Examples with CyTable org.cytoscape.model.CyTable used on opensource projects

Example 16 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class NNFParser method setNestedNetwork.

private void setNestedNetwork(CyNetwork sourceNetwork, CyNode node, CyNetwork targetNetwork) {
    // TODO: We should consider exposing a nested network API so we don't
    // have to do this everywhere we establish this link.
    node.setNetworkPointer(targetNetwork);
    CyTable nodeTable = sourceNetwork.getDefaultNodeTable();
    boolean attributeExists = nodeTable.getColumn(HAS_NESTED_NETWORK_ATTRIBUTE) != null;
    if (targetNetwork == null && attributeExists) {
        nodeTable.getRow(node.getSUID()).set(HAS_NESTED_NETWORK_ATTRIBUTE, false);
    } else if (targetNetwork != null) {
        if (!attributeExists) {
            nodeTable.createColumn(HAS_NESTED_NETWORK_ATTRIBUTE, Boolean.class, false);
        }
        CyRow row = nodeTable.getRow(node.getSUID());
        row.set(HAS_NESTED_NETWORK_ATTRIBUTE, true);
    }
}

Example 17 with CyTable

use of org.cytoscape.model.CyTable 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 18 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class Cy3SessionReaderImpl method mergeNetworkTable.

@SuppressWarnings("unchecked")
private final void mergeNetworkTable(CyNetwork network, CyTableMetadataBuilder builder, CyNetworkTableManager networkTableMgr) {
    final Class<? extends CyIdentifiable> type = (Class<? extends CyIdentifiable>) builder.getType();
    final String namespace = builder.getNamespace();
    final CyTable src = builder.getTable();
    final CyTable tgt = networkTableMgr.getTable(network, type, namespace);
    if (tgt == null) {
        // Just use the source table
        networkTableMgr.setTable(network, type, namespace, src);
        builder.setCyTable(src);
        suidUpdater.addTable(src);
    } else {
        mergeTables(src, tgt, type);
        builder.setCyTable(tgt);
        suidUpdater.addTable(tgt);
    }
}

Example 19 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class NetworkMediator method handleEvent.

@Override
public void handleEvent(final RowsSetEvent e) {
    if (loadingSession || networkMainPanel.getRootNetworkListPanel().isEmpty())
        return;
    // We only care about network name changes
    final Collection<RowSetRecord> nameRecords = e.getColumnRecords(CyNetwork.NAME);
    if (nameRecords == null || nameRecords.isEmpty())
        return;
    final CyTable tbl = e.getSource();
    final CyNetworkTableManager netTblMgr = serviceRegistrar.getService(CyNetworkTableManager.class);
    final CyNetwork net = netTblMgr.getNetworkForTable(tbl);
    // And if there is no related network, nothing needs to be done
    if (net != null && tbl.equals(net.getDefaultNetworkTable())) {
        invokeOnEDT(() -> {
            final AbstractNetworkPanel<?> item = networkMainPanel.getNetworkItem(net);
            if (item != null)
                item.update();
        });
    }
}

Example 20 with CyTable

use of org.cytoscape.model.CyTable in project cytoscape-impl by cytoscape.

the class DefaultTableBrowser method getPublicTables.

private Set<CyTable> getPublicTables(CyNetwork currentNetwork) {
    final Set<CyTable> tables = new LinkedHashSet<>();
    if (currentNetwork == null)
        return tables;
    final CyNetworkTableManager netTableManager = serviceRegistrar.getService(CyNetworkTableManager.class);
    final Map<String, CyTable> map = netTableManager.getTables(currentNetwork, objType);
    if (showPrivateTables()) {
        tables.addAll(map.values());
    } else {
        for (final CyTable tbl : map.values()) {
            if (tbl.isPublic())
                tables.add(tbl);
        }
    }
    return tables;
}