protected override void DoTest()
{
// Check backward compatibility with 19.1.9.338 and 350 when combined IMS got written to MsDataFilePath
string legacyFile_19_1_9 = TestFilesDirs[1].GetTestPath(@"BSA-Training.sky");
RunUI(() => SkylineWindow.OpenFile(legacyFile_19_1_9));
VerifyCombinedIonMobility(WaitForDocumentLoaded());
RunUI(() =>
{
SkylineWindow.SaveDocument();
SkylineWindow.NewDocument();
SkylineWindow.OpenFile(legacyFile_19_1_9);
});
VerifyCombinedIonMobility(WaitForDocumentLoaded());
var oldDoc = SkylineWindow.Document;
string skyFile = TestFilesDirs[0].GetTestPath(@"IMSFiltering\BSA-Training.sky");
RunUI(() => SkylineWindow.OpenFile(skyFile));
var document = WaitForDocumentChangeLoaded(oldDoc, 240 * 1000); // 4 minutes
RunUI(() => SkylineWindow.Size = new Size(880, 560));
RestoreViewOnScreen(2);
PauseForScreenShot("Document open - full window", 2);
AssertEx.IsDocumentState(document, null, 1, 34, 38, 404);
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(() =>
SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.FullScan));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Full-scan settings", 3);
RunUI(() =>
{
Assert.AreEqual(FullScanPrecursorIsotopes.Count, transitionSettingsUI.PrecursorIsotopesCurrent);
Assert.AreEqual(20 * 1000, transitionSettingsUI.PrecursorRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.PrecursorMassAnalyzer);
Assert.AreEqual(IsolationScheme.SpecialHandlingType.ALL_IONS, transitionSettingsUI.IsolationSchemeName);
Assert.AreEqual(20 * 1000, transitionSettingsUI.ProductRes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, transitionSettingsUI.ProductMassAnalyzer);
});
OkDialog(transitionSettingsUI, transitionSettingsUI.CancelDialog);
}
{
var importResults = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() => importResults.ImportSimultaneousIndex = 2);
PauseForScreenShot <ImportResultsDlg>("Import results form", 4);
// Importing raw data from a sample which is a mixture of yeast and BSA
var openDataSourceDialog = ShowDialog <OpenDataSourceDialog>(importResults.OkDialog);
RunUI(() =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(".d");
});
PauseForScreenShot <OpenDataSourceDialog>("Import results files", 5);
OkDialog(openDataSourceDialog, openDataSourceDialog.Open);
}
string yeastReplicateName = Path.GetFileNameWithoutExtension(Yeast_BSA);
PauseForScreenShot <AllChromatogramsGraph>("Importing results form", 6);
WaitForDocumentChangeLoaded(document, 1000 * 60 * 60 * 10); // 10 minutes
// Arrange graphs tiled
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
FindNode("R.FKDLGEEHFK.G");
RunUI(() => SkylineWindow.Size = new Size(1075, 799));
RestoreViewOnScreen(7);
PauseForScreenShot("Zoomed split graph panes only", 7);
RunUI(() => SkylineWindow.AutoZoomNone());
PauseForScreenShot("Unzoomed split graph panes only", 8);
const int wideWidth = 1547;
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.ShowPeakAreaLegend(false);
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL);
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.Size = new Size(wideWidth, 855);
});
RestoreViewOnScreen(9);
PauseForScreenShot("Full window", 9);
FindNode("TCVADESHAGCEK");
var noteDlg = ShowDialog <EditNoteDlg>(SkylineWindow.EditNote);
RunUI(() => noteDlg.NoteText = "Lost in yeast samples");
PauseForScreenShot("Peptide note", 10);
OkDialog(noteDlg, noteDlg.OkDialog);
FindNode("NECFLSHKDDSPDLPK");
RestoreViewOnScreen(11);
const int narrowWidth = 1350;
RunUI(() => SkylineWindow.Width = narrowWidth);
PauseForScreenShot("Yeast chromatograms and RT only - prtsc-paste-edit", 11);
PauseForScreenShot("Hover over BSA in water chromatogram - prtsc-paste-edit", 12);
RunUI(() => SkylineWindow.Width = wideWidth);
RestoreViewOnScreen(13);
{
const double clickTime1 = 41.06;
ClickChromatogram(clickTime1, 1.62E+6, PaneKey.PRECURSORS);
PauseForScreenShot("Full scan 2D MS1 graph", 13);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetSpectrum(false));
PauseForScreenShot("Full scan 3D MS1 graph", 13);
ValidateClickTime(fullScanGraph, clickTime1);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS1 graph", 14);
const double clickTime2 = 41.02;
RunUI(() => fullScanGraph.SetZoom(true));
ClickChromatogram(clickTime2, 5.8E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Full scan 3D MS/MS graph", 15);
ValidateClickTime(fullScanGraph, clickTime2);
RunUI(() => fullScanGraph.SetZoom(false));
PauseForScreenShot("Full scan unzoomed 3D MS/MS graph", 15);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
ClickChromatogram(clickTime2, 5.8E+4, PaneKey.PRODUCTS);
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RenameReplicate(manageResultsDlg, 0, "BSA");
RenameReplicate(manageResultsDlg, 1, "Yeast_BSA");
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
const double clickTime3 = 41.48;
ClickChromatogram(yeastReplicateName, clickTime3, 3.14E+4, PaneKey.PRODUCTS);
PauseForScreenShot("Interference full scan unzoomed 3D MS/MS graph", 16);
ValidateClickTime(fullScanGraph, clickTime3);
RunUI(SkylineWindow.HideFullScanGraph);
}
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
dlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Skip(1);
dlg.RemoveReplicates();
dlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.IonMobility;
transitionSettingsUI.IonMobilityControl.WindowWidthType = IonMobilityWindowWidthCalculator
.IonMobilityWindowWidthType.resolving_power;
transitionSettingsUI.IonMobilityControl.IonMobilityFilterResolvingPower = 50;
});
PauseForScreenShot("Setting ion mobility filter width calculation values", 17);
var editIonMobilityLibraryDlg = ShowDialog <EditIonMobilityLibraryDlg>(transitionSettingsUI.IonMobilityControl.AddIonMobilityLibrary);
const string libraryName = "BSA";
var databasePath = TestFilesDirs[1].GetTestPath(libraryName + IonMobilityDb.EXT);
RunUI(() =>
{
editIonMobilityLibraryDlg.LibraryName = libraryName;
editIonMobilityLibraryDlg.CreateDatabaseFile(databasePath); // Simulate user click on Create button
editIonMobilityLibraryDlg.SetOffsetHighEnergySpectraCheckbox(true);
editIonMobilityLibraryDlg.GetIonMobilitiesFromResults();
});
PauseForScreenShot("Edit ion mobility library form", 18);
// Check that a new value was calculated for all precursors
RunUI(() => Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroupCount, editIonMobilityLibraryDlg.LibraryMobilitiesFlatCount));
OkDialog(editIonMobilityLibraryDlg, () => editIonMobilityLibraryDlg.OkDialog());
PauseForScreenShot <TransitionSettingsUI.IonMobilityTab>("Transition Settings - Ion Mobility", 19);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, 3);
});
PauseForScreenShot("Transition Settings - Full-Scan", 20);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction);
PauseForScreenShot("Peptide Settings - Prediction", 21);
RunUI(() =>
{
Assert.IsTrue(peptideSettingsUI.IsUseMeasuredRT);
Assert.AreEqual(6, peptideSettingsUI.TimeWindow);
});
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
using (new WaitDocumentChange(1, true, 1000 * 60 * 60 * 5))
{
var choosePredictionReplicates = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
PauseForScreenShot("Choose Replicates form", 22);
RunUI(() => choosePredictionReplicates.SelectOrDeselectAll(true));
var importResults = ShowDialog <ImportResultsDlg>(choosePredictionReplicates.OkDialog);
RunDlg <OpenDataSourceDialog>(importResults.OkDialog, openDataSourceDialog =>
{
openDataSourceDialog.CurrentDirectory = new MsDataFilePath(DataPath);
openDataSourceDialog.SelectAllFileType(Yeast_BSA);
openDataSourceDialog.Open();
});
}
WaitForGraphs();
// Test to ensure the filtering happened
if (!IsPauseForScreenShots) // Don't bring up unexpected UI in a screenshot run
{
TestReports();
}
RestoreViewOnScreen(11);
RunUI(() => SkylineWindow.Width = narrowWidth);
PauseForScreenShot("Yeast chromatogram and RTs - prtsc-paste-edit", 23);
RunUI(() => SkylineWindow.Width = wideWidth);
RestoreViewOnScreen(13);
{
const double clickTime = 42.20;
ClickChromatogram(yeastReplicateName, clickTime, 2.904E+4, PaneKey.PRODUCTS);
var fullScanGraph = FindOpenForm <GraphFullScan>();
RunUI(() => fullScanGraph.SetZoom(true));
RunUI(() => fullScanGraph.Parent.Parent.Size = new Size(671, 332));
PauseForScreenShot("Full-scan graph zoomed", 24);
RunUI(() => Assert.IsTrue(fullScanGraph.TitleText.Contains(clickTime.ToString(CultureInfo.CurrentCulture))));
RunUI(SkylineWindow.HideFullScanGraph);
}
FindNode("FKDLGEEHFK");
RunUI(() =>
{
SkylineWindow.Size = new Size(1547, 689);
SkylineWindow.ShowProductTransitions();
SkylineWindow.ShowPeakAreaLegend(true);
});
RestoreViewOnScreen(25);
PauseForScreenShot("Chromatograms and Peak Areas - prtsc-paste-edit", 25);
var docFiltered = SkylineWindow.Document;
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageDlg =>
{
manageDlg.SelectedChromatograms = SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Take(1);
manageDlg.ReimportResults();
manageDlg.OkDialog();
});
WaitForDocumentChangeLoaded(docFiltered, 1000 * 60 * 60 * 5); // 5 minutes
// TODO: Check peak ranks before and after
AssertEx.IsFalse(IsRecordMode); // Make sure we turn this off before commit!
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.SetUIMode(SrmDocument.DOCUMENT_TYPE.small_molecules));
// Inserting a Transition List, p. 5
{
var doc = SkylineWindow.Document;
SetCsvFileClipboardText(GetTestPath("Energy_TransitionList.csv"));
RunUI(() =>
{
SkylineWindow.Paste();
AdjustSequenceTreePanelWidth();
});
PauseForScreenShot <SkylineWindow>("Main window after paste from csv", 5);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 3, 18, 36, 36);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.RegressionCEName = "Waters Xevo"; // Collision Energy
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 6);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes = TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 7);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
}
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("EnergyMet.sky")));
// Export method - 2 minutes
{
var exportMethodDlg2 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg2.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportMethodDlg2.MethodType = ExportMethodType.Standard;
exportMethodDlg2.RunLength = 2;
exportMethodDlg2.SetTemplateFile("VerifyETemplate.exp");
});
PauseForScreenShot <ExportMethodDlg>("Exporting 2 minute method", 9);
OkDialog(exportMethodDlg2, exportMethodDlg2.CancelDialog);
}
// Export transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Standard;
exportTransitionList.RunLength = 2;
});
PauseForScreenShot <ExportMethodDlg>("Exporting transition list", 10);
OkDialog(exportTransitionList, exportTransitionList.CancelDialog);
}
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Unscheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <OpenDataSourceDialog>("Import Results Files form", 11);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form", 12);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
OkDialog(importResultsDlg1, importResultsDlg1.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 13);
// Renaming replicates
{
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
string[] repNames = new[] { "2 min", "5 min" };
RunUI(() => manageResultsDlg.Left = SkylineWindow.Right + 50);
for (var i = 0; i < 2; i++)
{
doc = SkylineWindow.Document;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
var chrom = chromatograms[i];
RunUI(() =>
{
manageResultsDlg.SelectedChromatograms = new[] { chrom };
});
var renameDlg = ShowDialog <RenameResultDlg>(manageResultsDlg.RenameResult);
RunUI(() => renameDlg.ReplicateName = repNames[i]);
if (i == 0)
{
PauseForScreenShot <SkylineWindow>("Manage Results and Rename Replicate (PrtScn and select in Paint)", 14);
}
OkDialog(renameDlg, renameDlg.OkDialog);
}
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
}
PauseForScreenShot <SkylineWindow>("Skyline window (renamed)", 15);
var docResults = SkylineWindow.Document;
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 18, 18, 18, 18, 18);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ArrangeGraphsTiled();
});
RestoreViewOnScreen(16);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.Size = new Size(1054, 587);
AdjustSequenceTreePanelWidth(true);
});
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 16);
// Set zoom to show better peak separation in 5 minute run
for (var i = 0; i < 2; i++)
{
WaitForGraphs();
RunUI(() => SkylineWindow.GraphChromatograms.ToArray()[i].ZoomTo(.8, 1.8, 1.39e+8));
WaitForGraphs();
}
PauseForScreenShot <SkylineWindow>("Skyline window showing relative peak separation", 17);
// Set time window
{
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once RedundantCast
peptideSettingsDlg.SelectedTab = (PeptideSettingsUI.TABS) 0; //regular enum does not work because of the hidden tabs in the Small Molecule mode.
