private static void SetHeavyLabelNames(PeptideSettingsUI peptideSettingsUI, string[] heavyLabelNames)
{
var editLabelTypeListDlg = ShowEditLabelTypeListDlg(peptideSettingsUI);
RunUI(() =>
{
editLabelTypeListDlg.LabelTypeText = string.Join("\n", heavyLabelNames);
});
OkDialog(editLabelTypeListDlg, editLabelTypeListDlg.OkDialog);
}
private void SetUpTestLibraries()
{
PeptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
Assert.IsNotNull(PeptideSettingsUI);
var editListUI = ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(PeptideSettingsUI.EditLibraryList);
int numLibs = _testLibs.Length;
for (int i = 0; i < numLibs; i++)
{
AddLibrary(editListUI, _testLibs[i]);
}
RunUI(editListUI.OkDialog);
WaitForClosedForm(editListUI);
// Make sure the libraries actually show up in the peptide settings dialog before continuing.
WaitForConditionUI(() => _testLibs.Length == PeptideSettingsUI.AvailableLibraries.Count());
RunUI(() => Assert.IsFalse(PeptideSettingsUI.IsSettingsChanged));
RunUI(() => PeptideSettingsUI.OkDialog());
WaitForClosedForm(PeptideSettingsUI);
}
protected override void DoTest()
{
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot();
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");
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");
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { HEAVY_K, HEAVY_R });
PauseForScreenShot();
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
SetTransitionClipboardText(new[] { 0, 1, 7, 8 });
RunUI(() =>
{
SkylineWindow.Paste();
SkylineWindow.CollapsePeptides();
});
PauseForScreenShot();
const string peptideStandardsName = "Tr_peps_set2";
FindNode(peptideStandardsName);
RunUI(() =>
{
SkylineWindow.Cut();
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
SkylineWindow.Paste();
});
// Create auto-calculate regression RT predictor, p. 10
const string irtPredictorName = "iRT-OC-Study"; // Not L10N
{
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI2.SelectedTab = PeptideSettingsUI.TABS.Prediction);
var regressionDlg = ShowDialog <EditRTDlg>(peptideSettingsUI2.AddRTRegression);
const string irtCalcName = "iRT-OC-Study";
var editIrtCalcDlg = ShowDialog <EditIrtCalcDlg>(regressionDlg.AddCalculator);
RunUI(() =>
{
editIrtCalcDlg.CalcName = irtCalcName;
editIrtCalcDlg.CreateDatabase(GetOcRawTestPath("iRT-OC-Study.irtdb")); // Not L10N
SetTransitionClipboardText(new[] { 15, 17 }, c =>
{
if (string.Equals(c[8], "protein_name"))
{
return(null);
}
// c[17] = double.Parse(c[17], CultureInfo.InvariantCulture).ToString(LocalizationHelper.CurrentCulture);
return(string.Equals(c[8], peptideStandardsName) ? c : null);
});
editIrtCalcDlg.DoPasteStandard();
});
PauseForScreenShot();
RunUI(() =>
{
string carbC = string.Format("C[+{0:F01}]", 57.0);
SetTransitionClipboardText(new[] { 15, 17 }, c =>
{
if (string.Equals(c[8], peptideStandardsName) || string.Equals(c[8], "protein_name"))
{
return(null);
}
c[15] = c[15].Replace("[C160]", carbC).Replace("C[160]", carbC);
// c[17] = double.Parse(c[17], CultureInfo.InvariantCulture).ToString(LocalizationHelper.CurrentCulture);
return(c);
});
});
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalcDlg.DoPasteLibrary);
PauseForScreenShot(); // Add Peptides form
RunUI(() =>
{
Assert.AreEqual(71, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(0, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(0, addPeptidesDlg.RunsFailedCount);
addPeptidesDlg.OkDialog();
});
WaitForClosedForm(addPeptidesDlg);
PauseForScreenShot(); // Edit iRT Calculator form
RunUI(() => Assert.AreEqual(71, editIrtCalcDlg.LibraryPeptideCount));
OkDialog(editIrtCalcDlg, editIrtCalcDlg.OkDialog);
RunUI(() =>
{
regressionDlg.SetRegressionName(irtPredictorName);
regressionDlg.ChooseCalculator(irtCalcName);
regressionDlg.SetAutoCalcRegression(true);
regressionDlg.SetTimeWindow(3);
});
PauseForScreenShot(); // Edit retention time predictor form
OkDialog(regressionDlg, regressionDlg.OkDialog);
PauseForScreenShot(); // Prediction tab
RunUI(() => peptideSettingsUI2.SelectedTab = PeptideSettingsUI.TABS.Library);
var editLibListUI = ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI2.EditLibraryList);
var addLibUI = ShowDialog <EditLibraryDlg>(editLibListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(HUMAN_MINI, GetOcRawTestPath("h130kdp_consensus.blib"))); // Not L10N
PauseForScreenShot();
OkDialog(addLibUI, addLibUI.OkDialog);
OkDialog(editLibListUI, editLibListUI.OkDialog);
RunUI(() => peptideSettingsUI2.PickedLibraries = new[] { HUMAN_MINI });
PauseForScreenShot();
OkDialog(peptideSettingsUI2, peptideSettingsUI2.OkDialog);
}
RunUI(() => SkylineWindow.SaveDocument(GetOcRawTestPath("OC-study.sky")));
// Importing Data
ImportResultsFiles(GetOcRawTestPath(), ExtAbWiff,
IsFullData ? "R201217" : "R201217_plasma_revision_A", true);
WaitForCondition(5 * 60 * 1000, () =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
ImportResultsFiles(GetOcRawTestPath(), ExtAbWiff,
IsFullData ? "R201203" : "R201203_plasma_revision_F", true);
WaitForCondition(2 * 60 * 1000, () =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot();
}
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);
}
protected override void DoTest()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification over Transition Settings", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 11);
// Peptide Quantitification Settings p. 11
var peptideSettingsUi = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
const string quantUnits = "fmol/ul";
RunUI(() =>
{
peptideSettingsUi.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUi.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUi.QuantNormalizationMethod = new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUi.QuantUnits = quantUnits;
});
PauseForScreenShot("Peptide Settings Quantification Tab", 12);
OkDialog(peptideSettingsUi, peptideSettingsUi.OkDialog);
// Specify analyte concentrations of external standards
RunUI(() => 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 };
