public List <Task> getStandardTaskList(Run run) { Task peakChromGen = new PeakChromatogramGenerator(chromPPMTolerance); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5); Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET); MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task mspeakDet = new DeconToolsPeakDetector(peakParams); Task theorFeatureGen = new TomTheorFeatureGenerator(); Task finder = new N14N15TFFTask(5); Task quant = new N14N15QuantifierTask(1); Task fitScoreCalc = new IsotopicProfileFitScoreCalculator(); List <Task> taskList = new List <Task>(); taskList.Add(peakChromGen); taskList.Add(smoother); taskList.Add(peakDet); taskList.Add(chromPeakSel); taskList.Add(msgen); taskList.Add(mspeakDet); taskList.Add(theorFeatureGen); taskList.Add(finder); taskList.Add(quant); taskList.Add(fitScoreCalc); return(taskList); }
public SmartChromPeakSelector(SmartChromPeakSelectorParameters parameters) { this.Parameters = parameters; MSPeakDetector = new DeconToolsPeakDetectorV2(parameters.MSPeakDetectorPeakBR, parameters.MSPeakDetectorSigNoiseThresh, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, true); var iterativeTFFParams = new IterativeTFFParameters(); iterativeTFFParams.ToleranceInPPM = parameters.MSToleranceInPPM; iterativeTFFParams.MinimumRelIntensityForForPeakInclusion = parameters.IterativeTffMinRelIntensityForPeakInclusion; if (parameters.MSFeatureFinderType == DeconTools.Backend.Globals.TargetedFeatureFinderType.BASIC) { throw new NotSupportedException("Currently the Basic TFF is not supported in the SmartChromPeakSelector"); //TargetedMSFeatureFinder = new TargetedFeatureFinders.BasicTFF(parameters.MSToleranceInPPM); } else { TargetedMSFeatureFinder = new IterativeTFF(iterativeTFFParams); } resultValidator = new ResultValidatorTask(); fitScoreCalc = new IsotopicProfileFitScoreCalculator(); InterferenceScorer = new InterferenceScorer(); }
protected virtual void DoMainInitialization() { ValidateParameters(); TheorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); ChromGen = new PeakChromatogramGenerator(WorkflowParameters.ChromGenTolerance, WorkflowParameters.ChromGeneratorMode, DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED, WorkflowParameters.ChromGenToleranceUnit) { TopNPeaksLowerCutOff = 0.333, ChromWindowWidthForAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2, ChromWindowWidthForNonAlignedData = (float)WorkflowParameters.ChromNETTolerance * 2 }; //only var allowNegativeValues = false; ChromSmoother = new SavitzkyGolaySmoother(WorkflowParameters.ChromSmootherNumPointsInSmooth, 2, allowNegativeValues); ChromPeakDetector = new ChromPeakDetector(WorkflowParameters.ChromPeakDetectorPeakBR, WorkflowParameters.ChromPeakDetectorSigNoise); ChromPeakSelector = CreateChromPeakSelector(WorkflowParameters); ChromPeakAnalyzer = new ChromPeakAnalyzer(WorkflowParameters); IterativeTffParameters = new IterativeTFFParameters(); IterativeTffParameters.ToleranceInPPM = WorkflowParameters.MSToleranceInPPM; MsfeatureFinder = new IterativeTFF(IterativeTffParameters); FitScoreCalc = new IsotopicProfileFitScoreCalculator(); InterferenceScorer = new InterferenceScorer(); ResultValidator = new ResultValidatorTask(); ChromatogramCorrelator = new IqChromCorrelator(WorkflowParameters.ChromSmootherNumPointsInSmooth, 0.05, WorkflowParameters.ChromGenTolerance); }
public void test1() { Run run = new XCaliburRun(xcaliburTestfile); List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList(); MassTag mt = mass_tagList[0]; run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 }); run.CurrentMassTag = mt; MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task mspeakDet = new DeconToolsPeakDetector(peakParams); Task theorFeatureGen = new TomTheorFeatureGenerator(); Task targetedFeatureFinder = new BasicTFF(0.01); IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator(); msgen.Execute(run.ResultCollection); //run.XYData.Display(); mspeakDet.Execute(run.ResultCollection); theorFeatureGen.Execute(run.ResultCollection); targetedFeatureFinder.Execute(run.ResultCollection); fitScoreCalc.Execute(run.ResultCollection); MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt); TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile); Console.WriteLine("Fit val = " + result.IsotopicProfile.Score); /* * * * ------------------- MassTag = 24769--------------------------- * monoMass = 2086.0595; monoMZ = 1044.0370; ChargeState = 2; NET = 0.452; Sequence = DFNEALVHQVVVAYAANAR * ****** Match ****** ******NET = 0.452 ******ChromPeak ScanNum = 9016.48992535631 ******ChromPeak NETVal = 0.453 ******ScanSet = { 9010, 9017, 9024, } ******Observed MZ and intensity = 1044.03290771556 1.269842E+07 ******------------------------------ end -------------------------- * * * * * */ }
public ChromPeakAnalyzer(TargetedWorkflowParameters parameters) { Parameters = parameters; var iterativeTffParameters = new IterativeTFFParameters(); TargetedMSFeatureFinder = new IterativeTFF(iterativeTffParameters); InterferenceScorer = new InterferenceScorer(); MSPeakDetector = new DeconToolsPeakDetectorV2(); FitScoreCalc = new IsotopicProfileFitScoreCalculator(); ResultValidator = new ResultValidatorTask(); }
