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()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition 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", 4);
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", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
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", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
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", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
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");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
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(AreaNormalizeToView.area_percent_view);
});
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);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
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", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
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", 11);
// Peptide Quantitification Settings p. 11
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 12);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
RunUI(() => 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 };
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);
}
PauseForScreenShot("Document grid with concentrations filled in", 13);
// View the calibration curve p. 13
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
PauseForScreenShot("View calibration curve", 14);
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 arrangeTabbedMenuItem_Click(object sender, EventArgs e)
{
SkylineWindow.ArrangeGraphsTabbed();
}
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).");
}
}
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);
}
private void TofTest()
{
// Working wih High-Resolution Mass Spectra.
// Import a new Document. High-Resolution Mass Spectra, working with TOF p22.
string newDocumentFile = GetTestPath(@"TOF\BSA_Agilent.sky");
WaitForCondition(() => File.Exists(newDocumentFile));
RunUI(() => SkylineWindow.OpenFile(newDocumentFile));
bool asSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
if (asSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
}
var docCalibrate1 = WaitForDocumentLoaded();
const int pepCount1 = 5, preCount1 = 5, tranCount1 = 30;
AssertEx.IsDocumentState(docCalibrate1, null, 1, pepCount1, preCount1, tranCount1);
// Try to import a file to show it fails.
ImportResultsDlg importResultsDlg3 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() => importResultsDlg3.NamedPathSets = importResultsDlg3.GetDataSourcePathsFileReplicates(
new[] { MsDataFileUri.Parse(GetTestPath(@"TOF\6-BSA-500fmol" + ExtAgilentRaw)) }));
var importProgress = ShowDialog <AllChromatogramsGraph>(importResultsDlg3.OkDialog);
WaitForDocumentChangeLoaded(docCalibrate1);
WaitForConditionUI(() => importProgress.Finished);
string expectedErrorFormat = Resources.NoFullScanFilteringException_NoFullScanFilteringException_To_extract_chromatograms_from__0__full_scan_settings_must_be_enabled_;
WaitForConditionUI(() => !string.IsNullOrEmpty(importProgress.Error), "Missing expected error text: " + expectedErrorFormat);
RunUI(() => AssertEx.AreComparableStrings(expectedErrorFormat, importProgress.Error, 1));
RunUI(() =>
{
importProgress.ClickClose();
SkylineWindow.Undo();
});
var document = SkylineWindow.Document;
// Fill out Transition Settings Menu
int tranCount2 = (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? (tranCount1 + preCount1 * 3) : (tranCount1 + preCount1); // No iostopes for mass-only document
using (new CheckDocumentState(1, pepCount1, preCount1, tranCount2))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
transitionSettingsUI.Peaks = 3;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
transitionSettingsUI.ProductMassAnalyzer = FullScanMassAnalyzerType.tof;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab for TOF", 28);
RunUI(() =>
{
transitionSettingsUI.RetentionTimeFilterType = RetentionTimeFilterType.none;
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 29);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
var docHighRes = WaitForDocumentChange(document);
var tranSettingsHighRes = docHighRes.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsHighRes.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.tof, tranSettingsHighRes.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsHighRes.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsHighRes.Filter.IonTypes));
RunUI(() => SkylineWindow.ExpandPrecursors());
// Assert each peptide contains 3 precursors transitions (unless this is a masses-only small molecule doc).
