private void buildStatusBar() {
// create task monitor panel
StatusBarPanel taskMonitorPane = new TaskMonitorPanel();
// create notification handler
StatusBarPanel notificationPane = new NotificationPanel();
statusBar = new StatusBar(taskMonitorPane, notificationPane);
mainFrame.getContentPane().add(statusBar, BorderLayout.PAGE_END);
}
/** make menu bar a separate component */
private void buildMenuToolBar() {
// get property manager
PrideInspectorContext context = (PrideInspectorContext) getDesktopContext();
// create all the actions
// file open action
Icon openFileIcon = GUIUtilities.loadIcon(context.getProperty("open.file.icon.small"));
String openFileDesc = context.getProperty("open.file.title");
String openFileTooltip = context.getProperty("open.file.tooltip");
PrideAction openFileAction = new OpenFileAction(openFileDesc, openFileIcon);
// database open action
Icon openDbIcon = GUIUtilities.loadIcon(context.getProperty("open.database.icon.small"));
String openDbDesc = context.getProperty("open.database.title");
String openDbTooltip = context.getProperty("open.database.tooltip");
PrideAction openDbAction = new OpenDatabaseAction(openDbDesc, openDbIcon);
// open reviewer
Icon openReviewerIcon =
GUIUtilities.loadIcon(context.getProperty("reviewer.download.icon.small"));
String openReviewerDesc = context.getProperty("reviewer.download.title");
String openReviewerTooltip = context.getProperty("reviewer.download.tooltip");
PrideAction openReviewerAction = new OpenReviewAction(openReviewerDesc, openReviewerIcon);
// close
String closeDesc = context.getProperty("close.source.title");
String closeAllDesc = context.getProperty("close.all.soruce.title");
PrideAction closeAction = new CloseControllerAction(closeDesc, null);
PrideAction closeAllAction = new CloseAllControllersAction(closeAllDesc, null);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) closeAction);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) closeAllAction);
// try pride xml sample
String openPrideXmlExampleDesc = context.getProperty("open.pride.xml.example.title");
File prideXmlExampleFile =
getExampleFiles(context.getProperty("pride.inspector.pride.example.file"));
java.util.List<File> prideXmlFiles = new ArrayList<File>();
if (prideXmlExampleFile != null) {
prideXmlFiles.add(prideXmlExampleFile);
}
PrideAction openPrideXmlExampleAction =
new OpenFileAction(openPrideXmlExampleDesc, null, prideXmlFiles);
openPrideXmlExampleAction.setEnabled(
prideXmlExampleFile != null && prideXmlExampleFile.exists());
// try mzml sample
String openMzMLExampleDesc = context.getProperty("open.mzml.example.title");
File mzMLExampleFile =
getExampleFiles(context.getProperty("pride.inspector.mzml.example.file"));
java.util.List<File> mzMLFiles = new ArrayList<File>();
if (mzMLExampleFile != null) {
mzMLFiles.add(mzMLExampleFile);
}
PrideAction openMzMLExampleAction = new OpenFileAction(openMzMLExampleDesc, null, mzMLFiles);
openMzMLExampleAction.setEnabled(mzMLExampleFile != null && mzMLExampleFile.exists());
// help
Icon helpIcon = GUIUtilities.loadIcon(context.getProperty("help.icon.small"));
String helpDesc = context.getProperty("help.title");
String helpTooltip = context.getProperty("help.tooltip");
PrideAction helpAction = new OpenHelpAction(helpDesc, helpIcon);
// faq
String faqDesc = context.getProperty("faq.title");
PrideAction faqAction = new OpenFAQAction(faqDesc, null);
// pride website
String prideWeb = context.getProperty("open.pride.website.title");
String prideWebUrl = context.getProperty("pride.website");
PrideAction prideWebAction = new OpenUrlAction(prideWeb, null, prideWebUrl);
// pride website
String inspectorWeb = context.getProperty("open.pride.inspector.website.title");
String inspectorWebUrl = context.getProperty("pride.inspector.website");
PrideAction inspectorWebAction = new OpenUrlAction(inspectorWeb, null, inspectorWebUrl);
// feedback
String feedbackDesc = context.getProperty("feedback.title");
PrideAction feedBackAction = new FeedbackAction(feedbackDesc, null);
// export
String exportDesc = context.getProperty("export.title");
PrideAction exportAction = new ExportSpectrumAction(exportDesc, null);
context.addPropertyChangeListenerToDataAccessMonitor((PropertyChangeListener) exportAction);
// export identification