for (int iRow = 0; iRow < concentrations.Length; iRow++)
{
// ReSharper disable AccessToModifiedClosure
RunUI(() =>
{
var colSampleType = documentGridForm.FindColumn(PropertyPath.Root.Property("SampleType"));
documentGridForm.DataGridView.Rows[iRow].Cells[colSampleType.Index].Value = SampleType.STANDARD;
});
WaitForConditionUI(() => documentGridForm.IsComplete);
RunUI(() =>
{
var colAnalyteConcentration =
documentGridForm.FindColumn(PropertyPath.Root.Property("AnalyteConcentration"));
var cell = documentGridForm.DataGridView.Rows[iRow].Cells[colAnalyteConcentration.Index];
documentGridForm.DataGridView.CurrentCell = cell;
cell.Value = concentrations[iRow];
});
// ReSharper restore AccessToModifiedClosure
WaitForConditionUI(() => documentGridForm.IsComplete);
}
PauseForScreenShot("Document grid with concentrations filled in", 13);
// View the calibration curve p. 13
RunUI(() => SkylineWindow.ShowCalibrationForm());
var calibrationForm = FindOpenForm <CalibrationForm>();
PauseForScreenShot("View calibration curve", 14);
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);
}
private void MainTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
doc => doc.ChangeSettings(SrmSettingsList.GetDefault())));
// Check using libkey with small molecules
var adduct = Adduct.FromStringAssumeProtonated("M+3Na");
var z = adduct.AdductCharge;
const string caffeineFormula = "C8H10N4O2";
const string caffeineInChiKey = "RYYVLZVUVIJVGH-UHFFFAOYSA-N";
const string caffeineHMDB = "HMDB01847";
const string caffeineInChi = "InChI=1S/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3";
const string caffeineCAS = "58-08-2";
const string caffeineSMILES = "Cn1cnc2n(C)c(=O)n(C)c(=O)c12";
const string caffeineKEGG = "C07481";
var mId = new MoleculeAccessionNumbers(string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS, MoleculeAccessionNumbers.TagInChiKey + ":" + caffeineInChiKey,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
Assert.AreEqual(caffeineInChiKey, mId.GetInChiKey());
Assert.AreEqual(caffeineCAS, mId.GetCAS());
Assert.AreEqual(caffeineSMILES, mId.GetSMILES());
Assert.AreEqual(caffeineKEGG, mId.GetKEGG());
var moleculeName = "caffeine";
var smallMolAttributes = SmallMoleculeLibraryAttributes.Create(moleculeName, caffeineFormula, caffeineInChiKey,
string.Join("\t", MoleculeAccessionNumbers.TagHMDB + ":" + caffeineHMDB,
MoleculeAccessionNumbers.TagInChI + ":" + caffeineInChi, MoleculeAccessionNumbers.TagCAS + ":" + caffeineCAS,
MoleculeAccessionNumbers.TagSMILES + ":" + caffeineSMILES, MoleculeAccessionNumbers.TagKEGG + ":" + caffeineKEGG));
LibKey key;
for (var loop = 0; loop++ < 2;)
{
key = new LibKey(smallMolAttributes, adduct);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsFalse(key.IsProteomicKey);
Assert.IsTrue(key.IsSmallMoleculeKey);
Assert.IsFalse(key.IsModified);
Assert.AreEqual(0, key.ModificationCount);
Assert.AreEqual(z, key.Charge);
Assert.AreEqual(adduct, key.Adduct);
Assert.AreEqual(caffeineInChiKey, key.Target.ToString());
var viewLibPepInfo = new ViewLibraryPepInfo(key);
Assert.AreEqual(key, viewLibPepInfo.Key);
var smallMolInfo = viewLibPepInfo.GetSmallMoleculeLibraryAttributes();
Assert.AreEqual(moleculeName, smallMolInfo.MoleculeName);
Assert.AreEqual(caffeineInChiKey, smallMolInfo.InChiKey);
Assert.AreEqual(caffeineFormula, smallMolInfo.ChemicalFormula);
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineCAS));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineInChi));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineHMDB));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineSMILES));
Assert.IsTrue(smallMolInfo.OtherKeys.Contains(caffeineKEGG));
adduct = Adduct.FromString("M+3Si", Adduct.ADDUCT_TYPE.non_proteomic, z = -17); // Not realistic, but let's see if it's handled consistently
}
// Check general libkey operation
var seq = "YTQSNSVC[+57.0]YAK";
key = new LibKey(seq, Adduct.DOUBLY_PROTONATED);
Assert.IsFalse(key.IsPrecursorKey);
Assert.IsTrue(key.IsProteomicKey);
Assert.IsFalse(key.IsSmallMoleculeKey);
Assert.IsTrue(key.IsModified);
Assert.AreEqual(2, key.Charge);
Assert.AreEqual(1, key.ModificationCount);
Assert.AreEqual(Adduct.DOUBLY_PROTONATED, key.Adduct);
Assert.AreEqual(seq, key.Target.ToString());
// Test error conditions
BuildLibraryError("missing_charge.pep.XML", TestFilesDir.FullPath);
BuildLibraryError("non_int_charge.pep.XML", null);
BuildLibraryError("zero_charge.pep.XML", null);
BuildLibraryError("truncated.pep.XML", null);
BuildLibraryError("no_such_file.pep.XML", null, "Failed to open");
BuildLibraryError("missing_mzxml.pep.XML", null, "Could not find spectrum file");
// Check for proper handling of labeled addducts in small molecule files
// (formerly this would throw on a null object, fixed with the use of ExplicitMods.EMPTY)
BuildLibraryValid("heavy_adduct.ssl", true, false, false, 1);
// Make sure explorer handles this adduct type
var viewLibUI = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
RunUI(() => AssertEx.IsTrue(viewLibUI.GraphItem.IonLabels.Any()));
RunUI(viewLibUI.CancelDialog);
// Barbara added code to ProteoWizard to rebuild a missing or invalid mzXML index
// BuildLibraryError("bad_mzxml.pep.XML", "<index> not found");
BuildLibraryValid(TestFilesDir.GetTestPath("library_errors"), new[] { "bad_mzxml.pep.XML" }, false, false, false, 1);
string libraryBaseName = _libraryName;
// Test mascot parser
_libraryName = libraryBaseName + "mascot";
string libraryMascot = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("mascot"), new[] { "F027319.dat" },
true, false, false, 121, 4);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryMascot)));
// Test successful builds
_libraryName = libraryBaseName + "a";
string libraryA = _libraryName + BiblioSpecLiteSpec.EXT;
string libraryARedundant = _libraryName + BiblioSpecLiteSpec.EXT_REDUNDANT;
BuildLibraryValid("CPTAC_Set4_725_091509.pep.XML", true, false, false, 1);
BuildLibraryValid("CPTAC_Set4_610_080509.pep.XML", true, false, true, 2);
