private void DoStudy7Test()
{
// Preparing a Document to Accept the Study 7 Transition List, p. 15
RunUI(() => SkylineWindow.NewDocument());
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var mod13Cr = new StaticMod("Label:13C(6) (C-term R)", "R", ModTerminus.C, false, null, LabelAtoms.C13,
RelativeRT.Matching, null, null, null);
AddHeavyMod(mod13Cr, peptideSettingsUI1, "Edit Isotope Modification form", 17);
RunUI(() =>
{
peptideSettingsUI1.PickedHeavyMods = new[] { "Label:13C(6) (C-term R)", HEAVY_K };
peptideSettingsUI1.PickedLibraries = new[] { "" };
peptideSettingsUI1.SelectedBackgroundProteome = Resources.SettingsList_ELEMENT_NONE_None;
peptideSettingsUI1.OkDialog();
});
// Pasting a Transition List into the Document, p. 18.
string clipboardSaveText = string.Empty;
RunUI(() =>
{
var filePath = GetTestPath(@"Study 7\Study7 transition list.xls");
SetExcelFileClipboardText(filePath, "Simple", 6, false);
clipboardSaveText = ClipboardEx.GetText();
});
{
var messageDlg = ShowDialog <ImportTransitionListErrorDlg>(SkylineWindow.Paste);
PauseForScreenShot <ImportTransitionListErrorDlg>("Error message form (expected)", 18);
OkDialog(messageDlg, messageDlg.CancelDialog);
// Restore the clipboard text after pausing
ClipboardEx.SetText(clipboardSaveText);
}
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Instrument), transitionSettingsUI =>
{
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
SkylineWindow.Paste();
SkylineWindow.CollapsePeptides();
});
PauseForScreenShot("Targets tree (selected from main window)", 19);
// Adjusting Modifications Manually, p. 19.
AdjustModifications("AGLCQTFVYGGCR", true, 'V', 747.348);
PauseForScreenShot("Target tree clipped from main window", 22);
AdjustModifications("IVGGWECEK", true, 'V', 541.763);
AdjustModifications("YEVQGEVFTKPQLWP", false, 'L', 913.974);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"Study 7\Study7.sky")));
// Importing Data from a Multiple Sample WIFF file, p. 23.
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Study 7"));
openDataSourceDialog1.SelectAllFileType(IsFullData ? ".wiff" : ExtensionTestContext.ExtAbWiff); // Force true wiff for FullData
});
if (UseRawFilesOrFullData)
{
var importResultsSamplesDlg = ShowDialog <ImportResultsSamplesDlg>(openDataSourceDialog1.Open);
PauseForScreenShot <ImportResultsSamplesDlg>("Choose Samples form", 23);
RunUI(() =>
{
if (IsFullData)
{
importResultsSamplesDlg.CheckAll(true);
importResultsSamplesDlg.ExcludeSample(0); // Blank
importResultsSamplesDlg.ExcludeSample(25); // QC
importResultsSamplesDlg.ExcludeSample(26);
importResultsSamplesDlg.ExcludeSample(27);
importResultsSamplesDlg.ExcludeSample(28);
importResultsSamplesDlg.ExcludeSample(45); // A2
importResultsSamplesDlg.ExcludeSample(46);
importResultsSamplesDlg.ExcludeSample(47);
importResultsSamplesDlg.ExcludeSample(48);
importResultsSamplesDlg.ExcludeSample(49); // gradientwash
importResultsSamplesDlg.ExcludeSample(50);
importResultsSamplesDlg.ExcludeSample(51);
importResultsSamplesDlg.ExcludeSample(52);
importResultsSamplesDlg.ExcludeSample(53); // A3
importResultsSamplesDlg.ExcludeSample(54);
importResultsSamplesDlg.ExcludeSample(55);
importResultsSamplesDlg.ExcludeSample(56);
}
else
{
importResultsSamplesDlg.CheckAll(false);
importResultsSamplesDlg.IncludeSample(1);
importResultsSamplesDlg.IncludeSample(2);
importResultsSamplesDlg.IncludeSample(11);
importResultsSamplesDlg.IncludeSample(12);
}
});
OkDialog(importResultsSamplesDlg, importResultsSamplesDlg.OkDialog);
}
else
{
RunUI(openDataSourceDialog1.Open);
}
{
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportDocResultsDlg>("Import Results Common prefix form", 24);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
}
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RestoreViewOnScreen(25);
// Inspecting and Adjusting Peak Integration, p. 24.
