private void VerifyTransitionRatio(TransitionTreeNode transitionTreeNode, string ionName, double?ratioExpected = null) { Assert.AreEqual(ionName, transitionTreeNode.DocNode.FragmentIonName); var ratioActual = transitionTreeNode.DocNode.Results[0][0].Ratio; if (ratioExpected.HasValue) { Assert.AreEqual(ratioExpected.Value, ratioActual.Value, 0.005); } else { Assert.IsFalse(ratioActual.HasValue); } }
private void DoMrmerTest() { // Preparing a Document to Accept a Transition List, p. 2 var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI); var editListUI = ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList); RunDlg <EditLibraryDlg>(editListUI.AddItem, editLibraryDlg => { editLibraryDlg.LibrarySpec = new BiblioSpecLibSpec("Yeast_mini", GetTestPath(@"MRMer\Yeast_MRMer_min.blib")); // Not L10N editLibraryDlg.OkDialog(); }); OkDialog(editListUI, editListUI.OkDialog); RunUI(() => { peptideSettingsUI.PickedLibraries = new[] { "Yeast_mini" }; // Not L10N peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library; }); PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 3); RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Digest); RunDlg <BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg, buildBackgroundProteomeDlg => { buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast_mini"; // Not L10N buildBackgroundProteomeDlg.BackgroundProteomePath = GetTestPath(@"MRMer\Yeast_MRMer_mini.protdb"); // Not L10N buildBackgroundProteomeDlg.OkDialog(); }); PauseForScreenShot <PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 4); var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N RelativeRT.Matching, null, null, null); AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification form", 5); var modHeavyR = new StaticMod(HEAVY_R, "R", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N RelativeRT.Matching, null, null, null); AddHeavyMod(modHeavyR, peptideSettingsUI, "Edit Isotope Modification form", 6); RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { HEAVY_K, HEAVY_R }); var docBeforePeptideSettings = SkylineWindow.Document; OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog); WaitForDocumentChangeLoaded(docBeforePeptideSettings); // Inserting a Transition List With Associated Proteins, p. 6 RunUI(() => { var filePath = GetTestPath(@"MRMer\silac_1_to_4.xls"); // Not L10N SetExcelFileClipboardText(filePath, "Fixed", 3, false); // Not L10N }); using (new CheckDocumentState(24, 44, 88, 296)) { var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg); RunUI(() => pasteDlg.IsMolecule = false); // Make sure it's ready to accept peptides rather than small molecules RunUI(pasteDlg.PasteTransitions); PauseForScreenShot <PasteDlg.TransitionListTab>("Insert Transition List form", 8); OkDialog(pasteDlg, pasteDlg.OkDialog); } PauseForScreenShot("Main window with transitions added", 9); FindNode("LWDVAT"); RunUI(() => { Assert.IsTrue(((PeptideDocNode)((PeptideTreeNode)SkylineWindow.SelectedNode).Model).HasChildType(IsotopeLabelType.heavy)); SkylineWindow.ExpandPrecursors(); }); FindNode(string.Format("{0:F03}", 854.4)); // I18N WaitForGraphs(); // Unfortunately, label hiding may mean that the selected ion is not labeled Assert.IsTrue(SkylineWindow.GraphSpectrum.SelectedIonLabel != null ? SkylineWindow.GraphSpectrum.SelectedIonLabel.Contains("y7") // Not L10N : SkylineWindow.GraphSpectrum.IonLabels.Contains(ionLabel => ionLabel.Contains("y7"))); // Not L10N RunUI(() => { SkylineWindow.GraphSpectrumSettings.ShowBIons = true; SkylineWindow.GraphSpectrumSettings.ShowCharge2 = true; }); PauseForScreenShot <GraphSpectrum>("Main window with spectral library graph showing", 10); // Importing Data, p. 10. RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"MRMer\MRMer.sky"))); // Not L10N ImportResultsFile("silac_1_to_4.mzXML"); // Not L10N FindNode("ETFP"); // Not L10N RunUI(SkylineWindow.AutoZoomBestPeak); PauseForScreenShot("Main window with data imported", 12); RunUI(() => { var selNode = SkylineWindow.SequenceTree.SelectedNode; Assert.IsTrue(selNode.Text.Contains("ETFPILVEEK")); // Not L10N Assert.IsTrue(((PeptideDocNode)((PeptideTreeNode)selNode).Model).HasResults); Assert.IsTrue(Equals(selNode.StateImageIndex, (int)SequenceTree.StateImageId.keep)); SkylineWindow.ShowAllTransitions(); SkylineWindow.SelectedPath = SkylineWindow.SequenceTree.GetNodePath(selNode.Nodes[0].Nodes[2] as TreeNodeMS); Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.StateImageIndex, (int)SequenceTree.StateImageId.no_peak)); }); PauseForScreenShot("Main window", 13); // Removing a Transition with Interference, p. 13. FindNode(string.Format("{0:F04}", 504.2664)); // I18N RunUI(() => { TransitionTreeNode selNode = (TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode; SkylineWindow.RemovePeak( SkylineWindow.SequenceTree.SelectedPath.GetPathTo((int)SrmDocument.Level.TransitionGroups), ((TransitionGroupTreeNode)selNode.Parent).DocNode, selNode.DocNode); // Ensure that the Total Ratio is 0.62 // TODO(nicksh): Update tutorial Word Doc so that it has the right numbers. Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.StateImageIndex, (int)SequenceTree.StateImageId.no_peak) && SkylineWindow.SequenceTree.SelectedNode.Parent.Text.Contains((0.62).ToString(LocalizationHelper.CurrentCulture))); }); // Adjusting Peak Boundaries to Exclude Interference, p. 14. RunUI(() => SkylineWindow.Undo()); FindNode("ETFP"); RunUI(() => { var pathGroup = SkylineWindow.SequenceTree.GetNodePath((TreeNodeMS)SkylineWindow.SelectedNode.Nodes[0]); var graphChrom = SkylineWindow.GraphChromatograms.ToList()[0]; var listChanges = new List <ChangedPeakBoundsEventArgs> { new ChangedPeakBoundsEventArgs(pathGroup, null, graphChrom.NameSet, graphChrom.ChromGroupInfos[0].FilePath, new ScaledRetentionTime(29.8, 29.8), new ScaledRetentionTime(30.4, 30.4), PeakIdentification.FALSE, PeakBoundsChangeType.both) }; graphChrom.SimulateChangedPeakBounds(listChanges); foreach (TransitionTreeNode node in SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes) { Assert.IsTrue(((TransitionDocNode)node.Model).HasResults); } }); PauseForScreenShot("Main window", 14); FindNode("YVDP"); RunUI(() => Assert.IsTrue(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[2].StateImageIndex == (int)SequenceTree.StateImageId.peak_blank)); RunUI(() => SkylineWindow.SaveDocument()); PauseForAuditLog(); }
protected override void DoTest() { // Skyline Targeted Method Refinement var folderMethodRefine = UseRawFiles ? "MethodRefine" : "MethodRefineMzml"; // Not L10N // Results Data, p. 2 var doc = SkylineWindow.Document; RunUI(() => SkylineWindow.OpenFile(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\WormUnrefined.sky"))); // Not L10N WaitForDocumentChangeLoaded(doc); RunUI(() => { // Adjust font sizes for better screen shots Settings.Default.ChromatogramFontSize = 14; Settings.Default.SpectrumFontSize = 14; SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR); SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0]; SkylineWindow.AutoZoomBestPeak(); // TODO: Mention this in the tutorial SkylineWindow.Size = new Size(1160, 660); Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode.Text, "YLGAYLLATLGGNASPSAQDVLK"); // Not L10N }); PauseForScreenShot("Main window", 2); // TODO: Update tutorial to view b-ions. RunUI(() => SkylineWindow.GraphSpectrumSettings.ShowBIons = true); // Unrefined Methods, p. 3 { var exportDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List)); RunUI(() => { exportDlg.ExportStrategy = ExportStrategy.Buckets; exportDlg.MethodType = ExportMethodType.Standard; exportDlg.OptimizeType = ExportOptimize.NONE; exportDlg.MaxTransitions = 59; }); PauseForScreenShot("Export Transition List form", 3); // Not L10N OkDialog(exportDlg, () => exportDlg.OkDialog(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm"))); // Not L10N } for (int i = 1; i < 10; i++) { Assert.IsTrue(File.Exists(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm_000" + i + TextUtil.EXT_CSV))); // Not L10N } for (int i = 10; i < 40; i++) { Assert.IsTrue(File.Exists(TestFilesDirs[1].GetTestPath(folderMethodRefine + @"\worm_00" + i + TextUtil.EXT_CSV))); // Not L10N } // Importing Multiple Injection Data, p. 4 Assert.IsTrue(SkylineWindow.Document.Settings.HasResults); RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg => { manageResultsDlg.RemoveReplicates(); Assert.AreEqual(manageResultsDlg.Chromatograms.ToArray().Length, 0); manageResultsDlg.OkDialog(); }); RunUI(() => SkylineWindow.SaveDocument()); Assert.IsFalse(SkylineWindow.Document.Settings.HasResults); const string replicateName = "Unrefined"; // Not L10N RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg => { importResultsDlg.RadioAddNewChecked = true; var namedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray(); importResultsDlg.NamedPathSets = new[] { new KeyValuePair <string, MsDataFileUri[]>(replicateName, namedPathSets[0].Value.Take(15).ToArray()) }; importResultsDlg.OkDialog(); }); WaitForOpenForm <AllChromatogramsGraph>(); // To make the AllChromatogramsGraph form accessible to the SkylineTester forms tab PauseForScreenShot <AllChromatogramsGraph>("Loading Chromatograms: Take screenshot at about 25% loaded...", 5); WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes Assert.IsTrue(SkylineWindow.Document.Settings.HasResults); Assert.AreEqual(15, SkylineWindow.Document.Settings.MeasuredResults.CachedFilePaths.ToArray().Length); RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg => { importResultsDlg.RadioAddExistingChecked = true; var namedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray(); importResultsDlg.NamedPathSets = new[] { new KeyValuePair <string, MsDataFileUri[]>(replicateName, namedPathSets[0].Value.Skip(15).ToArray()) }; importResultsDlg.OkDialog(); }); WaitForCondition(20 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes Assert.AreEqual(39, SkylineWindow.Document.Settings.MeasuredResults.CachedFilePaths.ToArray().Length); RunUI(SkylineWindow.AutoZoomNone); RestoreViewOnScreen(7); PauseForScreenShot("Chromatogram graph metafile", 7); // Simple Manual Refinement, p. 6 int startingNodeCount = SkylineWindow.SequenceTree.Nodes[0].GetNodeCount(false); Assert.AreEqual("YLGAYLLATLGGNASPSAQDVLK", SkylineWindow.SequenceTree.Nodes[0].Nodes[0].Text); // Not L10N RunUI(() => { SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0]; SkylineWindow.AutoZoomNone(); SkylineWindow.AutoZoomBestPeak(); SkylineWindow.EditDelete(); SkylineWindow.ShowRTLinearRegressionGraph(); }); Assert.AreEqual(SkylineWindow.SequenceTree.Nodes[0].GetNodeCount(false), startingNodeCount - 1); Assert.AreEqual("VLEAGGLDCDMENANSVVDALK", SkylineWindow.SequenceTree.Nodes[0].Nodes[0].Text); // Not L10N PauseForScreenShot("Retention Times Regression plot metafile", 8); RunDlg <RegressionRTThresholdDlg>(SkylineWindow.ShowRegressionRTThresholdDlg, rtThresholdDlg => { rtThresholdDlg.Threshold = 0.95; rtThresholdDlg.OkDialog(); }); WaitForConditionUI(() => SkylineWindow.RTGraphController.RegressionRefined != null); WaitForGraphs(); PauseForScreenShot("Retention Times Regression plot metafile with 0.95 threshold", 9); // Not L10N TestRTResidualsSwitch(); RunDlg <EditRTDlg>(SkylineWindow.CreateRegression, editRTDlg => editRTDlg.OkDialog()); RunUI(() => SkylineWindow.ShowGraphRetentionTime(false)); RunUI(SkylineWindow.AutoZoomNone); PauseForScreenShot("Chromatogram graph metafile zoomed out", 10); // Not L10N // Missing Data, p. 10 RunUI(() => { SkylineWindow.RTGraphController.SelectPeptide(SkylineWindow.Document.GetPathTo(1, 163)); Assert.AreEqual("YLAEVASEDR", SkylineWindow.SequenceTree.SelectedNode.Text); // Not L10N }); RestoreViewOnScreen(11); // Restoring the view changes the selection RunUI(SkylineWindow.CollapsePeptides); FindNode("YLAEVASEDR"); RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[153]); PauseForScreenShot("Targets view clipped from the main window", 11); RunUI(() => { var nodePep = (PeptideDocNode)((SrmTreeNode)SkylineWindow.SequenceTree.SelectedNode).Model; Assert.AreEqual(null, nodePep.GetPeakCountRatio( SkylineWindow.SequenceTree.GetDisplayResultsIndex(nodePep))); SkylineWindow.SequenceTree.SelectedPath = SkylineWindow.Document.GetPathTo(1, 157); Assert.AreEqual("VTVVDDQSVILK", SkylineWindow.SequenceTree.SelectedNode.Text); }); WaitForGraphs(); RunUI(() => { SkylineWindow.ActivateReplicate("Unrefined"); SkylineWindow.AutoZoomNone(); }); PauseForScreenShot("Unrefined chromatogram graph page clipped from main window", 12); // Not L10N // foreach (var peptideDocNode in SkylineWindow.Document.Peptides) // { // var nodeGroup = ((TransitionGroupDocNode)peptideDocNode.Children[0]); // Console.WriteLine("{0} - {1}", peptideDocNode.Peptide.Sequence, // nodeGroup.GetDisplayText(SkylineWindow.SequenceTree.GetDisplaySettings(peptideDocNode))); // } // Console.WriteLine("---------------------------------"); RunUI(() => { var graphChrom = SkylineWindow.GetGraphChrom("Unrefined"); // Not L10N Assert.AreEqual(2, graphChrom.Files.Count); SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]; // Picking Measurable Peptides and Transitions, p. 12 SkylineWindow.ExpandPeptides(); SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0]; }); RunUI(SkylineWindow.AutoZoomBestPeak); RestoreViewOnScreen(13); RunUI(() => SkylineWindow.ShowGraphSpectrum(false)); PauseForScreenShot("Targets view clipped from the main window and chromatogram graph metafile", 13); RunUI(() => SkylineWindow.ShowGraphSpectrum(true)); PauseForScreenShot("Library Match plot metafile", 14); RunUI(() => { SkylineWindow.ShowGraphSpectrum(false); SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 0); SkylineWindow.SelectedNode.Expand(); SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0); }); PauseForScreenShot("Targetes view clipped from the main window", 14); // Not L10N RunUI(() => { double dotpExpect = Math.Round(Statistics.AngleToNormalizedContrastAngle(0.78), 2); // 0.57 AssertEx.Contains(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Text, dotpExpect.ToString(LocalizationHelper.CurrentCulture)); SkylineWindow.EditDelete(); dotpExpect = 0.34; // Math.Round(Statistics.AngleToNormalizedContrastAngle(0.633), 2); // 0.44 SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0]; AssertEx.Contains(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Text, dotpExpect.ToString(LocalizationHelper.CurrentCulture)); SkylineWindow.EditDelete(); PeptideTreeNode nodePep; for (int i = 0; i < 2; i++) { nodePep = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[i]; nodePep.ExpandAll(); foreach (TransitionTreeNode nodeTran in nodePep.Nodes[0].Nodes) { TransitionDocNode nodeTranDoc = (TransitionDocNode)nodeTran.Model; Assert.AreEqual((int)SequenceTree.StateImageId.peak, TransitionTreeNode.GetPeakImageIndex(nodeTranDoc, (PeptideDocNode)nodePep.Model, SkylineWindow.SequenceTree)); var resultsIndex = SkylineWindow.SequenceTree.GetDisplayResultsIndex(nodePep); var