_libraryName = libraryBaseName + "b";
string libraryB = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid("CPTAC_Set4_624_072409.pep.XML", false, false, false, 6);
_libraryName = libraryBaseName + "c";
string libraryC = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.FullPath, new[] { libraryA, libraryB },
false, false, false, 8);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryA)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryARedundant)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryB)));
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryC)));
// Test peptide filter
const string filterList = "ACARPIISVYSEK\n" +
// TODO: Having the modified sequence as the first line causes an error with European number formats
"ADRDESSPYAAM[+{0:F01}]IAAQDVAQR\n" +
"ADAIQAGASQFETSAAK";
PastePeptideList(string.Format(filterList, 16.0), true, 0, 3, true);
_libraryName = libraryBaseName + "filter";
string libraryFilter = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("maxquant"), new[] { "test.msms.txt" },
false, true, false, 2);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryFilter)));
RunUI(SkylineWindow.Undo);
RunUI(SkylineWindow.Undo);
// Test AddPathsDlg (file not found)
EnsurePeptideSettings();
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(PeptideSettingsUI.ShowBuildLibraryDlg);
string[] invalidPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.xml"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, invalidPaths, true);
// Test AddPathsDlg (file invalid type)
string[] invalidTypes =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "mqpar.xml")
};
TestAddPaths(buildLibraryDlg, invalidTypes, true);
// Test AddPathsDlg (valid files)
string[] goodPaths =
{
Path.Combine(TestFilesDir.GetTestPath("maxquant"), "test.msms.txt"),
Path.Combine(TestFilesDir.GetTestPath("library_valid"), "CPTAC_Set4_624_072409.pep.XML")
};
TestAddPaths(buildLibraryDlg, goodPaths, false);
OkDialog(buildLibraryDlg, buildLibraryDlg.CancelDialog);
const string heavyRPeptide = "TPAQFDADELR";
const string oxidizedMPeptide = "LVGNMHGDETVSR";
const string peptideList = heavyRPeptide + "\n" +
oxidizedMPeptide + "\n" +
"ALSIGFETCR\n" +
"GNMHGDETVSR\n" +
"VGNMHGDETVSR";
PastePeptideList(peptideList, true, 0, 1);
// Set modifications on peptides to verify they connect with library spectra.
const LabelAtoms labelAtoms = LabelAtoms.C13 | LabelAtoms.N15;
const string heavyR = "Heavy R";
Settings.Default.HeavyModList.Add(new StaticMod(heavyR, "R", ModTerminus.C, null, labelAtoms, null, null));
const string oMeth = "Oxidized Methionine";
Settings.Default.StaticModList.Add(new StaticMod(oMeth, "M", null, "O"));
var sequenceTree = SkylineWindow.SequenceTree;
var docCurrent = SkylineWindow.Document;
// Select the heavyR peptide
PeptideTreeNode nodePepTree = null;
IdentityPath pathPep = docCurrent.GetPathTo((int)SrmDocument.Level.Molecules, 0);
RunUI(() =>
{
sequenceTree.SelectedPath = pathPep;
nodePepTree = sequenceTree.SelectedNode as PeptideTreeNode;
});
Assert.IsNotNull(nodePepTree);
Assert.AreEqual(heavyRPeptide, nodePepTree.DocNode.Peptide.Sequence);
// Set the Heavy R modification explicitly
var editPepModsDlg = ShowDialog <EditPepModsDlg>(SkylineWindow.ModifyPeptide);
RunUI(() =>
{
editPepModsDlg.SetModification(heavyRPeptide.Length - 1, IsotopeLabelType.heavy, heavyR);
editPepModsDlg.OkDialog();
});
WaitForCondition(() => (SkylineWindow.Document.Molecules.First().TransitionGroupCount == 2));
// The peptide should now match the spectrum in the library, and have
// both heavy and light precursors, with ranked transitions
PeptideDocNode nodePep = null;
RunUI(() => nodePep = nodePepTree.DocNode);
Assert.IsNotNull(nodePep);
Debug.Assert(nodePep != null);
Assert.AreEqual(2, nodePep.Children.Count, "Missing precursor for heavy R peptide.");
docCurrent = SkylineWindow.Document;
foreach (TransitionGroupDocNode nodeGroup in nodePep.Children)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// Which means all transition groups should now have spectrum info
foreach (var nodeGroup in docCurrent.PeptideTransitionGroups)
{
AssertLibInfo(docCurrent, nodeGroup);
}
// New document
var docNew = new SrmDocument(SrmSettingsList.GetDefault());
var docNewCopy = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy, null));
const string idpList3 = "FHYKTDQGIK\n" +
"WCAIGHQER\n" +
"WCTISTHEANK";
int idpCount3 = idpList3.Split('\n').Length;
const string idpList = "ADVTLGGGAK\n" +
"AGFAGDDAPR\n" +
"ALEFAKK\n" +
"CCTESLVNR\n" +
"DSYVGDEAQSK\n" +
"YICDNQDTISSK\n" +
// charge 3 peptides all have 2 also
idpList3;
int idpCount = idpList.Split('\n').Length;
_libraryName = libraryBaseName + "_idp";
string libraryIdp = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("idp_xml"), new[] { "orbi-small-eg.idpXML" },
false, false, false, idpCount + idpCount3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryIdp)));
// Add peptides expected to have charge 2 spectra in the library
PastePeptideList(idpList, true, 0, 0);
// Undo the paste
RunUI(SkylineWindow.Undo);
// Try filtering for only charge 3 spectra
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.PrecursorCharges = "3";
transitionSettingsUI.OkDialog();
});
PastePeptideList(idpList, false, idpCount - idpCount3 + 1 /* missing cleavage*/, 0);
// New document
var docNewCopy2 = docNew;
RunUI(() => SkylineWindow.SwitchDocument(docNewCopy2, null));
_libraryName = libraryBaseName + "_cpas1";
string libraryCpas1 = _libraryName + BiblioSpecLiteSpec.EXT;
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 3);
Assert.IsTrue(File.Exists(TestFilesDir.GetTestPath(libraryCpas1)));
// These are very poor searches, so repeat with no filter
Settings.Default.LibraryResultCutOff = 0;
_libraryName = libraryBaseName + "_cpas2";
BuildLibraryValid(TestFilesDir.GetTestPath("cpas"), null,
false, false, false, 100, 100);
// And, since the spectra are really poor, allow lots of
// possibilities for fragment ions.
