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

Example 56 with CySubNetwork

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

the class RootNetworkPanelModel method getSubNetworkCount.

@Override
public int getSubNetworkCount() {
    int count = 0;
    final CyNetworkManager netManager = serviceRegistrar.getService(CyNetworkManager.class);
    // Count number of public subnetworks
    for (CySubNetwork net : getNetwork().getSubNetworkList()) {
        if (netManager.networkExists(net.getSUID()))
            count++;
    }
    return count;
}

Example 57 with CySubNetwork

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

the class GenerateNetworkViewsTask method run.

@Override
public void run(final TaskMonitor taskMonitor) throws Exception {
    final CyNetwork[] networks = viewReader.getNetworks();
    if (networks == null || networks.length == 0)
        return;
    taskMonitor.setProgress(0.0);
    final CyNetworkNaming networkNaming = serviceRegistrar.getService(CyNetworkNaming.class);
    double numNets = (double) networks.length;
    int i = 0;
    results = new ArrayList<>();
    largeNetworks = new ArrayList<>();
    for (CyNetwork net : networks) {
        // Use original name if exists
        String networkName = net.getRow(net).get(CyNetwork.NAME, String.class);
        if (networkName == null || networkName.trim().length() == 0)
            networkName = (name != null) ? name : "? (Name is missing)";
        net.getRow(net).set(CyNetwork.NAME, networkNaming.getSuggestedNetworkTitle(networkName));
        serviceRegistrar.getService(CyNetworkManager.class).addNetwork(net, false);
        final int numGraphObjects = net.getNodeCount() + net.getEdgeCount();
        if (numGraphObjects < viewThreshold)
            createNetworkView(net);
        else
            largeNetworks.add(net);
        taskMonitor.setProgress((double) (++i) / numNets);
    }
    // If there is no name yet for the root network, set it the same as its base subnetwork
    if (networks.length == 1) {
        if (networks[0] instanceof CySubNetwork) {
            CySubNetwork subnet = (CySubNetwork) networks[0];
            final CyRootNetwork rootNet = subnet.getRootNetwork();
            String rootNetName = rootNet.getRow(rootNet).get(CyNetwork.NAME, String.class);
            if (rootNetName == null || rootNetName.trim().length() == 0) {
                // The root network does not have a name yet, set it the same as the base subnetwork
                rootNet.getRow(rootNet).set(CyNetwork.NAME, networks[0].getRow(networks[0]).get(CyNetwork.NAME, String.class));
            }
        }
    }
    // Make sure rootNetwork has a name
    for (CyNetwork net : networks) {
        if (net instanceof CySubNetwork) {
            CySubNetwork subNet = (CySubNetwork) net;
            CyRootNetwork rootNet = subNet.getRootNetwork();
            String networkName = rootNet.getRow(rootNet).get(CyNetwork.NAME, String.class);
            if (networkName == null || networkName.trim().length() == 0) {
                networkName = name;
                if (networkName == null)
                    networkName = "? (Name is missing)";
                rootNet.getRow(rootNet).set(CyNetwork.NAME, networkNaming.getSuggestedNetworkTitle(networkName));
            }
        }
    }
    setCurrentNetworkAndViewTask(networks[0]);
    if (!largeNetworks.isEmpty())
        insertTasksAfterCurrentTask(new ConfirmCreateNetworkViewsTask(largeNetworks));
}

Example 58 with CySubNetwork

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

the class CloneNetworkTask method cloneGroups.

private void cloneGroups(final CyNetwork origNet, final CyNetwork newNet) {
    // Get all of the groups in our original network
    Set<CyGroup> origGroups = groupMgr.getGroupSet(origNet);
    // edges
    for (CyGroup origGroup : origGroups) {
        if (origGroup.isCollapsed(origNet)) {
            for (CyNode origNode : origGroup.getNodeList()) {
                // add the node back into the network
                ((CySubNetwork) origNet).addNode(origNode);
                cloneNode(origNet, newNet, origNode);
            }
        }
    }
    // Now, we can clone the group itself
    for (CyGroup origGroup : origGroups) {
        cloneGroup(origNet, newNet, origGroup);
    }
}

Example 59 with CySubNetwork

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

the class GroupUtils method updateMetaEdgeInformation.

public static void updateMetaEdgeInformation(CyNetwork origNet, CyNetwork newNet, CyEdge origEdge, CyEdge newEdge) {
    if (newEdge == null)
        return;
    CyRootNetwork newRoot = ((CySubNetwork) newNet).getRootNetwork();
    CyRootNetwork origRoot = ((CySubNetwork) origNet).getRootNetwork();
    CyTable newTable = newRoot.getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    if (newTable.getColumn(ISMETA_EDGE_ATTR) == null) {
        newTable.createColumn(ISMETA_EDGE_ATTR, Boolean.class, false);
    }
    CyRow origRow = origRoot.getRow(origEdge, CyNetwork.HIDDEN_ATTRS);
    if (origRow.isSet(ISMETA_EDGE_ATTR)) {
        CyRow newRow = newTable.getRow(newEdge.getSUID());
        Boolean isMeta = origRow.get(ISMETA_EDGE_ATTR, Boolean.class);
        newRow.set(ISMETA_EDGE_ATTR, isMeta);
    }
    return;
}

Example 60 with CySubNetwork

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

the class CloneNetworkTask method cloneGroup.

private CyGroup cloneGroup(final CyNetwork origNet, final CyNetwork newNet, final CyGroup origGroup) {
    List<CyNode> nodeList = new ArrayList<CyNode>();
    List<CyEdge> edgeList = new ArrayList<CyEdge>();
    // Check to see if the group node is already in the network
    boolean groupNodeExists = origNet.containsNode(origGroup.getGroupNode());
    boolean collapsed = origGroup.isCollapsed(origNet);
    if (collapsed)
        origGroup.expand(origNet);
    else {
        // If we're not collapsed, we need to clone the group node and it's edges
        CyNode groupNode = origGroup.getGroupNode();
        // If the node already exists, we shouldn't need to do anything
        if (!groupNodeExists) {
            ((CySubNetwork) origNet).addNode(groupNode);
            cloneNode(origNet, newNet, groupNode);
            // Now remove it
            ((CySubNetwork) origNet).removeNodes(Collections.singletonList(groupNode));
        // TODO: What about non-meta edges?
        }
    }
    // Get the list of nodes for the group
    for (CyNode node : origGroup.getNodeList()) {
        nodeList.add(orig2NewNodeMap.get(node));
    }
    for (CyEdge iEdge : origGroup.getInternalEdgeList()) {
        cloneEdge(origNet, newNet, iEdge);
    }
    for (CyEdge eEdge : origGroup.getExternalEdgeList()) {
        cloneEdge(origNet, newNet, eEdge);
    }
    // Get the group node
    CyNode newNode = orig2NewNodeMap.get(origGroup.getGroupNode());
    // Copy our metaEdge information (if any), which is stored in the root network hidden table
    cloneMetaEdgeInfo(origNet, newNet, origGroup);
    // Create the group
    CyGroup newGroup = groupFactory.createGroup(newNet, newNode, nodeList, null, true);
    // We need to update all of our positions hints
    cloneGroupTables(origNet, newNet, origGroup, newGroup);
    if (!groupNodeExists) {
        // Because we're providing a group node with a network pointer, the groups code
        // is going to think we're coming from a session.  We need to remove the group node
        newNet.removeNodes(Collections.singletonList(newNode));
    }
    if (collapsed) {
        // ...and collapse it...
        origGroup.collapse(origNet);
        newGroup.collapse(newNet);
    }
    return newGroup;
}