private static void TestAddingTransition()
{
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
var moleculeDlg = ShowDialog <EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
RunUI(() =>
{
moleculeDlg.FormulaBox.Formula = C12H12;
moleculeDlg.NameText = testNametextA;
moleculeDlg.Adduct = Adduct.NonProteomicProtonatedFromCharge(1);
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var newDoc = SkylineWindow.Document;
var compareIon = new CustomIon(C12H12, Adduct.NonProteomicProtonatedFromCharge(1), null, null, testNametextA);
Assert.AreEqual(compareIon, newDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
Assert.AreEqual(1, newDoc.MoleculeTransitions.ElementAt(0).Transition.Charge);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode);
});
}
private static void TestEditingTransition()
{
double massPrecisionTolerance = Math.Pow(10, -SequenceMassCalc.MassPrecision);
var doc = SkylineWindow.Document;
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode;
});
var editMoleculeDlg =
ShowDialog <EditCustomMoleculeDlg>(
() => SkylineWindow.ModifyTransition((TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode));
RunUI(() =>
{
Assert.AreEqual(C12H12, editMoleculeDlg.FormulaBox.Formula);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12), editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12), editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
editMoleculeDlg.FormulaBox.Formula = null;
editMoleculeDlg.Charge = 2; // If we set this after we set the mass, the mass will change since m/z is the actual input
editMoleculeDlg.FormulaBox.AverageMass = 800;
editMoleculeDlg.FormulaBox.MonoMass = 805;
editMoleculeDlg.NameText = "Fragment";
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newdoc = WaitForDocumentChange(doc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsFalse(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id)); // Changing the mass changes the Id
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
// And test undo/redo
RunUI(() => SkylineWindow.Undo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreNotEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreNotEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsTrue(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id));
RunUI(() => SkylineWindow.Redo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(805, 2), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
}
private static void TestAddingTransitionAsMasses()
{
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
var editMoleculeDlg = ShowDialog <EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
var formula = C12H12;
var monoMass = BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(formula);
var averageMass = BioMassCalc.AVERAGE.CalculateMassFromFormula(formula);
var adduct = Adduct.M_PLUS;
RunUI(() =>
{
// Verify the interaction of explicitly set mz and charge without formula
editMoleculeDlg.NameText = testNametextA;
editMoleculeDlg.Adduct = adduct;
var mzMono = editMoleculeDlg.Adduct.MzFromNeutralMass(monoMass);
var mzAverage = editMoleculeDlg.Adduct.MzFromNeutralMass(averageMass);
editMoleculeDlg.FormulaBox.MonoMass = monoMass;
editMoleculeDlg.FormulaBox.AverageMass = averageMass;
var massPrecisionTolerance = 0.00001;
Assert.AreEqual(mzMono, double.Parse(editMoleculeDlg.FormulaBox.MonoText), massPrecisionTolerance);
Assert.AreEqual(mzAverage, double.Parse(editMoleculeDlg.FormulaBox.AverageText), massPrecisionTolerance);
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newDoc = SkylineWindow.Document;
var compareIon = new CustomIon(null, adduct, monoMass, averageMass, testNametextA);
Assert.AreEqual(compareIon, newDoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon);
Assert.AreEqual(1, newDoc.MoleculeTransitions.ElementAt(0).Transition.Charge);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode);
});
}
private void DoMrmerTest()
{
// Preparing a Document to Accept a Transition List, p. 2
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList);
RunDlg <EditLibraryDlg>(editListUI.AddItem, editLibraryDlg =>
{
editLibraryDlg.LibrarySpec =
new BiblioSpecLibSpec("Yeast_mini", GetTestPath(@"MRMer\Yeast_MRMer_min.blib")); // Not L10N
editLibraryDlg.OkDialog();
});
OkDialog(editListUI, editListUI.OkDialog);
RunUI(() =>
{
peptideSettingsUI.PickedLibraries = new[] { "Yeast_mini" }; // Not L10N
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
});
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 3);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Digest);
RunDlg <BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg,
buildBackgroundProteomeDlg =>
{
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast_mini"; // Not L10N
buildBackgroundProteomeDlg.BackgroundProteomePath = GetTestPath(@"MRMer\Yeast_MRMer_mini.protdb"); // Not L10N
buildBackgroundProteomeDlg.OkDialog();
});
PauseForScreenShot <PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 4);
var modHeavyK = new StaticMod(HEAVY_K, "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification form", 5);
var modHeavyR = new StaticMod(HEAVY_R, "R", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15, // Not L10N
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyR, peptideSettingsUI, "Edit Isotope Modification form", 6);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { HEAVY_K, HEAVY_R });
var docBeforePeptideSettings = SkylineWindow.Document;
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChangeLoaded(docBeforePeptideSettings);
// Inserting a Transition List With Associated Proteins, p. 6
RunUI(() =>
{
var filePath = GetTestPath(@"MRMer\silac_1_to_4.xls"); // Not L10N
SetExcelFileClipboardText(filePath, "Fixed", 3, false); // Not L10N
});
using (new CheckDocumentState(24, 44, 88, 296))
{
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() => pasteDlg.IsMolecule = false); // Make sure it's ready to accept peptides rather than small molecules
RunUI(pasteDlg.PasteTransitions);
PauseForScreenShot <PasteDlg.TransitionListTab>("Insert Transition List form", 8);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
PauseForScreenShot("Main window with transitions added", 9);
FindNode("LWDVAT");
RunUI(() =>
{
Assert.IsTrue(((PeptideDocNode)((PeptideTreeNode)SkylineWindow.SelectedNode).Model).HasChildType(IsotopeLabelType.heavy));
SkylineWindow.ExpandPrecursors();
});
FindNode(string.Format("{0:F03}", 854.4)); // I18N
WaitForGraphs();
// Unfortunately, label hiding may mean that the selected ion is not labeled
Assert.IsTrue(SkylineWindow.GraphSpectrum.SelectedIonLabel != null
? SkylineWindow.GraphSpectrum.SelectedIonLabel.Contains("y7") // Not L10N
: SkylineWindow.GraphSpectrum.IonLabels.Contains(ionLabel => ionLabel.Contains("y7"))); // Not L10N
RunUI(() =>
{
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowCharge2 = true;
});
PauseForScreenShot <GraphSpectrum>("Main window with spectral library graph showing", 10);
// Importing Data, p. 10.
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"MRMer\MRMer.sky"))); // Not L10N
ImportResultsFile("silac_1_to_4.mzXML"); // Not L10N
FindNode("ETFP"); // Not L10N
RunUI(SkylineWindow.AutoZoomBestPeak);
PauseForScreenShot("Main window with data imported", 12);
RunUI(() =>
{
var selNode = SkylineWindow.SequenceTree.SelectedNode;
Assert.IsTrue(selNode.Text.Contains("ETFPILVEEK")); // Not L10N
Assert.IsTrue(((PeptideDocNode)((PeptideTreeNode)selNode).Model).HasResults);
Assert.IsTrue(Equals(selNode.StateImageIndex, (int)SequenceTree.StateImageId.keep));
SkylineWindow.ShowAllTransitions();
SkylineWindow.SelectedPath =
SkylineWindow.SequenceTree.GetNodePath(selNode.Nodes[0].Nodes[2] as TreeNodeMS);
Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.StateImageIndex,
(int)SequenceTree.StateImageId.no_peak));
});
PauseForScreenShot("Main window", 13);
// Removing a Transition with Interference, p. 13.