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
for (int i = 0; i < nodeGroup.Children.Count; i++)
{
var nodeTran = (TransitionDocNode)nodeGroup.Children[i];
if (i < ((AsSmallMoleculesTestMode == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 1 : 3))
{
Assert.AreEqual(IonType.precursor, nodeTran.Transition.IonType);
}
else
{
Assert.AreNotEqual(IonType.precursor, nodeTran.Transition.IonType);
}
}
}
RestoreViewOnScreen(30);
PauseForScreenShot("Targets View tree clipped from main window", 30);
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg2 =>
{
string[] filePaths =
{
GetTestPath(@"TOF\6-BSA-500fmol" + ExtAgilentRaw)
};
importResultsDlg2.NamedPathSets = importResultsDlg2.GetDataSourcePathsFileReplicates(filePaths.Select(MsDataFileUri.Parse));
importResultsDlg2.OkDialog();
});
WaitForDocumentChangeLoaded(docHighRes);
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(asSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
RunUI(() =>
{
SkylineWindow.CollapsePrecursors();
SkylineWindow.AutoZoomNone();
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.ShowProductTransitions();
});
RestoreViewOnScreen(31);
RunUI(() => SkylineWindow.Width = 1013);
PauseForScreenShot("Main window full gradient import of high concentration and Targets tree clipped", 31);
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
Assert.IsTrue(peptideSettingsUI.IsUseMeasuredRT);
Assert.AreEqual(2.0, peptideSettingsUI.TimeWindow);
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 32);
OkDialog(peptideSettingsUI, peptideSettingsUI.CancelDialog);
}
using (new CheckDocumentState(1, pepCount1, preCount1, tranCount2))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.scheduling_windows, 1);
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab wtih scheduled extraction", 33);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
var chooseSchedulingReplicateDlg = ShowDialog <ChooseSchedulingReplicatesDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
// Make sure UI is up to date to avoid race condition
chooseSchedulingReplicateDlg.UpdateUi();
chooseSchedulingReplicateDlg.SelectOrDeselectAll(true);
});
RunDlg <ImportResultsDlg>(chooseSchedulingReplicateDlg.OkDialog, importResultsDlg2 =>
{
string[] filePaths =
{
GetTestPath(@"TOF\1-BSA-50amol" + ExtAgilentRaw),
GetTestPath(@"TOF\2-BSA-100amol" + ExtAgilentRaw),
GetTestPath(@"TOF\3-BSA-1fmol" + ExtAgilentRaw),
GetTestPath(@"TOF\4-BSA-10fmol" + ExtAgilentRaw),
GetTestPath(@"TOF\5-BSA-100fmol" + ExtAgilentRaw),
};
importResultsDlg2.NamedPathSets = importResultsDlg2.GetDataSourcePathsFileReplicates(filePaths.Select(MsDataFileUri.Parse));
importResultsDlg2.OkDialog();
});
//Give the Raw files some time to be processed.
WaitForCondition(15 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 15 minutes
WaitForClosedAllChromatogramsGraph();
RunUI(() => SkylineWindow.ShowGraphSpectrum(false));
WaitForGraphs();
TryWaitForConditionUI(() => SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden) == 6);
RunUI(() =>
{
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
var listGraphs = SkylineWindow.GraphChromatograms.Where(graphChrom => !graphChrom.IsHidden).ToList();
if (listGraphs.Count != 6)
{
string hiddenGraphs = string.Empty;
var listHidden = SkylineWindow.GraphChromatograms.Where(graphChrom => graphChrom.IsHidden).ToList();
if (listHidden.Count != 0)
{
hiddenGraphs = TextUtil.LineSeparate(string.Empty, "Hidden:", TextUtil.LineSeparate(listHidden.Select(g => g.TabText)));
}
Assert.Fail(TextUtil.LineSeparate(string.Format("Expecting 6 visible graphs but found {0}", listGraphs.Count),
TextUtil.LineSeparate(listGraphs.Select(g => g.TabText)), hiddenGraphs));
}
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(6, chromGraphs.Length);
});
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, dlg =>
{
for (int i = 0; i < 5; i++)
{
dlg.MoveDown();
}
dlg.OkDialog();
});
RunDlg <ArrangeGraphsGroupedDlg>(SkylineWindow.ArrangeGraphsGrouped, dlg =>
{
dlg.Groups = 6;
dlg.GroupOrder = GroupGraphsOrder.Document;
dlg.OkDialog();
});
WaitForGraphs();
RunUI(() => SkylineWindow.Height = 768);
PauseForScreenShot("Chromatogram graphs clipped from main window", 34);
RunUI(() =>
{
var graphChrom6 = SkylineWindow.GetGraphChrom("6-BSA-500fmol");
var graphChrom5 = SkylineWindow.GetGraphChrom("5-BSA-100fmol");
var graphChrom4 = SkylineWindow.GetGraphChrom("4-BSA-10fmol");
var graphChrom3 = SkylineWindow.GetGraphChrom("3-BSA-1fmol");
var graphChrom2 = SkylineWindow.GetGraphChrom("2-BSA-100amol");
var graphChrom1 = SkylineWindow.GetGraphChrom("1-BSA-50amol");
Assert.AreEqual(13.3, graphChrom6.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.5, graphChrom5.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom4.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom3.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom2.BestPeakTime ?? 0, 0.05);
Assert.AreEqual(13.6, graphChrom1.BestPeakTime ?? 0, 0.05);
});
RunUI(SkylineWindow.AutoZoomBestPeak);
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window zoomed", 35);
