public PhosphoRSInput Read()
{
var input = new PhosphoRSInput();
while (_reader.Read())
{
if (_reader.NodeType == XmlNodeType.Element)
{
if (_reader.Name == "Spectra")
{
if (input.Spectra == null)
{
input.Spectra = new List <Spectrum>();
}
}
if (_reader.Name == "Spectrum")
{
input.Spectra?.Add(new Spectrum(
id: int.Parse(_reader["ID"]),
name: _reader["Name"],
precursorCharge: int.Parse(_reader["PrecursorCharge"]),
activationType: SpectrumTypeHelper.ParseSpectrumType(_reader["ActivationTypes"]),
peaks: null
));
}
if (_reader.Name == "Peaks")
{
var spectrum = input.Spectra?.LastOrDefault();
if (spectrum != null)
{
spectrum.Peaks = Peak.ParsePeaks(_reader.ReadElementContentAsString());
}
}
if (_reader.Name == "IdentifiedPhosphorPeptides")
{
var spectrum = input.Spectra?.LastOrDefault();
if (spectrum != null && spectrum.IdentifiedPhosphorPeptides == null)
{
spectrum.IdentifiedPhosphorPeptides = new List <Peptide>();
}
}
if (_reader.Name == "Peptide")
{
input.Spectra?.LastOrDefault()?.IdentifiedPhosphorPeptides?.Add(new Peptide(
id: int.Parse(_reader["ID"]),
sequence: _reader["Sequence"],
modification: _reader["ModificationInfo"]
));
}
if (_reader.Name == "MassTolerance")
{
if (input.Options == null)
{
input.Options = new PhosphoRSOptions();
}
input.Options.MassTolerance = double.Parse(_reader["Value"]);
}
if (_reader.Name == "MaxIsoformCount")
{
if (input.Options == null)
{
input.Options = new PhosphoRSOptions();
}
input.Options.MaxIsoformCount = int.Parse(_reader["Value"]);
}
if (_reader.Name == "MaxPTMCount")
{
if (input.Options == null)
{
input.Options = new PhosphoRSOptions();
}
input.Options.MaxPTMCount = int.Parse(_reader["Value"]);
}
if (_reader.Name == "ScoreNeutralLoss")
{
if (input.Options == null)
{
input.Options = new PhosphoRSOptions();
}
input.Options.ScoreNeutralLoss = bool.Parse(_reader["Value"]);
}
if (_reader.Name == "Phosphorylation")
{
if (input.Options == null)
{
input.Options = new PhosphoRSOptions();
}
input.Options.PhosphorylationSymbol = char.Parse(_reader["Symbol"]);
}
if (_reader.Name == "ModificationInfos")
{
if (input.Modifications == null)
{
input.Modifications = new List <Modification>();
}
}
if (_reader.Name == "ModificationInfo")
{
var s = _reader["Value"]?.Split(':');
input.Modifications?.Add(new Modification(
symbol: char.Parse(_reader["Symbol"]),
name: s[1],
abbreviation: s[2],
massDelta: double.Parse(s[3]),
neutralLossAbbreviation: s[4],
neutralLoss: double.Parse(s[5]),
targetAminoAcids: s[6]
));
}
}
}
return(input);
}
public PhosphoRSInput Read()
{
var spectra = new Dictionary <string, Spectral.Spectrum>();
while (true)
{
var spectrum = _spectralReader.Read();
if (spectrum == null)
{
break;
}
spectra.TryAdd(
key: spectrum.Title,
value: spectrum
);
}
var spectrumQueries = new List <SpectrumQuery>();
while (true)
{
var spectrumQuery = _peptideReader.Read();
if (spectrumQuery == null)
{
break;
}
spectrumQueries.Add(spectrumQuery);
}
var input = new PhosphoRSInput();
if (_options != null)
{
input.Options = _options;
}
input.Modifications.Add(Wrapper.Modification.PhosphoSTY);
input.Modifications.Add(Wrapper.Modification.OxidationM);
input.Modifications.Add(Wrapper.Modification.CarbamidomethylC);
input.Options.PhosphorylationSymbol = input.Modifications[0].Symbol;
spectrumQueries.ForEach((query, i) =>
{
if (query.SearchResults?.Count > 0)
{
if (spectra.TryGetValue(query.Spectrum, out var spec))
{
var spectrum = new Wrapper.Spectrum(
id: (int)i,
name: query.Spectrum,
precursorCharge: query.Charge,
activationType: input.Options.ActivationType,
peaks: spec.Peaks
);
query.SearchResults.ForEach(hit =>
{
if (_options.MaxHitRank > 0 && hit.Rank > _options.MaxHitRank)
{
return;
}
var modification = Enumerable.Repeat('0', hit.Peptide.Length).ToArray();
hit.Modifications.ForEach(mod =>
{
double Mass(char aminoAcid)
{
if (IMP.PhosphoRS.AminoAcid.FindAAResidue(aminoAcid, out var aa))
{
return(aa.MonoisotopicMass);
}
return(0);
};
modification[mod.Position - 1] =
input.Modifications
?.Where(m => m.TargetAminoAcids.Contains(hit.Peptide[mod.Position - 1]))
?.Where(m => Math.Abs(Mass(hit.Peptide[mod.Position - 1]) + m.MassDelta - mod.Mass) <= 0.5)
?.OrderBy(m => Math.Abs(Mass(hit.Peptide[mod.Position - 1]) + m.MassDelta - mod.Mass))
?.FirstOrDefault()
?.Symbol ?? '0';
});
var peptide = new Peptide(
id: (int)i + spectrumQueries.Count * (hit.Rank - 1),
sequence: hit.Peptide,
modification: "0." + string.Join("", modification) + ".0"
);
spectrum.IdentifiedPhosphorPeptides.Add(peptide);
});
input.Spectra.Add(spectrum);
}
}
});
return(input);
}
