private PhosphoRSOptions CreateOptions(
string activation, double tolerance, int maxIsoform, int maxPTM, bool neutralLoss
)
{
return(new PhosphoRSOptions()
{
ActivationType = SpectrumTypeHelper.ParseSpectrumType(activation),
MassTolerance = tolerance,
MaxIsoformCount = maxIsoform,
MaxPTMCount = maxPTM,
ScoreNeutralLoss = neutralLoss
});
}
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);
}