
ions.add(new PeptideFragmentIon(subType, faa, rewindMass + 2 * Atom.H.getMonoisotopicMass() - getLossesMass(losses), losses));
}</BUG>
} else {
<BUG>ions.add(new PeptideFragmentIon(subType, faa, rewindMass + 2 * Atom.H.getMonoisotopicMass(), null));
</BUG>
}
}
if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.Z_ION)) {
int subType = PeptideFragmentIon.Z_ION;

ions = new ArrayList<Ion>(1);
}
ionsMap.put(subType, ions);
}
if (neutralLossesCombinations != null) {
for (NeutralLossCombination losses : neutralLossesCombinations) {
ions.add(new PeptideFragmentIon(subType, faa, rewindMass + h2 - losses.getMass(), losses.getNeutralLossCombination()));
}
} else {
ions.add(new PeptideFragmentIon(subType, faa, rewindMass + h2, null));
}
}
if (specificAnnotationSettings == null || selectedIonTypes.keySet().contains(Ion.IonType.PEPTIDE_FRAGMENT_ION) && specificAnnotationSettings.getFragmentIonTypes().contains(PeptideFragmentIon.Z_ION)) {
int subType = PeptideFragmentIon.Z_ION;
