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);
}