protected override void DoTest()
{
// Exploring a Library, p. 1
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList);
RunDlg <EditLibraryDlg>(editListUI.AddItem, editLibraryDlg =>
{
editLibraryDlg.LibrarySpec =
new BiblioSpecLibSpec("Experiment 15N", GetTestPath(@"labeled_15N.blib"));
editLibraryDlg.OkDialog();
});
OkDialog(editListUI, editListUI.OkDialog);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI.PickedLibraries = new[] { "Experiment 15N" };
});
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 3);
// Modifications Tab in peptideSttingsUI to check "Carbamidomethyl Cysteine"
const string carbamidoName = StaticModList.DEFAULT_NAME;
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications;
peptideSettingsUI.PickedStaticMods = new[] { carbamidoName };
});
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modifications tab", 4);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
Assert.IsTrue(WaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
// Go to view menu and click Spectral Libraries
ViewLibraryDlg viewLibraryDlg = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
var matchedPepsDlg = WaitForOpenForm <AddModificationsDlg>();
RunUI(matchedPepsDlg.CancelDialog);
PauseForScreenShot <ViewLibraryDlg>("Library Explorer", 5);
// Types text in Peptide textbox in the Spectral Library Explorer Window
RunUI(() =>
{
viewLibraryDlg.FilterString = "Q"; // Not L10N
Assert.AreEqual(7, viewLibraryDlg.PeptideDisplayCount);
});
PauseForScreenShot("Library Explorere filtered for peptides beginning with Q", 6);
RunUI(() =>
{
viewLibraryDlg.FilterString = "I"; // Not L10N
viewLibraryDlg.SetObservedMzValues(true);
Assert.AreEqual(1, viewLibraryDlg.PeptideDisplayCount);
});
// Click B and 2 buttons on the right side of Spectral Library Explorer Window to show b-ions
RunUI(() =>
{
Assert.AreEqual(11, viewLibraryDlg.GraphItem.IonLabels.Count());
viewLibraryDlg.GraphSettings.ShowBIons = true;
viewLibraryDlg.GraphSettings.ShowCharge2 = true;
Assert.AreEqual(35, viewLibraryDlg.GraphItem.IonLabels.Count());
});
PauseForScreenShot <ViewLibraryDlg>("Library Explorer showing ISERT peptide with b and charge 2 ions", 7);
// Right click on spectrum chart and select Observed m/z Values
RunUI(() =>
{
if (!Settings.Default.ShowObservedMz)
{
if (!Settings.Default.ShowIonMz)
{
var labelsBefore = viewLibraryDlg.GraphItem.IonLabels.ToArray();
Assert.IsFalse(labelsBefore.Contains(label => label.Contains("\n"))); // Not L10N
}
viewLibraryDlg.SetObservedMzValues(true);
}
var labelsAfter = viewLibraryDlg.GraphItem.IonLabels;
Assert.IsTrue(labelsAfter.Contains(label => label.Contains("\n"))); // Not L10N
});
// Clearing Peptide Textbox...
