public void DoAgilentMseChromatogramTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, small_mol_mode smallMolMode = small_mol_mode.simple, string expectedError = null)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions && smallMolMode == small_mol_mode.simple)
{
System.Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath;
SrmDocument document = InitAgilentMseDocument(testFilesDir, out docPath);
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var refine = new RefinementSettings();
document = refine.ConvertToSmallMolecules(document, testFilesDir.FullPath, asSmallMolecules, smallMolMode == small_mol_mode.simple ? RefinementSettings.ConvertToSmallMoleculesChargesMode.none : RefinementSettings.ConvertToSmallMoleculesChargesMode.invert);
}
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var listChromatograms = new List <ChromatogramSet>();
var path = MsDataFileUri.Parse(smallMolMode == small_mol_mode.invert_charges_and_data ? @"AgilentMse\BSA-AI-0-10-25-41_first_100_scans_neg.mzML" : @"AgilentMse\BSA-AI-0-10-25-41_first_100_scans.mzML");
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
if (expectedError != null)
{
docContainer.AssertError(expectedError);
}
else
{
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var results = document.Settings.MeasuredResults;
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length);
VerifyMs1Truncated(chromGroupInfo.First());
}
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => !nodePep.Results[0].IsEmpty))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Any(chromInfo => chromInfo.PeakCountRatio > 0))
{
Assert.AreEqual(0.25205,
(double)nodePep.GetMeasuredRetentionTime(0), .0001, "averaged retention time differs in node " + nodePep.ModifiedTarget);
Assert.AreEqual(0.3333, (double)nodePep.GetPeakCountRatio(0), 0.0001);
nPeptides++;
}
}
Assert.AreEqual(smallMolMode == small_mol_mode.invert_charges ? 0 : 1, nPeptides); // If we switched document polarity, we'd expect no chromatograms extracted
}
}
testFilesDir.Dispose();
}
protected override void DoTest()
{
// iRT Retention Time Prediction
string standardDocumentFile = GetTestPath("iRT-C18 Standard.sky"); // Not L10N
RunUI(() => SkylineWindow.OpenFile(standardDocumentFile));
WaitForDocumentLoaded(); // might have some updating to do for protein metadata
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("iRT-C18 Calibrate.sky"))); // Not L10N
// Load raw files for iRT calculator calibration p. 2
const string unschedHuman1Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_1_30min-5-35"; // Not L10N
string unschedHuman1Name = unschedHuman1Fileroot.Substring(41);
const string unschedHuman2Fileroot = "A_D110907_SiRT_HELA_11_nsMRM_150selected_2_30min-5-35"; // Not L10N
string unschedHuman2Name = unschedHuman2Fileroot.Substring(41);
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, 41, false);
var docCalibrate = WaitForProteinMetadataBackgroundLoaderCompletedUI();
const int pepCount = 11, tranCount = 33;
AssertEx.IsDocumentState(docCalibrate, null, 1, pepCount, pepCount, tranCount);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman1Name, pepCount, pepCount, 0, tranCount, 0);
AssertResult.IsDocumentResultsState(docCalibrate, unschedHuman2Name, pepCount, pepCount, 0, tranCount, 0);
RunUI(() =>
{
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowRTPeptideGraph();
var enumLabels = SkylineWindow.RTGraphController.GraphSummary.Categories.GetEnumerator();
foreach (var nodePep in docCalibrate.Peptides)
{
Assert.IsTrue(enumLabels.MoveNext() && enumLabels.Current != null);
Assert.IsTrue(nodePep.Peptide.Sequence.StartsWith(enumLabels.Current.Substring(0, 3)));
}
});
// Page 3.
PauseForScreenShot <GraphSummary.RTGraphView>("RT graph metafile", 3); // Peptide RT graph
RunUI(() =>
{
SkylineWindow.ShowRTReplicateGraph();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, 0);
});
// Ensure graphs look like p. 3 and 4
WaitForGraphs();
RestoreViewOnScreen(04);
PauseForScreenShot("Main window showing chromatograms and RT graph", 4); // Skyline window with docked RT replicate comparison graph
RunUI(() =>
{
Assert.AreEqual(3, SkylineWindow.RTGraphController.GraphSummary.CurveCount);
Assert.AreEqual(2, SkylineWindow.RTGraphController.GraphSummary.Categories.Count());
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(11.3, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(11.2, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
});
var listTimes = new List <double>();
for (int i = 0; i < docCalibrate.PeptideCount; i++)
{
int iPeptide = i;
RunUI(() =>
{
SkylineWindow.SelectedPath = docCalibrate.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
});
WaitForGraphs();
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
double time1 = chromGraphs[0].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
double time2 = chromGraphs[1].GraphItems.First(g => g.BestPeakTime > 0).BestPeakTime;
listTimes.Add((time1 + time2) / 2);
Assert.AreEqual(time1, time2, 0.2);
});
}
// Calibrate a calculator p. 4-5
const string irtCalcName = "iRT-C18";
var peptideSettingsUI1 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var editIrtCalc1 = ShowDialog <EditIrtCalcDlg>(peptideSettingsUI1.AddCalculator);
RunUI(() =>
{
editIrtCalc1.CalcName = irtCalcName;
editIrtCalc1.CreateDatabase(GetTestPath("iRT-C18.irtdb")); // Not L10N
});
{
var calibrateDlg = ShowDialog <CalibrateIrtDlg>(editIrtCalc1.Calibrate);
RunUI(() =>
{
calibrateDlg.UseResults();
Assert.AreEqual(11, calibrateDlg.StandardPeptideCount);
calibrateDlg.SetFixedPoints(1, 10);
for (int i = 0; i < calibrateDlg.StandardPeptideCount; i++)
{
Assert.AreEqual(listTimes[i], calibrateDlg.StandardPeptideList[i].RetentionTime, 0.2);
}
});
PauseForScreenShot <CalibrateIrtDlg>("Calibrate iRT Calculator form", 5); // Calibrate iRT Calculator form
RunUI(calibrateDlg.OkDialog);
}
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc1.StandardPeptideCount == 11));
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculater form", 6); // Edit iRT Caclulator form
// Check iRT values and update to defined values p. 6-7
var irtDefinitionPath = GetTestPath("iRT definition.xlsx"); // Not L10N
string irtDefText = GetExcelFileText(irtDefinitionPath, "iRT-C18", 2, true); // Not L10N
RunUI(() =>
{
var standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.00001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.00001);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 6);
SetClipboardText(irtDefText);
editIrtCalc1.DoPasteStandard();
standardPeptidesArray = editIrtCalc1.StandardPeptides.ToArray();
Assert.AreEqual(11, standardPeptidesArray.Length);
Assert.AreEqual(0, standardPeptidesArray[1].Irt, 0.001);
Assert.AreEqual(100, standardPeptidesArray[10].Irt, 0.005);
CheckIrtStandardPeptides(standardPeptidesArray, irtDefText, 0.00001);
editIrtCalc1.OkDialog();
peptideSettingsUI1.OkDialog();
});
WaitForClosedForm(editIrtCalc1);
WaitForClosedForm(peptideSettingsUI1);
// Inspect RT regression graph p. 8
RunUI(SkylineWindow.ShowRTLinearRegressionGraph);
WaitForGraphs();
RestoreViewOnScreen(08);
PauseForScreenShot <GraphSummary.RTGraphView>("Retention Times Regression graph metafile", 8); // RT Regression graph
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
SkylineWindow.ShowSingleReplicate();
SkylineWindow.SequenceTree.Focus(); // If the focus is left on the results tab, then the next line does nothing
SkylineWindow.SelectedResultsIndex = 0;
});
WaitForGraphs();
RunUI(() =>
{
VerifyRTRegression(0.15, 15.15, 0.9991);
SkylineWindow.SelectedResultsIndex = 1;
});
WaitForGraphs();
RunUI(() => VerifyRTRegression(0.15, 15.04, 0.9991));
RunUI(() => SkylineWindow.ShowAverageReplicates());
RunUI(() => SkylineWindow.SaveDocument());
// Create a document containing human and standard peptides, p. 9
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human.sky")));
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RunUI(() =>
{
SkylineWindow.SelectedPath = new IdentityPath(SequenceTree.NODE_INSERT_ID);
SkylineWindow.ImportFiles(standardDocumentFile);
});
WaitForProteinMetadataBackgroundLoaderCompletedUI(); // let peptide metadata background loader do its work
RestoreViewOnScreen(09);
PauseForScreenShot("Targets tree clipped out of main winodw", 9); // Target tree
RunUI(() =>
{
Assert.AreEqual("iRT-C18 Standard Peptides", SkylineWindow.SelectedNode.Text); // Not L10N
Assert.AreEqual(1231, SkylineWindow.DocumentUI.PeptideTransitionCount);
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard.sky")); // Not L10N
SkylineWindow.SaveDocument(GetTestPath("iRT Human+Standard Calibrate.sky")); // Not L10N
});
// Remove heavy precursors, p. 10
var docHumanAndStandard = SkylineWindow.Document;
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.RefineLabelType = IsotopeLabelType.heavy;
refineDlg.OkDialog();
});
var docLightOnly = WaitForDocumentChange(docHumanAndStandard);
Assert.AreEqual(632, docLightOnly.PeptideTransitionCount);
// Create auto-calculate regression RT predictor, p. 10
const string irtPredictorName = "iRT-C18"; // Not L10N
{
var docPre = SkylineWindow.Document;
var peptideSettingsUI2 = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
var regressionDlg = ShowDialog <EditRTDlg>(peptideSettingsUI2.AddRTRegression);
RunUI(() =>
{
regressionDlg.SetRegressionName(irtPredictorName);
regressionDlg.ChooseCalculator(irtCalcName);
regressionDlg.SetAutoCalcRegression(true);
regressionDlg.SetTimeWindow(5);
});
PauseForScreenShot("Edit Retention Time Predictor form", 10); // Edit retention time predictor form
OkDialog(regressionDlg, regressionDlg.OkDialog);
OkDialog(peptideSettingsUI1, peptideSettingsUI2.OkDialog);
// Make sure iRT calculator is loaded
WaitForDocumentChangeLoaded(docPre);
}
// Export unscheduled transition list, p. 11
{
const string calibrateBasename = "iRT Human+Standard Calibrate"; // Not L10N
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.MaxTransitions = 335;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 11);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(calibrateBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
Assert.AreEqual(332, File.ReadAllLines(GetTestPath(calibrateBasename + "_0001.csv")).Length); // Not L10N
Assert.AreEqual(333 + (TestSmallMolecules ? 2 : 0), File.ReadAllLines(GetTestPath(calibrateBasename + "_0002.csv")).Length); // Not L10N
}
// Import human peptide calibration results p. 12
ImportNewResults(new[] { unschedHuman1Fileroot, unschedHuman2Fileroot }, -1, true);
// Review iRT-C18 graph p. 12-13
RunUI(() => SkylineWindow.ChooseCalculator(irtCalcName));
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 13);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.9991);
Assert.AreEqual(11, SkylineWindow.DocumentUI.PeptideCount -
SkylineWindow.RTGraphController.Outliers.Length);
});
// Find all unintegrated transitions, p. 13-14
{
var findDlg = ShowDialog <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg);
RunUI(() =>
{
findDlg.FindOptions = new FindOptions().ChangeText(string.Empty)
.ChangeCustomFinders(Finders.ListAllFinders().Where(f => f is UnintegratedTransitionFinder));
});
PauseForScreenShot <FindNodeDlg>("Find form", 14);
RestoreViewOnScreen(15);
RunUI(() =>
{
findDlg.FindAll();
findDlg.Close();
});
WaitForClosedForm(findDlg);
}
PauseForScreenShot <FindResultsForm>("Find Results pane", 14);
var findAllForm = WaitForOpenForm <FindResultsForm>();
Assert.IsNotNull(findAllForm);
const int expectedItems = 8;
RunUI(() =>
{
Assert.AreEqual(expectedItems, findAllForm.ItemCount);
SkylineWindow.ShowAllTransitions();
SkylineWindow.AutoZoomBestPeak();
});
// Review peaks with missing transitions, p. 15
for (int i = 0; i < expectedItems; i++)
{
int iItem = i;
RunUI(() => findAllForm.ActivateItem(iItem));
WaitForGraphs();
RunUI(() => Assert.AreEqual((int)SequenceTree.StateImageId.no_peak,
SkylineWindow.SelectedNode.StateImageIndex));
if (i == 2)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (1 of 2)", 15);
}
if (i == 3)
{
RunUI(() =>
{
var document = SkylineWindow.DocumentUI;
var nodeGroup = document.FindNode(SkylineWindow.SelectedPath.Parent) as TransitionGroupDocNode;
Assert.IsNotNull(nodeGroup);
var nodeTran = document.FindNode(SkylineWindow.SelectedPath) as TransitionDocNode;
Assert.IsNotNull(nodeTran);
var graph = SkylineWindow.GetGraphChrom(Resources.ImportResultsDlg_DefaultNewName_Default_Name);
// New peak picking picks correct peak
Assert.AreEqual(19.8, graph.BestPeakTime.Value, 0.05);
// TransitionGroupDocNode nodeGroupGraph;
// TransitionDocNode nodeTranGraph;
// var scaledRT = graph.FindAnnotatedPeakRetentionTime(19.8, out nodeGroupGraph, out nodeTranGraph);
// Assert.AreSame(nodeGroup, nodeGroupGraph);
// Assert.AreNotSame(nodeTran, nodeTranGraph);
// Assert.AreEqual(7, nodeTranGraph.Transition.Ordinal); // y7
// graph.FirePickedPeak(nodeGroupGraph, nodeTranGraph, scaledRT);
});
}
if (i == 4)
{
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile (2 of 2)", 15); // Chromatogram graph
}
}
// New peak picking picks correct peak
// RunUI(() => findAllForm.ActivateItem(3));
// PauseForScreenShot<GraphChromatogram>("Chromatogram graph metafile (3 of 3)", 15);
RunUI(SkylineWindow.ToggleIntegrateAll);
RunUI(findAllForm.Close);
WaitForClosedForm(findAllForm);
RestoreViewOnScreen(17);
// Calculate new iRT values for human peptides, p. 16
{
var editIrtCalc2 = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
RunUI(() => Assert.AreEqual(0, editIrtCalc2.LibraryPeptideCount));
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc2.AddResults);
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 15);
RunUI(() =>
{
Assert.AreEqual(148, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(0, addPeptidesDlg.RunsFailedCount);
addPeptidesDlg.OkDialog();
});
WaitForClosedForm(addPeptidesDlg);
PauseForScreenShot <EditIrtCalcDlg>("Edit iRT Calculator form", 16);
RunUI(() => Assert.AreEqual(148, editIrtCalc2.LibraryPeptideCount));
RunUI(editIrtCalc2.OkDialog);
WaitForClosedForm(editIrtCalc2);
}
// Check the RT regression, p. 17
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 17);
RunUI(() =>
{
VerifyRTRegression(0.15, 15.09, 0.99985);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
SkylineWindow.SaveDocument();
SkylineWindow.HideFindResults();
});
// Recalibrate method to 90-minute gradient, p. 18
RunUI(() => SkylineWindow.OpenFile(GetTestPath("iRT Human+Standard.sky"))); // Not L10N
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("NSAQ"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
RunUI(SkylineWindow.EditDelete);
{
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Prediction;
peptideSettingsUI.ChooseRegression(irtPredictorName);
peptideSettingsUI.IsUseMeasuredRT = true;
peptideSettingsUI.TimeWindow = 5;
});
PauseForScreenShot <PeptideSettingsUI.PredictionTab>("Peptide Settings - Prediction tab", 18);
RunUI(peptideSettingsUI.OkDialog);
WaitForClosedForm(peptideSettingsUI);
}
// Import 90-minute standard mix run, p. 19
const string unsched90MinFileroot = "A_D110913_SiRT_HELA_11_nsMRM_150selected_90min-5-40_TRID2215_01"; // Not L10N
ImportNewResults(new[] { unsched90MinFileroot }, -1, false);
WaitForGraphs();
// Verify regression graph, p. 19
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 19);
RunUI(() =>
{
VerifyRTRegression(0.40, 24.77, 0.9998);
Assert.AreEqual(147, SkylineWindow.RTGraphController.Outliers.Length);
});
// Check scheduling graph, p. 20
RunUI(SkylineWindow.ShowRTSchedulingGraph);
RunDlg <SchedulingGraphPropertyDlg>(SkylineWindow.ShowRTPropertyDlg, propertyDlg =>
{
propertyDlg.TimeWindows = new[] { 2.0, 5.0, 10.0 };
propertyDlg.OkDialog();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Scheduling graph metafile", 20);
// Export new 90-minute scheduled transition list, p. 22
const string scheduledBasename = "iRT Human+Standard"; // Not L10N
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 265;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 21);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath(scheduledBasename + TextUtil.EXT_CSV)));
WaitForClosedForm(exportMethodDlg);
}
Assert.AreEqual(1223 + (TestSmallMolecules ? 4 : 0), File.ReadAllLines(GetTestPath(scheduledBasename + "_0001.csv")).Length); // Not L10N
Assert.IsFalse(File.Exists(GetTestPath("iRT Human+Standard_0002.csv"))); // Not L10N
// Import scheduled data, p. 23
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, manageResultsDlg =>
{
manageResultsDlg.RemoveAllReplicates();
manageResultsDlg.OkDialog();
});
RunUI(() => SkylineWindow.SaveDocument());
const string sched90MinFileroot = "A_D110913_SiRT_HELA_11_sMRM_150selected_90min-5-40_SIMPLE"; // Not L10N
ImportNewResults(new[] { sched90MinFileroot }, -1, false);
RunUI(SkylineWindow.ShowRTLinearRegressionGraph);
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 23);
// Review regression and outliers, p. 24
RunUI(() =>
{
VerifyRTRegression(0.358, 25.920, 0.9162);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
RunDlg <RegressionRTThresholdDlg>(SkylineWindow.ShowRegressionRTThresholdDlg, thresholdDlg =>
{
thresholdDlg.Threshold = 0.998;
thresholdDlg.OkDialog();
});
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 24);
// Verify 2 outliers highlighed and removed, p. 25
WaitForConditionUI(() => SkylineWindow.RTGraphController.Outliers.Length == 2);
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
SkylineWindow.RemoveRTOutliers();
});
WaitForGraphs();
PauseForScreenShot <GraphSummary.RTGraphView>("RT Regression graph metafile", 25);
// Check outlier removal, p. 25
RunUI(() =>
{
VerifyRTRegression(0.393, 24.85, 0.9989);
Assert.AreEqual(0, SkylineWindow.RTGraphController.Outliers.Length);
});
// Review a peak and its predicted retention time, p. 26
RunDlg <FindNodeDlg>(SkylineWindow.ShowFindNodeDlg, findDlg =>
{
findDlg.FindOptions = new FindOptions().ChangeText("DATNVG"); // Not L10N
findDlg.FindNext();
findDlg.Close();
});
WaitForGraphs();
RestoreViewOnScreen(27);
PauseForScreenShot <GraphChromatogram>("Chromatogram graph metafile", 26); // Chromatogram graph
RunUI(() =>
{
var graphChrom = SkylineWindow.GetGraphChrom(sched90MinFileroot);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(47.3, graphChrom.BestPeakTime.Value, 0.05);
Assert.IsTrue(graphChrom.PredictedRT.HasValue);
Assert.AreEqual(47.6, graphChrom.PredictedRT.Value, 0.05);
});
// Import retention times from a spectral library, p. 27
RestoreViewOnScreen(17); // get regression graph back
{
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addLibrayDlg = ShowDialog <AddIrtSpectralLibrary>(editIrtCalc.AddLibrary);
RunUI(() =>
{
addLibrayDlg.Source = SpectralLibrarySource.file;
addLibrayDlg.FilePath = GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast_iRT_C18_0_00001.blib")); // Not L10N
});
PauseForScreenShot <AddIrtSpectralLibrary>("Add Spectral Library form", 27);
// Verify converted peptide iRT values and OK dialogs, p. 28
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(addLibrayDlg.OkDialog);
RunUI(() =>
{
Assert.AreEqual(558, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(3, addPeptidesDlg.KeepPeptidesCount);
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 28);
RunUI(addPeptidesDlg.OkDialog);
WaitForClosedForm(addPeptidesDlg);
RunUI(addLibrayDlg.OkDialog);
WaitForClosedForm(addLibrayDlg);
Assert.IsTrue(WaitForConditionUI(() => editIrtCalc.LibraryPeptideCount == 706));
RunUI(editIrtCalc.OkDialog);
WaitForClosedForm(editIrtCalc);
}
// Inspect MS1 filtered Skyline file created from library DDA data, p. 29
RunUI(() => SkylineWindow.OpenFile(GetTestPath(Path.Combine("Yeast+Standard", // Not L10N
"Yeast+Standard (refined) - 2min.sky"))));
WaitForDocumentLoaded();
RunUI(() => SkylineWindow.SelectedPath = SkylineWindow.DocumentUI.GetPathTo((int)SrmDocument.Level.Molecules, 0));
WaitForGraphs();
// Verify numbers that show up in the screenshot
RunUI(() =>
{
// If the cache gets rebuilt, then because the chromatograms
// were minimized, the peak picking is not exactly the same
// using the minimized chromatograms.
