spectrumCountingPreferences, sequenceMatchingPreferences, false);
// show the warnings
Iterator<String> iterator = peptideShaker.getWarnings().keySet().iterator();
while (iterator.hasNext()) {
FeedBack warning = peptideShaker.getWarnings().get(iterator.next());
if (warning.getType() == FeedBack.FeedBackType.WARNING) {
System.out.println(warning.getMessage()); // @TODO: better interaction between notes and feedback objetcs...
}
}
if (!waitingHandler.isRunCanceled()) {