private void TestExpansion() { SkylineWindow.ExpandProteins(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[0].Collapse(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[1].Nodes[0].Expand(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[1].Nodes[0].Nodes[1].Expand(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[2].Collapse(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[4].Nodes[0].ExpandAll(); CheckStateMaintained(); SkylineWindow.SequenceTree.Nodes[6].Nodes[1].Expand(); CheckStateMaintained(); }
protected override void DoTest() { LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-1_Settings.pdf"; //Tutorial 1 string fastaFile = GetTestPath("Tutorial-1_Settings/TubercuList_v2-6.fasta.txt"); WaitForCondition(() => File.Exists(fastaFile)); var pepSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI); RunUI(() => { SkylineWindow.Size = new Size(1600, 800); pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest; pepSettings.ComboEnzymeSelected = "Trypsin [KR | P]"; pepSettings.MaxMissedCleavages = 0; }); var backProteomeDlg = ShowDialog <BuildBackgroundProteomeDlg>(pepSettings.AddBackgroundProteome); RunUI(() => { backProteomeDlg.BackgroundProteomePath = GetTestPath("Skyline"); backProteomeDlg.BackgroundProteomeName = "TubercuList_v2-6"; backProteomeDlg.AddFastaFile(fastaFile); WaitForCondition(() => backProteomeDlg.StatusText.Length > 10); Assert.IsTrue(backProteomeDlg.StatusText.Contains("3982".ToString(CultureInfo.CurrentCulture))); }); OkDialog(backProteomeDlg, backProteomeDlg.OkDialog); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction); RunUI(() => { pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter; pepSettings.TextMinLength = 7; pepSettings.TextMaxLength = 25; pepSettings.TextExcludeAAs = 0; pepSettings.AutoSelectMatchingPeptides = true; }); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library); var editListDlg = ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(pepSettings.EditLibraryList); var editLibraryDlg = ShowDialog <EditLibraryDlg>(editListDlg.AddItem); RunUI(() => { editLibraryDlg.LibraryName = "Mtb_proteome_library"; editLibraryDlg.LibraryPath = GetTestPath("Skyline\\Mtb_DirtyPeptides_QT_filtered_cons.sptxt"); }); OkDialog(editLibraryDlg, editLibraryDlg.OkDialog); OkDialog(editListDlg, editListDlg.OkDialog); RunUI(() => pepSettings.SetLibraryChecked(0, true)); RunUI(() => { pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications; }); var editHeavyModListDlg = ShowDialog <EditListDlg <SettingsListBase <StaticMod>, StaticMod> >(pepSettings.EditHeavyMods); var addDlgOne = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem); RunUI(() => addDlgOne.SetModification("Label:13C(6)15N(2) (C-term K)")); PauseForScreenShot("Isotope modification 1", 3); OkDialog(addDlgOne, addDlgOne.OkDialog); var addDlgTwo = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem); RunUI(() => addDlgTwo.SetModification("Label:13C(6)15N(4) (C-term R)")); PauseForScreenShot("Isotope modification 2", 3); OkDialog(addDlgTwo, addDlgTwo.OkDialog); OkDialog(editHeavyModListDlg, editHeavyModListDlg.OkDialog); RunUI(() => { pepSettings.SetIsotopeModifications(0, true); pepSettings.SetIsotopeModifications(1, true); }); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest); PauseForScreenShot("Digestion tab", 4); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction); PauseForScreenShot("Prediction tab", 4); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter); PauseForScreenShot("Filter tab", 4); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library); PauseForScreenShot("Library tab", 4); RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications); PauseForScreenShot("Modifications tab", 4); OkDialog(pepSettings, pepSettings.OkDialog); WaitForCondition( () => SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('{').First()) && SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('}').Last())); WaitForCondition( () => SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('{').First()) && SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('}').Last())); WaitForCondition(() => SkylineWindow.Status.Contains(Resources.SkylineWindow_UpdateProgressUI_Ready)); WaitForDocumentLoaded(); var transitionDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); RunUI(() => { transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction; transitionDlg.PrecursorMassType = MassType.Monoisotopic; transitionDlg.FragmentMassType = MassType.Monoisotopic; transitionDlg.RegressionCEName = "ABI 5500 QTrap"; }); RunUI(() => { transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter; transitionDlg.PrecursorCharges = "2,3".ToString(CultureInfo.CurrentCulture); transitionDlg.ProductCharges = "1,2".ToString(CultureInfo.CurrentCulture); transitionDlg.FragmentTypes = "y"; transitionDlg.