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

Example 81 with CySubNetwork

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

the class GroupUtil method updateGroupAttribute.

private void updateGroupAttribute(final CyNetwork net, final CyGroup group) {
    CyNode node = group.getGroupNode();
    List<CyNode> nodeList;
    // to add it so that it will get serialized
    if (!net.containsNode(node)) {
        // Node not in this network.  Add it and mark it....
        CySubNetwork subNet = (CySubNetwork) net;
        // Temporarily add this to the network so we can serialize it
        subNet.addNode(node);
        // Remember it...
        if (addedNodes.containsKey(net))
            nodeList = addedNodes.get(net);
        else
            nodeList = new ArrayList<CyNode>();
        nodeList.add(node);
        addedNodes.put(net, nodeList);
    }
    CyTable hiddenTable = net.getTable(CyNode.class, CyNetwork.HIDDEN_ATTRS);
    if (hiddenTable.getColumn(GROUP_ATTRIBUTE) == null)
        hiddenTable.createColumn(GROUP_ATTRIBUTE, Boolean.class, false);
    hiddenTable.getRow(node.getSUID()).set(GROUP_ATTRIBUTE, Boolean.TRUE);
}

Example 82 with CySubNetwork

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

the class GroupUtil method updateMetaEdges.

private void updateMetaEdges(final CyNetwork net, final CyNode groupNode) {
    CyRootNetwork rootNetwork = ((CySubNetwork) net).getRootNetwork();
    // Find all of the edges from the group node and if they are
    // meta-edges, mark them as such
    List<CyEdge> edgeList = net.getAdjacentEdgeList(groupNode, CyEdge.Type.ANY);
    for (CyEdge edge : edgeList) {
        String interaction = net.getRow(edge).get(CyEdge.INTERACTION, String.class);
        if (interaction.startsWith("meta-")) {
            createColumn(rootNetwork.getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS), ISMETA_EDGE_ATTR, Boolean.class);
            rootNetwork.getRow(edge, CyNetwork.HIDDEN_ATTRS).set(ISMETA_EDGE_ATTR, Boolean.TRUE);
        }
    }
}

Example 83 with CySubNetwork

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

the class GroupUtil method updateCollapsedGroupsAttribute.

private void updateCollapsedGroupsAttribute(final CyGroup group) {
    // Get our subnetwork
    CySubNetwork np = (CySubNetwork) group.getGroupNode().getNetworkPointer();
    CyTable hiddenTable = np.getTable(CyNetwork.class, CyNetwork.HIDDEN_ATTRS);
    // We use our embedded network table for this
    CyRow netRow = hiddenTable.getRow(np.getSUID());
    CyColumn stateColumn = hiddenTable.getColumn(GROUP_COLLAPSED_ATTRIBUTE);
    if (stateColumn == null)
        hiddenTable.createListColumn(GROUP_COLLAPSED_ATTRIBUTE, Long.class, true);
    CyColumn groupShownColumn = hiddenTable.getColumn(GROUP_NODE_SHOWN_ATTRIBUTE);
    if (groupShownColumn == null)
        hiddenTable.createListColumn(GROUP_NODE_SHOWN_ATTRIBUTE, Long.class, true);
    List<Long> collapsedList = new ArrayList<Long>();
    List<Long> groupNodeShownList = new ArrayList<Long>();
    for (CyNetwork net : group.getNetworkSet()) {
        if (group.isCollapsed(net)) {
            collapsedList.add(net.getSUID());
        } else if (net.containsNode(group.getGroupNode())) {
            // We're not collapsed, but we're still showing the group node.
            groupNodeShownList.add(net.getSUID());
        }
    }
    netRow.set(GROUP_COLLAPSED_ATTRIBUTE, collapsedList);
    netRow.set(GROUP_NODE_SHOWN_ATTRIBUTE, groupNodeShownList);
    return;
}

Example 84 with CySubNetwork

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

the class ReadCache method getNetworkTables.

/**
 * @return All network tables, except DEFAULT_ATTRS and SHARED_DEFAULT_ATTRS ones.
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
public Set<CyTable> getNetworkTables() {
    final Set<CyTable> tables = new HashSet<>();
    final Set<CyNetwork> networks = new HashSet<>();
    final Class<?>[] types = new Class[] { CyNetwork.class, CyNode.class, CyEdge.class };
    if (networkByIdMap.values() != null)
        networks.addAll(networkByIdMap.values());
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    for (final CyNetwork n : networks) {
        for (final Class t : types) {
            Map<String, CyTable> tblMap = new HashMap<>(netTblMgr.getTables(n, t));
            tblMap.remove(CyNetwork.DEFAULT_ATTRS);
            if (tblMap != null)
                tables.addAll(tblMap.values());
            if (n instanceof CySubNetwork) {
                // Don't forget the root-network tables.
                tblMap = new HashMap<String, CyTable>(netTblMgr.getTables(((CySubNetwork) n).getRootNetwork(), t));
                tblMap.remove(CyRootNetwork.DEFAULT_ATTRS);
                tblMap.remove(CyRootNetwork.SHARED_DEFAULT_ATTRS);
                if (tblMap != null)
                    tables.addAll(tblMap.values());
            }
        }
    }
    return tables;
}

Example 85 with CySubNetwork

use of org.cytoscape.model.subnetwork.CySubNetwork in project clusterMaker2 by RBVI.

the class NodeCluster method getSubNetwork.

/* Method to get the subnetwork formed by the nodes in the cluster
	 *
	 * @param net parent network
	 * @param nodes
	 */
public CySubNetwork getSubNetwork(final CyNetwork net, final CyRootNetwork root, final SavePolicy policy) {
    // final CyRootNetwork root = rootNetworkMgr.getRootNetwork(net);
    final Set<CyEdge> edges = new HashSet<CyEdge>();
    for (CyNode n : this) {
        Set<CyEdge> adjacentEdges = new HashSet<CyEdge>(net.getAdjacentEdgeList(n, CyEdge.Type.ANY));
        // Get only the edges that connect nodes that belong to the subnetwork:
        for (CyEdge e : adjacentEdges) {
            if (this.contains(e.getSource()) && this.contains(e.getTarget())) {
                edges.add(e);
            }
        }
    }
    final CySubNetwork subNet = root.addSubNetwork(this, edges, policy);
    /*
		// Save it for later disposal
		Set<CySubNetwork> snSet = createdSubNetworks.get(root);

		if (snSet == null) {
			snSet = new HashSet<CySubNetwork>();
			createdSubNetworks.put(root, snSet);
		}

		snSet.add(subNet);
		*/
    return subNet;
}