/**
* Processing the input command line arguments
*
* @param args a list of pride db accessions
*/
private void processCmdArgs(String[] args) {
try {
// parse command line input
CommandLine cmd = cmdParser.parse(cmdOptions, args);
// get accessions
java.util.List<Comparable> accs = null;
if (cmd.hasOption(ACCESSION_CMD)) {
String accStr = cmd.getOptionValue(ACCESSION_CMD);
accs = new ArrayList<Comparable>(AccessionUtils.expand(accStr));
}
// get user name
String username = null;
if (cmd.hasOption(USER_NAME_CMD)) {
username = cmd.getOptionValue(USER_NAME_CMD);
}
// get password
String password = null;
if (cmd.hasOption(PASSWORD_CMD)) {
password = cmd.getOptionValue(PASSWORD_CMD);
}
if (accs != null || username != null) {
OpenValidPrideExperimentTask task =
new OpenValidPrideExperimentTask(accs, username, password);
task.setGUIBlocker(new DefaultGUIBlocker(task, GUIBlocker.Scope.NONE, null));
getDesktopContext().addTask(task);
}
} catch (ParseException e) {
System.err.println("Parsing command line option failed. Reason: " + e.getMessage());
}
}
public void cancelUpdate(String window_name) {
try {
saveUpdateSettings();
if (!cmd.getQuiet()) {
if (window_name == null) {
window = new MainWindow();
} else {
window = (AbstractWindow) newInstance(window_name);
}
addWindow(window);
window.setVisible(window.getWindowSettings().getVisible());
window.postLoad();
}
} catch (Exception ex) {
ex.printStackTrace();
logger.severe("Could not start application: " + ex.getMessage());
}
}
public Main(
String args[],
String cmd_name,
OSSpecific os_name,
String settings_name,
final String window_name,
String logger_name,
String about_name,
String pref_name) {
if (cmd == null) {
cmd = new CommandLine(args);
}
if (!cmd.getHelp()) {
if (os_name == null) {
os = OSSpecific.getInstance();
} else {
os = (OSSpecific) newInstance(cmd_name);
}
if (settings_name == null) {
settings = new Settings();
} else {
settings = (Settings) newInstance(settings_name);
}
settings.loadSettings();
if (logger_name == null) {
logger = initLogger();
} else {
logger = (Logger) newInstance(logger_name);
}
Logger().info("Custom logger now in use.");
aboutclass = about_name;
prefclass = pref_name;
ActionListener update =
new ActionListener() {
public void actionPerformed(ActionEvent e) {
saveUpdateSettings();
}
};
ActionListener cancel =
new ActionListener() {
public void actionPerformed(ActionEvent e) {
cancelUpdate(window_name);
}
};
WindowListener closewindow =
new WindowListener() {
public void windowClosing(WindowEvent e) {
cancelUpdate(window_name);
}
public void windowClosed(WindowEvent e) {}
public void windowOpened(WindowEvent e) {}
public void windowIconified(WindowEvent e) {}
public void windowDeiconified(WindowEvent e) {}
public void windowActivated(WindowEvent e) {}
public void windowDeactivated(WindowEvent e) {}
public void windowGainedFocus(WindowEvent e) {}
public void windowLostFocus(WindowEvent e) {}
public void windowStateChanged(WindowEvent e) {}
};
autoupdate = new AutoUpdate();
autoupdate.checkForUpdates(
settings.getTitle(),
settings.getUpdateUrl(),
settings.getVersion(),
settings.getBuild(),
settings.getAllowMinor(),
settings.getAllowExperimental(),
settings.getAllowAutoUpdate(),
settings.getMinor(),
settings.getExperimental(),
settings.getAutoUpdate(),
update,
cancel,
closewindow);
}
}