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_1; transitionDlg.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion; transitionDlg.SetListAlwaysAdd(0, false); transitionDlg.ExclusionWindow = 5; transitionDlg.SetAutoSelect = true; }); RunUI(() => { transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library; transitionDlg.IonMatchTolerance = 1.0; transitionDlg.UseLibraryPick = true; transitionDlg.IonCount = 5; transitionDlg.Filtered = true; }); RunUI(() => { transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument; transitionDlg.MinMz = 300; transitionDlg.MaxMz = 1250; }); RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction); PauseForScreenShot("Prediction Tab", 7); RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter); PauseForScreenShot("Filter Tab", 7); RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library); PauseForScreenShot("Library Tab", 7); RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument); PauseForScreenShot("Instrument Tab", 7); OkDialog(transitionDlg, transitionDlg.OkDialog); RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Tutorial-1_Settings\\SRMcourse_20140210_Settings.sky"))); //Tutorial 2 LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-2_TransitionList.pdf"; RunUI(() => { }); SetExcelFileClipboardText(GetTestPath(@"Tutorial-2_TransitionList\\target_peptides.xlsx"), "Sheet1", 1, false); var peptidePasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg); var matchingDlg = ShowDialog <FilterMatchedPeptidesDlg>(peptidePasteDlg.PastePeptides); PauseForScreenShot("Filter Peptides", 1); OkDialog(matchingDlg, matchingDlg.OkDialog); OkDialog(peptidePasteDlg, peptidePasteDlg.OkDialog); int expectedTrans = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 306 : 313; AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 68, expectedTrans); RunUI(() => { SkylineWindow.ExpandProteins(); SkylineWindow.ExpandPeptides(); SkylineWindow.ExpandPrecursors(); SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode; }); PauseForScreenShot("Skyline Window", 2); var exportDlg = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg); RunUI(() => { exportDlg.InstrumentType = "AB SCIEX"; exportDlg.ExportStrategy = ExportStrategy.Single; exportDlg.DwellTime = 20; }); PauseForScreenShot("Export Transition List", 3); var declusteringWarningDlg = ShowDialog <MultiButtonMsgDlg>( () => exportDlg.OkDialog(GetTestPath("Tutorial-2_TransitionList\\SRMcourse_20140210_MtbProteomeLib_TransList.csv"))); PauseForScreenShot("Decluster Window", 3); OkDialog(declusteringWarningDlg, declusteringWarningDlg.Btn1Click); WaitForClosedForm(exportDlg); //Tutorial 3 LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-3_Library.pdf"; var pepSettings2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI); RunUI(() => pepSettings2.SelectedTab = PeptideSettingsUI.TABS.Library); var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(pepSettings2.ShowBuildLibraryDlg); RunUI(() => { buildLibraryDlg.LibraryPath = GetTestPath("Skyline"); buildLibraryDlg.LibraryName = "Mtb_hDP_20140210"; buildLibraryDlg.LibraryCutoff = 0.9; buildLibraryDlg.LibraryAuthority = "SRMcourse"; }); PauseForScreenShot("Build Library Window", 2); RunUI(() => { buildLibraryDlg.OkWizardPage(); buildLibraryDlg.AddDirectory(GetTestPath("Tutorial-3_Library")); }); PauseForScreenShot("Build Library Window Next", 2); OkDialog(buildLibraryDlg, buildLibraryDlg.OkWizardPage); RunUI(() => { pepSettings2.SetLibraryChecked(0, true); pepSettings2.SetLibraryChecked(1, true); }); OkDialog(pepSettings2, pepSettings2.OkDialog); WaitForLibrary(20213); WaitForCondition(() => SkylineWindow.Document.PeptideTransitionCount != expectedTrans); int expectedTransAfter = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 444 : 450; AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 96, expectedTransAfter); var libraryExpl = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries); var messageWarning = WaitForOpenForm <MultiButtonMsgDlg>(); OkDialog(messageWarning, messageWarning.Btn1Click); PauseForScreenShot("Spectral Library Explorer Window", 3); OkDialog(libraryExpl, libraryExpl.Close); var exportDlg2 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg); RunUI(() => { exportDlg2.InstrumentType = "AB SCIEX"; exportDlg2.ExportStrategy = ExportStrategy.Buckets; exportDlg2.MaxTransitions = 150; exportDlg2.DwellTime = 20; exportDlg2.IgnoreProteins = true; }); var declusteringWarningDlg2 = ShowDialog <MultiButtonMsgDlg>(() => exportDlg2.OkDialog(GetTestPath("Tutorial-3_Library\\SRMcourse_20140210_MtbProteomeLib_hDP_TransList.csv"))); OkDialog(declusteringWarningDlg2, declusteringWarningDlg2.Btn1Click); WaitForClosedForm(exportDlg2); //Tutorial 4-A LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-4_Parameters.pdf"; SrmDocument smallDocument = SkylineWindow.Document; PeptideGroupDocNode[] newProteins = smallDocument.PeptideGroups.Take(0).ToArray(); smallDocument = (SrmDocument)smallDocument.ChangeChildren(newProteins); Assert.IsTrue(SkylineWindow.SetDocument(smallDocument, SkylineWindow.Document)); // TODO: Must be a better way to do this var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); RunUI(() => { transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Prediction; transitionSettings.RegressionCEName = "ABI QTrap 4000"; }); var editCollisionEnergy = ShowDialog <EditCEDlg>(() => transitionSettings.RegressionCEName = Resources.SettingsListComboDriver_Edit_current); RunUI(() => { editCollisionEnergy.StepSize = 2; editCollisionEnergy.StepCount = 5; }); PauseForScreenShot("Edit Collision Energy Equation Window", 2); OkDialog(editCollisionEnergy, editCollisionEnergy.OkDialog); OkDialog(transitionSettings, transitionSettings.OkDialog); SetExcelFileClipboardText(GetTestPath("Tutorial-4_Parameters\\transition_list_for_CEO.xlsx"), "Sheet1", 3, false); var insertTransitionDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg); RunUI(() => insertTransitionDlg.IsMolecule = false); // Make sure it's ready to accept peptides, not small molecules RunUI(insertTransitionDlg.PasteTransitions); OkDialog(insertTransitionDlg, insertTransitionDlg.OkDialog); AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 30, 143); var exportDlg3 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg); RunUI(() => { exportDlg3.InstrumentType = "AB SCIEX"; exportDlg3.ExportStrategy = ExportStrategy.Single; exportDlg3.OptimizeType = ExportOptimize.CE; exportDlg3.MethodType = ExportMethodType.Standard; exportDlg2.DwellTime = 20; }); PauseForScreenShot("Export Transition List", 3); var defaultWaringDlg = ShowDialog <MultiButtonMsgDlg>( () => exportDlg3.OkDialog(GetTestPath("Tutorial-4_Parameters\\SRMcourse_20140211_Parameters_CEO.csv"))); OkDialog(defaultWaringDlg, defaultWaringDlg.Btn1Click); WaitForClosedForm(exportDlg3); var paths = new string[4]; for (int i = 0; i < paths.Length; i++) { paths[i] = GetTestPath("Tutorial-4_Parameters\\CEO_" + (i + 1) + ".wiff"); } ImportResults("CEO", paths, ExportOptimize.CE); RestoreViewOnScreen(43); RunUI(() => SkylineWindow.ShowChromatogramLegends(false)); PauseForScreenShot("Skyline Window", 3); ImportResults("", new[] { GetTestPath("Tutorial-4_Parameters\\CE_plus10.wiff"), GetTestPath("Tutorial-4_Parameters\\CE_minus10.wiff") }, ExportOptimize.NONE, false); RunUI(() => { SkylineWindow.ShowAllTransitions(); SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_maximum_view); }); RestoreViewOnScreen(44); PauseForScreenShot("Skyline Window", 4); var transitionSettings2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); RunUI(() => { transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Prediction; }); var addCollisionEnergyDlg = ShowDialog <EditCEDlg>(transitionSettings2.AddToCEList); RunUI(() => { addCollisionEnergyDlg.UseCurrentData(); addCollisionEnergyDlg.RegressionName = "SRMcourse_20140211_Parameters_custom-CE-equation"; }); var