private void WriteSpectra(PhosphoRSOutput output)
{
_writer.WriteStartElement("Spectra");
output.Spectra.ForEach(spectrum =>
{
_writer.WriteStartElement("Spectrum");
_writer.WriteAttributeString("ID", spectrum.ID.ToString());
_writer.WriteAttributeString("Name", spectrum.Name?.ToString());
_writer.WriteAttributeString("PrecursorCharge", spectrum.PrecursorCharge.ToString());
_writer.WriteAttributeString("ActivationType", spectrum.ActivationType.ToString());
_writer.WriteStartElement("Peptides");
spectrum.Peptides.ForEach(peptide =>
{
_writer.WriteStartElement("Peptide");
_writer.WriteAttributeString("ID", peptide.ID.ToString());
_writer.WriteStartElement("SitePrediction");
peptide.SitePrediction.ForEach(site =>
{
_writer.WriteStartElement("Site");
_writer.WriteAttributeString("SeqPos", site.Position.ToString());
_writer.WriteAttributeString("SiteProb", site.Probability.ToString());
_writer.WriteEndElement();
});
_writer.WriteEndElement();
_writer.WriteStartElement("Isoforms");
peptide.Isoforms.ForEach(isoform =>
{
_writer.WriteStartElement("Isoform");
_writer.WriteAttributeString("ID", isoform.ID.ToString());
_writer.WriteAttributeString("PepScore", isoform.Score.ToString());
_writer.WriteAttributeString("PepProb", isoform.Probability.ToString());
_writer.WriteStartElement("PhosphoSites");
isoform.Sites.ForEach(site =>
{
_writer.WriteStartElement("PhosphoSite");
_writer.WriteAttributeString("SeqPos", site.ToString());
_writer.WriteEndElement();
});
_writer.WriteEndElement();
_writer.WriteEndElement();
});
_writer.WriteEndElement();
_writer.WriteEndElement();
});
_writer.WriteEndElement();
_writer.WriteEndElement();
});
_writer.WriteEndElement();
}
public void Write(PhosphoRSOutput output)
{
if (output == null)
{
throw new ArgumentNullException(nameof(output));
}
var s = JsonConvert.SerializeObject(output, Formatting.Indented);
_writer.Write(s);
}
public void Write(PhosphoRSOutput output)
{
if (output == null)
{
throw new ArgumentNullException(nameof(output));
}
_writer.WriteRow(
"Spectrum.ID",
"Spectrum.Name",
"Spectrum.PrecursorCharge",
"Spectrum.ActivationType",
"Peptide.ID",
"Peptide.Sequence",
"Peptide.SitePrediction",
"Isoform.ID",
"Isoform.Sites",
"Isoform.Score",
"Isoform.Probability"
);
string SitePredictionToString(Wrapper.PeptideResult peptide)
{
return(string.Join(
" ",
peptide.SitePrediction
.Select(site => $"{peptide.Sequence[site.Position - 1]}{site.Position}({site.Probability.ToString("0.###")})")
));
}
output.Spectra.ForEach(spectrum =>
{
spectrum.Peptides.ForEach(peptide =>
{
peptide.Isoforms.ForEach(isoform =>
{
_writer.WriteRow(new string[] {
spectrum.ID.ToString(),
spectrum.Name,
spectrum.PrecursorCharge.ToString(),
spectrum.ActivationType.ToString(),
peptide.ID.ToString(),
peptide.Sequence,
SitePredictionToString(peptide),
isoform.ID.ToString(),
string.Join(" ", isoform.Sites.Select(site => $"{peptide.Sequence[site - 1]}{site}")),
isoform.Score.ToString(),
isoform.Probability.ToString()
});
});
});
});
}
public void Write(PhosphoRSOutput output)
{
if (output == null)
{
throw new ArgumentNullException(nameof(output));
}
_writer.WriteStartDocument();
_writer.WriteStartElement("PhosphoRS_Results");
WriteGlobalParameters(output);
WriteSpectra(output);
_writer.WriteEndElement();
_writer.WriteEndDocument();
}
private void WriteGlobalParameters(PhosphoRSOutput output)
{
_writer.WriteStartElement("GlobalParameters");
_writer.WriteStartElement("MassTolerance");
_writer.WriteAttributeString("Value", output.Options.MassTolerance.ToString());
_writer.WriteEndElement();
_writer.WriteStartElement("Modifications");
output.Modifications.ForEach(modification =>
{
_writer.WriteStartElement("Modification");
_writer.WriteAttributeString("ID", modification.Symbol.ToString());
_writer.WriteAttributeString("Name", modification.Name.ToString());
_writer.WriteAttributeString("MassDelta", modification.MassDelta.ToString());
_writer.WriteEndElement();
});
_writer.WriteEndElement();
_writer.WriteStartElement("Phosphorylation");
_writer.WriteAttributeString("ID", output.Options.PhosphorylationSymbol.ToString());
_writer.WriteEndElement();
_writer.WriteStartElement("MaxIsoformCount");
_writer.WriteAttributeString("Value", output.Options.MaxIsoformCount.ToString());
_writer.WriteEndElement();
_writer.WriteStartElement("MaxPTMCount");
_writer.WriteAttributeString("Value", output.Options.MaxPTMCount.ToString());
_writer.WriteEndElement();
_writer.WriteStartElement("ScoreNeutralLoss");
_writer.WriteAttributeString("Value", output.Options.ScoreNeutralLoss.ToString());
_writer.WriteEndElement();
_writer.WriteEndElement();
}