FindNode(string.Format("{0:F04}", 504.2664)); // I18N
RunUI(() =>
{
TransitionTreeNode selNode = (TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode;
SkylineWindow.RemovePeak(
SkylineWindow.SequenceTree.SelectedPath.GetPathTo((int)SrmDocument.Level.TransitionGroups),
((TransitionGroupTreeNode)selNode.Parent).DocNode, selNode.DocNode);
// Ensure that the Total Ratio is 0.62
// TODO(nicksh): Update tutorial Word Doc so that it has the right numbers.
Assert.IsTrue(Equals(SkylineWindow.SequenceTree.SelectedNode.StateImageIndex,
(int)SequenceTree.StateImageId.no_peak) && SkylineWindow.SequenceTree.SelectedNode.Parent.Text.Contains((0.62).ToString(LocalizationHelper.CurrentCulture)));
});
// Adjusting Peak Boundaries to Exclude Interference, p. 14.
RunUI(() => SkylineWindow.Undo());
FindNode("ETFP");
RunUI(() =>
{
var pathGroup =
SkylineWindow.SequenceTree.GetNodePath((TreeNodeMS)SkylineWindow.SelectedNode.Nodes[0]);
var graphChrom = SkylineWindow.GraphChromatograms.ToList()[0];
var listChanges = new List <ChangedPeakBoundsEventArgs>
{
new ChangedPeakBoundsEventArgs(pathGroup, null, graphChrom.NameSet,
graphChrom.ChromGroupInfos[0].FilePath,
new ScaledRetentionTime(29.8, 29.8),
new ScaledRetentionTime(30.4, 30.4),
PeakIdentification.FALSE,
PeakBoundsChangeType.both)
};
graphChrom.SimulateChangedPeakBounds(listChanges);
foreach (TransitionTreeNode node in SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes)
{
Assert.IsTrue(((TransitionDocNode)node.Model).HasResults);
}
});
PauseForScreenShot("Main window", 14);
FindNode("YVDP");
RunUI(() =>
Assert.IsTrue(SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[2].StateImageIndex
== (int)SequenceTree.StateImageId.peak_blank));
RunUI(() => SkylineWindow.SaveDocument());
PauseForAuditLog();
}
protected override void DoTest()
{
// Clear all the settings lists that will be defined in this tutorial
ClearSettingsLists();
// Open the file
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_START_CHECKPOINT)));
WaitForDocumentLoaded();
// Specify DIA acquisition scheme and machine settings
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettings.AcquisitionMethod = FullScanAcquisitionMethod.DIA;
transitionSettings.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettings.PrecursorMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.PrecursorRes = 35000;
transitionSettings.PrecursorResMz = 200;
transitionSettings.ProductMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettings.ProductRes = 17500;
transitionSettings.ProductResMz = 200;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan", 4);
// Set up isolation scheme
var isolationSchemeDlg = ShowDialog <EditIsolationSchemeDlg>(transitionSettings.AddIsolationScheme);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme form", 5);
RunUI(() =>
{
isolationSchemeDlg.UseResults = false;
});
var calculateIsolationDlg = ShowDialog <CalculateIsolationSchemeDlg>(isolationSchemeDlg.Calculate);
RunUI(() =>
{
calculateIsolationDlg.WindowWidth = 20;
calculateIsolationDlg.Start = 500;
calculateIsolationDlg.End = 900;
calculateIsolationDlg.OptimizeWindowPlacement = true;
});
PauseForScreenShot <CalculateIsolationSchemeDlg>("Calculate Isolation Scheme form", 6);
OkDialog(calculateIsolationDlg, calculateIsolationDlg.OkDialog);
PauseForScreenShot <EditIsolationSchemeDlg>("Edit Isolation Scheme Dialog Filled", 7);
var isolationSchemeGraphDlg = ShowDialog <DiaIsolationWindowsGraphForm>(isolationSchemeDlg.OpenGraph);
PauseForScreenShot <DiaIsolationWindowsGraphForm>("Graph of Isolation Scheme", 8);
OkDialog(isolationSchemeGraphDlg, isolationSchemeGraphDlg.CloseButton);
RunUI(() => isolationSchemeDlg.IsolationSchemeName = "500 to 900 by 20");
OkDialog(isolationSchemeDlg, isolationSchemeDlg.OkDialog);
OkDialog(transitionSettings, transitionSettings.OkDialog);
// Export isolation scheme
var exportIsolationDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.IsolationList));
PauseForScreenShot <ExportMethodDlg>("Export Isolation List form", 9);
OkDialog(exportIsolationDlg, () => exportIsolationDlg.OkDialog(GetTestPath("DIA_tutorial_isolation_list.csv")));
// Adjust modifications and filter
var newPeptideSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => newPeptideSettings.AutoSelectMatchingPeptides = true);
OkDialog(newPeptideSettings, newPeptideSettings.OkDialog);
// Set up chromatogram retention time restriction
var newTransitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => newTransitionSettings.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 5.0));
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Retention time filtering options", 16);
// Adjust library transition ranking
RunUI(() =>
{
newTransitionSettings.SelectedTab = TransitionSettingsUI.TABS.Library;
newTransitionSettings.UseLibraryPick = true;
newTransitionSettings.Filtered = true;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 22);
OkDialog(newTransitionSettings, newTransitionSettings.OkDialog);
PauseForScreenShot <SequenceTreeForm>("Targets pane with precursors and best 5 transitions only", 23);
// Build spectral library using Import Peptide Search
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT)));
// "Build Spectral Library" page
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(() => SkylineWindow.ShowImportPeptideSearchDlg());
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(new[] { GetTestPath("interact-20130311_DDA_Pit01.pep.xml") }); // Not L10N
importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.dia;
});
PauseForScreenShot <BuildLibraryDlg>("Build Library form - input files", 10);
const string prefixKeep = "DIA_Pit0";
if (IsFullImportMode)
{
SrmDocument doc = SkylineWindow.Document;
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
doc = WaitForDocumentChange(doc);
// "Extract Chromatograms" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles =
_importFiles.Select(f => new ImportPeptideSearch.FoundResultsFile(f, GetTestPath(f + ExtensionTestContext.ExtThermoRaw))).ToList();
});
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
RunUI(() =>
{
string prefix = importResultsNameDlg.Prefix;
Assert.IsTrue(prefix.EndsWith(prefixKeep));
importResultsNameDlg.Prefix = prefix.Substring(0, prefix.Length - prefixKeep.Length);
importResultsNameDlg.YesDialog();
});
WaitForClosedForm(importResultsNameDlg);
// "Add Modifications" page
RunUI(() =>
{
const string modCarbamidomethyl = "Carbamidomethyl (C)";
const string modOxidation = "Oxidation (M)";
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
// Define expected matched/unmatched modifications
var expectedMatched = new[] { modCarbamidomethyl, modOxidation };
// Verify matched/unmatched modifications
AssertEx.AreEqualDeep(expectedMatched, importPeptideSearchDlg.MatchModificationsControl.MatchedModifications.ToArray());
