private IDictionary <int, Tuple <double, bool> > CalculateProteinAbundances()
{
var allTransitionIdentityPaths = new HashSet <IdentityPath>();
var quantifiers = Peptides.Select(peptide => peptide.GetPeptideQuantifier()).ToList();
int replicateCount = SrmDocument.Settings.HasResults
? SrmDocument.Settings.MeasuredResults.Chromatograms.Count : 0;
var abundances = new Dictionary <int, Tuple <double, int> >();
var srmSettings = SrmDocument.Settings;
bool allowMissingTransitions =
srmSettings.PeptideSettings.Quantification.NormalizationMethod is NormalizationMethod.RatioToLabel;
for (int iReplicate = 0; iReplicate < replicateCount; iReplicate++)
{
double totalNumerator = 0;
double totalDenomicator = 0;
int transitionCount = 0;
foreach (var peptideQuantifier in quantifiers)
{
foreach (var entry in peptideQuantifier.GetTransitionIntensities(SrmDocument.Settings, iReplicate,
false))
{
totalNumerator += Math.Max(entry.Value.Intensity, 1.0);
totalDenomicator += Math.Max(entry.Value.Denominator, 1.0);
allTransitionIdentityPaths.Add(entry.Key);
transitionCount++;
}
}
if (transitionCount != 0)
{
var abundance = totalNumerator / totalDenomicator;
abundances.Add(iReplicate, Tuple.Create(abundance, transitionCount));
}
}
var proteinAbundanceRecords = new Dictionary <int, Tuple <double, bool> >();
foreach (var entry in abundances)
{
bool incomplete;
if (allowMissingTransitions)
{
incomplete = true;
}
else
{
incomplete = entry.Value.Item2 != allTransitionIdentityPaths.Count;
}
proteinAbundanceRecords.Add(entry.Key, Tuple.Create(entry.Value.Item1, incomplete));
}
return(proteinAbundanceRecords);
}
