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

Example 56 with CyApplicationManager

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

the class NetworkSelectionMediator method updateApplicationManager.

private void updateApplicationManager(final CyNetwork currentNetwork, final CyNetworkView currentView, final Collection<CyNetwork> selectedNetworks, final Collection<CyNetworkView> selectedViews) {
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    appMgr.setSelectedNetworks(new ArrayList<>(selectedNetworks));
    appMgr.setCurrentNetwork(currentNetwork);
    appMgr.setSelectedNetworkViews(new ArrayList<>(selectedViews));
    appMgr.setCurrentNetworkView(currentView);
}

Example 57 with CyApplicationManager

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

the class DefaultTableBrowser method handleEvent.

@Override
public void handleEvent(final TableAddedEvent e) {
    final CyTable newTable = e.getTable();
    if (newTable.isPublic() || showPrivateTables()) {
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        final CyNetworkTableManager netTableManager = serviceRegistrar.getService(CyNetworkTableManager.class);
        final CyNetwork curNet = applicationManager.getCurrentNetwork();
        if (curNet != null && netTableManager.getTables(curNet, objType).containsValue(newTable)) {
            invokeOnEDT(() -> {
                if (((DefaultComboBoxModel<CyTable>) getTableChooser().getModel()).getIndexOf(newTable) < 0) {
                    getTableChooser().addItem(newTable);
                    getToolBar().updateEnableState(getTableChooser());
                }
            });
        }
    }
}

Example 58 with CyApplicationManager

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

the class DefaultTableBrowser method actionPerformed.

@Override
public void actionPerformed(final ActionEvent e) {
    if (!ignoreSetCurrentTable) {
        final CyTable table = (CyTable) getTableChooser().getSelectedItem();
        currentTable = table;
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        if (table != null && !table.equals(applicationManager.getCurrentTable())) {
            final CyTableManager tableManager = serviceRegistrar.getService(CyTableManager.class);
            if (tableManager.getTable(table.getSUID()) != null)
                applicationManager.setCurrentTable(table);
        }
        showSelectedTable();
        changeSelectionMode();
    }
}

Example 59 with CyApplicationManager

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

the class CyActivator method initComponents.

private void initComponents(final BundleContext bc, final CyServiceRegistrar serviceRegistrar) {
    CyApplicationManager applicationManager = getService(bc, CyApplicationManager.class);
    CyNetworkViewManager netViewManager = getService(bc, CyNetworkViewManager.class);
    final CytoscapeMenuBar cytoscapeMenuBar = new CytoscapeMenuBar(serviceRegistrar);
    final CytoscapeToolBar cytoscapeToolBar = new CytoscapeToolBar(serviceRegistrar);
    cytoscapeMenus = new CytoscapeMenus(cytoscapeMenuBar, cytoscapeToolBar);
    toolBarEnableUpdater = new ToolBarEnableUpdater(cytoscapeToolBar, serviceRegistrar);
    netSearchBar = new NetworkSearchBar(serviceRegistrar);
    netSearchMediator = new NetworkSearchMediator(netSearchBar, serviceRegistrar);
    netMainPanel = new NetworkMainPanel(netSearchBar, serviceRegistrar);
    netMediator = new NetworkMediator(netMainPanel, serviceRegistrar);
    commandToolPanel = new CommandToolDialog(serviceRegistrar);
    viewComparator = new ViewComparator(netMainPanel);
    gridViewToggleModel = new GridViewToggleModel(GridViewToggleModel.Mode.VIEW);
    netViewMainPanel = new NetworkViewMainPanel(gridViewToggleModel, cytoscapeMenus, viewComparator, serviceRegistrar);
    netViewMediator = new NetworkViewMediator(netViewMainPanel, netMediator, gridViewToggleModel, serviceRegistrar);
    cytoscapeDesktop = new CytoscapeDesktop(cytoscapeMenus, netViewMediator, serviceRegistrar);
    final SessionIO sessionIO = new SessionIO();
    sessionHandler = new SessionHandler(cytoscapeDesktop, netViewMediator, sessionIO, netMainPanel, serviceRegistrar);
    layoutMenuPopulator = new LayoutMenuPopulator(cytoscapeMenuBar, serviceRegistrar);
    cytoscapeMenuPopulator = new CytoscapeMenuPopulator(cytoscapeDesktop, serviceRegistrar);
    layoutSettingsManager = new LayoutSettingsManager(serviceRegistrar);
    helpUserManualTaskFactory = new HelpUserManualTaskFactory(serviceRegistrar);
    helpContactHelpDeskTaskFactory = new HelpContactHelpDeskTaskFactory(serviceRegistrar);
    helpReportABugTaskFactory = new HelpReportABugTaskFactory(serviceRegistrar);
    helpAboutTaskFactory = new HelpAboutTaskFactory(serviceRegistrar);
    cyDesktopManager = new CyDesktopManager(netViewMediator);
    arrangeGridTaskFactory = new ArrangeTaskFactory(GRID, cyDesktopManager, netViewMediator);
    arrangeCascadeTaskFactory = new ArrangeTaskFactory(CASCADE, cyDesktopManager, netViewMediator);
    arrangeHorizontalTaskFactory = new ArrangeTaskFactory(HORIZONTAL, cyDesktopManager, netViewMediator);
    arrangeVerticalTaskFactory = new ArrangeTaskFactory(VERTICAL, cyDesktopManager, netViewMediator);
    preferencesDialogFactory = new PreferencesDialogFactory(serviceRegistrar);
    // cy3preferencesDialogFactory = new Cy3PreferencesDialogFactory(serviceRegistrar);
    bookmarkDialogFactory = new BookmarkDialogFactory(serviceRegistrar);
    undoMonitor = new UndoMonitor(serviceRegistrar);
    rowViewTracker = new RowViewTracker();
    selecteEdgeViewUpdater = new SelectEdgeViewUpdater(rowViewTracker);
    selecteNodeViewUpdater = new SelectNodeViewUpdater(rowViewTracker);
    rowsSetViewUpdater = new RowsSetViewUpdater(rowViewTracker, netViewMediator, serviceRegistrar);
    recentSessionManager = new RecentSessionManager(serviceRegistrar);
    netSelectionMediator = new NetworkSelectionMediator(netMainPanel, netViewMainPanel, serviceRegistrar);
    // /// CyActions ////
    undoAction = new UndoAction(serviceRegistrar);
    redoAction = new RedoAction(serviceRegistrar);
    printAction = new PrintAction(applicationManager, netViewManager, serviceRegistrar);
    exitAction = new ExitAction(serviceRegistrar);
    // cy3preferenceAction = new Cy3PreferenceAction(cytoscapeDesktop, cy3preferencesDialogFactory);
    preferenceAction = new PreferenceAction(cytoscapeDesktop, preferencesDialogFactory);
    bookmarkAction = new BookmarkAction(cytoscapeDesktop, bookmarkDialogFactory);
    settingsAction = new SettingsAction(layoutSettingsManager, serviceRegistrar);
    cytoPanelWestAction = new CytoPanelAction(WEST, true, cytoscapeDesktop, 1.0f);
    cytoPanelSouthAction = new CytoPanelAction(SOUTH, true, cytoscapeDesktop, 1.1f);
    cytoPanelEastAction = new CytoPanelAction(EAST, false, cytoscapeDesktop, 1.2f);
    cytoPanelSouthWestAction = new CytoPanelAction(SOUTH_WEST, false, cytoscapeDesktop, 1.3f);
    cytoPanelCommandAction = new CytoPanelAction(BOTTOM, false, cytoscapeDesktop, 1.35f);
    starterPanelAction = new StarterPanelAction(1.4f, cytoscapeDesktop);
    detachedViewToolBarAction = new DetachedViewToolBarAction(1.5f, netViewMediator);
    closeWindowAction = new CloseWindowAction(6.1f, netViewMediator);
    createNetworkViewsAction = new CreateNetworkViewsAction(3.0f, serviceRegistrar);
    destroyNetworkViewsAction = new DestroyNetworkViewsAction(3.1f, serviceRegistrar);
    destroyNetworksAction = new DestroyNetworksAction(3.2f, netMainPanel, serviceRegistrar);
    exportNetworkAction = new ExportNetworkAction(1000.1f, serviceRegistrar);
    exportImageAction = new ExportImageAction(1000.2f, serviceRegistrar);
}

