private TransitionGroupChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionGroupChromInfo transitionGroupChromInfo, PeptideDocNode peptideDocNode, TransitionGroupDocNode transitionGroupDocNode)
: base(measuredResults, replicateIndex, chromFileInfo, transitionGroupChromInfo, peptideDocNode, transitionGroupDocNode)
{
}
public RatioValue GetTransitionGroupRatioValue(NormalizationMethod.RatioToLabel ratioToLabel,
PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionGroupChromInfo transitionGroupChromInfo)
{
if (peptideDocNode == null || transitionGroupChromInfo == null)
{
return(null);
}
if (transitionGroupDocNode.LabelType.Name == ratioToLabel.IsotopeLabelTypeName)
{
return(null);
}
var otherTransitionGroup =
FindMatchingTransitionGroup(ratioToLabel, peptideDocNode, transitionGroupDocNode);
if (otherTransitionGroup == null)
{
return(null);
}
var numerators = new List <double>();
var denominators = new List <double>();
if (SimpleRatios)
{
foreach (var tran in transitionGroupDocNode.Transitions.Where(tran =>
tran.IsQuantitative(Document.Settings)))
{
var chromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, tran);
if (chromInfo != null)
{
numerators.Add(chromInfo.Area);
}
}
foreach (var tran in otherTransitionGroup.Transitions.Where(tran =>
tran.IsQuantitative(Document.Settings)))
{
var chromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, tran);
if (chromInfo != null)
{
denominators.Add(chromInfo.Area);
}
}
if (numerators.Count == 0 || denominators.Count == 0)
{
return(null);
}
return(RatioValue.ValueOf(numerators.Sum() / denominators.Sum()));
}
var transitionMap = GetTransitionMap(otherTransitionGroup);
foreach (var transition in transitionGroupDocNode.Transitions)
{
if (!transition.IsQuantitative(Document.Settings))
{
continue;
}
var targetKey = new PeptideDocNode.TransitionKey(transitionGroupDocNode, new TransitionLossKey(transitionGroupDocNode, transition, transition.Losses), otherTransitionGroup.LabelType);
if (!transitionMap.TryGetValue(
targetKey,
out TransitionDocNode otherTransition))
{
continue;
}
if (!otherTransition.IsQuantitative(Document.Settings))
{
continue;
}
var transitionChromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, transition);
var otherTransitionChromInfo = FindMatchingTransitionChromInfo(transitionGroupChromInfo.FileId,
transitionGroupChromInfo.OptimizationStep, otherTransition);
if (transitionChromInfo == null || transitionChromInfo.IsEmpty || otherTransitionChromInfo == null || otherTransitionChromInfo.IsEmpty)
{
continue;
}
numerators.Add(transitionChromInfo.Area);
denominators.Add(otherTransitionChromInfo.Area);
}
return(RatioValue.Calculate(numerators, denominators));
}
private TransitionGroupChromInfoData(MeasuredResults measuredResults, int replicateIndex, ChromFileInfo chromFileInfo, TransitionGroupChromInfo transitionGroupChromInfo)
: base(measuredResults, replicateIndex, chromFileInfo, transitionGroupChromInfo)
{
}
public double?GetTransitionGroupValue(NormalizationMethod normalizationMethod, PeptideDocNode peptideDocNode,
TransitionGroupDocNode transitionGroupDocNode, TransitionGroupChromInfo transitionGroupChromInfo)
{
if (transitionGroupChromInfo == null)
{
return(null);
}
if (TryGetDenominator(normalizationMethod, transitionGroupDocNode.LabelType,
transitionGroupChromInfo.FileId, out double?denominator))
{
return(transitionGroupChromInfo.Area / denominator);
}
if (normalizationMethod is NormalizationMethod.RatioToLabel ratioToLabel)
{
return(GetTransitionGroupRatioValue(ratioToLabel, peptideDocNode, transitionGroupDocNode, transitionGroupChromInfo)?.Ratio);
}
return(null);
}
