private void WriteExplicitMods(XmlWriter writer, string name,
string nameElMod, IsotopeLabelType labelType, IEnumerable <ExplicitMod> mods,
string sequence)
{
if (mods == null || (labelType == null && string.IsNullOrEmpty(sequence)))
{
return;
}
writer.WriteStartElement(name);
if (labelType != null)
{
writer.WriteAttribute(ATTR.isotope_label, labelType);
}
if (!string.IsNullOrEmpty(sequence))
{
SequenceMassCalc massCalc = Settings.TransitionSettings.Prediction.PrecursorMassType == MassType.Monoisotopic ?
SrmSettings.MonoisotopicMassCalc : SrmSettings.AverageMassCalc;
foreach (ExplicitMod mod in mods)
{
writer.WriteStartElement(nameElMod);
writer.WriteAttribute(ATTR.index_aa, mod.IndexAA);
writer.WriteAttribute(ATTR.modification_name, mod.Modification.Name);
double massDiff = massCalc.GetModMass(sequence[mod.IndexAA], mod.Modification);
writer.WriteAttribute(ATTR.mass_diff,
string.Format(CultureInfo.InvariantCulture, @"{0}{1}", (massDiff < 0 ? string.Empty : @"+"),
Math.Round(massDiff, 1)));
writer.WriteEndElement();
}
}
writer.WriteEndElement();
}
public void Add(char aa, StaticMod mod, bool structural, bool allowDuplicates)
{
if (_completed)
{
throw new InvalidOperationException(Resources.ModMassLookup_Add_Invalid_attempt_to_add_data_to_completed_MassLookup);
}
// If structural, store in lowercase AA.
_aaMassLookups[structural ? ToStructuralIndex(aa) : ToIsotopeIndex(aa)]
.Add(CALC.GetModMass(aa, mod), mod, allowDuplicates);
}
private static double[] CalcModMasses(Peptide peptide, IEnumerable<ExplicitMod> mods,
SequenceMassCalc massCalc)
{
double[] masses = new double[peptide.Length];
string seq = peptide.Sequence;
foreach (ExplicitMod mod in mods)
masses[mod.IndexAA] += massCalc.GetModMass(seq[mod.IndexAA], mod.Modification);
return masses;
}