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowPeptideLogScale(true);
});
// p. 28
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 36);
WaitForDotProducts();
RunUI(() =>
{
Assert.AreEqual((AsSmallMoleculesTestMode == RefinementSettings.ConvertToSmallMoleculesMode.none) ? 7 : 6, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
VerifyDotProducts(0.87, 0.67, 0.91, 0.90, 0.90, 0.90);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(false);
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ActivateReplicate("6-BSA-500fmol");
SkylineWindow.Size = new Size(745, 545);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graph metafile for 500 fmol", 37);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPrecursorTransitions();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ActivateReplicate("4-BSA-10fmol");
});
WaitForDotProducts();
RunUI(() =>
{
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual((AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 3 : 1, SkylineWindow.GraphPeakArea.CurveCount);
});
VerifyDotProducts(0.99, 0.52, 0.98, 1.00, 1.00, 1.00);
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(false);
SkylineWindow.Size = new Size(1013, 768);
});
PauseForScreenShot("Main window", 38);
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 39);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition 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", 4);
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", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
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", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
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", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
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");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
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(AreaNormalizeToView.area_percent_view);
});
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);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
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", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
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", 11);
const int columnsToAddCount = 4;
var columnSeparator = TextUtil.CsvSeparator;
// Generating a Calibration Curve p. 11
var exportLiveReportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
var editReportListDlg = ShowDialog <ManageViewsForm>(exportLiveReportDlg.EditList);
const string reportName = "Peptide Ratio Results Test";
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Sequence"),
PropertyPath.Parse("Proteins!*.Name"),
PropertyPath.Parse("Replicates!*.Name"),
PropertyPath.Parse("Proteins!*.Peptides!*.Results!*.Value.RatioToStandard"),
};
Assert.AreEqual(columnsToAddCount, columnsToAdd.Length);
{
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
viewEditor.ViewName = reportName;
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(columnsToAdd.Length, viewEditor.ChooseColumnsTab.ColumnCount);
});
// TODO: MultiViewProvider not yet supported in Common
PauseForScreenShot <ViewEditor>("Edit Report form", 12);
OkDialog(viewEditor, viewEditor.OkDialog);
}
RunUI(editReportListDlg.OkDialog);
WaitForClosedForm(editReportListDlg);
RunUI(() =>
{
exportLiveReportDlg.ReportName = reportName;
exportLiveReportDlg.OkDialog(TestFilesDir.GetTestPath("Calibration.csv"), columnSeparator);
});
// Check if export file is correct.
string filePath = TestFilesDir.GetTestPath("Calibration.csv");
Assert.IsTrue(File.Exists(filePath));
string[] lines = File.ReadAllLines(filePath);
string[] line0 = lines[0].Split(columnSeparator);
int count = line0.Length;
Assert.IsTrue(lines.Count() == SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count + 1);
Assert.AreEqual(columnsToAddCount, count);
// Check export file data
double ratio1 = Double.Parse(lines[1].Split(new[] { columnSeparator }, 4)[3]);
double ratio2 = Double.Parse(lines[2].Split(new[] { columnSeparator }, 4)[3]);
double ratio3 = Double.Parse(lines[3].Split(new[] { columnSeparator }, 4)[3]);
double ratio4 = Double.Parse(lines[4].Split(new[] { columnSeparator }, 4)[3]);
double ratio5 = Double.Parse(lines[5].Split(new[] { columnSeparator }, 4)[3]);
double ratio6 = Double.Parse(lines[6].Split(new[] { columnSeparator }, 4)[3]);
double ratio7 = Double.Parse(lines[7].Split(new[] { columnSeparator }, 4)[3]);
double ratio8 = Double.Parse(lines[8].Split(new[] { columnSeparator }, 4)[3]);
double ratio9 = Double.Parse(lines[9].Split(new[] { columnSeparator }, 4)[3]);
Assert.AreEqual(21.4513, ratio1, 0.1);
Assert.AreEqual(6.2568, ratio2, 0.1);
Assert.AreEqual(2.0417, ratio3, 0.1);
Assert.AreEqual(0.8244, ratio4, 0.1);
Assert.AreEqual(0.2809, ratio5, 0.1);
Assert.AreEqual(0.1156, ratio6, 0.1);
Assert.AreEqual(0.0819, ratio7, 0.1);
Assert.AreEqual(0.0248, ratio8, 0.1);
Assert.AreEqual(0.7079, ratio9, 0.1);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
}