VerifyRTRegression(0.3, 19.47, 0.9998);
var graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_16"); // Not L10N
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[0], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.6, graphChrom.BestPeakTime.Value, 0.05);
graphChrom = SkylineWindow.GetGraphChrom("Velos_2011_1110_RJ_14"); // Not L10N
Assert.AreEqual(37.3, graphChrom.RetentionMsMs[0], 0.05);
Assert.AreEqual(37.6, graphChrom.RetentionMsMs[1], 0.05);
Assert.IsTrue(graphChrom.BestPeakTime.HasValue);
Assert.AreEqual(37.4, graphChrom.BestPeakTime.Value, 0.05);
});
PauseForScreenShot("Main window", 29);
// Add results and verify add dialog counts, p. 29-30
{
var editIrtCalc = ShowDialog <EditIrtCalcDlg>(SkylineWindow.ShowEditCalculatorDlg);
var addPeptidesDlg = ShowDialog <AddIrtPeptidesDlg>(editIrtCalc.AddResults);
RunUI(() =>
{
Assert.AreEqual(0, addPeptidesDlg.PeptidesCount);
Assert.AreEqual(2, addPeptidesDlg.RunsConvertedCount);
Assert.AreEqual(558, addPeptidesDlg.OverwritePeptidesCount);
Assert.AreEqual(3, addPeptidesDlg.ExistingPeptidesCount);
});
PauseForScreenShot <AddIrtPeptidesDlg>("Add Peptides form", 30);
RunUI(addPeptidesDlg.OkDialog);
WaitForClosedForm(addPeptidesDlg);
RunUI(editIrtCalc.OkDialog);
WaitForClosedForm(editIrtCalc);
}
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
private void WatersImsMseChromatogramTest(DriftFilterType mode,
IonMobilityWindowWidthCalculator.IonMobilityPeakWidthType driftPeakWidthCalcType,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions)
{
Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION);
return;
}
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, driftPeakWidthCalcType, withDriftTimeFilter, withDriftTimePredictor, out docPath);
AssertEx.IsDocumentState(document, null, 1, 1, 1, 8); // Drift time lib load bumps the doc version, so does small mol conversion
var listChromatograms = new List <ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
string mz5Path = "waters-mobility" + ExtensionTestContext.ExtMz5;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
testModeStr = "with drift times from spectral library";
}
listChromatograms.Add(AssertResult.FindChromatogramSet(document, new MsDataFilePath(mz5Path)) ??
new ChromatogramSet(Path.GetFileName(mz5Path).Replace('.', '_'), new[] { mz5Path }));
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
var doc = docContainer.Document;
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assume.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
document = docContainer.Document;
}
document = ConvertToSmallMolecules(document, ref docPath, new[] { mz5Path }, asSmallMolecules);
using (var docContainer = new ResultsTestDocumentContainer(document, docPath))
{
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assume.AreEqual(1, document.MoleculePrecursorPairs.Count());
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assume.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assume.AreEqual(1, chromGroupInfo.Length, testModeStr);
var chromGroup = chromGroupInfo[0];
int expectedPeaks;
if (withDriftTimeFilter)
{
expectedPeaks = 3;
}
else if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
expectedPeaks = 5;
}
else
{
expectedPeaks = 6; // No libraries
}
Assume.AreEqual(expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assume.AreEqual(withDriftTimeFilter ? 5226 : 20075, maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => !nodePep.Results[0].IsEmpty))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assume.AreEqual(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assume.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assume.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath =
testFilesDir.GetTestPath(complete == 1 ? "share_complete.zip" : "share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath,
new ShareType(complete == 1, SkylineVersion.CURRENT)); // Explicitly declaring version number forces a save before zip
share.Share(new SilentProgressMonitor());
var files = share.ListEntries().ToArray();
var imdbFile = withDriftTimePredictor ? "scaled.imdb" : "waters-mobility.filtered-scaled.blib";
if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)
{
var ext = "." + imdbFile.Split('.').Last();
imdbFile = imdbFile.Replace(ext, BiblioSpecLiteSpec.DotConvertedToSmallMolecules + ext);
}
Assume.IsTrue(files.Contains(imdbFile));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
share.Extract(new SilentProgressMonitor());
using (var cmdline = new CommandLine())
{
Assume.IsTrue(cmdline.OpenSkyFile(share.DocumentPath)); // Handles any path shifts in database files, like our .imdb file
var document2 = cmdline.Document;
Assume.IsNotNull(document2);
Assume.IsTrue(docContainer.SetDocument(document2, docContainer.Document, true));
docContainer.AssertComplete();
document2 = docContainer.Document;
var im = document2.Settings.GetIonMobilities(document2.MoleculeLibKeys.ToArray(), new MsDataFilePath(mz5Path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document2.Settings.GetIonMobility(
pep, nodeGroup, null, im, null, driftTimeMax, out windowDT);
Assume.AreEqual(3.86124, centerDriftTime.IonMobility.Mobility.Value, .0001, testModeStr);
Assume.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
}
}
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules,
out List <SrmDocument> docCheckpoints, bool centroided = false)
{
docCheckpoints = new List <SrmDocument>();
TestSmallMolecules = false; // We test small molecules explicitly
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
string docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_multi.sky");
var expectedPepCount = 7;
var expectedTransGroupCount = 7;
var expectedTransCount = 49;
var doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
if (centroided && ExtensionTestContext.CanImportThermoRaw)
{
const double ppm20 = 20.0;
doc = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm20, 0)));
}
using (var docContainer = new ResultsTestDocumentContainer(doc, docPath))
{
// Import the first RAW file (or mzML for international)
string rawPath = testFilesDir.GetTestPath("ah_20101011y_BSA_MS-MS_only_5-2" +
ExtensionTestContext.ExtThermoRaw);
var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { new MsDataFilePath(rawPath) }) });
SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21);
docCheckpoints.Add(docResults);
// Refilter allowing multiple precursors per spectrum
SrmDocument docMulti = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(
fs => fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.DIA, new IsolationScheme("Test", 2))));
AssertEx.Serializable(docMulti, AssertEx.DocumentCloned);
// Release data cache file
Assert.IsTrue(docContainer.SetDocument(docMulti, docResults));
// And remove it
FileEx.SafeDelete(Path.ChangeExtension(docPath, ChromatogramCache.EXT));
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 6, 6, 38));
// Import full scan Orbi-Velos data
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_long_acc_template.sky");
expectedPepCount = 3;
expectedTransGroupCount = 3;
expectedTransCount = 21;
doc = InitFullScanDocument(docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
docCheckpoints.Add(doc);
Assert.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
// Make sure saving this type of document works
AssertEx.Serializable(doc, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(doc, docContainer.Document));
rawPath = testFilesDir.GetTestPath("ah_20101029r_BSA_CID_FT_centroid_3uscan_3" +
ExtensionTestContext.ExtThermoRaw);
measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Accurate", new[] { rawPath }) });
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 3, 3, 21));
// Import LTQ data with MS1 and MS/MS
docPath = testFilesDir.GetTestPath("BSA_Protea_label_free_20100323_meth3_test4.sky");
expectedPepCount = 3;
expectedTransGroupCount = 4;
expectedTransCount = 32;
doc = InitFullScanDocument(docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
docCheckpoints.Add(doc);
var docBoth = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangeAcquisitionMethod(FullScanAcquisitionMethod.Targeted, null)
.ChangePrecursorResolution(FullScanMassAnalyzerType.qit, TransitionFullScan.DEFAULT_RES_QIT, null)));
docCheckpoints.Add(docBoth);
AssertEx.Serializable(docBoth, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docBoth, docContainer.Document));
string dataPath = testFilesDir.GetTestPath("klc_20100329v_Protea_Peptide_Curve_200fmol_uL_tech1.mzML");
var listResults = new List <ChromatogramSet>
{
new ChromatogramSet("MS1 and MS/MS", new[] { dataPath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount, expectedTransGroupCount, expectedTransCount - 6));
// The mzML was filtered for the m/z range 410 to 910.
foreach (var nodeTran in docContainer.Document.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.IsNotNull(nodeTran.Results[0]);
if (410 > nodeTran.Mz || nodeTran.Mz > 910)
{
Assert.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
else
{
Assert.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
}
// Import LTQ data with MS1 and MS/MS using multiple files for a single replicate
listResults.Add(new ChromatogramSet("Multi-file", new[]
{
testFilesDir.GetTestPath("both_DRV.mzML"),
testFilesDir.GetTestPath("both_KVP.mzML"),
}));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, expectedPepCount - 1, expectedTransGroupCount - 1, expectedTransCount - 6));
int indexResults = listResults.Count - 1;
foreach (var nodeTran in docContainer.Document.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(listResults.Count, nodeTran.Results.Count);
var peptide = nodeTran.Transition.Group.Peptide;
// DRV without FASTA sequence should not have data for non-precursor transitions
if (!peptide.Sequence.StartsWith("DRV") || !peptide.Begin.HasValue)
{
Assert.IsNotNull(nodeTran.Results[indexResults]);
Assert.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
}
else if (nodeTran.Transition.IonType != IonType.precursor)
{
Assert.IsNull(nodeTran.Results[indexResults]);
}
else
{
// Random, bogus peaks chosen in both files
Assert.IsNotNull(nodeTran.Results[indexResults]);
Assert.AreEqual(2, nodeTran.Results[indexResults].Count);
Assert.IsFalse(nodeTran.Results[indexResults][0].IsEmpty);
Assert.IsFalse(nodeTran.Results[indexResults][1].IsEmpty);
}
}
if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
return; // Can't work with isotope distributions when we don't have ion formulas
}
// Verify handling of bad request for vendor centroided data - out-of-range PPM
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docBad = doc;
AssertEx.ThrowsException <InvalidDataException>(() =>
docBad.ChangeSettings(docBad.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, 50 * 1000, 400))),
string.Format(Resources.TransitionFullScan_ValidateRes_Mass_accuracy_must_be_between__0__and__1__for_centroided_data_,
TransitionFullScan.MIN_CENTROID_PPM, TransitionFullScan.MAX_CENTROID_PPM));
// Verify relationship between PPM and resolving power
const double ppm = 20.0; // Should yield same filter width as resolving power 50,000 in TOF
var docNoCentroid = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0)));
AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document));
const double mzTest = 400.0;
var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest);
Assert.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth);
// Verify handling of bad request for vendor centroided data - ask for centroiding in mzML
const string fileName = "S_2_LVN.mzML";
var filePath = testFilesDir.GetTestPath(fileName);
AssertEx.ThrowsException <AssertFailedException>(() =>
{
listResults = new List <ChromatogramSet> {
new ChromatogramSet("rep1", new[] { new MsDataFilePath(filePath, null, true) }),
};
docContainer.ChangeMeasuredResults(new MeasuredResults(listResults.ToArray()), 1, 1, 1);
},
string.Format(Resources.NoCentroidedDataException_NoCentroidedDataException_No_centroided_data_available_for_file___0_____Adjust_your_Full_Scan_settings_, filePath));
// Import FT data with only MS1
docPath = testFilesDir.GetTestPath("Yeast_HI3 Peptides_test.sky");
expectedPepCount = 2;
expectedTransGroupCount = 2;
expectedTransCount = 2;
doc = InitFullScanDocument(docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer);
Assert.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer);
var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null)));
Assert.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest));
docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs =>
fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichments.DEFAULT)
.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest)));
AssertEx.Serializable(docMs1, AssertEx.DocumentCloned);
Assert.IsTrue(docContainer.SetDocument(docMs1, docContainer.Document));
const string rep1 = "rep1";
listResults = new List <ChromatogramSet>
{
new ChromatogramSet(rep1, new[] { filePath }),
};
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(1, nodeTran.Results.Count);
if ((nodeTran.Transition.Group.Peptide.IsCustomIon
? nodeTranGroup.CustomIon.Name
: nodeTran.Transition.Group.Peptide.Sequence).StartsWith("LVN"))
{
Assert.IsFalse(nodeTran.Results[0][0].IsEmpty);
}
else
{
Assert.IsTrue(nodeTran.Results[0][0].IsEmpty);
}
}
}
const string rep2 = "rep2";
listResults.Add(new ChromatogramSet(rep2, new[] { testFilesDir.GetTestPath("S_2_NVN.mzML") }));
measuredResults = new MeasuredResults(listResults.ToArray());
docCheckpoints.Add(docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 1));
// Because of the way the mzML files were filtered, all of the LVN peaks should be present
// in the first replicate, and all of the NVN peaks should be present in the other.
foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups)
{
foreach (var docNode in nodeTranGroup.Children)
{
var nodeTran = (TransitionDocNode)docNode;
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(2, nodeTran.Results.Count);
if ((nodeTran.Transition.Group.Peptide.IsCustomIon
? nodeTranGroup.CustomIon.Name
: nodeTran.Transition.Group.Peptide.Sequence).StartsWith("LVN"))
{
Assert.IsTrue(nodeTran.Results[1][0].IsEmpty);
}
else
{
Assert.IsFalse(nodeTran.Results[1][0].IsEmpty);
}
}
}
// Chromatograms should be present in the cache for a number of isotopes.
var docMs1Isotopes = docContainer.Document.ChangeSettings(doc.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count,
3, IsotopeEnrichments.DEFAULT))
.ChangeTransitionFilter(filter => filter.ChangeIonTypes(new[] { IonType.precursor })));
docCheckpoints.Add(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 2); // Need to reset auto-manage for transitions
var refineAutoSelect = new RefinementSettings {
AutoPickChildrenAll = PickLevel.transitions
};
docMs1Isotopes = refineAutoSelect.Refine(docMs1Isotopes);
AssertEx.IsDocumentState(docMs1Isotopes, null, 2, 2, 6);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep1, 1, 1, 0, 3, 0);
AssertResult.IsDocumentResultsState(docMs1Isotopes, rep2, 1, 1, 0, 3, 0);
docCheckpoints.Add(docMs1Isotopes);
// Add M-1 transitions, and verify that they have chromatogram data also, but
// empty peaks in all cases
var docMs1All = docMs1Isotopes.ChangeSettings(docMs1Isotopes.Settings
.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent,
0, IsotopeEnrichments.DEFAULT))
.ChangeTransitionIntegration(i => i.ChangeIntegrateAll(false))); // For compatibility with v2.5 and earlier
docCheckpoints.Add(docMs1All);
AssertEx.IsDocumentState(docMs1All, null, 2, 2, 10);
AssertResult.IsDocumentResultsState(docMs1All, rep1, 1, 1, 0, 4, 0);
AssertResult.IsDocumentResultsState(docMs1All, rep2, 1, 1, 0, 4, 0);
var ms1AllTranstions = docMs1All.MoleculeTransitions.ToArray();
var tranM1 = ms1AllTranstions[0];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(tranM1.Results[0] != null && tranM1.Results[1] != null);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsEmpty);
tranM1 = ms1AllTranstions[5];
Assert.AreEqual(-1, tranM1.Transition.MassIndex);
Assert.IsTrue(tranM1.Results[0] != null && tranM1.Results[1] != null);
Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsEmpty);
}
}
public INumberAssertion <T> IsLessThan(T comparedTo)
{
Extend(x => AssertResult.New(x.CompareTo(comparedTo) < 0, Resources.IsSmallerThan, comparedTo));
return(this);
}
protected override void DoTest()
{
var files = new [] {"8fmol.mz5", "20fmol.mz5", "40fmol.mz5", "200fmol.mz5"};
OpenDocument("RetentionTimeFilterTest.sky");
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("TestImportResultsCancel.sky"))); // Make a clean copy
// Try individual cancellation - can be timing dependent (do we get to the cancel button quickly enough?) so allow some retry
for (var retry = 10; retry-- > 0;)
{
OpenDocument("TestImportResultsCancel.sky");
ImportResultsAsync(files);
var dlg2 = WaitForOpenForm<AllChromatogramsGraph>();
WaitForCondition(30 * 1000, () => dlg2.ProgressTotalPercent >= 1); // Get a least a little way in
var cancelTarget = files[retry % 4].Replace(".mz5", "");
RunUI(() => dlg2.FileButtonClick(cancelTarget));
WaitForDocumentLoaded();
foreach (var file in files)
{
int index;
ChromatogramSet chromatogramSet;
var chromatogramSetName = file.Replace(".mz5", "");
// Can we find a loaded chromatogram set by this name?
SkylineWindow.Document.Settings.MeasuredResults.TryGetChromatogramSet(chromatogramSetName, out chromatogramSet, out index);
if (!chromatogramSetName.Equals(cancelTarget))
{
// Should always find it since we didn't try to cancel this one
Assert.AreNotEqual(-1, index);
}
else
{
// Should not find anything by that name, but sometimes we're not quick enough on the cancel button
if (retry == 0)
{
Assert.AreEqual(-1, index); // No more retries, declare failure or success
}
else if (index == -1)
{
retry = 0; // Success, no more retry needed
}
else
{
break; // Go back and retry
}
}
}
}
// Cancelled load should revert to initial document
OpenDocument("RetentionTimeFilterTest.sky");
var docUnloaded = SkylineWindow.Document;
ImportResultsAsync(files);
var dlg = WaitForOpenForm<AllChromatogramsGraph>();
WaitForCondition(30 * 1000, () => dlg.ProgressTotalPercent >= 1); // Get a least a little way in
RunUI(() => dlg.ClickCancel()); // Simulate user clicking the cancel button
Assert.AreEqual(docUnloaded, SkylineWindow.Document);
Assert.IsFalse(SkylineWindow.Document.Settings.HasResults);
// Now try a proper import
ImportResults(files);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "8fmol", 4, 4, 0, 13, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "20fmol", 5, 5, 0, 13, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "40fmol", 3, 3, 0, 11, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "200fmol", 4, 4, 0, 12, 0);
}
/* TODO bspratt drift time libs for small molecules
*
* [TestMethod]
* public void WatersImsMsePredictedDriftTimesChromatogramTestAsSmallMolecules()
* {
* WatersImsMseChromatogramTest(DriftFilterType.predictor, true);
* }
*
* [TestMethod]
* public void WatersImsMseLibraryDriftTimesChromatogramTestAsSmallMolecules()
* {
* WatersImsMseChromatogramTest(DriftFilterType.library, true);
* }
*
*/
private void WatersImsMseChromatogramTest(DriftFilterType mode,
RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules = RefinementSettings.ConvertToSmallMoleculesMode.none)
{
string subdir = (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.none) ? null : asSmallMolecules.ToString();
var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE, subdir);
TestSmallMolecules = false; // Don't need that extra magic node
bool withDriftTimePredictor = (mode == DriftFilterType.predictor); // Load the doc that has a drift time predictor?
bool withDriftTimeFilter = (mode != DriftFilterType.none); // Perform drift time filtering? (either with predictor, or with bare times in blib file)
string docPath;
SrmDocument document = InitWatersImsMseDocument(testFilesDir, withDriftTimePredictor ? "single_with_driftinfo.sky" : "single_no_driftinfo.sky", asSmallMolecules, out docPath);
AssertEx.IsDocumentState(document, (withDriftTimePredictor || (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none)) ? 1 : 0, 1, 1, 1, 8); // Drift time lib load bumps the doc version
var docContainer = new ResultsTestDocumentContainer(document, docPath);
var doc = docContainer.Document;
var docOriginal = doc;
string testModeStr = withDriftTimePredictor ? "with drift time predictor" : "without drift time info";
if (withDriftTimeFilter && !withDriftTimePredictor)
{
// Use the bare drift times in the spectral library
var librarySpec = new BiblioSpecLiteSpec("drift test",
testFilesDir.GetTestPath("mse-mobility.filtered-scaled.blib"));
doc = doc.ChangeSettings(
doc.Settings.ChangePeptideLibraries(lib => lib.ChangeLibrarySpecs(new[] { librarySpec })).
ChangePeptidePrediction(p => p.ChangeLibraryDriftTimesResolvingPower(100)).
