private static List <MeasuredPeptide> FindBestPeptides(SrmDocument doc, int peptideCount, ICollection <PeptideDocNode> exclude)
{
var docPeptides = new List <MeasuredPeptide>();
var cirtPeptides = new List <MeasuredPeptide>();
foreach (var pep in doc.Molecules)
{
if (pep.PercentileMeasuredRetentionTime.HasValue && !pep.IsDecoy && (exclude == null || !exclude.Contains(pep)))
{
var seq = doc.Settings.GetModifiedSequence(pep);
var time = pep.PercentileMeasuredRetentionTime.Value;
var measuredPeptide = new MeasuredPeptide(seq, time);
if (!IrtStandard.CIRT.Contains(seq))
{
docPeptides.Add(measuredPeptide);
}
else
{
cirtPeptides.Add(measuredPeptide);
}
}
}
if (cirtPeptides.Count >= peptideCount)
{
return(IrtPeptidePicker.Filter(cirtPeptides, peptideCount).ToList());
}
docPeptides.AddRange(cirtPeptides);
return(FindEvenlySpacedPeptides(docPeptides, peptideCount));
}
private static List <MeasuredPeptide> FindBestPeptides(SrmDocument doc, int peptideCount)
{
var docPeptides = new List <MeasuredPeptide>();
var cirtPeptides = new List <MeasuredPeptide>();
foreach (var pep in doc.Peptides)
{
if (pep.SchedulingTime.HasValue && !pep.IsDecoy)
{
var seq = doc.Settings.GetModifiedSequence(pep);
var schedulingTime = pep.SchedulingTime.Value;
var measuredPeptide = new MeasuredPeptide(seq, schedulingTime);
if (!IrtStandard.CIRT.Contains(seq))
{
docPeptides.Add(measuredPeptide);
}
else
{
cirtPeptides.Add(measuredPeptide);
}
}
}
if (cirtPeptides.Count >= peptideCount)
{
return(IrtPeptidePicker.Filter(cirtPeptides, peptideCount).ToList());
}
docPeptides.AddRange(cirtPeptides);
return(FindEvenlySpacedPeptides(docPeptides, peptideCount));
}
public Target TryResolveTarget(string text, out string errorMessage)
{
errorMessage = null;
if (string.IsNullOrEmpty(text))
{
return(null);
}
var matches = _targetsByName[text].ToArray();
if (matches.Length == 1)
{
return(matches.First());
}
if (matches.Length > 1)
{
errorMessage = string.Format(Resources.TargetResolver_TryResolveTarget_Unable_to_resolve_molecule_from___0____could_be_any_of__1_, text, string.Join(@", ", matches.Select(t => t.InvariantName)));
return(null);
}
Target target;
try
{
target = Target.FromSerializableString(text);
errorMessage = MeasuredPeptide.ValidateSequence(target);
if (errorMessage != null)
{
return(null);
}
}
catch (Exception)
{
target = null;
}
if (target == null)
{
errorMessage = string.Format(Resources.TargetResolver_TryResolveTarget_Unable_to_resolve_molecule_from___0___, text);
}
return(target);
}
