waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}</BUG>
waitingHandler.appendReport("MzIdentML export completed.", true, true);
System.exit(0);
<BUG>return null;

}</BUG>
private void setPathConfiguration() throws IOException {
File pathConfigurationFile = new File(PeptideShaker.getJarFilePath(), UtilitiesPathPreferences.configurationFileName);

waitingHandler.appendReport("An error occurred while closing PeptideShaker.", true, true);
e2.printStackTrace();
}
if (!waitingHandler.isRunCanceled()) {
waitingHandler.appendReport("MzIdentML export completed.", true, true);
System.exit(0);
return 0;
} else {
System.exit(1);
return 1;
}
}
private void setPathConfiguration() throws IOException {
File pathConfigurationFile = new File(PeptideShaker.getJarFilePath(), UtilitiesPathPreferences.configurationFileName);
