public PeptideQuantifier(PeptideGroupDocNode peptideGroup, PeptideDocNode peptideDocNode,
QuantificationSettings quantificationSettings)
{
PeptideGroupDocNode = peptideGroup;
PeptideDocNode = peptideDocNode;
QuantificationSettings = quantificationSettings;
}
protected bool Equals(QuantificationSettings other)
{
return(Equals(RegressionWeighting, other.RegressionWeighting) &&
Equals(RegressionFit, other.RegressionFit) &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
Equals(MsLevel, other.MsLevel) &&
Equals(Units, other.Units));
}
protected bool Equals(QuantificationSettings other)
{
return(Equals(RegressionWeighting, other.RegressionWeighting) &&
Equals(RegressionFit, other.RegressionFit) &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
Equals(MsLevel, other.MsLevel) &&
Equals(Units, other.Units) &&
Equals(LodCalculation, other.LodCalculation) &&
Equals(MaxLoqBias, other.MaxLoqBias) &&
Equals(MaxLoqCv, other.MaxLoqCv));
}
private SrmDocument ChangeQuantificationSettings(SrmDocument srmDocument, QuantificationSettings quantificationSettings)
{
return srmDocument.ChangeSettings(
srmDocument.Settings.ChangePeptideSettings(
srmDocument.Settings.PeptideSettings.ChangeAbsoluteQuantification(
quantificationSettings)));
}
protected bool Equals(QuantificationSettings other)
{
return Equals(RegressionWeighting, other.RegressionWeighting) &&
Equals(RegressionFit, other.RegressionFit) &&
Equals(NormalizationMethod, other.NormalizationMethod) &&
Equals(MsLevel, other.MsLevel) &&
Equals(Units, other.Units);
}
public void ReadXml(XmlReader reader)
{
// Consume tag
if (reader.IsEmptyElement)
reader.Read();
else
{
reader.ReadStartElement();
// Read child elements.
Enzyme = reader.DeserializeElement<Enzyme>();
DigestSettings = reader.DeserializeElement<DigestSettings>();
BackgroundProteome = reader.DeserializeElement<BackgroundProteome>();
Prediction = reader.DeserializeElement<PeptidePrediction>();
Filter = reader.DeserializeElement<PeptideFilter>();
Libraries = reader.DeserializeElement<PeptideLibraries>();
Modifications = reader.DeserializeElement<PeptideModifications>();
Integration = reader.DeserializeElement<PeptideIntegration>();
Quantification = reader.DeserializeElement<QuantificationSettings>();
reader.ReadEndElement();
}
Quantification = Quantification ?? QuantificationSettings.DEFAULT;
// Defer validation to the SrmSettings object
}
public PeptideSettings ChangeAbsoluteQuantification(QuantificationSettings prop)
{
prop = prop ?? QuantificationSettings.DEFAULT;
if (Equals(prop, Quantification))
{
return this;
}
return ChangeProp(ImClone(this), im => im.Quantification = prop);
}
