public void OpenDocumentNoWait(string documentPath)
{
var documentFile = TestFilesDir.GetTestPath(documentPath);
WaitForCondition(() => File.Exists(documentFile));
SkylineWindow.BeginInvoke((Action)(() => SkylineWindow.OpenFile(documentFile)));
}
protected bool RunAndMaybeTryCancel(Action action, bool tryToCancel)
{
bool finished = false;
SkylineWindow.BeginInvoke(new Action(() =>
{
action();
finished = true;
}));
bool triedToCancel = false;
while (!finished)
{
if (tryToCancel)
{
var longWaitDlg = FindOpenForm <LongWaitDlg>();
if (longWaitDlg != null)
{
RunUI(longWaitDlg.Close);
triedToCancel = true;
}
}
Thread.Sleep(0);
}
return(triedToCancel);
}
private static void PrepareLibraryDlg(ViewLibraryDlg libraryDlg, Action prepareAction = null)
{
if (prepareAction != null)
{
SkylineWindow.BeginInvoke(prepareAction);
}
if (!TryWaitForCondition(2000, () => libraryDlg.IsUpdateComplete))
{
libraryDlg.IsUpdateCanceled = true;
Assert.Fail("Unexpected long wait filling peptide list form");
}
}
protected void TestUsePredictedTime()
{
const double FILTER_LENGTH = 2.7;
RunUI(() => SkylineWindow.OpenFile(TestFilesDir.GetTestPath("RetentionTimeFilterTest.sky")));
var docStart = WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("TestUsePredictedTime.sky")));
SetUiDocument(docStart.ChangeSettings(docStart.Settings.ChangeTransitionFullScan(f =>
f.ChangeRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, FILTER_LENGTH))));
Assert.IsNull(SkylineWindow.Document.Settings.PeptideSettings.Prediction.RetentionTime);
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Prediction.UseMeasuredRTs);
// When we try to import a file, we should get an error about not having a peptide prediction algorithm
var messageDlg = ShowDialog <MessageDlg>(() => SkylineWindow.ImportResults());
RunUI(() =>
{
Assert.AreEqual(Resources.SkylineWindow_CheckRetentionTimeFilter_NoPredictionAlgorithm, messageDlg.Message);
messageDlg.Close();
});
var ssrCalcRegression = new RetentionTimeRegression("SSRCALC_FOR_RtFilterTest",
new RetentionScoreCalculator(RetentionTimeRegression.SSRCALC_100_A), .63,
5.8, 1.4, new MeasuredRetentionTime[0]);
// Now give the document a prediction algorithm
var docBeforeImport = SkylineWindow.Document;
docBeforeImport = docBeforeImport.ChangeSettings(docBeforeImport.Settings.ChangePeptidePrediction(p =>
p.ChangeRetentionTime(ssrCalcRegression)));
SetUiDocument(docBeforeImport);
// Now import two result files
{
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(() =>
{
openDataSourceDialog.SelectFile("200fmol" + extension);
openDataSourceDialog.SelectFile("20fmol" + extension);
});
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
{
var document = WaitForDocumentChangeLoaded(docBeforeImport);
foreach (var chromatogramSet in document.Settings.MeasuredResults.Chromatograms)
{
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
var peptide = tuple.Item1;
if (!peptide.IsProteomic)
{
continue;
}
var transitionGroup = tuple.Item2;
var predictedRetentionTime = ssrCalcRegression.GetRetentionTime(
document.Settings.GetModifiedSequence(peptide.Peptide.Sequence,
transitionGroup.TransitionGroup.LabelType, peptide.ExplicitMods)).Value;
AssertChromatogramWindow(document, chromatogramSet,
predictedRetentionTime - FILTER_LENGTH,
predictedRetentionTime + FILTER_LENGTH, tuple.Item3);
}
}
}
ChromatogramSet chromSetForScheduling = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms[1];
// Create a SrmDocument with just the one ChromatogramSet that we are going to use for scheduling, so that
// we can assert later that the chromatogram windows are where this document says they should be.