peptideSettingsDlg.TimeWindow = 1;
});
PauseForScreenShot <PeptideSettingsUI>("Setting scheduled transition list time window", 18);
OkDialog(peptideSettingsDlg, peptideSettingsDlg.OkDialog);
}
// Export transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
exportTransitionList.OptimizeType = ExportOptimize.NONE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 19);
var schedulingOptionsDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_scheduled.csv")));
RunUI(() =>
{
schedulingOptionsDlg.Algorithm = ExportSchedulingAlgorithm.Single;
schedulingOptionsDlg.ReplicateNum = 1; // 5 min
});
PauseForScreenShot <SchedulingOptionsDlg>("Exporting scheduled transition list - choose replicate", 19);
OkDialog(schedulingOptionsDlg, schedulingOptionsDlg.OkDialog);
WaitForClosedForm(exportTransitionList);
}
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Scheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
RunUI(() => importResultsNameDlg.IsRemove = false);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form, not changing names", 20);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
}
// Remove 2 minute gradient
// Renaming replicates
string[] newNames = { "1:1_1", "1:1_2", "2:1_2", "1:2_2" };
{
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
SelectReplicate(manageResultsDlg, 0);
PauseForScreenShot <SkylineWindow>("Manage Results removing 2 min", 21);
RunUI(manageResultsDlg.RemoveReplicates);
for (var i = 0; i < newNames.Length; i++)
{
SelectReplicate(manageResultsDlg, i + 1);
RunDlg <RenameResultDlg>(manageResultsDlg.RenameResult, renameDlg =>
{
renameDlg.ReplicateName = newNames[i];
renameDlg.OkDialog();
});
}
PauseForScreenShot <SkylineWindow>("Manage Results replicate renamed", 22);
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
var molNode = SkylineWindow.SelectedNode;
molNode.Expand();
Assert.AreEqual(2, molNode.Nodes.Count);
molNode.Nodes[0].Expand();
molNode.Nodes[1].Expand();
SkylineWindow.ArrangeGraphsTabbed();
});
PauseForScreenShot <SkylineWindow>("Skyline window with calibration data", 23);
// Linearity
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
double[] concentrations = { 1, 1, 2, 0.5 };
var namedConcentrations = newNames.Select((n, i) => new Tuple <string, double?>(n, concentrations[i]));
SetDocumentGridSampleTypesAndConcentrations(namedConcentrations.ToDictionary(t => t.Item1,
t => new Tuple <SampleType, double?>(SampleType.STANDARD, t.Item2)));
RunUI(() =>
{
var gridFloatingWindow = documentGrid.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 230);
gridFloatingWindow.Top = SkylineWindow.Top;
gridFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot <DocumentGridForm>("Document Grid - sample types and concentrations ", 23);
RunUI(() => SkylineWindow.ShowDocumentGrid(false));
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
// ReSharper disable once RedundantCast
peptideSettingsUI.SelectedTab = (PeptideSettingsUI.TABS) 3;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantUnits = "ratio to heavy";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 24);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
RunUI(() =>
{
var calibrationFloatingWindow = calibrationForm.Parent.Parent;
calibrationFloatingWindow.Width = 565;
calibrationFloatingWindow.Top = SkylineWindow.Top;
calibrationFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot <CalibrationForm>("Calibration Curve ", 25);
OkDialog(calibrationForm, calibrationForm.Close); // Hide the calibration window
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction);
var editCurrentCE = ShowDialog <EditCEDlg>(transitionSettingsUI.EditCECurrent);
RunUI(() =>
{
editCurrentCE.StepSize = 2;
editCurrentCE.StepCount = 5;
});
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 26);
RunUI(() =>
{
editCurrentCE.OkDialog();
transitionSettingsUI.UseOptimized = true;
transitionSettingsUI.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 27);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
// Export transition lists
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.ExportStrategy = ExportStrategy.Buckets;
exportTransitionList.IgnoreProteins = true;
exportTransitionList.MaxTransitions = 100;
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
exportTransitionList.OptimizeType = ExportOptimize.CE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 28);
var scheduleDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_ceopt.csv")));
PauseForScreenShot <SchedulingOptionsDlg>("Scheduling", 29);
OkDialog(scheduleDlg, scheduleDlg.OkDialog);
}
// Import CE optimization runs
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg1.RadioCreateMultipleChecked = true;
importResultsDlg1.OptimizationName = ExportOptimize.CE;
importResultsDlg1.ReplicateName = "CE Optimization";
});
PauseForScreenShot <ImportResultsDlg>("Setting new replicate name to CE Optimization", 30);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.OkDialog());
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("CE Optimization"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <OpenDataSourceDialog>("Import Results Files form", 31);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
}
PauseForScreenShot <SkylineWindow>("Skyline shows new replicate \"CE Optimization\"", 32);
RunUI(() =>
{
SkylineWindow.Size = new Size(1600, 960);
SkylineWindow.ShowGraphRetentionTime(false, GraphTypeSummary.replicate);
SkylineWindow.AutoZoomBestPeak();
AdjustSequenceTreePanelWidth();
SkylineWindow.ShowSingleTransition();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
PauseForScreenShot <SkylineWindow>("Split graph", 33);
RunUI(() =>
{
SkylineWindow.ShowPeakAreaLegend(false);
});
PauseForScreenShot <SkylineWindow>("No legend", 34);
// Show Pentose-P
SelectNode(SrmDocument.Level.Molecules, 6);
PauseForScreenShot <SkylineWindow>("Pentose-P", 35);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowChromatogramLegends(false);
});
RestoreCoverViewOnScreen();
TakeCoverShot();
return;
}
// Export final transition list
{
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.ExportStrategy = ExportStrategy.Single;
exportTransitionList.IgnoreProteins = true;
exportTransitionList.MaxTransitions = 100;
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg>("Exporting final optimized transition list", 36);
var scheduleDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList.OkDialog(GetTestPath("EnergyMet_5minutes_optimal.csv")));
PauseForScreenShot <SchedulingOptionsDlg>("Final Scheduling", 37);
OkDialog(scheduleDlg, scheduleDlg.OkDialog);
}
}
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 3);
var columnsOrdered = new[]
{
// Prepare transition list insert window to match tutorial
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.labelType,
SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.mzProduct,
SmallMoleculeTransitionListColumnHeaders.chargeProduct,
SmallMoleculeTransitionListColumnHeaders.coneVoltage,
SmallMoleculeTransitionListColumnHeaders.cePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
var text = "DrugX,Drug,light,283.04,1,129.96,1,26,16,2.7\r\nDrugX,Drug,heavy,286.04,1,133.00,1,26,16,2.7\r\n";
text = text.Replace(',', TextUtil.CsvSeparator).Replace(".", LocalizationHelper.CurrentCulture.NumberFormat.NumberDecimalSeparator);
SetClipboardText(text);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 1, 1, 2, 2);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
SelectNode(SrmDocument.Level.Transitions, 0);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 5);
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Waters Xevo"; // Collision Energy
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None; // Declustering Potential
transitionSettingsUI.OptimizationLibraryName = Resources.SettingsList_ELEMENT_NONE_None; // Optimization Library
transitionSettingsUI.RegressionCOVName = Resources.SettingsList_ELEMENT_NONE_None; // Compensation Voltage
transitionSettingsUI.UseOptimized = true;
transitionSettingsUI.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SelectedPeptidesSmallMolsSubTab = 1;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_PLUS_H.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_PLUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes = TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.SetAutoSelect = true;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 4);
RunUI(() =>
{
// Instrument Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettingsUI.MinMz = 50;
transitionSettingsUI.MaxMz = 1500;
transitionSettingsUI.MZMatchTolerance = .02;
transitionSettingsUI.MinTime = null;
transitionSettingsUI.MaxTime = null;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Instrument tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("SMQuant_v1.sky")));
ImportReplicates(true);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-precursor graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// peptide count, transition groups, heavy transition groups, tranistions, heavy transitions
{ "Blank_01", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank1", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank2", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank3", new[] { 1, 0, 1, 0, 1 } },
{ "47_0_1_1_00_1021523591", new[] { 1, 0, 1, 0, 1 } },
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = new[] { 1, 1, 1, 1, 1 }
}
; // Most have this value
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, transitions[0],
transitions[1], transitions[2], transitions[3], transitions[4]);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
SelectNode(SrmDocument.Level.Transitions, 0);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
// Peak integration correction
ActivateReplicate("DoubleBlank1"); // First with mismatched RT
PauseForScreenShot <SkylineWindow>("Selected replicate with unexpected RT", 10);
ChangePeakBounds("DoubleBlank2", 26.5, 27.5);
ChangePeakBounds("DoubleBlank3", 26.5, 27.5);
ChangePeakBounds("DoubleBlank1", 26.5, 27.5);
PauseForScreenShot <SkylineWindow>("Adjusted peak boundaries", 13);
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantRegressionWeighting = RegressionWeighting.ONE_OVER_X_SQUARED;
peptideSettingsUI.QuantMsLevel = null; // All
peptideSettingsUI.QuantUnits = "uM";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 14);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
// Setting sample types
WaitForClosedForm <DocumentGridForm>();
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
PauseForScreenShot <DocumentGridForm>("Document Grid - replicates", 15);
/*IDictionary<string, Tuple<SampleType, double?>> sampleTypes =
* new Dictionary<string, Tuple<SampleType, double?>> {
* {"Blank_01", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Blank_02", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Blank_03", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Cal_1_01", new Tuple<SampleType, double?>(SampleType.STANDARD,10)},
* {"Cal_1_02", new Tuple<SampleType, double?>(SampleType.STANDARD,10)},
* {"Cal_2_01", new Tuple<SampleType, double?>(SampleType.STANDARD,20)},
* {"Cal_2_02", new Tuple<SampleType, double?>(SampleType.STANDARD,20)},
* {"Cal_3_01", new Tuple<SampleType, double?>(SampleType.STANDARD,100)},
* {"Cal_3_02", new Tuple<SampleType, double?>(SampleType.STANDARD,100)},
* {"Cal_4_01", new Tuple<SampleType, double?>(SampleType.STANDARD,200)},
* {"Cal_4_02", new Tuple<SampleType, double?>(SampleType.STANDARD,200)},
* {"Cal_5_01", new Tuple<SampleType, double?>(SampleType.STANDARD,400)},
* {"Cal_5_02", new Tuple<SampleType, double?>(SampleType.STANDARD,400)},
* {"Cal_6_01", new Tuple<SampleType, double?>(SampleType.STANDARD,600)},
* {"Cal_6_02", new Tuple<SampleType, double?>(SampleType.STANDARD,600)},
* {"Cal_7_01", new Tuple<SampleType, double?>(SampleType.STANDARD,800)},
* {"Cal_7_02", new Tuple<SampleType, double?>(SampleType.STANDARD,800)},
* {"DoubleBlank1", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"DoubleBlank2", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"DoubleBlank3", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"QC_High_01", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_High_02", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_High_03", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_Low_01", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Low_02", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Low_03", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Mid_01", new Tuple<SampleType, double?>(SampleType.QC,346)},
* {"QC_Mid_02", new Tuple<SampleType, double?>(SampleType.QC,346)},
* {"QC_Mid_03", new Tuple<SampleType, double?>(SampleType.QC,346)}
* };*/
SetExcelFileClipboardText(GetTestPath("Concentrations.xlsx"), "Sheet1", 3, false);
RunUI(() =>
{
// Find and select Blank_01 cell
var replicateColumnIndex = documentGrid.FindColumn(PropertyPath.Root).Index;
documentGrid.DataGridView.CurrentCell = documentGrid.DataGridView.Rows.Cast <DataGridViewRow>()
.Select(row => row.Cells[replicateColumnIndex])
.FirstOrDefault(cell => ((Replicate)cell.Value).Name == "Blank_01");
documentGrid.DataGridView.SendPaste();
});
//SetDocumentGridSampleTypesAndConcentrations(sampleTypes);
PauseForScreenShot <DocumentGridForm>("Document Grid - sample types - enlarge for screenshot so all rows can be seen ", 16);
RunUI(() => SkylineWindow.ShowCalibrationForm());
PauseForScreenShot <CalibrationForm>("Calibration Curve ", 18);
EnableDocumentGridColumns(documentGrid, Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates, 47,
new[]
{
"Proteins!*.Peptides!*.Results!*.Value.Quantification.Accuracy",
"Proteins!*.Peptides!*.Results!*.Value.ExcludeFromCalibration"
},
"Replicates_custom_quant");
PauseForScreenShot <DocumentGridForm>("Custom document grid - resize so all rows are visible before screenshot", 19);
SetDocumentGridExcludeFromCalibration();
PauseForScreenShot <CalibrationForm>("Calibration Curve - outliers disabled", 20);
ImportReplicates(false); // Import the rest of the replicates
PauseForScreenShot <CalibrationForm>("Calibration Curve - all replicates loaded", 21);
RunUI(() => documentGrid.ChooseView(Resources.ReportSpecList_GetDefaults_Peptide_Ratio_Results));
WaitForConditionUI(() => documentGrid.ColumnCount > 6);
RunUI(() => {
var colReplicate = documentGrid.FindColumn(PropertyPath.Parse("Results!*.Value.ResultFile.Replicate"));
documentGrid.DataGridView.Sort(colReplicate, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Document Grid - Peptide Ratio Results", 15);
}
}
protected override void DoTest()
{
TestSmallMolecules = false; // The presence of the extra test node without any results is incompatible with what's being tested here.
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// show the empty Transition Setting dialog
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsDlg.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab nothing set", 2);
OkDialog(transitionSettingsDlg, transitionSettingsDlg.OkDialog);
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 5);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 6);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 7);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 10);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 11);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <MultiButtonMsgDlg>("Add mods alert", 12);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 13);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = 1160;
SkylineWindow.Height = 792;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 14);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 16);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 17);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 19);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
alignmentForm.Width = 711;
alignmentForm.Height = 561;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 20);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 21);
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 32.6, 41.4); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 22);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 23);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 24, "Transition pick list unfiltered", 24); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 39.6); // set the view for screenshot
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 25);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chhromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 26);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 27);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 28);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 29);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 30);
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
// page 32 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = SkylineWindow.GraphChromatograms.ToArray()[TIP3].GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 32);
RestoreViewOnScreen(33); // float the Library Match window TODO this causes a crash at next call to ChangePeakBounds, in pwiz.Skyline.Controls.Graphs.GraphChromatogram.ChromGroupInfos.get() Line 492 , why?
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 33);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 33);
RestoreViewOnScreen(34); // back to normal view
pepIndex = JumpToPeptide("GVVDSEDLPLNISR"); // Not L10N
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
PauseForScreenShot("upper - Chromatogram graph metafiles for peptide GVVDSEDLPLNISR", 34);
ZoomBoth(35.05, 36.9, 480);
PauseForScreenShot("lower - Chromatogram graph metafile - effect of zoom ", 34);
ChangePeakBounds(TIP3, pepIndex, 35.7, 36.5); // adjust integration per tutorial
CheckAnnotations(TIP3, pepIndex, atest++); // check the new idotp values
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 35);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 36); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // Not L10N
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio;
dlg.OkDialog();
});
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
// Setting the UI mode, p 2
var startPage = WaitForOpenForm <StartPage>();
RunUI(() => startPage.SetUIMode(SrmDocument.DOCUMENT_TYPE.proteomic));
PauseForScreenShot <StartPage>("Start Window proteomic", 2);
RunUI(() => startPage.SetUIMode(SrmDocument.DOCUMENT_TYPE.small_molecules));
PauseForScreenShot <StartPage>("Start Window small molecule", 3);
RunUI(() => startPage.DoAction(skylineWindow => true));
WaitForOpenForm <SkylineWindow>();
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
for (var retry = 0; retry < 2; retry++)
{
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 3);
}
var columnsOrdered = new[]
{
// Prepare transition list insert window to match tutorial
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Adduct,Label Type,Precursor m/z,Precursor Charge,Explicit Retention Time
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
SmallMoleculeTransitionListColumnHeaders.adductPrecursor,
SmallMoleculeTransitionListColumnHeaders.labelType,
SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
}
var text = GetCsvFileText(GetTestPath("PUFA_TransitionList.csv"), true);
if (retry > 0)
{
// Fix bad charge declaration
var z = string.Format("{0}1{0}", TextUtil.CsvSeparator);
var zneg = string.Format("{0}-1{0}", TextUtil.CsvSeparator);
text = text.Replace(z, zneg);
}
SetClipboardText(text);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents showing charge problem", 5);
OkDialog(pasteDlg, pasteDlg.CancelDialog);
}
else
{
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
}
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 1, 4, 7, 7);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => !t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
SkylineWindow.ExpandPeptides();
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets - show the right-click menu for setting DHA to be a surrogate standard", 5);
// Set the standard type of the surrogate standards to StandardType.SURROGATE_STANDARD
RunUI(() =>
{
List <IdentityPath> pathsToSelect = SkylineWindow.SequenceTree.Nodes.OfType <PeptideGroupTreeNode>()
.SelectMany(peptideGroup => peptideGroup.Nodes.OfType <PeptideTreeNode>())
.Where(peptideTreeNode => peptideTreeNode.DocNode.RawTextId.Contains("(DHA)"))
.Select(treeNode => treeNode.Path)
.ToList();
SkylineWindow.SequenceTree.SelectedPaths = pathsToSelect;
SkylineWindow.SetStandardType(StandardType.SURROGATE_STANDARD);
});
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SelectedPeptidesSmallMolsSubTab = 1;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_PLUS_H.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_PLUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes =
TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR + "," + TransitionFilter.PRECURSOR_ION_CHAR;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.SetAutoSelect = true;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 4);
RunUI(() =>
{
// Full Scan Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.Peaks = 2;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettingsUI.PrecursorRes = 70000;
transitionSettingsUI.PrecursorResMz = 200;
transitionSettingsUI.RetentionTimeFilterType = RetentionTimeFilterType.none;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Full Scan tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("FattyAcids_demo.sky")));
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(Path.Combine(TestFilesDirs.First().PersistentFilesDir, GetDataFolder()));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
OkDialog(importResultsDlg1, importResultsDlg1.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// peptides, transition groups, heavy transition groups, tranistions, heavy transitions
{ "default", new[] { 4, 4, 3, 8, 6 } }, // Most have these values
{ "ID31609_01_E749_4745_091517", new[] { 4, 4, 3, 7, 6 } },
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = expectedTransCount["default"];
}
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, transitions[0], transitions[1], transitions[2], transitions[3], transitions[4]);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
var documentGrid = FindOpenForm <DocumentGridForm>();
if (documentGrid == null)
{
// When running offscreen, can't depend on RestoreViewOnScreen to open document grid
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
documentGrid = FindOpenForm <DocumentGridForm>();
}
RunUI(() => documentGrid.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification));
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR_THROUGH_ZERO;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantRegressionWeighting = RegressionWeighting.NONE;
peptideSettingsUI.QuantMsLevel = null; // All
peptideSettingsUI.QuantUnits = "uM";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 10);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
var documentGrid2 = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGrid2.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => (documentGrid2.RowCount == 16)); // Let it initialize
RunUI(() =>
{
var gridView = documentGrid2.DataGridView;
for (var index = 0; index < gridView.Rows.Count; index++)
{
var row = gridView.Rows[index];
if (row.Cells[0].Value.ToString().StartsWith("NIST"))
{
row.Cells[1].Value = SampleType.STANDARD;
row.Cells[2].Value = 1.0;
}
else if (row.Cells[0].Value.ToString().StartsWith("GW"))
{
row.Cells[1].Value = SampleType.QC;
}
}
});
// Make sure the edits have flowed to the document
WaitForConditionUI(() => SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms.Where(c => c.Name.StartsWith("GW")).All(c => c.SampleType.Equals(SampleType.QC)));
PauseForScreenShot <DocumentGridForm>("Document Grid - replicates", 11);
// Finish setting up quant
var documentGrid3 = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGrid3.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification);
});
WaitForConditionUI(() => (documentGrid3.RowCount > 0 &&
documentGrid3.ColumnCount > 6)); // Let it initialize
RunUI(() =>
{
var gridView = documentGrid3.DataGridView;
var methods = ((DataGridViewComboBoxCell)gridView.Rows[0].Cells[6]).Items;
var ratioToSurrogateHeavyDHA = ((Tuple <String, NormalizationMethod>)methods[6]).Item2;
gridView.Rows[0].Cells[5].Value = 2838.0;
gridView.Rows[1].Cells[5].Value = 54.0;
gridView.Rows[1].Cells[6].Value = ratioToSurrogateHeavyDHA;
gridView.Rows[2].Cells[5].Value = 984.0;
gridView.Rows[3].Cells[5].Value = 118.0;
});
PauseForScreenShot <DocumentGridForm>("Document Grid - peptide quant again", 11);
RunUI(() => SkylineWindow.ShowCalibrationForm());
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <DocumentGridForm>("Calibration curve", 12);
}
}
protected override void DoTest()
{
// iRT Retention Time Prediction
string standardDocumentFile = GetTestPath("iRT-C18 Standard.sky"); // Not L10N
RunUI(() => SkylineWindow.OpenFile(standardDocumentFile));
WaitForDocumentLoaded(); // might have some updating to do for protein metadata
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("iRT-C18 Calibrate.sky"))); // Not L10N
// Load raw files for iRT calculator calibration p. 2
const string unschedHuman1Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_1_30min-5-35"; // Not L10N
string unschedHuman1Name = unschedHuman1Fileroot.Substring(41, 7);
const string unschedHuman2Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_2_30min-5-35"; // Not L10N
string unschedHuman2Name = unschedHuman2Fileroot.Substring(41, 7);
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, 5, false, true, "Names form", 3);
var docCalibrate = WaitForProteinMetadataBackgroundLoaderCompletedUI();
const int pepCount = 11, tranCount = 33;
AssertEx.IsDocumentState(docCalibrate, null, 1, pepCount, pepCount, tranCount);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman1Name, pepCount, pepCount, 0, tranCount, 0);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman2Name, pepCount, pepCount, 0, tranCount, 0);
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowRTPeptideGraph();
using (var enumLabels = SkylineWindow.RTGraphController.GraphSummary.Categories.GetEnumerator())
{
foreach (var nodePep in docCalibrate.Peptides)
{
Assert.IsTrue(enumLabels.MoveNext() && enumLabels.Current != null);
Assert.IsTrue(nodePep.Peptide.Sequence.StartsWith(enumLabels.Current.Substring(0, 3)));
}
}
});
// Page 3.