RunUI(() =>
{
viewLibraryDlg.FilterString = string.Empty;
Assert.AreEqual(43, viewLibraryDlg.PeptideDisplayCount);
});
// Matching Modifications p. 7
// Settings > Peptides Settings
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string glnPyroGluName = "Gln->pyro-Glu (N-term Q)"; // Not L10N
var glnPyroGlu = UniMod.GetModification(glnPyroGluName, out _);
glnPyroGlu = glnPyroGlu.ChangeVariable(true);
AddStaticMod(glnPyroGlu, peptideSettingsUI1, "Edit Structural Modification form", 8);
RunUI(() => peptideSettingsUI1.PickedStaticMods = new[] { carbamidoName, glnPyroGluName });
const string label15NName = "Label:15N"; // Not L10N
var mod15N = UniMod.GetModification(label15NName, out _);
AddHeavyMod(mod15N, peptideSettingsUI1, "Edit Structural Modification form", 9);
RunUI(() => peptideSettingsUI1.PickedHeavyMods = new[] { label15NName });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modificatoins tab", 10);
OkDialog(peptideSettingsUI1, peptideSettingsUI1.OkDialog);
Assert.IsTrue(WaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications.Count > 0 &&
SkylineWindow.Document.Settings.PeptideSettings.Modifications.AllHeavyModifications.Any()));
PauseForScreenShot("Peptide list clipped from Library Explorer", 11);
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen(false);
RunUI(() =>
{
viewLibraryDlg.SetBounds(SkylineWindow.Left, SkylineWindow.Top, SkylineWindow.Width, SkylineWindow.Height);
});
TakeCoverShot();
OkDialog(viewLibraryDlg, viewLibraryDlg.CancelDialog);
return;
}
// Adding Library Peptides to the Document p. 11
// Adding AEVNGLAAQGKYEGSGEDGGAAAQSLYIANHAY
var docInitial = WaitForProteinMetadataBackgroundLoaderCompletedUI();
const string peptideSequence1 = "AEVNGLAAQGKYEGSGEDGGAAAQSLYIANHAY"; // Not L10N
RunUI(() =>
{
viewLibraryDlg.FilterString = peptideSequence1;
Assert.AreEqual(1, viewLibraryDlg.PeptideDisplayCount);
});
{
var msgDlg = ShowDialog <FilterMatchedPeptidesDlg>(viewLibraryDlg.AddPeptide);
PauseForScreenShot <FilterMatchedPeptidesDlg>("Filter peptides form", 11);
OkDialog(msgDlg, msgDlg.OkDialog);
}
var docAdd1 = WaitForDocumentChange(docInitial);
Assert.AreEqual(1, docAdd1.PeptideCount);
Assert.AreEqual(peptideSequence1, docAdd1.Peptides.ToArray()[0].Peptide.Sequence);
// Adding DNAGAATEEFIK++ (no ok dialog)
const string peptideSequence2 = "DNAGAATEEFIK"; // Not L10N
RunUI(() =>
{
viewLibraryDlg.FilterString = peptideSequence2 + "++"; // Not L10N
Assert.AreEqual(2, viewLibraryDlg.PeptideDisplayCount);
});
RunUI(viewLibraryDlg.AddPeptide);
var docAdd2 = WaitForDocumentChange(docAdd1);
Assert.AreEqual(2, docAdd2.PeptideCount);
Assert.AreEqual(peptideSequence2, docAdd2.Peptides.ToArray()[1].Peptide.Sequence);
// Edit > ExpandAll > Peptides
RunUI(() =>
{
SkylineWindow.ExpandPeptides();
SkylineWindow.Size = new Size(918, 553);
});
RestoreViewOnScreen(12);
PauseForScreenShot("Main window", 12);
// Adding DNAGAATEEFIKR++ (has ok)
const string peptideSequence3 = "DNAGAATEEFIKR"; // Not L10N
RunUI(() =>
{
viewLibraryDlg.FilterString = peptideSequence3 + "++"; // Not L10N
Assert.AreEqual(2, viewLibraryDlg.PeptideDisplayCount);
});
RunDlg <FilterMatchedPeptidesDlg>(viewLibraryDlg.AddPeptide, msgDlg => msgDlg.OkDialog());
var docAdd3 = WaitForDocumentChange(docAdd2);
Assert.AreEqual(3, docAdd3.PeptideCount);
Assert.AreEqual(2, docAdd3.Peptides.ToArray()[2].Children.Count);
Assert.AreEqual(peptideSequence3, docAdd3.Peptides.ToArray()[2].Peptide.Sequence);
// Adding DNAGAATEEFIKR+++ (has ok)
RunUI(() =>
{
viewLibraryDlg.FilterString = peptideSequence3 + "+++"; // Not L10N
Assert.AreEqual(1, viewLibraryDlg.PeptideDisplayCount);
});
WaitForGraphs();
RunDlg <FilterMatchedPeptidesDlg>(viewLibraryDlg.AddPeptide, msgDlg => msgDlg.OkDialog());
var docAdd4 = WaitForDocumentChange(docAdd3);
// peptideSequence4 is considered a sub of peptideSequence3
Assert.AreEqual(3, docAdd4.PeptideCount);
Assert.AreEqual(4, docAdd4.Peptides.ToArray()[2].Children.Count);
// Close the Library Explorer dialog
OkDialog(viewLibraryDlg, viewLibraryDlg.CancelDialog);
// Save current document as 15N_library_peptides.sky
