private static FileRetentionTimeAlignments CalculateFileRetentionTimeAlignments(
string dataFileName, ResultNameMap <IDictionary <Target, double> > libraryRetentionTimes, IProgressMonitor progressMonitor)
{
var targetTimes = libraryRetentionTimes.Find(dataFileName);
if (targetTimes == null)
{
return(null);
}
var alignments = new List <RetentionTimeAlignment>();
foreach (var entry in libraryRetentionTimes)
{
if (dataFileName == entry.Key)
{
continue;
}
var alignedFile = AlignedRetentionTimes.AlignLibraryRetentionTimes(targetTimes, entry.Value, REFINEMENT_THRESHHOLD, RegressionMethodRT.linear, new CustomCancellationToken(CancellationToken.None, () => progressMonitor.IsCanceled));
if (alignedFile == null || alignedFile.RegressionRefinedStatistics == null ||
!RetentionTimeRegression.IsAboveThreshold(alignedFile.RegressionRefinedStatistics.R, REFINEMENT_THRESHHOLD))
{
continue;
}
var regressionLine = alignedFile.RegressionRefined.Conversion as RegressionLineElement;
if (regressionLine != null)
{
alignments.Add(new RetentionTimeAlignment(entry.Key, regressionLine));
}
}
return(new FileRetentionTimeAlignments(dataFileName, alignments));
}
private void AlignDataRow(int index, CancellationToken cancellationToken)
{
var dataRow = _dataRows[index];
if (dataRow.TargetTimes == null || dataRow.SourceTimes == null)
{
return;
}
Task.Factory.StartNew(
() => {
try
{
return(AlignedRetentionTimes.AlignLibraryRetentionTimes(
dataRow.TargetTimes, dataRow.SourceTimes,
DocumentRetentionTimes.REFINEMENT_THRESHHOLD,
RegressionMethodRT.linear,
() => cancellationToken.IsCancellationRequested));
}
catch (OperationCanceledException operationCanceledException)
{
throw new OperationCanceledException(operationCanceledException.Message, operationCanceledException, cancellationToken);
}
}, cancellationToken)
.ContinueWith(alignedTimesTask => UpdateDataRow(index, alignedTimesTask), TaskScheduler.FromCurrentSynchronizationContext());
}
private void AlignDataRowAsync(DataRow dataRow, int index, CancellationToken cancellationToken)
{
try
{
var alignedTimes = AlignedRetentionTimes.AlignLibraryRetentionTimes(
dataRow.TargetTimes, dataRow.SourceTimes,
DocumentRetentionTimes.REFINEMENT_THRESHHOLD,
RegressionMethodRT.linear,
new CustomCancellationToken(cancellationToken));
if (!cancellationToken.IsCancellationRequested)
{
RunUI(() => UpdateDataRow(index, alignedTimes, cancellationToken));
}
}
catch (OperationCanceledException operationCanceledException)
{
throw new OperationCanceledException(operationCanceledException.Message, operationCanceledException, cancellationToken);
}
}
public bool BuildLibrary(IProgressMonitor progress)
{
RetentionTimeRegression regr = null;
var standardSpectra = new List <SpectrumMzInfo>();
if (IrtStandard != null && !ReferenceEquals(IrtStandard, IrtStandard.EMPTY))
{
// Align Prosit iRTs with iRT standard
var standardPeptidesToAdd = SkylineWindow.ReadStandardPeptides(IrtStandard);
if (standardPeptidesToAdd != null && standardPeptidesToAdd.Count > 0)
{
// Get iRTs
var standardIRTMap = _rtModel.Predict(_prositClient, _document.Settings,
standardPeptidesToAdd.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p.NodePep).ToArray(),
CancellationToken.None);
var original = standardIRTMap.ToDictionary(p => p.Key.ModifiedTarget, p => p.Value);
var target = IrtStandard.Peptides.ToDictionary(p => p.ModifiedTarget, p => p.Irt);
var aligned = AlignedRetentionTimes.AlignLibraryRetentionTimes(target, original, 0.0, RegressionMethodRT.linear,
CancellationToken.None);
regr = aligned.Regression;
// Get spectra
var standardMS = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
standardPeptidesToAdd.Select(p => p.WithNCE(_nce)).ToArray(),
CancellationToken.None);
// Merge iRT and MS2 into SpecMzInfos