PauseForScreenShot <GraphSummary.RTGraphView>("RT graph metafile", 3); // Peptide RT graph
RunUI(() =>
{
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.Size = new Size(914, 560);
});
// Ensure graphs look like p. 5
WaitForGraphs();
RestoreViewOnScreen(5);
PauseForScreenShot("Main window showing chromatograms and RT graph", 5); // Skyline window with docked RT replicate comparison graph
RunUI(() =>
{
Assert.AreEqual(3, SkylineWindow.RTGraphController.GraphSummary.CurveCount);
Assert.AreEqual(2, SkylineWindow.RTGraphController.GraphSummary.Categories.Count());
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(11.3, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(11.2, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
});
var listTimes = new List <double>();
for (int i = 0; i < docCalibrate.PeptideCount; i++)
{
int iPeptide = i;
RunUI(() =>
{
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
});
WaitForGraphs();
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
double time1 = chromGraphs[0].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
double time2 = chromGraphs[1].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
listTimes.Add((time1 + time2) / 2);
Assert.AreEqual(time1, time2, 0.2);
});
}
// Calibrate a calculator p. 7
const string irtCalcName = "iRT-C18";
string irtCalcPath = GetTestPath(irtCalcName + IrtDb.EXT);
const string irtCalcPathScreenShot = @"C:\Users\Brendan\Documents\iRT\iRT-C18.irtdb";
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editIrtCalc1 = ShowDialog <EditIrtCalcDlg>(peptideSettingsUI1.AddCalculator);
RunUI(() =>
{
editIrtCalc1.CalcName = irtCalcName;
editIrtCalc1.CreateDatabase(irtCalcPath); // Not L10N
});
{
var calibrateDlg = ShowDialog <CalibrateIrtDlg>(editIrtCalc1.Calibrate);
RunUI(() =>
{
calibrateDlg.StandardName = "Biognosys (30 min cal)";
calibrateDlg.UseResults();
Assert.AreEqual(11, calibrateDlg.StandardPeptideCount);
calibrateDlg.SetFixedPoints(1, 10);
for (int i = 0; i < calibrateDlg.StandardPeptideCount; i++)
{
Assert.AreEqual(listTimes[i], calibrateDlg.StandardPeptideList[i].RetentionTime, 0.2);
}
});
PauseForScreenShot <CalibrateIrtDlg>("Calibrate iRT Calculator form", 6); // Calibrate iRT Calculator form
RunDlg <GraphRegression>(calibrateDlg.GraphRegression, dlg => dlg.CloseDialog());
RunDlg <GraphRegression>(calibrateDlg.GraphIrts, dlg => dlg.CloseDialog());
RunUI(calibrateDlg.OkDialog);
}
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc1.StandardPeptideCount == 11));
if (IsPauseForScreenShots)
{
RunUI(() => editIrtCalc1.CalcPath = irtCalcPathScreenShot);
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculator form", 7); // Edit iRT Calculator form
RunUI(() => editIrtCalc1.CalcPath = irtCalcPath);
}
// Check iRT values and update to defined values p. 7-8
var irtDefinitionPath = GetTestPath("iRT definition.xlsx"); // Not L10N
string irtDefText = GetExcelFileText(irtDefinitionPath, "iRT-C18", 2, true); // Not L10N
RunUI(() =>
{
var standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.00001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.00001);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 6);
SetClipboardText(irtDefText);
editIrtCalc1.DoPasteStandard();
standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.005);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 0.00001);
});
OkDialog(editIrtCalc1, editIrtCalc1.OkDialog);
OkDialog(peptideSettingsUI1, peptideSettingsUI1.OkDialog);
// Inspect RT regression graph p. 9
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
RestoreViewOnScreen(9);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times Regression graph metafile", 9); // RT Regression graph
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
SkylineWindow.ShowSingleReplicate();
SkylineWindow.SequenceTree.Focus(); // If the focus is left on the results tab, then the next line does nothing
SkylineWindow.SelectedResultsIndex = 0;
});
WaitForRegression();
RunUI(() =>
{
VerifyRTRegression(0.15, 15.15, 0.9991);
SkylineWindow.SelectedResultsIndex = 1;
});
WaitForRegression();
RunUI(() => VerifyRTRegression(0.15, 15.04, 0.9991));
RunUI(() => SkylineWindow.ShowAverageReplicates());
RunUI(() => SkylineWindow.SaveDocument());
// Create a document containing human and standard peptides, p. 10
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human.sky")));
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.ImportFiles(standardDocumentFile);
});
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RestoreViewOnScreen(10);
PauseForScreenShot("Targets tree clipped out of main window", 10); // Target tree
RunUI(() =>
{
Assert.AreEqual("iRT-C18 Standard Peptides", SkylineWindow.SelectedNode.Text); // Not L10N
Assert.AreEqual(1231, SkylineWindow.DocumentUI.PeptideTransitionCount);
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard.sky")); // Not L10N
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard Calibrate.sky")); // Not L10N
});
// Remove heavy precursors, p. 11
var docHumanAndStandard = SkylineWindow.Document;
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.RefineLabelType = IsotopeLabelType.heavy;
refineDlg.OkDialog();
});
var docLightOnly = WaitForDocumentChange(docHumanAndStandard);
Assert.AreEqual(632, docLightOnly.PeptideTransitionCount);
// Create auto-calculate regression RT predictor, p. 11
const string irtPredictorName = "iRT-C18"; // Not L10N
{
var docPre = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI2.ChooseRegression(irtPredictorName));
var regressionDlg = ShowDialog <EditRTDlg>(peptideSettingsUI2.EditRegression);
RunUI(() =>
{
Assert.AreEqual(irtPredictorName, regressionDlg.Regression.Name);
Assert.AreEqual(irtCalcName, regressionDlg.Regression.Calculator.Name);
regressionDlg.SetAutoCalcRegression(true);
regressionDlg.SetTimeWindow(5);
});
PauseForScreenShot("Edit Retention Time Predictor form", 11); // Edit retention time predictor form
OkDialog(regressionDlg, regressionDlg.OkDialog);
OkDialog(peptideSettingsUI1, peptideSettingsUI2.OkDialog);
// Make sure iRT calculator is loaded
WaitForDocumentChangeLoaded(docPre);
}
// Export unscheduled transition list, p. 12
{
const string calibrateBasename = "iRT Human+Standard Calibrate"; // Not L10N
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.MaxTransitions = 335;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 12);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(calibrateBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
Assert.AreEqual(332, File.ReadAllLines(GetTestPath(calibrateBasename + "_0001.csv")).Length); // Not L10N
Assert.AreEqual(333, File.ReadAllLines(GetTestPath(calibrateBasename + "_0002.csv")).Length); // Not L10N
}
// Import human peptide calibration results p. 13
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, -1, true);
// Review iRT-C18 graph p. 13-14
RunUI(() => SkylineWindow.ChooseCalculator(irtCalcName));
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 14);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
Assert.AreEqual(11, SkylineWindow.DocumentUI.PeptideCount -
SkylineWindow.RTGraphController.Outliers.Length);
});
// Find all unintegrated transitions, p. 14-15
{
var findDlg = ShowDialog <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() =>
{
findDlg.FindOptions = new FindOptions().ChangeText(string.Empty)
.ChangeCustomFinders(Finders.ListAllFinders().Where(f => f is UnintegratedTransitionFinder));
});
PauseForScreenShot <FindNodeDlg>("Find form", 15);
RestoreViewOnScreen(15);
RunUI(() =>
{
findDlg.FindAll();
findDlg.Close();
});
WaitForClosedForm(findDlg);
}
PauseForScreenShot <FindResultsForm>("Find Results pane", 15);
var findAllForm = WaitForOpenForm <FindResultsForm>();
Assert.IsNotNull(findAllForm);
const int expectedItems = 6;
RunUI(() =>
{
Assert.AreEqual(expectedItems, findAllForm.ItemCount);
SkylineWindow.ShowAllTransitions();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.Size = new Size(657, 632);
});
// Review peaks with missing transitions, p. 16
for (int i = 0; i < expectedItems; i++)
{
int iItem = i;
RunUI(() => findAllForm.ActivateItem(iItem));
WaitForGraphs();
RunUI(() => Assert.AreEqual((int)SequenceTree.StateImageId.no_peak,
SkylineWindow.SelectedNode.StateImageIndex));
if (i == 1)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (1 of 2)", 16); // Chromatogram graph
}
if (i == 2)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (2 of 2)", 16);
}
if (i == 3)
{
RunUI(() =>
{
var document = SkylineWindow.DocumentUI;
var nodeGroup = document.FindNode(SkylineWindow.SelectedPath.Parent) as TransitionGroupDocNode;
Assert.IsNotNull(nodeGroup);
var nodeTran = document.FindNode(SkylineWindow.SelectedPath) as TransitionDocNode;
Assert.IsNotNull(nodeTran);
var graph = SkylineWindow.GetGraphChrom(Resources.ImportResultsDlg_DefaultNewName_Default_Name);
// New peak picking picks correct peak
Assert.AreEqual(19.8, graph.BestPeakTime.Value, 0.05);
// TransitionGroupDocNode nodeGroupGraph;
// TransitionDocNode nodeTranGraph;
// var scaledRT = graph.FindAnnotatedPeakRetentionTime(19.8, out nodeGroupGraph, out nodeTranGraph);
// Assert.AreSame(nodeGroup, nodeGroupGraph);
// Assert.AreNotSame(nodeTran, nodeTranGraph);
// Assert.AreEqual(7, nodeTranGraph.Transition.Ordinal); // y7
// graph.FirePickedPeak(nodeGroupGraph, nodeTranGraph, scaledRT);
});
}
}
// New peak picking picks correct peak
// RunUI(() => findAllForm.ActivateItem(3));
// PauseForScreenShot<GraphChromatogram>("Chromatogram graph metafile (3 of 3)", 15);
RunUI(SkylineWindow.ToggleIntegrateAll);
RunUI(findAllForm.Close);
WaitForClosedForm(findAllForm);
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
// Calculate new iRT values for human peptides, p. 18
{
WaitForConditionUI(() =>
SkylineWindow.IsGraphRetentionTimeShown(GraphTypeSummary.score_to_run_regression) &&
SkylineWindow.RTGraphController.RegressionRefined != null);
var editIrtCalc2 = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
RunUI(() => Assert.AreEqual(0, editIrtCalc2.LibraryPeptideCount));
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc2.AddResults);
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 17);
RunUI(() =>
{
Assert.AreEqual(148, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(0, addPeptidesDlg.RunsFailedCount);
});
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
if (IsPauseForScreenShots)
{
RunUI(() => editIrtCalc2.CalcPath = irtCalcPathScreenShot);
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculator form", 18); // Edit iRT Calculator form
RunUI(() => editIrtCalc2.CalcPath = irtCalcPath);
}
RunUI(() => Assert.AreEqual(148, editIrtCalc2.LibraryPeptideCount));
CommitIrtCalcChange(editIrtCalc2);
}
// Check the RT regression, p. 19
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 19);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.99985);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
SkylineWindow.SaveDocument();
SkylineWindow.HideFindResults();
});
// Recalibrate method to 90-minute gradient, p. 20
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human+Standard.sky"))); // Not L10N
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("NSAQ"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
RunUI(SkylineWindow.EditDelete);
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
peptideSettingsUI.ChooseRegression(irtPredictorName);
peptideSettingsUI.IsUseMeasuredRT = true;
peptideSettingsUI.TimeWindow = 5;
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 21);
RunUI(peptideSettingsUI.OkDialog);
WaitForClosedForm(peptideSettingsUI);
}
// Import 90-minute standard mix run, p. 19
const string unsched90MinFileroot = "A_D110913_SiRT_HELA_11_nsMRM_150selected_90min-5-40_TRID2215_01"; // Not L10N
ImportNewResults(new[] { unsched90MinFileroot }, -1, false);
WaitForGraphs();
// Verify regression graph, p. 19
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 22);
RunUI(() =>
{
VerifyRTRegression(0.40, 24.77, 0.9998);
Assert.AreEqual(147, SkylineWindow.RTGraphController.Outliers.Length);
});
// Check scheduling graph, p. 20
RunUI(SkylineWindow.ShowRTSchedulingGraph);
RunDlg <SchedulingGraphPropertyDlg>(() => SkylineWindow.ShowRTPropertyDlg(SkylineWindow.GraphRetentionTime), propertyDlg =>
{
propertyDlg.TimeWindows = new[] { 2.0, 5.0, 10.0 };
propertyDlg.OkDialog();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Scheduling graph metafile", 23);
// Export new 90-minute scheduled transition list, p. 22
const string scheduledBasename = "iRT Human+Standard"; // Not L10N
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 265;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 24);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(scheduledBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
}
Assert.AreEqual(1223, File.ReadAllLines(GetTestPath(scheduledBasename + "_0001.csv")).Length); // Not L10N
Assert.IsFalse(File.Exists(GetTestPath("iRT Human+Standard_0002.csv"))); // Not L10N
// Import scheduled data, p. 23
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg =>
{
manageResultsDlg.RemoveAllReplicates();
manageResultsDlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
const string sched90MinFileroot = "A_D110913_SiRT_HELA_11_sMRM_150selected_90min-5-40_SIMPLE"; // Not L10N
ImportNewResults(new[] { sched90MinFileroot }, -1, false);
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 26);
// Review regression and outliers, p. 24
RunUI(() =>
{
VerifyRTRegression(0.358, 25.920, 0.91606);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
RunDlg <RegressionRTThresholdDlg>(SkylineWindow.ShowRegressionRTThresholdDlg, thresholdDlg =>
{
thresholdDlg.Threshold = 0.998;
thresholdDlg.OkDialog();
});
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 27);
// Verify 2 outliers highlighted and removed, p. 25
WaitForConditionUI(() => SkylineWindow.RTGraphController.Outliers.Length == 2);
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
SkylineWindow.RemoveRTOutliers();
SkylineWindow.ShowPlotType(PlotTypeRT.residuals);
});
WaitForRegression();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 28);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RenameReplicate(manageResultsDlg, 0, "HELA_11_sMRM_150selected_90min");
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.Top = SkylineWindow.Top;
peptideSettingsUI.Left = SkylineWindow.Left - peptideSettingsUI.Width - 20;
});
var irtEditor = ShowDialog <EditIrtCalcDlg>(peptideSettingsUI.EditCalculator);
RunUI(() =>
{
irtEditor.Height = SkylineWindow.DockPanel.Height + 10;
irtEditor.Width += 25;
irtEditor.Top = SkylineWindow.Bottom - irtEditor.Height - SkylineWindow.StatusBarHeight - 5;
irtEditor.Left = SkylineWindow.Right - irtEditor.Width - 5;
});
TakeCoverShot();
OkDialog(irtEditor, irtEditor.CancelDialog);
OkDialog(peptideSettingsUI, peptideSettingsUI.CancelDialog);
return;
}
// Check outlier removal, p. 25
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
RunUI(() =>
{
SkylineWindow.ShowPlotType(PlotTypeRT.correlation);
SkylineWindow.ShowGraphRetentionTime(false, GraphTypeSummary.score_to_run_regression);
SkylineWindow.ShowGraphRetentionTime(false, GraphTypeSummary.schedule);
});
// Review a peak and its predicted retention time, p. 26
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("DATNVG"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 29); // Chromatogram graph
RunUI(() =>
{
var graphChrom = SkylineWindow.GetGraphChrom(sched90MinFileroot);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(47.3, graphChrom.BestPeakTime.Value, 0.05);
Assert.IsTrue(graphChrom.PredictedRT.HasValue);
Assert.AreEqual(47.6, graphChrom.PredictedRT.Value, 0.05);
});
RunUI(SkylineWindow.ShowRTRegressionGraphScoreToRun);
// Import retention times from a spectral library, p. 31
{
WaitForConditionUI(() =>
SkylineWindow.IsGraphRetentionTimeShown(GraphTypeSummary.score_to_run_regression) &&
SkylineWindow.RTGraphController.RegressionRefined != null);
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addLibraryDlg = ShowDialog <AddIrtSpectralLibrary>(editIrtCalc.AddLibrary);
RunUI(() =>
{
addLibraryDlg.Source = SpectralLibrarySource.file;
addLibraryDlg.FilePath = GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast_iRT_C18_0_00001.blib")); // Not L10N
addLibraryDlg.FilePathFocus();
});
PauseForScreenShot <AddIrtSpectralLibrary>("Add Spectral Library form", 31);
// Verify converted peptide iRT values and OK dialogs, p. 31
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(addLibraryDlg.OkDialog);
RunUI(() =>
{
Assert.AreEqual(558, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(1, addPeptidesDlg.RunsConvertedCount); // Libraries now convert through internal alignment to single RT scale
Assert.AreEqual(3, addPeptidesDlg.KeepPeptidesCount);
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 31);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc.LibraryPeptideCount == 706));
CommitIrtCalcChange(editIrtCalc);
}
// Inspect MS1 filtered Skyline file created from library DDA data, p. 32
RunUI(() => SkylineWindow.OpenFile(GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast+Standard (refined) - 2min.sky"))));
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForRegression();
// Verify numbers that show up in the screenshot
RunUI(() =>
{
// If the cache gets rebuilt, then because the chromatograms
// were minimized, the peak picking is not exactly the same
// using the minimized chromatograms.