ChangePeptidePrediction(p => p.ChangeUseLibraryDriftTimes(true))
);
testModeStr = "with drift times from spectral library";
}
var listChromatograms = new List <ChromatogramSet>();
// A small subset of the QC_HDMSE_02_UCA168_3495_082213 data set (RT 21.5-22.5) from Will Thompson
const string path = @"waters-mobility.mz5";
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, new MsDataFilePath(path)) ??
new ChromatogramSet(Path.GetFileName(path).Replace('.', '_'), new[] { path }));
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, docOriginal, true));
docContainer.AssertComplete();
document = docContainer.Document;
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
double maxHeight = 0;
var results = document.Settings.MeasuredResults;
Assert.AreEqual(1, document.MoleculePrecursorPairs.Count());
foreach (var pair in document.MoleculePrecursorPairs)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(results.TryLoadChromatogram(0, pair.NodePep, pair.NodeGroup,
tolerance, true, out chromGroupInfo));
Assert.AreEqual(1, chromGroupInfo.Length, testModeStr);
var chromGroup = chromGroupInfo[0];
var expectedPeaks = ((asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) ? 6 : 5);
Assert.AreEqual(withDriftTimeFilter ? 3 : expectedPeaks, chromGroup.NumPeaks, testModeStr); // This will be higher if we don't filter on DT
foreach (var tranInfo in chromGroup.TransitionPointSets)
{
maxHeight = Math.Max(maxHeight, tranInfo.MaxIntensity);
}
}
Assert.AreEqual(withDriftTimeFilter? 5226 : 20075, maxHeight, 1, testModeStr); // Without DT filtering, this will be much greater
// now drill down for specific values
int nPeptides = 0;
foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null))
{
// expecting just one peptide result in this small data set
if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0)
{
Assert.AreEqual(21.94865, (double)nodePep.GetMeasuredRetentionTime(0), .0001, testModeStr);
Assert.AreEqual(1.0, (double)nodePep.GetPeakCountRatio(0), 0.0001, testModeStr);
nPeptides++;
}
}
Assert.AreEqual(1, nPeptides);
if (withDriftTimePredictor || withDriftTimeFilter)
{
// Verify that the .imdb pr .blib file goes out in the share zipfile
for (int complete = 0; complete <= 1; complete++)
{
var sharePath = testFilesDir.GetTestPath(complete == 1?"share_complete.zip":"share_minimized.zip");
var share = new SrmDocumentSharing(document, docPath, sharePath, complete == 1);
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest -- sharing document",
})
{
longWaitDlg.PerformWork(null, 1000, share.Share);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
var files = share.ListEntries().ToArray();
Assert.IsTrue(files.Contains(withDriftTimePredictor ? "scaled.imdb" : "mse-mobility.filtered-scaled.blib"));
// And round trip it to make sure we haven't left out any new features in minimized imdb or blib files
using (var longWaitDlg = new LongWaitDlg
{
// ReSharper disable once LocalizableElement
Text = "unit test WatersImsTest",
})
{
longWaitDlg.PerformWork(null, 1000, share.Extract);
Assert.IsFalse(longWaitDlg.IsCanceled);
}
using (TextReader reader = new StreamReader(share.DocumentPath))
{
XmlSerializer documentSerializer = new XmlSerializer(typeof(SrmDocument));
var document2 = (SrmDocument)documentSerializer.Deserialize(reader);
Assert.IsNotNull(document2);
var im = document.Settings.GetIonMobilities(new MsDataFilePath(path));
var pep = document2.Molecules.First();
foreach (TransitionGroupDocNode nodeGroup in pep.Children)
{
double windowDT;
var centerDriftTime = document.Settings.PeptideSettings.Prediction.GetDriftTime(
pep, nodeGroup, im, out windowDT);
Assert.AreEqual(3.86124, centerDriftTime.DriftTimeMsec(false) ?? 0, .0001, testModeStr);
Assert.AreEqual(0.077224865797235934, windowDT, .0001, testModeStr);
}
}
}
}
// Release file handles
docContainer.Release();
testFilesDir.Dispose();
string cachePath = ChromatogramCache.FinalPathForName(docPath, null);
FileEx.SafeDelete(cachePath);
}
protected override void DoTest()
{
RunUI(() => SkylineWindow.SetUIMode(SrmDocument.DOCUMENT_TYPE.small_molecules));
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 4);
var columnsOrdered = new[]
{
// Prepare transition list insert window to match tutorial
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.labelType,
SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.mzProduct,
SmallMoleculeTransitionListColumnHeaders.chargeProduct,
SmallMoleculeTransitionListColumnHeaders.coneVoltage,
SmallMoleculeTransitionListColumnHeaders.cePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 6);
var text = "DrugX,Drug,light,283.04,1,129.96,1,26,16,2.7\r\nDrugX,Drug,heavy,286.04,1,133.00,1,26,16,2.7\r\n";
text = text.Replace(',', TextUtil.CsvSeparator).Replace(".", LocalizationHelper.CurrentCulture.NumberFormat.NumberDecimalSeparator);
SetClipboardText(text);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 6);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 1, 1, 2, 2);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
SelectNode(SrmDocument.Level.Transitions, 0);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 7);
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Waters Xevo"; // Collision Energy
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None; // Declustering Potential
transitionSettingsUI.OptimizationLibraryName = Resources.SettingsList_ELEMENT_NONE_None; // Optimization Library
transitionSettingsUI.RegressionCOVName = Resources.SettingsList_ELEMENT_NONE_None; // Compensation Voltage
transitionSettingsUI.UseOptimized = true;
transitionSettingsUI.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SelectedPeptidesSmallMolsSubTab = 1;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_PLUS_H.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_PLUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes = TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.SetAutoSelect = true;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 4);
RunUI(() =>
{
// Instrument Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettingsUI.MinMz = 50;
transitionSettingsUI.MaxMz = 1500;
transitionSettingsUI.MZMatchTolerance = .02;
transitionSettingsUI.MinTime = null;
transitionSettingsUI.MaxTime = null;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Instrument tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("SMQuant_v1.sky")));
ImportReplicates(true);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-precursor graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// peptide count, transition groups, heavy transition groups, tranistions, heavy transitions
{ "Blank_01", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank1", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank2", new[] { 1, 0, 1, 0, 1 } },
{ "DoubleBlank3", new[] { 1, 0, 1, 0, 1 } },
{ "47_0_1_1_00_1021523591", new[] { 1, 0, 1, 0, 1 } },
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = new[] { 1, 1, 1, 1, 1 }
}
; // Most have this value
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, transitions[0],
transitions[1], transitions[2], transitions[3], transitions[4]);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
SelectNode(SrmDocument.Level.Transitions, 0);
SelectNode(SrmDocument.Level.Transitions, 1);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
// Peak integration correction
ActivateReplicate("DoubleBlank1"); // First with mismatched RT
PauseForScreenShot <SkylineWindow>("Selected replicate with unexpected RT", 10);
ChangePeakBounds("DoubleBlank2", 26.5, 27.5);
ChangePeakBounds("DoubleBlank3", 26.5, 27.5);
ChangePeakBounds("DoubleBlank1", 26.5, 27.5);
PauseForScreenShot <SkylineWindow>("Adjusted peak boundaries", 13);
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantRegressionWeighting = RegressionWeighting.ONE_OVER_X_SQUARED;
peptideSettingsUI.QuantMsLevel = null; // All
peptideSettingsUI.QuantUnits = "uM";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 14);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
// Setting sample types
WaitForClosedForm <DocumentGridForm>();
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
PauseForScreenShot <DocumentGridForm>("Document Grid - replicates", 15);
/*IDictionary<string, Tuple<SampleType, double?>> sampleTypes =
* new Dictionary<string, Tuple<SampleType, double?>> {
* {"Blank_01", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Blank_02", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Blank_03", new Tuple<SampleType, double?>(SampleType.BLANK,null)},
* {"Cal_1_01", new Tuple<SampleType, double?>(SampleType.STANDARD,10)},
* {"Cal_1_02", new Tuple<SampleType, double?>(SampleType.STANDARD,10)},
* {"Cal_2_01", new Tuple<SampleType, double?>(SampleType.STANDARD,20)},
* {"Cal_2_02", new Tuple<SampleType, double?>(SampleType.STANDARD,20)},
* {"Cal_3_01", new Tuple<SampleType, double?>(SampleType.STANDARD,100)},
* {"Cal_3_02", new Tuple<SampleType, double?>(SampleType.STANDARD,100)},
* {"Cal_4_01", new Tuple<SampleType, double?>(SampleType.STANDARD,200)},
* {"Cal_4_02", new Tuple<SampleType, double?>(SampleType.STANDARD,200)},
* {"Cal_5_01", new Tuple<SampleType, double?>(SampleType.STANDARD,400)},
* {"Cal_5_02", new Tuple<SampleType, double?>(SampleType.STANDARD,400)},
* {"Cal_6_01", new Tuple<SampleType, double?>(SampleType.STANDARD,600)},
* {"Cal_6_02", new Tuple<SampleType, double?>(SampleType.STANDARD,600)},
* {"Cal_7_01", new Tuple<SampleType, double?>(SampleType.STANDARD,800)},
* {"Cal_7_02", new Tuple<SampleType, double?>(SampleType.STANDARD,800)},
* {"DoubleBlank1", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"DoubleBlank2", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"DoubleBlank3", new Tuple<SampleType, double?>(SampleType.DOUBLE_BLANK,null)},
* {"QC_High_01", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_High_02", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_High_03", new Tuple<SampleType, double?>(SampleType.QC,589)},
* {"QC_Low_01", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Low_02", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Low_03", new Tuple<SampleType, double?>(SampleType.QC,121)},
* {"QC_Mid_01", new Tuple<SampleType, double?>(SampleType.QC,346)},
* {"QC_Mid_02", new Tuple<SampleType, double?>(SampleType.QC,346)},
* {"QC_Mid_03", new Tuple<SampleType, double?>(SampleType.QC,346)}
* };*/
string concentrationsFileName;
if (CultureInfo.CurrentUICulture.Name.StartsWith("zh"))
{
concentrationsFileName = "Concentrations_zh.xlsx";
}
else if (CultureInfo.CurrentUICulture.Name.StartsWith("ja"))
{
concentrationsFileName = "Concentrations_ja.xlsx";
}
else
{
concentrationsFileName = "Concentrations.xlsx";
}
SetExcelFileClipboardText(GetTestPath(concentrationsFileName), "Sheet1", 3, false);
RunUI(() =>
{
// Find and select Blank_01 cell
var replicateColumnIndex = documentGrid.FindColumn(PropertyPath.Root).Index;
documentGrid.DataGridView.CurrentCell = documentGrid.DataGridView.Rows.Cast <DataGridViewRow>()
.Select(row => row.Cells[replicateColumnIndex])
.FirstOrDefault(cell => ((Replicate)cell.Value).Name == "Blank_01");
documentGrid.DataGridView.SendPaste();
});
//SetDocumentGridSampleTypesAndConcentrations(sampleTypes);
PauseForScreenShot <DocumentGridForm>("Document Grid - sample types - enlarge for screenshot so all rows can be seen ", 16);
foreach (var chromatogramSet in SkylineWindow.Document.MeasuredResults.Chromatograms)
{
if (chromatogramSet.Name.StartsWith("DoubleBlank"))
{
Assert.AreEqual(SampleType.DOUBLE_BLANK, chromatogramSet.SampleType);
}
else if (chromatogramSet.Name.StartsWith("Blank"))
{
Assert.AreEqual(SampleType.BLANK, chromatogramSet.SampleType);
}
else if (chromatogramSet.Name.StartsWith("QC"))
{
Assert.AreEqual(SampleType.QC, chromatogramSet.SampleType);
}
else if (chromatogramSet.Name.StartsWith("Cal"))
{
Assert.AreEqual(SampleType.STANDARD, chromatogramSet.SampleType);
}
else
{
Assert.AreEqual(SampleType.UNKNOWN, chromatogramSet.SampleType);
}
}
RunUI(() => SkylineWindow.ShowCalibrationForm());
PauseForScreenShot <CalibrationForm>("Calibration Curve ", 18);
EnableDocumentGridColumns(documentGrid, Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates, 47,
new[]
{
"Proteins!*.Peptides!*.Results!*.Value.Quantification.Accuracy",
"Proteins!*.Peptides!*.Results!*.Value.ExcludeFromCalibration"
},
"Replicates_custom_quant");
PauseForScreenShot <DocumentGridForm>("Custom document grid - resize so all rows are visible before screenshot", 19);
SetDocumentGridExcludeFromCalibration();
PauseForScreenShot <CalibrationForm>("Calibration Curve - outliers disabled", 20);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.AutoZoomBestPeak();
});
RestoreCoverViewOnScreen();
RunDlg <ManageResultsDlg>(SkylineWindow.ManageResults, resultsDlg =>
{
resultsDlg.SelectedChromatograms =
SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms.Take(15);
resultsDlg.RemoveReplicates();
resultsDlg.OkDialog();
});
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
ImportReplicates(false); // Import the rest of the replicates
PauseForScreenShot <CalibrationForm>("Calibration Curve - all replicates loaded", 21);
RunUI(() => documentGrid.ChooseView(Resources.ReportSpecList_GetDefaults_Peptide_Ratio_Results));
WaitForConditionUI(() => documentGrid.ColumnCount > 6);
RunUI(() => {
var colReplicate = documentGrid.FindColumn(PropertyPath.Parse("Results!*.Value.ResultFile.Replicate"));
documentGrid.DataGridView.Sort(colReplicate, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Document Grid - Peptide Ratio Results", 15);
Settings.Default.CalibrationCurveOptions.LogXAxis = true;
Settings.Default.CalibrationCurveOptions.LogYAxis = true;
var calibrationForm = FindOpenForm <CalibrationForm>();
RunUI(() => calibrationForm.UpdateUI(false));
PauseForScreenShot <CalibrationForm>("Calibration Curve: Log");
}
}
private void TestCancellation(bool initiallyVisible)
{
string mz5 = ExtensionTestContext.ExtMz5;
int initialStatusHeight = 0;
RunUI(() => initialStatusHeight = SkylineWindow.StatusBarHeight);
var files = new[] { "8fmol" + mz5, "20fmol" + mz5, "40fmol" + mz5, "200fmol" + mz5 };
OpenDocument("RetentionTimeFilterTest.sky");
var skyfile = initiallyVisible ? "TestImportResultsCancelA.sky" : "TestImportResultsCancelB.sky";
RunUI(() => { SkylineWindow.SaveDocument(TestFilesDir.GetTestPath(skyfile)); }); // Make a clean copy
// Try individual cancellation - can be timing dependent (do we get to the cancel button quickly enough?) so allow some retry
int retry = 0;
for (; retry < maxTries; retry++)
{
RemovePartialCacheFiles(files);
OpenDocument(skyfile);
Assert.IsFalse(SkylineWindow.Document.Settings.HasResults);
Settings.Default.AutoShowAllChromatogramsGraph = initiallyVisible; // Start with progress window hidden?
Settings.Default.ImportResultsSimultaneousFiles =
(int)MultiFileLoader.ImportResultsSimultaneousFileOptions.many; // Ensure all buttons are enabled
ImportResultsAsync(files);
WaitForConditionUI(
() => SkylineWindow.Document.IsLoaded ||
(SkylineWindow.ImportingResultsWindow != null &&
SkylineWindow.ImportingResultsWindow.ProgressTotalPercent >= 1)); // Get at least partway in
// Make sure status bar height does not change showing import progress
// Failure here is usually caused by statusProgress.Size y-dimension getting reset to 20 instead of 16
RunUI(() => Assert.AreEqual(initialStatusHeight, SkylineWindow.StatusBarHeight, "Progress indicator changed status bar height"));
if (!initiallyVisible)
{
RunUI(() => SkylineWindow.ShowAllChromatogramsGraph()); // Turn it on
}
var dlg2 = TryWaitForOpenForm <AllChromatogramsGraph>(30000, () => SkylineWindow.Document.IsLoaded);
if (dlg2 == null)
{
if (SkylineWindow.Document.IsLoaded)
{
continue; // Loaded faster than we could react
}
else
{
dlg2 = WaitForOpenForm <AllChromatogramsGraph>();
}
}
WaitForConditionUI(30 * 1000, () => dlg2.ProgressTotalPercent >= 1 && dlg2.Files.Count() == 4); // Get a least a little way in
int cancelIndex = retry % 4;
string cancelTarget = null;
RunUI(() =>
{
var fileStatus = dlg2.Files.ToArray();
Assert.AreEqual(4, fileStatus.Length);
for (int i = 0; i < files.Length; i++)
{
var statusCancel = fileStatus[(cancelIndex + i) % 4];
if (0 < statusCancel.Progress && statusCancel.Progress < 100)
{
cancelTarget = Path.GetFileNameWithoutExtension(statusCancel.FilePath.GetFilePath());
dlg2.FileButtonClick(cancelTarget);
Assert.AreEqual(3, SkylineWindow.Document.Settings.MeasuredResults.Chromatograms.Count);
Assert.IsFalse(SkylineWindow.Document.Settings.MeasuredResults.ContainsChromatogram(cancelTarget));
break;
}
}
});
WaitForDocumentLoaded();
WaitForClosedAllChromatogramsGraph();
if (cancelTarget == null)
{
continue; // Found everything at 100%
}
int fileCheck = 0;
foreach (var file in files)
{
int index;
ChromatogramSet chromatogramSet;
var chromatogramSetName = file.Replace(mz5, "");
// Can we find a loaded chromatogram set by this name?
SkylineWindow.Document.Settings.MeasuredResults.TryGetChromatogramSet(chromatogramSetName,
out chromatogramSet, out index);
if (!chromatogramSetName.Equals(cancelTarget))
{
// Should always find it since we didn't try to cancel this one
if (index == -1)
{
Assert.AreNotEqual(-1, index, string.Format("Missing chromatogram set {0} after cancelling {1}", chromatogramSetName, cancelTarget));
}
fileCheck++;
}
else if (index == -1)
{
fileCheck++;
}
}
if (fileCheck == files.Length)
{
break; // Success
}
}
if (retry >= maxTries)
{
Assert.Fail("Failed to cancel individual file import after {0} tries", retry);
}
// Cancelled load should revert to initial document
if (initiallyVisible)
{
CancelAll(new[] { files[0] }, false);
CancelAll(new[] { files[3] }, true);
CancelAll(files, false);
CancelAll(files, true);
}
for (retry = 0; retry < maxTries; retry++)
{
// Now try a proper import
Settings.Default.AutoShowAllChromatogramsGraph = initiallyVisible;
RemovePartialCacheFiles(files);
OpenDocument("RetentionTimeFilterTest.sky");
ImportResultsAsync(files);
if (!TryWaitForConditionUI(() =>
SkylineWindow.ImportingResultsWindow != null &&
SkylineWindow.ImportingResultsWindow.ProgressTotalPercent >= 1)) // Get at least partway in
{
Assert.Fail("AllChromagotramsGraph missing in action");
}
if (!initiallyVisible)
{
RunUI(() => SkylineWindow.ShowAllChromatogramsGraph()); // Turn it on
}
var dlgACG = TryWaitForOpenForm <AllChromatogramsGraph>(5000, () => SkylineWindow.Document.IsLoaded);
if (dlgACG == null)
{
continue; // Try again
}
Assert.IsTrue(dlgACG.ChromatogramManager.SupportAllGraphs);
Assert.IsNotNull(dlgACG.SelectedControl,
"unable to select a loader control in chromatogram progress window");
Assert.IsTrue(dlgACG.Width > 500,
"Initially hidden chromatogram progress window did not size properly when enabled by user");
// Did it resize properly?
