public void DoTestTargetedMSMSTutorial(RefinementSettings.ConvertToSmallMoleculesMode smallMoleculesTestMode) { // Set true to look at tutorial screenshots. //IsPauseForScreenShots = true; if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions) { Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION); return; } TestSmallMolecules = false; // Don't need that magic extra node, we have an explict test ForceMzml = true; // 2-3x faster than raw files for this test. AsSmallMoleculesTestMode = smallMoleculesTestMode; if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) { TestDirectoryName = "AsSmMol_" + smallMoleculesTestMode; } LinkPdf = "https://skyline.gs.washington.edu/labkey/_webdav/home/software/Skyline/%40files/tutorials/TargetedMSMS-2_5.pdf"; TestFilesZipPaths = new[] { UseRawFiles ? @"http://skyline.gs.washington.edu/tutorials/TargetedMSMS_2.zip" : @"http://skyline.gs.washington.edu/tutorials/TargetedMSMSMzml_2.zip", @"TestTutorial\TargetedMSMSViews.zip" }; RunFunctionalTest(); }
public void DoTestExportIsolationList(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, bool asExplicitRetentionTimes = false, bool negativeCharges = false, bool withSLens = false) { SmallMoleculeTestMode = asSmallMolecules; AsSmallMoleculesNegative = (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) && negativeCharges; AsExplicitRetentionTimes = asExplicitRetentionTimes; WithSLens = withSLens; TestFilesZip = @"TestFunctional\ExportIsolationListTest.zip"; // Avoid trying to reuse the .skyd file while another test is still extant if (AsExplicitRetentionTimes) { TestDirectoryName = "AsExplicitRetentionTimes"; } else if (AsSmallMoleculesNegative) { TestDirectoryName = "AsSmallMoleculesNegative_" + SmallMoleculeTestMode; } else if (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) { TestDirectoryName = "AsSmallMolecules_" + SmallMoleculeTestMode; } if (WithSLens) { TestDirectoryName += "WithSLens"; } RunFunctionalTest(); }
public void DoTestExportIsolationList(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, bool asExplicitRetentionTimes = false, RefinementSettings.ConvertToSmallMoleculesChargesMode negativeCharges = RefinementSettings.ConvertToSmallMoleculesChargesMode.none, bool withSLens = false) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions) { Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION); return; } SmallMoleculeTestMode = asSmallMolecules; AsSmallMoleculesNegativeMode = negativeCharges; AsSmallMoleculesNegative = negativeCharges != RefinementSettings.ConvertToSmallMoleculesChargesMode.none; AsExplicitRetentionTimes = asExplicitRetentionTimes; WithSLens = withSLens; TestFilesZip = @"TestFunctional\ExportIsolationListTest.zip"; // Avoid trying to reuse the .skyd file while another test is still extant if (AsExplicitRetentionTimes) { TestDirectoryName = "AsExplicitRetentionTimes"; } else if (SmallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) { TestDirectoryName = "AsSmallMolecules_" + SmallMoleculeTestMode; } if (AsSmallMoleculesNegative) { TestDirectoryName += "_Negative_" + AsSmallMoleculesNegativeMode; } if (WithSLens) { TestDirectoryName += "WithSLens"; } RunFunctionalTest(); }
public void ConvertDocumentToSmallMolecules(RefinementSettings.ConvertToSmallMoleculesMode mode = RefinementSettings.ConvertToSmallMoleculesMode.formulas, RefinementSettings.ConvertToSmallMoleculesChargesMode invertCharges = RefinementSettings.ConvertToSmallMoleculesChargesMode.none, bool ignoreDecoys = false) { var doc = WaitForDocumentLoaded(); RunUI(() => SkylineWindow.ModifyDocument("Convert to small molecules", document => { var refine = new RefinementSettings(); var path = Path.GetDirectoryName(SkylineWindow.DocumentFilePath); var smallMolDoc = refine.ConvertToSmallMolecules(document, path, mode, invertCharges, ignoreDecoys); CheckConsistentLibraryInfo(smallMolDoc); return(smallMolDoc); })); WaitForDocumentChange(doc); var newDocFileName = SkylineWindow.DocumentFilePath.Contains(BiblioSpecLiteSpec.DotConvertedToSmallMolecules) ? SkylineWindow.DocumentFilePath : SkylineWindow.DocumentFilePath.Replace(".sky", BiblioSpecLiteSpec.DotConvertedToSmallMolecules + ".sky"); RunUI(() => SkylineWindow.SaveDocument(newDocFileName)); WaitForCondition(() => File.Exists(newDocFileName)); RunUI(() => SkylineWindow.OpenFile(newDocFileName)); WaitForDocumentLoaded(); CheckConsistentLibraryInfo(); Thread.Sleep(1000); }
public void DoAgilentMseChromatogramTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions) { System.Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION); return; } var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); TestSmallMolecules = false; // We have an explicit test for that here string docPath; SrmDocument document = InitAgilentMseDocument(testFilesDir, out docPath); if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none) { var refine = new RefinementSettings(); document = refine.ConvertToSmallMolecules(document, asSmallMolecules); } using (var docContainer = new ResultsTestDocumentContainer(document, docPath)) { var doc = docContainer.Document; var listChromatograms = new List <ChromatogramSet>(); var path = MsDataFileUri.Parse(@"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)); 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); } // 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(0.2462, (double)nodePep.GetMeasuredRetentionTime(0), .0001, "averaged retention time differs in node " + nodePep.RawTextId); Assert.AreEqual(0.3333, (double)nodePep.GetPeakCountRatio(0), 0.0001); nPeptides++; } } Assert.AreEqual(1, nPeptides); } testFilesDir.Dispose(); }
