// ReSharper restore AccessToModifiedClosure
protected bool ExportAndMaybeTryToCancel(ExportLiveReportDlg exportLiveReportDlg, string filename, bool tryToCancel)
{
Assert.AreSame(exportLiveReportDlg, FindOpenForm <ExportLiveReportDlg>());
bool triedToCancel = RunAndMaybeTryCancel(() => exportLiveReportDlg.OkDialog(filename, SEPARATOR_TO_USE), tryToCancel);
if (!triedToCancel)
{
return(true);
}
var remainingForm = FindOpenForm <ExportLiveReportDlg>();
if (remainingForm != null)
{
Assert.AreSame(exportLiveReportDlg, remainingForm);
return(remainingForm.DialogResult != DialogResult.None);
}
return(true);
}
private void LowResTest()
{
string documentFile = GetTestPath(@"Low Res\BSA_Protea_label_free_meth3.sky");
WaitForCondition(() => File.Exists(documentFile));
RunUI(() => SkylineWindow.OpenFile(documentFile));
bool AsSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
const int expectedMoleculeCount = 9;
int expectedTransitionGroupCount = 10;
int expectedTransitionCount = 78;
var document = SkylineWindow.Document;
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
document = SkylineWindow.Document;
Assert.AreEqual(document.PeptideTransitionGroupCount, 0);
Assert.AreEqual(document.MoleculeTransitionGroupCount, expectedTransitionGroupCount);
Assert.AreEqual(document.PeptideTransitionCount, 0);
Assert.AreEqual(document.MoleculeTransitionCount, expectedTransitionCount);
}
AssertEx.IsDocumentState(document, null, 3, expectedMoleculeCount, expectedTransitionGroupCount, expectedTransitionCount);
// p. 3 Select first peptide
RunUI(() => SkylineWindow.SelectedPath = document.GetPathTo((int)SrmDocument.Level.Molecules, 0));
PauseForScreenShot("Main window", 3);
// p. 4 Configure Document for Thermo raw files
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab blank", 5);
RunUI(() =>
{
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.qit;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab low res", 6);
RunUI(() =>
{
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 2);
// p.6 - library ion match tolerance same as extraction window
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonMatchTolerance = 0.7;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab match tolerance same as MS/MS resolution", 8);
RunUI(() =>
{
// p.6
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var docFullScan = WaitForDocumentChange(document);
var tranSettingsFullScan = docFullScan.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsFullScan.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.qit, tranSettingsFullScan.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsFullScan.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsFullScan.Filter.IonTypes));
}
RunUI(() => SkylineWindow.ExpandPrecursors());
// Check all the precursors on picklists
bool pausedForScreenShot = false;
foreach (PeptideGroupTreeNode node in SkylineWindow.SequenceTree.GetSequenceNodes())
{
foreach (TreeNode child in node.Nodes)
{
foreach (SrmTreeNodeParent grandChild in child.Nodes)
{
// Because of RunUI must copy to local variable first.
SrmTreeNodeParent child1 = grandChild;
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = child1);
var picklist = ShowDialog <PopupPickList>(() => SkylineWindow.SequenceTree.ShowPickList(false));
RunUI(() =>
{
picklist.SetItemChecked(0, true);
Assert.IsTrue(picklist.GetItemLabel(0).Contains(IonType.precursor.GetLocalizedString()));
Assert.IsTrue(picklist.GetItemChecked(0));
});
if (!pausedForScreenShot)
{
PauseForScreenShot <PopupPickList>("Transitions popup pick-list", 10);
pausedForScreenShot = true;
}
OkDialog(picklist, picklist.OnOk);
}
}
}
WaitForDocumentLoaded();
if (!AsSmallMolecules) // No libraries for small molecules, yet
{
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.IsFalse(nodeGroup.HasLibInfo && nodeGroup.Transitions.All(nodeTran => !nodeTran.HasLibInfo));
}
}
// All transition groups should now have a precursor transition
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.AreEqual(IonType.precursor, nodeGroup.Transitions.First().Transition.IonType);
}
// p.8
ExportMethodDlg exportMethodDlg =
ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.SetInstrument("Thermo LTQ");
Assert.AreEqual("Thermo LTQ", exportMethodDlg.InstrumentType);
exportMethodDlg.SetMethodType(ExportMethodType.Standard);
exportMethodDlg.SetTemplateFile(GetTestPath(@"Low Res\TargetedMSMS_template.meth"));
});
PauseForScreenShot <ExportMethodDlg.MethodView>("Export Method form", 11);
// p. 10 Ok the error box.