VerifyRTRegression(0.3, 19.37, 0.9998);
var graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_16"); // Not L10N
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[0], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.6, graphChrom.BestPeakTime.Value, 0.05);
graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_14"); // Not L10N
Assert.AreEqual(37.3, graphChrom.RetentionMsMs[0], 0.05);
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[1], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.4, graphChrom.BestPeakTime.Value, 0.05);
SkylineWindow.Size = new Size(1250, 660);
});
PauseForScreenShot("Main window", 33);
// Add results and verify add dialog counts, p. 33
{
RunUI(() => SkylineWindow.Width = 500); // Make room for the form below
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc.AddResults);
RunUI(() =>
{
Assert.AreEqual(0, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(558, addPeptidesDlg.OverwritePeptidesCount);
Assert.AreEqual(3, addPeptidesDlg.ExistingPeptidesCount);
addPeptidesDlg.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 34);
var recalibrateDlg = ShowDialog <MultiButtonMsgDlg>(addPeptidesDlg.OkDialog);
OkDialog(recalibrateDlg, recalibrateDlg.Btn1Click);
RunUI(editIrtCalc.OkDialog);
WaitForClosedForm(editIrtCalc);
}
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
// Skyline Collision Energy Optimization
RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules();
}
// 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, new [] { 120 }, 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.HasResults &&
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, 0);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
});
RestoreViewOnScreen(5);
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, new[] { 220, 220, 264, 308, 308 }, 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
string decorator = AsSmallMolecules
? RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator
: string.Empty;
FindNode(decorator + "IHGFDLAAINLQR");
RestoreViewOnScreen(8);
RunUI(() => SkylineWindow.Size = new Size(984, 553));
PauseForScreenShot("Main Skyline window", 8);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowPeakAreaLegend(false);
});
RestoreCoverViewOnScreen();
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
// p. 8
// Not L10N
RemoveTargetByDisplayName(decorator + "EGIHAQQK");
FindNode(decorator + "IDALNENK");
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
PauseForScreenShot("Main Skyline window", 9);
RunUI(SkylineWindow.EditDelete);
RemoveTargetByDisplayName(AsSmallMolecules ? decorator + "LIC[+57.0]DNTHITK" : "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, new[] { 108 }, 9);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 5, 6
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Prediction Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 5);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 6);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 7, 8
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null,
LabelAtoms.C13 | LabelAtoms.N15, RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi, "Edit Isotope Modification over Transition Settings", 7);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 8);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Inserting a peptide sequence p. 9
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
RunUI(() => pasteDlg.Size = new Size(700, 210));
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 9);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
RunUI(() => SkylineWindow.Size = new Size(840, 410));
PauseForScreenShot("Main window with Targets view", 9);
// Exporting a transition list p. 10
{
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", 10);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 11, 12
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 11);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
RunUI(() =>
{ //resize the window and activate the first standard chromatogram pane.
RunUI(() => SkylineWindow.Size = new Size(1330, 720));
var chrom = SkylineWindow.GraphChromatograms.First();
chrom.Select();
});
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 13);
// Analyzing SRM Data from FOXN1-GST Sample p. 14
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
RunUI(() => SkylineWindow.Size = new Size(1470, 656));
RestoreViewOnScreen(14);
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 14);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 14);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.FromIsotopeLabelType(IsotopeLabelType.heavy)));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 15);
// Peptide Quantitification Settings p. 16
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 16);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
var documentGridForm = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
for (int iRow = 0; iRow < concentrations.Length; iRow++)
{
// ReSharper disable AccessToModifiedClosure
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.Rows[iRow].Cells[colSampleType.Index].Value = SampleType.STANDARD;
});
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var colAnalyteConcentration =
documentGridForm.FindColumn(PropertyPath.Root.Property("AnalyteConcentration"));
var cell = documentGridForm.DataGridView.Rows[iRow].Cells[colAnalyteConcentration.Index];
documentGridForm.DataGridView.CurrentCell = cell;
cell.Value = concentrations[iRow];
});
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
}
if (IsPauseForScreenShots)
{
RunUI(() =>
{
SkylineWindow.Width = 500;
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Top;
gridFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot("Document grid with concentrations filled in", 17);
}
// View the calibration curve p. 18
RunUI(() => SkylineWindow.ShowDocumentGrid(false));
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowPeakAreaLegend(false);
SkylineWindow.ShowRTLegend(false);
});
RestoreCoverViewOnScreen();
RunUI(() =>
{
var calibrationOpenForm = WaitForOpenForm <CalibrationForm>();
var calibrationFloatingWindow = calibrationOpenForm.Parent.Parent;
calibrationFloatingWindow.Top = SkylineWindow.Bottom - calibrationFloatingWindow.Height - 35;
calibrationFloatingWindow.Left = SkylineWindow.Left + 15;
});
TakeCoverShot();
return;
}
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
if (IsPauseForScreenShots)
{
RunUI(() =>
{
var calibrationFloatingWindow = calibrationForm.Parent.Parent;
calibrationFloatingWindow.Width = 565;
calibrationFloatingWindow.Top = SkylineWindow.Top;
calibrationFloatingWindow.Left = SkylineWindow.Right + 20;
});
PauseForScreenShot("View calibration curve", 18);
}
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
}
private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 18
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
if (IsCoverShotMode)
{
var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI1, "Edit Isotope Modification form", 6);
}
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", 18);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new string[0];
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 19.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
// We expect this to fail due to instrument settings rather than format issues eg "The product m/z 1519.78 is out of range for the instrument settings, in the peptide sequence YEVQGEVFTKPQLWP. Check the Instrument tab in the Transition Settings."
{
var transitionSelectdgl = ShowDialog <ImportTransitionListColumnSelectDlg>(SkylineWindow.Paste);
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(transitionSelectdgl.AcceptButton.PerformClick);
AssertEx.AreComparableStrings(TextUtil.SpaceSeparate(Resources.MassListRowReader_CalcTransitionExplanations_The_product_m_z__0__is_out_of_range_for_the_instrument_settings__in_the_peptide_sequence__1_,
Resources.MassListRowReader_CalcPrecursorExplanations_Check_the_Instrument_tab_in_the_Transition_Settings),
messageDlg.ErrorList[0].ErrorMessage,
2);
RunUI(() => messageDlg.Size = new Size(838, 192));
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 19);
OkDialog(messageDlg, messageDlg.CancelButton.PerformClick); // Acknowledge the error but decline to proceed with import
RunUI(() => transitionSelectdgl.DialogResult = DialogResult.Cancel); // Cancel the import
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
PasteTransitionListSkipColumnSelect();
RunUI(SkylineWindow.CollapsePeptides);
PauseForScreenShot("Targets tree (selected from main window)", 20);
// 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(UseRawFilesOrFullData ? ".wiff" : ".mzML"); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 24);
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 <ImportResultsNameDlg>("Import Results Common prefix form", 25);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(26);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
SkylineWindow.Size = new Size(1029, 659);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 26);
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. 29.
RestoreViewOnScreen(28);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 31);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 32);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.ActivateReplicate("E_03");
SkylineWindow.Size = new Size(757, 655);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 32);
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", 33);
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
var pathConcentration = PropertyPath.Parse("AnalyteConcentration");
var pathSampleType = PropertyPath.Parse("SampleType");
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
WaitForConditionUI(() => documentGrid.RowCount == (IsFullData ? concentrations.Length * 4 : 4) &&
documentGrid.FindColumn(pathConcentration) != null &&
documentGrid.FindColumn(pathSampleType) != null); // Let it initialize
RunUI(() =>
{
// Parent is a DocPane and Parent.Parent is the floating window
documentGrid.Parent.Parent.Size = new Size(585, 325);
var documentGridView = documentGrid.DataGridView;
var colConcentration = documentGrid.FindColumn(pathConcentration);
var colStandardType = documentGrid.FindColumn(pathSampleType);
if (IsFullData)
{
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
double?concentration = concentrations[i];
SetCellValue(documentGridView, j, colConcentration.Index, concentration);
SetCellValue(documentGridView, j, colStandardType.Index,
concentration == 0 ? SampleType.BLANK : SampleType.STANDARD);
}
}
}
else
{
SetCellValue(documentGridView, 0, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 0, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 1, colConcentration.Index, 0.0);
SetCellValue(documentGridView, 1, colStandardType.Index, SampleType.BLANK);
SetCellValue(documentGridView, 2, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 2, colStandardType.Index, SampleType.STANDARD);
SetCellValue(documentGridView, 3, colConcentration.Index, 175.0);
SetCellValue(documentGridView, 3, colStandardType.Index, SampleType.STANDARD);
}
});
WaitForGraphs();
PauseForScreenShot <DocumentGridForm>("Document grid filled (scrolled to the end)", 35);
RunUI(() => documentGrid.Close());
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
var settings = SkylineWindow.DocumentUI.Settings;
var valConcentration = ReplicateValue.GetAllReplicateValues(settings).Skip(1).First();
SkylineWindow.GroupByReplicateValue(valConcentration);
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", 37);
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);
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 38);
FindNode("LSEPAELTDAVK");
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.Width = 920;
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", 39);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.AutoZoomBestPeak();
});
RestoreCoverViewOnScreen();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Parent);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.Nodes[0]);
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 40);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 41);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 41);
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.ResetDefaultSettings();
SkylineWindow.NewDocument();
});
ShowAndPositionAuditLog(false);
PauseForScreenShot <AuditLogForm>("Empty Audit Log form.", 2);
// Configuring Settings for Inserting a New Peptide, p. 3
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
});
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
PeptideSettingsUI peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Modifications);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUi);
RunUI(() => peptideSettingsUi.PickedHeavyMods = new[] { modHeavyK.Name });
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with settings modifications.", 4);
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.Width = 1010;
});
PauseForScreenShot("Undo list expanded. (manual)", 4);
RunUI(SkylineWindow.Undo);
PauseForScreenShot("Redo list expanded. (manual)", 5);
RunUI(SkylineWindow.Redo);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
WaitForProteinMetadataBackgroundLoaderCompletedUI();
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
RunUI(pasteDlg.PastePeptides);
RunUI(() =>
{
pasteDlg.Size = new Size(700, 210);
pasteDlg.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
using (new WaitDocumentChange())
{
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
WaitForConditionUI(() => SkylineWindow.SequenceTree.Nodes.Count > 0);
}
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Height = 390;
});
PauseForScreenShot("Main window with Targets view", 6);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with inserted peptide.", 7);
ShowLastExtraInfo("Extra info form with inserted peptide info.", 7);
string documentPath = GetTestPath("AuditLogTutorial" + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentPath));
WaitForCondition(() => File.Exists(documentPath));
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value;
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
OkDialog(importResultsDlg, importResultsDlg.OkDialog);
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(9, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <AuditLogForm>("Audit Log form with imported data files.", 9);
ShowLastExtraInfo("Extra info form for the import.", 9);
// Peptide Quantitification Settings p. 9
peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUi.SelectedTab = (PeptideSettingsUI.TABS) 5);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
PauseForScreenShot <AuditLogForm>("Audit Log form with quantification settings.", 10);
// Specify analyte concentrations of external standards
RunUI(() =>
{
SkylineWindow.AuditLogForm.Close();
SkylineWindow.ShowDocumentGrid(true);
});
var documentGridForm = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGridForm.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => documentGridForm.IsComplete);
var concentrations = new[] { 40, 12.5, 5, 2.5, 1, .5, .25, .1 };
string pasteString = TextUtil.LineSeparate(concentrations.Select((f, i) =>
QuantificationStrings.SampleType_STANDARD_Standard + "\t" + f));
ClipboardEx.SetText(pasteString);
using (new WaitDocumentChange())
{
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.CurrentCell = documentGridForm.DataGridView.Rows[1].Cells[colSampleType.Index];
documentGridForm.DataGridView.SendPaste();
});
}
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var gridFloatingWindow = documentGridForm.Parent.Parent;
gridFloatingWindow.Size = new Size(370, 315);
gridFloatingWindow.Top = SkylineWindow.Bottom + 20;
});
PauseForScreenShot <DocumentGridForm>("Document grid with concentrations filled in", 11);
RunUI(documentGridForm.Close);
ShowAndPositionAuditLog(true);
PauseForScreenShot <AuditLogForm>("Audit Log form with grid changes", 12);
ShowLastExtraInfo("Extra Info for the analyte data import.", 12);
RunUI(SkylineWindow.AuditLogForm.Close);
const string unknownReplicate = "FOXN1-GST";
RestoreViewOnScreen(13);
ActivateReplicate(unknownReplicate);
SelectNode(SrmDocument.Level.TransitionGroups, 1);
RunUI(() => SkylineWindow.Size = new Size(936, 527));
WaitForGraphs();
PauseForScreenShot("Heavy precursor chromatogram", 13);
RunUI(() =>
{