Example 60 with CyApplicationManager

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

the class PopupMenuHelper method createTableCellMenu.

@SuppressWarnings("serial")
public void createTableCellMenu(final CyColumn column, final Object primaryKeyValue, final Class<? extends CyIdentifiable> tableType, final Component invoker, final int x, final int y, final JTable table) {
    final JPopupMenu menu = new JPopupMenu();
    // Add preset menu items
    menu.add(new JMenuItem(new AbstractAction("Edit") {

        @Override
        public void actionPerformed(ActionEvent e) {
            Point point = new Point(x, y);
            int row = table.rowAtPoint(point);
            int column = table.columnAtPoint(point);
            table.editCellAt(row, column);
            table.transferFocus();
        }
    }));
    final Object value = column.getTable().getRow(primaryKeyValue).get(column.getName(), column.getType());
    if (value != null) {
        String urlString = value.toString();
        if (urlString != null && (urlString.startsWith("http:") || urlString.startsWith("https:")))
            menu.add(getOpenLinkMenu(value.toString()));
    }
    final PopupMenuGravityTracker tracker = new PopupMenuGravityTracker(menu);
    for (final Map.Entry<TableCellTaskFactory, Map<?, ?>> mapEntry : tableCellFactoryMap.entrySet()) {
        TableCellTaskFactory taskFactory = mapEntry.getKey();
        TaskFactory provisioner = factoryProvisioner.createFor(taskFactory, column, primaryKeyValue);
        createMenuItem(provisioner, tracker, mapEntry.getValue(), tableType);
    }
    if (tableType == CyNode.class || tableType == CyEdge.class) {
        menu.add(new JSeparator());
        final String name = String.format("Select %s from selected rows", tableType == CyNode.class ? "nodes" : "edges");
        final JMenuItem mi = new JMenuItem(new AbstractAction(name) {

            @Override
            public void actionPerformed(ActionEvent e) {
                selectElementsFromSelectedRows(table, tableType);
            }

            @Override
            public boolean isEnabled() {
                final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
                return table.getSelectedRowCount() > 0 && applicationManager.getCurrentNetwork() != null;
            }
        });
        menu.add(mi);
    }
    if (menu.getSubElements().length > 0)
        menu.show(invoker, x, y);
}