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

Example 31 with CySubNetwork

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

the class GenericXGMMLWriter method getRowFromNetOrRoot.

protected CyRow getRowFromNetOrRoot(final CyNetwork network, final CyIdentifiable entry, String namespace) {
    CyRow row = null;
    try {
        row = namespace == null ? network.getRow(entry) : network.getRow(entry, namespace);
    } catch (final IllegalArgumentException e) {
    // Ignore this exception
    } catch (final RuntimeException e) {
        logger.error("Cannot get \"" + namespace + "\" row for entry \"" + entry + "\" in network \"" + network + "\".", e);
    }
    if (row == null && network instanceof CySubNetwork) {
        // Doesn't exist in subnetwork? Try to get it from the root network.
        final CyRootNetwork root = ((CySubNetwork) network).getRootNetwork();
        row = namespace == null ? root.getRow(entry) : root.getRow(entry, namespace);
    }
    return row;
}

Example 32 with CySubNetwork

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

the class GenericXGMMLWriter method getSerializableSubNetworks.

/**
 * @param rootNet
 * @return A set with all the subnetworks that should be serialized.
 */
protected Set<CySubNetwork> getSerializableSubNetworks(final CyRootNetwork rootNet) {
    final Set<CySubNetwork> serializableSet = new LinkedHashSet<CySubNetwork>();
    final List<CySubNetwork> subNetList = rootNet.getSubNetworkList();
    final CySubNetwork baseNetwork = rootNet.getBaseNetwork();
    // The base network must be the first one!
    if (isSerializable(baseNetwork))
        serializableSet.add(baseNetwork);
    for (final CySubNetwork sn : subNetList) {
        if (isSerializable(sn))
            serializableSet.add(sn);
    }
    return serializableSet;
}

Example 33 with CySubNetwork

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

the class ReadDataManager method createNode.

protected CyNode createNode(final Object oldId, final String label, final CyNetwork net) {
    if (oldId == null)
        throw new NullPointerException("'oldId' is null.");
    CyNode node = null;
    if (net instanceof CySubNetwork && getParentNetwork() != null) {
        // Do not create the element again if the network is a sub-network!
        node = cache.getNode(oldId);
        if (node != null)
            ((CySubNetwork) net).addNode(node);
    }
    if (node == null) {
        node = this.nMap.get(label);
        if (node == null) {
            // OK, create it
            node = net.addNode();
        }
    }
    if (net instanceof CySubNetwork && getParentNetwork() != null) {
        // cache the parent node, not the node from subnetwork
        CySubNetwork subnet = (CySubNetwork) net;
        node = subnet.getRootNetwork().getNode(node.getSUID());
    }
    // Add to internal cache:
    cache.cache(oldId, node);
    cache.cacheNodeByName(label, node);
    mapSUIDs(oldId, node.getSUID());
    return node;
}

Example 34 with CySubNetwork

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

the class GroupUtil method updateGroupNodeLocation.

private void updateGroupNodeLocation(final CyNetworkView view, final CyNode groupNode) {
    if (view == null)
        return;
    CyRootNetwork rootNetwork = ((CySubNetwork) view.getModel()).getRootNetwork();
    View<CyNode> nView = view.getNodeView(groupNode);
    double x = nView.getVisualProperty(BasicVisualLexicon.NODE_X_LOCATION);
    double y = nView.getVisualProperty(BasicVisualLexicon.NODE_Y_LOCATION);
    // Save it
    // TODO these attributes will not work with multiple views per network!
    CyRow hRow = rootNetwork.getRow(groupNode, CyNetwork.HIDDEN_ATTRS);
    createColumn(hRow.getTable(), X_LOCATION_ATTR, Double.class);
    createColumn(hRow.getTable(), Y_LOCATION_ATTR, Double.class);
    hRow.set(X_LOCATION_ATTR, new Double(x));
    hRow.set(Y_LOCATION_ATTR, new Double(y));
}

Example 35 with CySubNetwork

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

the class GroupUtil method getGroupNodeEdges.

public List<CyEdge> getGroupNodeEdges(final CyNetwork network) {
    CyRootNetwork rootNetwork = ((CySubNetwork) network).getRootNetwork();
    // Don't need to worry about this for collapsed groups
    List<CyNode> groupNodes = getExpandedGroups(network);
    List<CyEdge> groupNodeEdges = new ArrayList<>();
    for (CyNode groupNode : groupNodes) {
        groupNodeEdges.addAll(rootNetwork.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY));
    }
    return groupNodeEdges;
}