID(), rootNet, (parentNet != null ? parentNet.getSUID() : null));
}

Example 2 with CySubNetwork

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

the class GroupUtils method addGroupToNetwork.

public static void addGroupToNetwork(CyGroup group, CyNetwork origNet, CyNetwork newNet) {
    CyNetwork groupNetwork = group.getGroupNetwork();
    Dimension d = getPosition(origNet, group, groupNetwork.getSUID(), CyNetwork.class);
    updatePosition(newNet, group, groupNetwork.getSUID(), CyNetwork.class, d);
    for (CyNode node : group.getNodeList()) {
        Long nodeSUID = node.getSUID();
        d = getPosition(origNet, group, nodeSUID, CyNode.class);
        updatePosition(newNet, group, nodeSUID, CyNode.class, d);
        // This helps out collapse
        ((CySubNetwork) newNet).addNode(node);
    }
    for (CyEdge edge : group.getInternalEdgeList()) {
        // This helps out collapse
        ((CySubNetwork) newNet).addEdge(edge);
    }
    for (CyEdge edge : group.getExternalEdgeList()) {
        // This helps out collapse
        ((CySubNetwork) newNet).addEdge(edge);
    }
    group.addGroupToNetwork(newNet);
    group.collapse(newNet);
}

Example 3 with CySubNetwork

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

the class AddTask method run.

@Override
public void run(final TaskMonitor taskMonitor) {
    network = nodesAndEdges.getNetwork();
    if (network == null) {
        taskMonitor.showMessage(TaskMonitor.Level.ERROR, "Network must be specified for add command");
        return;
    }
    nodeList = nodesAndEdges.getNodeList(false);
    edgeList = nodesAndEdges.getEdgeList(false);
    if ((nodeList == null || nodeList.size() == 0) && (edgeList == null || edgeList.size() == 0)) {
        taskMonitor.showMessage(TaskMonitor.Level.WARN, "Nothing to add");
        return;
    }
    int nodeCount = nodeList.size();
    int edgeCount = 0;
    for (CyNode node : nodeList) ((CySubNetwork) network).addNode(node);
    // nodes and "all" edges
    for (CyEdge edge : edgeList) {
        if (network.containsNode(edge.getSource()) && network.containsNode(edge.getTarget())) {
            ((CySubNetwork) network).addEdge(edge);
            edgeCount++;
        }
    }
    eventHelper.flushPayloadEvents();
    taskMonitor.showMessage(TaskMonitor.Level.INFO, "Added " + nodeCount + " nodes and " + edgeCount + " edges to network " + network.toString());
}

Example 4 with CySubNetwork

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

the class Cy2SessionReaderImpl method extractNetworksAndViews.

