private void TestHistogramRatios <T>(Action showHistogram, int statsStartIndex) where T : SummaryGraphPane
{
RunUI(() =>
{
showHistogram();
SkylineWindow.SetAreaCVPointsType(PointsTypePeakArea.targets);
SkylineWindow.SetNormalizationMethod(NormalizeOption.RatioToFirstStandard(SkylineWindow.Document.Settings));
});
WaitForGraphs();
var graph = SkylineWindow.GraphPeakArea;
var toolbar = graph.Toolbar as AreaCVToolbar;
Assert.IsNotNull(toolbar);
RunUI(() => toolbar.SetMinimumDetections(2));
OpenAndChangeAreaCVProperties(graph, p => p.QValueCutoff = double.NaN);
// Make sure toolbar is there, combo box items are correct and data is correct
T pane;
Assert.IsTrue(graph.TryGetGraphPane(out pane));
Assert.IsTrue(pane.HasToolbar);
CollectionAssert.AreEqual(new[] { NormalizeOption.DEFAULT.Caption, "Light", "Heavy", "All 15N", NormalizationMethod.EQUALIZE_MEDIANS.NormalizeToCaption, NormalizationMethod.NONE.NormalizeToCaption }, toolbar.NormalizationMethods.ToArray());
AssertDataCorrect(pane, statsStartIndex++); // Light
RunUI(() => SkylineWindow.SetNormalizationMethod(NormalizeOption.FromIsotopeLabelType(SkylineWindow.Document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[1])));
WaitForGraphs();
AssertDataCorrect(pane, statsStartIndex++); // Heavy
RunUI(() => SkylineWindow.SetNormalizationMethod(NormalizeOption.FromIsotopeLabelType(SkylineWindow.Document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[2])));
WaitForGraphs();
AssertDataCorrect(pane, statsStartIndex++, allowInvalid: true); // All 15N
}
private static void NormalizeGraphToHeavy()
{
AreaGraphController.AreaNormalizeOption = NormalizeOption.FromIsotopeLabelType(IsotopeLabelType.heavy);
Settings.Default.AreaLogScale = false;
SkylineWindow.UpdatePeakAreaGraph();
}
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);
}