private void RunMultiplePeptidesSameMz(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none) { TestDirectoryName = asSmallMolecules.ToString(); } TestSmallMolecules = false; // Don't need the magic test node, we have an explicit test var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); string docPath; SrmDocument document = InitMultiplePeptidesSameMzDocument(testFilesDir, out docPath); document = (new RefinementSettings()).ConvertToSmallMolecules(document, asSmallMolecules); var docContainer = new ResultsTestDocumentContainer(document, docPath); var doc = docContainer.Document; var listChromatograms = new List <ChromatogramSet>(); var path = MsDataFileUri.Parse(@"AMultiplePeptidesSameMz\ljz_20131201k_Newvariant_standards_braf.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)); 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); // without the fix, only the first pair will have a chromatogram } // now drill down for specific values int nPeptides = 0; foreach (var nodePep in document.Molecules.Where(nodePep => nodePep.Results[0] != null)) { // expecting three peptide result in this small data set if (nodePep.Results[0].Sum(chromInfo => chromInfo.PeakCountRatio > 0 ? 1 : 0) > 0) { Assert.AreEqual(34.2441024780273, (double)nodePep.GetMeasuredRetentionTime(0), .0001); nPeptides++; } } Assert.AreEqual(3, nPeptides); // without the fix this will give just one result // Release file handles docContainer.Release(); testFilesDir.Dispose(); }
public void ConvertDocumentToSmallMolecules(RefinementSettings.ConvertToSmallMoleculesMode mode = RefinementSettings.ConvertToSmallMoleculesMode.formulas, bool invertCharges = false, bool ignoreDecoys = false) { WaitForDocumentLoaded(); RunUI(() => SkylineWindow.ModifyDocument("Convert to small molecules", document => { var refine = new RefinementSettings(); return(refine.ConvertToSmallMolecules(document, mode, invertCharges, ignoreDecoys)); })); }
private string InitRefineDocument(RefinementSettings.ConvertToSmallMoleculesMode mode) { TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestData\CommandLineRefine.zip", mode.ToString()); string docPath = testFilesDir.GetTestPath("SRM_mini_single_replicate.sky"); // if (mode != RefinementSettings.ConvertToSmallMoleculesMode.none) // { // var dataPaths = new[] { testFilesDir.GetTestPath("worm1.mzML") }; // doc = ConvertToSmallMolecules(null, ref docPath, dataPaths, mode); // } IsDocumentState(docPath, _initProt, _initList, _initPep, _initMol, _initPrec, _initTran); return(docPath); }
private static SrmDocument InitWatersImsMseDocument(TestFilesDir testFilesDir, string skyFile, RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, out string docPath) { docPath = testFilesDir.GetTestPath(skyFile); var cmdline = new CommandLine(); Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imdb file SrmDocument doc = cmdline.Document; var refine = new RefinementSettings(); doc = refine.ConvertToSmallMolecules(doc, asSmallMolecules); return(doc); }
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions) { Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION); return; } TestSmallMolecules = false; // We test small molecules explicitly in this test LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); string docPath = testFilesDir.GetTestPath("TROUBLED_File.sky"); string cachePath = ChromatogramCache.FinalPathForName(docPath, null); FileEx.SafeDelete(cachePath); SrmDocument doc = ResultsUtil.DeserializeDocument(docPath); var refine = new RefinementSettings(); doc = refine.ConvertToSmallMolecules(doc, testFilesDir.FullPath, asSmallMolecules); const int expectedMoleculeCount = 1; // At first small molecules did not support multiple label types AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 6); using (var docContainer = new ResultsTestDocumentContainer(doc, docPath)) { // Import the first RAW file (or mzML for international) string rawPath = testFilesDir.GetTestPath("Rush_p3_96_21May16_Smeagol.mzML"); var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) }); { // Import with symmetric isolation window var docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 3, 3); var nodeGroup = docResults.MoleculeTransitionGroups.First(); double ratio = nodeGroup.Results[0][0].Ratio ?? 0; // The expected ratio is 1.0, but the symmetric isolation window should produce poor results if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula { Assert.AreEqual(0.008, ratio, 0.001); } } } testFilesDir.Dispose(); }
private SrmDocument InitRefineDocument(RefinementSettings.ConvertToSmallMoleculesMode mode) { TestFilesDir testFilesDir = new TestFilesDir(TestContext, @"TestData\Refine.zip", mode.ToString()); if (mode == RefinementSettings.ConvertToSmallMoleculesMode.none) { var doc = ResultsUtil.DeserializeDocument(testFilesDir.GetTestPath("SRM_mini.sky")); AssertEx.IsDocumentState(doc, null, 4, 36, 38, 334); return(doc); } var docPath = testFilesDir.GetTestPath("SRM_mini_single_replicate.sky"); var dataPaths = new[] { testFilesDir.GetTestPath("worm1.mzML") }; var converted = ConvertToSmallMolecules(null, ref docPath, dataPaths, mode); AssertEx.IsDocumentState(converted, null, 4, 36, 38, 334); return(converted); }
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); } } } } } }
public void DoTestTargetedMSMSTutorial(RefinementSettings.ConvertToSmallMoleculesMode smallMoleculesTestMode) { // Set true to look at tutorial screenshots. //IsPauseForScreenShots = true; TestSmallMolecules = false; // Don't need that magic extra node, we have an explict test ForceMzml = true; // 2-3x faster than raw files for this test. AsSmallMoleculesTestMode = smallMoleculesTestMode; if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) TestDirectoryName = "AsSmMol_" + smallMoleculesTestMode; LinkPdf = "https://skyline.gs.washington.edu/labkey/_webdav/home/software/Skyline/%40files/tutorials/TargetedMSMS-2_5.pdf"; TestFilesZipPaths = new[] { UseRawFiles ? @"http://skyline.gs.washington.edu/tutorials/TargetedMSMS_2.zip" : @"http://skyline.gs.washington.edu/tutorials/TargetedMSMSMzml_2.zip", @"TestTutorial\TargetedMSMSViews.zip" }; RunFunctionalTest(); }
