/**
* @param title Title of the new Visual Style
* @param lexManager
*/
public VisualStyleImpl(
final String title,
final VisualLexiconManager lexManager,
final CyServiceRegistrar serviceRegistrar,
final CyEventHelper eventHelper) {
if (lexManager == null) throw new NullPointerException("Lexicon Manager is missing.");
if (title == null) this.title = DEFAULT_TITLE;
else this.title = title;
this.eventHelper = eventHelper;
mappings = new HashMap<VisualProperty<?>, VisualMappingFunction<?, ?>>();
styleDefaults = new HashMap<VisualProperty<?>, Object>();
// Init Apply handlers for node, egde and network.
applyHandlersMap = new HashMap<Class<? extends CyIdentifiable>, ApplyHandler>();
applyHandlersMap.put(CyNetwork.class, new ApplyToNetworkHandler(this, lexManager));
applyHandlersMap.put(CyNode.class, new ApplyToNodeHandler(this, lexManager));
applyHandlersMap.put(CyEdge.class, new ApplyToEdgeHandler(this, lexManager));
dependencies = new HashSet<VisualPropertyDependency<?>>();
// Listening to dependencies
serviceRegistrar.registerServiceListener(
this,
"registerDependencyFactory",
"unregisterDependencyFactory",
VisualPropertyDependencyFactory.class);
serviceRegistrar.registerService(
this, VisualMappingFunctionChangedListener.class, new Properties());
logger.info("New Visual Style Created: Style Name = " + this.title);
}
@Override
public void run(TaskMonitor taskMonitor) throws Exception {
taskMonitor.setTitle("Loading Gene Association File");
taskMonitor.setStatusMessage("Importing annotation file. Please wait...");
taskMonitor.setProgress(-1.0);
this.ontologyDAG = OntologyDAGManager.getOntologyDAG(ontologyDagName);
if (ontologyDAG == null) logger.warn("Could not find associated Ontology DAG.");
else {
termIDList =
ontologyDAG.getDefaultNodeTable().getColumn(CyNetwork.NAME).getValues(String.class);
}
BufferedReader bufRd =
new BufferedReader(new InputStreamReader(is, Charset.forName("UTF-8").newDecoder()));
String line = null;
String[] parts;
while ((line = bufRd.readLine()) != null) {
// Validate.
if (line.contains(COMPATIBLE_VERSION)) break;
}
// Create result table
table =
serviceRegistrar
.getService(CyTableFactory.class)
.createTable(tableName, CyNetwork.NAME, String.class, true, true);
createColumns();
while ((line = bufRd.readLine()) != null) {
if (line.startsWith("!")) continue;
parts = line.split(GA_DELIMITER);
// GA is a fixed format file. Read only valid lines.
if (parts.length >= EXPECTED_COL_COUNT) {
parseGA(parts);
}
}
bufRd.close();
is.close();
is = null;
tables = new CyTable[1];
tables[0] = table;
serviceRegistrar.getService(CyTableManager.class).addTable(table);
}
/** Initializes the button. */
private void initButtons() {
final IconManager iconManager = serviceRegistrar.getService(IconManager.class);
// Create Float / Dock Button
floatButton = new JButton(ICON_SQUARE_O);
floatButton.setToolTipText(TOOL_TIP_FLOAT);
CytoPanelUtil.styleButton(floatButton);
floatButton.setFont(iconManager.getIconFont(12));
floatButton.setSelected(true);
// Create close button
closeButton = new JButton(ICON_REMOVE);
closeButton.setToolTipText(TOOL_TIP_CLOSE);
CytoPanelUtil.styleButton(closeButton);
closeButton.setFont(iconManager.getIconFont(13));
closeButton.setSelected(true);
floatButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
if (isFloating()) DockCytoPanel();
else FloatCytoPanel();
notifyListeners(NOTIFICATION_STATE_CHANGE);
}
});
closeButton.addActionListener(
new ActionListener() {
public void actionPerformed(ActionEvent e) {
setState(CytoPanelState.HIDE);
notifyListeners(NOTIFICATION_STATE_CHANGE);
}
});
}
void setNetworkView(final CyNetworkView view) {
getApplyBtn().setEnabled(view != null);
if (layoutAttrPnl == null) return;
layoutAttrPnl.removeAll();
layoutAttrTunable = new LayoutAttributeTunable();
if (view != null) {
List<String> attributeList =
getAttributeList(
view.getModel(),
currentLayout.getSupportedNodeAttributeTypes(),
currentLayout.getSupportedEdgeAttributeTypes());
if (attributeList.size() > 0) {
layoutAttrTunable.layoutAttribute = new ListSingleSelection<String>(attributeList);
layoutAttrTunable.layoutAttribute.setSelectedValue(attributeList.get(0));
final PanelTaskManager taskMgr = serviceRegistrar.getService(PanelTaskManager.class);