WaitForDocumentLoaded();
WaitForClosedAllChromatogramsGraph();
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "8fmol", 4, 4, 0, 13, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "20fmol", 5, 5, 0, 13, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "40fmol", 3, 3, 0, 11, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, "200fmol", 4, 4, 0, 12, 0);
break;
}
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
SetCsvFileClipboardText(GetTestPath("Energy_TransitionList.csv"));
RunUI(SkylineWindow.Paste);
PauseForScreenShot <SkylineWindow>("after paste from csv", 3);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 3, 18, 36, 36);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.RegressionCEName = "Waters Xevo"; // Collision Energy
transitionSettingsUI.RegressionDPName = Resources.SettingsList_ELEMENT_NONE_None; // Declustering Potential
transitionSettingsUI.OptimizationLibraryName = Resources.SettingsList_ELEMENT_NONE_None; // Optimization Library
transitionSettingsUI.RegressionCOVName = Resources.SettingsList_ELEMENT_NONE_None; // Compensation Voltage
transitionSettingsUI.UseOptimized = false;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 4);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SelectedPeptidesSmallMolsSubTab = 1;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_MINUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes = TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.SetAutoSelect = true;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 4);
RunUI(() =>
{
// Instrument Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Instrument;
transitionSettingsUI.MinMz = 50;
transitionSettingsUI.MaxMz = 1500;
transitionSettingsUI.MZMatchTolerance = .055;
transitionSettingsUI.MinTime = null;
transitionSettingsUI.MaxTime = null;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Instrument tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("EnergyMet_demo.sky")));
// Export method - 2 minutes
var exportMethodDlg2 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg2.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportMethodDlg2.MethodType = ExportMethodType.Standard;
exportMethodDlg2.RunLength = 2;
exportMethodDlg2.OptimizeType = ExportOptimize.NONE;
exportMethodDlg2.SetTemplateFile("VerifyETemplate.exp");
});
PauseForScreenShot <ExportMethodDlg>("Exporting 2 minute method", 5);
OkDialog(exportMethodDlg2, exportMethodDlg2.CancelDialog);
WaitForClosedForm(exportMethodDlg2);
// Export transition list
var exportTransitionList = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList.MethodType = ExportMethodType.Standard;
exportTransitionList.RunLength = 2;
exportTransitionList.OptimizeType = ExportOptimize.NONE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting transition list", 6);
OkDialog(exportTransitionList, exportTransitionList.CancelDialog);
WaitForClosedForm(exportTransitionList);
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Unscheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 7);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form", 7);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
OkDialog(importResultsDlg1, importResultsDlg1.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
// Renaming replicates
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
for (var i = 0; i < 2; i++)
{
doc = SkylineWindow.Document;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
var chrom = chromatograms[i];
RunUI(() =>
{
manageResultsDlg.SelectedChromatograms = new[] { chrom };
});
var renameDlg = ShowDialog <RenameResultDlg>(manageResultsDlg.RenameResult);
var newName = i == 0 ? "unscheduled_2min" : "unscheduled_5min";
RunUI(() =>
{
renameDlg.ReplicateName = newName;
});
if (i == 0)
{
PauseForScreenShot <SkylineWindow>("Renaming replicate", 10);
}
RunUI(() =>
{
renameDlg.OkDialog();
});
WaitForClosedForm(renameDlg);
}
RunUI(manageResultsDlg.OkDialog);
WaitForClosedForm(manageResultsDlg);
var docResults = SkylineWindow.Document;
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 18, 18, 18, 18, 18);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 10);
// Set zoom to show better peak seperation in 5 minute run
for (var index = 0; index < 2; index++)
{
var indexChrom = index;
WaitForGraphs();
RunUI(() => SkylineWindow.GraphChromatograms.ToArray()[indexChrom].ZoomTo(.8, 1.8));
WaitForGraphs();
}
PauseForScreenShot <SkylineWindow>("Skyline window showing relative peak seperation", 12);
// Set time window
var peptideSettingsDlg = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsDlg.SelectedTab = PeptideSettingsUI.TABS.Prediction;
peptideSettingsDlg.UseMeasuredRT(true);
peptideSettingsDlg.TimeWindow = 1;
});
PauseForScreenShot <PeptideSettingsUI>("Setting scheduled transition list time window", 12);
RunUI(() => peptideSettingsDlg.OkDialog());
// Export transition list
var exportTransitionList2 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList2.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList2.MethodType = ExportMethodType.Scheduled;
exportTransitionList2.OptimizeType = ExportOptimize.NONE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 12);
var schedulingOptionsDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList2.OkDialog(GetTestPath("scheduled_5min.csv")));
RunUI(() =>
{
schedulingOptionsDlg.Algorithm = ExportSchedulingAlgorithm.Single;
schedulingOptionsDlg.ReplicateNum = 1;
});
PauseForScreenShot <SchedulingOptionsDlg>("Exporting scheduled transition list - choose replicate", 12);
OkDialog(schedulingOptionsDlg, schedulingOptionsDlg.OkDialog);
WaitForClosedForm(exportTransitionList2);
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("Scheduled"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
RunUI(() => importResultsNameDlg.IsRemove = false);
PauseForScreenShot <ImportResultsNameDlg>("Import Results common name form, not changing names", 14);
OkDialog(importResultsNameDlg, importResultsNameDlg.OkDialog);
}
// Remove 2 minute gradient
// Renaming replicates
var manageResultsDlg2 = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
RunUI(() =>
{
doc = SkylineWindow.DocumentUI;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
var chrom = chromatograms[0];
manageResultsDlg2.SelectedChromatograms = new[] { chrom };
manageResultsDlg2.RemoveReplicates();
});
for (var i = 1; i < 5; i++)
{
var iC = i;
RunUI(() =>
{
doc = SkylineWindow.DocumentUI;
var chromatograms = doc.Settings.MeasuredResults.Chromatograms;
var chrom = chromatograms[iC];
manageResultsDlg2.SelectedChromatograms = new[] { chrom };
});
var renameDlg = ShowDialog <RenameResultDlg>(manageResultsDlg2.RenameResult);
string newName;
switch (i)
{
case 1:
newName = "1:1_1";
break;
case 2:
newName = "1:1_2";
break;
case 3:
newName = "2:1_2";
break;
default:
newName = "1:2_2";
break;
}
RunUI(() =>
{
renameDlg.ReplicateName = newName;
renameDlg.OkDialog();
});
WaitForClosedForm(renameDlg);
}
PauseForScreenShot <SkylineWindow>("Renaming replicates", 15);
RunUI(manageResultsDlg2.OkDialog);
WaitForClosedForm(manageResultsDlg2);
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <SkylineWindow>("Inspecting ratios", 16);
// Linearity
var documentGrid = ShowDialog <DocumentGridForm>(() => SkylineWindow.ShowDocumentGrid(true));
RunUI(() => documentGrid.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates));
IDictionary <string, Tuple <SampleType, double?> > sampleTypes =
new Dictionary <string, Tuple <SampleType, double?> > {
{ "1:1_1", new Tuple <SampleType, double?>(SampleType.STANDARD, 1) },
{ "1:1_2", new Tuple <SampleType, double?>(SampleType.STANDARD, 1) },
{ "2:1_2", new Tuple <SampleType, double?>(SampleType.STANDARD, 2) },
{ "1:2_2", new Tuple <SampleType, double?>(SampleType.STANDARD, .5) },
};
SetDocumentGridSampleTypesAndConcentrations(sampleTypes);
PauseForScreenShot <DocumentGridForm>("Document Grid - sample types and concentrations ", 17);
OkDialog(documentGrid, documentGrid.Close); // Hide the document grid
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantRegressionWeighting = RegressionWeighting.NONE;
peptideSettingsUI.QuantMsLevel = null; // All
peptideSettingsUI.QuantUnits = "ratio to heavy";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 17);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
var calibrationForm = ShowDialog <CalibrationForm>(() => SkylineWindow.ShowCalibrationForm());
PauseForScreenShot <CalibrationForm>("Calibration Curve ", 18);
OkDialog(calibrationForm, calibrationForm.Close); // Hide the calibration window
var transitionSettingsUI2 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Predicition Settings
transitionSettingsUI2.SelectedTab = TransitionSettingsUI.TABS.Prediction;
transitionSettingsUI2.PrecursorMassType = MassType.Monoisotopic;
transitionSettingsUI2.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI2.RegressionCEName = "Waters Xevo"; // Collision Energy
transitionSettingsUI2.RegressionDPName =
Resources.SettingsList_ELEMENT_NONE_None; // Declustering Potential
transitionSettingsUI2.OptimizationLibraryName =
Resources.SettingsList_ELEMENT_NONE_None; // Optimization Library
transitionSettingsUI2.RegressionCOVName =
Resources.SettingsList_ELEMENT_NONE_None; // Compensation Voltage
});
var editCurrentCE = ShowDialog <EditCEDlg>(transitionSettingsUI2.EditCECurrent);
RunUI(() =>
{
editCurrentCE.StepSize = 2;
editCurrentCE.StepCount = 5;
});
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 18);
RunUI(() =>
{
editCurrentCE.OkDialog();
transitionSettingsUI2.UseOptimized = true;
transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings - Prediction tab", 18);
RunUI(transitionSettingsUI2.OkDialog);
// Export transition lists
var exportTransitionList3 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList3.ExportStrategy = ExportStrategy.Buckets;
exportTransitionList3.IgnoreProteins = true;
exportTransitionList3.MaxTransitions = 100;
exportTransitionList3.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList3.MethodType = ExportMethodType.Scheduled;
exportTransitionList3.OptimizeType = ExportOptimize.CE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting scheduled transition list", 19);
var schedDlg = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList3.OkDialog(GetTestPath("TL_CE_Opt")));
PauseForScreenShot <SchedulingOptionsDlg>("Scheduling", 19);
RunUI(schedDlg.OkDialog);
WaitForClosedForm(exportTransitionList3);
// Import CE optimization runs
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
RunUI(() =>
{
importResultsDlg1.RadioCreateMultipleChecked = true;
importResultsDlg1.OptimizationName = ExportOptimize.CE;
importResultsDlg1.ReplicateName = "CE Optimization";
});
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.OkDialog());
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath("CE Optimization"));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 20);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
RunUI(() =>
{
SkylineWindow.ShowSingleTransition();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
PauseForScreenShot <SkylineWindow>("Split graph", 21);
RunUI(() =>
{
SkylineWindow.ShowPeakAreaLegend(false);
});
PauseForScreenShot <SkylineWindow>("No legend", 24);
// Show Pentose-P
SelectNode(SrmDocument.Level.Molecules, 6);
PauseForScreenShot <SkylineWindow>("Pentose-P", 24);
// Export final transition list
var exportTransitionList4 = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportTransitionList4.ExportStrategy = ExportStrategy.Single;
exportTransitionList4.IgnoreProteins = true;
exportTransitionList4.MaxTransitions = 100;
exportTransitionList4.InstrumentType = ExportInstrumentType.WATERS_XEVO_TQ;
exportTransitionList4.MethodType = ExportMethodType.Scheduled;
exportTransitionList4.OptimizeType = ExportOptimize.NONE;
});
PauseForScreenShot <ExportMethodDlg>("Exporting final optimized transition list", 25);
var schedDlg2 = ShowDialog <SchedulingOptionsDlg>(() => exportTransitionList4.OkDialog(GetTestPath("TL_CE_Final.csv")));
PauseForScreenShot <SchedulingOptionsDlg>("Final Scheduling", 26);
RunUI(schedDlg2.OkDialog);
}
}
}
protected override void DoTest()
{
var docInitial = SkylineWindow.Document;
// Set up necessary modifications
var peptideSettingsUI = ShowPeptideSettings();
const string oxidationMName = "Oxidation (M)";
AddStaticMod(oxidationMName, true, peptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.PickedStaticMods = new[] { oxidationMName };
peptideSettingsUI.MissedCleavages = 1;
});
// Build the library from the pepXML
var buildLibraryDlg = ShowDialog <BuildLibraryDlg>(peptideSettingsUI.ShowBuildLibraryDlg);
const string libraryName = "FullScanIdTest";
string libraryPath = TestFilesDir.GetTestPath(libraryName + BiblioSpecLiteSpec.EXT);
string pepXmlPath = TestFilesDir.GetTestPath("CAexample.pep.xml");
RunUI(() =>
{
buildLibraryDlg.LibraryName = libraryName;
buildLibraryDlg.LibraryPath = libraryPath;
buildLibraryDlg.LibraryKeepRedundant = true;
buildLibraryDlg.LibraryBuildAction = LibraryBuildAction.Create;
buildLibraryDlg.OkWizardPage();
buildLibraryDlg.AddInputFiles(new [] { pepXmlPath });
});
OkDialog(buildLibraryDlg, buildLibraryDlg.OkWizardPage);
Assert.IsTrue(WaitForCondition(() =>
peptideSettingsUI.AvailableLibraries.Contains(libraryName)));
// Add the library to the document
RunUI(() => peptideSettingsUI.PickedLibraries = new[] { libraryName });
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
WaitForDocumentChange(docInitial);
try
{
WaitForCondition(() =>
{
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
return(librarySettings.IsLoaded &&
librarySettings.Libraries.Count > 0 &&
librarySettings.Libraries[0].Keys.Count() == 43);
});
}
catch (Exception e)
{
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
var libraryKeysCounts = string.Join(",", librarySettings.Libraries.Select(
library => null == library ? "null" : string.Empty + library.Keys.Count()));
string message =
string.Format(
"Timeout waiting for libraries. IsLoaded:{0} Libraries.Count:{1} LibrariesKeysCounts:{2}",
librarySettings.IsLoaded,
librarySettings.Libraries.Count,
libraryKeysCounts);
throw new Exception(message, e);
}
var docSetup = SkylineWindow.Document;
// Add all but 2 of the peptides in the library to the document
var libraryExplorer = ShowDialog <ViewLibraryDlg>(SkylineWindow.ViewSpectralLibraries);
var matchedPepsDlg = WaitForOpenForm <AddModificationsDlg>();
RunUI(matchedPepsDlg.CancelDialog);
WaitForClosedForm <AddModificationsDlg>(); // Wait for cancellation to take effect
var filterMatchedPeptidesDlg = ShowDialog <FilterMatchedPeptidesDlg>(libraryExplorer.AddAllPeptides);
RunDlg <MultiButtonMsgDlg>(filterMatchedPeptidesDlg.OkDialog, addLibraryPepsDlg =>
{
Assert.AreEqual(2, (int)addLibraryPepsDlg.Tag);
addLibraryPepsDlg.Btn1Click();
});
RunUI(libraryExplorer.Close);
var docPeptides = WaitForDocumentChange(docSetup);
AssertEx.IsDocumentState(docPeptides, null, 1, 33, 41, 123);
// Switch to full-scan filtering of precursors in MS1
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI =>
{
transitionSettingsUI.FragmentTypes = "p";
transitionSettingsUI.PrecursorCharges = "2, 3";
transitionSettingsUI.UseLibraryPick = false;
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.qit;
transitionSettingsUI.OkDialog();
});
var docFullScan = WaitForDocumentChange(docPeptides);
AssertEx.IsDocumentState(docFullScan, null, 1, 33, 41, 41); // precursors only
foreach (var chromInfo in docFullScan.PeptideTransitionGroups.SelectMany(nodeGroup => nodeGroup.ChromInfos))
{
Assert.IsTrue(chromInfo.IsIdentified);
}
RunUI(() => SkylineWindow.SaveDocument(TestFilesDir.GetTestPath("CAexample.sky")));
// Import results
const string importFileName = "CAexample.mzXML";
ImportResultsFile(importFileName);
var docResults = WaitForDocumentChange(docFullScan);
AssertResult.IsDocumentResultsState(docResults, Path.GetFileNameWithoutExtension(importFileName),
33, 41, 0, 41, 0);
// Make sure spectrum and chromatogram graphs behave as expected in
// relation to MS/MS spectrum selection.
const int level = (int)SrmDocument.Level.TransitionGroups;
RunUI(() => SkylineWindow.SelectedPath = docResults.GetPathTo(level, 0));
// CONSIDER: This could be a lot more interesting with a multi-replicate data set,
// but it is hard to get one small enough.