var transitionSettingsCpas = ShowDialog <TransitionSettingsUI>(
SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsCpas.PrecursorCharges =
transitionSettingsCpas.ProductCharges = "1,2,3";
transitionSettingsCpas.FragmentTypes = "y,b";
transitionSettingsCpas.InstrumentMaxMz = 2000;
transitionSettingsCpas.OkDialog();
});
EnsurePeptideSettings();
RunUI(() =>
{
// Turn off carbamidomethyl cys, since not in these searches
PeptideSettingsUI.PickedStaticMods = new string[0];
PeptideSettingsUI.OkDialog();
});
// Get the set of peptides to paste from the library, since there
// are a lot.
var setPeptides = new HashSet <Target>();
var library = SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries[0];
foreach (var libKey in library.Keys)
{
if (!libKey.IsModified)
{
setPeptides.Add(libKey.Target);
}
}
string cpasPeptides = string.Join("\n", setPeptides.Select(p => p.ToString()).ToArray());
var pasteFilteredPeptideDlg = ShowDialog <PasteFilteredPeptidesDlg>(
() => SkylineWindow.Paste(cpasPeptides));
RunUI(pasteFilteredPeptideDlg.NoDialog);
Assert.IsTrue(WaitForCondition(() => SkylineWindow.Document.PeptideCount == setPeptides.Count),
string.Format("Expecting {0} peptides, found {1}.", setPeptides.Count, SkylineWindow.Document.PeptideCount));
Assert.AreEqual(setPeptides.Count, SkylineWindow.Document.PeptideTransitionGroupCount,
"Expecting precursors for peptides matched to library spectrum.");
// New document
docNew = new SrmDocument(SrmSettingsList.GetDefault());
RunUI(() => SkylineWindow.SwitchDocument(docNew, null));
// Tests for adding iRTs to spectral library after building
// 1. ask to recalibrate iRTs
// 2. ask to add iRTs
// 3. if added iRTs, ask to add RT predictor
// no recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt1"; // library_test_irt1
BuildLibraryIrt(true, false, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime == null));
// no recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt2"; // library_test_irt2
BuildLibraryIrt(true, false, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg2 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg2.IrtStandards, IrtStandard.BIOGNOSYS_10)));
OkDialog(editIrtDlg2, editIrtDlg2.CancelDialog);
// recalibrate, add iRTs, no add predictor
_libraryName = libraryBaseName + "_irt3"; // library_test_irt3
BuildLibraryIrt(true, true, false);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(libraryBaseName + "_irt2")));
// recalibrate, add iRTs, add predictor
_libraryName = libraryBaseName + "_irt4"; // library_test_irt4
BuildLibraryIrt(true, true, true);
RunUI(() => Assert.IsTrue(PeptideSettingsUI.Prediction.RetentionTime.Name.Equals(_libraryName)));
var editIrtDlg4 = ShowDialog <EditIrtCalcDlg>(PeptideSettingsUI.EditCalculator);
RunUI(() => Assert.IsTrue(ReferenceEquals(editIrtDlg4.IrtStandards, IrtStandard.EMPTY)));
OkDialog(editIrtDlg4, editIrtDlg4.CancelDialog);
OkDialog(PeptideSettingsUI, PeptideSettingsUI.CancelDialog);
}
private static EditLabelTypeListDlg ShowEditLabelTypeListDlg(PeptideSettingsUI peptideSettingsUI)
{
return(ShowDialog <EditLabelTypeListDlg>(peptideSettingsUI.EditLabelTypeList));
}
private void EnsurePeptideSettings()
{
PeptideSettingsUI = FindOpenForm <PeptideSettingsUI>() ??
ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
}
protected override void DoTest()
{
// Creating a MS/MS Spectral Library, p. 1
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunDlg <BuildLibraryDlg>(peptideSettingsUI.ShowBuildLibraryDlg, buildLibraryDlg =>
{
buildLibraryDlg.LibraryPath = TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\"); // Not L10N
buildLibraryDlg.LibraryName = YEAST_ATLAS;
buildLibraryDlg.LibraryCutoff = 0.95;
buildLibraryDlg.LibraryAuthority = "peptideatlas.org"; // Not L10N
buildLibraryDlg.OkWizardPage();
IList <string> inputPaths = new List <string>
{
TestFilesDirs[0].GetTestPath(@"MethodEdit\Yeast_atlas\interact-prob.pep.xml") // Not L10N
};
buildLibraryDlg.AddInputFiles(inputPaths);
buildLibraryDlg.OkWizardPage();
});
PeptideSettingsUI peptideSettingsUI1 = peptideSettingsUI;
RunUI(() =>
{
peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI1.PickedLibraries = new[] { YEAST_ATLAS };
});
WaitForOpenForm <PeptideSettingsUI>(); // To show Library tab for Forms testing
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 4); // Not L10N
RunUI(() => peptideSettingsUI1.SelectedTab = PeptideSettingsUI.TABS.Digest);
WaitForOpenForm <PeptideSettingsUI>(); // To show Digestion tab for Forms testing
// Creating a Background Proteome File, p. 3
FileEx.SafeDelete(TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast" + ProteomeDb.EXT_PROTDB)); // Not L10N
var buildBackgroundProteomeDlg =
ShowDialog <BuildBackgroundProteomeDlg>(peptideSettingsUI.ShowBuildBackgroundProteomeDlg);
RunUI(() =>
{
buildBackgroundProteomeDlg.BackgroundProteomePath =
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\Yeast"); // Not L10N
buildBackgroundProteomeDlg.BackgroundProteomeName = "Yeast"; // Not L10N
buildBackgroundProteomeDlg.AddFastaFile(
TestFilesDirs[0].GetTestPath(@"MethodEdit\FASTA\sgd_yeast.fasta")); // Not L10N
});
PauseForScreenShot <BuildBackgroundProteomeDlg>("Edit Background Proteome form", 5); // Not L10N
OkDialog(buildBackgroundProteomeDlg, buildBackgroundProteomeDlg.OkDialog);
PauseForScreenShot <PeptideSettingsUI.DigestionTab>("Peptide Settings - Digestion tab", 6); // Not L10N
var docB = SkylineWindow.Document;
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChange(docB);
if (!TryWaitForCondition(() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0))
{
Assert.Fail("Timed out loading libraries: libCount={0}, NotLoadedExplained={1}",
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count,
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsNotLoadedExplained ?? "<null>");
}
WaitForCondition(() =>
{
var peptideSettings = SkylineWindow.Document.Settings.PeptideSettings;
var backgroundProteome = peptideSettings.BackgroundProteome;
return(backgroundProteome.HasDigestion(peptideSettings));
}, "backgroundProteome.HasDigestion");
// Wait a bit in case web access is turned on and backgroundProteome is actually resolving protein metadata
int millis = (AllowInternetAccess ? 300 : 60) * 1000;
WaitForCondition(millis, () => !SkylineWindow.Document.Settings.PeptideSettings.BackgroundProteome.NeedsProteinMetadataSearch, "backgroundProteome.NeedsProteinMetadataSearch");
// Pasting FASTA Sequences, p. 5
RunUI(() => SetClipboardFileText(@"MethodEdit\FASTA\fasta.txt")); // Not L10N
// New in v0.7 : Skyline asks about removing empty proteins.
using (new CheckDocumentState(35, 25, 25, 75))
{
var emptyProteinsDlg = ShowDialog <EmptyProteinsDlg>(SkylineWindow.Paste);
RunUI(() => emptyProteinsDlg.IsKeepEmptyProteins = true);
OkDialog(emptyProteinsDlg, emptyProteinsDlg.OkDialog);
WaitForCondition(millis, () => SkylineWindow.SequenceTree.Nodes.Count > 4);
}
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[3].Nodes[0];
});
RestoreViewOnScreen(07);
PauseForScreenShot("Main window", 7); // Not L10N
RunUI(() =>
{
Settings.Default.ShowBIons = true;
SkylineWindow.SequenceTree.SelectedNode.Expand();
SkylineWindow.SequenceTree.SelectedNode =
SkylineWindow.SequenceTree.SelectedNode.Nodes[0].Nodes[1];
});
PauseForScreenShot("Main window showing effect of selection on Library Match graph", 8); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 3); // Not L10N
using (new CheckDocumentState(35, 28, 31, 155))
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2, 3"; // Not L10N
transitionSettingsUI.ProductCharges = "1"; // Not L10N
transitionSettingsUI.FragmentTypes = "y, b"; // Not L10N
});
WaitForOpenForm <TransitionSettingsUI>(); // To show Filter tab for Forms testing
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9); // Not L10N
RunUI(() =>
{
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonCount = 5;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab", 10); // Not L10N
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
}
PauseForScreenShot("Targets tree clipped from main window", 11); // Not L10N
CheckTransitionCount("VDIIANDQGNR", 5); // Not L10N
// Using a Public Spectral Library, p. 9
peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editListUI =
ShowDialog <EditListDlg <SettingsListBase <LibrarySpec>, LibrarySpec> >(peptideSettingsUI.EditLibraryList);
var addLibUI = ShowDialog <EditLibraryDlg>(editListUI.AddItem);
RunUI(() => addLibUI.LibrarySpec =
new BiblioSpecLibSpec(YEAST_GPM, TestFilesDirs[0].GetTestPath(@"MethodEdit\Library\yeast_cmp_20.hlf"))); // Not L10N
OkDialog(addLibUI, addLibUI.OkDialog);
WaitForClosedForm(addLibUI);
OkDialog(editListUI, editListUI.OkDialog);
// Limiting Peptides per Protein, p. 11
using (new CheckDocumentState(35, 182, 219, 1058))
{
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Library;
peptideSettingsUI.PickedLibraries = new[] { YEAST_ATLAS, YEAST_GPM };
});
PauseForScreenShot <PeptideSettingsUI.LibraryTab>("Peptide Settings - Library tab", 12); // Not L10N
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
Assert.IsTrue(WaitForCondition(
() =>
SkylineWindow.Document.Settings.PeptideSettings.Libraries.IsLoaded &&
SkylineWindow.Document.Settings.PeptideSettings.Libraries.Libraries.Count > 0));
}
using (new CheckDocumentState(35, 47, 47, 223, 2, true)) // Wait for change loaded, and expect 2 document revisions.
