public SrmDocument RemoveBelowCutoffs(SrmDocument document)
{
var intersection = new HashSet <int>();
foreach (var data in Data)
{
if (_progressMonitor != null && _progressMonitor.IsCanceled())
{
throw new OperationCanceledException();
}
if (_progressMonitor != null)
{
_progressMonitor.ProcessMolecule(null);
}
var filterByCutoff = data.ToArray();
var toRemove = IndicesBelowCutoff(_adjustedPValCutoff, _foldChangeCutoff, _msLevel, null,
filterByCutoff);
if (intersection.Count == 0)
{
intersection.UnionWith(toRemove);
}
else
{
intersection.IntersectWith(toRemove);
}
}
return((SrmDocument)document.RemoveAll(intersection));
}
public SrmDocument RemoveAboveCVCutoff(SrmDocument document)
{
var filterByCutoff = Data;
if (!double.IsNaN(_settings.CVCutoff))
{
var cutoff = _settings.CVCutoff / 100.0;
filterByCutoff = Data.Where(d => d.CV < cutoff).ToList();
}
var ids = new HashSet <int>(filterByCutoff
.SelectMany(d => d.PeptideAnnotationPairs)
.Select(pair => pair.TransitionGroup.Id.GlobalIndex));
var setRemove = IndicesToRemove(document, ids);
return((SrmDocument)document.RemoveAll(setRemove, null, (int)SrmDocument.Level.Molecules));
}
public SrmDocument RemoveDecoys(SrmDocument document)
{
// Remove the existing decoys
return (SrmDocument) document.RemoveAll(document.MoleculeGroups.Where(nodePeptideGroup => nodePeptideGroup.IsDecoy)
.Select(nodePeptideGroup => nodePeptideGroup.Id.GlobalIndex).ToArray());
}