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowGraphRetentionTime(true);
});
if (!IsPauseForScreenShots && !IsFullData)
{
TestApplyToAll();
}
PauseForScreenShot <GraphSummary.RTGraphView>("Main window with peaks and retention times showing", 25);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
RunUI(SkylineWindow.EditDelete);
FindNode("IVGGWECEK"); // Not L10N
TransitionGroupTreeNode selNodeGroup = null;
RunUI(() =>
{
selNodeGroup = (TransitionGroupTreeNode)SkylineWindow.SequenceTree.SelectedNode.Nodes[1];
Assert.AreEqual(selNodeGroup.StateImageIndex, (int)SequenceTree.StateImageId.peak_blank);
});
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.MZMatchTolerance = 0.065;
transitionSettingsUI.OkDialog();
});
RunUI(() =>
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, selNodeGroup.StateImageIndex);
SkylineWindow.ToggleIntegrateAll();
});
RunUI(() =>
{
foreach (PeptideDocNode nodePep in SkylineWindow.Document.Molecules)
{
string sequence = nodePep.Peptide.Sequence;
int imageIndex = PeptideTreeNode.GetPeakImageIndex(nodePep, SkylineWindow.SequenceTree);
if ((sequence != null) && (sequence.StartsWith("YLA") || sequence.StartsWith("YEV"))) // Not L10N
{
Assert.AreEqual((int)SequenceTree.StateImageId.keep, imageIndex,
string.Format("Expected keep icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else if (sequence != null)
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak, imageIndex,
string.Format("Expected peak icon for the peptide {0}, found {1}", sequence, imageIndex));
}
else // Custom Ion
{
Assert.AreEqual((int)SequenceTree.StateImageId.peak_blank, imageIndex,
string.Format("Expected peak_blank icon for the custom ion {0}, found {1}", nodePep.ModifiedTarget, imageIndex));
}
}
});
PauseForScreenShot("Main window", 27);
// Data Inspection with Peak Areas View, p. 27.
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(NormalizeGraphToHeavy);
RestoreViewOnScreen(28);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 28);
FindNode((564.7746).ToString(LocalizationHelper.CurrentCulture) + "++"); // ESDTSYVSLK - Not L10N
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 29);
RunUI(SkylineWindow.ExpandPeptides);
string hgflprLight = (363.7059).ToString(LocalizationHelper.CurrentCulture) + "++"; // HGFLPR - Not L10N
FindNode(hgflprLight);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 30);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view));
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph normalized metafile", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_03"));
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile with interference", 31);
RunUI(() => SkylineWindow.ShowGraphPeakArea(true));
RunUI(() =>
{
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowTotalTransitions();
SkylineWindow.ShowCVValues(true);
SkylineWindow.ShowPeptideOrder(SummaryPeptideOrder.document);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Peptide Comparison graph metafile", 32);
// Annotating replicates with concentration values
var chooseAnnotationsDlg = ShowDialog <DocumentSettingsDlg>(SkylineWindow.ShowDocumentSettingsDialog);
var editListDlg = ShowDialog <EditListDlg <SettingsListBase <AnnotationDef>, AnnotationDef> >(chooseAnnotationsDlg.EditAnnotationList);
RunUI(editListDlg.ResetList);
var defineAnnotationDlg = ShowDialog <DefineAnnotationDlg>(editListDlg.AddItem);
RunUI(() =>
{
defineAnnotationDlg.AnnotationName = "Concentration";
defineAnnotationDlg.AnnotationType = AnnotationDef.AnnotationType.number;
defineAnnotationDlg.AnnotationTargets = AnnotationDef.AnnotationTargetSet.Singleton(AnnotationDef.AnnotationTarget.replicate);
});
PauseForScreenShot <DefineAnnotationDlg>("Define Annotation form", 33);
OkDialog(defineAnnotationDlg, defineAnnotationDlg.OkDialog);
OkDialog(editListDlg, () => editListDlg.DialogResult = DialogResult.OK);
RunUI(() => chooseAnnotationsDlg.AnnotationsCheckedListBox.SetItemChecked(0, true));
PauseForScreenShot <DocumentSettingsDlg>("Annotation Settings form", 34);
OkDialog(chooseAnnotationsDlg, chooseAnnotationsDlg.OkDialog);
RunUI(() => SkylineWindow.ShowResultsGrid(true));
RunUI(() =>
{
SkylineWindow.SelectedPath =
SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.MoleculeGroups, 0);
});
WaitForGraphs();
WaitForConditionUI(() => FindOpenForm <LiveResultsGrid>().IsComplete);
RunUI(() =>
{
Settings.Default.ResultsGridSynchSelection = false;
var resultsGrid = FindOpenForm <LiveResultsGrid>().DataGridView;
var colConcentration =
// ReSharper disable LocalizableElement
resultsGrid.Columns.Cast <DataGridViewColumn>().First(col => "Concentration" == col.HeaderText); // Not L10N
// ReSharper restore LocalizableElement
if (IsFullData)
{
float[] concentrations = { 0f, 60, 175, 513, 1500, 2760, 4980, 9060, 16500, 30000 };
for (int i = 0; i < concentrations.Length; i++)
{
for (int j = i * 4; j < (i + 1) * 4; j++)
{
SetCellValue(resultsGrid, j, colConcentration.Index, concentrations[i]);
}
}
}
else
{
SetCellValue(resultsGrid, 0, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 1, colConcentration.Index, 0f);
SetCellValue(resultsGrid, 2, colConcentration.Index, 175f);
SetCellValue(resultsGrid, 3, colConcentration.Index, 175f);
}
});
WaitForGraphs();
PauseForScreenShot <LiveResultsGrid>("Results grid with annotations (scrolled to the end)", 35);
FindNode("SSDLVALSGGHTFGK"); // Not L10N
RunUI(() =>
{
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.GroupByReplicateAnnotation("Concentration");
NormalizeGraphToHeavy();
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph with CVs metafile", 36);
RunUI(() => SkylineWindow.ShowCVValues(false));
RunUI(() => SkylineWindow.SaveDocument());
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph grouped by concentration metafile", 36);
PauseForAuditLog();
// Further Exploration, p. 33.
