public NormalizationData GetNormalizationData()
{
if (_normalizationData == null)
{
_normalizationData = _getNormalizationDataFunc();
}
return(_normalizationData);
}
public NormalizationData GetNormalizationData()
{
if (_normalizationData == null)
{
_normalizationData = NormalizationData.GetNormalizationData(SrmDocument, ComparisonDef.UseZeroForMissingPeaks, ComparisonDef.QValueCutoff);
}
return(_normalizationData);
}
public NormalizationData GetNormalizationData()
{
if (!NormalizationMethod.EQUALIZE_MEDIANS.Equals(ComparisonDef.NormalizationMethod))
{
return(null);
}
return(_normalizationData = _normalizationData ?? NormalizationData.GetNormalizationData(SrmDocument));
}
public static PeptideQuantifier GetPeptideQuantifier(SrmDocument document, PeptideGroupDocNode peptideGroup,
PeptideDocNode peptide)
{
return(GetPeptideQuantifier(() => NormalizationData.GetNormalizationData(document, false, null),
document.Settings, peptideGroup, peptide));
}
private Quantity GetTransitionQuantity(
SrmSettings srmSettings,
IDictionary <PeptideDocNode.TransitionKey, TransitionChromInfo> peptideStandards,
int replicateIndex,
TransitionGroupDocNode transitionGroup, TransitionDocNode transition)
{
if (null == transition.Results)
{
return(null);
}
if (replicateIndex >= transition.Results.Count)
{
return(null);
}
var chromInfos = transition.Results[replicateIndex];
if (null == chromInfos)
{
return(null);
}
var chromInfo = GetTransitionChromInfo(transition, replicateIndex);
if (null == chromInfo || chromInfo.IsEmpty)
{
return(null);
}
double normalizedArea = chromInfo.Area;
double denominator = 1.0;
if (null != peptideStandards)
{
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))
{
denominator = srmSettings.CalcGlobalStandardArea(replicateIndex, chromInfo.FileId);
}
else if (Equals(NormalizationMethod, NormalizationMethod.EQUALIZE_MEDIANS))
{
if (null == NormalizationData)
{
throw new InvalidOperationException(string.Format("Normalization method '{0}' is not supported here.", NormalizationMethod)); // Not L10N
}
double?median = NormalizationData.GetMedian(chromInfo.FileId, transitionGroup.TransitionGroup.LabelType);
if (!median.HasValue)
{
return(null);
}
denominator = Math.Pow(2.0, median.Value);
}
}
return(new Quantity(normalizedArea, denominator));
}
