protected override string GetValue(SapPredicted predict)
{
var fs = predict.Ms2.FileScans.FirstOrDefault(m => expectScans.ContainsKey(m.LongFileName));
predict.Expect = fs != null ? new TargetVariant()
{
Source = expectScans[fs.LongFileName].Source.ToString(),
Target = new HashSet <string>(new[] { expectScans[fs.LongFileName].Target.ToString() })
} : null;
return(base.GetValue(predict) + string.Format("\t{0}\t{1}",
predict.Expect == null ? string.Empty : string.Format("{0} => {1}", predict.Expect.Source, predict.Expect.Target.Merge(",")),
predict.IsExpect));
}
protected void CheckSAP(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
foreach (var aa in libms2.AminoacidCompsition)
{
var lst = options.SubstitutionDeltaMassMap[aa];
//the list has been ordered by deltamass
foreach (var ts in lst)
{
var targetMz = libms2.Precursor + ts.DeltaMass / query.Charge;
if (targetMz < query.MinPrecursorMz)
{
continue;
}
if (targetMz > query.MaxPrecursorMz)
{
break;
}
var curp = new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = ts.Source,
Target = ts.Target,
DeltaMass = ts.DeltaMass,
TargetType = ts.TargetType
}
};
predicted.Add(curp);
}
}
}
protected void CheckTerminalLoss(List <SapPredicted> predicted, MS2Item query, MS2Item libms2, SapMatchedCount ms3match)
{
foreach (var nl in libms2.TerminalLoss)
{
if (nl.Precursor >= query.MinPrecursorMz && nl.Precursor <= query.MaxPrecursorMz)
{
var curp = new SapPredicted()
{
Ms2 = query,
LibMs2 = libms2,
Matched = ms3match,
Target = new TargetVariant()
{
Source = PeptideUtils.GetPureSequence(libms2.Peptide),
Target = new HashSet <string>(new[] { nl.Sequence }),
DeltaMass = (nl.Precursor - libms2.Precursor) * libms2.Charge,
TargetType = nl.IsNterminal ? VariantType.NTerminalLoss : VariantType.CTerminalLoss
}
};
predicted.Add(curp);
}
}
}
