public ProteinGroup ConstructSubsetProteinGroup(string fullFilePath)
{
var allPsmsForThisFile = new HashSet <PeptideSpectralMatch>(AllPsmsBelowOnePercentFDR.Where(p => p.FullFilePath.Equals(fullFilePath)));
var allPeptidesForThisFile = new HashSet <PeptideWithSetModifications>(allPsmsForThisFile.SelectMany(p => p.BestMatchingPeptides.Select(v => v.Peptide)));
var allUniquePeptidesForThisFile = new HashSet <PeptideWithSetModifications>(UniquePeptides.Intersect(allPeptidesForThisFile));
ProteinGroup subsetPg = new ProteinGroup(Proteins, allPeptidesForThisFile, allUniquePeptidesForThisFile)
{
AllPsmsBelowOnePercentFDR = allPsmsForThisFile,
DisplayModsOnPeptides = DisplayModsOnPeptides
};
SpectraFileInfo spectraFileInfo = null;
if (FilesForQuantification != null)
{
spectraFileInfo = FilesForQuantification.Where(p => p.FullFilePathWithExtension == fullFilePath).First();
subsetPg.FilesForQuantification = new List <SpectraFileInfo> {
spectraFileInfo
};
}
if (IntensitiesByFile == null)
{
subsetPg.IntensitiesByFile = null;
}
else
{
subsetPg.IntensitiesByFile = new Dictionary <SpectraFileInfo, double> {
{ spectraFileInfo, IntensitiesByFile[spectraFileInfo] }
};
}
return(subsetPg);
}
// this method is only used internally, to make protein grouping faster
// this is NOT an output and is NOT used for protein FDR calculations
public void Score()
{
// sum the scores of the best PSM per base sequence
ProteinGroupScore = AllPsmsBelowOnePercentFDR.GroupBy(p => p.BaseSequence).Select(p => p.Select(x => x.Score).Max()).Sum();
}
