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

Example 51 with CyApplicationManager

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

the class CellEditorEventHandler method switchMappingType.

private VisualMappingFunction<?, ?> switchMappingType(final VizMapperProperty<?, ?, ?> prop, final VisualProperty<?> vp, final VisualMappingFunctionFactory oldFactory, final VisualMappingFunctionFactory newFactory, final String controllingAttrName, final PropertySheetPanel propertySheetPanel) {
    // This is the currently selected Visual Style.
    final VisualStyle style = servicesUtil.get(VisualMappingManager.class).getCurrentVisualStyle();
    final VisualMappingFunction<?, ?> mapping = style.getVisualMappingFunction(vp);
    VisualMappingFunction<?, ?> newMapping = mapping;
    final Class<?> newMappingType = newFactory.getMappingFunctionType();
    if (mapping == null || mapping.getClass() != newMappingType || !mapping.getMappingColumnName().equals(controllingAttrName)) {
        final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
        final CyNetwork currentNet = appMgr.getCurrentNetwork();
        if (currentNet == null)
            return newMapping;
        // Mapping does not exist. Need to create new one.
        final AttributeSet attrSet = attrProxy.getAttributeSet(currentNet, vp.getTargetDataType());
        Class<?> attributeDataType = attrSet.getAttrMap().get(controllingAttrName);
        if (attributeDataType == null) {
            JOptionPane.showMessageDialog(null, "The current table does not have the selected column (\"" + controllingAttrName + "\").\nPlease select another column.", "Invalid Column.", JOptionPane.WARNING_MESSAGE);
            prop.setValue(oldFactory);
            return newMapping;
        }
        if (newMappingType == ContinuousMapping.class) {
            if (!Number.class.isAssignableFrom(attributeDataType)) {
                JOptionPane.showMessageDialog(null, "Selected column data type is not Number.\nPlease select a numerical column type.", "Incompatible Column Type.", JOptionPane.WARNING_MESSAGE);
                prop.setValue(oldFactory);
                return newMapping;
            }
        } else if (newMappingType == DiscreteMapping.class) {
            if (attributeDataType == List.class)
                attributeDataType = String.class;
        }
        // Create new mapping
        newMapping = newFactory.createVisualMappingFunction(controllingAttrName, attributeDataType, vp);
        // Keep old mapping values if the new mapping has the same type
        if (oldFactory != null && oldFactory.getMappingFunctionType() == newMappingType)
            copyMappingValues(mapping, newMapping);
    }
    // Disable listeners to avoid unnecessary updates
    final PropertySheetTableModel model = (PropertySheetTableModel) propertySheetPanel.getTable().getModel();
    final TableModelListener[] modelListeners = model.getTableModelListeners();
    for (final TableModelListener tm : modelListeners) model.removeTableModelListener(tm);
    vizMapPropertyBuilder.createMappingProperties(newMapping, propertySheetPanel, newFactory);
    // Restore listeners
    for (final TableModelListener tm : modelListeners) model.addTableModelListener(tm);
    return newMapping;
}

Example 52 with CyApplicationManager

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

the class CellEditorEventHandler method switchColumn.

@SuppressWarnings("unchecked")
private VisualMappingFunction<?, ?> switchColumn(final VisualMappingFunctionFactory factory, final AttributeComboBoxPropertyEditor editor, final VizMapperProperty<?, ?, ?> prop, final String columnName, final PropertySheetPanel propertySheetPanel) {
    final VisualStyle currentStyle = servicesUtil.get(VisualMappingManager.class).getCurrentVisualStyle();
    final VisualProperty<?> vp = (VisualProperty<?>) prop.getKey();
    VisualMappingFunction<?, ?> mapping = currentStyle.getVisualMappingFunction(vp);
    // Ignore if not compatible.
    final CyNetworkTableManager netTblMgr = servicesUtil.get(CyNetworkTableManager.class);
    final CyApplicationManager appMgr = servicesUtil.get(CyApplicationManager.class);
    Class<? extends CyIdentifiable> type = (Class<? extends CyIdentifiable>) editor.getTargetObjectType();
    final CyTable table = netTblMgr.getTable(appMgr.getCurrentNetwork(), type, CyNetwork.DEFAULT_ATTRS);
    final CyColumn column = table.getColumn(columnName);
    if (column == null) {
        JOptionPane.showMessageDialog(null, "The current table does not have the selected column (\"" + columnName + "\").\nPlease select another column.", "Invalid Column.", JOptionPane.WARNING_MESSAGE);
        prop.setValue(mapping != null ? mapping.getMappingColumnName() : null);
        return mapping;
    }
    final Class<?> dataType = column.getType();
    if (factory != null && (mapping == null || !columnName.equals(mapping.getMappingColumnName()))) {
        // Need to create new mapping function
        if (ContinuousMapping.class.isAssignableFrom(factory.getMappingFunctionType()) && !Number.class.isAssignableFrom(dataType)) {
            JOptionPane.showMessageDialog(null, "Continuous Mapper can be used with numbers only.\nPlease select a numerical column type.", "Incompatible Mapping Type.", JOptionPane.INFORMATION_MESSAGE);
            prop.setValue(mapping != null ? mapping.getMappingColumnName() : null);
            return mapping;
        }
        return switchMappingType(prop, vp, factory, factory, columnName, propertySheetPanel);
    }
    return mapping;
}

