public double?GetTransitionDataValue(NormalizeOption ratioIndex, TransitionChromInfoData transitionChromInfoData)
{
var normalizationMethod = NormalizationMethodForPrecursor(transitionChromInfoData.PeptideDocNode,
transitionChromInfoData.TransitionGroupDocNode, ratioIndex);
return(GetTransitionValue(normalizationMethod, transitionChromInfoData.PeptideDocNode,
transitionChromInfoData.TransitionGroupDocNode, transitionChromInfoData.TransitionDocNode,
transitionChromInfoData.ChromInfo));
}
public static NormalizeOption Constrain(SrmSettings settings, NormalizeOption currentNormalizeOption)
{
return((currentNormalizeOption ?? RatioToFirstStandard(settings)).Constrain(settings));
}
protected bool Equals(NormalizeOption other)
{
return(PersistedName == other.PersistedName);
}
public NormalizationMethod NormalizationMethodForPrecursor(PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroup, NormalizeOption normalizeOption)
{
var normalizationMethod = NormalizationMethodForMolecule(peptideDocNode, normalizeOption);
if (normalizationMethod is NormalizationMethod.RatioToLabel ratioToLabel)
{
if (ratioToLabel.IsotopeLabelTypeName == transitionGroup.LabelType.Name)
{
return(NormalizationMethod.NONE);
}
}
return(normalizationMethod);
}
public NormalizationMethod NormalizationMethodForMolecule(PeptideDocNode peptideDocNode, NormalizeOption normalizeOption)
{
if (normalizeOption.NormalizationMethod != null)
{
return(normalizeOption.NormalizationMethod);
}
if (normalizeOption == NormalizeOption.CALIBRATED)
{
normalizeOption = NormalizeOption.DEFAULT;
}
if (normalizeOption == NormalizeOption.DEFAULT)
{
return(peptideDocNode.NormalizationMethod ??
Document.Settings.PeptideSettings.Quantification.NormalizationMethod);
}
return(NormalizationMethod.NONE);
}