public void RunTestFindNode(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none) { TestDirectoryName = asSmallMolecules.ToString(); } SrmDocument doc = CreateStudy7Doc(); doc = new RefinementSettings().ConvertToSmallMolecules(doc, TestDirectoryName, asSmallMolecules); var displaySettings = new DisplaySettings(null, false, 0, 0); //, ProteinDisplayMode.ByName); // Find every other transition, searching down. List <TransitionDocNode> listTransitions = doc.MoleculeTransitions.ToList(); var pathFound = doc.GetPathTo(0, 0); int i; for (i = 0; i < doc.MoleculeTransitionCount; i += 2) { pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[i].Mz), displaySettings, false, false); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, i), pathFound); } // Test wrapping in search down. pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitions[0].Mz), displaySettings, false, false); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Transitions, 0), pathFound); // Find every other peptide searching up while for each finding one of its children searching down. pathFound = doc.LastNodePath; List <PeptideDocNode> listPeptides = new List <PeptideDocNode>(); listPeptides.AddRange(doc.Molecules); List <TransitionGroupDocNode> listTransitionGroups = new List <TransitionGroupDocNode>(); listTransitionGroups.AddRange(doc.MoleculeTransitionGroups); for (int x = doc.MoleculeCount; x > 0; x -= 2) { // Test case insensitivity. pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound); // Test parents can find children. pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[x * 2 - 1].PrecursorMz.Value), displaySettings, false, true); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, x * 2 - 1), pathFound); // Test Children can find parents. pathFound = doc.SearchDocumentForString(pathFound, listPeptides[x - 1].ToString().ToLower(), displaySettings, true, false); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, x - 1), pathFound); } // Test wrapping in search up. pathFound = doc.SearchDocumentForString(pathFound, String.Format("{0:F04}", listTransitionGroups[listTransitionGroups.Count - 1].PrecursorMz.Value), displaySettings, false, true); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.TransitionGroups, listTransitionGroups.Count - 1), pathFound); // Test children can find other parents. pathFound = doc.SearchDocumentForString(pathFound, listPeptides[0].ToString().ToLowerInvariant(), displaySettings, true, false); Assert.AreEqual(doc.GetPathTo((int)SrmDocument.Level.Molecules, 0), pathFound); // Test forward and backward searching in succession const string heavyText = "heavy"; int countHeavyForward = CountOccurrances(doc, heavyText, displaySettings, false, true); Assert.IsTrue(countHeavyForward > 0); Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText, displaySettings, true, true)); // More tests of case insensitive searching Assert.AreEqual(0, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, true)); Assert.AreEqual(countHeavyForward, CountOccurrances(doc, heavyText.ToUpperInvariant(), displaySettings, false, false)); if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) { Assert.AreEqual(1, CountOccurrances(doc, "hgflpr", displaySettings, true, false)); } // Test mismatched transitions finder var missmatchFinder = new FindOptions().ChangeCustomFinders(new[] { new MismatchedIsotopeTransitionsFinder() }); Assert.AreEqual(4, CountOccurrances(doc, missmatchFinder, displaySettings)); var docRemoved = (SrmDocument)doc.RemoveChild(doc.Children[1]).RemoveChild(doc.Children[2]); Assert.AreEqual(0, CountOccurrances(docRemoved, missmatchFinder, displaySettings)); var refineRemoveHeavy = new RefinementSettings { RefineLabelType = IsotopeLabelType.heavy }; var docLight = refineRemoveHeavy.Refine(doc); Assert.AreEqual(0, CountOccurrances(docLight, missmatchFinder, displaySettings)); var refineRemoveLight = new RefinementSettings { RefineLabelType = IsotopeLabelType.light }; var docHeavy = refineRemoveLight.Refine(doc); Assert.AreEqual(0, CountOccurrances(docHeavy, missmatchFinder, displaySettings)); var docMulti = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType()); docMulti = (new RefinementSettings()).ConvertToSmallMolecules(docMulti, TestContext.TestDir, asSmallMolecules); Assert.AreEqual(0, CountOccurrances(docMulti, missmatchFinder, displaySettings)); var pathTranMultiRemove = docMulti.GetPathTo((int)SrmDocument.Level.Transitions, 7); var tranMultiRemove = docMulti.FindNode(pathTranMultiRemove); var docMultiRemoved = (SrmDocument)docMulti.RemoveChild(pathTranMultiRemove.Parent, tranMultiRemove); Assert.AreEqual(2, CountOccurrances(docMultiRemoved, missmatchFinder, displaySettings)); var tranGroupMultiRemove = docMulti.FindNode(pathTranMultiRemove.Parent); var docMultiGroupRemoved = (SrmDocument) docMulti.RemoveChild(pathTranMultiRemove.Parent.Parent, tranGroupMultiRemove); Assert.AreEqual(0, CountOccurrances(docMultiGroupRemoved, missmatchFinder, displaySettings)); }
public void DoThermoRatioTest(RefinementSettings.ConvertToSmallMoleculesMode smallMoleculesTestMode) { TestSmallMolecules = false; // We do this explicitly var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); string docPath; SrmDocument doc = InitThermoDocument(testFilesDir, out docPath); SrmSettings settings = doc.Settings.ChangePeptideModifications(mods => mods.ChangeInternalStandardTypes(new[] { IsotopeLabelType.light })); doc = doc.ChangeSettings(settings); if (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) { var docOrig = doc; var refine = new RefinementSettings(); doc = refine.ConvertToSmallMolecules(doc, smallMoleculesTestMode); // This is our first example of a converted label doc - check roundtripping AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(docOrig, doc); AssertEx.Serializable(doc); } var docContainer = new ResultsTestDocumentContainer(doc, docPath); string extRaw = ExtensionTestContext.ExtThermoRaw; var listChromatograms = new List <ChromatogramSet> { new ChromatogramSet("rep03", new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath( "Site20_STUDY9P_PHASEII_QC_03" + extRaw)) }), new ChromatogramSet("rep05", new[] { MsDataFileUri.Parse(testFilesDir.GetTestPath( "Site20_STUDY9P_PHASEII_QC_05" + extRaw)) }) }; var docResults = doc.ChangeMeasuredResults(new MeasuredResults(listChromatograms)); Assert.IsTrue(docContainer.SetDocument(docResults, doc, true)); docContainer.AssertComplete(); docResults = docContainer.Document; // Make sure all groups have at least 5 transitions (of 6) with ratios int ratioGroupMissingCount = 0; foreach (var nodeGroup