Example 53 with CyApplicationManager

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

the class NetworkCollectionHelper method init.

void init() {
    final CyApplicationManager appMgr = serviceRegistrar.getService(CyApplicationManager.class);
    final CyRootNetworkManager rootNetMgr = serviceRegistrar.getService(CyRootNetworkManager.class);
    // initialize the network Collection
    name2RootMap = getRootNetworkMap();
    final List<String> rootNames = new ArrayList<>();
    rootNames.addAll(name2RootMap.keySet());
    if (!rootNames.isEmpty()) {
        sort(rootNames);
        rootNames.add(0, CREATE_NEW_COLLECTION_STRING);
    }
    rootNetworkList = new ListSingleSelection<>(rootNames);
    final CyNetwork net = appMgr != null ? appMgr.getCurrentNetwork() : null;
    final CyRootNetwork rootNet = net != null ? rootNetMgr.getRootNetwork(net) : null;
    final String rootNetName = rootNet != null ? rootNet.getRow(rootNet).get(CyRootNetwork.NAME, String.class) : CREATE_NEW_COLLECTION_STRING;
    if (rootNames.contains(rootNetName))
        rootNetworkList.setSelectedValue(rootNetName);
    else if (rootNames.contains(CREATE_NEW_COLLECTION_STRING))
        rootNetworkList.setSelectedValue(CREATE_NEW_COLLECTION_STRING);
    if (rootNet != null)
        targetColumnList = getTargetColumns(rootNet);
    else
        targetColumnList = new ListSingleSelection<>();
    // initialize renderer list
    final List<NetworkViewRenderer> renderers = new ArrayList<>();
    final Set<NetworkViewRenderer> rendererSet = appMgr.getNetworkViewRendererSet();
    // so the combo-box does not appear to the user, since there is nothing to select anyway.
    if (rendererSet.size() > 1) {
        renderers.addAll(rendererSet);
        Collections.sort(renderers, new Comparator<NetworkViewRenderer>() {

            @Override
            public int compare(NetworkViewRenderer r1, NetworkViewRenderer r2) {
                return r1.toString().compareToIgnoreCase(r2.toString());
            }
        });
    }
    rendererList = new ListSingleSelection<>(renderers);
    final NetworkViewRenderer defViewRenderer = appMgr.getDefaultNetworkViewRenderer();
    if (defViewRenderer != null && renderers.contains(defViewRenderer))
        rendererList.setSelectedValue(defViewRenderer);
}

Example 54 with CyApplicationManager

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

the class CyNetworkViewManagerImpl method addNetworkView.

@Override
public void addNetworkView(final CyNetworkView view, final boolean setCurrent) {
    if (view == null) {
        // Do nothing if view is null.
        logger.warn("Network view is null.");
        return;
    }
    final CyNetwork network = view.getModel();
    final CyNetworkManager netMgr = serviceRegistrar.getService(CyNetworkManager.class);
    synchronized (lock) {
        if (!netMgr.networkExists(network.getSUID()))
            throw new IllegalArgumentException("Network view cannot be added, because its network (" + network + ") is not registered");
        Collection<CyNetworkView> existingSet = networkViewMap.get(network);
        if (existingSet == null)
            existingSet = new LinkedHashSet<>();
        existingSet.add(view);
        networkViewMap.put(network, existingSet);
    }
    fireEvent(new NetworkViewAddedEvent(this, view));
    if (setCurrent) {
        final CyApplicationManager applicationManager = serviceRegistrar.getService(CyApplicationManager.class);
        if (// It may be null when running unit tests
        applicationManager != null)
            applicationManager.setCurrentNetworkView(view);
    }
}

Example 55 with CyApplicationManager

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

the class CyActivator method start.

@Override
public void start(BundleContext bc) {
    final CyServiceRegistrar serviceRegistrar = getService(bc, CyServiceRegistrar.class);
    final CySwingApplication cySwingApplicationServiceRef = getService(bc, CySwingApplication.class);
    final CyApplicationManager cyApplicationManagerServiceRef = getService(bc, CyApplicationManager.class);
    final CyNetworkViewManager cyNetworkViewManagerServiceRef = getService(bc, CyNetworkViewManager.class);
    invokeOnEDTAndWait(() -> {
        controlPanel = new ControlPanel(serviceRegistrar);
        controlPanelAction = new ControlPanelAction(controlPanel, cySwingApplicationServiceRef, cyApplicationManagerServiceRef, cyNetworkViewManagerServiceRef);
    }, logger);
    registerAllServices(bc, controlPanelAction, new Properties());
    registerAllServices(bc, controlPanel, new Properties());
}