private SrmDocument GetDocumentFinal(CancellationToken cancellationToken, SrmDocument doc, int minPeptides, bool removeRepeated, bool removeDuplicate, out int?emptyProteins)
{
emptyProteins = null;
// Remove repeated/duplicate peptides
var newDoc = removeRepeated || removeDuplicate
? new RefinementSettings {
RemoveRepeatedPeptides = removeRepeated, RemoveDuplicatePeptides = removeDuplicate
}.Refine(doc)
: doc;
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Remove proteins without enough peptides
newDoc = ImportPeptideSearch.RemoveProteinsByPeptideCount(newDoc, minPeptides);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Move iRT proteins to top
var irtPeptides = new HashSet <Target>(RCalcIrt.IrtPeptides(newDoc));
var proteins = new List <PeptideGroupDocNode>(newDoc.PeptideGroups);
var proteinsIrt = new List <PeptideGroupDocNode>();
for (var i = 0; i < proteins.Count; i++)
{
var nodePepGroup = proteins[i];
if (nodePepGroup.Peptides.All(nodePep => irtPeptides.Contains(new Target(nodePep.ModifiedSequence))))
{
proteinsIrt.Add(nodePepGroup);
proteins.RemoveAt(i--);
}
}
if (proteinsIrt.Any())
{
newDoc = (SrmDocument)newDoc.ChangeChildrenChecked(proteinsIrt.Concat(proteins).Cast <DocNode>().ToArray());
}
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Add decoys
newDoc = AddDecoys(newDoc);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
// Count empty proteins
emptyProteins = newDoc.PeptideGroups.Count(pepGroup => pepGroup.PeptideCount == 0);
if (cancellationToken.IsCancellationRequested)
{
return(null);
}
return(newDoc);
}