{
var messageDlg = ShowDialog <MessageDlg>(() => exportMethodDlg.OkDialog(GetTestPath(@"Low Res\TargetedMSMS_BSA_Protea.meth")));
PauseForScreenShot <MessageDlg>("Error message (expected)", 12);
OkDialog(messageDlg, messageDlg.OkDialog);
}
// Making a report by hand p.11
ExportLiveReportDlg exportReportDlg = ShowDialog <ExportLiveReportDlg>(() => SkylineWindow.ShowExportReportDialog());
var editReportListDlg = ShowDialog <ManageViewsForm>(exportReportDlg.EditList);
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(PropertyPath.Parse("Proteins!*.Name")));
viewEditor.ChooseColumnsTab.AddSelectedColumn();
Assert.AreEqual(1, viewEditor.ChooseColumnsTab.ColumnCount);
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.ModifiedSequence"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Charge"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Mz"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(4, viewEditor.ChooseColumnsTab.ColumnCount);
});
PauseForScreenShot <ViewEditor>("Edit Report form", 13);
{
var previewReportDlg = ShowDialog <DocumentGridForm>(viewEditor.ShowPreview);
var expectedRows = 10 + (TestSmallMolecules ? 1 : 0);
WaitForConditionUI(() => previewReportDlg.IsComplete && previewReportDlg.RowCount == expectedRows);
RunUI(() =>
{
Assert.AreEqual(4, previewReportDlg.ColumnCount);
var precursors =
SkylineWindow.Document.MoleculeTransitionGroups.ToArray();
const int precursorIndex = 3;
for (int i = 0; i < expectedRows; i++)
{
Assert.AreEqual(precursors[i].PrecursorMz, double.Parse(previewReportDlg.DataGridView.Rows[i].Cells[precursorIndex].Value.ToString()), 0.000001);
}
var precursorMzCol = previewReportDlg.DataGridView.Columns[precursorIndex];
Assert.IsNotNull(precursorMzCol);
previewReportDlg.DataGridView.Sort(precursorMzCol, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Preview New Report window", 14);
OkDialog(previewReportDlg, previewReportDlg.Close);
}
// Press the Esc key until all forms have been dismissed.
RunUI(() =>
{
viewEditor.Close();
editReportListDlg.Close();
exportReportDlg.CancelClick();
});
WaitForClosedForm(viewEditor);
WaitForClosedForm(editReportListDlg);
WaitForClosedForm(exportReportDlg);
//p. 12 Import Full-Scan Data
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
RunUI(() => importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm);
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library blank page", 15);
const int prefixLen = 35;
const string lowResDir = "Low Res";
const string searchDir = "search";
const string lowRes20Base = "klc_20100329v_Protea_Peptide_Curve_20fmol_uL_tech1";
string lowRes20File = GetTestPath(Path.Combine(lowResDir, lowRes20Base + ExtThermoRaw));
string lowRes20FileRaw = Path.ChangeExtension(lowRes20File, ExtThermoRaw);
string lowRes20Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes20Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes20FileName = (Path.GetFileNameWithoutExtension(lowRes20File) ?? "").Substring(prefixLen);
const string lowRes80Base = "klc_20100329v_Protea_Peptide_Curve_80fmol_uL_tech1";
string lowRes80File = GetTestPath(Path.Combine(lowResDir, lowRes80Base + ExtThermoRaw));
string lowRes80Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes80Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes80FileName = (Path.GetFileNameWithoutExtension(lowRes80File) ?? "").Substring(prefixLen);
string[] searchFiles = { lowRes20Search, lowRes80Search };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.99;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library with files page", 16);
RunDlg <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck, dlg => dlg.OkDialog());
doc = WaitForDocumentChangeLoaded(doc);
// 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);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search Extract Chromatograms page", 17);
// 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.
TryWaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
var correctPage = false;
ImportPeptideSearchDlg.Pages currentPage = 0;
RunUI(() => correctPage = ImportPeptideSearchDlg.Pages.chromatograms_page == (currentPage = importPeptideSearchDlg.CurrentPage));
if (!correctPage)
{
WaitForConditionUI(1, // Immediate timeout - just want the richer error message that WaitForConditionUI provides
() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page,
string.Format("Expected to be on chromatograms_page, on {0} instead", currentPage));
}
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Modifications are already set up, so that page should get skipped.
// We're on the "Configure Transition Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// We're on the "Configure Full-Scan Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
doc = WaitForDocumentChange(doc);
// Add FASTA also skipped because filter for document peptides was chosen.
WaitForClosedForm(importPeptideSearchDlg);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 18);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
WaitForClosedAllChromatogramsGraph();
expectedTransitionGroupCount = 10; // Expect this many with results
expectedTransitionCount = 87; // Expect this many with results
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes20FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes80FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.CollapsePrecursors();
SkylineWindow.Width = 1070;
});
// Select the first precursor.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
// Ensure Graphs look like p17. (checked)
WaitForGraphs();
RestoreViewOnScreen(18);
PauseForScreenShot("Main window with data imported", 19);
const double minDotp = 0.9;
foreach (var nodeGroup in SkylineWindow.Document.PeptideTransitionGroups)
{
double dotp = nodeGroup.Results[0][0].LibraryDotProduct ?? 0;
Assert.IsTrue(Math.Round(dotp, 2) >= minDotp, string.Format("Library dot-product {0} found below {1}", dotp, minDotp));
}
RunUI(() => SkylineWindow.AutoZoomBestPeak());
// Ensure Graphs look like p18. (checked)
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window with zoomed peaks", 20);
RestoreViewOnScreen(21);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(lowRes20FileRaw, 77.7722)));
PauseForScreenShot <GraphSpectrum>("Library Match view clipped from main window with noisy spectrum", 21);
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ShowPeptideIDTimes(false);
});
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(46.8, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(46.8, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowProductTransitions();
});
WaitForCondition(() => !SkylineWindow.GraphPeakArea.IsHidden);
if (!AsSmallMolecules) // No libraries (yet?)
{
WaitForDotProducts();
}
RunUI(() =>
{
// Graph p.15
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 22);
if (!AsSmallMolecules) // No libraries (yet?)
{
VerifyDotProducts(0.99, 0.98);
}
// Check graph p15. (checked)
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
// p. 16 screenshot of full 5-point dilution curve
// Select precursor
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "DRVYIHPF" : "R.DRVYIHPF.- [34, 41]"); // May be localized " (missed 1)"
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1047");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile with split graphs", 24);
RunUI(() =>
{
SkylineWindow.Size = new Size(990, 620);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graphs clipped from main window with split graphs", 25);
// PeakAreaGraph Normalize to total p.20.
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowProductTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
// Ensure graph looks like p20.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]");
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]"); // Phosphorylated
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1333");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("figure 1a - Area Replicate graph metafile for IKNLQSLDPSH", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(9, SkylineWindow.GraphPeakArea.CurveCount);
});
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "HLVDEPQNLIK" : "K.HLVDEPQNLIK.Q [401, 411]");
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1306");
}
WaitForGraphs();
PauseForScreenShot("figure 1b - Area replicate graph metafile for HLVDEPQNLIK", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.CurveCount);
});
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
WaitForCondition(() => SkylineWindow.GraphPeakArea.IsHidden);
RunUI(() => SkylineWindow.SaveDocument());
}
