private void DoStudy7Test() { // Preparing a Document to Accept the Study 7 Transition List, p. 15 RunUI(() => SkylineWindow.NewDocument()); var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI); var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13, RelativeRT.Matching, null, null, null); AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 17); RunUI(() => { peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K }; peptideSettingsUI1.PickedLibraries = new[] { "" }; peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None; peptideSettingsUI1.OkDialog(); }); // Pasting a Transition List into the Document, p. 18. string clipboardSaveText = string.Empty; RunUI(() => { var filePath = GetTestPath(@"Study 7\Study7 transition list.xls"); SetExcelFileClipboardText(filePath, "Simple", 6, false); clipboardSaveText = ClipboardEx.GetText(); }); { var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(SkylineWindow.Paste); PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 18); OkDialog(messageDlg, messageDlg.CancelDialog); // Restore the clipboard text after pausing ClipboardEx.SetText(clipboardSaveText); } RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI => { transitionSettingsUI.InstrumentMaxMz = 1800; transitionSettingsUI.OkDialog(); }); RunUI(() => { SkylineWindow.Paste(); SkylineWindow.CollapsePeptides(); }); PauseForScreenShot("Targets tree (selected from main window)", 19); // Adjusting Modifications Manually, p. 19. AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348); PauseForScreenShot("Target tree clipped from main window", 22); AdjustModifications("IVGGWECEK", true, 'V', 541.763); AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974); RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky"))); // Importing Data from a Multiple Sample WIFF file, p. 23. var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults); var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets = importResultsDlg1.GetDataSourcePathsFile(null)); RunUI(() => { openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7")); openDataSourceDialog1.SelectAllFileType(IsFullData ? ".wiff" : ExtensionTestContext.ExtAbWiff); // Force true wiff for FullData }); if (UseRawFilesOrFullData) { var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open); PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 23); RunUI(() => { if (IsFullData) { importResultsSamplesDlg.CheckAll(true); importResultsSamplesDlg.ExcludeSample(0); // Blank importResultsSamplesDlg.ExcludeSample(25); // QC importResultsSamplesDlg.ExcludeSample(26); importResultsSamplesDlg.ExcludeSample(27); importResultsSamplesDlg.ExcludeSample(28); importResultsSamplesDlg.ExcludeSample(45); // A2 importResultsSamplesDlg.ExcludeSample(46); importResultsSamplesDlg.ExcludeSample(47); importResultsSamplesDlg.ExcludeSample(48); importResultsSamplesDlg.ExcludeSample(49); // gradientwash importResultsSamplesDlg.ExcludeSample(50); importResultsSamplesDlg.ExcludeSample(51); importResultsSamplesDlg.ExcludeSample(52); importResultsSamplesDlg.ExcludeSample(53); // A3 importResultsSamplesDlg.ExcludeSample(54); importResultsSamplesDlg.ExcludeSample(55); importResultsSamplesDlg.ExcludeSample(56); } else { importResultsSamplesDlg.CheckAll(false); importResultsSamplesDlg.IncludeSample(1); importResultsSamplesDlg.IncludeSample(2); importResultsSamplesDlg.IncludeSample(11); importResultsSamplesDlg.IncludeSample(12); } }); OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog); } else { RunUI(openDataSourceDialog1.Open); } { var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog); PauseForScreenShot <ImportDocResultsDlg>("Import Results Common prefix form", 24); OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog); } WaitForCondition(() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); RestoreViewOnScreen(25); // Inspecting and Adjusting Peak Integration, p. 24. RunUI(() => { SkylineWindow.ShowPeakAreaReplicateComparison(); SkylineWindow.ShowGraphRetentionTime(true); }); if (!IsPauseForScreenShots && !IsFullData) { TestApplyToAll(); } PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 25); CheckReportCompatibility.CheckAll(SkylineWindow.Document); RunUI(SkylineWindow.EditDelete); FindNode("IVGGWECEK"); // Not L10N TransitionGroupTreeNode selNodeGroup = null; RunUI(() => { selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1]; Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank); }); RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI => { transitionSettingsUI.MZMatchTolerance = 0.065; transitionSettingsUI.OkDialog(); }); RunUI(() => { Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex); SkylineWindow.ToggleIntegrateAll(); }); RunUI(() => { foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules) { string sequence = nodePep.Peptide.Sequence; int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree); if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N { Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex, string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex)); } else if (sequence != null) { Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex, string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex)); } else // Custom Ion { Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex, string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex)); } } }); PauseForScreenShot("Main window", 27); // Data Inspection with Peak Areas View, p. 27. FindNode("SSDLVALSGGHTFGK"); // Not L10N RunUI(NormalizeGraphToHeavy); RestoreViewOnScreen(28); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 28); FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29); RunUI(SkylineWindow.ExpandPeptides); string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N FindNode(hgflprLight); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30); RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view)); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 31); RunUI(() => SkylineWindow.ShowGraphPeakArea(false)); RunUI(() => SkylineWindow.ActivateReplicate("E_03")); PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 31); RunUI(() => SkylineWindow.ShowGraphPeakArea(true)); RunUI(() => { SkylineWindow.ShowPeakAreaPeptideGraph(); SkylineWindow.ShowTotalTransitions(); SkylineWindow.ShowCVValues(true); SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document); }); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 