{
RunDlg <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI, peptideSettingsUI2 =>
{
peptideSettingsUI2.PickedLibraries = new[] { YEAST_GPM };
peptideSettingsUI2.LimitPeptides = true;
peptideSettingsUI2.RankID = XHunterLibSpec.PEP_RANK_EXPECT;
peptideSettingsUI2.PeptidesPerProtein = 3;
peptideSettingsUI2.OkDialog();
});
}
using (new CheckDocumentState(19, 47, 47, 223))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {
MinPeptidesPerProtein = 1
};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Protein List, p. 11
using (new CheckDocumentState(36, 58, 58, 278))
{
PasteDlg pasteProteinsDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteProteinsDlg);
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - 1];
SkylineWindow.SequenceTree.SelectedNode = node;
SetClipboardFileText(@"MethodEdit\FASTA\Protein list.txt"); // Not L10N
pasteProteinsDlg.SelectedPath = SkylineWindow.SequenceTree.SelectedPath;
pasteProteinsDlg.PasteProteins();
});
PauseForScreenShot <PasteDlg.ProteinListTab>("Insert Protein List - For Screenshot, select last (empty) item in list", 14); // Not L10N
OkDialog(pasteProteinsDlg, pasteProteinsDlg.OkDialog);
}
using (new CheckDocumentState(24, 58, 58, 278))
{
RunUI(() =>
{
var refinementSettings = new RefinementSettings {
MinPeptidesPerProtein = 1
};
SkylineWindow.ModifyDocument("Remove empty proteins", refinementSettings.Refine); // Not L10N
});
}
// Inserting a Peptide List, p. 13
using (new CheckDocumentState(25, 70, 70, 338))
{
RunUI(() =>
{
SetClipboardFileText(@"MethodEdit\FASTA\Peptide list.txt"); // Not L10N
SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0];
SkylineWindow.Paste();
// ReSharper disable LocalizableElement
SkylineWindow.SequenceTree.Nodes[0].Text = "Primary Peptides"; // Not L10N
// ReSharper restore LocalizableElement
});
FindNode("TLTAQSMQNSTQSAPNK"); // Not L10N
PauseForScreenShot("Main window", 16); // Not L10N
}
using (new CheckDocumentState(35, 70, 70, 338))
{
RunUI(() => SkylineWindow.Undo());
PasteDlg pastePeptidesDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pastePeptidesDlg.PastePeptides);
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List - For screenshot, select last (empty) line in list", 17); // Not L10N
OkDialog(pastePeptidesDlg, pastePeptidesDlg.OkDialog);
}
// Simple Refinement, p. 16
var findPeptideDlg = ShowDialog <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() => findPeptideDlg.SearchString = "IPEE"); // Not L10N
OkDialog(findPeptideDlg, () =>
{
findPeptideDlg.FindNext();
findPeptideDlg.Close();
});
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile", 18); // Not L10N
using (new CheckDocumentState(35, 64, 64, 320))
{
RefineDlg refineDlg = ShowDialog <RefineDlg>(SkylineWindow.ShowRefineDlg);
RunUI(() => refineDlg.MinTransitions = 5);
OkDialog(refineDlg, refineDlg.OkDialog);
PauseForScreenShot("29/35 prot 50/64 pep 50/64 prec 246/320 tran", 18); // Not L10N
}
// Checking Peptide Uniqueness, p. 18
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 3 : 2)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
using (new CheckDocumentState(34, 63, 63, 315))
{
var uniquePeptidesDlg = ShowDialog <UniquePeptidesDlg>(SkylineWindow.ShowUniquePeptidesDlg);
WaitForConditionUI(() => uniquePeptidesDlg.GetDataGridView().RowCount == 1);
RunUI(() =>
{
Assert.AreEqual(1, uniquePeptidesDlg.GetDataGridView().RowCount);
Assert.AreEqual(7, uniquePeptidesDlg.GetDataGridView().ColumnCount);
});
PauseForScreenShot <UniquePeptidesDlg>("Unique Peptides form", 19); // Not L10N
OkDialog(uniquePeptidesDlg, uniquePeptidesDlg.OkDialog);
RunUI(() => SkylineWindow.EditDelete());
}
// Protein Name Auto-Completion
PauseForScreenShot("(fig. 1): For screenshot, click at bottom of document tree, type 'ybl087' and see the autocomplete text. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("ybl087", 0); // Not L10N
var peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YBL087C", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Protein Description Auto-Completion
PauseForScreenShot("(fig. 2): For screenshot, click at bottom of document tree, type 'eft2' and see the autocomplete text, then down-arrow twice. Make sure to undo this new entry before proceeding.", 20); // Not L10N
TestAutoComplete("eft2", 0); // Sorting logic puts this at the 0th entry in the list - Not L10N
peptideGroups = new List <PeptideGroupDocNode>(Program.ActiveDocument.PeptideGroups);
Assert.AreEqual("YDR385W", peptideGroups[peptideGroups.Count - 1].Name); // Not L10N
// Peptide Sequence Auto-Completion, p. 21
TestAutoComplete("IQGP", 0); // Not L10N
var peptides = new List <PeptideDocNode>(Program.ActiveDocument.Peptides);
Assert.AreEqual("K.AYLPVNESFGFTGELR.Q [769, 784]", peptides[peptides.Count - 1].Peptide.ToString()); // Not L10N
PauseForScreenShot("(fig. 1) - For screenshot, click at the bottom of the document tree", 21); // Not L10N
// Pop-up Pick-Lists, p. 21
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
var node = SkylineWindow.SequenceTree.Nodes[SkylineWindow.SequenceTree.Nodes.Count - (TestSmallMolecules ? 4 : 3)];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList.ApplyFilter(false);
pickList.SetItemChecked(8, true);
pickList.AutoManageChildren = false; // TODO: Because calling SetItemChecked does not do this
});
PauseForScreenShot <PopupPickList>("(fig. 2) - YBL087C Peptides picklist", 21); // Not L10N
RunUI(pickList.OnOk);
}
using (new CheckDocumentState(36, 71, 71, 355))
{
RunUI(() =>
{
SkylineWindow.SequenceTree.Nodes[34].ExpandAll();
var node =
SkylineWindow.SequenceTree.Nodes[34].Nodes[0].Nodes[0];
SkylineWindow.SequenceTree.SelectedNode = node;
});
var pickList1 = ShowDialog <PopupPickList>(SkylineWindow.ShowPickChildrenInTest);