public void test1() { Run run = new XCaliburRun(xcaliburTestfile); List <MassTag> mass_tagList = TestUtilities.CreateTestMassTagList(); MassTag mt = mass_tagList[0]; run.CurrentScanSet = new ScanSet(9017, new int[] { 9010, 9017, 9024 }); run.CurrentMassTag = mt; MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 1.3, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task mspeakDet = new DeconToolsPeakDetector(peakParams); Task theorFeatureGen = new TomTheorFeatureGenerator(); Task targetedFeatureFinder = new BasicTFF(0.01); IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator(); Task exporter = new BasicMTResultSQLiteExporter(exporterOutputFile1); msgen.Execute(run.ResultCollection); //run.XYData.Display(); mspeakDet.Execute(run.ResultCollection); theorFeatureGen.Execute(run.ResultCollection); targetedFeatureFinder.Execute(run.ResultCollection); fitScoreCalc.Execute(run.ResultCollection); exporter.Execute(run.ResultCollection); exporter.Cleanup(); MassTagResultBase result = run.ResultCollection.GetMassTagResult(mt); TestUtilities.DisplayIsotopicProfileData(result.IsotopicProfile); }
public void find_targetMassTag_131959Test1() { var run = new RunFactory().CreateRun(xcaliburTestfile); var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1); var massTagColl = masstagImporter.Import(); Assert.AreEqual(2719, massTagColl.TargetList.Count); var chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); var peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); //int mtID = 635428; var mtID = 131959; Task peakChromGen = new PeakChromatogramGenerator(20); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.SavitzkyGolaySmoother(23, 2); Task zeroFill = new DeconTools.Backend.ProcessingTasks.ZeroFillers.DeconToolsZeroFiller(3); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 1); Task msPeakDet = new DeconToolsPeakDetectorV2(1.3, 2, Globals.PeakFitType.QUADRATIC, true); var basicChromPeakSelParam = new ChromPeakSelectorParameters(); basicChromPeakSelParam.NETTolerance = 0.1f; basicChromPeakSelParam.PeakSelectorMode = Globals.PeakSelectorMode.ClosestToTarget; Task chromPeakSel = new BasicChromPeakSelector(basicChromPeakSelParam); Task msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); run.CurrentMassTag = massTagColl.TargetList.Find(p => p.ID == mtID); var mt = run.CurrentMassTag; mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS; Task theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); Task targetedFeatureFinder = new BasicTFF(); Task fitScoreCalc = new IsotopicProfileFitScoreCalculator(); theorFeatureGen.Execute(run.ResultCollection); Console.WriteLine(); Console.WriteLine(); Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------"); Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NormalizedElutionTime.ToString("0.000") + "; Sequence = " + mt.Code + "; EmpiricalFormula= " + mt.EmpiricalFormula + "\n"); peakChromGen.Execute(run.ResultCollection); smoother.Execute(run.ResultCollection); //TestUtilities.DisplayXYValues(run.ResultCollection); peakDet.Execute(run.ResultCollection); TestUtilities.DisplayPeaks(run.PeakList); chromPeakSel.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); //TestUtilities.DisplayXYValues(run.ResultCollection); msPeakDet.Execute(run.ResultCollection); targetedFeatureFinder.Execute(run.ResultCollection); fitScoreCalc.Execute(run.ResultCollection); var massTagResult = run.ResultCollection.MassTagResultList[mt]; massTagResult.DisplayToConsole(); //Console.WriteLine("------------------------------ end --------------------------"); }
public void test1() { Run run = new XCaliburRun(xcaliburTestfile); MassTagCollection massTagColl = new MassTagCollection(); MassTagIDGenericImporter mtidImporter = new MassTagIDGenericImporter(cysteineMassTagSourceFile1, '\t'); mtidImporter.Import(massTagColl); MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_Shewanella_ProdTest_P352", "porky"); importer.Import(massTagColl); Assert.AreEqual(737, massTagColl.MassTagIDList.Count); Assert.AreEqual(826, massTagColl.MassTagList.Count); ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburAllPeaksFile); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); Task peakChromGen = new PeakChromatogramGenerator(20); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5); Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET); MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 0.75, true, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task mspeakDet = new DeconToolsPeakDetector(peakParams); Task theorFeatureGen = new TomTheorFeatureGenerator(); Task targetedFeatureFinder = new BasicTFF(6); Task exporter = new BasicMTResultSQLiteExporter(cysteineAnalysisOutput1); IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator(); int successCounter = 0; List <long> timingResults = new List <long>(); foreach (MassTag mt in massTagColl.MassTagList) { run.CurrentMassTag = mt; mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS; Console.WriteLine(); Console.WriteLine(); Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------"); Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n"); Stopwatch sw = new Stopwatch(); sw.Start(); try { peakChromGen.Execute(run.ResultCollection); smoother.