WaitForGraphs();
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.GraphSpectrum.SelectedSpectrum.IsBest);
var availableSpectra = SkylineWindow.GraphSpectrum.AvailableSpectra.ToArray();
Assert.AreEqual(2, availableSpectra.Length);
var graphChrom = SkylineWindow.GraphChromatograms.First();
double idTime = availableSpectra[0].RetentionTime ?? 0;
Assert.AreEqual(idTime, graphChrom.SelectedRetentionTimeMsMs);
graphChrom.FirePickedSpectrum(new ScaledRetentionTime(idTime, idTime));
});
WaitForGraphs();
RunUI(() => Assert.IsFalse(SkylineWindow.GraphSpectrum.SelectedSpectrum.IsBest));
}
protected override void DoTest()
{
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
foreach (var searchFile in searchFiles)
{
Assert.IsTrue(File.Exists(searchFile), string.Format("File {0} does not exist.", searchFile));
}
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
// Sanity check here, because of failure getting both files for results import below
var searchNames = importPeptideSearchDlg.BuildPepSearchLibControl.SearchFilenames;
Assert.AreEqual(searchFiles.Length, searchNames.Length,
PathsMessage("Unexpected search files found.", searchNames));
var builder = importPeptideSearchDlg.BuildPepSearchLibControl.ImportPeptideSearch.GetLibBuilder(
SkylineWindow.DocumentUI, SkylineWindow.DocumentFilePath, false);
Assert.IsTrue(ArrayUtil.EqualsDeep(searchFiles, builder.InputFiles),
PathsMessage("Unexpected BlibBuild input files.", builder.InputFiles));
importPeptideSearchDlg.BuildPepSearchLibControl.DebugMode = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
var ambiguousDlg = ShowDialog <MessageDlg>(() => importPeptideSearchDlg.ClickNextButton());
RunUI(() => AssertEx.Contains(ambiguousDlg.Message,
Resources.BiblioSpecLiteBuilder_AmbiguousMatches_The_library_built_successfully__Spectra_matching_the_following_peptides_had_multiple_ambiguous_peptide_matches_and_were_excluded_));
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// Verify input paths sent to BlibBuild
string buildArgs = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildCommandArgs;
string buildOutput = importPeptideSearchDlg.BuildPepSearchLibControl.LastBuildOutput;
var argLines = buildArgs.Split(new[] { Environment.NewLine }, StringSplitOptions.None);
var dirCommon = PathEx.GetCommonRoot(searchFiles);
var searchLines = searchFiles.Select(f => PathEx.RemovePrefix(f, dirCommon)).ToArray();
Assert.IsTrue(ArrayUtil.EqualsDeep(searchLines, argLines.Skip(1).ToArray()), buildArgs);
// Verify resulting .blib file contains the expected files
var docLib = librarySettings.Libraries[0];
int expectedFileCount = searchFiles.Length;
int expectedRedundantSpectra = 813; // 446 with TiTip only
int expectedSpectra = 552; // 428 with TiTip3 only
if (expectedFileCount != docLib.FileCount)
{
var searchFileNames = searchFiles.Select(Path.GetFileName).ToArray();
using (var blibDbRedundant = BlibDb.OpenBlibDb(redundantDocLibPath))
{
VerifyLib(searchFileNames, expectedRedundantSpectra, blibDbRedundant.GetIdFilePaths(), blibDbRedundant.GetSpectraCount(),
"redundant library", buildArgs, buildOutput);
}
using (var blibDb = BlibDb.OpenBlibDb(docLibPath))
{
VerifyLib(searchFileNames, expectedSpectra, blibDb.GetIdFilePaths(), blibDb.GetSpectraCount(),
"SQLite library", buildArgs, buildOutput);
}
VerifyLib(searchFileNames, expectedSpectra, docLib.LibraryDetails.DataFiles.Select(d => d.IdFilePath).ToArray(), docLib.SpectrumCount,
"in memory", buildArgs, buildOutput);
}
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page &&
importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count > 0 &&
importPeptideSearchDlg.IsNextButtonEnabled);
// Wait for extra for both source files in the list
TryWaitForConditionUI(10 * 1000, () => importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count == searchFiles.Length);
RunUI(() =>
{
// Check for missing files
var missingFiles = importPeptideSearchDlg.ImportResultsControl.MissingResultsFiles.ToArray();
Assert.AreEqual(0, missingFiles.Length,
PathsMessage("Unexpected missing file found.", missingFiles));
// Check for expected results files
var resultsNames = importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Select(f => f.Name).ToArray();
Assert.AreEqual(searchFiles.Length, importPeptideSearchDlg.ImportResultsControl.FoundResultsFiles.Count,
PathsMessage("Unexpected results files found.", resultsNames));
// Check for expected common prefix
var commonPrefix = ImportResultsDlg.GetCommonPrefix(resultsNames);
Assert.IsFalse(string.IsNullOrEmpty(commonPrefix),
PathsMessage("File names do not have a common prefix.", resultsNames));
Assert.AreEqual("100803_000", commonPrefix);
});
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 6);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 7);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 9);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 12);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
var allChromGraph = WaitForOpenForm <AllChromatogramsGraph>();
RunUI(() =>
{
allChromGraph.Left = SkylineWindow.Right + 20;
allChromGraph.Activate();
});
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 13);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <AddModificationsDlg>("Add mods alert", 14);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 15);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.01);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
const int skylineWindowWidth = 1160;
const int skylineWindowHeight = 792;
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = skylineWindowHeight;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 16);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.NONE);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
RunUI(() =>
{
SkylineWindow.Width = 500;
var peakAreas = SkylineWindow.GraphPeakArea;
var peakAreasFloating = peakAreas.Parent.Parent;
peakAreasFloating.Left = SkylineWindow.Right + 20;
peakAreasFloating.Top = SkylineWindow.Top;
peakAreasFloating.Size = new Size(504, 643);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 18);
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 19);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
const int skylineWindowNarrowWidth = 788;
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
alignmentForm.Width = 660;
alignmentForm.Height = 561;
alignmentForm.Left = SkylineWindow.Right + 20;
alignmentForm.Splitter.SplitterDistance = 75;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 22);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 23);
const string TIP_NAME = "5b_MCF7_TiTip3";
if (IsCoverShotMode)
{
RestoreCoverViewOnScreen();
ClickChromatogram(TIP_NAME, 34.5, 366);
TreeNode selectedNode = null;
RunUI(() => selectedNode = SkylineWindow.SequenceTree.SelectedNode);
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = SkylineWindow.SequenceTree.Nodes[0]);
WaitForGraphs();
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = selectedNode);
TakeCoverShot();
return;
}
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 31.8, 42.2, 280); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 24);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
RunUI(() => SkylineWindow.Width = skylineWindowWidth);
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 25);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 26, "Transition pick list unfiltered", 26); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 42.2, 520); // set the view for screenshot
RunUI(() =>
{
SkylineWindow.Height = 550;
SkylineWindow.ArrangeGraphsTabbed();
});
ActivateReplicate(TIP_NAME);
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
ActivateReplicate(TIP_NAME);
ClickChromatogram(TIP_NAME, 37.3, 142);
PauseForScreenShot("MS1 spectrum graph 37.32 minutes", 28);
ClickChromatogram(TIP_NAME, 33.2, 328.1);
PauseForScreenShot("MS1 spectrum graph 33.19 minutes", 29);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
SkylineWindow.ArrangeGraphs(DisplayGraphsType.Column);
});
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11, 300); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 31);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 31);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 32);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 33);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
if (IsPauseForScreenShots)
{
RestoreViewOnScreen(34);
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 34);
}
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 34);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
// page 36 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = GetGraphChromatogram(TIP3).GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(false);
SkylineWindow.Width = skylineWindowWidth;
SkylineWindow.Height = 720;
});
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 35);
ClickChromatogram(TIP_NAME, 37.5, 1107.3);
PauseForScreenShot("MS1 spectrum graph 37.50 minutes", 36);
RunUI(() => SkylineWindow.HideFullScanGraph());
RunUI(() =>
{
SkylineWindow.ShowChromatogramLegends(true);
SkylineWindow.Width = skylineWindowNarrowWidth;
SkylineWindow.Height = skylineWindowHeight;
});
RestoreViewOnScreen(36); // float the Library Match window
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 37);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 37);
RestoreViewOnScreen(37); // back to normal view
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 38);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 39); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
doc = WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
// CONSIDER: This refinement seems to be a no-op. Not sure why it is here.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // This would get rid of proteins with no peptides (none exist)
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio; // This would get rid of undetected transitions (none exist)
dlg.OkDialog(); // Will not change the document or add an Undo entry
});
// Nothing should have changed on the UI thread
RunUI(() => Assert.AreSame(doc, SkylineWindow.DocumentUI));
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
// Because this was showing up in the nightly test failures
WaitForConditionUI(() => exportMethodDlg.IsDisposed);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
private void LowResTest()
{
string documentFile = GetTestPath(@"Low Res\BSA_Protea_label_free_meth3.sky");
WaitForCondition(() => File.Exists(documentFile));
RunUI(() => SkylineWindow.OpenFile(documentFile));
bool AsSmallMolecules = AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none;
const int expectedMoleculeCount = 9;
int expectedTransitionGroupCount = 10;
int expectedTransitionCount = 78;
var document = SkylineWindow.Document;
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules(AsSmallMoleculesTestMode);
document = SkylineWindow.Document;
Assert.AreEqual(document.PeptideTransitionGroupCount, 0);
Assert.AreEqual(document.MoleculeTransitionGroupCount, expectedTransitionGroupCount);
Assert.AreEqual(document.PeptideTransitionCount, 0);
Assert.AreEqual(document.MoleculeTransitionCount, expectedTransitionCount);
}
AssertEx.IsDocumentState(document, null, 3, expectedMoleculeCount, expectedTransitionGroupCount, expectedTransitionCount);
// p. 3 Select first peptide
RunUI(() => SkylineWindow.SelectedPath = document.GetPathTo((int)SrmDocument.Level.Molecules, 0));
PauseForScreenShot("Main window", 3);
// p. 4 Configure Document for Thermo raw files
{
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab blank", 5);
RunUI(() =>
{
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.qit;
transitionSettingsUI.AcquisitionMethod = FullScanAcquisitionMethod.Targeted;
});
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Peptide Settings - Full-Scan tab low res", 6);
RunUI(() =>
{
transitionSettingsUI.SetRetentionTimeFilter(RetentionTimeFilterType.ms2_ids, 2);
// p.6 - library ion match tolerance same as extraction window
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Library;
transitionSettingsUI.IonMatchTolerance = 0.7;
});
PauseForScreenShot <TransitionSettingsUI.LibraryTab>("Transition Settings - Library tab match tolerance same as MS/MS resolution", 8);
RunUI(() =>
{
// p.6
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.FragmentTypes += ", p";
});
PauseForScreenShot <TransitionSettingsUI.FilterTab>("Transition Settings - Filter tab", 9);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
var docFullScan = WaitForDocumentChange(document);
var tranSettingsFullScan = docFullScan.Settings.TransitionSettings;
Assert.AreEqual(FullScanPrecursorIsotopes.Count, tranSettingsFullScan.FullScan.PrecursorIsotopes);
Assert.AreEqual(FullScanMassAnalyzerType.qit, tranSettingsFullScan.FullScan.PrecursorMassAnalyzer);
Assert.AreEqual(FullScanAcquisitionMethod.Targeted, tranSettingsFullScan.FullScan.AcquisitionMethod);
Assert.IsTrue(ArrayUtil.EqualsDeep(new[] { IonType.y, IonType.b, IonType.precursor },
tranSettingsFullScan.Filter.IonTypes));
}
RunUI(() => SkylineWindow.ExpandPrecursors());
// Check all the precursors on picklists
bool pausedForScreenShot = false;
foreach (PeptideGroupTreeNode node in SkylineWindow.SequenceTree.GetSequenceNodes())
{
foreach (TreeNode child in node.Nodes)
{
foreach (SrmTreeNodeParent grandChild in child.Nodes)
{
// Because of RunUI must copy to local variable first.
SrmTreeNodeParent child1 = grandChild;
RunUI(() => SkylineWindow.SequenceTree.SelectedNode = child1);
var picklist = ShowDialog <PopupPickList>(() => SkylineWindow.SequenceTree.ShowPickList(false));
RunUI(() =>
{
picklist.SetItemChecked(0, true);
Assert.IsTrue(picklist.GetItemLabel(0).Contains(IonType.precursor.GetLocalizedString()));
Assert.IsTrue(picklist.GetItemChecked(0));
});
if (!pausedForScreenShot)
{
PauseForScreenShot <PopupPickList>("Transitions popup pick-list", 10);
pausedForScreenShot = true;
}
OkDialog(picklist, picklist.OnOk);
}
}
}
WaitForDocumentLoaded();
if (!AsSmallMolecules) // No libraries for small molecules, yet
{
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.IsFalse(nodeGroup.HasLibInfo && nodeGroup.Transitions.All(nodeTran => !nodeTran.HasLibInfo));
}
}
// All transition groups should now have a precursor transition
foreach (var nodeGroup in SkylineWindow.Document.MoleculeTransitionGroups)
{
Assert.AreEqual(IonType.precursor, nodeGroup.Transitions.First().Transition.IonType);
}
// p.8
ExportMethodDlg exportMethodDlg =
ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.SetInstrument("Thermo LTQ");
Assert.AreEqual("Thermo LTQ", exportMethodDlg.InstrumentType);
exportMethodDlg.SetMethodType(ExportMethodType.Standard);
exportMethodDlg.SetTemplateFile(GetTestPath(@"Low Res\TargetedMSMS_template.meth"));
});
PauseForScreenShot <ExportMethodDlg.MethodView>("Export Method form", 11);
// p. 10 Ok the error box.
{
var messageDlg = ShowDialog <MessageDlg>(() => exportMethodDlg.OkDialog(GetTestPath(@"Low Res\TargetedMSMS_BSA_Protea.meth")));
PauseForScreenShot <MessageDlg>("Error message (expected)", 12);
OkDialog(messageDlg, messageDlg.OkDialog);
}
// Making a report by hand p.11
ExportLiveReportDlg exportReportDlg = ShowDialog <ExportLiveReportDlg>(() => SkylineWindow.ShowExportReportDialog());
var editReportListDlg = ShowDialog <ManageViewsForm>(exportReportDlg.EditList);
var viewEditor = ShowDialog <ViewEditor>(editReportListDlg.AddView);
RunUI(() =>
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(PropertyPath.Parse("Proteins!*.Name")));
viewEditor.ChooseColumnsTab.AddSelectedColumn();
Assert.AreEqual(1, viewEditor.ChooseColumnsTab.ColumnCount);
var columnsToAdd = new[]
{
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.ModifiedSequence"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Charge"),
PropertyPath.Parse("Proteins!*.Peptides!*.Precursors!*.Mz"),
};
foreach (var id in columnsToAdd)
{
Assert.IsTrue(viewEditor.ChooseColumnsTab.TrySelect(id), "Unable to select {0}", id);
viewEditor.ChooseColumnsTab.AddSelectedColumn();
}
Assert.AreEqual(4, viewEditor.ChooseColumnsTab.ColumnCount);
});
PauseForScreenShot <ViewEditor>("Edit Report form", 13);
{
var previewReportDlg = ShowDialog <DocumentGridForm>(viewEditor.ShowPreview);
var expectedRows = 10 + (TestSmallMolecules ? 1 : 0);
WaitForConditionUI(() => previewReportDlg.IsComplete && previewReportDlg.RowCount == expectedRows);
RunUI(() =>
{
Assert.AreEqual(4, previewReportDlg.ColumnCount);
var precursors =
SkylineWindow.Document.MoleculeTransitionGroups.ToArray();
const int precursorIndex = 3;
for (int i = 0; i < expectedRows; i++)
{
Assert.AreEqual(precursors[i].PrecursorMz, double.Parse(previewReportDlg.DataGridView.Rows[i].Cells[precursorIndex].Value.ToString()), 0.000001);
}
var precursorMzCol = previewReportDlg.DataGridView.Columns[precursorIndex];
Assert.IsNotNull(precursorMzCol);
previewReportDlg.DataGridView.Sort(precursorMzCol, ListSortDirection.Ascending);
});
PauseForScreenShot <DocumentGridForm>("Preview New Report window", 14);
OkDialog(previewReportDlg, previewReportDlg.Close);
}
// Press the Esc key until all forms have been dismissed.
RunUI(() =>
{
viewEditor.Close();
editReportListDlg.Close();
exportReportDlg.CancelClick();
});
WaitForClosedForm(viewEditor);
WaitForClosedForm(editReportListDlg);
WaitForClosedForm(exportReportDlg);
//p. 12 Import Full-Scan Data
// Launch import peptide search wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
RunUI(() => importPeptideSearchDlg.BuildPepSearchLibControl.WorkflowType = ImportPeptideSearchDlg.Workflow.prm);
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library blank page", 15);
const int prefixLen = 35;
const string lowResDir = "Low Res";
const string searchDir = "search";
const string lowRes20Base = "klc_20100329v_Protea_Peptide_Curve_20fmol_uL_tech1";
string lowRes20File = GetTestPath(Path.Combine(lowResDir, lowRes20Base + ExtThermoRaw));
string lowRes20FileRaw = Path.ChangeExtension(lowRes20File, ExtThermoRaw);
string lowRes20Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes20Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes20FileName = (Path.GetFileNameWithoutExtension(lowRes20File) ?? "").Substring(prefixLen);
const string lowRes80Base = "klc_20100329v_Protea_Peptide_Curve_80fmol_uL_tech1";
string lowRes80File = GetTestPath(Path.Combine(lowResDir, lowRes80Base + ExtThermoRaw));
string lowRes80Search = GetTestPath(Path.Combine(lowResDir, Path.Combine(searchDir, lowRes80Base + BiblioSpecLiteBuilder.EXT_PERCOLATOR)));
string shortLowRes80FileName = (Path.GetFileNameWithoutExtension(lowRes80File) ?? "").Substring(prefixLen);
string[] searchFiles = { lowRes20Search, lowRes80Search };
var doc = SkylineWindow.Document;
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
importPeptideSearchDlg.BuildPepSearchLibControl.CutOffScore = 0.99;
importPeptideSearchDlg.BuildPepSearchLibControl.FilterForDocumentPeptides = true;
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search Build Spectral Library with files page", 16);
RunDlg <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck, dlg => dlg.OkDialog());
doc = WaitForDocumentChangeLoaded(doc);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search Extract Chromatograms page", 17);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
TryWaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
var correctPage = false;
ImportPeptideSearchDlg.Pages currentPage = 0;
RunUI(() => correctPage = ImportPeptideSearchDlg.Pages.chromatograms_page == (currentPage = importPeptideSearchDlg.CurrentPage));
if (!correctPage)
{
WaitForConditionUI(1, // Immediate timeout - just want the richer error message that WaitForConditionUI provides
() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page,
string.Format("Expected to be on chromatograms_page, on {0} instead", currentPage));
}
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Modifications are already set up, so that page should get skipped.
// We're on the "Configure Transition Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.transition_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
// We're on the "Configure Full-Scan Settings" page of the wizard.
// We've already set up these settings, so just click next.
WaitForConditionUI(() => importPeptideSearchDlg.IsNextButtonEnabled);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
Assert.IsTrue(importPeptideSearchDlg.ClickNextButton());
});
doc = WaitForDocumentChange(doc);
// Add FASTA also skipped because filter for document peptides was chosen.
WaitForClosedForm(importPeptideSearchDlg);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 18);
WaitForDocumentChangeLoaded(doc, 15 * 60 * 1000); // 15 minutes
WaitForClosedAllChromatogramsGraph();
expectedTransitionGroupCount = 10; // Expect this many with results
expectedTransitionCount = 87; // Expect this many with results
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes20FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, shortLowRes80FileName, expectedMoleculeCount, expectedTransitionGroupCount, 0, expectedTransitionCount, 0);
RunUI(() =>
{
Assert.IsTrue(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.CollapsePrecursors();
SkylineWindow.Width = 1070;
});
// Select the first precursor.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "LVNELTEFAK" : "K.LVNELTEFAK.T [65, 74]");
}
else
{
FindNode(document.MoleculeTransitionGroups.First().CustomIon.DisplayName);
}
// Ensure Graphs look like p17. (checked)
WaitForGraphs();
RestoreViewOnScreen(18);
PauseForScreenShot("Main window with data imported", 19);
const double minDotp = 0.9;
foreach (var nodeGroup in SkylineWindow.Document.PeptideTransitionGroups)
{
double dotp = nodeGroup.Results[0][0].LibraryDotProduct ?? 0;
Assert.IsTrue(Math.Round(dotp, 2) >= minDotp, string.Format("Library dot-product {0} found below {1}", dotp, minDotp));
}
RunUI(() => SkylineWindow.AutoZoomBestPeak());
// Ensure Graphs look like p18. (checked)
WaitForGraphs();
PauseForScreenShot("Chromatogram graphs clipped from main window with zoomed peaks", 20);
RestoreViewOnScreen(21);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(lowRes20FileRaw, 77.7722)));
PauseForScreenShot <GraphSpectrum>("Library Match view clipped from main window with noisy spectrum", 21);
RunUI(() =>
{
SkylineWindow.ShowGraphSpectrum(false);
Assert.IsFalse(SkylineWindow.IsGraphSpectrumVisible);
SkylineWindow.ShowPeptideIDTimes(false);
});
RunUI(() =>
{
var chromGraphs = SkylineWindow.GraphChromatograms.ToArray();
Assert.AreEqual(2, chromGraphs.Length);
Assert.AreEqual(46.8, chromGraphs[0].GraphItems.First().BestPeakTime, 0.05);
Assert.AreEqual(46.8, chromGraphs[1].GraphItems.First().BestPeakTime, 0.05);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.ShowProductTransitions();
});
WaitForCondition(() => !SkylineWindow.GraphPeakArea.IsHidden);
if (!AsSmallMolecules) // No libraries (yet?)
{
WaitForDotProducts();
}
RunUI(() =>
{
// Graph p.15
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(6, SkylineWindow.GraphPeakArea.CurveCount);
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile", 22);
if (!AsSmallMolecules) // No libraries (yet?)
{
VerifyDotProducts(0.99, 0.98);
}
// Check graph p15. (checked)
RunUI(() =>
{
SkylineWindow.ShowAllTransitions();
SkylineWindow.ShowSplitChromatogramGraph(true);
});
// p. 16 screenshot of full 5-point dilution curve
// Select precursor
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "DRVYIHPF" : "R.DRVYIHPF.- [34, 41]"); // May be localized " (missed 1)"
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1047");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas Replicate Comparison graph metafile with split graphs", 24);
RunUI(() =>
{
SkylineWindow.Size = new Size(990, 620);
SkylineWindow.ShowGraphPeakArea(false);
});
PauseForScreenShot("Chromatogram graphs clipped from main window with split graphs", 25);
// PeakAreaGraph Normalize to total p.20.
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowProductTransitions();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.area_percent_view);
});
// Ensure graph looks like p20.
