/**
* 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());
}
}
