private Quantity GetTransitionQuantity(
SrmSettings srmSettings,
IDictionary <PeptideDocNode.TransitionKey, TransitionChromInfo> peptideStandards,
NormalizationMethod normalizationMethod,
int replicateIndex,
TransitionGroupDocNode transitionGroup, TransitionDocNode transition,
bool treatMissingAsZero)
{
if (null == transition.Results)
{
return(null);
}
if (replicateIndex >= transition.Results.Count)
{
return(null);
}
var chromInfos = transition.Results[replicateIndex];
if (chromInfos.IsEmpty)
{
return(null);
}
var chromInfo = GetTransitionChromInfo(transition, replicateIndex);
if (null == chromInfo)
{
return(null);
}
double?normalizedArea = GetArea(treatMissingAsZero, QValueCutoff, IncludeTruncatedPeaks, transitionGroup, transition, replicateIndex, chromInfo);
if (!normalizedArea.HasValue)
{
return(null);
}
double denominator = 1.0;
if (null != peptideStandards)
{
if (QuantificationSettings.SimpleRatios)
{
if (peptideStandards.Count == 0)
{
return(null);
}
denominator = peptideStandards.Values.Sum(value => value.Area);
}
else
{
TransitionChromInfo chromInfoStandard;
if (!peptideStandards.TryGetValue(GetRatioTransitionKey(transitionGroup, transition), out chromInfoStandard))
{
return(null);
}
else
{
denominator = chromInfoStandard.Area;
}
}
}
else
{
if (chromInfo.IsTruncated.GetValueOrDefault())
{
return(null);
}
if (Equals(normalizationMethod, NormalizationMethod.GLOBAL_STANDARDS))
{
var fileInfo = srmSettings.MeasuredResults.Chromatograms[replicateIndex]
.GetFileInfo(chromInfo.FileId);
if (fileInfo == null)
{
return(null);
}
denominator = srmSettings.CalcGlobalStandardArea(replicateIndex, fileInfo);
}
else if (normalizationMethod is NormalizationMethod.RatioToSurrogate)
{
denominator = ((NormalizationMethod.RatioToSurrogate)NormalizationMethod)
.GetStandardArea(srmSettings, replicateIndex, chromInfo.FileId);
}
else if (Equals(normalizationMethod, NormalizationMethod.EQUALIZE_MEDIANS))
{
var normalizationData = GetNormalizationData();
if (null == normalizationData)
{
throw new InvalidOperationException(string.Format(@"Normalization method '{0}' is not supported here.", NormalizationMethod));
}
double?medianAdjustment = normalizationData.GetMedian(chromInfo.FileId, transitionGroup.TransitionGroup.LabelType)
- normalizationData.GetMedianMedian(srmSettings.MeasuredResults.Chromatograms[replicateIndex].SampleType, transitionGroup.TransitionGroup.LabelType);
if (!medianAdjustment.HasValue)
{
return(null);
}
normalizedArea /= Math.Pow(2.0, medianAdjustment.Value);
}
else if (Equals(normalizationMethod, NormalizationMethod.TIC))
{
var factor = srmSettings.GetTicNormalizationDenominator(replicateIndex, chromInfo.FileId);
if (!factor.HasValue)
{
return(null);
}
denominator = factor.Value;
}
}
return(new Quantity(normalizedArea.Value, denominator));
}