Assert.IsFalse(importPeptideSearchDlg.MatchModificationsControl.UnmatchedModifications.Any());
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = new[] { modCarbamidomethyl };
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
WaitForDocumentChange(doc);
// "Configure Transition Settings" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
importPeptideSearchDlg.TransitionSettingsControl.PrecursorCharges = new[] { 1, 2, 3, 4 };
importPeptideSearchDlg.TransitionSettingsControl.IonCharges = new[] { 1, 2 };
importPeptideSearchDlg.TransitionSettingsControl.IonTypes = new[] { IonType.y, IonType.b, IonType.precursor };
importPeptideSearchDlg.TransitionSettingsControl.ExclusionUseDIAWindow = true;
importPeptideSearchDlg.TransitionSettingsControl.IonCount = 5;
importPeptideSearchDlg.TransitionSettingsControl.IonMatchTolerance = 0.05;
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Configure Full-Scan Settings" page
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// "Import FASTA" page
RunUI(() =>
{
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(GetTestPath("pituitary_database.fasta"));
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
WaitForClosedForm(importPeptideSearchDlg);
WaitForCondition(10 * 60 * 1000, () => SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 10 minutes
RunUI(() =>
{
SkylineWindow.SaveDocument(GetTestPath(DIA_IMPORTED_CHECKPOINT));
SkylineWindow.SaveDocument(GetTestPath(DIA_TUTORIAL_CHECKPOINT));
});
}
else
{
OkDialog(importPeptideSearchDlg, importPeptideSearchDlg.CancelDialog);
RunUI(() => SkylineWindow.OpenFile(GetTestPath(DIA_IMPORTED_CHECKPOINT)));
}
WaitForDocumentLoaded();
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.Size = new Size(750, 788);
});
// Generate decoys
// var decoysDlg = ShowDialog<GenerateDecoysDlg>(SkylineWindow.ShowGenerateDecoysDlg);
// PauseForScreenShot<GenerateDecoysDlg>("Add Decoy Peptides form", 24);
// RunUI(() =>
// {
// decoysDlg.NumDecoys = 26;
// Assert.AreEqual(decoysDlg.DecoysMethod, DecoyGeneration.SHUFFLE_SEQUENCE);
// });
// OkDialog(decoysDlg, decoysDlg.OkDialog);
// RunUI(() => SkylineWindow.SequenceTree.TopNode = SkylineWindow.SequenceTree.SelectedNode.PrevNode.Nodes[6]);
// PauseForScreenShot<SequenceTreeForm>("Targets pane with decoys added", 25);
RunUI(() =>
{
SkylineWindow.CollapsePeptides();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 6);
var nodePepTree = SkylineWindow.SelectedNode as PeptideTreeNode;
Assert.IsNotNull(nodePepTree);
Assert.AreEqual("VLQAVLPPLPQVVCTYR", nodePepTree.DocNode.Peptide.Sequence);
SkylineWindow.ShowSplitChromatogramGraph(true);
SkylineWindow.AutoZoomBestPeak();
var graphChrom = SkylineWindow.GetGraphChrom(prefixKeep + "1");
var labelStrings = graphChrom.GetAnnotationLabelStrings().ToArray();
Assert.IsTrue(labelStrings.Contains(string.Format("{0}\n+{1} ppm\n(idotp {2})", 75.4, 3, 0.59)),
string.Format("Missing expected label in {0}", string.Join("|", labelStrings)));
SkylineWindow.Width = 1250;
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RestoreViewOnScreen(27);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 26);
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
Assert.AreEqual((int)SequenceTree.StateImageId.no_peak, nodeTree.StateImageIndex);
});
PauseForScreenShot <SequenceTreeForm>("Targets view - ", 27);
RunUI(() =>
{
SkylineWindow.SetIntegrateAll(true);
var nodeTree = SkylineWindow.SelectedNode.Nodes[0].Nodes[0] as SrmTreeNode;
Assert.IsNotNull(nodeTree);
Assert.AreEqual((int)SequenceTree.StateImageId.peak, nodeTree.StateImageIndex);
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.83, nodeGroupTree.DocNode.GetLibraryDotProduct(0) ?? 0, 0.005);
SkylineWindow.ShowOtherRunPeptideIDTimes(true);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - with ID lines", 28);
RunUI(() =>
{
SkylineWindow.AutoZoomNone();
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 1);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed out and small peak", 30);
RunUI(SkylineWindow.AutoZoomBestPeak);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - zoomed to peak", 31);
if (IsFullImportMode)
{
ClickChromatogram(74.9, 1.775E+7, PaneKey.PRECURSORS);
RestoreViewOnScreen(33);
PauseForScreenShot <GraphFullScan>("Full Scan graph with precursors - zoom manually", 32);
ClickChromatogram(74.8, 1.753E+6, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y7", 33);
ClickChromatogram(74.9, 9.64E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing b3 - zoom manually", 34);
ClickChromatogram(74.9, 1.25E+5, PaneKey.PRODUCTS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing y3 - zoom manually", 34);
}
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 2);
Assert.AreEqual("CNTDYSDCIHEAIK", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - split between two precursors", 35);
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
SkylineWindow.SelectedPath = ((SrmTreeNode)SkylineWindow.SelectedNode.Nodes[0]).Path;
});
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile - double charged precursor", 36);
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 3);
Assert.AreEqual("ELVYETVR", ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode.Peptide.Sequence);
});
RunUI(() =>
{
SkylineWindow.SelectedNode.Expand();
var nodeGroupTree = SkylineWindow.SelectedNode.Nodes[0] as TransitionGroupTreeNode;
Assert.IsNotNull(nodeGroupTree);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
Assert.AreEqual(0.99, nodeGroupTree.DocNode.GetIsotopeDotProduct(0) ?? 0, 0.005);
});
RestoreViewOnScreen(38);
PauseForScreenShot <GraphSpectrum>("Library Match view - zoom manually", 37);
RestoreViewOnScreen(39);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 38);
if (IsFullImportMode)
{
RestoreViewOnScreen(40);
ClickChromatogram(41.9, 1.166E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing precursor interference - zoom manually", 39);
RunUI(() => SkylineWindow.GraphFullScan.ChangeScan(-12));
CheckFullScanSelection(41.7, 1.532E+8, PaneKey.PRECURSORS);
PauseForScreenShot <GraphFullScan>("Full Scan graph showing transition between interference and real peak - zoom manually", 39);
}
// Clear all the settings lists that were defined in this tutorial
ClearSettingsLists();
}
protected override void DoTest()
{
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-1_Settings.pdf";
//Tutorial 1
string fastaFile = GetTestPath("Tutorial-1_Settings/TubercuList_v2-6.fasta.txt");
WaitForCondition(() => File.Exists(fastaFile));
var pepSettings = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
SkylineWindow.Size = new Size(1600, 800);
pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest;
pepSettings.ComboEnzymeSelected = "Trypsin [KR | P]";
pepSettings.MaxMissedCleavages = 0;
});
