for (int advocateIndex : inputMap.getIntermediateScoreInputAlgorithms(spectrumFileName)) {
ArrayList<Integer> scores = processingPreferences.getScores(advocateIndex);
if (scores.size() > 1) {
for (int scoreIndex : scores) {
TargetDecoyMap targetDecoyMap = inputMap.getIntermediateScoreMap(spectrumFileName, advocateIndex, scoreIndex);
targetDecoyMap.estimateProbabilities(waitingHandler);
if (waitingHandler.isRunCanceled()) {
return;
}
}
}