in docResults.MoleculeTransitionGroups) { if (nodeGroup.TransitionGroup.LabelType.IsLight) { foreach (var result in nodeGroup.Results) { Assert.IsFalse(result[0].Ratio.HasValue, "Light group found with a ratio"); } foreach (TransitionDocNode nodeTran in nodeGroup.Children) { foreach (var resultTran in nodeTran.Results) { Assert.IsFalse(resultTran[0].Ratio.HasValue, "Light transition found with a ratio"); } } } else { bool missingRatio = false; foreach (ChromInfoList <TransitionGroupChromInfo> chromInfoList in nodeGroup.Results) { var ratioHeavy = chromInfoList[0].Ratio; if (!ratioHeavy.HasValue) { missingRatio = true; } } int ratioCount1 = 0; int ratioCount2 = 0; foreach (TransitionDocNode nodeTranHeavy in nodeGroup.Children) { float?ratioHeavy = nodeTranHeavy.Results[0][0].Ratio; if (ratioHeavy.HasValue) { Assert.IsFalse(float.IsNaN(ratioHeavy.Value) || float.IsInfinity(ratioHeavy.Value)); ratioCount1++; } ratioHeavy = nodeTranHeavy.Results[1][0].Ratio; if (ratioHeavy.HasValue) { Assert.IsFalse(float.IsNaN(ratioHeavy.Value) || float.IsInfinity(ratioHeavy.Value)); ratioCount2++; } } Assert.AreEqual(3, ratioCount1); if (ratioCount2 < 2) { ratioGroupMissingCount++; } else { Assert.IsFalse(missingRatio, "Precursor missing ratio when transitions have ratios"); } } } // 3 groups with less than 2 transition ratios Assert.AreEqual(3, ratioGroupMissingCount); // Remove the first light transition, checking that this removes the ratio // from the corresponding heavy transition, but not the entire group, until // after all light transitions have been removed. IdentityPath pathFirstPep = docResults.GetPathTo((int)SrmDocument.Level.Molecules, 0); var nodePep = (PeptideDocNode)docResults.FindNode(pathFirstPep); Assert.AreEqual(2, nodePep.Children.Count); var nodeGroupLight = (TransitionGroupDocNode)nodePep.Children[0]; IdentityPath pathGroupLight = new IdentityPath(pathFirstPep, nodeGroupLight.TransitionGroup); Assert.IsNull(nodeGroupLight.Results[0][0].Ratio, "Light group has ratio"); var nodeGroupHeavy = (TransitionGroupDocNode)nodePep.Children[1]; IdentityPath pathGroupHeavy = new IdentityPath(pathFirstPep, nodeGroupHeavy.TransitionGroup); float? ratioStart = nodeGroupHeavy.Results[0][0].Ratio; Assert.IsTrue(ratioStart.HasValue, "No starting heavy group ratio"); var expectedValues = new[] { 1.403414, 1.38697791, 1.34598482 }; for (int i = 0; i < 3; i++) { var pathLight = docResults.GetPathTo((int)SrmDocument.Level.Transitions, 0); var pathHeavy = docResults.GetPathTo((int)SrmDocument.Level.Transitions, 3); TransitionDocNode nodeTran = (TransitionDocNode)docResults.FindNode(pathHeavy); float? ratioTran = nodeTran.Results[0][0].Ratio; Assert.IsTrue(ratioTran.HasValue, "Expected transition ratio not found"); Assert.AreEqual(ratioTran.Value, expectedValues[i], 1.0e-5); docResults = (SrmDocument)docResults.RemoveChild(pathLight.Parent, docResults.FindNode(pathLight)); nodeTran = (TransitionDocNode)docResults.FindNode(pathHeavy); Assert.IsFalse(nodeTran.Results[0][0].Ratio.HasValue, "Unexpected transiton ratio found"); Assert.AreEqual(pathGroupHeavy, pathHeavy.Parent, "Transition found outside expected group"); // nodePep = (PeptideDocNode) docResults.FindNode(pathFirstPep); nodeGroupHeavy = (TransitionGroupDocNode)docResults.FindNode(pathGroupHeavy); // Assert.AreEqual(nodePep.Results[0][0].RatioToStandard, nodeGroupHeavy.Results[0][0].Ratio, // "Peptide and group ratios not equal"); if (i < 2) { float?ratioGroup = nodeGroupHeavy.Results[0][0].Ratio; Assert.IsTrue(ratioGroup.HasValue, "Group ratio removed with transition ratios"); Assert.AreEqual(ratioStart.Value, ratioGroup.Value, 0.1, "Unexpected group ratio change by more than 0.1"); } else { Assert.IsFalse(nodeGroupHeavy.Results[0][0].Ratio.HasValue, "Group ratio still present with no transition ratios"); } } bool asSmallMolecules = (smallMoleculesTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none); if (!asSmallMolecules) // GetTransitions() doesn't work the same way for small molecules - it only lists existing ones { bool firstAdd = true; var nodeGroupLightOrig = (TransitionGroupDocNode)doc.FindNode(pathGroupLight); DocNode[] lightChildrenOrig = nodeGroupLightOrig.Children.ToArray(); foreach (var nodeTran in nodeGroupLightOrig.GetTransitions(docResults.Settings, null, nodeGroupLightOrig.PrecursorMz, null, null, null, false)) { var transition = nodeTran.Transition; if (!firstAdd && lightChildrenOrig.IndexOf(node => Equals(node.Id, transition)) == -1) { continue; } // Add the first transition, and then the original transitions docResults = (SrmDocument)docResults.Add(pathGroupLight, nodeTran); nodeGroupHeavy = (TransitionGroupDocNode)docResults.FindNode(pathGroupHeavy); if (firstAdd) { Assert.IsNull(nodeGroupHeavy.Results[0][0].Ratio, "Unexpected heavy ratio found"); } else { Assert.IsNotNull(nodeGroupHeavy.Results[0][0].Ratio, "Heavy ratio null after adding light children"); } firstAdd = false; } Assert.AreEqual(ratioStart, nodeGroupHeavy.Results[0][0].Ratio); } // Release file handles docContainer.Release(); testFilesDir.Dispose(); }
public void DoFullScanSettingsTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, out List <SrmDocument> docCheckPoints) { docCheckPoints = new List <SrmDocument>(); var doc0 = ResultsUtil.DeserializeDocument("MultiLabel.sky", GetType()); var refine = new RefinementSettings(); var docSM = refine.ConvertToSmallMolecules(doc0, ".", asSmallMolecules); docCheckPoints.Add(docSM); Assert.IsFalse(docSM.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist != null)); AssertEx.Serializable(docSM, AssertEx.Cloned); double c13Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C13) - BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.C); double n15Delta = BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N15) - BioMassCalc.MONOISOTOPIC.GetMass(BioMassCalc.N); // Verify isotope distributions calculated when MS1 filtering enabled var enrichments = IsotopeEnrichmentsList.DEFAULT; var docIsotopes = docSM.ChangeSettings(docSM.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 3, enrichments))); docCheckPoints.Add(docIsotopes); Assert.AreEqual(FullScanMassAnalyzerType.tof, docIsotopes.