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

Example 46 with CyApplicationManager

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

the class IndexAndSearchTask method updateView.

/**
 * If view(s) exists for the current network, update them.
 */
private void updateView() {
    final CyNetworkViewManager viewManager = serviceRegistrar.getService(CyNetworkViewManager.class);
    final CyApplicationManager appManager = serviceRegistrar.getService(CyApplicationManager.class);
    final Collection<CyNetworkView> views = viewManager.getNetworkViews(network);
    CyNetworkView targetView = null;
    if (views.size() != 0)
        targetView = views.iterator().next();
    if (targetView != null)
        targetView.updateView();
    final CyNetworkView view = appManager.getCurrentNetworkView();
    if (view != null)
        view.updateView();
}

Example 47 with CyApplicationManager

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

the class SessionHandler method setSessionNetworks.

/**
 * @param netOrder Maps CyNetwork SUID to the network position
 */
private void setSessionNetworks(final Map<Long, Integer> netOrder) {
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    final List<CySubNetwork> sortedNetworks = new ArrayList<>();
    for (CyNetwork n : netMgr.getNetworkSet()) {
        if (n instanceof CySubNetwork && netMgr.networkExists(n.getSUID()))
            sortedNetworks.add((CySubNetwork) n);
    }
    Collections.sort(sortedNetworks, new Comparator<CySubNetwork>() {

        @Override
        public int compare(final CySubNetwork n1, final CySubNetwork n2) {
            try {
                Integer o1 = netOrder.get(n1.getSUID());
                Integer o2 = netOrder.get(n2.getSUID());
                if (o1 == null)
                    o1 = -1;
                if (o2 == null)
                    o2 = -1;
                return o1.compareTo(o2);
            } catch (final Exception e) {
                logger.error("Cannot sort networks", e);
            }
            return 0;
        }
    });
    final CyApplicationManager applicationMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final CyNetworkViewManager netViewMgr = serviceRegistrar.getService(CyNetworkViewManager.class);
    final List<CyNetwork> selectedNetworks = applicationMgr.getSelectedNetworks();
    final List<CyNetworkView> selectedViews = applicationMgr.getSelectedNetworkViews();
    invokeOnEDT(() -> {
        netPanel.setNetworks(sortedNetworks);
        for (SubNetworkPanel snp : netPanel.getAllSubNetworkItems()) {
            final int count = netViewMgr.getNetworkViews(snp.getModel().getNetwork()).size();
            snp.getModel().setViewCount(count);
        }
        netPanel.setSelectedNetworks(selectedNetworks);
        netViewMediator.getNetworkViewMainPanel().setSelectedNetworkViews(selectedViews);
    });
}

Example 48 with CyApplicationManager

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

the class BrowserTable method selectFromTable.

private void selectFromTable() {
    final TableModel model = this.getModel();
    if (model instanceof BrowserTableModel == false)
        return;
    final BrowserTableModel btModel = (BrowserTableModel) model;
    if (btModel.getViewMode() != BrowserTableModel.ViewMode.ALL)
        return;
    final CyTable table = btModel.getDataTable();
    final CyColumn pKey = table.getPrimaryKey();
    final String pKeyName = pKey.getName();
    final int[] rowsSelected = getSelectedRows();
    if (rowsSelected.length == 0)
        return;
    final int selectedRowCount = getSelectedRowCount();
    final Set<CyRow> targetRows = new HashSet<CyRow>();
    for (int i = 0; i < selectedRowCount; i++) {
        // 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) btModel.getValueAt(convertRowIndexToModel(rowsSelected[i]), pKeyName);
        targetRows.add(btModel.getRow(selected.getValidatedObject()));
    }
    // Clear selection for non-global table
    final CyTableManager tableManager = serviceRegistrar.getService(CyTableManager.class);
    if (tableManager.getGlobalTables().contains(table) == false) {
        List<CyRow> allRows = btModel.getDataTable().getAllRows();
        try {
            ignoreRowSetEvents = true;
            for (CyRow row : allRows) {
                final Boolean val = row.get(CyNetwork.SELECTED, Boolean.class);
                if (targetRows.contains(row)) {
                    row.set(CyNetwork.SELECTED, true);
                    continue;
                }
                if (val != null && (val == true))
                    row.set(CyNetwork.SELECTED, false);
            }
            final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
            final CyNetworkView curView = applicationManager.getCurrentNetworkView();
            if (curView != null) {
                final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
                eventHelper.flushPayloadEvents();
                curView.updateView();
            }
        } finally {
            ignoreRowSetEvents = false;
        }
        repaint();
    }
}

