public static void GetLibIrtProviders(Library lib, IrtStandard standard, IProgressMonitor monitor,
out IRetentionTimeProvider[] irtProviders, out List <IrtStandard> autoStandards, out DbIrtPeptide[] cirtPeptides)
{
monitor?.UpdateProgress(new ProgressStatus().ChangePercentComplete(-1));
irtProviders = lib.RetentionTimeProvidersIrt.ToArray();
if (!irtProviders.Any())
{
irtProviders = lib.RetentionTimeProviders.ToArray();
}
var isAuto = ReferenceEquals(standard, IrtStandard.AUTO);
autoStandards = isAuto
? IrtStandard.BestMatch(irtProviders.SelectMany(provider => provider.PeptideRetentionTimes).Select(rt => rt.PeptideSequence))
: null;
if (ReferenceEquals(standard, IrtStandard.CIRT_SHORT) || isAuto && autoStandards.Count == 0)
{
var libPeptides = new TargetMap <bool>(irtProviders
.SelectMany(provider => provider.PeptideRetentionTimes)
.Select(rt => new KeyValuePair <Target, bool>(rt.PeptideSequence, true)));
cirtPeptides = IrtStandard.CIRT.Peptides.Where(pep => libPeptides.ContainsKey(pep.ModifiedTarget)).ToArray();
}
else
{
cirtPeptides = new DbIrtPeptide[0];
}
}
public void CheckDecoys(SrmDocument document, out int decoysNoSource, out int decoysWrongTransitionCount, out double proportionDecoysMatch)
{
var targets = document.Peptides.Where(pep => !pep.IsDecoy).ToArray();
var targetMap = new TargetMap <HashSet <int> >(targets.Select(target =>
new KeyValuePair <Target, HashSet <int> >(target.ModifiedTarget, new HashSet <int>())));
foreach (var target in targets)
{
foreach (var nodeTranGroup in target.TransitionGroups)
{
targetMap[target.ModifiedTarget].Add(nodeTranGroup.TransitionCount);
}
}
decoysNoSource = 0;
decoysWrongTransitionCount = 0;
var decoys = Peptides.Where(pep => pep.IsDecoy).ToArray();
foreach (var decoy in decoys)
{
if (!targetMap.TryGetValue(decoy.SourceModifiedTarget, out var transitionCounts))
{
decoysNoSource++;
}
else if (decoy.TransitionGroups.All(nodeTranGroup => !transitionCounts.Contains(nodeTranGroup.TransitionCount)))
{
decoysWrongTransitionCount++;
}
}
proportionDecoysMatch = 1 - (double)(decoysNoSource + decoysWrongTransitionCount) / decoys.Length;
}