var backProteomeDlg = ShowDialog <BuildBackgroundProteomeDlg>(pepSettings.AddBackgroundProteome);
RunUI(() =>
{
backProteomeDlg.BackgroundProteomePath = GetTestPath("Skyline");
backProteomeDlg.BackgroundProteomeName = "TubercuList_v2-6";
backProteomeDlg.AddFastaFile(fastaFile);
WaitForCondition(() => backProteomeDlg.StatusText.Length > 10);
Assert.IsTrue(backProteomeDlg.StatusText.Contains("3982".ToString(CultureInfo.CurrentCulture)));
});
OkDialog(backProteomeDlg, backProteomeDlg.OkDialog);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction);
RunUI(() =>
{
pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter;
pepSettings.TextMinLength = 7;
pepSettings.TextMaxLength = 25;
pepSettings.TextExcludeAAs = 0;
pepSettings.AutoSelectMatchingPeptides = true;
});
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library);
var editListDlg =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(pepSettings.EditLibraryList);
var editLibraryDlg = ShowDialog <EditLibraryDlg>(editListDlg.AddItem);
RunUI(() =>
{
editLibraryDlg.LibraryName = "Mtb_proteome_library";
editLibraryDlg.LibraryPath = GetTestPath("Skyline\\Mtb_DirtyPeptides_QT_filtered_cons.sptxt");
});
OkDialog(editLibraryDlg, editLibraryDlg.OkDialog);
OkDialog(editListDlg, editListDlg.OkDialog);
RunUI(() => pepSettings.SetLibraryChecked(0, true));
RunUI(() => { pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications; });
var editHeavyModListDlg =
ShowDialog <EditListDlg <SettingsListBase <StaticMod>, StaticMod> >(pepSettings.EditHeavyMods);
var addDlgOne = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem);
RunUI(() => addDlgOne.SetModification("Label:13C(6)15N(2) (C-term K)"));
PauseForScreenShot("Isotope modification 1", 3);
OkDialog(addDlgOne, addDlgOne.OkDialog);
var addDlgTwo = ShowDialog <EditStaticModDlg>(editHeavyModListDlg.AddItem);
RunUI(() => addDlgTwo.SetModification("Label:13C(6)15N(4) (C-term R)"));
PauseForScreenShot("Isotope modification 2", 3);
OkDialog(addDlgTwo, addDlgTwo.OkDialog);
OkDialog(editHeavyModListDlg, editHeavyModListDlg.OkDialog);
RunUI(() =>
{
pepSettings.SetIsotopeModifications(0, true);
pepSettings.SetIsotopeModifications(1, true);
});
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Digest);
PauseForScreenShot("Digestion tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Prediction);
PauseForScreenShot("Prediction tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Filter);
PauseForScreenShot("Filter tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Library);
PauseForScreenShot("Library tab", 4);
RunUI(() => pepSettings.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot("Modifications tab", 4);
OkDialog(pepSettings, pepSettings.OkDialog);
WaitForCondition(
() => SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('{').First()) &&
SkylineWindow.Status.Contains(Resources.BackgroundProteomeSpec_Digest_Digesting__0__.Split('}').Last()));
WaitForCondition(
() => SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('{').First()) &&
SkylineWindow.Status.Contains(Resources.BackgroundProteomeManager_LoadBackground_Resolving_protein_details_for__0__proteome.Split('}').Last()));
WaitForCondition(() => SkylineWindow.Status.Contains(Resources.SkylineWindow_UpdateProgressUI_Ready));
WaitForDocumentLoaded();
var transitionDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionDlg.PrecursorMassType = MassType.Monoisotopic;
transitionDlg.FragmentMassType = MassType.Monoisotopic;
transitionDlg.RegressionCEName = "ABI 5500 QTrap";
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionDlg.PrecursorCharges = "2,3".ToString(CultureInfo.CurrentCulture);
transitionDlg.ProductCharges = "1,2".ToString(CultureInfo.CurrentCulture);
transitionDlg.FragmentTypes = "y";
transitionDlg.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_1;
transitionDlg.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion;
transitionDlg.SetListAlwaysAdd(0, false);
transitionDlg.ExclusionWindow = 5;
transitionDlg.SetAutoSelect = true;
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionDlg.IonMatchTolerance = 1.0;
transitionDlg.UseLibraryPick = true;
transitionDlg.IonCount = 5;
transitionDlg.Filtered = true;
});
RunUI(() =>
{
transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionDlg.MinMz = 300;
transitionDlg.MaxMz = 1250;
});
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Prediction);
PauseForScreenShot("Prediction Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Filter);
PauseForScreenShot("Filter Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Library);
PauseForScreenShot("Library Tab", 7);
RunUI(() => transitionDlg.SelectedTab = TransitionSettingsUI.TABS.Instrument);
PauseForScreenShot("Instrument Tab", 7);
OkDialog(transitionDlg, transitionDlg.OkDialog);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Tutorial-1_Settings\\SRMcourse_20140210_Settings.sky")));
//Tutorial 2
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-2_TransitionList.pdf";
RunUI(() => { });
SetExcelFileClipboardText(GetTestPath(@"Tutorial-2_TransitionList\\target_peptides.xlsx"), "Sheet1", 1,
false);
var peptidePasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
var matchingDlg = ShowDialog <FilterMatchedPeptidesDlg>(peptidePasteDlg.PastePeptides);
PauseForScreenShot("Filter Peptides", 1);
OkDialog(matchingDlg, matchingDlg.OkDialog);
OkDialog(peptidePasteDlg, peptidePasteDlg.OkDialog);
int expectedTrans = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 306 : 313;
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 68, expectedTrans);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
});
PauseForScreenShot("Skyline Window", 2);
var exportDlg = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg.InstrumentType = "AB SCIEX";
exportDlg.ExportStrategy = ExportStrategy.Single;
exportDlg.DwellTime = 20;
});
PauseForScreenShot("Export Transition List", 3);
var declusteringWarningDlg = ShowDialog <MultiButtonMsgDlg>(
() => exportDlg.OkDialog(GetTestPath("Tutorial-2_TransitionList\\SRMcourse_20140210_MtbProteomeLib_TransList.csv")));
PauseForScreenShot("Decluster Window", 3);
OkDialog(declusteringWarningDlg, declusteringWarningDlg.Btn1Click);
WaitForClosedForm(exportDlg);
//Tutorial 3
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-3_Library.pdf";
var pepSettings2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => pepSettings2.SelectedTab = PeptideSettingsUI.TABS.Library);
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(pepSettings2.ShowBuildLibraryDlg);
RunUI(() =>
{
buildLibraryDlg.LibraryPath = GetTestPath("Skyline");
buildLibraryDlg.LibraryName = "Mtb_hDP_20140210";
buildLibraryDlg.LibraryCutoff = 0.9;
buildLibraryDlg.LibraryAuthority = "SRMcourse";
});
PauseForScreenShot("Build Library Window", 2);
RunUI(() =>
{
buildLibraryDlg.OkWizardPage();