var pathHeavy = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1);
var graphChrom = SkylineWindow.GetGraphChrom(unknownReplicate);
Assert.IsNotNull(graphChrom);
Assert.AreEqual(unknownReplicate, graphChrom.NameSet);
var firstGroupInfo = graphChrom.ChromGroupInfos.FirstOrDefault();
Assert.IsNotNull(firstGroupInfo, "Missing group info");
var firstChromItem = graphChrom.GraphItems.FirstOrDefault(gci => gci.TransitionChromInfo != null);
Assert.IsNotNull(firstChromItem, "Missing graph item");
var listChanges = new List <ChangedPeakBoundsEventArgs>
{
new ChangedPeakBoundsEventArgs(pathHeavy,
null,
graphChrom.NameSet,
firstGroupInfo.FilePath,
firstChromItem.GetValidPeakBoundaryTime(20.65),
firstChromItem.GetValidPeakBoundaryTime(21.15),
PeakIdentification.FALSE,
PeakBoundsChangeType.both)
};
graphChrom.SimulateChangedPeakBounds(listChanges);
});
ShowAndPositionAuditLog(true, 50, 200);
WaitForConditionUI(500, () => SkylineWindow.AuditLogForm.DataGridView.Rows.Count > 0);
PauseForScreenShot <AuditLogForm>("Audit Log form with changed integration boundary.", 14);
int reasonIndex = 2;
using (new WaitDocumentChange())
{
RunUI(() =>
{
var pathReason = PropertyPath.Root.Property("Reason");
var colReason = SkylineWindow.AuditLogForm.FindColumn(pathReason);
reasonIndex = colReason.Index;
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex,
"Changed peak integration as instructed by the tutorial");
});
}
RunUI(() => SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex));
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
PauseForScreenShot <AuditLogForm>("Audit Log form with updated reason.", 14);
// View the calibration curve p. 15
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
var priorZoomState = ZoomCalibrationCurve(calibrationForm, 0.52);
RunUI(() =>
{
Assert.AreEqual(CalibrationCurveFitter.AppendUnits(QuantificationStrings.Analyte_Concentration, quantUnits), calibrationForm.ZedGraphControl.GraphPane.XAxis.Title.Text);
Assert.AreEqual(string.Format(QuantificationStrings.CalibrationCurveFitter_PeakAreaRatioText__0___1__Peak_Area_Ratio, IsotopeLabelType.light.Title, IsotopeLabelType.heavy.Title),
calibrationForm.ZedGraphControl.GraphPane.YAxis.Title.Text);
VerifyCalibrationCurve(calibrationForm, 5.4065E-1, -2.9539E-1, 0.999);
});
PauseForScreenShot <CalibrationForm>("Calibration curve zoomed", 15);
RunUI(() =>
{
priorZoomState?.ApplyState(calibrationForm.ZedGraphControl.GraphPane);
var chromatograms = SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms;
new [] { 5, 6, 7, 8 }.ForEach((index) =>
{
int replicateIdx = chromatograms.IndexOf((ch) => ch.Name.Equals("Standard_" + index));
Assert.IsTrue(replicateIdx >= 0);
using (var excludeStandardMenu = calibrationForm.MakeExcludeStandardMenuItem(replicateIdx))
{
excludeStandardMenu?.PerformClick();
}
});
});
WaitForGraphs();
RunUI(() => VerifyCalibrationCurve(calibrationForm, 5.52E-1, -6.3678E-1, 1));
OkDialog(calibrationForm, calibrationForm.Close);
PauseForScreenShot <AuditLogForm>("Audit Log with excluded standard records", 16);
PauseForScreenShot <AuditLogForm>("Audit Log Reports menu (manual)", 16);
// TODO(nicksh): Audit log reason field does not currently support fill down
// RunUI(() =>
// {
// SetCellValue(SkylineWindow.AuditLogForm.DataGridView, 0, reasonIndex, "Excluded standard below LOD");
// for (int i = 0; i < 4; i++)
// SkylineWindow.AuditLogForm.DataGridView.Rows[i].Cells[reasonIndex].Selected = true;
// });
// RunUI(() => SkylineWindow.AuditLogForm.DataboundGridControl.FillDown());
RunUI(() =>
{
for (int i = 0; i < 4; i++)
{
SetCellValue(SkylineWindow.AuditLogForm.DataGridView, i, reasonIndex, "Excluded standard below LOD");
}
});
RunUI(() =>
{
SkylineWindow.AuditLogForm.ChooseView(AuditLogStrings.AuditLogForm_MakeAuditLogForm_Undo_Redo);
});
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() =>
{
var floatingWindow = SkylineWindow.AuditLogForm.Parent.Parent;
floatingWindow.Height = 334;
floatingWindow.Width -= 15;
});
PauseForScreenShot <AuditLogForm>("Audit Log with UndoRedo view.", 17);
if (IsCoverShotMode)
{
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
var calibrationCoverForm = WaitForOpenForm <CalibrationForm>();
ZoomCalibrationCurve(calibrationCoverForm, 0.53);
var floatingLogWindow = SkylineWindow.AuditLogForm.Parent.Parent;
var floatingCalWindow = calibrationCoverForm.Parent.Parent;
RunUI(() =>
{
floatingLogWindow.Top = SkylineWindow.Bottom - floatingLogWindow.Height - 8;
floatingLogWindow.Left =
(SkylineWindow.Left + SkylineWindow.Right) / 2 - floatingLogWindow.Width / 2;
floatingCalWindow.Top = SkylineWindow.Top + 8;
floatingCalWindow.Left = SkylineWindow.Right - floatingCalWindow.Width - 8;
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex);
SkylineWindow.AuditLogForm.DataGridView.AutoResizeColumn(reasonIndex - 1);
});
TakeCoverShot();
}
var customizeDialog = ShowDialog <ViewEditor>(SkylineWindow.AuditLogForm.NavBar.CustomizeView);
RunUI(() =>
{
customizeDialog.ViewName = "Custom Columns";
var columnsToAdd = new[]
{
PropertyPath.Parse("SkylineVersion"),
PropertyPath.Parse("User"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(customizeDialog.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
customizeDialog.ChooseColumnsTab.AddSelectedColumn();
}
customizeDialog.Height = 370;
});
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Custom Columns report template", 17);
OkDialog(customizeDialog, customizeDialog.OkDialog);
SetGridFormToFullWidth(SkylineWindow.AuditLogForm);
RunUI(() => SkylineWindow.AuditLogForm.Parent.Parent.Height += 10); // Extra for 2-line headers
PauseForScreenShot <AuditLogForm>("Audit Log with custom view.", 18);
var registrationDialog = ShowDialog <MultiButtonMsgDlg>(() => SkylineWindow.ShowPublishDlg(null));
PauseForScreenShot <MultiButtonMsgDlg>("Upload confirmation dialog.", 19);
var loginDialog = ShowDialog <EditServerDlg>(registrationDialog.ClickNo);
PauseForScreenShot <EditServerDlg>("Login dialog.", 20);
RunUI(() =>
{
loginDialog.URL = SERVER_URL;
loginDialog.Username = PANORAMA_USER_NAME;
});
if (!IsPauseForScreenShots)
{
OkDialog(loginDialog, loginDialog.CancelButton.PerformClick);
}
else
{
PauseTest("Enter password. (manual) No screen shot.");
var publishDialog = ShowDialog <PublishDocumentDlg>(loginDialog.OkDialog);
WaitForCondition(() => publishDialog.IsLoaded);
RunUI(() =>
{
publishDialog.SelectItem(testFolderName);
});
PauseForScreenShot <PublishDocumentDlg>("Folder selection dialog.", 21);
var browserConfirmationDialog = ShowDialog <MultiButtonMsgDlg>(publishDialog.OkDialog);
OkDialog(browserConfirmationDialog, browserConfirmationDialog.ClickYes);
PauseForScreenShot("Uploaded document in Panorama (in browser).");
Regex reDocId = new Regex(@"\?id=([0-9]+)");
Assert.IsTrue(reDocId.IsMatch(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()));
string docId = reDocId.Match(publishDialog.PanoramaPublishClient.UploadedDocumentUri.ToString()).Groups[1].Captures[0].Value;
Uri serverUri = new Uri(SERVER_URL);
Uri requestUri = PanoramaUtil.Call(serverUri, "targetedms", String.Format("{0}/{1}", PANORAMA_FOLDER, testFolderName),
"showSkylineAuditLog", "id=" + docId);
Process.Start(requestUri.ToString());
PauseForScreenShot("Uploaded document audit log in Panorama (in browser).");
}
}
public void ChangeTextSize(double textFactor)
{
SkylineWindow.ChangeTextSize(textFactor);
}
protected override void DoTest()
{
// Clear all the settings lists that will be defined in this tutorial
ClearSettingsLists();
// Open the file
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_START_CHECKPOINT)));
WaitForDocumentLoaded();
// Specify DIA acquisition scheme and machine settings
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettings.AcquisitionMethod = FullScanAcquisitionMethod.DIA;
transitionSettings.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettings.PrecursorMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.PrecursorRes = 35000;
transitionSettings.PrecursorResMz = 200;
transitionSettings.ProductMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.ProductRes = 17500;
transitionSettings.ProductResMz = 200;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan", 4);
// Set up isolation scheme
var isolationSchemeDlg = ShowDialog <EditIsolationSchemeDlg>(transitionSettings.AddIsolationScheme);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme form", 5);
RunUI(() =>
{
isolationSchemeDlg.UseResults = false;
});
var calculateIsolationDlg = ShowDialog <CalculateIsolationSchemeDlg>(isolationSchemeDlg.Calculate);
RunUI(() =>
{
calculateIsolationDlg.WindowWidth = 20;
calculateIsolationDlg.Start = 500;
calculateIsolationDlg.End = 900;
calculateIsolationDlg.OptimizeWindowPlacement = true;
});
PauseForScreenShot <CalculateIsolationSchemeDlg>("Calculate Isolation Scheme form", 6);
OkDialog(calculateIsolationDlg, calculateIsolationDlg.OkDialog);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme Dialog Filled", 7);
var isolationSchemeGraphDlg = ShowDialog <DiaIsolationWindowsGraphForm>(isolationSchemeDlg.OpenGraph);
PauseForScreenShot <DiaIsolationWindowsGraphForm>("Graph of Isolation Scheme", 8);
OkDialog(isolationSchemeGraphDlg, isolationSchemeGraphDlg.CloseButton);
const string isolationSchemeName = "500 to 900 by 20";
RunUI(() => isolationSchemeDlg.IsolationSchemeName = isolationSchemeName);
OkDialog(isolationSchemeDlg, isolationSchemeDlg.OkDialog);
OkDialog(transitionSettings, transitionSettings.OkDialog);
// Export isolation scheme
var exportIsolationDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
PauseForScreenShot <ExportMethodDlg>("Export Isolation List form", 9);
OkDialog(exportIsolationDlg, () => exportIsolationDlg.OkDialog(GetTestPath("DIA_tutorial_isolation_list.csv")));
// Adjust modifications and filter
var newPeptideSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => newPeptideSettings.AutoSelectMatchingPeptides = true);
OkDialog(newPeptideSettings, newPeptideSettings.OkDialog);
// Set up chromatogram retention time restriction
var newTransitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => newTransitionSettings.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 5.0));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Retention time filtering options", 16);
// Adjust library transition ranking
RunUI(() =>
{
newTransitionSettings.SelectedTab = TransitionSettingsUI.TABS.Library;
newTransitionSettings.UseLibraryPick = true;
newTransitionSettings.Filtered = true;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 22);
OkDialog(newTransitionSettings, newTransitionSettings.OkDialog);
PauseForScreenShot <SequenceTreeForm>("Targets pane with precursors and best 5 transitions only", 23);
// Build spectral library using Import Peptide Search
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT)));
// "Build Spectral Library" page
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(() => SkylineWindow.ShowImportPeptideSearchDlg());
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(new[] { GetTestPath("interact-20130311_DDA_Pit01.pep.xml") }); // Not L10N
importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia;
});
PauseForScreenShot <ImportPeptideSearchDlg>("Build Library form - input files", 24);
const string prefixKeep = "DIA_Pit0";
if (IsFullImportMode)
{
SrmDocument doc = SkylineWindow.Document;
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsDiaPage>("Import Results page", 25);
// "Extract Chromatograms" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles =
_importFiles.Select(f => new ImportPeptideSearch.FoundResultsFile(f, GetTestPath(f + ExtensionTestContext.ExtThermoRaw))).ToList();
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
string prefix = importResultsNameDlg.Prefix;
Assert.IsTrue(prefix.EndsWith(prefixKeep));
importResultsNameDlg.Prefix = prefix.Substring(0, prefix.Length - prefixKeep.Length);
importResultsNameDlg.YesDialog();
});
WaitForClosedForm(importResultsNameDlg);
// "Add Modifications" page
RunUI(() =>
{
const string modCarbamidomethyl = "Carbamidomethyl (C)";
const string modOxidation = "Oxidation (M)";
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
// Define expected matched/unmatched modifications
var expectedMatched = new[] { modCarbamidomethyl, modOxidation };
// Verify matched/unmatched modifications
AssertEx.AreEqualDeep(expectedMatched, importPeptideSearchDlg.MatchModificationsControl.MatchedModifications.ToArray());
Assert.IsFalse(importPeptideSearchDlg.MatchModificationsControl.UnmatchedModifications.Any());
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = new[] { modCarbamidomethyl };
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.transition_settings_page);
// "Configure Transition Settings" page
RunUI(() =>
{
importPeptideSearchDlg.TransitionSettingsControl.PeptidePrecursorCharges = Adduct.ProtonatedFromCharges(1, 2, 3, 4);
importPeptideSearchDlg.TransitionSettingsControl.PeptideIonCharges = Adduct.ProtonatedFromCharges(1, 2);
importPeptideSearchDlg.TransitionSettingsControl.PeptideIonTypes = new[] { IonType.y, IonType.b, IonType.precursor };
importPeptideSearchDlg.TransitionSettingsControl.ExclusionUseDIAWindow = true;
importPeptideSearchDlg.TransitionSettingsControl.IonCount = 5;
importPeptideSearchDlg.TransitionSettingsControl.IonMatchTolerance = 0.05;
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Configure Full-Scan Settings" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.IsolationSchemeName = isolationSchemeName;
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Import FASTA" page
RunUI(() =>
{
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("pituitary_database.fasta"));
});
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(6, proteinCount);
Assert.AreEqual(26, peptideCount);
Assert.AreEqual(31, precursorCount);
Assert.AreEqual(246, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(6, proteinCount);
Assert.AreEqual(26, peptideCount);
Assert.AreEqual(31, precursorCount);
Assert.AreEqual(246, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
WaitForClosedForm(importPeptideSearchDlg);
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
RunUI(() =>
{
SkylineWindow.SaveDocument(GetTestPath(DIA_IMPORTED_CHECKPOINT));
SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT));
});
}
else
{
OkDialog(importPeptideSearchDlg, importPeptideSearchDlg.CancelDialog);
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_IMPORTED_CHECKPOINT)));
}
WaitForDocumentLoaded();
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Size = new Size(750, 788);
});
// Generate decoys
// var decoysDlg = ShowDialog<GenerateDecoysDlg>(SkylineWindow.ShowGenerateDecoysDlg);
// PauseForScreenShot<GenerateDecoysDlg>("Add Decoy Peptides form", 24);
// RunUI(() =>
// {
// decoysDlg.NumDecoys = 26;
// Assert.AreEqual(decoysDlg.DecoysMethod, DecoyGeneration.SHUFFLE_SEQUENCE);
// });
// OkDialog(decoysDlg, decoysDlg.OkDialog);
// RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.SelectedNode.PrevNode.Nodes[6]);
// PauseForScreenShot<SequenceTreeForm>("Targets pane with decoys added", 25);
RunUI(() =>
{
SkylineWindow.CollapsePeptides();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 6);
var nodePepTree = SkylineWindow.SelectedNode as PeptideTreeNode;
Assert.IsNotNull(nodePepTree);
Assert.AreEqual("VLQAVLPPLPQVVCTYR", nodePepTree.DocNode.Peptide.Sequence);
SkylineWindow.ShowSplitChromatogramGraph(true);
SkylineWindow.AutoZoomBestPeak();
var graphChrom = SkylineWindow.GetGraphChrom(prefixKeep + "1");
var labelStrings = graphChrom.GetAnnotationLabelStrings().ToArray();
Assert.IsTrue(labelStrings.Contains(string.Format("{0}\n+{1} ppm", 75.4, 3)),
string.Format("Missing expected label in {0}", string.Join("|", labelStrings)));
SkylineWindow.Width = 1250;
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RestoreViewOnScreen(27);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 26);
RunUI(SkylineWindow.SelectedNode.Expand);
RunUI(() =>
{
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
var expectedImageId = IsFullImportMode ? SequenceTree.StateImageId.peak : SequenceTree.StateImageId.no_peak;
Assert.AreEqual((int)expectedImageId, nodeTree.StateImageIndex);
});
PauseForScreenShot <SequenceTreeForm>("Targets view - ", 27);
RunUI(() =>
{
SkylineWindow.SetIntegrateAll(true);
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
Assert.AreEqual((int)SequenceTree.StateImageId.peak, nodeTree.StateImageIndex);