/**
 * @param is
 * @param entryName
 * @param parent
 * @param createView
 * @return The top-level network that was extracted from the XGMML file.
 * @throws Exception
 */
private CyNetwork extractNetworksAndViews(final InputStream is, final String entryName, final CyNetwork parent, final boolean createView) throws Exception {
    CyNetwork topNetwork = null;
    final CyNetworkReader reader = networkReaderMgr.getReader(is, entryName);
    if (parent != null) {
        if (reader instanceof SessionXGMMLNetworkReader) {
            ((SessionXGMMLNetworkReader) reader).setParent(parent);
        } else {
            logger.error("CyNetworkReader should be an instance of XGMMLNetworkReader. " + "Cannot extract network as sub-nertwork of: " + entryName);
        }
    }
    reader.run(taskMonitor);
    final CyNetwork[] netArray = reader.getNetworks();
    if (netArray != null && netArray.length > 0) {
        topNetwork = netArray[0];
        for (int i = 0; i < netArray.length; i++) {
            // Process each CyNetwork
            final CyNetwork net = netArray[i];
            final String netName = net.getRow(net).get(CyNetwork.NAME, String.class);
            networkLookup.put(netName, net);
            // Add parent network attribute to a column in the hidden table,
            // to preserve the network hierarchy info from Cytoscape 2.x
            final CyRow hRow = net.getRow(net, CyNetwork.HIDDEN_ATTRS);
            final CyTable hTbl = hRow.getTable();
            if (parent instanceof CySubNetwork) {
                if (hTbl.getColumn(CY3_PARENT_NETWORK_COLUMN) == null)
                    hTbl.createColumn(CY3_PARENT_NETWORK_COLUMN, Long.class, false);
                hRow.set(CY3_PARENT_NETWORK_COLUMN, parent.getSUID());
            }
            final CyTable tbl = net.getRow(net, CyNetwork.LOCAL_ATTRS).getTable();
            // (e.g. the user imported a Cy3 XGMML that contains this attribute into Cy2)
            if (tbl.getColumn(CY2_PARENT_NETWORK_COLUMN) != null && parent instanceof CySubNetwork == false)
                tbl.deleteColumn(CY2_PARENT_NETWORK_COLUMN);
            // Restore node/edge selection
            List<Node> selNodes = nodeSelectionLookup.get(netName);
            List<Edge> selEdges = edgeSelectionLookup.get(netName);
            if (selNodes != null)
                setBooleanNodeAttr(net, selNodes, SELECTED, DEFAULT_ATTRS);
            if (selEdges != null)
                setBooleanEdgeAttr(net, selEdges, SELECTED, DEFAULT_ATTRS);
            networks.add(net);
            if (!cancelled && i == 0 && createView) {
                // Create a network view for the first network only,
                // which is supposed to be the top-level one
                final CyNetworkView view = reader.buildCyNetworkView(net);
                networkViewLookup.put(netName, view);
                networkViews.add(view);
                cache.cache(netName, view);
            }
        }
    }
    return topNetwork;
}

Example 5 with CySubNetwork

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

the class HandleGraphDone method handle.

@Override
public ParseState handle(String tag, Attributes atts, ParseState current) throws SAXException {
    graphDone();
    // End of document?
    if (manager.graphDoneCount != manager.graphCount)
        return current;
    // Resolve any unresolved node and edge references
    Map<CyNetwork, Set<Long>> nodeMap = manager.getCache().getNodeLinks();
    for (Map.Entry<CyNetwork, Set<Long>> entry : nodeMap.entrySet()) {
        CyNetwork net = entry.getKey();
        Set<Long> ids = entry.getValue();
        if (net != null && ids != null && !ids.isEmpty()) {
            if (net instanceof CySubNetwork) {
                final CySubNetwork sn = (CySubNetwork) net;
                for (Long id : ids) {
                    CyNode n = manager.getCache().getNode(id);
                    if (n != null)
                        sn.addNode(n);
                    else
                        logger.error("Cannot find XLink node with id \"" + id + "\".");
                }
            } else {
                logger.error("Cannot add existing nodes \"" + ids.toArray() + "\" to a network which is not a CySubNetwork");
            }
        }
    }
    // TODO: refactor
    Map<CyNetwork, Set<Long>> edgeMap = manager.getCache().getEdgeLinks();
    for (Map.Entry<CyNetwork, Set<Long>> entry : edgeMap.entrySet()) {
        CyNetwork net = entry.getKey();
        Set<Long> ids = entry.getValue();
        if (net != null && ids != null && !ids.isEmpty()) {
            if (net instanceof CySubNetwork) {
                final CySubNetwork sn = (CySubNetwork) net;
                for (Long id : ids) {
                    final CyEdge e = manager.getCache().getEdge(id);
                    if (e != null)
                        sn.addEdge(e);
                    else
                        logger.error("Cannot find XLink edge with id \"" + id + "\".");
                }
            } else {
                logger.error("Cannot add existing edges \"" + ids.toArray() + "\" to a network which is not a CySubNetwork");
            }
        }
    }
    manager.getCache().deleteUnresolvedNodes();
    resolveEquations();
    resolveNetworkPointers();
    updateSUIDAttributes();
    // TODO: we should not create (and specially register) groups here!
    createGroups();
    return ParseState.NONE;
}