Examples with CyApplicationManager org.cytoscape.application.CyApplicationManager used on opensource projects

Example 11 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class CySessionManagerImpl method disposeCurrentSession.

@Override
public void disposeCurrentSession() {
    logger.debug("Disposing current session...");
    // Destroy network views
    final CyNetworkViewManager nvMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
    final Set<CyNetworkView> netViews = nvMgr.getNetworkViewSet();
    for (final CyNetworkView nv : netViews) nvMgr.destroyNetworkView(nv);
    nvMgr.reset();
    // Destroy networks
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    final Set<CyNetwork> networks = netMgr.getNetworkSet();
    for (final CyNetwork n : networks) netMgr.destroyNetwork(n);
    netMgr.reset();
    // Destroy styles
    logger.debug("Removing current visual styles...");
    final VisualMappingManager vmMgr = serviceRegistrar.getService(VisualMappingManager.class);
    final VisualStyle defaultStyle = vmMgr.getDefaultVisualStyle();
    final List<VisualStyle> allStyles = new ArrayList<>(vmMgr.getAllVisualStyles());
    for (final VisualStyle vs : allStyles) {
        if (!vs.equals(defaultStyle))
            vmMgr.removeVisualStyle(vs);
    }
    // Destroy tables
    final CyTableManager tblMgr = serviceRegistrar.getService(CyTableManager.class);
    tblMgr.reset();
    // Reset groups
    serviceRegistrar.getService(CyGroupManager.class).reset();
    // Unregister session properties
    final Set<CyProperty<?>> cyPropsClone = getAllProperties();
    for (CyProperty<?> cyProps : cyPropsClone) {
        if (cyProps.getSavePolicy().equals(CyProperty.SavePolicy.SESSION_FILE)) {
            serviceRegistrar.unregisterAllServices(cyProps);
            sessionProperties.remove(cyProps.getName());
        }
    }
    // Clear undo stack
    serviceRegistrar.getService(UndoSupport.class).reset();
    // Reset current table and rendering engine
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    appMgr.reset();
    currentFileName = null;
    disposed = true;
}

Example 12 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class LayoutMenuPopulator method checkEnabled.

private boolean checkEnabled() {
    CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetwork network = appMgr.getCurrentNetwork();
    if (network == null)
        return false;
    CyNetworkView view = appMgr.getCurrentNetworkView();
    if (view == null)
        return false;
    else
        return true;
}

Example 13 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class EnhancedSearchPanel method doSearching.

// Do searching based on the query string from user on text-field
private void doSearching() {
    final String queryStr = tfSearchText.getText().trim();
    // Ignore if the search term is empty
    if (queryStr == null || queryStr.length() == 0)
        return;
    final CyApplicationManager appManager = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetwork currentNetwork = appManager.getCurrentNetwork();
    if (currentNetwork != null) {
        final SearchTaskFactory factory = new SearchTaskFactory(searchMgr, queryStr, serviceRegistrar);
        final DialogTaskManager taskMgr = serviceRegistrar.getService(DialogTaskManager.class);
        taskMgr.execute(factory.createTaskIterator(currentNetwork));
    } else {
        logger.error("Could not find network for search");
    }
}

Example 14 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class ExportSelectedNetworkTaskFactoryImpl method createTaskIterator.

@Override
public TaskIterator createTaskIterator() {
    final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
    CyNetworkView view = applicationManager.getCurrentNetworkView();
    if (view != null)
        return getExportNetworkViewTaskFactory().createTaskIterator(view);
    CyNetwork network = applicationManager.getCurrentNetwork();
    if (network != null)
        return getExportNetworkTaskFactory().createTaskIterator(network);
    return null;
}

Example 15 with CyApplicationManager

use of org.cytoscape.application.CyApplicationManager in project cytoscape-impl by cytoscape.

the class PopupMenuHelper method selectElementsFromSelectedRows.

private void selectElementsFromSelectedRows(final JTable table, final Class<? extends CyIdentifiable> tableType) {
    final Thread t = new Thread() {

        @Override
        public void run() {
            final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
            final CyNetwork net = applicationManager.getCurrentNetwork();
            if (net != null) {
                final BrowserTableModel tableModel = (BrowserTableModel) table.getModel();
                final int[] selectedRows = table.getSelectedRows();
                final Set<CyRow> targetRows = new HashSet<CyRow>();
                for (final int rowIndex : selectedRows) {
                    // Getting the row from data table solves the problem with hidden or moved SUID column.
                    // However, since the rows might be sorted we need to convert the index to model.
                    final ValidatedObjectAndEditString selected = (ValidatedObjectAndEditString) tableModel.getValueAt(table.convertRowIndexToModel(rowIndex), CyNetwork.SUID);
                    targetRows.add(tableModel.getRow(selected.getValidatedObject()));
                }
                final CyTable cyTable = tableType == CyNode.class ? net.getDefaultNodeTable() : net.getDefaultEdgeTable();
                for (final CyRow cyRow : cyTable.getAllRows()) cyRow.set(CyNetwork.SELECTED, targetRows.contains(cyRow));
                final CyNetworkView view = applicationManager.getCurrentNetworkView();
                if (view != null) {
                    final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
                    eventHelper.flushPayloadEvents();
                    view.updateView();
                }
            }
        }
    };
    t.start();
}