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.83, nodeGroupTree.DocNode.GetLibraryDotProduct(0) ?? 0, 0.005);
SkylineWindow.ShowOtherRunPeptideIDTimes(true);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - with ID lines", 28);
RunUI(() =>
{
SkylineWindow.AutoZoomNone();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed out and small peak", 30);
RunUI(SkylineWindow.AutoZoomBestPeak);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed to peak", 31);
if (IsFullImportMode)
{
ClickChromatogram(74.9, 1.775E+7, PaneKey.PRECURSORS);
RestoreViewOnScreen(33);
PauseForScreenShot <GraphFullScan>("Full Scan graph with precursors - zoom manually", 32);
ClickChromatogram(74.8, 1.753E+6, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y7", 33);
ClickChromatogram(74.9, 9.64E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing b3 - zoom manually", 34);
ClickChromatogram(74.9, 1.25E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y3 - zoom manually", 34);
}
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 2);
Assert.AreEqual("CNTDYSDCIHEAIK", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - split between two precursors", 35);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen();
// RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.PrevNode);
WaitForGraphs();
ClickChromatogram("DIA_Pit01", 75.3468, 104968093, PaneKey.PRODUCTS);
TreeNode selectedNode = null;
RunUI(() => selectedNode = SkylineWindow.SequenceTree.SelectedNode);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.PrevNode);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = selectedNode);
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.Top = SkylineWindow.Top;
transitionSettingsUI.Left = SkylineWindow.Left - transitionSettingsUI.Width - 20;
});
var isolationSchemeForm = ShowDialog <EditIsolationSchemeDlg>(transitionSettingsUI.EditCurrentIsolationScheme);
RunUI(() =>
{
isolationSchemeForm.Top = SkylineWindow.Bottom - isolationSchemeForm.Height - 34;
isolationSchemeForm.Left = SkylineWindow.Left + 40;
isolationSchemeForm.Width = 400;
});
var isolationSchemeGraph = ShowDialog <DiaIsolationWindowsGraphForm>(isolationSchemeForm.OpenGraph);
RunUI(() =>
{
isolationSchemeGraph.Height -= 58;
isolationSchemeGraph.Top = SkylineWindow.Bottom - isolationSchemeGraph.Height;
isolationSchemeGraph.Left = SkylineWindow.Left;
isolationSchemeGraph.Width = 480;
});
TakeCoverShot();
OkDialog(isolationSchemeGraph, isolationSchemeGraph.CloseButton);
OkDialog(isolationSchemeForm, isolationSchemeForm.OkDialog);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
return;
}
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
SkylineWindow.SelectedPath = ((SrmTreeNode)SkylineWindow.SelectedNode.Nodes[0]).Path;
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - double charged precursor", 36);
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 3);
Assert.AreEqual("ELVYETVR", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
});
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSpectrum>("Library Match view - zoom manually", 37);
RestoreViewOnScreen(39);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 38);
if (IsFullImportMode)
{
RestoreViewOnScreen(40);
ClickChromatogram(41.9, 1.166E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing precursor interference - zoom manually", 39);
RunUI(() => SkylineWindow.GraphFullScan.ChangeScan(-12));
CheckFullScanSelection(41.7, 1.532E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing transition between interference and real peak - zoom manually", 39);
}
// Clear all the settings lists that were defined in this tutorial
ClearSettingsLists();
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
foreach (var searchFile in searchFiles)
{
Assert.IsTrue(File.Exists(searchFile), string.Format("File {0} does not exist.", searchFile));
}
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
// Sanity check here, because of failure getting both files for results import below
var searchNames = importPeptideSearchDlg.BuildPepSearchLibControl.SearchFilenames;
Assert.AreEqual(searchFiles.Length, searchNames.Length,
PathsMessage("Unexpected search files found.", searchNames));
var builder = importPeptideSearchDlg.BuildPepSearchLibControl.ImportPeptideSearch.GetLibBuilder(
SkylineWindow.DocumentUI, SkylineWindow.DocumentFilePath, false);
Assert.IsTrue(ArrayUtil.EqualsDeep(searchFiles, builder.InputFiles),
PathsMessage("Unexpected BlibBuild input files.", builder.InputFiles));
importPeptideSearchDlg.BuildPepSearchLibControl.DebugMode = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
var ambiguousDlg = ShowDialog <MessageDlg>(() => importPeptideSearchDlg.ClickNextButton());
RunUI(() => AssertEx.Contains(ambiguousDlg.Message,
Resources.BiblioSpecLiteBuilder_AmbiguousMatches_The_library_built_successfully__Spectra_matching_the_following_peptides_had_multiple_ambiguous_peptide_matches_and_were_excluded_));
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// Verify input paths sent to BlibBuild
string buildArgs = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildCommandArgs;
string buildOutput = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildOutput;
var argLines = buildArgs.Split(new[] { Environment.NewLine }, StringSplitOptions.None);
var dirCommon = PathEx.GetCommonRoot(searchFiles);
var searchLines = searchFiles.Select(f => PathEx.RemovePrefix(f, dirCommon)).ToArray();
Assert.IsTrue(ArrayUtil.EqualsDeep(searchLines, argLines.Skip(1).ToArray()), buildArgs);
// Verify resulting .blib file contains the expected files
var docLib = librarySettings.Libraries[0];
int expectedFileCount = searchFiles.Length;
int expectedRedundantSpectra = 813; // 446 with TiTip only
int expectedSpectra = 552; // 428 with TiTip3 only
if (expectedFileCount != docLib.FileCount)
{
var searchFileNames = searchFiles.Select(Path.GetFileName).ToArray();
using (var blibDbRedundant = BlibDb.OpenBlibDb(redundantDocLibPath))
{
VerifyLib(searchFileNames, expectedRedundantSpectra, blibDbRedundant.GetIdFilePaths(), blibDbRedundant.GetSpectraCount(),
"redundant library", buildArgs, buildOutput);
}
using (var blibDb = BlibDb.OpenBlibDb(docLibPath))
{
VerifyLib(searchFileNames, expectedSpectra, blibDb.GetIdFilePaths(), blibDb.GetSpectraCount(),
"SQLite library", buildArgs, buildOutput);
}
VerifyLib(searchFileNames, expectedSpectra, docLib.LibraryDetails.DataFiles.Select(d => d.IdFilePath).ToArray(), docLib.SpectrumCount,
"in memory", buildArgs, buildOutput);
}
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page &&
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count > 0 &&
importPeptideSearchDlg.IsNextButtonEnabled);
// Wait for extra for both source files in the list
TryWaitForConditionUI(10 * 1000, () => importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count == searchFiles.Length);
RunUI(() =>
{
// Check for missing files
var missingFiles = importPeptideSearchDlg.ImportResultsControl.MissingResultsFiles.ToArray();
Assert.AreEqual(0, missingFiles.Length,
PathsMessage("Unexpected missing file found.", missingFiles));
// Check for expected results files
var resultsNames = importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Select(f => f.Name).ToArray();
Assert.AreEqual(searchFiles.Length, importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count,
PathsMessage("Unexpected results files found.", resultsNames));
// Check for expected common prefix
var commonPrefix = ImportResultsDlg.GetCommonPrefix(resultsNames);
Assert.IsFalse(string.IsNullOrEmpty(commonPrefix),
PathsMessage("File names do not have a common prefix.", resultsNames));
Assert.AreEqual("100803_000", commonPrefix);
});
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 6);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 7);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 9);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 12);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
var allChromGraph = WaitForOpenForm <AllChromatogramsGraph>();
RunUI(() =>
{
allChromGraph.Left = SkylineWindow.Right + 20;
allChromGraph.Activate();
});
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 13);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <AddModificationsDlg>("Add mods alert", 14);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 15);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
const int skylineWindowWidth = 1160;
const int skylineWindowHeight = 792;
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = skylineWindowHeight;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 16);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
RunUI(() =>
{
SkylineWindow.Width = 500;
var peakAreas = SkylineWindow.GraphPeakArea;
var peakAreasFloating = peakAreas.Parent.Parent;
peakAreasFloating.Left = SkylineWindow.Right + 20;
peakAreasFloating.Top = SkylineWindow.Top;
peakAreasFloating.Size = new Size(504, 643);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 18);
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 19);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
const int skylineWindowNarrowWidth = 788;
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
alignmentForm.Width = 660;
alignmentForm.Height = 561;
alignmentForm.Left = SkylineWindow.Right + 20;
alignmentForm.Splitter.SplitterDistance = 75;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 22);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 23);
const string TIP_NAME = "5b_MCF7_TiTip3";
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
ClickChromatogram(TIP_NAME, 34.5, 366);
TreeNode selectedNode = null;
RunUI(() => selectedNode = SkylineWindow.SequenceTree.SelectedNode);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = selectedNode);
TakeCoverShot();
return;
}
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 31.8, 42.2, 280); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 25);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 26, "Transition pick list unfiltered", 26); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 42.2, 520); // set the view for screenshot
RunUI(() =>
{
SkylineWindow.Height = 550;
SkylineWindow.ArrangeGraphsTabbed();
});
ActivateReplicate(TIP_NAME);
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
ActivateReplicate(TIP_NAME);
ClickChromatogram(TIP_NAME, 37.3, 142);
PauseForScreenShot("MS1 spectrum graph 37.32 minutes", 28);
ClickChromatogram(TIP_NAME, 33.2, 328.1);
PauseForScreenShot("MS1 spectrum graph 33.19 minutes", 29);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
SkylineWindow.ArrangeGraphs(DisplayGraphsType.Column);
});
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11, 300); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 31);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 31);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 32);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 33);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
if (IsPauseForScreenShots)
{
RestoreViewOnScreen(34);
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 34);
}
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 34);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
// page 36 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = GetGraphChromatogram(TIP3).GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = 720;
});
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 35);
ClickChromatogram(TIP_NAME, 37.5, 1107.3);
PauseForScreenShot("MS1 spectrum graph 37.50 minutes", 36);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(true);
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
});
RestoreViewOnScreen(36); // float the Library Match window
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 37);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 37);
RestoreViewOnScreen(37); // back to normal view
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 38);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 39); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
doc = WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
// CONSIDER: This refinement seems to be a no-op. Not sure why it is here.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // This would get rid of proteins with no peptides (none exist)
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio; // This would get rid of undetected transitions (none exist)
dlg.OkDialog(); // Will not change the document or add an Undo entry
});
// Nothing should have changed on the UI thread
RunUI(() => Assert.AreSame(doc, SkylineWindow.DocumentUI));
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
// Because this was showing up in the nightly test failures
WaitForConditionUI(() => exportMethodDlg.IsDisposed);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
// Creating a MS/MS Spectral Library, p. 1
PeptideSettingsUI peptideSettingsUI = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg<BuildLibraryDlg>(peptideSettingsUI.ShowBuildLibraryDlg, buildLibraryDlg =>
{
buildLibraryDlg.LibraryPath = TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\"); // Not L10N
buildLibraryDlg.LibraryName = YEAST_ATLAS;
buildLibraryDlg.LibraryCutoff = 0.95;
buildLibraryDlg.OkWizardPage();
IList<string> inputPaths = new List<string>
{
TestFilesDirs[0].GetTestPath(@"MethodEdit\Yeast_atlas\interact-prob.pep.xml") // Not L10N
};
buildLibraryDlg.AddInputFiles(inputPaths);
buildLibraryDlg.OkWizardPage();
});
PeptideSettingsUI peptideSettingsUI1 = peptideSettingsUI;
RunUI(() =>
{
peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI1.PickedLibraries = new[] { YEAST_ATLAS };
});
WaitForOpenForm<PeptideSettingsUI>(); // To show Library tab for Forms testing
PauseForScreenShot<PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 4); // Not L10N
RunUI(() => peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Digest);
WaitForOpenForm<PeptideSettingsUI>(); // To show Digestion tab for Forms testing
// Creating a Background Proteome File, p. 3
FileEx.SafeDelete(TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast" + ProteomeDb.EXT_PROTDB)); // Not L10N
var buildBackgroundProteomeDlg =
ShowDialog<BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg);
RunUI(() =>
{
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast"; // Not L10N
buildBackgroundProteomeDlg.CreateDb(TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast" + ProteomeDb.EXT_PROTDB)); // Not L10N
});
AddFastaToBackgroundProteome(buildBackgroundProteomeDlg, TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\sgd_yeast.fasta"), 61);
RunUI(buildBackgroundProteomeDlg.SelToEndBackgroundProteomePath);
PauseForScreenShot<BuildBackgroundProteomeDlg>("Edit Background Proteome form", 5); // Not L10N
OkDialog(buildBackgroundProteomeDlg, buildBackgroundProteomeDlg.OkDialog);
PauseForScreenShot<PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 6); // Not L10N
var docB = SkylineWindow.Document;
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChange(docB);
if (!TryWaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0))
{
Assert.Fail("Timed out loading libraries: libCount={0}, NotLoadedExplained={1}",
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count,
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsNotLoadedExplained ?? "<null>");
}
// Wait a bit in case web access is turned on and backgroundProteome is actually resolving protein metadata
int millis = (AllowInternetAccess ? 300 : 60) * 1000;
WaitForConditionUI(millis, () =>
SkylineWindow.DocumentUI.Settings.HasBackgroundProteome &&
!SkylineWindow.DocumentUI.Settings.PeptideSettings.BackgroundProteome.NeedsProteinMetadataSearch,
() => "backgroundProteome.NeedsProteinMetadataSearch");
WaitForConditionUI(() => SkylineWindow.DocumentUI.RevisionIndex == 3);
// FASTA paste will happen on the UI thread
RunUI(() =>
{
// Really truly fully loaded?
var allDescriptions = SkylineWindow.DocumentUI.NonLoadedStateDescriptionsFull.ToArray();
if (allDescriptions.Length > 0)
Assert.Fail(TextUtil.LineSeparate("Document not fully loaded:", TextUtil.LineSeparate(allDescriptions)));
// Should have been 3 changes: 1. peptide settings, 2. library load, 3. background proteome completion
AssertEx.IsDocumentState(SkylineWindow.DocumentUI, 3, 0, 0, 0, 0);
});
// Pasting FASTA Sequences, p. 5
RunUI(() => SetClipboardFileText(@"MethodEdit\FASTA\fasta.txt")); // Not L10N
// New in v0.7 : Skyline asks about removing empty proteins.
