HashMap<Peptide, HashMap<String, ArrayList<Integer>>> proteinMapping = proteinTree.getProteinMapping(extendedAssumption.getTag(), tagMatcher, sequenceMatchingPreferences, searchParameters.getFragmentIonAccuracy());
for (Peptide peptide : proteinMapping.keySet()) {
String peptideKey = peptide.getKey();
if (!peptidesFound.contains(peptideKey)) {
PeptideAssumption peptideAssumption = new PeptideAssumption(peptide, extendedAssumption.getRank(), advocateId, tagAssumption.getIdentificationCharge(), tagAssumption.getScore(), tagAssumption.getIdentificationFile());
peptideAssumption.addUrParam(tagAssumption);
spectrumMatch.addHit(advocateId, peptideAssumption, true);
peptidesFound.add(peptideKey);
}
}
String extendedSequence = extendedAssumption.getTag().asSequence();