File destinationFile = new File(getJarFilePath(), UtilitiesPathPreferences.configurationFileName);
try {
PeptideShakerPathPreferences.writeConfigurationToFile(destinationFile);
} catch (Exception e) {
System.out.println("An error occurred when saving the path preference to " + destinationFile.getAbsolutePath() + ".");
<BUG>e.printStackTrace();
}
System.out.println("Path configuration completed.");
}</BUG>
public String getJarFilePath() {

File destinationFile = new File(getJarFilePath(), UtilitiesPathPreferences.configurationFileName);
try {
PeptideShakerPathPreferences.writeConfigurationToFile(destinationFile);
} catch (Exception e) {
System.out.println("An error occurred when saving the path preference to " + destinationFile.getAbsolutePath() + ".");
e.printStackTrace();
waitingHandler.setRunCanceled();
}
if (!waitingHandler.isRunCanceled()) {
System.out.println("Path configuration completed.");
}
}
public String getJarFilePath() {