RunUI(() => SkylineWindow.SaveDocument(GetTestPath(@"15N_library_peptides.sky")));
RunUI(() => SkylineWindow.NewDocument());
// Neutral Losses p. 13
PeptideSettingsUI settingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
settingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications;
settingsUI.PickedStaticMods = new[] { carbamidoName }; // Not L10N
settingsUI.PickedHeavyMods = new string[0];
settingsUI.PickedLibraries = new string[0];
});
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modifications tab", 14);
var editListUI1 =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(settingsUI.EditLibraryList);
const string humanPhosphoLibName = "Human Phospho"; // Not L10N
RunDlg <EditLibraryDlg>(editListUI1.AddItem, editLibraryDlg =>
{
editLibraryDlg.LibrarySpec =
new BiblioSpecLibSpec(humanPhosphoLibName, GetTestPath(@"phospho.blib"));
editLibraryDlg.OkDialog();
});
OkDialog(editListUI1, editListUI1.OkDialog);
RunUI(() =>
{
settingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
settingsUI.PickedLibraries = new[] { humanPhosphoLibName };
});
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 15);
{
var msgDlg = ShowDialog <MultiButtonMsgDlg>(() => settingsUI.ShowViewLibraryDlg());
PauseForScreenShot <MultiButtonMsgDlg>("Save changes", 15);
OkDialog(msgDlg, msgDlg.Btn0Click);
}
Assert.IsTrue(WaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Modifications.StaticModifications.Count == 1 &&
!SkylineWindow.Document.Settings.PeptideSettings.Modifications.AllHeavyModifications.Any() &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
// Ignore modification matching form
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
RunUI(matchedPepModsDlg.CancelDialog);
var viewLibraryDlg1 = WaitForOpenForm <ViewLibraryDlg>();
const int countLabels1 = 15;
const int countLabels2 = 18;
RunUI(() =>
{
viewLibraryDlg1.FilterString = "AISS"; // Not L10N
Assert.AreEqual(2, viewLibraryDlg1.PeptideDisplayCount);
Assert.AreEqual(countLabels1, viewLibraryDlg1.GraphItem.IonLabels.Count());
});
PauseForScreenShot <GraphSpectrum>("Spectrum graph metafile", 16); // p. 16, figure 1a
RunUI(() =>
{
viewLibraryDlg1.SelectedIndex = 1;
Assert.AreEqual(countLabels2, viewLibraryDlg1.GraphItem.IonLabels.Count());
});
PauseForScreenShot <GraphSpectrum>("Spectrum graph metafile", 16); // p. 16, figure 1b
docInitial = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string phosphoModName = "Phospho (ST)"; // Not L10N
var phosphoSt = new StaticMod(phosphoModName, "S, T", null, true, "HPO3", LabelAtoms.None, // Not L10N
RelativeRT.Unknown, null, null, new[] { new FragmentLoss("H3PO4"), }); // Not L10N
AddStaticMod(phosphoSt, peptideSettingsUI2, "Edit Structural Modifcation form", 17);
// Check Phospho (ST) and Carbamidomethyl Cysteine
RunUI(() => peptideSettingsUI2.PickedStaticMods = new[] { phosphoModName, carbamidoName }); // Not L10N
OkDialog(peptideSettingsUI2, peptideSettingsUI2.OkDialog);
var docPhospho = WaitForDocumentChange(docInitial);
Assert.IsTrue(docPhospho.Settings.PeptideSettings.Modifications.StaticModifications.Count == 2);
string lossText = Math.Round(-phosphoSt.Losses[0].MonoisotopicMass, 1).ToString(LocalizationHelper.CurrentCulture);
const int countLossLabels1 = 12;
const int countLossLabels2 = 15;
const int countPrecursors1 = 1;
const int countPrecursors2 = 2;
RunUI(() =>
{
// New ions should be labeled, because of the added modification with loss
viewLibraryDlg1.SelectedIndex = 0;
Assert.AreEqual(countLabels1 + countLossLabels1, viewLibraryDlg1.GraphItem.IonLabels.Count());
viewLibraryDlg1.GraphSettings.ShowPrecursorIon = true;
// Make sure the precursor -98 ion was added
var labelsPhospho = viewLibraryDlg1.GraphItem.IonLabels.ToList();
Assert.AreEqual(countLossLabels1 + 1, labelsPhospho.Count(label => label.Contains(lossText)));
Assert.IsTrue(labelsPhospho.Contains(label => label.Contains(string.Format("{0} {1}", IonType.precursor.GetLocalizedString(), lossText))));
Assert.AreEqual(countLabels1 + countLossLabels1 + countPrecursors1, labelsPhospho.Count);
});
PauseForScreenShot <GraphSpectrum>("Spectrum graph metafile", 18); // p. 18, figure 1a.
