private void AddPeptideGroup(ICollection<PeptideGroupDocNode> listGroups,
PeptideGroupBuilder builder,
List<MeasuredRetentionTime> irtPeptides,
List<SpectrumMzInfo> librarySpectra,
List<TransitionImportErrorInfo> errorList)
{
PeptideGroupDocNode nodeGroup = builder.ToDocNode();
listGroups.Add(nodeGroup);
irtPeptides.AddRange(builder.IrtPeptides);
librarySpectra.AddRange(builder.LibrarySpectra);
if (builder.PeptideGroupErrorInfo.Count > 0)
errorList.AddRange(builder.PeptideGroupErrorInfo);
_countPeptides += nodeGroup.MoleculeCount;
_countIons += nodeGroup.TransitionCount;
}
private void AddPeptideGroup(List<PeptideGroupDocNode> listGroups,
ICollection<FastaSequence> set, PeptideGroupBuilder builder)
{
PeptideGroupDocNode nodeGroup = builder.ToDocNode();
FastaSequence fastaSeq = nodeGroup.Id as FastaSequence;
if (fastaSeq != null && set.Contains(fastaSeq))
return;
if (nodeGroup.MoleculeCount == 0)
{
EmptyPeptideGroupCount++;
// If more than MaxEmptyPeptideGroupCount, then don't keep the empty peptide groups
// This is not useful and is likely to cause memory and performance issues
if (EmptyPeptideGroupCount > MaxEmptyPeptideGroupCount)
{
if (EmptyPeptideGroupCount == MaxEmptyPeptideGroupCount + 1)
{
var nonEmptyGroups = listGroups.Where(g => g.MoleculeCount > 0).ToArray();
listGroups.Clear();
listGroups.AddRange(nonEmptyGroups);
}
return;
}
}
listGroups.Add(nodeGroup);
_countPeptides += nodeGroup.MoleculeCount;
_countIons += nodeGroup.TransitionCount;
}