buildLibraryDlg.AddDirectory(GetTestPath("Tutorial-3_Library"));
});
PauseForScreenShot("Build Library Window Next", 2);
OkDialog(buildLibraryDlg, buildLibraryDlg.OkWizardPage);
RunUI(() =>
{
pepSettings2.SetLibraryChecked(0, true);
pepSettings2.SetLibraryChecked(1, true);
});
OkDialog(pepSettings2, pepSettings2.OkDialog);
WaitForLibrary(20213);
WaitForCondition(() => SkylineWindow.Document.PeptideTransitionCount != expectedTrans);
int expectedTransAfter = TransitionGroup.IsAvoidMismatchedIsotopeTransitions ? 444 : 450;
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 96, expectedTransAfter);
var libraryExpl = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
var messageWarning = WaitForOpenForm <MultiButtonMsgDlg>();
OkDialog(messageWarning, messageWarning.Btn1Click);
PauseForScreenShot("Spectral Library Explorer Window", 3);
OkDialog(libraryExpl, libraryExpl.Close);
var exportDlg2 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg2.InstrumentType = "AB SCIEX";
exportDlg2.ExportStrategy = ExportStrategy.Buckets;
exportDlg2.MaxTransitions = 150;
exportDlg2.DwellTime = 20;
exportDlg2.IgnoreProteins = true;
});
var declusteringWarningDlg2 = ShowDialog <MultiButtonMsgDlg>(() =>
exportDlg2.OkDialog(GetTestPath("Tutorial-3_Library\\SRMcourse_20140210_MtbProteomeLib_hDP_TransList.csv")));
OkDialog(declusteringWarningDlg2, declusteringWarningDlg2.Btn1Click);
WaitForClosedForm(exportDlg2);
//Tutorial 4-A
LinkPdf = "http://www.srmcourse.ch/tutorials2014/Tutorial-4_Parameters.pdf";
SrmDocument smallDocument = SkylineWindow.Document;
PeptideGroupDocNode[] newProteins = smallDocument.PeptideGroups.Take(0).ToArray();
smallDocument = (SrmDocument)smallDocument.ChangeChildren(newProteins);
Assert.IsTrue(SkylineWindow.SetDocument(smallDocument, SkylineWindow.Document)); // TODO: Must be a better way to do this
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettings.RegressionCEName = "ABI QTrap 4000";
});
var editCollisionEnergy = ShowDialog <EditCEDlg>(() =>
transitionSettings.RegressionCEName = Resources.SettingsListComboDriver_Edit_current);
RunUI(() =>
{
editCollisionEnergy.StepSize = 2;
editCollisionEnergy.StepCount = 5;
});
PauseForScreenShot("Edit Collision Energy Equation Window", 2);
OkDialog(editCollisionEnergy, editCollisionEnergy.OkDialog);
OkDialog(transitionSettings, transitionSettings.OkDialog);
SetExcelFileClipboardText(GetTestPath("Tutorial-4_Parameters\\transition_list_for_CEO.xlsx"), "Sheet1", 3,
false);
var insertTransitionDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() => insertTransitionDlg.IsMolecule = false); // Make sure it's ready to accept peptides, not small molecules
RunUI(insertTransitionDlg.PasteTransitions);
OkDialog(insertTransitionDlg, insertTransitionDlg.OkDialog);
AssertEx.IsDocumentState(SkylineWindow.Document, null, 10, 30, 30, 143);
var exportDlg3 = ShowDialog <ExportMethodDlg>(SkylineWindow.ShowExportTransitionListDlg);
RunUI(() =>
{
exportDlg3.InstrumentType = "AB SCIEX";
exportDlg3.ExportStrategy = ExportStrategy.Single;
exportDlg3.OptimizeType = ExportOptimize.CE;
exportDlg3.MethodType = ExportMethodType.Standard;
exportDlg2.DwellTime = 20;
});
PauseForScreenShot("Export Transition List", 3);
var defaultWaringDlg = ShowDialog <MultiButtonMsgDlg>(
() => exportDlg3.OkDialog(GetTestPath("Tutorial-4_Parameters\\SRMcourse_20140211_Parameters_CEO.csv")));
OkDialog(defaultWaringDlg, defaultWaringDlg.Btn1Click);
WaitForClosedForm(exportDlg3);
var paths = new string[4];
for (int i = 0; i < paths.Length; i++)
{
paths[i] = GetTestPath("Tutorial-4_Parameters\\CEO_" + (i + 1) + ".wiff");
}
ImportResults("CEO", paths, ExportOptimize.CE);
RestoreViewOnScreen(43);
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Skyline Window", 3);
ImportResults("", new[]
{
GetTestPath("Tutorial-4_Parameters\\CE_plus10.wiff"),
GetTestPath("Tutorial-4_Parameters\\CE_minus10.wiff")
}, ExportOptimize.NONE, false);
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_maximum_view);
});
RestoreViewOnScreen(44);
PauseForScreenShot("Skyline Window", 4);
var transitionSettings2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => { transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Prediction; });
var addCollisionEnergyDlg = ShowDialog <EditCEDlg>(transitionSettings2.AddToCEList);
RunUI(() =>
{
addCollisionEnergyDlg.UseCurrentData();
addCollisionEnergyDlg.RegressionName = "SRMcourse_20140211_Parameters_custom-CE-equation";
});
var equationGraphDlg = ShowDialog <GraphRegression>(addCollisionEnergyDlg.ShowGraph);
PauseForScreenShot("Collision Energy Equation Graph", 6);
OkDialog(equationGraphDlg, equationGraphDlg.CloseDialog);
OkDialog(addCollisionEnergyDlg, addCollisionEnergyDlg.OkDialog);
RunUI(() =>
{
transitionSettings2.RegressionCEName = "SRMcourse_20140211_Parameters_custom-CE-equation";
transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings2.MZMatchTolerance = 0.01;
});
PauseForScreenShot("Instrument Tab", 7);
OkDialog(transitionSettings2, transitionSettings2.OkDialog);
//Tutorial 4-B
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RunUI(manageResultsDlg.RemoveAllReplicates);
OkDialog(manageResultsDlg, manageResultsDlg.OkDialog);
string[] paths2 =
{
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 10)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 20)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 40)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 60)),
GetTestPath(string.Format("Tutorial-4_Parameters\\unscheduled_dwell{0}ms.wiff", 100))
};
ImportResults("", paths2, null, false);
RestoreViewOnScreen(48);
RunUI(() => SkylineWindow.AutoZoomBestPeak());
PauseForScreenShot("Skyline Window", 8);
}
/// <summary>
/// Test tree state restoration from a persistent string. Tests for proper expansion and
/// selection of nodes, and correct vertical scrolling
/// </summary>
protected override void DoTest()
{
// tests for a blank document
RunUI(() =>
{
SkylineWindow.NewDocument();
SetCurrentState();
SkylineWindow.SaveDocument(TestContext.GetTestPath("blank.sky"));
// reload file from persistent string
SkylineWindow.OpenFile(TestContext.GetTestPath("blank.sky"));
CompareStates();
});
_documentFile = TestFilesDir.GetTestPath("Study7_0-7.sky");
// tests for a fully collapsed tree
RunUI(() =>
{
SkylineWindow.OpenFile(_documentFile);
SkylineWindow.CollapseProteins();
CheckStateMaintained();
});
// tests for a fully expanded tree and scrolling
RunUI(() =>
{
SkylineWindow.OpenFile(_documentFile);
SkylineWindow.ExpandPrecursors();
CheckStateMaintained();
SkylineWindow.SelectAll();
CheckStateMaintained();
// select last node in tree for scrolling test
SelectNode(SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1], null);
CheckStateMaintained();
});
// tests for expansion
RunUI(() =>
{
SkylineWindow.OpenFile(_documentFile);
SkylineWindow.CollapseProteins();