RunUI(() =>
{
pickList1.SearchString = "y"; // Not L10N
pickList1.SetItemChecked(0, false);
pickList1.SetItemChecked(1, false);
pickList1.ApplyFilter(false);
pickList1.ToggleFind();
pickList1.SearchString = "b ++"; // Not L10N
pickList1.SetItemChecked(4, true);
pickList1.SetItemChecked(6, true);
});
PauseForScreenShot <PopupPickList>("b ++ filtered picklist", 22); // Not L10N
RunUI(pickList1.OnOk);
}
// Bigger Picture, p. 22. Drag and Drop, p. 23
RunUI(() =>
{
ITipProvider nodeTip = SkylineWindow.SequenceTree.SelectedNode as ITipProvider;
Assert.IsTrue(nodeTip != null && nodeTip.HasTip);
var nodeName = SkylineWindow.SequenceTree.Nodes[1].Name;
IdentityPath selectPath;
SkylineWindow.ModifyDocument("Drag and drop", // Not L10N
doc => doc.MoveNode(SkylineWindow.Document.GetPathTo(0, 1), SkylineWindow.Document.GetPathTo(0, 0), out selectPath));
Assert.IsTrue(SkylineWindow.SequenceTree.Nodes[0].Name == nodeName);
});
FindNode(string.Format("L [b5] - {0:F04}+", 484.3130)); // Not L10N - may be localized " (rank 3)"
PauseForScreenShot("For Screenshots, First hover over YBL087C, then over 672.671+++", 23); // Not L10N
// Preparing to Measure, p. 25
RunDlg <TransitionSettingsUI>(() => SkylineWindow.ShowTransitionSettingsUI(TransitionSettingsUI.TABS.Prediction), transitionSettingsUI =>
{
transitionSettingsUI.RegressionCE = Settings.Default.GetCollisionEnergyByName("ABI 4000 QTrap"); // Not L10N
transitionSettingsUI.RegressionDP = Settings.Default.GetDeclusterPotentialByName("ABI"); // Not L10N
transitionSettingsUI.InstrumentMaxMz = 1800;
transitionSettingsUI.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument(TestFilesDirs[0].GetTestPath("MethodEdit Tutorial.sky"))); // Not L10N
var exportDialog = ShowDialog <ExportMethodDlg>(() =>
SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportDialog.ExportStrategy = ExportStrategy.Buckets;
exportDialog.MethodType = ExportMethodType.Standard;
exportDialog.OptimizeType = ExportOptimize.NONE;
exportDialog.IgnoreProteins = true;
exportDialog.MaxTransitions = 75;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 25); // Not L10N
const string basename = "Yeast_list"; // Not L10N
OkDialog(exportDialog, () => exportDialog.OkDialog(TestFilesDirs[0].GetTestPath(basename))); // write Yeast_list_000n.csv
// check the output files
for (int n = 0; n++ < 5;)
{
var csvname = String.Format("{0}_{1}.csv", basename, n.ToString("D4")); // Not L10N
// AssertEx.FieldsEqual is hard-coded with CultureInfo.InvariantCulture, but so is transition list CSV export, so OK
using (TextReader actual = new StreamReader(TestFilesDirs[0].GetTestPath(csvname)))
using (TextReader target = new StreamReader(TestFilesDirs[1].GetTestPath(csvname)))
{
AssertEx.FieldsEqual(target, actual, 6, null, true, TestSmallMolecules ? 3 : 0);
}
}
}
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()
{
var folderAbsoluteQuant = UseRawFiles ? "AbsoluteQuant" : "AbsoluteQuantMzml";
// Generating a Transition List, p. 4
{
var doc = SkylineWindow.Document;
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Thermo TSQ Vantage";
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.PrecursorCharges = "2";
transitionSettingsUI.ProductCharges = "1";
transitionSettingsUI.FragmentTypes = "y";
transitionSettingsUI.RangeFrom = Resources.TransitionFilter_FragmentStartFinders_ion_3;
transitionSettingsUI.RangeTo = Resources.TransitionFilter_FragmentEndFinders_last_ion_minus_1;
transitionSettingsUI.SpecialIons = new string[0];
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(doc);
}
// Configuring Peptide settings p. 4
PeptideSettingsUI peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() => peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Modifications);
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab", 5);
var modHeavyK = new StaticMod("Label:13C(6)15N(2) (C-term K)", "K", ModTerminus.C, false, null, LabelAtoms.C13 | LabelAtoms.N15,
RelativeRT.Matching, null, null, null);
AddHeavyMod(modHeavyK, peptideSettingsUI, "Edit Isotope Modification over Transition Settings", 5);
RunUI(() => peptideSettingsUI.PickedHeavyMods = new[] { modHeavyK.Name });
PauseForScreenShot <PeptideSettingsUI.ModificationsTab>("Peptide Settings - Modification tab with mod added", 5);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
// Inserting a peptide sequence p. 5
using (new CheckDocumentState(1, 1, 2, 10))
{
RunUI(() => SetClipboardText("IEAIPQIDK\tGST-tag"));
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPastePeptidesDlg);
RunUI(pasteDlg.PastePeptides);
WaitForProteinMetadataBackgroundLoaderCompletedUI();
PauseForScreenShot <PasteDlg.PeptideListTab>("Insert Peptide List", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
RunUI(SkylineWindow.ExpandPrecursors);
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
WaitForCondition(() => File.Exists(TestFilesDir.GetTestPath(folderAbsoluteQuant + @"test_file.sky")));
PauseForScreenShot("Main window with Targets view", 6);
// Exporting a transition list p. 6
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OptimizeType = ExportOptimize.NONE;
exportMethodDlg.MethodType = ExportMethodType.Standard;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List", 7);
OkDialog(exportMethodDlg, () =>
exportMethodDlg.OkDialog(TestFilesDir.GetTestPath("Quant_Abs_Thermo_TSQ_Vantage.csv")));
}
// Importing RAW files into Skyline p. 7
var importResultsDlg = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
PauseForScreenShot <ImportResultsDlg>("Import Results - click OK to get shot of Import Results Files and then cancel", 8);
RunUI(() =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Skip(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg.NamedPathSets = namedPathSets.ToArray();