equationGraphDlg = ShowDialog <GraphRegression>(addCollisionEnergyDlg.ShowGraph); PauseForScreenShot("Collision Energy Equation Graph", 6); OkDialog(equationGraphDlg, equationGraphDlg.CloseDialog); OkDialog(addCollisionEnergyDlg, addCollisionEnergyDlg.OkDialog); RunUI(() => { transitionSettings2.RegressionCEName = "SRMcourse_20140211_Parameters_custom-CE-equation"; transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument; transitionSettings2.MZMatchTolerance = 0.01; }); PauseForScreenShot("Instrument Tab", 7); OkDialog(transitionSettings2, transitionSettings2.OkDialog); //Tutorial 4-B var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults); RunUI(manageResultsDlg.RemoveAllReplicates); OkDialog(manageResultsDlg, manageResultsDlg.OkDialog); string[] paths2 = { GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 10)), GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 20)), GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 40)), GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 60)), GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 100)) }; ImportResults("", paths2, null, false); RestoreViewOnScreen(48); RunUI(() => SkylineWindow.AutoZoomBestPeak()); PauseForScreenShot("Skyline Window", 8); }
protected override void DoTest() { // Lest we get "To export a scheduled method, you must first choose a retention time predictor in Peptide Settings / Prediction, or import results for all peptides in the document." TestSmallMolecules = false; // Skyline Collision Energy Optimization RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N if (AsSmallMolecules) { var doc = WaitForDocumentLoaded(); var refine = new RefinementSettings(); SkylineWindow.SetDocument(refine.ConvertToSmallMolecules(doc), doc); } // Deriving a New Linear Equation, p. 2 var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); var editList = ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> > (transitionSettingsUI.EditCEList); RunUI(() => editList.SelectItem("Thermo")); // Not L10N EditCEDlg editItem = ShowDialog <EditCEDlg>(editList.EditItem); PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 3); ChargeRegressionLine regressionLine2 = new ChargeRegressionLine(2, 0.034, 3.314); ChargeRegressionLine regressionLine3 = new ChargeRegressionLine(3, 0.044, 3.314); CheckRegressionLines(new[] { regressionLine2, regressionLine3 }, editItem.Regression.Conversions); RunUI(() => { editItem.DialogResult = DialogResult.OK; editList.DialogResult = DialogResult.Cancel; transitionSettingsUI.DialogResult = DialogResult.Cancel; }); WaitForClosedForm(transitionSettingsUI); // Measuring Retention Times for Method Scheduling, p. 3 { var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List)); RunUI(() => { exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO; exportMethodDlg.ExportStrategy = ExportStrategy.Single; exportMethodDlg.OptimizeType = ExportOptimize.NONE; exportMethodDlg.MethodType = ExportMethodType.Standard; }); PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 4); RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"))); // Not L10N WaitForClosedForm(exportMethodDlg); } string filePathTemplate = GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"); // Not L10N CheckTransitionList(filePathTemplate, 1, 6); const string unscheduledName = "Unscheduled"; // Not L10N RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg => { importResultsDlg.RadioAddNewChecked = true; var path = new[] { new KeyValuePair <string, MsDataFileUri[]>(unscheduledName, // This is not actually a valid file path (missing OptimizeCE) // but Skyline should correctly find the file in the same folder // as the document. new[] { MsDataFileUri.Parse(GetTestPath("CE_Vantage_15mTorr_unscheduled" + ExtThermoRaw)) }) }; // Not L10N importResultsDlg.NamedPathSets = path; importResultsDlg.OkDialog(); }); WaitForCondition(5 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 5 minutes AssertEx.IsDocumentState(SkylineWindow.Document, null, 7, 27, 30, 120); var docUnsched = SkylineWindow.Document; AssertResult.IsDocumentResultsState(SkylineWindow.Document, unscheduledName, docUnsched.MoleculeCount, docUnsched.MoleculeTransitionGroupCount, 0, docUnsched.MoleculeTransitionCount - 1, 0); RunUI(() => { SkylineWindow.ExpandProteins(); SkylineWindow.ExpandPeptides(); }); PauseForScreenShot("Main Skyline window", 5); // Creating Optimization Methods, p. 5 { var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List)); RunUI(() => { exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO; exportMethodDlg.ExportStrategy = ExportStrategy.Buckets; exportMethodDlg.MaxTransitions = 110; exportMethodDlg.IgnoreProteins = true; exportMethodDlg.OptimizeType = ExportOptimize.CE; exportMethodDlg.MethodType = ExportMethodType.Scheduled; }); PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 6); RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr.csv"))); // Not L10N WaitForClosedForm(exportMethodDlg); } string filePathTemplate1 = GetTestPath("CE_Vantage_15mTorr_000{0}.csv"); // Not L10N CheckTransitionList(filePathTemplate1, 5, 9); var filePath = GetTestPath("CE_Vantage_15mTorr_0001.csv"); // Not L10N CheckCEValues(filePath, 11); // Analyze Optimization Data, p. 7 RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg => { importResultsDlg.RadioAddNewChecked = true; importResultsDlg.OptimizationName = ExportOptimize.CE; importResultsDlg.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray(); importResultsDlg.NamedPathSets[0] = new KeyValuePair <string, MsDataFileUri[]>("Optimize CE", importResultsDlg.NamedPathSets[0].Value.Take(5).ToArray()); // Not L10N importResultsDlg.OkDialog(); }); RunUI(() => { SkylineWindow.ShowSingleTransition(); SkylineWindow.AutoZoomBestPeak(); SkylineWindow.ShowPeakAreaReplicateComparison(); }); WaitForDocumentLoaded(15 * 60 * 1000); // 10 minutes if (AsSmallMolecules) { return; // Too peptide-centric from here to end of test } FindNode("IHGFDLAAINLQR"); RestoreViewOnScreen(8); PauseForScreenShot("Main Skyline window", 8); // p. 8 // Not L10N RemovePeptide("EGIHAQQK"); FindNode("IDALNENK"); RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view)); PauseForScreenShot("Main Skyline window", 9); RunUI(SkylineWindow.EditDelete); RemovePeptide("LICDNTHITK"); // Creating a New Equation for CE, p. 9 var transitionSettingsUI1 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI); var editCEDlg1 = ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >(transitionSettingsUI1.EditCEList); var addItem = ShowDialog <EditCEDlg>(editCEDlg1.AddItem); RunUI(() => { addItem.RegressionName = "Thermo Vantage Tutorial"; // Not L10N addItem.UseCurrentData(); }); var graphRegression = ShowDialog <GraphRegression>(addItem.ShowGraph); PauseForScreenShot <GraphRegression>("Collision Energy Regression graphs", 10); var graphDatas = graphRegression.RegressionGraphDatas.ToArray(); Assert.AreEqual(2, graphDatas.Length); ChargeRegressionLine regressionLine21 = new ChargeRegressionLine(2, 0.0305, 2.5061); ChargeRegressionLine regressionLine31 = new ChargeRegressionLine(3, 0.0397, 1.4217); var expectedRegressions = new[] { regressionLine21, regressionLine31 }; CheckRegressionLines(expectedRegressions, new[] { new ChargeRegressionLine(2, Math.Round(graphDatas[0].RegressionLine.Slope, 4), Math.Round(graphDatas[0].RegressionLine.Intercept, 4)), new ChargeRegressionLine(3, Math.Round(graphDatas[1].RegressionLine.Slope, 4), Math.Round(graphDatas[1].RegressionLine.Intercept, 4)), }); RunUI(graphRegression.CloseDialog); WaitForClosedForm(graphRegression); RunUI(addItem.OkDialog); WaitForClosedForm(addItem); RunUI(editCEDlg1.OkDialog); WaitForClosedForm(editCEDlg1); RunUI(transitionSettingsUI1.OkDialog); WaitForClosedForm(transitionSettingsUI1); // Optimizing Each Transition, p. 10 RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI2 => { transitionSettingsUI2.UseOptimized = true; transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString(); transitionSettingsUI2.OkDialog(); }); RunDlg <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List), exportMethodDlg => { exportMethodDlg.ExportStrategy = ExportStrategy.Single; exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_optimized.csv")); // Not L10N }); var filePathTemplate2 = GetTestPath("CE_Vantage_15mTorr_optimized.csv"); // Not L10N CheckTransitionList(filePathTemplate2, 1, 9); RunUI(() => SkylineWindow.SaveDocument()); WaitForConditionUI(() => !SkylineWindow.Dirty); }