SelectNode(SkylineWindow.SequenceTree.TopNode, null);
CheckStateMaintained();
TestExpansion();
});
// tests for selection
RunUI(() =>
{
SkylineWindow.OpenFile(_documentFile);
TestSingleSelect();
TestSelectLastNode();
TestRangeSelect();
TestDisjointSelect();
TestCombinedRangeDisjoint();
});
// tests that Skyline will not crash when there is a mismatch between stored data in the
// .sky.view file and that in the tree
RunUI(() =>
{
SelectNode(SkylineWindow.SequenceTree.Nodes[1], null);
SkylineWindow.SaveDocument(_documentFile);
System.IO.File.Copy(SkylineWindow.GetViewFile(_documentFile), _documentFile + ".copy");
SkylineWindow.EditDelete();
CheckStateMaintained();
System.IO.File.Delete(SkylineWindow.GetViewFile(_documentFile));
System.IO.File.Copy(_documentFile + ".copy", SkylineWindow.GetViewFile(_documentFile));
SkylineWindow.OpenFile(_documentFile);
});
}
private static void TestEditingTransition()
{
double massPrecisionTolerance = Math.Pow(10, -SequenceMassCalc.MassPrecision);
var doc = SkylineWindow.Document;
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode;
});
var editMoleculeDlg =
ShowDialog <EditCustomMoleculeDlg>(
() => SkylineWindow.ModifyTransition((TransitionTreeNode)SkylineWindow.SequenceTree.SelectedNode));
var monoMass = new TypedMass(805, MassType.Monoisotopic);
RunUI(() =>
{
Assert.AreEqual(C12H12 + Adduct.NonProteomicProtonatedFromCharge(1).AdductFormula, editMoleculeDlg.FormulaBox.Formula);
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(Adduct.NonProteomicProtonatedFromCharge(1).AdductFormula, editMoleculeDlg.FormulaBox.Adduct.AdductFormula);
editMoleculeDlg.FormulaBox.Formula = editMoleculeDlg.FormulaBox.Adduct.AdductFormula; // Remove neutral formula, should leave masses unchanged
Assert.AreEqual(BioMassCalc.MONOISOTOPIC.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.MonoMass ?? -1, massPrecisionTolerance);
Assert.AreEqual(BioMassCalc.AVERAGE.CalculateMassFromFormula(C12H12),
editMoleculeDlg.FormulaBox.AverageMass ?? -1, massPrecisionTolerance);
editMoleculeDlg.FormulaBox.AverageMass = 800;
editMoleculeDlg.FormulaBox.MonoMass = monoMass.Value;
editMoleculeDlg.NameText = "Fragment";
});
OkDialog(editMoleculeDlg, editMoleculeDlg.OkDialog);
var newdoc = WaitForDocumentChange(doc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsFalse(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id)); // Changing the mass changes the Id
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
// And test undo/redo
RunUI(() => SkylineWindow.Undo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreNotEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreNotEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
Assert.IsTrue(ReferenceEquals(doc.MoleculeTransitions.ElementAt(0).Id, newdoc.MoleculeTransitions.ElementAt(0).Id));
RunUI(() => SkylineWindow.Redo());
newdoc = WaitForDocumentChange(newdoc);
Assert.AreEqual("Fragment", newdoc.MoleculeTransitions.ElementAt(0).Transition.CustomIon.ToString());
Assert.AreEqual(BioMassCalc.CalculateIonMz(monoMass, editMoleculeDlg.Adduct), newdoc.MoleculeTransitions.ElementAt(0).Mz, massPrecisionTolerance);
// Verify that tree selection doesn't change just because we changed an ID object
// (formerly the tree node would collapse and focus would jump up a level)
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SequenceTree.SelectedNode, SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode.FirstNode);
});
}
protected override void DoTest()
{
const int molCount = 1;
var doc = SkylineWindow.Document;
for (var loop = 0; loop < 3; loop++)
{
// Should be able to synchronize if both sibs have formula, or neither, but not one of each
string testname;
switch (loop)
{
case 0:
testname = "ions_testing_masses.sky"; // Masses only
break;
case 1:
testname = "ions_testing_mixed.sky"; // Starts out as two precursors, with no transitions, one is labeled 15N
break;
default:
testname = "ions_testing.sky"; // Starts out as two precursors, first has a precursor transition, other has label 15N and serialized ion formula
break;
}
string testPath = TestFilesDir.GetTestPath(testname);
RunUI(() => SkylineWindow.OpenFile(testPath));
doc = WaitForDocumentChange(doc);
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add precursor transition to it
var pickList = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
var lloop = loop;
RunUI(() =>
{
pickList.ApplyFilter(false);
switch (lloop)
{
default:
pickList.SetItemChecked(0, true); // 0th item is M transition
break;
case 1:
pickList.SetItemChecked(0, true); // 0th item is the M-1 transition
pickList.SetItemChecked(1, true); // 1th item is the M transition
break;
}
pickList.AutoManageChildren = false;
pickList.IsSynchSiblings = true; // Cause a precursor transition to be added to heavy group
});
OkDialog(pickList, pickList.OnOk);
WaitForClosedForm(pickList);
doc = WaitForDocumentChange(doc);
switch (loop)
{
default:
// There should now be a precursor transition for the second, heavy labeled transition group, and it
// should match the mz of the transition group
Assert.AreEqual(2, doc.MoleculeTransitions.Count());
Assert.AreNotEqual(doc.MoleculeTransitionGroups.ToArray()[0].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
Assert.AreEqual(doc.MoleculeTransitionGroups.ToArray()[1].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
break;
case 1:
// There should now be two precursor transitions M-1 and M for the second, heavy labeled transition group, and the
// second precursor transition should match the mz of the transition group
Assert.AreEqual(4, doc.MoleculeTransitions.Count());
Assert.AreNotEqual(doc.MoleculeTransitionGroups.ToArray()[0].PrecursorMz, doc.MoleculeTransitions.ToArray()[3].Mz);
Assert.AreEqual(doc.MoleculeTransitionGroups.ToArray()[1].PrecursorMz, doc.MoleculeTransitions.ToArray()[3].Mz);
break;
}
}
//
// Now with isotope distributions
//
var documentPath = TestFilesDir.GetTestPath("ions_testing_isotopes.sky");
RunUI(() => SkylineWindow.OpenFile(documentPath));
var newDoc = WaitForDocumentLoaded();
var transitionSettingsFilter = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsFilter.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsFilter.SmallMoleculeFragmentTypes = "p"; // Allow precursors
transitionSettingsFilter.SmallMoleculePrecursorAdducts = "[M+H]"; // Allow precursors
});
OkDialog(transitionSettingsFilter, transitionSettingsFilter.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add isotope labeled precursor transitions to it
var pickList0 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList0.ApplyFilter(false);
pickList0.SetItemChecked(0, true);
pickList0.SetItemChecked(1, true);
pickList0.SetItemChecked(2, true);
pickList0.AutoManageChildren = false;
Assert.IsTrue(pickList0.CanSynchSiblings);