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]");
FindNode(AsSmallMolecules ? "KNLQSLDPSH" : "R.IKNLQSLDPSH.- [80, 90]"); // Phosphorylated
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1333");
}
WaitForGraphs();
PauseForScreenShot <GraphSummary.AreaGraphView>("figure 1a - Area Replicate graph metafile for IKNLQSLDPSH", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(9, SkylineWindow.GraphPeakArea.CurveCount);
});
if (AsSmallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.masses_only)
{
FindNode(AsSmallMolecules ? "HLVDEPQNLIK" : "K.HLVDEPQNLIK.Q [401, 411]");
}
else
{
FindNode(Resources.CustomIon_DisplayName_Ion + " [1306");
}
WaitForGraphs();
PauseForScreenShot("figure 1b - Area replicate graph metafile for HLVDEPQNLIK", 26);
RunUI(() =>
{
Assert.AreEqual(AsSmallMolecules ? 2 : 3, SkylineWindow.GraphPeakArea.Categories.Count());
Assert.AreEqual(7, SkylineWindow.GraphPeakArea.CurveCount);
});
RunUI(() => SkylineWindow.ShowGraphPeakArea(false));
WaitForCondition(() => SkylineWindow.GraphPeakArea.IsHidden);
RunUI(() => SkylineWindow.SaveDocument());
}
protected override void DoTest()
{
var testFilesDir = TestFilesDir;
var skyFile = "test_b.sky";
var basename = "289_97";
var sourceData = TestFilesDir.GetTestPath(basename + ExtensionTestContext.ExtMzml);
string docPath;
var doc = InitHighReplicateCountDocument(testFilesDir, skyFile, out docPath);
Settings.Default.ImportResultsSimultaneousFiles =
(int)MultiFileLoader.ImportResultsSimultaneousFileOptions
.many; // use maximum threads for multiple file import
var listChromatograms = new List <ChromatogramSet>();
var filenames = new List <string>();
var TOO_MANY_FILES = Skyline.SkylineWindow.MAX_GRAPH_CHROM * 2;
int count;
for (count = 0; count < TOO_MANY_FILES; count++)
{
var fname = TestFilesDir.GetTestPath(GetReplicateNameFromIndex(count));
filenames.Add(fname);
if (count != Skyline.SkylineWindow.MAX_GRAPH_CHROM)
{
File.Copy(sourceData, fname);
}
var path = MsDataFileUri.Parse(fname);
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(SkylineWindow.SetDocument(docResults, doc));
var document = WaitForDocumentLoaded();
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
foreach (var pair in document.MoleculePrecursorPairs)
{
for (var f = 0; f < filenames.Count; f++)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(f, pair.NodePep, pair.NodeGroup,
tolerance,
true, out chromGroupInfo));
}
}
WaitForClosedAllChromatogramsGraph();
// We expect 0th display to be R0, then as we move on to high undisplayed chromatograms we expect r0 to be replaced with R100, R1 with R101 etc
var graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
Assert.IsTrue(graphChromatograms.Any(g => g.NameSet.Equals("R0_mzML")));
var oldest = graphChromatograms[0].NameSet;
var newest = "distinct_mzML"; // This replicate should have a different peak
Assert.IsFalse(graphChromatograms.Any(g => g.NameSet.Equals(newest)));
// Now select a graph not currently displayed
RunUI(() => SkylineWindow.SelectedResultsIndex = Skyline.SkylineWindow.MAX_GRAPH_CHROM);
WaitForGraphs();
graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
Assert.IsFalse(graphChromatograms.Any(g => g.NameSet.Equals(oldest)));
Assert.IsTrue(graphChromatograms.Any(g => g.NameSet.Equals(newest)));
RunUI(() => SkylineWindow.ArrangeGraphsTiled()); // Arrange so that all are fully visible, so we can use .Visible in test below
// Now close all, then open them back up again with ctrl-up/ctrl-down hotkeys, and verify that we see the ones we expect
RunUI(() => SkylineWindow.CloseAllChromatograms());
WaitForClosedAllChromatogramsGraph();
// Now run through the replicates
for (count = 0; count < TOO_MANY_FILES; count++)
{
RunUI(() => SkylineWindow.SelectedResultsIndex = count);
var name = GetReplicateNameFromIndex(count).Replace(@".", @"_");
WaitForConditionUI(() => SkylineWindow.GraphChromatograms.Any(g => g.NameSet.Equals(name) && g.Visible));
graphChromatograms = SkylineWindow.GraphChromatograms.ToList();
for (var index = 0; index < TOO_MANY_FILES; index++)
{
name = GetReplicateNameFromIndex(index).Replace(@".", @"_");
var visible = graphChromatograms.Any(g => g.NameSet.Equals(name) && g.Visible);
var shouldBeVisible = (index > count - Skyline.SkylineWindow.MAX_GRAPH_CHROM) && (index <= count);
Assert.IsTrue(visible == shouldBeVisible);
if (shouldBeVisible)
{
// Make sure it's showing the right data
Assert.IsTrue(graphChromatograms.First(g => g.NameSet.Equals(name)).FilePath.ToString().Contains(GetReplicateNameFromIndex(index)));
}
}
}
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
for (var retry = 0; retry < 2; retry++)
{
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
}
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 3);
}
var columnsOrdered = new[]
{
// Prepare transition list insert window to match tutorial
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Adduct,Label Type,Precursor m/z,Precursor Charge,Explicit Retention Time
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
SmallMoleculeTransitionListColumnHeaders.adductPrecursor,
SmallMoleculeTransitionListColumnHeaders.labelType,
SmallMoleculeTransitionListColumnHeaders.mzPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
}
var text = GetCsvFileText(GetTestPath("PUFA_TransitionList.csv"), true);
if (retry > 0)
{
// Fix bad charge declaration
var z = string.Format("{0}1{0}", TextUtil.CsvSeparator);
var zneg = string.Format("{0}-1{0}", TextUtil.CsvSeparator);
text = text.Replace(z, zneg);
}
SetClipboardText(text);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
if (retry == 0)
{
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents showing charge problem", 5);
OkDialog(pasteDlg, pasteDlg.CancelDialog);
}
else
{
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
}
}
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 1, 4, 7, 7);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => !t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
SkylineWindow.ExpandPeptides();
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets - show the right-click menu for setting DHA to be a surrogate standard", 5);
// Set the standard type of the surrogate standards to StandardType.SURROGATE_STANDARD
RunUI(() =>
{
List <IdentityPath> pathsToSelect = SkylineWindow.SequenceTree.Nodes.OfType <PeptideGroupTreeNode>()
.SelectMany(peptideGroup => peptideGroup.Nodes.OfType <PeptideTreeNode>())
.Where(peptideTreeNode => peptideTreeNode.DocNode.RawTextId.Contains("(DHA)"))
.Select(treeNode => treeNode.Path)
.ToList();
SkylineWindow.SequenceTree.SelectedPaths = pathsToSelect;
SkylineWindow.SetStandardType(StandardType.SURROGATE_STANDARD);
});
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() =>
{
// Filter Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.Filter;
transitionSettingsUI.SelectedPeptidesSmallMolsSubTab = 1;
transitionSettingsUI.SmallMoleculePrecursorAdducts = Adduct.M_PLUS_H.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentAdducts = Adduct.M_PLUS.AdductFormula;
transitionSettingsUI.SmallMoleculeFragmentTypes =
TransitionFilter.SMALL_MOLECULE_FRAGMENT_CHAR + "," + TransitionFilter.PRECURSOR_ION_CHAR;
transitionSettingsUI.FragmentMassType = MassType.Monoisotopic;
transitionSettingsUI.SetAutoSelect = true;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Filter tab", 4);
RunUI(() =>
{
// Full Scan Settings
transitionSettingsUI.SelectedTab = TransitionSettingsUI.TABS.FullScan;
transitionSettingsUI.PrecursorIsotopesCurrent = FullScanPrecursorIsotopes.Count;
transitionSettingsUI.PrecursorMassAnalyzer = FullScanMassAnalyzerType.orbitrap;
transitionSettingsUI.PrecursorRes = 70000;
transitionSettingsUI.PrecursorResMz = 200;
transitionSettingsUI.RetentionTimeFilterType = RetentionTimeFilterType.none;
});
PauseForScreenShot <TransitionSettingsUI.PredictionTab>("Transition Settings -Full Scan tab", 4);
OkDialog(transitionSettingsUI, transitionSettingsUI.OkDialog);
WaitForDocumentChange(docTargets);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("FattyAcids_demo.sky")));
using (new WaitDocumentChange(1, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(Path.Combine(TestFilesDirs.First().PersistentFilesDir, GetDataFolder()));
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
OkDialog(importResultsDlg1, importResultsDlg1.OkDialog);
}
SelectNode(SrmDocument.Level.Molecules, 0);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// transition groups, heavy transition groups, tranistions, heavy transitions
{ "ID31609_01_E749_4745_091517", new[] { 3, 3, 3, 10, 9 } },
{ "ID31627_01_E749_4745_091517", new[] { 4, 4, 3, 12, 9 } },
{ "ID31624_01_E749_4745_091517", new[] { 4, 4, 3, 12, 9 } },
{ "ID31653_01_E749_4745_091517", new[] { 4, 4, 3, 12, 9 } },
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = new[] { 4, 4, 3, 11, 9 }
}
; // Most have this value
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, transitions[0], transitions[1], transitions[2], transitions[3], transitions[4]);
}
catch (Exception x)
{
msg += TextUtil.LineSeparate(x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
var documentGrid = FindOpenForm <DocumentGridForm>();
if (documentGrid == null)
{
// When running offscreen, can't depend on RestoreViewOnScreen to open document grid
RunUI(() => SkylineWindow.ShowDocumentGrid(true));
documentGrid = FindOpenForm <DocumentGridForm>();
}
RunUI(() => documentGrid.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification));
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
using (new WaitDocumentChange(1, true))
{
// Quant settings
var peptideSettingsUI = ShowDialog <PeptideSettingsUI>(SkylineWindow.ShowPeptideSettingsUI);
RunUI(() =>
{
peptideSettingsUI.SelectedTab = PeptideSettingsUI.TABS.Quantification;
peptideSettingsUI.QuantRegressionFit = RegressionFit.LINEAR_THROUGH_ZERO;
peptideSettingsUI.QuantNormalizationMethod =
new NormalizationMethod.RatioToLabel(IsotopeLabelType.heavy);
peptideSettingsUI.QuantRegressionWeighting = RegressionWeighting.NONE;
peptideSettingsUI.QuantMsLevel = null; // All
peptideSettingsUI.QuantUnits = "uM";
});
PauseForScreenShot <PeptideSettingsUI.QuantificationTab>("Peptide Settings - Quantitation", 10);
OkDialog(peptideSettingsUI, peptideSettingsUI.OkDialog);
}
var documentGrid2 = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGrid2.ChooseView(Resources.SkylineViewContext_GetDocumentGridRowSources_Replicates);
});
WaitForConditionUI(() => (documentGrid2.RowCount == 16)); // Let it initialize
RunUI(() =>
{
var gridView = documentGrid2.DataGridView;
for (var index = 0; index < gridView.Rows.Count; index++)
{
var row = gridView.Rows[index];
if (row.Cells[0].Value.ToString().StartsWith("NIST"))
{
row.Cells[1].Value = SampleType.STANDARD;
row.Cells[2].Value = 2838.0;
}
else if (row.Cells[0].Value.ToString().StartsWith("GW"))
{
row.Cells[1].Value = SampleType.QC;
}
}
});
// Make sure the edits have flowed to the document
WaitForConditionUI(() => SkylineWindow.DocumentUI.Settings.MeasuredResults.Chromatograms.Where(c => c.Name.StartsWith("GW")).All(c => c.SampleType.Equals(SampleType.QC)));
PauseForScreenShot <DocumentGridForm>("Document Grid - replicates", 11);
// Finish setting up quant
var documentGrid3 = FindOpenForm <DocumentGridForm>();
RunUI(() =>
{
documentGrid3.ChooseView(Resources.Resources_ReportSpecList_GetDefaults_Peptide_Quantification);
});
WaitForConditionUI(() => (documentGrid3.RowCount > 0 &&
documentGrid3.ColumnCount > 6)); // Let it initialize
RunUI(() =>
{
var gridView = documentGrid3.DataGridView;
var methods = ((DataGridViewComboBoxCell)gridView.Rows[0].Cells[6]).Items;
var ratioToHeavy = ((Tuple <String, NormalizationMethod>)methods[3]).Item2;
var ratioToSurrogateHeavyDHA = ((Tuple <String, NormalizationMethod>)methods[6]).Item2;
gridView.Rows[0].Cells[5].Value = 1.0;
gridView.Rows[0].Cells[6].Value = ratioToHeavy;
gridView.Rows[1].Cells[5].Value = .0192;
gridView.Rows[1].Cells[6].Value = ratioToSurrogateHeavyDHA;
gridView.Rows[2].Cells[5].Value = .3467;
gridView.Rows[2].Cells[6].Value = ratioToHeavy;
gridView.Rows[3].Cells[5].Value = .0416;
gridView.Rows[3].Cells[6].Value = ratioToHeavy;
});
PauseForScreenShot <DocumentGridForm>("Document Grid - peptide quant again", 11);
RunUI(() => SkylineWindow.ShowCalibrationForm());
SelectNode(SrmDocument.Level.Molecules, 0);
PauseForScreenShot <DocumentGridForm>("Calibration curve", 12);
}
}
}
internal static StringAssertion IsEmpty(this StringAssertion source)
{
source.Extend(x => AssertResult.New(x.Length <= 0, Resources.IsEmpty));
return(source);
}
public void WiffResultsTest()
{
TestFilesDir testFilesDir = new TestFilesDir(TestContext, ZIP_FILE);
SrmDocument doc = InitWiffDocument(testFilesDir);
using (var docContainer = new ResultsTestDocumentContainer(doc,
testFilesDir.GetTestPath("SimpleWiffTest.sky")))
{
FileEx.SafeDelete(ChromatogramCache.FinalPathForName(docContainer.DocumentFilePath, null));
var listChromatograms = new List <ChromatogramSet>();
if (ExtensionTestContext.CanImportAbWiff)
{
string pathWiff = testFilesDir.GetTestPath("051309_digestion.wiff");
string[] dataIds = MsDataFileImpl.ReadIds(pathWiff);
for (int i = 0; i < dataIds.Length; i++)
{
string nameSample = dataIds[i];
if (!Equals(nameSample, "test") && listChromatograms.Count == 0)
{
continue;
}
string pathSample = SampleHelp.EncodePath(pathWiff, nameSample, i, LockMassParameters.EMPTY, false, false);
listChromatograms.Add(new ChromatogramSet(nameSample, new[] { MsDataFileUri.Parse(pathSample) }));
}
}
else
{
listChromatograms.Add(new ChromatogramSet("test",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-test.mzML")) }));
listChromatograms.Add(new ChromatogramSet("rfp9,before,h,1",
new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-rfp9,before,h,1.mzML")) }));
}
// Should have added test and one after
Assert.AreEqual(2, listChromatograms.Count);
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docResults, doc, true));
docContainer.AssertComplete();
docResults = docContainer.Document;
AssertEx.IsDocumentState(docResults, 6, 9, 9, 18, 54);
Assert.IsTrue(docResults.Settings.MeasuredResults.IsLoaded);
foreach (var nodeTran in docResults.PeptideTransitions)
{
Assert.IsTrue(nodeTran.HasResults);
Assert.AreEqual(2, nodeTran.Results.Count);
}
// Remove the last chromatogram
listChromatograms.RemoveAt(1);
var docResultsSingle = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
AssertResult.IsDocumentResultsState(docResultsSingle, "test", 9, 2, 9, 10, 27);
// Add mzXML version of test sample
listChromatograms.Add(new ChromatogramSet("test-mzXML", new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath("051309_digestion-s3.mzXML")) }));
var docMzxml = docResults.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(docContainer.SetDocument(docMzxml, docResults, true));
docContainer.AssertComplete();
docMzxml = docContainer.Document;
// Verify mzXML and native contained same results
// Unfortunately mzWiff produces chromatograms with now zeros, which
// need to be interpolated into place. This means a .wiff file and
// its mzWiff mzXML file will never be the same.
AssertResult.MatchChromatograms(docMzxml, 0, 1, -1, 0);
}
// TODO: Switch to a using clause when PWiz is fixed, and this assertion fails
// AssertEx.ThrowsException<IOException>(() => testFilesDir.Dispose());
}
internal static StringAssertion IsEmptyOrWhitespace(this StringAssertion source)
{
source.Extend(x => AssertResult.New(string.IsNullOrWhiteSpace(x), Resources.IsEmpty));
return(source);
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns - show Columns checklist", 3);
var columnsOrdered = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Charge,Precursor RT,Precursor CE,Product m/z,Product Charge, label type
SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
SmallMoleculeTransitionListColumnHeaders.namePrecursor,
SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
SmallMoleculeTransitionListColumnHeaders.adductPrecursor,
SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
SmallMoleculeTransitionListColumnHeaders.cePrecursor,
SmallMoleculeTransitionListColumnHeaders.mzProduct,
SmallMoleculeTransitionListColumnHeaders.chargeProduct,
SmallMoleculeTransitionListColumnHeaders.labelType
}.ToList();
if (_inferredLabels)
{
columnsOrdered.Remove(SmallMoleculeTransitionListColumnHeaders.labelType);
}
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
SetCsvFileClipboardText(GetTestPath("SMTutorial_TransitionList.csv"), true);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 6, 12, 19, 21);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 5);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Amino Acid Metabolism.sky")));
using (new WaitDocumentChange(null, true))
{
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath());
openDataSourceDialog1.SelectAllFileType(ExtWatersRaw);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
}
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int[]>
{
// transition groups, heavy transition groups, tranistions, heavy transitions
{ "ID15656_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15658_01_WAA263_3976_020415", new[] { 12, 6, 13, 7 } },
{ "ID15659_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15661_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15662_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15663_01_WAA263_3976_020415", new[] { 11, 7, 12, 8 } },
{ "ID15664_01_WAA263_3976_020415", new[] { 11, 6, 12, 7 } },
{ "ID15739_01_WAA263_3976_020415", new[] { 10, 6, 10, 7 } },
{ "ID15740_01_WAA263_3976_020415", new[] { 12, 6, 12, 7 } },
{ "ID15740_02_WAA263_3976_020415", new[] { 11, 5, 11, 6 } },
{ "ID15740_04_WAA263_3976_020415", new[] { 12, 6, 12, 7 } },
{ "ID15741_01_WAA263_3976_020415", new[] { 12, 7, 13, 8 } },
{ "ID15741_02_WAA263_3976_020415", new[] { 12, 6, 13, 7 } }
};
var msg = "";
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int[] transitions;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out transitions))
{
transitions = new[] { 12, 7, 13, 8 }
}
; // Most have this value
try
{
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 12, transitions[0], transitions[1], transitions[2], transitions[3]);
}
catch (Exception x)
{
msg = TextUtil.LineSeparate(msg, x.Message);
}
}
if (!string.IsNullOrEmpty(msg))
{
Assert.IsTrue(string.IsNullOrEmpty(msg), msg);
}
RestoreViewOnScreen(9);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
}
}
}
internal static StringAssertion IsLongerThan(this StringAssertion source, int length)
{
source.Extend(x => AssertResult.New(x.Length > length, Resources.IsLongerThan, length + 1));
return(source);
}
protected override void DoTest()
{
int countRep = EXPECTED_REPLICATES.Length;
// Open the .sky file
string documentPath1 = TestFilesDir.GetTestPath("SRMCourse_DosR-hDP__20130501.sky");
RunUI(() => SkylineWindow.OpenFile(documentPath1));
WaitForDocumentLoaded();
// Check expected initial state
const int protCount = 13, pepCount = 71, tranCount = 312;
var document = SkylineWindow.Document;
AssertEx.IsDocumentState(document, null, protCount, pepCount, pepCount, tranCount);
int[] missing = { 1, 0, 0, 0 };
for (int i = 0; i < EXPECTED_REPLICATES.Length; i++)
{
string replicateName = EXPECTED_REPLICATES[i];
AssertResult.IsDocumentResultsState(document, replicateName,
pepCount, pepCount, 0, tranCount - missing[i], 0);
}
VerifyUserSets(document,
new[] { new UserSetCount(UserSet.FALSE, countRep * pepCount) },
new[] { new UserSetCount(UserSet.FALSE, countRep * tranCount) });
// Add heavy precursors
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, refineDlg =>
{
refineDlg.RefineLabelType = IsotopeLabelType.heavy;
refineDlg.AddLabelType = true;
refineDlg.OkDialog();
});
// Check changed result state
const int pepStandardCount = 13, tranStandardCount = 34;
document = WaitForDocumentChange(document);
AssertEx.IsDocumentState(document, null, protCount, pepCount, pepCount * 2 - pepStandardCount, tranCount * 2 - tranStandardCount);
int[] missingHeavy = { 1, 1, 2, 2 };
for (int i = 0; i < EXPECTED_REPLICATES.Length; i++)
{
string replicateName = EXPECTED_REPLICATES[i];
AssertResult.IsDocumentResultsState(document, replicateName,
pepCount, pepCount, pepCount - pepStandardCount,
tranCount - missing[i],
tranCount - tranStandardCount - missingHeavy[i]);
}
const int pepRandomCount = 8; // Randomly need no changes from default to match
// TODO: Figure out what is up with the 6
var matchedUserSetGroups = new[]
{
new UserSetCount(UserSet.FALSE, 4 * pepStandardCount + pepRandomCount),
new UserSetCount(UserSet.MATCHED, 8 * (pepCount - pepStandardCount) - pepRandomCount),
};
var matchedUserSetTrans = new[]
{
new UserSetCount(UserSet.FALSE, countRep * tranStandardCount + countRep * pepRandomCount + 6),
new UserSetCount(UserSet.MATCHED, 2 * countRep * (tranCount - tranStandardCount) - countRep * pepRandomCount - 6),
};
VerifyUserSets(document, matchedUserSetGroups, matchedUserSetTrans);
VerifyMatchingPeakBoundaries(document, true); // CONSIDER: Strange that these peak times match exactly
// Test limited scoring model
{
var reintegrateDlg = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
RunDlg <EditPeakScoringModelDlg>(reintegrateDlg.AddPeakScoringModel, scoringModelDlg =>
{
scoringModelDlg.TrainModelClick();
Assert.IsNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestWeightedReferenceShapeCalc)));
Assert.IsNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestWeightedReferenceCoElutionCalc)));
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestReferenceCorrelationCalc)));
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(LegacyUnforcedCountScoreStandardCalc)));
Assert.AreEqual(16, scoringModelDlg.GetTargetCount());
Assert.AreEqual(4, scoringModelDlg.GetDecoyCount());
scoringModelDlg.CancelDialog();
});
OkDialog(reintegrateDlg, reintegrateDlg.CancelDialog);
}
// Rescore
var manageResults = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var rescoreResultsDlg = ShowDialog <RescoreResultsDlg>(manageResults.Rescore);
RunUI(() => rescoreResultsDlg.Rescore(false));
WaitForClosedForm(rescoreResultsDlg);
WaitForClosedForm(manageResults);
var documentRescore = WaitForDocumentChangeLoaded(document, 5 * 60 * 1000); // 5 minutes
WaitForClosedForm <AllChromatogramsGraph>();
VerifyUserSets(documentRescore, matchedUserSetGroups, matchedUserSetTrans);
// Test corrected scoring model
{
const string peakScoringModelName = "Test Model";
var reintegrateDlg = ShowDialog <ReintegrateDlg>(SkylineWindow.ShowReintegrateDialog);
RunDlg <EditPeakScoringModelDlg>(reintegrateDlg.AddPeakScoringModel, scoringModelDlg =>
{
scoringModelDlg.PeakScoringModelName = peakScoringModelName;
scoringModelDlg.TrainModelClick();
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestWeightedReferenceShapeCalc)));
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestWeightedReferenceCoElutionCalc)));
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(MQuestReferenceCorrelationCalc)));
Assert.IsNotNull(scoringModelDlg.GetCalculatorWeight(typeof(LegacyUnforcedCountScoreStandardCalc)));
const int pepTargetCount = (pepCount - pepStandardCount) / 2;
Assert.AreEqual(pepTargetCount * countRep, scoringModelDlg.GetTargetCount());
Assert.AreEqual(pepTargetCount * countRep, scoringModelDlg.GetDecoyCount());
scoringModelDlg.OkDialog();
});
RunUI(() =>
{
reintegrateDlg.OverwriteManual = true;
reintegrateDlg.ComboPeakScoringModelSelected = peakScoringModelName;
});
OkDialog(reintegrateDlg, reintegrateDlg.OkDialog);
}
WaitForClosedForm <AllChromatogramsGraph>();
documentRescore = WaitForDocumentChangeLoaded(documentRescore);
matchedUserSetGroups = new[]
{
new UserSetCount(UserSet.FALSE, 274),
new UserSetCount(UserSet.REINTEGRATED, 10),
};
matchedUserSetTrans = new[]
{
new UserSetCount(UserSet.FALSE, 1202),
new UserSetCount(UserSet.REINTEGRATED, 46),
};
VerifyUserSets(documentRescore, matchedUserSetGroups, matchedUserSetTrans, true);
VerifyMatchingPeakBoundaries(documentRescore, true);
int changeCount = CountChangedPeaks(document, documentRescore);
Assert.IsTrue(changeCount > 200);
}
internal static IStringAssertion DoesNotContain(this StringAssertion source, string text)
{
source.Extend(x => AssertResult.New(!x.Contains(text), Resources.DoesNotContain, text));
return(source);
}
protected override void DoTest()
{
// Skyline Collision Energy Optimization
RunUI(() => SkylineWindow.OpenFile(GetTestPath("CE_Vantage_15mTorr.sky"))); // Not L10N
if (AsSmallMolecules)
{
ConvertDocumentToSmallMolecules();
}
// Deriving a New Linear Equation, p. 2
var transitionSettingsUI = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editList =
ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >
(transitionSettingsUI.EditCEList);
RunUI(() => editList.SelectItem("Thermo")); // Not L10N
EditCEDlg editItem = ShowDialog <EditCEDlg>(editList.EditItem);
PauseForScreenShot <EditCEDlg>("Edit Collision Energy Equation form", 3);
ChargeRegressionLine regressionLine2 = new ChargeRegressionLine(2, 0.034, 3.314);
ChargeRegressionLine regressionLine3 = new ChargeRegressionLine(3, 0.044, 3.314);
CheckRegressionLines(new[] { regressionLine2, regressionLine3 }, editItem.Regression.Conversions);
RunUI(() =>
{
editItem.DialogResult = DialogResult.OK;
editList.DialogResult = DialogResult.Cancel;
transitionSettingsUI.DialogResult = DialogResult.Cancel;
});
WaitForClosedForm(transitionSettingsUI);
// Measuring Retention Times for Method Scheduling, p. 3
{
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 form", 4);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate = GetTestPath("CE_Vantage_15mTorr_unscheduled.csv"); // Not L10N
CheckTransitionList(filePathTemplate, new [] { 120 }, 6);
const string unscheduledName = "Unscheduled"; // Not L10N
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
var path =
new[] { new KeyValuePair <string, MsDataFileUri[]>(unscheduledName,
// This is not actually a valid file path (missing OptimizeCE)
// but Skyline should correctly find the file in the same folder
// as the document.
