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); 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, 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(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); } } } } } }
/* 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); }