rank = nodeTranDoc.GetPeakRank(resultsIndex); if (rank == null || rank > 3) { SkylineWindow.SequenceTree.SelectedNode = nodeTran; } SkylineWindow.SequenceTree.KeysOverride = Keys.Control; } } nodePep = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[2]; nodePep.ExpandAll(); foreach (TransitionTreeNode nodeTran in nodePep.Nodes[0].Nodes) { TransitionDocNode nodeTranDoc = (TransitionDocNode)nodeTran.Model; Assert.AreEqual((int)SequenceTree.StateImageId.peak, TransitionTreeNode.GetPeakImageIndex(nodeTranDoc, (PeptideDocNode)nodePep.Model, SkylineWindow.SequenceTree)); var name = ((TransitionDocNode)nodeTran.Model).FragmentIonName; if (!(name == "y11" || name == "y13" || name == "y14")) // Not L10N { SkylineWindow.SequenceTree.SelectedNode = nodeTran; } SkylineWindow.SequenceTree.KeysOverride = Keys.Control; } SkylineWindow.SequenceTree.KeysOverride = Keys.None; SkylineWindow.EditDelete(); for (int i = 0; i < 3; i++) { Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Nodes[i].Nodes[0].Nodes.Count == 3); } SkylineWindow.AutoZoomNone(); SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 5); SkylineWindow.Size = new Size(722, 449); }); RunUI(SkylineWindow.AutoZoomBestPeak); RestoreViewOnScreen(15); PauseForScreenShot("Targetes view clipped from main window and chromatogram graph metafile", 15); // Automated Refinement, p. 16 RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg => { refineDlg.MaxTransitionPeakRank = 3; refineDlg.PreferLargerIons = true; refineDlg.RemoveMissingResults = true; refineDlg.RTRegressionThreshold = 0.95; refineDlg.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.95); // Convert from original cos(angle) dot-product refineDlg.OkDialog(); }); WaitForCondition(() => SkylineWindow.Document.PeptideCount < 73); // foreach (var peptideDocNode in SkylineWindow.Document.Peptides) // { // var nodeGroup = ((TransitionGroupDocNode) peptideDocNode.Children[0]); // Console.WriteLine("{0} - {1}", peptideDocNode.Peptide.Sequence, // nodeGroup.GetDisplayText(SkylineWindow.SequenceTree.GetDisplaySettings(peptideDocNode))); // } RunUI(() => { Assert.AreEqual(72, SkylineWindow.Document.PeptideCount); Assert.AreEqual(216, SkylineWindow.Document.PeptideTransitionCount); SkylineWindow.CollapsePeptides(); SkylineWindow.Undo(); }); RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg => { refineDlg.MaxTransitionPeakRank = 6; refineDlg.RemoveMissingResults = true; refineDlg.RTRegressionThreshold = 0.90; refineDlg.DotProductThreshold = Statistics.AngleToNormalizedContrastAngle(0.90); // Convert from original cos(angle) dot-product refineDlg.OkDialog(); }); WaitForCondition(() => SkylineWindow.Document.PeptideCount < 120); RunUI(() => { Assert.AreEqual(113, SkylineWindow.Document.PeptideCount); // Scheduling for Efficient Acquisition, p. 17 SkylineWindow.Undo(); }); RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, mResults => { Assert.AreEqual(1, mResults.Chromatograms.Count()); mResults.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Where( set => Equals("Unrefined", set.Name)); // Not L10N mResults.RemoveReplicates(); Assert.AreEqual(0, mResults.Chromatograms.Count()); mResults.OkDialog(); }); var importResultsDlg0 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults); RunUI(() => { SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]; importResultsDlg0.RadioCreateMultipleMultiChecked = true; importResultsDlg0.