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer); Assert.IsFalse(docIsotopes.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null)); foreach (var nodeGroup in docIsotopes.MoleculeTransitionGroups) { Assert.AreEqual(3, nodeGroup.Children.Count); var isotopePeaks = nodeGroup.IsotopeDist; Assert.IsNotNull(isotopePeaks); Assert.IsTrue(nodeGroup.HasIsotopeDist); // The peaks should always includ at least M-1 Assume.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0); // Within 2.5% of 100% of the entire isotope distribution Assert.AreEqual(1.0, isotopePeaks.ExpectedProportions.Sum(), 0.025); // Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip accuracy anyway) Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.IsotopeDist.GetMZI(0), SequenceMassCalc.MassTolerance); Assert.AreEqual(nodeGroup.PrecursorMz, nodeGroup.TransitionGroup.IsCustomIon ? BioMassCalc.CalculateIonMz(nodeGroup.IsotopeDist.GetMassI(0), nodeGroup.TransitionGroup.PrecursorAdduct.Unlabeled) : SequenceMassCalc.GetMZ(nodeGroup.IsotopeDist.GetMassI(0), nodeGroup.TransitionGroup.PrecursorAdduct), SequenceMassCalc.MassTolerance); // Check isotope distribution masses for (int i = 1; i < isotopePeaks.CountPeaks; i++) { int massIndex = isotopePeaks.PeakIndexToMassIndex(i); Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex)); double massDelta = GetMassDelta(isotopePeaks, massIndex); if (nodeGroup.TransitionGroup.LabelType.IsLight) { // All positive should be close to 13C - C, and 0 should be the same as the next delta double expectedDelta = (massIndex > 0 ? c13Delta : GetMassDelta(isotopePeaks, massIndex + 1)); Assert.AreEqual(expectedDelta, massDelta, 0.001); } else if (nodeGroup.TransitionGroup.LabelType.Name.Contains("15N")) { // All positive should be close to 13C, and all negative 15N double expectedDelta = (massIndex > 0 ? c13Delta : n15Delta); Assert.AreEqual(expectedDelta, massDelta, 0.0015); } else if (massIndex == 0) { double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0 ? GetMassDelta(isotopePeaks, massIndex + 1) : 1.0017); Assert.AreEqual(expectedDelta, massDelta, 0.001); } else { Assert.AreEqual(c13Delta, massDelta, 0.001); } } } AssertEx.Serializable(docIsotopes, AssertEx.Cloned); // Narrow the resolution, and verify that predicted proportion of the isotope // distribution captured is reduced for all precursors var docIsotopesFt = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 500 * 1000, 400))); docCheckPoints.Add(docIsotopesFt); var tranGroupsOld = docIsotopes.MoleculeTransitionGroups.ToArray(); var tranGroupsNew = docIsotopesFt.MoleculeTransitionGroups.ToArray(); Assume.AreEqual(tranGroupsOld.Length, tranGroupsNew.Length); for (int i = 0; i < tranGroupsOld.Length; i++) { Assert.AreNotSame(tranGroupsOld[i], tranGroupsNew[i]); Assert.AreNotSame(tranGroupsOld[i].IsotopeDist, tranGroupsNew[i].IsotopeDist); Assert.IsTrue(tranGroupsOld[i].IsotopeDist.ExpectedProportions.Sum() > tranGroupsNew[i].IsotopeDist.ExpectedProportions.Sum()); } // Use Min % of base peak and verify variation in transitions used const float minPercent1 = 10; var docIsotopesP1 = docIsotopes.ChangeSettings(docIsotopes.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent1, enrichments))); docCheckPoints.Add(docIsotopesP1); tranGroupsNew = docIsotopesP1.MoleculeTransitionGroups.ToArray(); int maxTran = 0; for (int i = 0; i < tranGroupsOld.Length; i++) { // Isotope distributions should not have changed var isotopePeaks = tranGroupsNew[i].IsotopeDist; Assert.AreSame(tranGroupsOld[i].IsotopeDist, isotopePeaks); // Expected transitions should be present maxTran = Math.Max(maxTran, tranGroupsNew[i].Children.Count); foreach (TransitionDocNode nodeTran in tranGroupsNew[i].Children) { int massIndex = nodeTran.Transition.MassIndex; Assume.IsTrue(minPercent1 <= isotopePeaks.GetProportionI(massIndex) * 100.0 / isotopePeaks.BaseMassPercent); } } Assume.AreEqual(5, maxTran); AssertEx.Serializable(docIsotopesP1, AssertEx.Cloned); // Express any failure in terms of XML diffs // Use 10%, and check that 15N modifications all have M-1 const float minPercent2 = 5; var docIsotopesP2 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichments))); docCheckPoints.Add(docIsotopesP2); foreach (var nodeGroup in docIsotopesP2.MoleculeTransitionGroups) { var firstChild = (TransitionDocNode)nodeGroup.Children[0]; if (nodeGroup.TransitionGroup.LabelType.Name.EndsWith("15N")) { Assume.AreEqual(-1, firstChild.Transition.MassIndex); } else { Assume.AreNotEqual(-1, firstChild.Transition.MassIndex); } } AssertEx.Serializable(docIsotopesP2, AssertEx.Cloned); // Use lower enrichment of 13C, and verify that this add M-1 for 13C labeled precursors var enrichmentsLow13C = enrichments.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.C13, 0.9)); var docIsotopesLow13C = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, minPercent2, enrichmentsLow13C))); tranGroupsNew = docIsotopesLow13C.MoleculeTransitionGroups.ToArray(); for (int i = 0; i < tranGroupsOld.Length; i++) { var nodeGroup = tranGroupsNew[i]; if (!Equals(nodeGroup.TransitionGroup.LabelType.Name, "heavy")) { Assert.AreSame(tranGroupsOld[i].IsotopeDist, nodeGroup.IsotopeDist); } else { var firstChild = (TransitionDocNode)nodeGroup.Children[0]; Assert.IsTrue(firstChild.Transition.MassIndex < 0); } } AssertEx.Serializable(docIsotopesLow13C, AssertEx.Cloned); // Express any failure as XML diffs // Use 0%, and check that everything has M-1 and lower var enrichmentsLow = enrichmentsLow13C.ChangeEnrichment(new IsotopeEnrichmentItem(BioMassCalc.N15, 0.97)); var docIsotopesLowP0 = docIsotopesP1.ChangeSettings(docIsotopesP1.