using (new CheckDocumentState(35, 25, 25, 75, null, true))
// using (new ImportFastaDocChangeLogger()) // Log any unexpected document changes (i.e. changes not due to import fasta)
{
var emptyProteinsDlg = ShowDialog<EmptyProteinsDlg>(SkylineWindow.Paste);
RunUI(() => emptyProteinsDlg.IsKeepEmptyProteins = true);
OkDialog(emptyProteinsDlg, emptyProteinsDlg.OkDialog);
WaitForCondition(millis, () => SkylineWindow.SequenceTree.Nodes.Count > 4);
}
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[3].Nodes[0];
SkylineWindow.Size = new Size(1035, 511);
});
RestoreViewOnScreen(07);
PauseForScreenShot("Main window", 7); // Not L10N
RunUI(() =>
{
Settings.Default.ShowBIons = true;
SkylineWindow.SequenceTree.SelectedNode.Expand();
SkylineWindow.SequenceTree.SelectedNode =
SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[1];
});
PauseForScreenShot("Main window showing effect of selection on Library Match graph", 8); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 3); // Not L10N
using (new CheckDocumentState(35, 28, 31, 155, null, true))
{
var transitionSettingsUI = ShowDialog<TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2, 3"; // Not L10N
transitionSettingsUI.ProductCharges = "1"; // Not L10N
transitionSettingsUI.FragmentTypes = "y, b"; // Not L10N
});
WaitForOpenForm<TransitionSettingsUI>(); // To show Filter tab for Forms testing
PauseForScreenShot<TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9); // Not L10N
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonCount = 5;
});
PauseForScreenShot<TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 10); // Not L10N
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
PauseForScreenShot("Targets tree clipped from main window", 11); // Not L10N
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.SpectrumFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RestoreCoverViewOnScreen(false);
RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SelectedNode.Parent.Parent.Parent);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.PrevNode);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SelectedNode.NextNode);
TakeCoverShot();
return;
}
CheckTransitionCount("VDIIANDQGNR", 5); // Not L10N
// Using a Public Spectral Library, p. 9
peptideSettingsUI = ShowDialog<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog<EditListDlg<SettingsListBase<LibrarySpec>, LibrarySpec>>(peptideSettingsUI.EditLibraryList);
var addLibUI = ShowDialog<EditLibraryDlg>(editListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(YEAST_GPM, TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\yeast_cmp_20.hlf"))); // Not L10N
OkDialog(addLibUI, addLibUI.OkDialog);
WaitForClosedForm(addLibUI);
OkDialog(editListUI, editListUI.OkDialog);
// Limiting Peptides per Protein, p. 11
using (new CheckDocumentState(35, 182, 219, 1058, null, true))
{
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI.PickedLibraries = new[] {YEAST_ATLAS, YEAST_GPM};
});
PauseForScreenShot<PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 12); // Not L10N
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
Assert.IsTrue(WaitForCondition(
() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
}
using (new CheckDocumentState(35, 47, 47, 223, 2, true)) // Wait for change loaded, and expect 2 document revisions.
{
RunDlg<PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUI2 =>
{
peptideSettingsUI2.PickedLibraries = new[] {YEAST_GPM};
peptideSettingsUI2.LimitPeptides = true;
peptideSettingsUI2.RankID = XHunterLibSpec.PEP_RANK_EXPECT;
peptideSettingsUI2.PeptidesPerProtein = 3;
peptideSettingsUI2.OkDialog();
});
}
using (new CheckDocumentState(19, 47, 47, 223, null, true))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {MinPeptidesPerProtein = 1};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Protein List, p. 11
using (new CheckDocumentState(36, 58, 58, 278, null, true))
{
PasteDlg pasteProteinsDlg = ShowDialog<PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = node;
SetClipboardFileText(@"MethodEdit\FASTA\Protein list.txt"); // Not L10N
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
PauseForScreenShot<PasteDlg.ProteinListTab>("Insert Protein List - For Screenshot, select last (empty) item in list", 14); // Not L10N
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
}
using (new CheckDocumentState(24, 58, 58, 278, null, true))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {MinPeptidesPerProtein = 1};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Wait for protein metadata again to avoid changes during paste
WaitForProteinMetadataBackgroundLoaderCompleted(millis);
// Inserting a Peptide List, p. 13
using (new CheckDocumentState(25, 70, 70, 338, null, true))
// using (new ImportFastaDocChangeLogger()) // Log any unexpected document changes (i.e. changes not due to import fasta)
{
RunUI(() =>
{
SetClipboardFileText(@"MethodEdit\FASTA\Peptide list.txt"); // Not L10N
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.Paste();
});
}
RunUI(() => SkylineWindow.SequenceTree.Nodes[0].Text = @"Primary Peptides");
FindNode("TLTAQSMQNSTQSAPNK"); // Not L10N
PauseForScreenShot("Main window", 16); // Not L10N
using (new CheckDocumentState(35, 70, 70, 338, null, true))
{
RunUI(() => SkylineWindow.Undo());
PasteDlg pastePeptidesDlg = ShowDialog<PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pastePeptidesDlg.PastePeptides);
PauseForScreenShot<PasteDlg.PeptideListTab>("Insert Peptide List - For screenshot, select last (empty) line in list", 17); // Not L10N
OkDialog(pastePeptidesDlg, pastePeptidesDlg.OkDialog);
}
// Simple Refinement, p. 16
var findPeptideDlg = ShowDialog<FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() => findPeptideDlg.SearchString = "IPEE"); // Not L10N
OkDialog(findPeptideDlg, () =>
{
findPeptideDlg.FindNext();
findPeptideDlg.Close();
});
PauseForScreenShot<GraphSpectrum>("Library Match graph metafile", 18); // Not L10N
using (new CheckDocumentState(35, 64, 64, 320, null, true))
{
RefineDlg refineDlg = ShowDialog<RefineDlg>(SkylineWindow.ShowRefineDlg);
PauseForForm(typeof(RefineDlg.DocumentTab));
RunUI(() => refineDlg.MinTransitions = 5);
OkDialog(refineDlg, refineDlg.OkDialog);
PauseForScreenShot("29/35 prot 50/64 pep 50/64 prec 246/320 tran", 18); // Not L10N
}
// Checking Peptide Uniqueness, p. 18
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 2];
SkylineWindow.SequenceTree.SelectedNode = node;
});
using (new CheckDocumentState(34, 63, 63, 315, null, true))
{
var uniquePeptidesDlg = ShowDialog<UniquePeptidesDlg>(SkylineWindow.ShowUniquePeptidesDlg);
WaitForConditionUI(() => uniquePeptidesDlg.GetDataGridView().RowCount == 1);
RunUI(() =>
{
Assert.AreEqual(1, uniquePeptidesDlg.GetDataGridView().RowCount);
Assert.AreEqual(7, uniquePeptidesDlg.GetDataGridView().ColumnCount);
});
PauseForScreenShot<UniquePeptidesDlg>("Unique Peptides form", 19); // Not L10N
var oldDoc = SkylineWindow.Document;
OkDialog(uniquePeptidesDlg, uniquePeptidesDlg.OkDialog);
RunUI(() => Assert.AreSame(oldDoc, SkylineWindow.DocumentUI));
RunUI(() => SkylineWindow.EditDelete());
}
// Protein Name Auto-Completion
PauseForScreenShot("(fig. 1): For screenshot, click at bottom of document tree, type 'ybl087' and see the autocomplete text. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("ybl087", 0); // Not L10N
var peptideGroups = new List<PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YBL087C", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Protein Description Auto-Completion
PauseForScreenShot("(fig. 2): For screenshot, click at bottom of document tree, type 'eft2' and see the autocomplete text, then down-arrow twice. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("eft2", 0); // Sorting logic puts this at the 0th entry in the list - Not L10N
peptideGroups = new List<PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YDR385W", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Peptide Sequence Auto-Completion, p. 21
TestAutoComplete("IQGP", 0); // Not L10N
var peptides = new List<PeptideDocNode>(Program.ActiveDocument.Peptides);
Assert.AreEqual("K.AYLPVNESFGFTGELR.Q [769, 784]", peptides[peptides.Count - 1].Peptide.ToString()); // Not L10N
PauseForScreenShot("(fig. 1) - For screenshot, click at the bottom of the document tree", 21); // Not L10N
// Pop-up Pick-Lists, p. 21
using (new CheckDocumentState(36, 71, 71, 355, null, true))
{
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 3];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(8, true);
pickList.AutoManageChildren = false; // TODO: Because calling SetItemChecked does not do this
});
PauseForScreenShot<PopupPickList>("(fig. 2) - YBL087C Peptides picklist", 21); // Not L10N
RunUI(pickList.OnOk);
}
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
SkylineWindow.SequenceTree.Nodes[34].ExpandAll();
var node =
SkylineWindow.SequenceTree.Nodes[34].Nodes[0].Nodes[0];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList1 = ShowDialog<PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.SearchString = "y"; // Not L10N
pickList1.SetItemChecked(0, false);
pickList1.SetItemChecked(1, false);
pickList1.ApplyFilter(false);
pickList1.ToggleFind();
pickList1.SearchString = "b ++"; // Not L10N
pickList1.SetItemChecked(4, true);
pickList1.SetItemChecked(6, true);
});
PauseForScreenShot<PopupPickList>("b ++ filtered picklist", 22); // Not L10N
RunUI(pickList1.OnOk);
}
// Bigger Picture, p. 22. Drag and Drop, p. 23
RunUI(() =>
{
ITipProvider nodeTip = SkylineWindow.SequenceTree.SelectedNode as ITipProvider;
Assert.IsTrue(nodeTip != null && nodeTip.HasTip);
var nodeName = SkylineWindow.SequenceTree.Nodes[1].Name;
IdentityPath selectPath;
SkylineWindow.ModifyDocument("Drag and drop", // Not L10N
doc => doc.MoveNode(SkylineWindow.Document.GetPathTo(0, 1), SkylineWindow.Document.GetPathTo(0, 0), out selectPath));
Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Name == nodeName);
});
FindNode(string.Format("L [b5] - {0:F04}+", 484.3130)); // Not L10N - may be localized " (rank 3)"
ShowNodeTip("YBL087C");
ShowNodeTip(string.Format("{0:F04}+++", 672.6716));
ShowNodeTip(null);
PauseForScreenShot("For Screenshots, First hover over YBL087C, then over 672.671+++", 23); // Not L10N
// Preparing to Measure, p. 25
RunDlg<TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction), transitionSettingsUI =>
{
transitionSettingsUI.RegressionCE = Settings.Default.GetCollisionEnergyByName("SCIEX"); // Not L10N
transitionSettingsUI.RegressionDP = Settings.Default.GetDeclusterPotentialByName("SCIEX"); // Not L10N
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument(TestFilesDirs[0].GetTestPath("MethodEdit Tutorial.sky"))); // Not L10N
var exportDialog = ShowDialog<ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportDialog.ExportStrategy = ExportStrategy.Buckets;
exportDialog.MethodType = ExportMethodType.Standard;
exportDialog.OptimizeType = ExportOptimize.NONE;
exportDialog.IgnoreProteins = true;
exportDialog.MaxTransitions = 75;
});
PauseForScreenShot<ExportMethodDlg.TransitionListView>("Export Transition List form", 25); // Not L10N
const string basename = "Yeast_list"; // Not L10N
OkDialog(exportDialog, () => exportDialog.OkDialog(TestFilesDirs[0].GetTestPath(basename))); // write Yeast_list_000n.csv
// check the output files
for (int n = 0; n++ < 5;)
{
var csvname = String.Format("{0}_{1}.csv", basename, n.ToString("D4")); // Not L10N
// AssertEx.FieldsEqual is hard-coded with CultureInfo.InvariantCulture, but so is transition list CSV export, so OK
using (TextReader actual = new StreamReader(TestFilesDirs[0].GetTestPath(csvname)))
using (TextReader target = new StreamReader(TestFilesDirs[1].GetTestPath(csvname)))
{
AssertEx.FieldsEqual(target, actual, 6, null, true);
}
}
}
protected override void DoTest()
{
Settings.Default.PeakScoringModelList.Clear();
// Open the file
RunUI(() => SkylineWindow.OpenFile(GetTestPath("SRMCourse_DosR-hDP__20130501-tutorial-empty.sky"))); // Not L10N
WaitForDocumentLoaded();
// Add decoys
var generateDecoysDlg = ShowDialog <GenerateDecoysDlg>(() => SkylineWindow.ShowGenerateDecoysDlg());
RunUI(() =>
{
generateDecoysDlg.DecoysMethod = DecoyGeneration.REVERSE_SEQUENCE;
generateDecoysDlg.NumDecoys = 29;
});
PauseForScreenShot <GenerateDecoysDlg>("Add Decoy Peptides form", 2);
RunUI(generateDecoysDlg.OkDialog);
WaitForClosedForm(generateDecoysDlg);
RestoreViewOnScreen(3);
RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.Nodes[11]);
PauseForScreenShot("Targets view clipped from main window", 3);
// Open the file with decoys
RunUI(() => SkylineWindow.OpenFile(GetTestPath("SRMCourse_DosR-hDP__20130501-tutorial-empty-decoys.sky"))); // Not L10N
WaitForDocumentLoaded();
// Import the raw data
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg.RadioAddNewChecked = true;
var path = new KeyValuePair <string, MsDataFileUri[]> [5];
for (int i = 0; i < 5; ++i)
{
path[i] = new KeyValuePair <string, MsDataFileUri[]>(_importFiles[i],
new[] { MsDataFileUri.Parse(GetTestPath(_importFiles[i] + ExtAbWiff)) });
}
importResultsDlg.NamedPathSets = path;
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common prefix form", 4);
RunUI(() =>
{
string prefix = importResultsNameDlg.Prefix;
importResultsNameDlg.Prefix = prefix.Substring(0, prefix.Length - 1);
importResultsNameDlg.YesDialog();
});
WaitForClosedForm(importResultsNameDlg);
WaitForClosedForm(importResultsDlg);
WaitForConditionUI(5 * 60 * 1000, () =>
SkylineWindow.DocumentUI.Settings.HasResults &&
SkylineWindow.DocumentUI.Settings.MeasuredResults.IsLoaded); // 5 minutes
RestoreViewOnScreen(5);
const string peptideSeqHighlight = "LPDGNGIELCR";
RunUI(() =>
{
var nodeGroup = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[71];
Assert.AreEqual(nodeGroup.TransitionGroup.Peptide.Sequence, peptideSeqHighlight);
var chromGroupInfo = nodeGroup.ChromInfos.ToList()[0];
Assert.IsNotNull(chromGroupInfo.RetentionTime);
// TODO: Fix the tutorial. This was supposed to be an incorrectly picked peak, but our default scoring is now good enough to pick it correctly
Assert.AreEqual(chromGroupInfo.RetentionTime.Value, 18.0, 0.1);
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.LARGE;
dlg.OkDialog();
});
PauseForScreenShot("Main window", 5);
// Test different point types on RTLinearRegressionGraph
RunUI(() =>
{
SkylineWindow.ShowRTRegressionGraphScoreToRun();
SkylineWindow.ShowPlotType(PlotTypeRT.correlation);
SkylineWindow.ChooseCalculator("iRT_SRMAtlas_20121202_noLGG");
});
const int numDecoys = 30;
CheckPointsTypeRT(PointsTypeRT.targets, SkylineWindow.Document.PeptideCount - numDecoys);
CheckPointsTypeRT(PointsTypeRT.standards, SkylineWindow.Document.GetRetentionTimeStandards().Count);
CheckPointsTypeRT(PointsTypeRT.decoys, numDecoys);
RunUI(() => SkylineWindow.ShowGraphRetentionTime(false));
WaitForDocumentLoaded();
// Train the peak scoring model
var reintegrateDlg = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
PauseForScreenShot <ReintegrateDlg>("Reintegrate form", 6);
var editDlg = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlg.AddPeakScoringModel);
RunUI(() => editDlg.TrainModel());
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form trained model", 6);
RunUI(() => Assert.AreEqual(0.5926, editDlg.PeakCalculatorsGrid.Items[3].PercentContribution ?? 0, 0.005));
RunUI(() => editDlg.SelectedGraphTab = 2);
PauseForScreenShot <EditPeakScoringModelDlg.PvalueTab>("Edit Peak Scoring Model form p value graph metafile", 7);
RunUI(() => editDlg.SelectedGraphTab = 3);
PauseForScreenShot <EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph metafile", 8);