pickList0.IsSynchSiblings = true; // Cause precursor transitions to be added to heavy group
});
OkDialog(pickList0, pickList0.OnOk);
WaitForClosedForm(pickList0);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz,
SkylineWindow.Document.MoleculeTransitions.ToArray()[4].Mz);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz + 1.003492,
SkylineWindow.Document.MoleculeTransitions.ToArray()[5].Mz, 1e-6);
// Verify that adding a custom transition prevents the synch siblings checkbox from appearing
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
newDoc = WaitForDocumentChange(newDoc);
var moleculeDlg = ShowDialog <EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
var C12H12 = "C12H12";
var testNametextA = "y1";
RunUI(() =>
{
moleculeDlg.FormulaBox.Formula = C12H12;
moleculeDlg.NameText = testNametextA;
moleculeDlg.Adduct = Adduct.SINGLY_PROTONATED;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
var compareIon = new CustomIon(C12H12, Adduct.SINGLY_PROTONATED, null, null, testNametextA);
const int transY1Index = 3;
Assert.AreEqual(compareIon, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.CustomIon);
Assert.AreEqual(1, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.Charge);
var pickList1 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.AutoManageChildren = true;
Assert.IsFalse(pickList1.CanSynchSiblings);
});
OkDialog(pickList1, pickList1.OnOk);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
// Long as we're here, check mz filtering
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings.MinMz = 160; // Should drop that custom ion
});
OkDialog(transitionSettings, transitionSettings.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
RunUI(() => { SkylineWindow.Undo(); });
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.Nodes[1];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList2 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsFalse(pickList2.CanSynchSiblings); // The light set has a non-precursor transition
});
OkDialog(pickList2, pickList2.OnOk);
var transitionSettings2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings2.MinMz = 300; // Should drop that custom ion
});
OkDialog(transitionSettings2, transitionSettings2.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
var pickList3 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsTrue(pickList3.CanSynchSiblings);
});
OkDialog(pickList3, pickList3.OnOk);
// Add another precursor, with explicit isotope declaration in the adduct [M4C13+H]
// Open its picklist, clear filter so all isotopes appear
// Select them all, and check synch siblings
// Should be 3*3 transitions in doc
SelectNode(SrmDocument.Level.Molecules, 0);
var moleculeDlg2 = ShowDialog <EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
var adduct = moleculeDlg.FormulaBox.Adduct.ChangeIsotopeLabels(new Dictionary <string, int> {
{ "C'", 4 }
}); // Not L10N
RunUI(() =>
{
moleculeDlg2.Adduct = adduct;
});
OkDialog(moleculeDlg2, moleculeDlg2.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
// Select the new transition group
SelectNode(SrmDocument.Level.TransitionGroups, 2);
// Add precursor transition to it
var pickList4 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList4.ApplyFilter(false);
pickList4.SetItemChecked(0, true);
pickList4.SetItemChecked(1, true);
pickList4.SetItemChecked(2, true);
pickList4.AutoManageChildren = false;
pickList4.IsSynchSiblings = true; // Cause a precursor transition to be added to heavy group
});
OkDialog(pickList4, pickList4.OnOk);
WaitForClosedForm(pickList4);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(9, newDoc.MoleculeTransitionCount);
}
protected override void DoTest()
{
RunUI(() =>
{
SkylineWindow.OpenFile(TestFilesDir.GetTestPath("SimpleRatiosTest.sky"));
SkylineWindow.ExpandPrecursors();
});
Assert.IsFalse(SkylineWindow.Document.Settings.PeptideSettings.Quantification.SimpleRatios);
Assert.AreEqual(new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy),
SkylineWindow.Document.Settings.PeptideSettings.Quantification.NormalizationMethod);
PeptideTreeNode peptideTreeNode = (PeptideTreeNode)SkylineWindow.SequenceTree.Nodes[0].Nodes[0];
TransitionGroupTreeNode lightTreeNode =
(TransitionGroupTreeNode)peptideTreeNode.Nodes[0];
TransitionGroupTreeNode heavyTreeNode = (TransitionGroupTreeNode)peptideTreeNode.Nodes[1];
var lightTransitionAreas =
lightTreeNode.DocNode.Transitions.Select(tran => tran.Results[0][0].Area).ToList();
Assert.AreEqual(4, lightTransitionAreas.Count);
var heavyTransitionAreas =
heavyTreeNode.DocNode.Transitions.Select(tran => tran.Results[0][0].Area).ToList();
Assert.AreEqual(2, heavyTransitionAreas.Count);
// Verify that only the first two transition areas in both precursors contribute to the displayed ratio
var expectedRatio = lightTransitionAreas.Take(2).Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
RunUI(() =>
{
SkylineWindow.ShowResultsGrid(true);
SkylineWindow.SelectedPath = peptideTreeNode.Path;
});
var resultsGridForm = FindOpenForm <LiveResultsGrid>();
WaitForConditionUI(() => resultsGridForm.IsComplete);
RunDlg <ViewEditor>(resultsGridForm.DataboundGridControl.NavBar.CustomizeView, viewEditor =>
{
viewEditor.ChooseColumnsTab.AddColumn(propertyPathNormalizedArea);
viewEditor.ViewName = "PeptideResultsWithNormalizedArea";
viewEditor.OkDialog();
});
VerifyExpectedRatio(resultsGridForm, expectedRatio);
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUi =>
{
peptideSettingsUi.SimpleRatios = true;
peptideSettingsUi.OkDialog();
});
Assert.IsTrue(SkylineWindow.Document.Settings.PeptideSettings.Quantification.SimpleRatios);
// When SimpleRatios is true, verify that all transitions contribute to the ratio
expectedRatio = lightTransitionAreas.Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
VerifyExpectedRatio(resultsGridForm, expectedRatio);
// Verify that deleting a transition from the light precursor does not affect the heavy precursor
Assert.AreEqual(4, lightTreeNode.DocNode.TransitionCount);
Assert.AreEqual(2, heavyTreeNode.DocNode.TransitionCount);
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPaths = new[]
{ SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Transitions, 0) };
SkylineWindow.EditDelete();
});
Assert.AreEqual(3, lightTreeNode.DocNode.TransitionCount);
Assert.AreEqual(2, heavyTreeNode.DocNode.TransitionCount);
expectedRatio = lightTransitionAreas.Skip(1).Sum() / heavyTransitionAreas.Sum();
StringAssert.Contains(lightTreeNode.Text, GetTransitionGroupRatioText(expectedRatio));
RunUI(() => SkylineWindow.SelectedPath = peptideTreeNode.Path);
VerifyExpectedRatio(resultsGridForm, expectedRatio);
}
protected override void DoTest()
{
TestSmallMolecules = false; // The presence of the extra test node without any results is incompatible with what's being tested here.