new[] { MsDataFileUri.Parse(GetTestPath("CE_Vantage_15mTorr_unscheduled" + ExtThermoRaw)) }) }; // Not L10N
importResultsDlg.NamedPathSets = path;
importResultsDlg.OkDialog();
});
WaitForCondition(5 * 60 * 1000, () => SkylineWindow.Document.Settings.HasResults &&
SkylineWindow.Document.Settings.MeasuredResults.IsLoaded); // 5 minutes
AssertEx.IsDocumentState(SkylineWindow.Document, null, 7, 27, 30, 120);
var docUnsched = SkylineWindow.Document;
AssertResult.IsDocumentResultsState(SkylineWindow.Document,
unscheduledName,
docUnsched.MoleculeCount,
docUnsched.MoleculeTransitionGroupCount, 0,
docUnsched.MoleculeTransitionCount, 0);
RunUI(() =>
{
SkylineWindow.ExpandProteins();
SkylineWindow.ExpandPeptides();
});
RestoreViewOnScreen(5);
PauseForScreenShot("Main Skyline window", 5);
// Creating Optimization Methods, p. 5
{
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.THERMO;
exportMethodDlg.ExportStrategy = ExportStrategy.Buckets;
exportMethodDlg.MaxTransitions = 110;
exportMethodDlg.IgnoreProteins = true;
exportMethodDlg.OptimizeType = ExportOptimize.CE;
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
});
PauseForScreenShot <ExportMethodDlg.TransitionListView>("Export Transition List form", 6);
RunUI(() => exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr.csv"))); // Not L10N
WaitForClosedForm(exportMethodDlg);
}
string filePathTemplate1 = GetTestPath("CE_Vantage_15mTorr_000{0}.csv"); // Not L10N
CheckTransitionList(filePathTemplate1, new[] { 220, 220, 264, 308, 308 }, 9);
var filePath = GetTestPath("CE_Vantage_15mTorr_0001.csv"); // Not L10N
CheckCEValues(filePath, 11);
// Analyze Optimization Data, p. 7
RunDlg <ImportResultsDlg>(SkylineWindow.ImportResults, importResultsDlg =>
{
importResultsDlg.RadioAddNewChecked = true;
importResultsDlg.OptimizationName = ExportOptimize.CE;
importResultsDlg.NamedPathSets = DataSourceUtil.GetDataSourcesInSubdirs(TestFilesDirs[0].FullPath).ToArray();
importResultsDlg.NamedPathSets[0] =
new KeyValuePair <string, MsDataFileUri[]>("Optimize CE", importResultsDlg.NamedPathSets[0].Value.Take(5).ToArray()); // Not L10N
importResultsDlg.OkDialog();
});
RunUI(() =>
{
SkylineWindow.ShowSingleTransition();
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ShowPeakAreaReplicateComparison();
});
WaitForDocumentLoaded(15 * 60 * 1000); // 10 minutes
string decorator = AsSmallMolecules
? RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator
: string.Empty;
FindNode(decorator + "IHGFDLAAINLQR");
RestoreViewOnScreen(8);
RunUI(() => SkylineWindow.Size = new Size(984, 553));
PauseForScreenShot("Main Skyline window", 8);
if (IsCoverShotMode)
{
RunUI(() =>
{
Settings.Default.ChromatogramFontSize = 14;
Settings.Default.AreaFontSize = 14;
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.ShowPeakAreaLegend(false);
});
RestoreCoverViewOnScreen();
RunUI(SkylineWindow.FocusDocument);
TakeCoverShot();
return;
}
// p. 8
// Not L10N
RemoveTargetByDisplayName(decorator + "EGIHAQQK");
FindNode(decorator + "IDALNENK");
RunUI(() => SkylineWindow.NormalizeAreaGraphTo(NormalizeOption.TOTAL));
PauseForScreenShot("Main Skyline window", 9);
RunUI(SkylineWindow.EditDelete);
RemoveTargetByDisplayName(AsSmallMolecules ? decorator + "LIC[+57.0]DNTHITK" : "LICDNTHITK");
// Creating a New Equation for CE, p. 9
var transitionSettingsUI1 = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
var editCEDlg1 = ShowDialog <EditListDlg <SettingsListBase <CollisionEnergyRegression>, CollisionEnergyRegression> >(transitionSettingsUI1.EditCEList);
var addItem = ShowDialog <EditCEDlg>(editCEDlg1.AddItem);
RunUI(() =>
{
addItem.RegressionName = "Thermo Vantage Tutorial"; // Not L10N
addItem.UseCurrentData();
});
var graphRegression = ShowDialog <GraphRegression>(addItem.ShowGraph);
PauseForScreenShot <GraphRegression>("Collision Energy Regression graphs", 10);
var graphDatas = graphRegression.RegressionGraphDatas.ToArray();
Assert.AreEqual(2, graphDatas.Length);
ChargeRegressionLine regressionLine21 = new ChargeRegressionLine(2, 0.0305, 2.5061);
ChargeRegressionLine regressionLine31 = new ChargeRegressionLine(3, 0.0397, 1.4217);
var expectedRegressions = new[] { regressionLine21, regressionLine31 };
CheckRegressionLines(expectedRegressions, new[]
{
new ChargeRegressionLine(2,
Math.Round(graphDatas[0].RegressionLine.Slope, 4),
Math.Round(graphDatas[0].RegressionLine.Intercept, 4)),
new ChargeRegressionLine(3,
Math.Round(graphDatas[1].RegressionLine.Slope, 4),
Math.Round(graphDatas[1].RegressionLine.Intercept, 4)),
});
RunUI(graphRegression.CloseDialog);
WaitForClosedForm(graphRegression);
RunUI(addItem.OkDialog);
WaitForClosedForm(addItem);
RunUI(editCEDlg1.OkDialog);
WaitForClosedForm(editCEDlg1);
RunUI(transitionSettingsUI1.OkDialog);
WaitForClosedForm(transitionSettingsUI1);
// Optimizing Each Transition, p. 10
RunDlg <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI, transitionSettingsUI2 =>
{
transitionSettingsUI2.UseOptimized = true;
transitionSettingsUI2.OptimizeType = OptimizedMethodType.Transition.GetLocalizedString();
transitionSettingsUI2.OkDialog();
});
RunDlg <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.List), exportMethodDlg =>
{
exportMethodDlg.ExportStrategy = ExportStrategy.Single;
exportMethodDlg.OkDialog(GetTestPath("CE_Vantage_15mTorr_optimized.csv")); // Not L10N
});
var filePathTemplate2 = GetTestPath("CE_Vantage_15mTorr_optimized.csv"); // Not L10N
CheckTransitionList(filePathTemplate2, new[] { 108 }, 9);
RunUI(() => SkylineWindow.SaveDocument());
WaitForConditionUI(() => !SkylineWindow.Dirty);
}
internal static IStringAssertion DoesNotStartWith(this StringAssertion source, string text)
{
source.Extend(x => AssertResult.New(!x.StartsWith(text, StringComparison.CurrentCultureIgnoreCase), Resources.DoesNotStartWith, text));
return(source);
}
public INumberAssertion <T> IsGreaterThanOrEqualTo(T comparedTo)
{
Extend(x => AssertResult.New(x.CompareTo(comparedTo) >= 0, Resources.IsGreaterThan, comparedTo));
return(this);
}
private void DoSubTest(TestFilesDir testFilesDir, string skyFile, double[] expectedRTs, string[] filenames, double?expectedRatio,
Adduct[] expectedAdducts)
{
string docPath;
var doc = InitExplicitRTDocument(testFilesDir, skyFile, out docPath);
// These test files are some of our oldest small molecule docs, let's see if we can roundtrip them
AssertEx.Serializable(doc, 3, AssertEx.DocumentCloned);
var listChromatograms = new List <ChromatogramSet>();
foreach (var filename in filenames)
{
var path = MsDataFileUri.Parse(filename + ExtensionTestContext.ExtMzml);
listChromatograms.Add(AssertResult.FindChromatogramSet(doc, path) ??
new ChromatogramSet(path.GetFileName().Replace('.', '_'), new[] { path }));
}
var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms));
Assert.IsTrue(SkylineWindow.SetDocument(docResults, doc));
var document = WaitForDocumentLoaded();
float tolerance = (float)document.Settings.TransitionSettings.Instrument.MzMatchTolerance;
var infos = new List <ChromatogramGroupInfo[]>();
int adductIndex = 0;
foreach (var pair in document.MoleculePrecursorPairs)
{
if (!pair.NodeGroup.PrecursorAdduct.Equals(expectedAdducts[adductIndex++]))
{
// These test files are some of our oldest small molecule docs, let's see if we can pull adducts from ion formulas
Assert.Fail("Expected adduct {0}, read as {1} instead", expectedAdducts[adductIndex - 1], pair.NodeGroup.PrecursorAdduct);
}
for (var f = 0; f < filenames.Length; f++)
{
ChromatogramGroupInfo[] chromGroupInfo;
Assert.IsTrue(document.Settings.MeasuredResults.TryLoadChromatogram(f, pair.NodePep, pair.NodeGroup, tolerance,
true, out chromGroupInfo));
infos.Add(chromGroupInfo);
}
}
for (int i = 0; i < infos.Count; i++)
{
if (infos[i].Length == 0)
{
Assert.AreEqual(0, expectedRTs[i], "expected to find a peak at " + expectedRTs[i]);
continue;
}
var chromatogramInfo = infos[i][0].GetTransitionInfo(0);
var chromPeaks = chromatogramInfo.Peaks.ToList();
if (expectedRTs[i] == 0) // Not expecting to find a good peak
{
var errmsg = chromatogramInfo.BestPeakIndex >= 0 ? string.Format("Did not expect to find a peak at RT {0} in {1} ", chromPeaks[chromatogramInfo.BestPeakIndex].RetentionTime, skyFile) : string.Empty;
Assert.AreEqual(-1, chromatogramInfo.BestPeakIndex, errmsg);
}
else if (chromatogramInfo.BestPeakIndex == -1)
{
Assert.Fail("expected to find a peak at {0} in {1}", expectedRTs[i], skyFile);
}
else
{
var peakRT = chromPeaks[chromatogramInfo.BestPeakIndex].RetentionTime;
Assert.AreEqual(expectedRTs[i], peakRT, 0.1, string.Format("Expected to find a peak at RT {0} in {1}", expectedRTs[i], skyFile));
}
}
if (expectedRatio.HasValue)
{
var nResults = 0;
foreach (var nodePep in document.Molecules)
{
foreach (var results in nodePep.Results)
{
foreach (var result in results)
{
Assert.IsNotNull(result.LabelRatios[0].Ratio);
Assert.AreEqual(expectedRatio.Value, result.LabelRatios[0].Ratio.Ratio, .1);
nResults++;
}
}
}
Assert.AreEqual(filenames.Length * document.MoleculeCount, nResults);
}
WaitForClosedAllChromatogramsGraph();
}
protected override void DoTest()
{
TestSmallMolecules = false; // The presence of the extra test node without any results is incompatible with what's being tested here.
// Clean-up before running the test
RunUI(() => SkylineWindow.ModifyDocument("Set default settings",
d => d.ChangeSettings(SrmSettingsList.GetDefault())));
SrmDocument doc = SkylineWindow.Document;
const string documentBaseName = "Ms1FilterTutorial";
string documentFile = GetTestPath(documentBaseName + SrmDocument.EXT);
RunUI(() => SkylineWindow.SaveDocument(documentFile));
// show the empty Transition Setting dialog
var transitionSettingsDlg = ShowDialog <TransitionSettingsUI>(SkylineWindow.ShowTransitionSettingsUI);
RunUI(() => transitionSettingsDlg.SelectedTab = TransitionSettingsUI.TABS.FullScan);
PauseForScreenShot <TransitionSettingsUI.FullScanTab>("Transition Settings - Full-Scan tab nothing set", 2);
OkDialog(transitionSettingsDlg, transitionSettingsDlg.OkDialog);
// Launch the wizard
var importPeptideSearchDlg = ShowDialog <ImportPeptideSearchDlg>(SkylineWindow.ShowImportPeptideSearchDlg);
// We're on the "Build Spectral Library" page of the wizard.
// Add the test xml file to the search files list and try to
// build the document library.
string[] searchFiles =
{
GetTestPath("100803_0001_MCF7_TiB_L.group.xml"), // Not L10N
GetTestPath("100803_0005b_MCF7_TiTip3.group.xml") // Not L10N
};
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library empty page", 3);
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage ==
ImportPeptideSearchDlg.Pages.spectra_page);
importPeptideSearchDlg.BuildPepSearchLibControl.AddSearchFiles(searchFiles);
});
PauseForScreenShot <ImportPeptideSearchDlg.SpectraPage>("Import Peptide Search - Build Spectral Library populated page", 4);
var ambiguousDlg = ShowDialog <MessageDlg>(importPeptideSearchDlg.ClickNextButtonNoCheck);
OkDialog(ambiguousDlg, ambiguousDlg.OkDialog);
// Verify document library was built
string docLibPath = BiblioSpecLiteSpec.GetLibraryFileName(documentFile);
string redundantDocLibPath = BiblioSpecLiteSpec.GetRedundantName(docLibPath);
Assert.IsTrue(File.Exists(docLibPath) && File.Exists(redundantDocLibPath));
var librarySettings = SkylineWindow.Document.Settings.PeptideSettings.Libraries;
Assert.IsTrue(librarySettings.HasDocumentLibrary);
// We're on the "Extract Chromatograms" page of the wizard.
// All the test results files are in the same directory as the
// document file, so all the files should be found, and we should
// just be able to move to the next page.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.chromatograms_page);
PauseForScreenShot <ImportPeptideSearchDlg.ChromatogramsPage>("Import Peptide Search - Extract Chromatograms page", 5);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(() => importPeptideSearchDlg.ClickNextButton());
PauseForScreenShot <ImportResultsNameDlg>("Import Results - Common prefix form", 6);
OkDialog(importResultsNameDlg, importResultsNameDlg.YesDialog);
// Wait for the "Add Modifications" page of the wizard.
WaitForConditionUI(() => importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.match_modifications_page);
List <string> modsToCheck = new List <string> {
"Phospho (ST)", "Phospho (Y)", "Oxidation (M)"
}; // Not L10N
RunUI(() =>
{
importPeptideSearchDlg.MatchModificationsControl.CheckedModifications = modsToCheck;
});
PauseForScreenShot <ImportPeptideSearchDlg.MatchModsPage>("Import Peptide Search - Add Modifications page", 7);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// We're on the "Configure MS1 Full-Scan Settings" page of the wizard.
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.full_scan_settings_page);
importPeptideSearchDlg.FullScanSettingsControl.PrecursorCharges = new[] { 2, 3, 4 };
importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer = FullScanMassAnalyzerType.tof;
importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes = 10 * 1000;
Assert.AreEqual(importPeptideSearchDlg.FullScanSettingsControl.PrecursorIsotopesCurrent, FullScanPrecursorIsotopes.Count);
Assert.AreEqual(FullScanMassAnalyzerType.tof, importPeptideSearchDlg.FullScanSettingsControl.PrecursorMassAnalyzer);
Assert.AreEqual(10 * 1000, importPeptideSearchDlg.FullScanSettingsControl.PrecursorRes);
Assert.AreEqual(3, importPeptideSearchDlg.FullScanSettingsControl.Peaks);
Assert.AreEqual(RetentionTimeFilterType.ms2_ids, importPeptideSearchDlg.FullScanSettingsControl.RetentionTimeFilterType);
Assert.AreEqual(5, importPeptideSearchDlg.FullScanSettingsControl.TimeAroundMs2Ids);
});
PauseForScreenShot <ImportPeptideSearchDlg.Ms1FullScanPage>("Import Peptide Search - Configure MS1 Full-Scan Settings page", 8);
RunUI(() => Assert.IsTrue(importPeptideSearchDlg.ClickNextButton()));
// Last page of wizard - Import Fasta.
string fastaPath = GetTestPath("12_proteins.062011.fasta");
RunUI(() =>
{
Assert.IsTrue(importPeptideSearchDlg.CurrentPage == ImportPeptideSearchDlg.Pages.import_fasta_page);
Assert.AreEqual("Trypsin [KR | P]", importPeptideSearchDlg.ImportFastaControl.Enzyme.GetKey());
importPeptideSearchDlg.ImportFastaControl.MaxMissedCleavages = 2;
importPeptideSearchDlg.ImportFastaControl.SetFastaContent(fastaPath);
Assert.IsFalse(importPeptideSearchDlg.ImportFastaControl.DecoyGenerationEnabled);
});
PauseForScreenShot <ImportPeptideSearchDlg.FastaPage>("Import Peptide Search - Import FASTA page", 10);
var peptidesPerProteinDlg = ShowDialog <PeptidesPerProteinDlg>(() => importPeptideSearchDlg.ClickNextButton());
WaitForCondition(() => peptidesPerProteinDlg.DocumentFinalCalculated);
RunUI(() =>
{
int proteinCount, peptideCount, precursorCount, transitionCount;
peptidesPerProteinDlg.NewTargetsAll(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
peptidesPerProteinDlg.NewTargetsFinal(out proteinCount, out peptideCount, out precursorCount, out transitionCount);
Assert.AreEqual(11, proteinCount);
Assert.AreEqual(51, peptideCount);
Assert.AreEqual(52, precursorCount);
Assert.AreEqual(156, transitionCount);
});
OkDialog(peptidesPerProteinDlg, peptidesPerProteinDlg.OkDialog);
PauseForScreenShot <AllChromatogramsGraph>("Loading chromatograms window", 11);
WaitForDocumentChangeLoaded(doc, 8 * 60 * 1000); // 10 minutes
var libraryExplorer = ShowDialog <ViewLibraryDlg>(() => SkylineWindow.OpenLibraryExplorer(documentBaseName));
var matchedPepModsDlg = WaitForOpenForm <AddModificationsDlg>();
PauseForScreenShot <MultiButtonMsgDlg>("Add mods alert", 12);
RunUI(() =>
{
Assert.AreEqual(13, matchedPepModsDlg.NumMatched);
Assert.AreEqual(0, matchedPepModsDlg.NumUnmatched);
matchedPepModsDlg.CancelDialog();
});
RunUI(() =>
{
libraryExplorer.GraphSettings.ShowBIons = true;
libraryExplorer.GraphSettings.ShowYIons = true;
libraryExplorer.GraphSettings.ShowCharge1 = true;
libraryExplorer.GraphSettings.ShowCharge2 = true;
libraryExplorer.GraphSettings.ShowPrecursorIon = true;
});
PauseForScreenShot <ViewLibraryDlg>("Spectral Library Explorer", 13);
RunUI(() =>
{
const string sourceFirst = "100803_0005b_MCF7_TiTip3.wiff";
const double timeFirst = 35.2128;
Assert.AreEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
libraryExplorer.SelectedIndex++;
Assert.AreNotEqual(sourceFirst, libraryExplorer.SourceFile);
Assert.AreNotEqual(timeFirst, libraryExplorer.RetentionTime, 0.0001);
});
OkDialog(libraryExplorer, libraryExplorer.CancelDialog);
const int TIB_L = 0; // index for Tib_L
const int TIP3 = 1; // index for Tip3
AssertEx.IsDocumentState(SkylineWindow.Document, null, 11, 51, 52, 156);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIB_L]), 51, 52, 0, 156, 0);
AssertResult.IsDocumentResultsState(SkylineWindow.Document, GetFileNameWithoutExtension(searchFiles[TIP3]), 51, 52, 0, 156, 0);
string Tib_LFilename = searchFiles[TIB_L].Replace(".group.xml", PreferedExtAbWiff);
string Tip3Filename = searchFiles[TIP3].Replace(".group.xml", PreferedExtAbWiff);
// Select the first transition group.