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Percent, 0, enrichmentsLow))); docCheckPoints.Add(docIsotopesLowP0); foreach (var nodeGroup in docIsotopesLowP0.MoleculeTransitionGroups) { Assume.AreEqual(nodeGroup.IsotopeDist.CountPeaks, nodeGroup.Children.Count); var firstChild = (TransitionDocNode)nodeGroup.Children[0]; if (nodeGroup.TransitionGroup.LabelType.IsLight) { Assert.AreEqual(-1, firstChild.Transition.MassIndex); } else { Assert.IsTrue(-1 > firstChild.Transition.MassIndex); } } AssertEx.Serializable(docIsotopesLowP0, AssertEx.Cloned); // Test a document with variable and heavy modifications, which caused problems for // the original implementation var docVariable = ResultsUtil.DeserializeDocument("HeavyVariable.sky", GetType()); Assert.IsFalse(docVariable.MoleculeTransitionGroups.Any(nodeGroup => nodeGroup.IsotopeDist == null)); foreach (var nodeGroup in docVariable.MoleculeTransitionGroups) { var isotopePeaks = nodeGroup.IsotopeDist; Assert.IsNotNull(isotopePeaks); // The peaks should always includ at least M-1 Assert.IsTrue(isotopePeaks.MassIndexToPeakIndex(0) > 0); // Precursor mass and m/z values are expected to match exactly (well, within XML roundtrip tolerance anyway) var mzI = nodeGroup.IsotopeDist.GetMZI(0); Assert.AreEqual(nodeGroup.PrecursorMz, mzI, SequenceMassCalc.MassTolerance); // Check isotope distribution masses for (int i = 1; i < isotopePeaks.CountPeaks; i++) { int massIndex = isotopePeaks.PeakIndexToMassIndex(i); Assert.IsTrue(isotopePeaks.GetMZI(massIndex - 1) < isotopePeaks.GetMZI(massIndex)); double massDelta = GetMassDelta(isotopePeaks, massIndex); bool containsSulfur = nodeGroup.TransitionGroup.Peptide.IsCustomMolecule ? (nodeGroup.CustomMolecule.Formula.IndexOfAny("S".ToCharArray()) != -1) : (nodeGroup.TransitionGroup.Peptide.Sequence.IndexOfAny("CM".ToCharArray()) != -1); if (massIndex == 0) { double expectedDelta = (isotopePeaks.GetProportionI(massIndex - 1) == 0 ? GetMassDelta(isotopePeaks, massIndex + 1) : 1.0017); Assert.AreEqual(expectedDelta, massDelta, 0.001); } else if (!containsSulfur || massIndex == 1) { Assert.AreEqual(c13Delta, massDelta, 0.001); } else { Assert.AreEqual(1.00075, massDelta, 0.001); } } } docCheckPoints.Add(docVariable); }
private SrmDocument InitFullScanDocument(ref string docPath, int prot, ref int pep, ref int prec, ref int tran, RefinementSettings.ConvertToSmallMoleculesMode smallMoleculeTestMode) { SrmDocument doc = ResultsUtil.DeserializeDocument(docPath); int? expectedRevisionNumber = 0; if (smallMoleculeTestMode != RefinementSettings.ConvertToSmallMoleculesMode.none) { var oldDoc = doc; AssertEx.Serializable(oldDoc); doc = ConvertToSmallMolecules(doc, ref docPath, null, smallMoleculeTestMode); AssertEx.Serializable(doc); expectedRevisionNumber = null; } AssertEx.IsDocumentState(doc, expectedRevisionNumber, prot, pep, prec, tran); return(doc); }
private void DoFullScanFilterTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules, out List <SrmDocument> docCheckpoints, bool centroided = false) { docCheckpoints = new List <SrmDocument>(); 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(ref 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 Assume.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(ref docPath, 1, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules); docCheckpoints.Add(doc); Assume.AreEqual(FullScanMassAnalyzerType.orbitrap, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer); // Make sure saving this type of document works AssertEx.Serializable(doc, AssertEx.DocumentCloned); Assume.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(ref docPath, 3, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules); Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer); Assume.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); Assume.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.MoleculeTransitions) { Assume.IsTrue(nodeTran.HasResults); Assume.IsNotNull(nodeTran.Results[0]); if (410 > nodeTran.Mz || nodeTran.Mz > 910) { Assume.IsTrue(nodeTran.Results[0][0].IsForcedIntegration); } else { Assume.IsFalse(nodeTran.Results[0][0].IsForcedIntegration); } } // 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)); if (asSmallMolecules == RefinementSettings.ConvertToSmallMoleculesMode.masses_only) { return; // Can't work with isotope distributions when we don't have ion formulas } int indexResults = listResults.Count - 1; var matchIdentifierDRV = "DRV"; if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none) { matchIdentifierDRV = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierDRV; } int index = 0; foreach (var nodeTran in docContainer.Document.MoleculeTransitions) { Assume.IsTrue(nodeTran.HasResults); Assume.AreEqual(listResults.Count, nodeTran.Results.Count); var peptide = nodeTran.Transition.Group.Peptide; if (peptide.IsCustomMolecule && index == 24) { // Conversion to small molecule loses some of the nuance of "Sequence" vs "FastaSequence", comparisons are inexact Assume.AreEqual("pep_DRVY[+80.0]IHPF", nodeTran.PrimaryCustomIonEquivalenceKey); break; } // DRV without FASTA sequence should not have data for non-precursor transitions if (!peptide.TextId.StartsWith(matchIdentifierDRV) || (!peptide.IsCustomMolecule && !peptide.Begin.HasValue)) { Assume.IsNotNull(nodeTran.Results[indexResults]); Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty); } else if (nodeTran.Transition.IonType != IonType.precursor) { Assert.IsTrue(nodeTran.Results[indexResults].IsEmpty); } else { // Random, bogus peaks chosen in both files Assume.IsNotNull(nodeTran.Results[indexResults]); Assume.AreEqual(2, nodeTran.Results[indexResults].Count); Assume.IsFalse(nodeTran.Results[indexResults][0].IsEmpty); Assume.IsFalse(nodeTran.Results[indexResults][1].IsEmpty); } index++; } // 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(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules); Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer); Assume.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, IsotopeEnrichmentsList.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, IsotopeEnrichmentsList.DEFAULT) .ChangePrecursorResolution(FullScanMassAnalyzerType.centroided, ppm, 0))); AssertEx.Serializable(docNoCentroid, AssertEx.DocumentCloned); Assume.IsTrue(docContainer.SetDocument(docNoCentroid, docContainer.Document)); const double mzTest = 400.0; var filterWidth = docNoCentroid.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest); Assume.AreEqual(mzTest * 2.0 * ppm * 1E-6, filterWidth); // Verify relationship between normal and high-selectivity extraction var docTofNormal = docNoCentroid.