public double?CalculateIonRatio(Replicate replicate, Peptide peptide)
{
var numerator = new List <double>();
var denominator = new List <double>();
foreach (var transition in peptide.Precursors.SelectMany(precursor => precursor.Transitions))
{
var transitionDocNode = transition.DocNode;
var chromInfo = transitionDocNode.Results[replicate.ReplicateIndex].FirstOrDefault();
if (chromInfo == null || chromInfo.IsEmpty || chromInfo.IsTruncated.GetValueOrDefault())
{
continue;
}
if (transition.Quantitative)
{
denominator.Add(chromInfo.Area);
}
else
{
numerator.Add(chromInfo.Area);
}
}
if (numerator.Count == 0 || denominator.Count == 0)
{
return(null);
}
return(numerator.Sum() / denominator.Sum());
}
private void VerifyQuantificationResults(bool hasBatchNames)
{
var documentGrid = FindOpenForm <DocumentGridForm>();
RunUI(() => documentGrid.ChooseView("PeptideQuantificationResults"));
WaitForConditionUI(() => documentGrid.IsComplete);
var propertyPathResults = PropertyPath.Root
.Property(nameof(Peptide.Results)).LookupAllItems()
.Property(nameof(KeyValuePair <ResultKey, PeptideResult> .Value));
var colPeptide = documentGrid.FindColumn(PropertyPath.Root);
var colReplicate = documentGrid.FindColumn(propertyPathResults
.Property(nameof(PeptideResult.ResultFile))
.Property(nameof(ResultFile.Replicate)));
var colCalibrationCurve =
documentGrid.FindColumn(PropertyPath.Root.Property(nameof(Peptide.CalibrationCurve)));
var colReplicateCalibrationCurve =
documentGrid.FindColumn(propertyPathResults.Property(nameof(PeptideResult.ReplicateCalibrationCurve)));
var colQuantification =
documentGrid.FindColumn(propertyPathResults.Property(nameof(PeptideResult.Quantification)));
for (int iRow = 0; iRow < documentGrid.RowCount; iRow++)
{
Peptide peptide = null;
Replicate replicate = null;
var calibrationCurve = default(LinkValue <CalibrationCurve>);
var replicateCalibrationCurve = default(LinkValue <CalibrationCurve>);
RunUI(() =>
{
var row = documentGrid.DataGridView.Rows[iRow];
peptide = (Peptide)row.Cells[colPeptide.Index].Value;
replicate = (Replicate)row.Cells[colReplicate.Index].Value;
calibrationCurve = (LinkValue <CalibrationCurve>)row.Cells[colCalibrationCurve.Index].Value;
replicateCalibrationCurve =
(LinkValue <CalibrationCurve>)row.Cells[colReplicateCalibrationCurve.Index].Value;
});
if (hasBatchNames)
{
Assert.AreNotEqual(calibrationCurve.Value.PointCount, replicateCalibrationCurve.Value.PointCount);
}
else
{
Assert.AreEqual(calibrationCurve.Value.PointCount, replicateCalibrationCurve.Value.PointCount);
Assert.AreEqual(calibrationCurve.Value.Slope, replicateCalibrationCurve.Value.Slope);
}
int selectedResultsIndexOld = SkylineWindow.SelectedResultsIndex;
RunUI(() => calibrationCurve.ClickEventHandler(new object(), new EventArgs()));
var calibrationForm = FindOpenForm <CalibrationForm>();
Assert.IsNotNull(calibrationForm);
WaitForGraphs();
Assert.AreEqual(peptide.IdentityPath, SkylineWindow.SelectedPath);
Assert.AreEqual(selectedResultsIndexOld, SkylineWindow.SelectedResultsIndex);
RunUI(() => replicateCalibrationCurve.ClickEventHandler(new object(), new EventArgs()));
Assert.AreEqual(peptide.IdentityPath, SkylineWindow.SelectedPath);
Assert.AreEqual(replicate.ReplicateIndex, SkylineWindow.SelectedResultsIndex);
}
}
private CalibrationCurveFitter GetCalibrationCurveFitter()
{
if (string.IsNullOrEmpty(ResultFile.Replicate.BatchName) && !Peptide.DocNode.HasPrecursorConcentrations)
{
return(Peptide.GetCalibrationCurveFitter());
}
var calibrationCurveFitter =
new CalibrationCurveFitter(Peptide.GetPeptideQuantifier(), SrmDocument.Settings);
calibrationCurveFitter.SingleBatchReplicateIndex = ResultFile.Replicate.ReplicateIndex;
return(calibrationCurveFitter);
}
public PeptideResult(Peptide peptide, ResultFile file) : base(peptide, file)
{
_chromInfo = CachedValue.Create(DataSchema, () => ResultFile.FindChromInfo(peptide.DocNode.Results));
_quantificationResult = CachedValue.Create(DataSchema, GetQuantification);
_calibrationCurveFitter = CachedValue.Create(DataSchema, GetCalibrationCurveFitter);
}
public override ElementRef GetElementRef()
{
return(MoleculeResultRef.PROTOTYPE.ChangeChromInfo(ResultFile.Replicate.ChromatogramSet, ChromInfo)
.ChangeParent(Peptide.GetElementRef()));
}
public void ChangeChromInfo(EditDescription editDescription, Func <PeptideChromInfo, PeptideChromInfo> newChromInfo)
{
Peptide.ChangeDocNode(editDescription, docNode => docNode.ChangeResults(GetResultFile().ChangeChromInfo(docNode.Results, newChromInfo)));
}
public QuantificationResult GetQuantification()
{
CalibrationCurveFitter curveFitter = Peptide.GetCalibrationCurveFitter();
return(curveFitter.GetQuantificationResult(ResultFile.Replicate.ReplicateIndex));
}