RunUI(() =>
{
SkylineWindow.SequenceTree.SelectedPath =
SkylineWindow.Document.GetPathTo((int)SrmDocument.Level.Molecules, 0);
SkylineWindow.GraphSpectrumSettings.ShowAIons = true;
SkylineWindow.GraphSpectrumSettings.ShowBIons = true;
SkylineWindow.GraphSpectrumSettings.ShowYIons = true;
SkylineWindow.GraphSpectrumSettings.ShowPrecursorIon = true;
SkylineWindow.ExpandPrecursors();
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
});
RunDlg <SpectrumChartPropertyDlg>(SkylineWindow.ShowSpectrumProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunDlg <ChromChartPropertyDlg>(SkylineWindow.ShowChromatogramProperties, dlg =>
{
dlg.FontSize = GraphFontSize.NORMAL;
dlg.OkDialog();
});
RunUI(() =>
{
// Make window screenshot size
if (IsPauseForScreenShots && SkylineWindow.WindowState != FormWindowState.Maximized)
{
SkylineWindow.Width = 1160;
SkylineWindow.Height = 792;
}
});
RestoreViewOnScreen(13);
PauseForScreenShot("Main window with imported data", 14);
// RunUIWithDocumentWait(() =>
// {
// SkylineWindow.ToggleIntegrateAll(); // TODO: No longer necessary. Change in tutorial
// });
RunUI(() =>
{
SkylineWindow.ShowGraphPeakArea(true);
SkylineWindow.ShowPeakAreaReplicateComparison();
SkylineWindow.NormalizeAreaGraphTo(AreaNormalizeToView.none);
Settings.Default.ShowDotProductPeakArea = true;
Settings.Default.ShowLibraryPeakArea = true;
});
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas view (show context menu)", 16);
RestoreViewOnScreen(15);
RunUI(() =>
{
SkylineWindow.AutoZoomBestPeak();
SkylineWindow.ArrangeGraphsTiled();
SkylineWindow.ShowChromatogramLegends(false);
});
PauseForScreenShot("Main window layout", 17);
int atest = 0;
CheckAnnotations(TIB_L, 0, atest++);
int pepIndex = 3;
RunUI(() => SkylineWindow.CollapsePeptides());
RunUI(() => SkylineWindow.ShowAlignedPeptideIDTimes(true));
ChangePeakBounds(TIB_L, pepIndex, 38.79, 39.385);
PauseForScreenShot("Chromatogram graphs clipped from main window", 19);
CheckAnnotations(TIB_L, pepIndex, atest++);
var alignmentForm = ShowDialog <AlignmentForm>(() => SkylineWindow.ShowRetentionTimeAlignmentForm());
RunUI(() =>
{
alignmentForm.Width = 711;
alignmentForm.Height = 561;
alignmentForm.ComboAlignAgainst.SelectedIndex = 0; // to match what's in the tutorial doc
});
PauseForScreenShot <AlignmentForm>("Retention time alignment form", 20);
OkDialog(alignmentForm, alignmentForm.Close);
PauseForScreenShot("Status bar clipped from main window - 4/51 pep 4/52 prec 10/156 tran", 21);
pepIndex = JumpToPeptide("SSKASLGSLEGEAEAEASSPK");
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
Assert.IsTrue(8 == pepIndex);
PauseForScreenShot("Chromatogram graph metafiles for 9th peptide", 21);
CheckAnnotations(TIB_L, pepIndex, atest++);
ZoomSingle(TIP3, 32.6, 41.4); // simulate the wheel scroll described in tutorial
PauseForScreenShot("Chromatogram graph metafile showing all peaks for 1_MCF_TiB_L", 22);
CheckAnnotations(TIB_L, pepIndex, atest++);
// current TIB_L peak should have idotp .87 and ppm -6.9
Assert.AreEqual(0.87, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-10.8, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
ChangePeakBounds(TIB_L, pepIndex, 36.5, 38.0);
// now current TIB_L peak should have idotp .9 and ppm -6.5
Assert.AreEqual(0.9, GetTransitionGroupChromInfo(TIB_L, pepIndex).IsotopeDotProduct ?? -1, .005);
Assert.AreEqual(-9.4, GetTransitionChromInfo(TIB_L, pepIndex, 0).MassError ?? -1, .05);
CheckAnnotations(TIB_L, pepIndex, atest++);
var undoIndex = SkylineWindow.Document.RevisionIndex; // preserve for simulating ctrl-z
PickPeakBoth(pepIndex, 40.471035, 40.8134); // select peak for both chromatograms at these respective retention times
PauseForScreenShot <GraphSummary.AreaGraphView>("Peak Areas graph metafile", 23);
int[] m1Thru4 = { 1, 2, 3, 4, 5 };
PickTransitions(pepIndex, m1Thru4, "Transition pick list filtered", 24, "Transition pick list unfiltered", 24); // turn on chromatograms
PickPeakBoth(pepIndex, 36.992836, 37.3896027); // select peak for both chromatograms at these respective retention times
ZoomSingle(TIP3, 32.4, 39.6); // set the view for screenshot
PauseForScreenShot("Chromatogram graph metafile comparing 33 and 37 minute peaks", 25);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("ASLGSLEGEAEAEASSPKGK"); // Not L10N
Assert.IsTrue(10 == pepIndex);
PauseForScreenShot("Chhromatogram graph meta files for peptide ASLGSLEGEAEAEASSPKGK", 26);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
PickTransitions(pepIndex, m1Thru4); // turn on M+3 and M+4
ChangePeakBounds(TIP3, pepIndex, 37.35, 38.08);
ZoomSingle(TIP3, 36.65, 39.11); // simulate the wheel scroll described in tutorial
PauseForScreenShot("upper - Chromatogram graph metafile for peptide ASLGSLEGEAEAEASSPKGK with adjusted integration", 27);
CheckAnnotations(TIP3, pepIndex, atest++);
RevertDoc(undoIndex); // undo changes
pepIndex = JumpToPeptide("AEGEWEDQEALDYFSDKESGK"); // Not L10N
PauseForScreenShot("lower - Chromatogram graph metafiles for peptide AEGEWEDQEALDYFSDKESGK", 27);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
int[] m1Thru5 = { 1, 2, 3, 4, 5, 6 };
PickTransitions(pepIndex, m1Thru5); // turn on M+3 M+4 and M+5
PauseForScreenShot("Chromatogram graph metafiles with M+3, M+4 and M+5 added", 28);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
JumpToPeptide("ALVEFESNPEETREPGSPPSVQR"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide ALVEFESNPEETREPGSPPSVQR", 29);
pepIndex = JumpToPeptide("YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR"); // Not L10N
PauseForScreenShot("upper - Peak Areas graph metafile for peptide YGPADVEDTTGSGATDSKDDDDIDLFGSDDEEESEEAKR", 30);
int[] m1Thru7 = { 1, 2, 3, 4, 5, 6, 7, 8 };
PickTransitions(pepIndex, m1Thru7); // enable [M+3] [M+4] [M+5] [M+6] [M+7]
PauseForScreenShot("lower - Peak Areas graph metafile with M+3 through M+7 added", 30);
CheckAnnotations(TIB_L, pepIndex, atest++);
CheckAnnotations(TIP3, pepIndex, atest++);
// page 32 zooming setup
RunUI(() =>
{
SkylineWindow.SynchronizeZooming(true);
SkylineWindow.LockYChrom(false);
SkylineWindow.AlignToFile = SkylineWindow.GraphChromatograms.ToArray()[TIP3].GetChromFileInfoId(); // align to Tip3
});
ZoomBoth(36.5, 39.5, 1600); // simulate the wheel scroll described in tutorial
RunUI(() => SkylineWindow.ShowChromatogramLegends(false));
PauseForScreenShot("Chromatogram graphs clipped from main window with synchronized zooming", 32);
RestoreViewOnScreen(33); // float the Library Match window TODO this causes a crash at next call to ChangePeakBounds, in pwiz.Skyline.Controls.Graphs.GraphChromatogram.ChromGroupInfos.get() Line 492 , why?
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tip3Filename), 37.6076f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 5b_MCF7_TiTip3 (37.61 Min)", 33);
RunUI(() => SkylineWindow.GraphSpectrum.SelectSpectrum(new SpectrumIdentifier(MsDataFileUri.Parse(Tib_LFilename), 37.0335f))); // set the Library Match view
PauseForScreenShot <GraphSpectrum>("Library Match graph metafile - 1_MCF_TiB_L (37.03 min)", 33);
RestoreViewOnScreen(34); // back to normal view
pepIndex = JumpToPeptide("GVVDSEDLPLNISR"); // Not L10N
RunUI(() => SkylineWindow.ShowChromatogramLegends(true));
PauseForScreenShot("upper - Chromatogram graph metafiles for peptide GVVDSEDLPLNISR", 34);
ZoomBoth(35.05, 36.9, 480);
PauseForScreenShot("lower - Chromatogram graph metafile - effect of zoom ", 34);
ChangePeakBounds(TIP3, pepIndex, 35.7, 36.5); // adjust integration per tutorial
CheckAnnotations(TIP3, pepIndex, atest++); // check the new idotp values
/* pepIndex = */ JumpToPeptide("DQVANSAFVER"); // Not L10N
PauseForScreenShot("Chromatogram graph metafiles for peptide DQVANSAFVER", 35);
// int[] m1 = {2};
// PickTransitions(pepIndex, m1); // enable [M+1] only
// // Measured times in TIB_L are different from displayed times, because of alignment
// ChangePeakBounds(TIB_L, pepIndex, 23.99, 25.29);
// ChangePeakBounds(TIP3, pepIndex, 23.81, 25.21);
// // First transition selected for screenshot
// RunUI(() =>
// {
// var pathPep = SkylineWindow.SelectedPath;
// var nodePep = ((PeptideTreeNode)SkylineWindow.SelectedNode).DocNode;
// var nodeGroup = nodePep.TransitionGroups.First();
// var nodeTran = nodeGroup.Transitions.First();
// SkylineWindow.SelectedPath = new IdentityPath(
// new IdentityPath(pathPep, nodeGroup.TransitionGroup), nodeTran.Transition);
// });
// PauseForScreenShot("page 36 - M+1 only, with adjusted integration");
// CheckAnnotations(TIB_L, pepIndex, atest++);
// CheckAnnotations(TIP3, pepIndex, EXPECTED_ANNOTATIONS[atest]);
var docAfter = WaitForProteinMetadataBackgroundLoaderCompletedUI();
// Minimizing a chromatogram cache file.
RunUI(SkylineWindow.CollapsePeptides);
for (int i = 0; i < 5; i++) // just do the first 5
{
int iPeptide = i;
var path = docAfter.GetPathTo((int)SrmDocument.Level.Molecules, iPeptide);
RunUI(() =>
{
SkylineWindow.SelectedPath = path;
});
WaitForGraphs();
}
// Eliminate extraneous chromatogram data.
doc = WaitForProteinMetadataBackgroundLoaderCompletedUI();
var minimizedFile = GetTestPath("Ms1FilteringTutorial-2min.sky"); // Not L10N
var cacheFile = Path.ChangeExtension(minimizedFile, ChromatogramCache.EXT);
{
// TODO: Figure out why the minimize fails to unlock the .skyd file, if not minimized to current file
RunUI(() => SkylineWindow.SaveDocument(minimizedFile));
var manageResultsDlg = ShowDialog <ManageResultsDlg>(SkylineWindow.ManageResults);
var minimizeResultsDlg = ShowDialog <MinimizeResultsDlg>(manageResultsDlg.MinimizeResults);
RunUI(() =>
{
minimizeResultsDlg.LimitNoiseTime = true;
minimizeResultsDlg.NoiseTimeRange = 2; // Not L10N
});
PauseForScreenShot <MinimizeResultsDlg>("Minimize Results form (percentages vary slightly)", 36); // old p. 23
OkDialog(minimizeResultsDlg, () => minimizeResultsDlg.MinimizeToFile(minimizedFile));
WaitForCondition(() => File.Exists(cacheFile));
WaitForClosedForm(manageResultsDlg);
}
WaitForDocumentChange(doc);
// Inclusion list method export for MS1 filtering
doc = SkylineWindow.Document;
RunDlg <PeptideSettingsUI>(() => SkylineWindow.ShowPeptideSettingsUI(PeptideSettingsUI.TABS.Prediction), dlg =>
{
dlg.IsUseMeasuredRT = true;
dlg.TimeWindow = 10;
dlg.OkDialog();
});
WaitForDocumentChangeLoaded(doc);
// Now deviating from the tutorial script for a moment to make sure we can choose a Scheduled export method.
RunDlg <RefineDlg>(SkylineWindow.ShowRefineDlg, dlg =>
{
dlg.MinPeptides = 1; // Not L10N
const double minPeakFoundRatio = 0.1;
dlg.MinPeakFoundRatio = minPeakFoundRatio;
dlg.OkDialog();
});
// Ready to export, although we will just cancel out of the dialog.
var exportMethodDlg = ShowDialog <ExportMethodDlg>(() => SkylineWindow.ShowExportMethodDialog(ExportFileType.Method));
RunUI(() =>
{
exportMethodDlg.InstrumentType = ExportInstrumentType.ABI_TOF; // Not L10N
exportMethodDlg.MethodType = ExportMethodType.Scheduled;
exportMethodDlg.CancelButton.PerformClick();
});
WaitForClosedForm(exportMethodDlg);
RunUI(() => SkylineWindow.SaveDocument());
RunUI(SkylineWindow.NewDocument);
}
protected override void DoTest()
{
// Inserting a Transition List, p. 2
{
var doc = SkylineWindow.Document;
var pasteDlg = ShowDialog <PasteDlg>(SkylineWindow.ShowPasteTransitionListDlg);
RunUI(() =>
{
pasteDlg.IsMolecule = false; // Default peptide view
pasteDlg.Size = new Size(800, 275);
});
PauseForScreenShot <PasteDlg>("Paste Dialog in peptide mode", 2);
RunUI(() =>
{
pasteDlg.IsMolecule = true;
pasteDlg.SetSmallMoleculeColumns(null); // Default columns
});
PauseForScreenShot <PasteDlg>("Paste Dialog in small molecule mode, default columns", 3);
if (IsPauseForScreenShots)
{
var columnsRestricted = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Product m/z,Precursor Charge,Product Charge,Precursor RT,Precursor CE
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
}.ToList();
RunUI(() =>
{
pasteDlg.SetSmallMoleculeColumns(columnsRestricted);
pasteDlg.Height = 339;
});
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsRestricted.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected columns - show Columns checklist", 4);
}
var columnsOrdered = new[]
{
// Molecule List Name,Precursor Name,Precursor Formula,Precursor Charge,Precursor RT,Precursor CE,Product m/z,Product Charge
PasteDlg.SmallMoleculeTransitionListColumnHeaders.moleculeGroup,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.namePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.formulaPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.rtPrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.cePrecursor,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.mzProduct,
PasteDlg.SmallMoleculeTransitionListColumnHeaders.chargeProduct
}.ToList();
RunUI(() => { pasteDlg.SetSmallMoleculeColumns(columnsOrdered); });
WaitForConditionUI(() => pasteDlg.GetUsableColumnCount() == columnsOrdered.Count);
PauseForScreenShot <PasteDlg>("Paste Dialog with selected and ordered columns", 4);
SetCsvFileClipboardText(GetTestPath("SMTutorial_TransitionList.csv"), true);
RunUI(pasteDlg.PasteTransitions);
RunUI(pasteDlg.ValidateCells);
PauseForScreenShot <PasteDlg>("Paste Dialog with validated contents", 5);
OkDialog(pasteDlg, pasteDlg.OkDialog);
var docTargets = WaitForDocumentChange(doc);
AssertEx.IsDocumentState(docTargets, null, 6, 19, 19, 21);
Assert.IsFalse(docTargets.MoleculeTransitions.Any(t => t.Transition.IsPrecursor()));
RunUI(() =>
{
SkylineWindow.ChangeTextSize(TreeViewMS.LRG_TEXT_FACTOR);
SkylineWindow.Size = new Size(957, 654);
});
RestoreViewOnScreen(5);
PauseForScreenShot <SkylineWindow>("Skyline with small molecule targets", 5);
RunUI(() => SkylineWindow.SaveDocument(GetTestPath("Amino Acid Metabolism.sky")));
var importResultsDlg1 = ShowDialog <ImportResultsDlg>(SkylineWindow.ImportResults);
var openDataSourceDialog1 = ShowDialog <OpenDataSourceDialog>(() => importResultsDlg1.NamedPathSets =
importResultsDlg1.GetDataSourcePathsFile(null));
RunUI(() =>
{
openDataSourceDialog1.CurrentDirectory = new MsDataFilePath(GetTestPath());
openDataSourceDialog1.SelectAllFileType(UseRawFiles
? ExtensionTestContext.ExtWatersRaw
: ExtensionTestContext.ExtMzml);
});
PauseForScreenShot <ImportResultsSamplesDlg>("Import Results Files form", 6);
OkDialog(openDataSourceDialog1, openDataSourceDialog1.Open);
var importResultsNameDlg = ShowDialog <ImportResultsNameDlg>(importResultsDlg1.OkDialog);
OkDialog(importResultsNameDlg, importResultsNameDlg.NoDialog);
WaitForCondition(() =>
SkylineWindow.Document.Settings.HasResults && SkylineWindow.Document.Settings.MeasuredResults.IsLoaded);
SelectNode(SrmDocument.Level.MoleculeGroups, 0);
PauseForScreenShot <SkylineWindow>("Skyline window multi-target graph", 8);
var docResults = SkylineWindow.Document;
var expectedTransCount = new Dictionary <string, int>
{
{ "ID15655_01_WAA263_3976_020415", 21 },
{ "ID15657_01_WAA263_3976_020415", 21 },
{ "ID15658_01_WAA263_3976_020415", 21 },
{ "ID15662_01_WAA263_3976_020415", 21 },
{ "ID15740_02_WAA263_3976_020415", 19 },
{ "ID15741_01_WAA263_3976_020415", 21 },
};
foreach (var chromatogramSet in docResults.Settings.MeasuredResults.Chromatograms)
{
int trans;
if (!expectedTransCount.TryGetValue(chromatogramSet.Name, out trans))
{
trans = 20; // Most have this value
}
AssertResult.IsDocumentResultsState(docResults, chromatogramSet.Name, 19, 19, 0, trans, 0);
}
RestoreViewOnScreen(9);
PauseForScreenShot <SkylineWindow>("Skyline window multi-replicate layout", 9);
}
}
