if (ptmCandidate == null) {
throw new IllegalArgumentException("No PTM found for site " + newLocalization + " on peptide " + peptide.getSequence() + " in spectrum " + spectrumKey + ".");
}
modificationMatch.setModificationSite(newLocalization);
PSPtmScores psmScores = (PSPtmScores) spectrumMatch.getUrParam(new PSPtmScores());
psmScores.changeRepresentativeSite(ptmCandidate.getName(), oldLocalization, newLocalization);
}
modificationMatch.setInferred(true);
}
}
}