String exportIdentDesc = context.getProperty("export.identification.title");
PrideAction exportIdentAction = new ExportIdentificationPeptideAction(exportIdentDesc, null);
// export spectrum description
String exportSpectrumDesc = context.getProperty("export.spectrum.desc.title");
PrideAction exportSpectrumDescAction = new ExportSpectrumDescAction(exportSpectrumDesc, null);
// export identification description
String exportIdentDescTitle = context.getProperty("export.identification.desc.title");
PrideAction exportIdentDescAction =
new ExportIdentificationDescAction(exportIdentDescTitle, null);
// export peptide description
String exportPeptideDescTitle = context.getProperty("export.peptide.desc.title");
PrideAction exportPeptideAction = new ExportPeptideDescAction(exportPeptideDescTitle, null);
// make experiment public
String makeExpPublicTitle = context.getProperty("make.experiment.public.title");
PrideAction makeExpPublicAction = new MakeExperimentPublicAction(makeExpPublicTitle, null);
String createReviewerTitle = context.getProperty("create.reviewer.title");
PrideAction createReviewerAction = new CreateReviewerAction(createReviewerTitle, null);
// check update
String updateDescTitle = context.getProperty("check.update.desc.title");
PrideAction updateAction = new UpdateAction(updateDescTitle, null);
// about
String aboutDesc = context.getProperty("about.title");
PrideAction aboutAction = new AboutAction(aboutDesc, null);
// exit
String exitDesc = context.getProperty("exit.title");
PrideAction exitAction = new ExitAction(exitDesc, null);
// menu items
menuBar = new JMenuBar();
// file menu
JMenu fileMenu =
MenuFactory.createMenu(
"File",
openFileAction,
openDbAction,
openReviewerAction,
MenuFactory.ACTION_SEPARATOR,
closeAction,
closeAllAction,
MenuFactory.ACTION_SEPARATOR,
exitAction);
fileMenu.setMnemonic(java.awt.event.KeyEvent.VK_F);
menuBar.add(fileMenu);
// try samples
JMenu trySampleMenu =
MenuFactory.createMenu("Examples", openPrideXmlExampleAction, openMzMLExampleAction);
trySampleMenu.setMnemonic(java.awt.event.KeyEvent.VK_X);
menuBar.add(trySampleMenu);
// export menu
JMenu exportMenu =
MenuFactory.createMenu(
"Export",
exportAction,
exportSpectrumDescAction,
exportIdentAction,
exportIdentDescAction,
exportPeptideAction);
exportMenu.setMnemonic(java.awt.event.KeyEvent.VK_E);
menuBar.add(exportMenu);
// curation menu
boolean showCurationMenu = Boolean.parseBoolean(context.getProperty("include.curation.menu"));
if (showCurationMenu) {
JMenu curationMenu =
MenuFactory.createMenu("Curation", makeExpPublicAction, createReviewerAction);
curationMenu.setMnemonic(java.awt.event.KeyEvent.VK_C);
menuBar.add(curationMenu);
}
// help menu
JMenu helpMenu =
MenuFactory.createMenu(
"Help",
helpAction,
faqAction,
MenuFactory.ACTION_SEPARATOR,
prideWebAction,
inspectorWebAction,
MenuFactory.ACTION_SEPARATOR,
feedBackAction,
MenuFactory.ACTION_SEPARATOR,
updateAction,
aboutAction);
helpMenu.setMnemonic(java.awt.event.KeyEvent.VK_H);
menuBar.add(helpMenu);
// add menus
mainFrame.setJMenuBar(menuBar);
// tool bar
toolBar = new JToolBar();
// open file
JButton openFileButton = new JButton();
openFileButton.setAction(openFileAction);
openFileButton.setText("");
openFileButton.setToolTipText(openFileTooltip);
openFileButton.setFocusable(false);
toolBar.add(openFileButton);
// open database
JButton openDbButton = new JButton();
openDbButton.setAction(openDbAction);
openDbButton.setText("");
openDbButton.setToolTipText(openDbTooltip);
openDbButton.setFocusable(false);
toolBar.add(openDbButton);
// open reviewer download
JButton openReviewerButton = new JButton();
openReviewerButton.setAction(openReviewerAction);
openReviewerButton.setText("");
openReviewerButton.setToolTipText(openReviewerTooltip);
openReviewerButton.setFocusable(false);
toolBar.add(openReviewerButton);
// separator
toolBar.addSeparator();
// help
JButton helpButton = new JButton(helpIcon);
helpButton.setAction(helpAction);
helpButton.setText("");
helpButton.setToolTipText(helpTooltip);
helpButton.setFocusable(false);
toolBar.add(helpButton);
mainFrame.getContentPane().add(toolBar, BorderLayout.PAGE_START);
}
private void buildMainDisplay() {
visualizer = new MainDataVisualizer();
mainFrame.getContentPane().add(visualizer, BorderLayout.CENTER);
}