private void SetModifications(PhosphoRSInput input)
{
_modifications = input.Modifications;
_aminoAcidModifications = _modifications.Select(
modification => new AminoAcidModification(
modification.Symbol,
modification.Name,
modification.Abbreviation,
modification.NeutralLossAbbreviation,
modification.MassDelta,
modification.NeutralLoss,
AminoAcidSequence.ParseAASequence(modification.TargetAminoAcids)
)
).ToList();
_phosphoModification = _aminoAcidModifications
.Where(modification => modification.ID == _options.PhosphorylationSymbol)
.First();
_phosphoTargetAminoAcids = _phosphoModification.TargetAminoAcids
.Select(a => a.OneLetterCode)
.ToArray();
}
private void SetSpectra(PhosphoRSInput input)
{
_spectra = input.Spectra;
_spectrumMap = new Dictionary <int, Spectrum>();
_peptideMap = new Dictionary <int, Peptide>();
_phosphoSiteMap = new Dictionary <int, List <int> >();
_items = new List <Tuple <PeptideSpectrumMatch, List <Tuple <int, List <int> > > > >();
var count = 0;
foreach (var spectrum in input.Spectra)
{
var rank = 0;
foreach (var peptide in spectrum.IdentifiedPhosphorPeptides)
{
if (_options.MaxHitRank > 0 && rank >= _options.MaxHitRank)
{
break;
}
rank += 1;
var isoformMap = new List <Tuple <int, List <int> > >();
var aas = AminoAcidSequence.Create(
peptide.ID,
peptide.Sequence,
_aminoAcidModifications,
peptide.Modification
);
var psm = new PeptideSpectrumMatch(
peptide.ID,
spectrum.ActivationType,
spectrum.PrecursorCharge,
1,
spectrum.Peaks.ToArray(),
aas
);
var phosphoCount = peptide.Modification
.Skip(2).SkipLast(2)
.Where(c => c == _options.PhosphorylationSymbol)
.Count();
if (phosphoCount == 0)
{
continue;
}
var targetSites = peptide.Sequence
.Select((c, i) => _phosphoTargetAminoAcids.Contains(c) ? i : -1)
.Where(i => i >= 0)
.ToList();
targetSites.Combinations(phosphoCount).Take(_options.MaxIsoformCount).ForEach(sites =>
{
var list = sites.ToList();
isoformMap.Add(
new Tuple <int, List <int> >(
count,
list
)
);
_spectrumMap.Add(count, spectrum);
_peptideMap.Add(count, peptide);
_phosphoSiteMap.Add(count, list);
count += 1;
});
_items.Add(Tuple.Create <PeptideSpectrumMatch, List <Tuple <int, List <int> > > >(
psm,
isoformMap
));
}
}
}
private void SetOptions(PhosphoRSInput input)
{
_options = input.Options;
}
public PhosphoRSDataSource(PhosphoRSInput input)
{
SetOptions(input);
SetModifications(input);
SetSpectra(input);
}