});
RunDlg <ImportResultsNameDlg>(importResultsDlg.OkDialog,
importResultsNameDlg => importResultsNameDlg.NoDialog());
WaitForGraphs();
RunUI(() =>
{
SkylineWindow.SelectedPath = SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
Settings.Default.ArrangeGraphsOrder = GroupGraphsOrder.Document.ToString();
Settings.Default.ArrangeGraphsReversed = false;
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.AutoZoomBestPeak();
});
WaitForCondition(() => Equals(8, SkylineWindow.GraphChromatograms.Count(graphChrom => !graphChrom.IsHidden)),
"unexpected visible graphChromatogram count");
WaitForCondition(10 * 60 * 1000, // ten minutes
() => SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
PauseForScreenShot("Main window with imported data", 9);
// Analyzing SRM Data from FOXN1-GST Sample p. 9
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults,
importResultsDlg1 =>
{
var rawFiles = DataSourceUtil.GetDataSources(TestFilesDirs[0].FullPath).First().Value.Take(1);
var namedPathSets = from rawFile in rawFiles
select new KeyValuePair <string, MsDataFileUri[]>(
rawFile.GetFileNameWithoutExtension(), new[] { rawFile });
importResultsDlg1.NamedPathSets = namedPathSets.ToArray();
importResultsDlg1.OkDialog();
});
WaitForGraphs();
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
WaitForCondition(5 * 60 * 1000, // five minutes
() =>
SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
RunUI(() =>
{
SkylineWindow.ToggleIntegrateAll();
SkylineWindow.ArrangeGraphsTabbed();
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.ShowPeakAreaReplicateComparison();
// Total normalization
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
RunUI(() => SkylineWindow.ActivateReplicate("FOXN1-GST"));
WaitForGraphs();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 0));
WaitForGraphs();
RunUI(() =>
{
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphPeakArea.ResultsIndex);
Assert.AreEqual(SkylineWindow.SelectedResultsIndex, SkylineWindow.GraphRetentionTime.ResultsIndex);
});
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.First().TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for light", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.TransitionGroups, 1));
WaitForGraphs();
RunUI(() =>
{
int transitionCount = SkylineWindow.DocumentUI.PeptideTransitionGroups.ToArray()[1].TransitionCount;
CheckGstGraphs(transitionCount, transitionCount);
});
PauseForScreenShot("Main window with Peak Areas, Retention Times and FOXN1-GST for heavy", 10);
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Heavy normalization
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_ratio_view));
WaitForGraphs();
RunUI(() =>
{
int transitionGroupCount = SkylineWindow.DocumentUI.Peptides.First().TransitionGroupCount;
CheckGstGraphs(transitionGroupCount, transitionGroupCount - 1);
});
PauseForScreenShot("Main window with totals graphs for light and heavy and FOXN1-GST", 11);
const int columnsToAddCount = 4;
var columnSeparator = TextUtil.CsvSeparator;
// Generating a Calibration Curve p. 11
var exportLiveReportDlg = ShowDialog <ExportLiveReportDlg>(SkylineWindow.ShowExportReportDialog);
var editReportListDlg = ShowDialog <ManageViewsForm>(exportLiveReportDlg.EditList);
const string reportName = "Peptide Ratio Results Test";
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Sequence"),
PropertyPath.Parse("Proteins!*.Name"),
PropertyPath.Parse("Replicates!*.Name"),
PropertyPath.Parse("Proteins!*.Peptides!*.Results!*.Value.RatioToStandard"),
};
Assert.AreEqual(columnsToAddCount, columnsToAdd.Length);
{
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
viewEditor.ViewName = reportName;
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(columnsToAdd.Length, viewEditor.ChooseColumnsTab.ColumnCount);
});
// TODO: MultiViewProvider not yet supported in Common
PauseForScreenShot <ViewEditor>("Edit Report form", 12);
OkDialog(viewEditor, viewEditor.OkDialog);
}
RunUI(editReportListDlg.OkDialog);
WaitForClosedForm(editReportListDlg);
RunUI(() =>
{
exportLiveReportDlg.ReportName = reportName;
exportLiveReportDlg.OkDialog(TestFilesDir.GetTestPath("Calibration.csv"), columnSeparator);
});
// Check if export file is correct.
string filePath = TestFilesDir.GetTestPath("Calibration.csv");
Assert.IsTrue(File.Exists(filePath));
string[] lines = File.ReadAllLines(filePath);
string[] line0 = lines[0].Split(columnSeparator);
int count = line0.Length;
Assert.IsTrue(lines.Count() == SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count + 1);
Assert.AreEqual(columnsToAddCount, count);
// Check export file data
double ratio1 = Double.Parse(lines[1].Split(new[] { columnSeparator }, 4)[3]);
double ratio2 = Double.Parse(lines[2].Split(new[] { columnSeparator }, 4)[3]);
double ratio3 = Double.Parse(lines[3].Split(new[] { columnSeparator }, 4)[3]);
double ratio4 = Double.Parse(lines[4].Split(new[] { columnSeparator }, 4)[3]);
double ratio5 = Double.Parse(lines[5].Split(new[] { columnSeparator }, 4)[3]);
double ratio6 = Double.Parse(lines[6].Split(new[] { columnSeparator }, 4)[3]);
double ratio7 = Double.Parse(lines[7].Split(new[] { columnSeparator }, 4)[3]);
double ratio8 = Double.Parse(lines[8].Split(new[] { columnSeparator }, 4)[3]);
double ratio9 = Double.Parse(lines[9].Split(new[] { columnSeparator }, 4)[3]);
Assert.AreEqual(21.4513, ratio1, 0.1);
Assert.AreEqual(6.2568, ratio2, 0.1);
Assert.AreEqual(2.0417, ratio3, 0.1);
Assert.AreEqual(0.8244, ratio4, 0.1);
Assert.AreEqual(0.2809, ratio5, 0.1);
Assert.AreEqual(0.1156, ratio6, 0.1);
Assert.AreEqual(0.0819, ratio7, 0.1);
Assert.AreEqual(0.0248, ratio8, 0.1);
Assert.AreEqual(0.7079, ratio9, 0.1);
CheckReportCompatibility.CheckAll(SkylineWindow.Document);
}