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(Path.Combine(TestFilesDirs[1].FullPath, Path.GetFileName(TestFilesDirs[1].FullPath) ?? string.Empty)).ToArray(); }); var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg0.OkDialog); RunUI(importResultsNameDlg.NoDialog); WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes var docCurrent = SkylineWindow.Document; RunUI(SkylineWindow.RemoveMissingResults); WaitForDocumentChange(docCurrent); Assert.AreEqual(86, SkylineWindow.Document.PeptideCount); Assert.AreEqual(255, SkylineWindow.Document.PeptideTransitionCount); TestRTResidualsSwitch(); // Measuring Retention Times, p. 17 { var exportDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List)); RunUI(() => exportDlg.MaxTransitions = 130); PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 18); OkDialog(exportDlg, () => exportDlg.OkDialog(TestFilesDirs[1].FullPath + "\\unscheduled")); // Not L10N } /////////////////////// // Reviewing Retention Time Runs, p. 18 RunUI(() => { SkylineWindow.ShowGraphSpectrum(false); SkylineWindow.ArrangeGraphsTiled(); SkylineWindow.AutoZoomNone(); SkylineWindow.AutoZoomBestPeak(); }); FindNode("FWEVISDEHGIQPDGTFK"); RunUI(() => SkylineWindow.Size = new Size(1060, 550)); RestoreViewOnScreen(19); PauseForScreenShot("Main window", 19); // Not L10N RunUI(() => SkylineWindow.ShowRTSchedulingGraph()); WaitForCondition(() => SkylineWindow.GraphRetentionTime != null); PauseForScreenShot("Retention Times - Scheduling graph metafile", 19); RestoreViewOnScreen(20); // Creating a Scheduled Transition List, p. 20 { var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI); RunUI(() => { peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction; peptideSettingsUI.TimeWindow = 4; }); PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 21); OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog); // Not L10N } var exportMethodDlg1 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List)); RunUI(() => { exportMethodDlg1.ExportStrategy = ExportStrategy.Single; exportMethodDlg1.MethodType = ExportMethodType.Scheduled; }); // TODO: Update tutorial to mention the scheduling options dialog. PauseForScreenShot("Export Transition List form", 22); // Not L10N RunDlg <SchedulingOptionsDlg>(() => exportMethodDlg1.OkDialog(TestFilesDirs[1].FullPath + "\\scheduled"), // Not L10N schedulingOptionsDlg => schedulingOptionsDlg.OkDialog()); WaitForClosedForm(exportMethodDlg1); // Reviewing Multi-Replicate Data, p. 22 RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg => { manageResultsDlg.RemoveAllReplicates(); manageResultsDlg.OkDialog(); }); var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults); RunDlg <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets = importResultsDlg1.GetDataSourcePathsFile(null), openDataSourceDialog => { openDataSourceDialog.SelectAllFileType(ExtThermoRaw); openDataSourceDialog.Open(); }); RunDlg <ImportResultsNameDlg>(importResultsDlg1.OkDialog, importResultsNameDlg0 => { importResultsNameDlg0.Prefix = "Scheduled_"; // Not L10N importResultsNameDlg0.YesDialog(); }); WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes Assert.AreEqual(5, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)); RunUI(() => { SkylineWindow.RemoveMissingResults(); SkylineWindow.ArrangeGraphsTiled(); SkylineWindow.ShowGraphRetentionTime(false); }); WaitForCondition(() => SkylineWindow.GraphRetentionTime.IsHidden); RunUI(() => { SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].Nodes[0]; SkylineWindow.ShowRTReplicateGraph(); SkylineWindow.ShowPeakAreaReplicateComparison(); SkylineWindow.CollapsePeptides(); SkylineWindow.ShowChromatogramLegends(false); SkylineWindow.Size = new Size(1024, 768); }); RestoreViewOnScreen(24); WaitForGraphs(); PauseForScreenShot("Main window", 24); // Not L10N RunUI(() => SkylineWindow.SaveDocument()); RunUI(SkylineWindow.NewDocument); }
public override string GetDisplayText(DisplaySettings settings) { return(TransitionTreeNode.DisplayText(this, settings)); }