standardSpectra = standardMS.Spectra.Select(m => m.SpecMzInfo).ToList();
for (var i = 0; i < standardSpectra.Count; ++i)
{
if (standardIRTMap.TryGetValue(standardMS.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
standardSpectra[i].RetentionTime = iRT;
}
}
}
}
// Predict fragment intensities
PrositMS2Spectra ms = _intensityModel.PredictBatches(_prositClient, progress, _document.Settings,
_peptides.Zip(_precursors,
(pep, prec) =>
new PrositIntensityModel.PeptidePrecursorNCE(pep, prec, _nce)).ToArray(),
CancellationToken.None);
var specMzInfo = ms.Spectra.Select(m => m.SpecMzInfo).ToList();
// Predict iRTs for peptides
var distinctPeps = _peptides.Select(p => (PrositRetentionTimeModel.PeptideDocNodeWrapper)p).Distinct(
new SystemLinqExtensionMethods.FuncEqualityComparer <PrositRetentionTimeModel.PeptideDocNodeWrapper>(
(p1, p2) => p1.Node.ModifiedSequence == p2.Node.ModifiedSequence)).ToArray();
var iRTMap = _rtModel.PredictBatches(_prositClient, progress, _document.Settings,
distinctPeps, CancellationToken.None);
for (var i = 0; i < specMzInfo.Count; ++i)
{
if (iRTMap.TryGetValue(ms.Spectra[i].PeptidePrecursorNCE.NodePep, out var iRT))
{
specMzInfo[i].RetentionTime = regr?.Conversion?.GetY(iRT) ?? iRT;
}
}
// Build library
var librarySpectra = SpectrumMzInfo.RemoveDuplicateSpectra(standardSpectra.Concat(specMzInfo).ToList());
// Delete if already exists, no merging with Prosit
var libraryExists = File.Exists(LibrarySpec.FilePath);
if (libraryExists)
{
var replace = _replaceLibrary();
if (!replace)
{
return(false);
}
FileEx.SafeDelete(LibrarySpec.FilePath);
}
if (!librarySpectra.Any())
{
return(true);
}
// Build the library
using (var blibDb = BlibDb.CreateBlibDb(LibrarySpec.FilePath))
{
var docLibrarySpec = new BiblioSpecLiteSpec(LibrarySpec.Name, LibrarySpec.FilePath);
BiblioSpecLiteLibrary docLibraryNew = null;
var docLibrarySpec2 = docLibrarySpec;
docLibraryNew =
blibDb.CreateLibraryFromSpectra(docLibrarySpec2, librarySpectra, LibrarySpec.Name, progress);
if (docLibraryNew == null)
{
return(false);
}
}
return(true);
}
protected override void DoTest()
{
const string seqWithOneId = "TFAEALR";
const string seqWithTwoIds = "AADALLLK";
SetPeptideSettings();
SetTransitionSettings();
InsertPeptides();
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("RetentionTimeAlignmentTest.sky")));
ImportResultsFile("S_1.mzML");
ImportResultsFile("S_10.mzML");
WaitForDocumentLoaded();
var document = SkylineWindow.Document;
CollectionAssert.AreEqual(
new[] { "S_1", "S_10" },
document.Settings.MeasuredResults.Chromatograms.Select(c => c.Name).ToArray());
var peptideWithOneId =
document.Peptides.First(
peptideDocNode => seqWithOneId.Equals(peptideDocNode.Peptide.Sequence));
var precursorWithOneId = peptideWithOneId.TransitionGroups.First();
var peptideWithTwoIds =
document.Peptides.First(
peptideDocNode => seqWithTwoIds.Equals(peptideDocNode.Peptide.Sequence));
var precursorWithTwoIds = peptideWithTwoIds.TransitionGroups.First();
Assert.IsTrue(precursorWithOneId.Results[0][0].IsIdentified);
Assert.IsFalse(precursorWithOneId.Results[1][0].Identified == PeakIdentification.TRUE);
Assert.IsTrue(precursorWithOneId.Results[1][0].Identified == PeakIdentification.ALIGNED);
Assert.IsTrue(precursorWithTwoIds.Results[0][0].IsIdentified);
Assert.IsTrue(precursorWithTwoIds.Results[1][0].IsIdentified);
var documentRetentionTimes = document.Settings.DocumentRetentionTimes;
var alignedTo1 = documentRetentionTimes.FileAlignments.Find("S_1");
var alignedTo10 = documentRetentionTimes.FileAlignments.Find("S_10");
var af10To1 = alignedTo1.RetentionTimeAlignments.Find("S_10");
var af1To10 = alignedTo10.RetentionTimeAlignments.Find("S_1");
// Verify that the slopes and intercepts are reciprocals of each other.
