/** * 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()); } }