Example 49 with CyApplicationManager

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

the class LayoutMenuPopulator method menuSelected.

@Override
public void menuSelected(MenuEvent e) {
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final DialogTaskManager tm = serviceRegistrar.getService(DialogTaskManager.class);
    CyNetworkView view = appMgr.getCurrentNetworkView();
    CyNetwork network = appMgr.getCurrentNetwork();
    // Figure out if we have anything selected
    boolean someSelected = false;
    if (network != null)
        someSelected = network.getDefaultNodeTable().countMatchingRows(CyNetwork.SELECTED, true) > 0;
    boolean enableMenuItem = checkEnabled();
    // Get all of the algorithms
    for (CyLayoutAlgorithm layout : algorithmMap.keySet()) {
        Map props = algorithmMap.get(layout);
        double gravity = 1000.0;
        if (props.get(MENU_GRAVITY) != null)
            gravity = Double.parseDouble((String) props.get(MENU_GRAVITY));
        boolean separatorAfter = false;
        if (props.get(INSERT_SEPARATOR_AFTER) != null)
            separatorAfter = Boolean.parseBoolean((String) props.get(INSERT_SEPARATOR_AFTER));
        boolean separatorBefore = false;
        if (props.get(INSERT_SEPARATOR_BEFORE) != null)
            separatorBefore = Boolean.parseBoolean((String) props.get(INSERT_SEPARATOR_BEFORE));
        // Remove the old menu
        if (menuMap.containsKey(layout)) {
            layoutMenu.remove(menuMap.remove(layout));
        }
        boolean usesNodeAttrs = false;
        if (network != null)
            usesNodeAttrs = hasValidAttributes(layout.getSupportedNodeAttributeTypes(), network.getDefaultNodeTable());
        boolean usesEdgeAttrs = false;
        if (network != null)
            usesEdgeAttrs = hasValidAttributes(layout.getSupportedEdgeAttributeTypes(), network.getDefaultEdgeTable());
        boolean usesSelected = (layout.getSupportsSelectedOnly() && someSelected);
        if (usesNodeAttrs || usesEdgeAttrs || usesSelected) {
            JMenu newMenu = new DynamicLayoutMenu(layout, network, enableMenuItem, appMgr, tm, usesNodeAttrs, usesEdgeAttrs, usesSelected);
            menuMap.put(layout, newMenu);
            gravityTracker.addMenu(newMenu, gravity);
        } else {
            JMenuItem newMenu = new StaticLayoutMenu(layout, enableMenuItem, appMgr, tm);
            menuMap.put(layout, newMenu);
            gravityTracker.addMenuItem(newMenu, gravity);
        }
        if (separatorAfter && !separatorMap.containsKey(layout)) {
            gravityTracker.addMenuSeparator(gravity + 0.0001);
            separatorMap.put(layout, Boolean.TRUE);
        } else if (separatorBefore && !separatorMap.containsKey(layout)) {
            gravityTracker.addMenuSeparator(gravity - 0.0001);
            separatorMap.put(layout, Boolean.TRUE);
        }
    }
}

Example 50 with CyApplicationManager

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

the class CyNetworkViewManagerTest method setUp.

@Before
public void setUp() throws Exception {
    super.setUp();
    CyApplicationManager applicationManager = mock(CyApplicationManager.class);
    when(serviceRegistrar.getService(CyApplicationManager.class)).thenReturn(applicationManager);
}