public double?GetTransitionValue(NormalizationMethod normalizationMethod, PeptideDocNode peptideDocNode, TransitionGroupDocNode transitionGroupDocNode, TransitionDocNode transitionDocNode, TransitionChromInfo transitionChromInfo)
{
if (!transitionDocNode.IsQuantitative(Document.Settings))
{
return(null);
}
if (transitionChromInfo == null || transitionChromInfo.IsEmpty)
{
return(null);
}
if (TryGetDenominator(normalizationMethod, transitionGroupDocNode.LabelType, transitionChromInfo.FileId,
out double?denominator))
{
return(transitionChromInfo.Area / denominator);
}
if (normalizationMethod is NormalizationMethod.RatioToLabel ratioToLabel)
{
if (ratioToLabel.IsotopeLabelTypeName == transitionGroupDocNode.LabelType.Name)
{
return(null);
}
if (SimpleRatios)
{
return(null);
}
var otherTransitionGroup =
FindMatchingTransitionGroup(ratioToLabel, peptideDocNode, transitionGroupDocNode);
if (otherTransitionGroup == null)
{
return(null);
}
var otherTransition = FindMatchingTransition(transitionGroupDocNode, transitionDocNode, otherTransitionGroup);
if (otherTransition == null)
{
return(null);
}
if (!otherTransition.IsQuantitative(Document.Settings))
{
return(null);
}
var otherChrominfo = FindMatchingTransitionChromInfo(transitionChromInfo, otherTransition);
if (otherChrominfo == null || otherChrominfo.IsEmpty)
{
return(null);
}
return(transitionChromInfo.Area / otherChrominfo.Area);
}
return(null);
}
public bool SkipTransition(SrmSettings settings, TransitionDocNode transitionDocNode)
{
if (!transitionDocNode.IsQuantitative(settings))
{
return(true);
}
if (MsLevel.HasValue)
{
if (MsLevel == 1)
{
return(!transitionDocNode.IsMs1);
}
return(transitionDocNode.IsMs1);
}
return(false);
}