32); // Annotating replicates with concentration values var chooseAnnotationsDlg = ShowDialog <DocumentSettingsDlg>(SkylineWindow.ShowDocumentSettingsDialog); var editListDlg = ShowDialog <EditListDlg <SettingsListBase <AnnotationDef>, AnnotationDef> >(chooseAnnotationsDlg.EditAnnotationList); RunUI(editListDlg.ResetList); var defineAnnotationDlg = ShowDialog <DefineAnnotationDlg>(editListDlg.AddItem); RunUI(() => { defineAnnotationDlg.AnnotationName = "Concentration"; defineAnnotationDlg.AnnotationType = AnnotationDef.AnnotationType.number; defineAnnotationDlg.AnnotationTargets = AnnotationDef.AnnotationTargetSet.Singleton(AnnotationDef.AnnotationTarget.replicate); }); PauseForScreenShot <DefineAnnotationDlg>("Define Annotation form", 33); OkDialog(defineAnnotationDlg, defineAnnotationDlg.OkDialog); OkDialog(editListDlg, () => editListDlg.DialogResult = DialogResult.OK); RunUI(() => chooseAnnotationsDlg.AnnotationsCheckedListBox.SetItemChecked(0, true)); PauseForScreenShot <DocumentSettingsDlg>("Annotation Settings form", 34); OkDialog(chooseAnnotationsDlg, chooseAnnotationsDlg.OkDialog); RunUI(() => SkylineWindow.ShowResultsGrid(true)); RunUI(() => { SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0); }); WaitForGraphs(); WaitForConditionUI(() => FindOpenForm <LiveResultsGrid>().IsComplete); RunUI(() => { Settings.Default.ResultsGridSynchSelection = false; var resultsGrid = FindOpenForm <LiveResultsGrid>().DataGridView; var colConcentration = // ReSharper disable LocalizableElement resultsGrid.Columns.Cast <DataGridViewColumn>().First(col => "Concentration" == col.HeaderText); // Not L10N // ReSharper restore LocalizableElement if (IsFullData) { float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 }; for (int i = 0; i < concentrations.Length; i++) { for (int j = i * 4; j < (i + 1) * 4; j++) { SetCellValue(resultsGrid, j, colConcentration.Index, concentrations[i]); } } } else { SetCellValue(resultsGrid, 0, colConcentration.Index, 0f); SetCellValue(resultsGrid, 1, colConcentration.Index, 0f); SetCellValue(resultsGrid, 2, colConcentration.Index, 175f); SetCellValue(resultsGrid, 3, colConcentration.Index, 175f); } }); WaitForGraphs(); PauseForScreenShot <LiveResultsGrid>("Results grid with annotations (scrolled to the end)", 35); FindNode("SSDLVALSGGHTFGK"); // Not L10N RunUI(() => { SkylineWindow.ShowPeakAreaReplicateComparison(); SkylineWindow.GroupByReplicateAnnotation("Concentration"); NormalizeGraphToHeavy(); }); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36); RunUI(() => SkylineWindow.ShowCVValues(false)); RunUI(() => SkylineWindow.SaveDocument()); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 36); PauseForAuditLog(); // Further Exploration, p. 33. RunUI(() => { SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N SkylineWindow.ShowPeakAreaPeptideGraph(); SkylineWindow.ShowCVValues(true); }); WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 37); FindNode("LSEPAELTDAVK"); RunUI(SkylineWindow.ShowRTReplicateGraph); PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38); FindNode("INDISHTQSVSAK"); RunUI(SkylineWindow.ShowPeakAreaReplicateComparison); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 38); RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none)); WaitForGraphs(); PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 39); FindNode(hgflprLight); RunUI(() => { SkylineWindow.ShowAllTransitions(); NormalizeGraphToHeavy(); }); WaitForGraphs(); PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 40); RunUI(() => SkylineWindow.ShowGraphPeakArea(false)); RunUI(() => SkylineWindow.ActivateReplicate("E_ 03")); WaitForGraphs(); PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 40); }
protected override void DoTest() { OpenDocument(@"Rat_plasma.sky"); RunUI(SkylineWindow.ShowRTReplicateGraph); RunUI(SkylineWindow.ShowPeakAreaReplicateComparison); SelectNode(SrmDocument.Level.MoleculeGroups, 3); WaitForGraphs(); const int repCount = 42; const int removedPeaks = 5; VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 3, repCount); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.bars, 3, repCount); RunUI(() => SkylineWindow.ShowRTPeptideValue(RTPeptideValue.FWHM)); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, 3, repCount); SelectNode(SrmDocument.Level.MoleculeGroups, 2); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 1, repCount - removedPeaks); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, 1, repCount - removedPeaks); SelectNode(SrmDocument.Level.Molecules, 3); WaitForGraphs(); const int tranCount = 5; VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.bars, tranCount, repCount + 1); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks); RunUI(() => SkylineWindow.SetAreaGraphDisplayType(AreaGraphDisplayType.lines)); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks + 1); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks); RunUI(() => SkylineWindow.GroupByReplicateAnnotation("SubjectId")); WaitForGraphs(); int subjectCount = repCount / 3; VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, subjectCount, subjectCount); ActivateReplicate("D_103_REP1"); WaitForGraphs(); RunUI(() => SkylineWindow.RemovePeak()); ActivateReplicate("D_103_REP2"); WaitForGraphs(); RunUI(() => SkylineWindow.RemovePeak()); WaitForGraphs(); subjectCount--; VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount); VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, subjectCount, subjectCount); RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.GLOBAL_STANDARDS)); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount); VerifyGraphYRange(SkylineWindow.GraphPeakArea, 5E-5, 2E-2, subjectCount + 1, subjectCount); RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL)); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount); VerifyGraphYRange(SkylineWindow.GraphPeakArea, 5, 50, subjectCount + 1, subjectCount); subjectCount++; SelectNode(SrmDocument.Level.MoleculeGroups, 13); WaitForGraphs(); VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 2, subjectCount, subjectCount); VerifyGraphYRange(SkylineWindow.GraphPeakArea, 4E+4, 1.5E+5, subjectCount, subjectCount); }