var docForScheduling = SkylineWindow.Document.ChangeMeasuredResults(
SkylineWindow.Document.Settings.MeasuredResults.ChangeChromatograms(new[] { chromSetForScheduling }));
docForScheduling = docForScheduling.ChangeSettings(docForScheduling.Settings.ChangePeptidePrediction(p =>
p.ChangeUseMeasuredRTs(true).ChangeRetentionTime(null)));
SetUiDocument(docForScheduling);
{
var chooseSchedulingReplicatesDlg = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
// Choose a scheduling replicate (the one saved above)
RunUI(() => Assert.IsTrue(chooseSchedulingReplicatesDlg.TrySetReplicateChecked(
chromSetForScheduling, true)));
var importResultsDlg = ShowDialog <ImportResultsDlg>(chooseSchedulingReplicatesDlg.OkDialog);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(() => openDataSourceDialog.SelectFile("40fmol" + extension));
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
{
var document = WaitForDocumentChangeLoaded(docForScheduling);
var chromatogramSet = document.Settings.MeasuredResults.Chromatograms.First(cs => cs.Name == "40fmol");
int countNull = 0;
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
var prediction = new PeptidePrediction(null, null, true, 1, false, 0);
double windowRtIgnored;
var schedulingPeptide =
docForScheduling.Molecules.First(pep => ReferenceEquals(pep.Peptide, tuple.Item1.Peptide));
var schedulingTransitionGroup = (TransitionGroupDocNode)schedulingPeptide.FindNode(tuple.Item2.TransitionGroup);
double?predictedRt = prediction.PredictRetentionTime(docForScheduling,
schedulingPeptide,
schedulingTransitionGroup,
null, ExportSchedulingAlgorithm.Average, true, out windowRtIgnored);
if (!predictedRt.HasValue)
{
countNull++;
continue;
}
AssertChromatogramWindow(document, chromatogramSet, predictedRt.Value - FILTER_LENGTH, predictedRt.Value + FILTER_LENGTH, tuple.Item3);
}
Assert.AreEqual((TestSmallMolecules ? 1 : 0), countNull);
}
// Test using iRT with auto-calculated regression
{
const string calcName = "TestCalculator";
const string regressionName = "TestCalculatorAutoCalcRegression";
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editIrtDlg = ShowDialog <EditIrtCalcDlg>(peptideSettingsDlg.AddCalculator);
RunUI(() =>
{
editIrtDlg.OpenDatabase(TestFilesDir.GetTestPath("RetentionTimeFilterTest.irtdb"));
editIrtDlg.CalcName = calcName;
});
SkylineWindow.BeginInvoke(new Action(editIrtDlg.OkDialog));
var multiButtonMsgDlg = WaitForOpenForm <MultiButtonMsgDlg>();
OkDialog(multiButtonMsgDlg, () => multiButtonMsgDlg.DialogResult = DialogResult.Yes);
var editRtDlg = ShowDialog <EditRTDlg>(peptideSettingsDlg.AddRTRegression);
RunUI(() =>
{
editRtDlg.ChooseCalculator(calcName);
editRtDlg.SetAutoCalcRegression(true);
editRtDlg.SetRegressionName(regressionName);
editRtDlg.SetTimeWindow(1.0);
});
OkDialog(editRtDlg, editRtDlg.OkDialog);
RunUI(() =>
{
peptideSettingsDlg.ChooseRegression(regressionName);
peptideSettingsDlg.UseMeasuredRT(false);
});
OkDialog(peptideSettingsDlg, peptideSettingsDlg.OkDialog);
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Prediction.UseMeasuredRTs);
docBeforeImport = SkylineWindow.Document;
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResultsDlg.OkDialog);
RunUI(() => openDataSourceDialog.SelectFile("8fmol" + extension));
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
var document = WaitForDocumentChangeLoaded(docBeforeImport);
var chromatogramSet = document.Settings.MeasuredResults.Chromatograms.First(cs => cs.Name == "8fmol");
var regressionLine =
document.Settings.PeptideSettings.Prediction.RetentionTime.GetConversion(
chromatogramSet.MSDataFileInfos.First().FileId);
var calculator = document.Settings.PeptideSettings.Prediction.RetentionTime.Calculator;
double fullGradientStartTime;
double fullGradientEndTime;
using (var msDataFile = new MsDataFileImpl(TestFilesDir.GetTestPath("8fmol" + extension)))
{
fullGradientStartTime = msDataFile.GetSpectrum(0).RetentionTime.Value;
fullGradientEndTime = msDataFile.GetSpectrum(msDataFile.SpectrumCount - 1).RetentionTime.Value;
}
foreach (var tuple in LoadAllChromatograms(document, chromatogramSet))
{
if (tuple.Item1.GlobalStandardType != PeptideDocNode.STANDARD_TYPE_IRT)
{
double?score =
calculator.ScoreSequence(document.Settings.GetModifiedSequence(tuple.Item1.Peptide.Sequence,
tuple.Item2.TransitionGroup.LabelType, tuple.Item1.ExplicitMods));
if (score.HasValue)
{
double?predictedRt = regressionLine.GetY(score.Value);
AssertChromatogramWindow(document, chromatogramSet, predictedRt.Value - FILTER_LENGTH,
predictedRt.Value + FILTER_LENGTH, tuple.Item3);
}
}
else
{
// IRT Standards get extracted for the full gradient
AssertChromatogramWindow(document, chromatogramSet, fullGradientStartTime, fullGradientEndTime, tuple.Item3);
}
}
}
}