JPanel panel = taskMgr.getConfiguration(null, layoutAttrTunable);
setPanelsTransparent(panel);
layoutAttrPnl.add(panel);
panel.invalidate();
}
}
}
private void updatePrefAlgorithmCmb() {
final CyLayoutAlgorithm defLayout =
serviceRegistrar.getService(CyLayoutAlgorithmManager.class).getDefaultLayout();
if (defLayout != null && !defLayout.equals(getPrefAlgorithmCmb().getSelectedItem()))
getPrefAlgorithmCmb().setSelectedItem(defLayout);
}
private void initialize() {
initializing = true;
try {
final Collator collator = Collator.getInstance(Locale.getDefault());
final TreeSet<CyLayoutAlgorithm> allLayouts =
new TreeSet<>(
new Comparator<CyLayoutAlgorithm>() {
@Override
public int compare(CyLayoutAlgorithm o1, CyLayoutAlgorithm o2) {
return collator.compare(o1.toString(), o2.toString());
}
});
allLayouts.addAll(
serviceRegistrar.getService(CyLayoutAlgorithmManager.class).getAllLayouts());
// Populate the algorithm selectors
getAlgorithmCmb().removeAllItems();
getPrefAlgorithmCmb().removeAllItems();
for (CyLayoutAlgorithm algo : allLayouts) {
getAlgorithmCmb().addItem(algo);
getPrefAlgorithmCmb().addItem(algo);
}
} finally {
initializing = false;
}
if (currentLayout != null) getAlgorithmCmb().setSelectedItem(currentLayout);
else if (getAlgorithmCmb().getModel().getSize() > 0) getAlgorithmCmb().setSelectedIndex(0);
}
private void saveLayoutContexts() {
final PanelTaskManager taskMgr = serviceRegistrar.getService(PanelTaskManager.class);
for (CyLayoutAlgorithm layout : tunablesToSave) {
layoutSettingsMgr.saveLayoutContext(taskMgr, layout);
}
tunablesToSave.clear();
}
public ResultPanel registerPanel(final Component panel, final String panelTitle) {
final ResultPanel resPanel = new ResultPanel(panelTitle);
JScrollPane pane = new JScrollPane(panel);
// pane.setViewportView(panel);
resPanel.setLayout(new BorderLayout());
resPanel.add(pane, BorderLayout.CENTER);
registrar.registerAllServices(resPanel, new Properties());
return resPanel;
}
public GUICyJobMonitor(
CyServiceRegistrar registrar, CyJobManagerImpl jobManager, JobStatusBar statusBar) {
this.serviceRegistrar = registrar;
this.jobManager = jobManager;
this.statusBar = statusBar;
jobManager.setJobMonitor(this);
logger = Logger.getLogger(CyUserLog.NAME);
statusMap = new ConcurrentHashMap<>();
CySwingApplication swingApp = registrar.getService(CySwingApplication.class);
dialog = new GUIJobDialog(serviceRegistrar, swingApp, statusMap, jobManager, this);
statusBar.setDialog(dialog);
}
@Before
public void setUp() throws Exception {
NetworkTestSupport netSupport = new NetworkTestSupport();
TableTestSupport tableSupport = new TableTestSupport();
CyNetworkFactory cyNetworkFactory = netSupport.getNetworkFactory();
tableFactory = tableSupport.getTableFactory();
tableManager = mock(CyTableManager.class);
dag = cyNetworkFactory.createNetwork();
tm = mock(TaskMonitor.class);
serviceRegistrar = mock(CyServiceRegistrar.class);
when(serviceRegistrar.getService(CyTableFactory.class)).thenReturn(tableFactory);
when(serviceRegistrar.getService(CyTableManager.class)).thenReturn(tableManager);
}
@Override
public void actionPerformed(ActionEvent e) {
// Initialize and display
if (isVisible()) {
requestFocus();
} else {
if (!initialized) {
initialize();
updatePrefAlgorithmCmb();
setLocationRelativeTo(getOwner());
pack();
}
setVisible(true);
initialized = true;
}
setNetworkView(serviceRegistrar.getService(CyApplicationManager.class).getCurrentNetworkView());
}
/**
* Code to notify our listeners of some particular event.
*
* @param notificationType What type of notification to perform.
*/
private void notifyListeners(int notificationType) {
final CyEventHelper eventHelper = serviceRegistrar.getService(CyEventHelper.class);
// determine what event to fire
switch (notificationType) {
case NOTIFICATION_STATE_CHANGE:
eventHelper.fireEvent(new CytoPanelStateChangedEvent(this, this, cytoPanelState));
break;
case NOTIFICATION_COMPONENT_SELECTED:
int selectedIndex = tabbedPane.getSelectedIndex();
eventHelper.fireEvent(new CytoPanelComponentSelectedEvent(this, this, selectedIndex));
break;
case NOTIFICATION_COMPONENT_ADDED:
break;
case NOTIFICATION_COMPONENT_REMOVED:
break;
}
}
public void removePanel(ResultPanel panel) {
if (panel != null) {
registrar.unregisterAllServices(panel);
}
}