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

Example 46 with CyTable

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

the class StringToModelImpl method getTable.

@Override
public CyTable getTable(String strTable) {
    if (strTable == null || strTable.length() == 0 || strTable.equalsIgnoreCase(CURRENT))
        return serviceRegistrar.getService(CyApplicationManager.class).getCurrentTable();
    // Look for any special prefix
    CyNetwork network;
    String[] splitString = strTable.split(":");
    if (splitString.length > 1) {
        if (splitString[0].equalsIgnoreCase("node")) {
            network = getNetwork(splitString[1]);
            if (network != null)
                return network.getDefaultNodeTable();
        }
        if (splitString[0].equalsIgnoreCase("edge")) {
            network = getNetwork(splitString[1]);
            if (network != null)
                return network.getDefaultEdgeTable();
        }
        if (splitString[0].equalsIgnoreCase("network")) {
            network = getNetwork(splitString[1]);
            if (network != null)
                return network.getDefaultNetworkTable();
        }
    } else {
        final CyTableManager tableMgr = serviceRegistrar.getService(CyTableManager.class);
        for (CyTable tab : tableMgr.getGlobalTables()) {
            if (tab.getTitle().contains(strTable))
                return tab;
        }
    }
    return null;
}

Example 47 with CyTable

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

the class ThumbnailView method handleEvent.

@Override
public void handleEvent(RowsSetEvent e) {
    if (!e.containsColumn(CyNetwork.SELECTED))
        return;
    CyTable source = e.getSource();
    CyNetwork model = viewModel.getModel();
    if (!viewModel.getComponent().isShowing() && (source == model.getDefaultNodeTable() || source == model.getDefaultEdgeTable())) {
        forceRender = true;
        repaint();
    }
}

Example 48 with CyTable

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

the class DGraphView method select.

public void select(Collection<? extends CyIdentifiable> nodesOrEdges, Class<? extends CyIdentifiable> type, boolean selected) {
    if (nodesOrEdges.isEmpty())
        return;
    List<RowSetRecord> records = new ArrayList<>();
    CyTable table = type.equals(CyNode.class) ? getModel().getDefaultNodeTable() : getModel().getDefaultEdgeTable();
    // Disable events
    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
    eventHelper.silenceEventSource(table);
    try {
        for (final CyIdentifiable nodeOrEdge : nodesOrEdges) {
            CyRow row = getModel().getRow(nodeOrEdge);
            row.set(CyNetwork.SELECTED, selected);
            // Add to paylod
            records.add(new RowSetRecord(row, CyNetwork.SELECTED, selected, selected));
        }
    } finally {
        eventHelper.unsilenceEventSource(table);
    }
    // Update the selection before firing the event to prevent race conditions
    updateSelection(type, records);
    // Only now it can fire the RowsSetEvent
    fireRowsSetEvent(table, records, eventHelper);
}

Example 49 with CyTable

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

the class CyRootNetworkImpl method createRootNetworkTables.

private void createRootNetworkTables() {
    final CyTable rawEdgeSharedTable = tableFactory.createTable(suid + " shared edge", CyIdentifiable.SUID, Long.class, false, /*all root tables are private*/
    false, getInitialTableSize(subNetworks.size()));
    final CyTable edgeSharedTable = new SharedTableFacade(rawEdgeSharedTable, this, CyEdge.class, networkTableMgr, eventHelper);
    edgeSharedTable.setPublic(false);
    networkTableMgr.setTable(this, CyEdge.class, CyRootNetwork.SHARED_ATTRS, rawEdgeSharedTable);
    networkTableMgr.setTable(this, CyEdge.class, CyRootNetwork.SHARED_DEFAULT_ATTRS, edgeSharedTable);
    edgeSharedTable.createColumn(CyRootNetwork.SHARED_NAME, String.class, true);
    edgeSharedTable.createColumn(CyRootNetwork.SHARED_INTERACTION, String.class, true);
    final CyTable rawNetworkSharedTable = tableFactory.createTable(suid + " shared network", CyIdentifiable.SUID, Long.class, false, /*all root tables are private*/
    false, InitialTableSize.SMALL);
    final CyTable networkSharedTable = new SharedTableFacade(rawNetworkSharedTable, this, CyNetwork.class, networkTableMgr, eventHelper);
    networkSharedTable.setPublic(false);
    networkTableMgr.setTable(this, CyNetwork.class, CyRootNetwork.SHARED_ATTRS, rawNetworkSharedTable);
    networkTableMgr.setTable(this, CyNetwork.class, CyRootNetwork.SHARED_DEFAULT_ATTRS, networkSharedTable);
    networkSharedTable.createColumn(CyRootNetwork.SHARED_NAME, String.class, true);
    final CyTable rawNodeSharedTable = tableFactory.createTable(suid + " shared node", CyIdentifiable.SUID, Long.class, false, /*all root tables are private*/
    false, getInitialTableSize(subNetworks.size()));
    final CyTable nodeSharedTable = new SharedTableFacade(rawNodeSharedTable, this, CyNode.class, networkTableMgr, eventHelper);
    nodeSharedTable.setPublic(false);
    networkTableMgr.setTable(this, CyNode.class, CyRootNetwork.SHARED_ATTRS, rawNodeSharedTable);
    networkTableMgr.setTable(this, CyNode.class, CyRootNetwork.SHARED_DEFAULT_ATTRS, nodeSharedTable);
    nodeSharedTable.createColumn(CyRootNetwork.SHARED_NAME, String.class, true);
}

Example 50 with CyTable

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

the class CySubNetworkImpl method removeEdges.

@Override
public boolean removeEdges(final Collection<CyEdge> edges) {
    if (edges == null || edges.isEmpty())
        return false;
    // Possible error if one of the edges isn't contained in subnetwork, but
    // since this is only a notification, maybe that's OK.
    eventHelper.fireEvent(new AboutToRemoveEdgesEvent(this, edges));
    CyTable hiddenTable = getTable(CyEdge.class, CyNetwork.HIDDEN_ATTRS);
    CyTable localTable = getTable(CyEdge.class, CyNetwork.LOCAL_ATTRS);
    CyTable defaultTable = getTable(CyEdge.class, CyNetwork.DEFAULT_ATTRS);
    List<Long> suids = new ArrayList<>();
    for (CyEdge edge : edges) {
        if (containsEdge(edge)) {
            // getRow(edge).set(CyNetwork.SELECTED, false);
            suids.add(edge.getSUID());
        }
    }
    boolean ret = removeEdgesInternal(edges);
    hiddenTable.deleteRows(suids);
    defaultTable.deleteRows(suids);
    if (ret) {
        parent.subnetworkEdgesRemoved(edges);
    }
    if (ret) {
        eventHelper.fireEvent(new RemovedEdgesEvent(this));
    }
    return ret;
}