public void addModification(int zero_based_index, double modMass)
throws UnimodRepositoryException {
ModificationType modType = new ModificationType();
modType.setLocation(zero_based_index + 1);
List<String> residues = modType.getResidues();
residues.add(String.valueOf(sequence.charAt(zero_based_index)));
modType.setMonoisotopicMassDelta(modMass);
// get the Unimod entry for this modification
ModT unimod_mod =
unimodRepository.getModification(
sequence.charAt(zero_based_index),
modMass,
UnimodRepository.DELTA_MASS_TOLERANCE_1,
true);
if (unimod_mod != null) {
CvParamMaker paramMaker = CvParamMaker.getInstance();
CVParamType param =
paramMaker.make(
"UNIMOD:" + unimod_mod.getRecordId(), unimod_mod.getTitle(), CvConstants.UNIMOD_CV);
modType.getCvParam().add(param);
}
modifications.add(modType);
}