// We can only verify this with very coarse precision
Assert.AreEqual(af10To1.RegressionLine.Slope, 1 / af1To10.RegressionLine.Slope, .03);
Assert.AreEqual(af10To1.RegressionLine.Intercept, -af1To10.RegressionLine.Intercept * af10To1.RegressionLine.Slope, 1);
var alignedRetentionTimes10To1 = AlignedRetentionTimes.AlignLibraryRetentionTimes(
document.Settings.GetRetentionTimes("S_1").GetFirstRetentionTimes(),
document.Settings.GetRetentionTimes("S_10").GetFirstRetentionTimes(),
DocumentRetentionTimes.REFINEMENT_THRESHHOLD, () => false);
var alignedRetentionTimes1To10 = AlignedRetentionTimes.AlignLibraryRetentionTimes(
document.Settings.GetRetentionTimes("S_10").GetFirstRetentionTimes(),
document.Settings.GetRetentionTimes("S_1").GetFirstRetentionTimes(),
DocumentRetentionTimes.REFINEMENT_THRESHHOLD, () => false);
Assert.AreEqual(af10To1.RegressionLine.Slope, alignedRetentionTimes10To1.RegressionRefined.Conversion.Slope);
Assert.AreEqual(af10To1.RegressionLine.Intercept, alignedRetentionTimes10To1.RegressionRefined.Conversion.Intercept);
Assert.AreEqual(af1To10.RegressionLine.Slope, alignedRetentionTimes1To10.RegressionRefined.Conversion.Slope);
Assert.AreEqual(af1To10.RegressionLine.Intercept, alignedRetentionTimes1To10.RegressionRefined.Conversion.Intercept);
// Verify that the generated chromatogram is of the expected length around the actual or aligned ID's
var idTimes = document.Settings.GetRetentionTimes("S_1", seqWithOneId, peptideWithOneId.ExplicitMods);
VerifyStartEndTime(document, peptideWithOneId, precursorWithOneId, 0,
idTimes.Min() - CHROMATOGRAM_WINDOW_LENGTH_MINUTES,
idTimes.Max() + CHROMATOGRAM_WINDOW_LENGTH_MINUTES);
var alignedTimes = document.Settings.GetAllRetentionTimes("S_10", seqWithOneId, peptideWithOneId.ExplicitMods);
Assert.AreEqual(0, document.Settings.GetRetentionTimes("S_10").GetRetentionTimes(seqWithOneId).Length);
VerifyStartEndTime(document, peptideWithOneId, precursorWithOneId, 1,
alignedTimes.Min() - CHROMATOGRAM_WINDOW_LENGTH_MINUTES,
alignedTimes.Max() + CHROMATOGRAM_WINDOW_LENGTH_MINUTES);
RunUI(() => SkylineWindow.ComboResults.SelectedIndex = 1);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
var alignAgainstOptions = alignmentForm.ComboAlignAgainst.Items.Cast <object>()
.Select(item => item.ToString())
.ToArray();
CollectionAssert.AreEqual(new[] { "S_1", "S_10" }, alignAgainstOptions);
Assert.AreEqual("S_10", alignmentForm.ComboAlignAgainst.SelectedItem.ToString());
});
WaitForConditionUI(10000, () => alignmentForm.RegressionGraph.GraphPane.XAxis.Title.Text == string.Format(Resources.AlignmentForm_UpdateGraph_Time_from__0__, "S_1"));
RunUI(() =>
{
var curves = alignmentForm.RegressionGraph.GraphPane.CurveList;
var outlierCurve = curves.Find(curveItem => Resources.AlignmentForm_UpdateGraph_Outliers == curveItem.Label.Text);
var goodPointsCurve = curves.Find(curveItem => curveItem.Label.Text == Resources.AlignmentForm_UpdateGraph_Peptides_Refined);
Assert.AreEqual(alignedRetentionTimes1To10.OutlierIndexes.Count, outlierCurve.Points.Count);
Assert.AreEqual(alignedRetentionTimes1To10.RegressionPointCount, outlierCurve.Points.Count + goodPointsCurve.Points.Count);
});
RunUI(alignmentForm.Close);
RunUI(() => SkylineWindow.ComboResults.SelectedIndex = 0);
var alignmentForm2 = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() => Assert.AreEqual("S_1", alignmentForm2.ComboAlignAgainst.SelectedItem.ToString()));
RunUI(alignmentForm2.Close);
RunUI(() => SkylineWindow.SaveDocument());
}