RunUI(() =>
{
SkylineWindow.OpenFile(GetTestPath(@"Study 7\Study II\Study 7ii (site 52).sky")); // Not L10N
SkylineWindow.ShowPeakAreaPeptideGraph();
SkylineWindow.ShowCVValues(true);
});
WaitForCondition(() => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas peptide comparison graph metafile", 37);
FindNode("LSEPAELTDAVK");
RunUI(SkylineWindow.ShowRTReplicateGraph);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times replicate graph metafile", 38);
FindNode("INDISHTQSVSAK");
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas normalized to heave graph metafile", 38);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none));
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas no normalization graph metafile", 39);
FindNode(hgflprLight);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
NormalizeGraphToHeavy();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Area Ratio to Heavy graph showing interference metafile", 40);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
RunUI(() => SkylineWindow.ActivateReplicate("E_ 03"));
WaitForGraphs();
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile showing slight interference", 40);
}
protected override void DoTest()
{
OpenDocument(@"Rat_plasma.sky");
RunUI(SkylineWindow.ShowRTReplicateGraph);
RunUI(SkylineWindow.ShowPeakAreaReplicateComparison);
SelectNode(SrmDocument.Level.MoleculeGroups, 3);
WaitForGraphs();
const int repCount = 42;
const int removedPeaks = 5;
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 3, repCount);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.bars, 3, repCount);
RunUI(() => SkylineWindow.ShowRTPeptideValue(RTPeptideValue.FWHM));
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, 3, repCount);
SelectNode(SrmDocument.Level.MoleculeGroups, 2);
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 1, repCount - removedPeaks);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, 1, repCount - removedPeaks);
SelectNode(SrmDocument.Level.Molecules, 3);
WaitForGraphs();
const int tranCount = 5;
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.bars, tranCount, repCount + 1);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks);
RunUI(() => SkylineWindow.SetAreaGraphDisplayType(AreaGraphDisplayType.lines));
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks + 1);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, repCount - removedPeaks);
RunUI(() => SkylineWindow.GroupByReplicateAnnotation("SubjectId"));
WaitForGraphs();
int subjectCount = repCount / 3;
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, subjectCount, subjectCount);
ActivateReplicate("D_103_REP1");
WaitForGraphs();
RunUI(() => SkylineWindow.RemovePeak());
ActivateReplicate("D_103_REP2");
WaitForGraphs();
RunUI(() => SkylineWindow.RemovePeak());
WaitForGraphs();
subjectCount--;
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount);
VerifyGraphState(SkylineWindow.GraphRetentionTime, AreaGraphDisplayType.lines, tranCount, subjectCount, subjectCount);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.GLOBAL_STANDARDS));
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount);
VerifyGraphYRange(SkylineWindow.GraphPeakArea, 5E-5, 2E-2, subjectCount + 1, subjectCount);
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, tranCount, subjectCount + 1, subjectCount);
VerifyGraphYRange(SkylineWindow.GraphPeakArea, 5, 50, subjectCount + 1, subjectCount);
subjectCount++;
SelectNode(SrmDocument.Level.MoleculeGroups, 13);
WaitForGraphs();
VerifyGraphState(SkylineWindow.GraphPeakArea, AreaGraphDisplayType.lines, 2, subjectCount, subjectCount);
VerifyGraphYRange(SkylineWindow.GraphPeakArea, 4E+4, 1.5E+5, subjectCount, subjectCount);
}