RunUI(() =>
{
viewLibraryDlg1.SelectedIndex = 1;
var labelsPhospho = viewLibraryDlg1.GraphItem.IonLabels.ToList();
Assert.AreEqual(countLossLabels2 + 1, labelsPhospho.Count(label => label.Contains(lossText)));
Assert.IsTrue(labelsPhospho.Contains(label => label.Contains(string.Format("{0} {1}", IonType.precursor.GetLocalizedString(), lossText))));
Assert.AreEqual(countLabels2 + countLossLabels2 + countPrecursors2, labelsPhospho.Count);
});
PauseForScreenShot <GraphSpectrum>("Spectrum graph metafile", 18); // p. 18, figure 1b.
// Matching Library Peptides to Proteins p. 18
var peptideSettingsUI3 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var buildBackgroundProteomeDlg =
ShowDialog <BuildBackgroundProteomeDlg>(peptideSettingsUI3.ShowBuildBackgroundProteomeDlg);
RunUI(() =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath = GetTestPath(@"human.protdb");
buildBackgroundProteomeDlg.BackgroundProteomeName = "Human (mini)";
});
PauseForScreenShot <BuildBackgroundProteomeDlg>("Edit Background Proteome", 19); // p. 19
OkDialog(buildBackgroundProteomeDlg, buildBackgroundProteomeDlg.OkDialog);
// Select Max Missed Cleavages to be 2
RunUI(() =>
{
peptideSettingsUI3.MissedCleavages = 2;
});
OkDialog(peptideSettingsUI3, peptideSettingsUI3.OkDialog);
WaitForBackgroundProteomeLoaderCompleted(); // wait for protDB to populate protein metadata
RunUI(() =>
{
viewLibraryDlg1.FilterString = string.Empty;
Assert.AreEqual(100, viewLibraryDlg1.PeptideDisplayCount);
});
// Check Associate Proteins check box on Spectral Library Explorer form
RunUI(() =>
{
viewLibraryDlg1.AssociateMatchingProteins = true;
});
docInitial = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var confirmUpgrade = ShowDialog <AlertDlg>(viewLibraryDlg1.AddAllPeptides);
// Add everything in the library to the document.
var filterMatchedPeptidesDlg =
ShowDialog <FilterMatchedPeptidesDlg>(confirmUpgrade.ClickYes);
RunUI(() =>
{
filterMatchedPeptidesDlg.DuplicateProteinsFilter =
BackgroundProteome.DuplicateProteinsFilter.FirstOccurence;
filterMatchedPeptidesDlg.AddUnmatched = true;
filterMatchedPeptidesDlg.AddFiltered = true;
// Checks that Peptides were added with the correct buttons selected...
Assert.AreEqual(163, filterMatchedPeptidesDlg.DuplicateMatchesCount);
Assert.AreEqual(2, filterMatchedPeptidesDlg.UnmatchedCount);
});
PauseForScreenShot <FilterMatchedPeptidesDlg>("Filter Peptides", 20); // p. 20, figure 1
{
var msgDlg = ShowDialog <MultiButtonMsgDlg>(filterMatchedPeptidesDlg.OkDialog);
PauseForScreenShot("Message form", 20); // p. 20, figure 2
OkDialog(msgDlg, msgDlg.Btn1Click);
}
OkDialog(viewLibraryDlg1, viewLibraryDlg1.CancelDialog);
var docProteins = WaitForDocumentChange(docInitial);
AssertEx.IsDocumentState(docProteins, null, 250, 346, 347, 1041);
RestoreViewOnScreen(21);
PauseForScreenShot("Main window", 21);
OkDialog(viewLibraryDlg, viewLibraryDlg.Close);
}