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null))); AssertEx.Serializable(docTofNormal, AssertEx.DocumentCloned); var docTofSelective = docTofNormal.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 25 * 1000, null) .ChangeUseSelectiveExtraction(true))); AssertEx.Serializable(docTofSelective, AssertEx.DocumentCloned); var filterWidthTof = docTofNormal.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest); var filterWidthSelective = docTofSelective.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest); Assume.AreEqual(filterWidth, filterWidthTof); Assume.AreEqual(filterWidth, filterWidthSelective); // 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) }), }; 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(ref docPath, 2, ref expectedPepCount, ref expectedTransGroupCount, ref expectedTransCount, asSmallMolecules); Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.ProductMassAnalyzer); Assume.AreEqual(FullScanMassAnalyzerType.none, doc.Settings.TransitionSettings.FullScan.PrecursorMassAnalyzer); var docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT) .ChangePrecursorResolution(FullScanMassAnalyzerType.tof, 50 * 1000, null))); Assume.AreEqual(filterWidth, docMs1.Settings.TransitionSettings.FullScan.GetPrecursorFilterWindow(mzTest)); docMs1 = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fs => fs.ChangePrecursorIsotopes(FullScanPrecursorIsotopes.Count, 1, IsotopeEnrichmentsList.DEFAULT) .ChangePrecursorResolution(FullScanMassAnalyzerType.ft_icr, 50 * 1000, mzTest))); AssertEx.Serializable(docMs1, AssertEx.DocumentCloned); Assume.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. var matchIdentifierLVN = "LVN"; if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none) { matchIdentifierLVN = RefinementSettings.TestingConvertedFromProteomicPeptideNameDecorator + matchIdentifierLVN; } foreach (var nodeTranGroup in docContainer.Document.MoleculeTransitionGroups) { foreach (var docNode in nodeTranGroup.Children) { var nodeTran = (TransitionDocNode)docNode; Assume.IsTrue(nodeTran.HasResults); Assume.AreEqual(1, nodeTran.Results.Count); if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN)) { Assume.IsFalse(nodeTran.Results[0][0].IsEmpty); } else { Assume.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; Assume.IsTrue(nodeTran.HasResults); Assume.AreEqual(2, nodeTran.Results.Count); if (nodeTran.Transition.Group.Peptide.Target.ToString().StartsWith(matchIdentifierLVN)) { Assume.IsTrue(nodeTran.Results[1][0].IsEmpty); } else { Assume.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, IsotopeEnrichmentsList.DEFAULT)) .ChangeTransitionFilter(filter => filter.ChangePeptideIonTypes(new[] { IonType.precursor }) .ChangeSmallMoleculeIonTypes(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, IsotopeEnrichmentsList.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].IsEmpty && !tranM1.Results[1].IsEmpty); Assert.IsTrue(tranM1.Results[0][0].IsEmpty && tranM1.Results[1][0].IsForcedIntegration); tranM1 = ms1AllTranstions[5]; Assert.AreEqual(-1, tranM1.Transition.MassIndex); Assert.IsTrue(!tranM1.Results[0].IsEmpty && !tranM1.Results[1].IsEmpty); Assert.IsTrue(tranM1.Results[0][0].IsForcedIntegration && tranM1.Results[1][0].IsEmpty); } }
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(); }
public SrmDocument ConvertToSmallMolecules(SrmDocument doc, ref string docPath, IEnumerable <string> dataPaths, RefinementSettings.ConvertToSmallMoleculesMode mode) { if (doc == null) { using (var cmd = new CommandLine()) { Assert.IsTrue(cmd.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imsdb file var docLoad = cmd.Document; using (var docContainer = new ResultsTestDocumentContainer(null, docPath)) { docContainer.SetDocument(docLoad, null, true); docContainer.AssertComplete(); doc = docContainer.Document; } } } if (mode == RefinementSettings.ConvertToSmallMoleculesMode.none) { return(doc); } var docOriginal = doc; var refine = new RefinementSettings(); docPath = docPath.Replace(".sky", "_converted_to_small_molecules.sky"); var docSmallMol = refine.ConvertToSmallMolecules(doc, Path.GetDirectoryName(docPath), mode); var listChromatograms = new List <ChromatogramSet>(); if (dataPaths != null) { foreach (var dataPath in dataPaths) { if (!string.IsNullOrEmpty(dataPath)) { listChromatograms.Add(AssertResult.FindChromatogramSet(docSmallMol, new MsDataFilePath(dataPath)) ?? new ChromatogramSet(Path.GetFileName(dataPath).Replace('.', '_'), new[] { dataPath })); } } } var docResults = docSmallMol.ChangeMeasuredResults(listChromatograms.Any() ? new MeasuredResults(listChromatograms) : null); // Since refine isn't in a document container, have to close the streams manually to avoid file locking trouble (thanks, Nick!) foreach (var library in docResults.Settings.PeptideSettings.Libraries.Libraries) { foreach (var stream in library.ReadStreams) { stream.CloseStream(); } } // Save and restore to ensure library caches var cmdline = new CommandLine(); cmdline.SaveDocument(docResults, docPath, TextWriter.Null); Assert.IsTrue(cmdline.OpenSkyFile(docPath)); // Handles any path shifts in database files, like our .imsdb file docResults = cmdline.Document; using (var docContainer = new ResultsTestDocumentContainer(null, docPath)) { docContainer.SetDocument(docResults, null, true); docContainer.AssertComplete(); doc = docContainer.Document; } AssertEx.ConvertedSmallMoleculeDocumentIsSimilar(docOriginal, doc, Path.GetDirectoryName(docPath), mode); return(doc); }