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// show the empty Transition Setting dialog
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsDlg.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab nothing set", 2);
OkDialog(transitionSettingsDlg, transitionSettingsDlg.OkDialog);
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 5);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 6);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 7);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 10);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 11);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <MultiButtonMsgDlg>("Add mods alert", 12);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 13);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = 1160;
SkylineWindow.Height = 792;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 14);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 16);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 17);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 19);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
alignmentForm.Width = 711;
alignmentForm.Height = 561;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 20);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 21);
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 32.6, 41.4); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 22);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 23);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 24, "Transition pick list unfiltered", 24); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 39.6); // set the view for screenshot
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 25);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chhromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 26);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 27);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 28);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 29);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 30);
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
// page 32 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = SkylineWindow.GraphChromatograms.ToArray()[TIP3].GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 32);
RestoreViewOnScreen(33); // float the Library Match window TODO this causes a crash at next call to ChangePeakBounds, in pwiz.Skyline.Controls.Graphs.GraphChromatogram.ChromGroupInfos.get() Line 492 , why?
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 33);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 33);
RestoreViewOnScreen(34); // back to normal view
pepIndex = JumpToPeptide("GVVDSEDLPLNISR"); // Not L10N
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
PauseForScreenShot("upper - Chromatogram graph metafiles for peptide GVVDSEDLPLNISR", 34);
ZoomBoth(35.05, 36.9, 480);
PauseForScreenShot("lower - Chromatogram graph metafile - effect of zoom ", 34);
ChangePeakBounds(TIP3, pepIndex, 35.7, 36.5); // adjust integration per tutorial
CheckAnnotations(TIP3, pepIndex, atest++); // check the new idotp values
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 35);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 36); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // Not L10N
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio;
dlg.OkDialog();
});
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
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()
{
const int molCount = 1;
var doc = SkylineWindow.Document;
for (var loop = 0; loop < 3; loop++)
{
// Should be able to synchronize of both sibs have formula, or neither, but not one of each
string testname;
switch (loop)
{
case 0:
testname = "ions_testing_mixed.sky";
break;
case 1:
testname = "ions_testing.sky";
break;
default:
testname = "ions_testing_masses.sky";
break;
}
string testPath = TestFilesDir.GetTestPath(testname);
RunUI(() => SkylineWindow.OpenFile(testPath));
doc = WaitForDocumentChange(doc);
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add precursor transition to it
var pickList = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(0, true);
pickList.AutoManageChildren = false;
pickList.IsSynchSiblings = true; // Cause a precursor transition to be added to heavy group
});
OkDialog(pickList, pickList.OnOk);
WaitForClosedForm(pickList);
doc = WaitForDocumentChange(doc);
if (loop == 0)
{
// No synch is possible - one ion is formula based, the other mass only
Assert.AreEqual(1, doc.MoleculeTransitions.Count());
}
else
{
// There should now be a precursor transition for the second, heavy labeled transition group, and it
// should match the mz of the transition group
Assert.AreNotEqual(doc.MoleculeTransitionGroups.ToArray()[0].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
Assert.AreEqual(doc.MoleculeTransitionGroups.ToArray()[1].PrecursorMz, doc.MoleculeTransitions.ToArray()[1].Mz);
}
}
//
// Now with isotope distributions
//
var documentPath = TestFilesDir.GetTestPath("ions_testing_isotopes.sky");
RunUI(() => SkylineWindow.OpenFile(documentPath));
WaitForDocumentLoaded();
SelectNode(SrmDocument.Level.Molecules, 0);
Assert.AreEqual(molCount, SkylineWindow.Document.MoleculeCount);
RunUI(SkylineWindow.ExpandPrecursors);
Settings.Default.SynchronizeIsotopeTypes = true;
// Select the first transition group
SelectNode(SrmDocument.Level.TransitionGroups, 0);
// Add isotope labeled precursor transitions to it
var pickList0 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList0.ApplyFilter(false);
pickList0.SetItemChecked(0, true);
pickList0.SetItemChecked(1, true);
pickList0.SetItemChecked(2, true);
pickList0.AutoManageChildren = false;
Assert.IsTrue(pickList0.CanSynchSiblings);
pickList0.IsSynchSiblings = true; // Cause precursor transitions to be added to heavy group
});
OkDialog(pickList0, pickList0.OnOk);
WaitForClosedForm(pickList0);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz,
SkylineWindow.Document.MoleculeTransitions.ToArray()[4].Mz);
Assert.AreEqual(SkylineWindow.Document.MoleculeTransitionGroups.ToArray()[1].PrecursorMz + 1.00349556477,
SkylineWindow.Document.MoleculeTransitions.ToArray()[5].Mz, 1e-6);
// Verify that adding a custom transition prevents the synch siblings checkbox from appearing
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.FirstNode;
SkylineWindow.SequenceTree.SelectedNode = node;
});
var moleculeDlg = ShowDialog <EditCustomMoleculeDlg>(SkylineWindow.AddSmallMolecule);
var C12H12 = "C12H12";
var testNametextA = "y1";
RunUI(() =>
{
moleculeDlg.FormulaBox.Formula = C12H12;
moleculeDlg.NameText = testNametextA;
moleculeDlg.Charge = 1;
});
OkDialog(moleculeDlg, moleculeDlg.OkDialog);
var newDoc = SkylineWindow.Document;
var compareIon = new DocNodeCustomIon(C12H12, testNametextA);
const int transY1Index = 3;
Assert.AreEqual(compareIon, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.CustomIon);
Assert.AreEqual(1, newDoc.MoleculeTransitions.ElementAt(transY1Index).Transition.Charge);
var pickList1 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.AutoManageChildren = true;
Assert.IsFalse(pickList1.CanSynchSiblings);
});
OkDialog(pickList1, pickList1.OnOk);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
// Long as we're here, check mz filtering
var transitionSettings = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings.MinMz = 160; // Should drop that custom ion
});
OkDialog(transitionSettings, transitionSettings.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
RunUI(() => { SkylineWindow.Undo(); });
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(7, newDoc.MoleculeTransitions.Count());
RunUI(() =>
{
SkylineWindow.ExpandPrecursors();
var node = SkylineWindow.SequenceTree.Nodes[0].FirstNode.Nodes[1];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList2 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsFalse(pickList2.CanSynchSiblings); // The light set has a non-precursor transition
});
OkDialog(pickList2, pickList2.OnOk);
var transitionSettings2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettings2.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettings2.MinMz = 300; // Should drop that custom ion
});
OkDialog(transitionSettings2, transitionSettings2.OkDialog);
newDoc = WaitForDocumentChange(newDoc);
Assert.AreEqual(6, newDoc.MoleculeTransitions.Count());
var pickList3 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
Assert.IsTrue(pickList3.CanSynchSiblings);
});
OkDialog(pickList3, pickList3.OnOk);
}
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);
}
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());
}