RunUI(() => editDlg.SelectedGraphTab = 1);
RunUI(() => editDlg.PeakCalculatorsGrid.SelectRow(3));
PauseForScreenShot <EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form feature score", 10);
RunUI(() =>
{
Assert.AreEqual(18, editDlg.PeakCalculatorsGrid.RowCount);
// The rows which the tutorial says are missing scores are in fact missing scores
foreach (int i in new[] { 2, 7, 8, 9, 10, 11, 13, 15 }) // MS1 scores are now missing, 19, 20, 21, 22
{
Assert.IsFalse(editDlg.IsActiveCell(i, 0));
}
editDlg.IsFindButtonVisible = true;
editDlg.FindMissingValues(2); // Retention time
editDlg.PeakScoringModelName = "test1";
});
PauseForScreenShot <EditPeakScoringModelDlg.FeaturesTab>("Edit Peak Scoring Model form find missing scores", 11);
OkDialog(editDlg, editDlg.OkDialog);
OkDialog(reintegrateDlg, reintegrateDlg.CancelDialog);
PauseForScreenShot <FindResultsForm>("Find Results view clipped from main window", 12);
// Remove the peptide with no library dot product, and train again
FindResultsForm findResultsForm = null;
var missingPeptides = new List <string> {
"LGGNEQVTR", "IPVDSIYSPVLK", "YFNDGDIVEGTIVK",
"DFDSLGTLR", "GGYAGMLVGSVGETVAQLAR", "GGYAGMLVGSVGETVAQLAR"
};
var isDecoys = new List <bool> {
false, false, false, false, false, true
};
RunUI(() =>
{
findResultsForm = FormUtil.OpenForms.OfType <FindResultsForm>().FirstOrDefault();
Assert.IsNotNull(findResultsForm);
// ReSharper disable once PossibleNullReferenceException
Assert.AreEqual(findResultsForm.ItemCount, 6);
for (int i = 0; i < 6; ++i)
{
findResultsForm.ActivateItem(i);
Assert.AreEqual(SkylineWindow.SelectedPeptideSequence, missingPeptides[i]);
if (0 < i && i < 5)
{
SkylineWindow.SetStandardType(PeptideDocNode.STANDARD_TYPE_QC);
}
}
});
RunUI(() => findResultsForm.Close());
for (int i = 0; i < 6; ++i)
{
if (!(0 < i && i < 5))
{
RemovePeptide(missingPeptides[i], isDecoys[i]);
}
}
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
var reintegrateDlgCover = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
var editModelCover = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlgCover.AddPeakScoringModel);
RunUI(() =>
{
editModelCover.Top = SkylineWindow.Top + 8;
editModelCover.Left = SkylineWindow.Right - editModelCover.Width - 8;
editModelCover.PeakScoringModelName = "SRMCourse";
editModelCover.TrainModelClick();
});
TakeCoverShot();
OkDialog(editModelCover, editModelCover.CancelDialog);
OkDialog(reintegrateDlgCover, reintegrateDlgCover.CancelDialog);
return;
}
var reintegrateDlgNew = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
var editListLibrary = ShowDialog <EditListDlg <SettingsListBase <PeakScoringModelSpec>, PeakScoringModelSpec> >(
reintegrateDlgNew.EditPeakScoringModel);
RunUI(() => editListLibrary.SelectItem("test1"));
var editDlgLibrary = ShowDialog <EditPeakScoringModelDlg>(editListLibrary.EditItem);
RunUI(() =>
{
foreach (int i in new[] { 2, 8, 9, 10, 11 })
{
Assert.IsTrue(editDlgLibrary.IsActiveCell(i, 0));
Assert.IsFalse(editDlgLibrary.PeakCalculatorsGrid.Items[i].IsEnabled);
editDlgLibrary.PeakCalculatorsGrid.Items[i].IsEnabled = true;
}
editDlgLibrary.TrainModel(true);
});
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form with library score", 13);
RunUI(() => editDlgLibrary.SelectedGraphTab = 3);
PauseForScreenShot <EditPeakScoringModelDlg.QvalueTab>("Edit Peak Scoring Model form q value graph with library score metafile", 14);
OkDialog(editDlgLibrary, editDlgLibrary.OkDialog);
// Open up the model again for editing, re-train with second best peaks and removing some scores
RunUI(() => editListLibrary.SelectItem("test1")); // Not L10N
var editDlgNew = ShowDialog <EditPeakScoringModelDlg>(editListLibrary.EditItem);
RunUI(() =>
{
Assert.IsFalse(editDlgNew.UsesSecondBest);
Assert.IsTrue(editDlgNew.UsesDecoys);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[4].IsEnabled);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[4].PercentContribution < 0);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[2].IsEnabled);
Assert.IsTrue(editDlgNew.PeakCalculatorsGrid.Items[2].PercentContribution > 0);
editDlgNew.UsesSecondBest = true;
editDlgNew.PeakCalculatorsGrid.Items[4].IsEnabled = false;
editDlgNew.PeakCalculatorsGrid.Items[2].IsEnabled = false;
editDlgNew.TrainModel(true);
// Check that these cells are still active even though they've been unchecked
Assert.IsTrue(editDlgNew.IsActiveCell(6, 0));
});
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form with second best", 15);
OkDialog(editDlgNew, editDlgNew.CancelDialog);
OkDialog(editListLibrary, editListLibrary.OkDialog);
// Apply the model to reintegrate peaks
RunUI(() =>
{
reintegrateDlgNew.ComboPeakScoringModelSelected = "test1";
reintegrateDlgNew.ReintegrateAll = true;
reintegrateDlgNew.OverwriteManual = true;
});
PauseForScreenShot <ReintegrateDlg>("Reintegrate form", 16);
OkDialog(reintegrateDlgNew, reintegrateDlgNew.OkDialog);
RunUI(() =>
{
var nodeGroup = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[70];
Assert.AreEqual(nodeGroup.TransitionGroup.Peptide.Sequence, peptideSeqHighlight);
var chromGroupInfo = nodeGroup.ChromInfos.ToList()[0];
Assert.IsNotNull(chromGroupInfo.RetentionTime);
Assert.AreEqual(18.0, chromGroupInfo.RetentionTime.Value, 0.1);
});
FindNode(peptideSeqHighlight);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile corrected peak at 18.0", 17);
// Reintegrate slightly differently, with a q value cutoff
var reintegrateDlgQ = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
RunUI(() =>
{
reintegrateDlgQ.ReintegrateAll = false;
reintegrateDlgQ.Cutoff = 0.001;
reintegrateDlgQ.OverwriteManual = true;
});
OkDialog(reintegrateDlgQ, reintegrateDlgQ.OkDialog);
PauseForScreenShot("Targets view with some null peaks clipped from main window", 17);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with no picked peak", 18);
RestoreViewOnScreen(14);
FindNode((622.3086).ToString(CultureInfo.CurrentCulture) + "++");
PauseForScreenShot("Main window with interference on transition", 19);
// Export the mProphet features
var mProphetExportDlg = ShowDialog <MProphetFeaturesDlg>(SkylineWindow.ShowMProphetFeaturesDialog);
RunUI(() => mProphetExportDlg.BestScoresOnly = true);
PauseForScreenShot <MProphetFeaturesDlg>("Export mProphet Features form", 20);
// TODO: actually write the features here using WriteFeatures
OkDialog(mProphetExportDlg, mProphetExportDlg.CancelDialog);
// Export a report
string pathReport = GetTestPath("qValues_Exported_report.csv");
const string qvalueHeader = "annotation_QValue";
string reportName = Resources.ReportSpecList_GetDefaults_Peptide_RT_Results;
var reportExportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
var manageViewsForm = ShowDialog <ManageViewsForm>(reportExportDlg.EditList);
RunUI(() => manageViewsForm.SelectView(reportName));
PauseForScreenShot <ManageViewsForm>("Edit Reports form", 21);
var customizeViewDlg = ShowDialog <ViewEditor>(manageViewsForm.EditView);
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Edit Report form", 22);
RunUI(() => customizeViewDlg.ChooseColumnsTab.AddColumn(PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Results!*.Value")
.Property(AnnotationDef.ANNOTATION_PREFIX + qvalueHeader)));
PauseForScreenShot <ViewEditor.ChooseColumnsView>("Edit Report form with selected columns", 23);
OkDialog(customizeViewDlg, customizeViewDlg.OkDialog);
OkDialog(manageViewsForm, manageViewsForm.Close);
RunUI(() => reportExportDlg.ReportName = reportName);
OkDialog(reportExportDlg, () => reportExportDlg.OkDialog(pathReport, TextUtil.CsvSeparator));
Assert.IsTrue(File.Exists(pathReport));
using (var reader = new StreamReader(pathReport))
{
string line = reader.ReadLine();
Assert.IsNotNull(line);
var fieldHeaders = line.Split(TextUtil.CsvSeparator);
const int qvalueColumnIndex = 6;
Assert.AreEqual(qvalueColumnIndex + 1, fieldHeaders.Length);
Assert.AreEqual(qvalueHeader, fieldHeaders[qvalueColumnIndex]);
int qvalueCount = 0;
while ((line = reader.ReadLine()) != null)
{
var fields = line.Split(TextUtil.CsvSeparator);
double qvalue;
if (double.TryParse(fields[qvalueColumnIndex], out qvalue))
{
qvalueCount++;
}
}
Assert.AreEqual(290, qvalueCount); // PrecursorResults field means 29 peptides * 5 replicates * 2 label types
}
// Open OpenSWATH gold standard dataset
RunUI(() => SkylineWindow.OpenFile(GetTestPath("AQUA4_Human_picked_napedro2-mod2.sky"))); // Not L10N
WaitForDocumentLoaded();
// Perform re-score of DIA data
var manageResults = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
PauseForScreenShot <ManageResultsDlg>("Manage Results form", 25);
var rescoreResultsDlg = ShowDialog <RescoreResultsDlg>(manageResults.Rescore);
PauseForScreenShot <RescoreResultsDlg>("Re-score Results form", 25);
RunUI(() => rescoreResultsDlg.Rescore(false));
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes (usually needs less, but code coverage analysis can be slow)
WaitForClosedForm(rescoreResultsDlg);
WaitForClosedForm(manageResults);
WaitForConditionUI(() => FindOpenForm <AllChromatogramsGraph>() == null);
WaitForDocumentLoaded();
// Train the peak scoring model for the DIA dataset
var reintegrateDlgDia = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
// Open the previous scoring model for use with the DIA dataset
var editListDia = ShowDialog <EditListDlg <SettingsListBase <PeakScoringModelSpec>, PeakScoringModelSpec> >(
reintegrateDlgDia.EditPeakScoringModel);
RunUI(() => editListDia.SelectItem("test1"));
var editDlgFromSrm = ShowDialog <EditPeakScoringModelDlg>(editListDia.EditItem);
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form SRM model applied to DIA data", 26);
RunUI(() =>
{
ValidateCoefficients(editDlgFromSrm, 0);
for (int j = 0; j < editDlgFromSrm.PeakCalculatorsGrid.Items.Count; ++j)
{
Assert.AreEqual(editDlgFromSrm.PeakCalculatorsGrid.Items[j].PercentContribution, null);
}
int i = 0;
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
// Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsTrue(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i++, 0));
Assert.IsFalse(editDlgFromSrm.IsActiveCell(i, 0));
});
OkDialog(editDlgFromSrm, editDlgFromSrm.CancelDialog);
OkDialog(editListDia, editListDia.CancelDialog);
// Train a new model for the DIA dataset
var editDlgDia = ShowDialog <EditPeakScoringModelDlg>(reintegrateDlgDia.AddPeakScoringModel);
RunUI(() =>
{
editDlgDia.UsesDecoys = false;
editDlgDia.UsesSecondBest = true;
editDlgDia.TrainModel();
});
RunUI(() => ValidateCoefficients(editDlgDia, 1));
PauseForScreenShot <EditPeakScoringModelDlg.ModelTab>("Edit Peak Scoring Model form DIA peak scoring dialog with second best", 27);
RunUI(() =>
{
editDlgDia.SelectedGraphTab = 1;
editDlgDia.PeakCalculatorsGrid.SelectRow(2);
editDlgDia.IsFindButtonVisible = true;
editDlgDia.FindMissingValues(2); // Retention times
editDlgDia.PeakScoringModelName = "testDIA";
});
OkDialog(editDlgDia, editDlgDia.OkDialog);
RunUI(() =>
{
reintegrateDlgDia.ReintegrateAll = true;
reintegrateDlgDia.OverwriteManual = true;
});
OkDialog(reintegrateDlgDia, reintegrateDlgDia.OkDialog);
findResultsForm = FormUtil.OpenForms.OfType <FindResultsForm>().FirstOrDefault();
Assert.IsNotNull(findResultsForm);
Assert.AreEqual(34, findResultsForm.ItemCount);
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 3);
var columnsOrdered = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Charge,Precursor RT,Precursor CE,Product m/z,Product Charge, label type
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
SmallMoleculeTransitionListColumnHeaders.adductPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
SmallMoleculeTransitionListColumnHeaders.cePrecursor,
SmallMoleculeTransitionListColumnHeaders.mzProduct,
SmallMoleculeTransitionListColumnHeaders.chargeProduct,
SmallMoleculeTransitionListColumnHeaders.labelType
}.ToList();
if (_inferredLabels)
{
columnsOrdered.Remove(SmallMoleculeTransitionListColumnHeaders.labelType);
}
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
SetCsvFileClipboardText(GetTestPath("SMTutorial_TransitionList.csv"), true);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 6, 12, 19, 21);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 5);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Amino Acid Metabolism.sky")));
using (new WaitDocumentChange(null, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath());
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
}
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// transition groups, heavy transition groups, tranistions, heavy transitions
{ "ID15656_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15658_01_WAA263_3976_020415", new[] { 12, 6, 13, 7 } },
{ "ID15659_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15661_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15662_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15663_01_WAA263_3976_020415", new[] { 11, 7, 12, 8 } },
{ "ID15664_01_WAA263_3976_020415", new[] { 11, 6, 12, 7 } },
{ "ID15739_01_WAA263_3976_020415", new[] { 10, 6, 10, 7 } },
{ "ID15740_01_WAA263_3976_020415", new[] { 12, 6, 12, 7 } },
{ "ID15740_02_WAA263_3976_020415", new[] { 11, 5, 11, 6 } },
{ "ID15740_04_WAA263_3976_020415", new[] { 12, 6, 12, 7 } },
{ "ID15741_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15741_02_WAA263_3976_020415", new[] { 12, 6, 13, 7 } }
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = new[] { 12, 7, 13, 8 }
}
; // Most have this value
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 12, transitions[0], transitions[1], transitions[2], transitions[3]);
}
catch (Exception x)
{
msg = TextUtil.LineSeparate(msg, x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
}
}
}
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);
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns", 3);
if (IsPauseForScreenShots)
{
var columnsRestricted = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Product m/z,Precursor Charge,Product Charge,Precursor RT,Precursor CE
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
}.ToList();
RunUI(() =>
{
pasteDlg.SetSmallMoleculeColumns(columnsRestricted);
pasteDlg.Height = 339;
});
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsRestricted.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected columns - show Columns checklist", 4);
}
var columnsOrdered = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Charge,Precursor RT,Precursor CE,Product m/z,Product Charge
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
SetCsvFileClipboardText(GetTestPath("SMTutorial_TransitionList.csv"), true);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 6, 19, 19, 21);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 5);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Amino Acid Metabolism.sky")));
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath());
openDataSourceDialog1.SelectAllFileType(UseRawFiles
? ExtensionTestContext.ExtWatersRaw
: ExtensionTestContext.ExtMzml);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int>
{
{ "ID15655_01_WAA263_3976_020415", 21 },
{ "ID15657_01_WAA263_3976_020415", 21 },
{ "ID15658_01_WAA263_3976_020415", 21 },
{ "ID15662_01_WAA263_3976_020415", 21 },
{ "ID15740_02_WAA263_3976_020415", 19 },
{ "ID15741_01_WAA263_3976_020415", 21 },
};
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int trans;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out trans))
{
trans = 20; // Most have this value
}
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 19, 19, 0, trans, 0);
}
RestoreViewOnScreen(9);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
}
}