public void DoAsymmetricIsolationTest(RefinementSettings.ConvertToSmallMoleculesMode asSmallMolecules) { if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.none && !RunSmallMoleculeTestVersions) { Console.Write(MSG_SKIPPING_SMALLMOLECULE_TEST_VERSION); return; } LocalizationHelper.InitThread(); // TODO: All unit tests should be correctly initialized var testFilesDir = new TestFilesDir(TestContext, ZIP_FILE); string docPath = testFilesDir.GetTestPath("Asym_DIA.sky"); string cachePath = ChromatogramCache.FinalPathForName(docPath, null); FileEx.SafeDelete(cachePath); SrmDocument doc = ResultsUtil.DeserializeDocument(docPath); var refine = new RefinementSettings(); doc = refine.ConvertToSmallMolecules(doc, testFilesDir.FullPath, asSmallMolecules); const int expectedMoleculeCount = 1; // At first small molecules did not support multiple charge states, and this was 2 for that test mode AssertEx.IsDocumentState(doc, null, 1, expectedMoleculeCount, 2, 4); var fullScanInitial = doc.Settings.TransitionSettings.FullScan; Assert.IsTrue(fullScanInitial.IsEnabledMsMs); Assert.AreEqual(FullScanAcquisitionMethod.DIA, fullScanInitial.AcquisitionMethod); Assert.AreEqual(25, fullScanInitial.PrecursorFilter); AssertEx.Serializable(doc); using (var docContainer = new ResultsTestDocumentContainer(doc, docPath)) { // Import the first RAW file (or mzML for international) string rawPath = testFilesDir.GetTestPath("Asym_DIA_data.mzML"); var measuredResults = new MeasuredResults(new[] { new ChromatogramSet("Single", new[] { rawPath }) }); TransitionGroupDocNode nodeGroup; double ratio; const double poorRatio = 0.25; const double fixedRatio = 1.05; { // Import with symmetric isolation window SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2); nodeGroup = docResults.MoleculeTransitionGroups.First(); ratio = nodeGroup.Results[0][0].Ratio ?? 0; // The expected ratio is 1.0, but the symmetric isolation window should produce poor results if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula { Assert.AreEqual(poorRatio, ratio, 0.05); } // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docResults, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } { // Import with asymmetric isolation window SrmDocument docAsym = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan => fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test asym", 5, 20)))); AssertEx.Serializable(docAsym); Assert.IsTrue(docContainer.SetDocument(docAsym, doc, false)); SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2); nodeGroup = docResults.MoleculeTransitionGroups.First(); ratio = nodeGroup.Results[0][0].Ratio ?? 0; // Asymmetric should be a lot closer to 1.0 if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula { Assert.AreEqual(fixedRatio, ratio, 0.05); } // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docResults, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } { // Import with prespecified isolation windows var windowList = new List <IsolationWindow> { new IsolationWindow(999.2702214, 1024.270221), new IsolationWindow(1024.27267, 1049.27267) }; SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan => fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test prespecified", windowList)))); AssertEx.Serializable(docPrespecified); Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false)); SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2); nodeGroup = docResults.MoleculeTransitionGroups.First(); ratio = nodeGroup.Results[0][0].Ratio ?? 0; // Asymmetric should be a lot closer to 1.0 if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula { Assert.AreEqual(fixedRatio, ratio, 0.05); } // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docResults, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } { // Import with prespecified targets var windowList = new List <IsolationWindow> { new IsolationWindow(999.2702214, 1024.270221, 1004.27), new IsolationWindow(1024.27267, 1049.27267, 1029.27) }; SrmDocument docPrespecified = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan => fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test target", windowList)))); AssertEx.Serializable(docPrespecified); Assert.IsTrue(docContainer.SetDocument(docPrespecified, doc, false)); SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2); nodeGroup = docResults.MoleculeTransitionGroups.First(); ratio = nodeGroup.Results[0][0].Ratio ?? 0; // Asymmetric should be a lot closer to 1.0 if (asSmallMolecules != RefinementSettings.ConvertToSmallMoleculesMode.masses_only) // Can't use labels without a formula { Assert.AreEqual(fixedRatio, ratio, 0.05); } // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docResults, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } { // Import with ambiguous prespecified targets var windowList = new List <IsolationWindow> { new IsolationWindow(999.2702214, 1024.270221, 1004.27), new IsolationWindow(1000.0, 1049.27267, 1004.28) }; SrmDocument docAmbiguous = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan => fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test ambiguous", windowList)))); AssertEx.Serializable(docAmbiguous); Assert.IsTrue(docContainer.SetDocument(docAmbiguous, doc, false)); try { docContainer.ChangeMeasuredResults(measuredResults, expectedMoleculeCount, 1, 1, 2, 2); Assert.Fail("Expected ambiguous isolation targets."); } catch (Exception x) { AssertEx.AreComparableStrings(Resources.SpectrumFilter_FindFilterPairs_Two_isolation_windows_contain_targets_which_match_the_isolation_target__0__, x.Message, 1); } // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docContainer.Document, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } { // Import with one isolation window, so one result is discarded. var windowList = new List <IsolationWindow> { new IsolationWindow(999.2702214, 1024.270221), }; SrmDocument docOneWindow = doc.ChangeSettings(doc.Settings.ChangeTransitionFullScan(fullScan => fullScan.ChangeAcquisitionMethod(fullScan.AcquisitionMethod, new IsolationScheme("Test one window", windowList)))); AssertEx.Serializable(docOneWindow); Assert.IsTrue(docContainer.SetDocument(docOneWindow, doc, false)); SrmDocument docResults = docContainer.ChangeMeasuredResults(measuredResults, 1, 1, 0, 2, 0); nodeGroup = docResults.MoleculeTransitionGroups.First(); Assert.IsNull(nodeGroup.Results[0][0].Ratio); // Revert to original document, and get rid of results cache Assert.IsTrue(docContainer.SetDocument(doc, docResults, false)); FileEx.SafeDelete(testFilesDir.GetTestPath("Asym_DIA.skyd")); } } testFilesDir.Dispose(); }
/* 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); }