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); chromPeakSel.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); mspeakDet.Execute(run.ResultCollection); theorFeatureGen.Execute(run.ResultCollection); targetedFeatureFinder.Execute(run.ResultCollection); fitScoreCalc.Execute(run.ResultCollection); MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt]; massTagResult.DisplayToConsole(); Console.WriteLine("------------------------------ end --------------------------"); } catch (Exception ex) { Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace); } sw.Stop(); timingResults.Add(sw.ElapsedMilliseconds); if (mt == massTagColl.MassTagList.Last()) { exporter.Execute(run.ResultCollection); } } exporter.Cleanup(); //List<IMassTagResult> successfulResults = run.ResultCollection.GetSuccessfulMassTagResults(); foreach (long tr in timingResults) { Console.WriteLine(tr); } Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum()); Console.WriteLine("-------- Average time for each MT = " + timingResults.Average()); Console.WriteLine(); }
protected override void DoPostInitialization() { base.DoPostInitialization(); ValidateParameters(); theorFeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); theorN15FeatureGen = new JoshTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.N15, 0.005); chromGenN14 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, _workflowParameters.ChromGeneratorMode); chromGenN14.TopNPeaksLowerCutOff = 0.333; chromGenN15 = new PeakChromatogramGenerator(_workflowParameters.ChromGenTolerance, DeconTools.Backend.Globals.ChromatogramGeneratorMode.MOST_ABUNDANT_PEAK, DeconTools.Backend.Globals.IsotopicProfileType.LABELLED); chromGenN15.TopNPeaksLowerCutOff = 0.333; var pointsToSmooth = (_workflowParameters.ChromSmootherNumPointsInSmooth + 1) / 2; chromSmoother = new SavitzkyGolaySmoother(_workflowParameters.ChromSmootherNumPointsInSmooth, 2); chromPeakDetector = new ChromPeakDetector(_workflowParameters.ChromPeakDetectorPeakBR, _workflowParameters.ChromPeakDetectorSigNoise); var smartchrompeakSelectorParams = new SmartChromPeakSelectorParameters(); smartchrompeakSelectorParams.MSFeatureFinderType = DeconTools.Backend.Globals.TargetedFeatureFinderType.ITERATIVE; smartchrompeakSelectorParams.MSPeakDetectorPeakBR = _workflowParameters.MSPeakDetectorPeakBR; smartchrompeakSelectorParams.MSPeakDetectorSigNoiseThresh = _workflowParameters.MSPeakDetectorSigNoise; smartchrompeakSelectorParams.MSToleranceInPPM = _workflowParameters.MSToleranceInPPM; smartchrompeakSelectorParams.NETTolerance = (float)_workflowParameters.ChromNETTolerance; smartchrompeakSelectorParams.NumScansToSum = _workflowParameters.NumMSScansToSum; smartchrompeakSelectorParams.NumChromPeaksAllowed = 10; smartchrompeakSelectorParams.IterativeTffMinRelIntensityForPeakInclusion = 0.5; chromPeakSelectorN14 = new SmartChromPeakSelector(smartchrompeakSelectorParams); var chromPeakSelectorParameters = new ChromPeakSelectorParameters(); chromPeakSelectorParameters.NumScansToSum = _workflowParameters.NumMSScansToSum; chromPeakSelectorParameters.NETTolerance = (float)_workflowParameters.ChromNETTolerance; chromPeakSelectorParameters.PeakSelectorMode = DeconTools.Backend.Globals.PeakSelectorMode.N15IntelligentMode; chromPeakSelectorN15 = new BasicChromPeakSelector(chromPeakSelectorParameters); chromPeakSelectorN15.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED; msPeakDetector = new DeconToolsPeakDetectorV2(_workflowParameters.MSPeakDetectorPeakBR, _workflowParameters.MSPeakDetectorSigNoise, DeconTools.Backend.Globals.PeakFitType.QUADRATIC, false); var iterativeTFFParameters = new IterativeTFFParameters(); iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM; iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33; iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.UNLABELLED; unlabelledProfilefinder = new IterativeTFF(iterativeTFFParameters); iterativeTFFParameters = new IterativeTFFParameters(); iterativeTFFParameters.ToleranceInPPM = _n14N15Workflow2Parameters.TargetedFeatureFinderToleranceInPPM; iterativeTFFParameters.MinimumRelIntensityForForPeakInclusion = 0.33; iterativeTFFParameters.IsotopicProfileType = DeconTools.Backend.Globals.IsotopicProfileType.LABELLED; labelledProfileFinder = new IterativeTFF(iterativeTFFParameters); quantifier = new N14N15QuantifierTask(_n14N15Workflow2Parameters.NumPeaksUsedInQuant, _workflowParameters.MSToleranceInPPM); fitScoreCalc = new IsotopicProfileFitScoreCalculator(); var minRelativeIntensityForScore = 0.2; resultValidatorN14 = new ResultValidatorTask(minRelativeIntensityForScore, true); resultValidatorN15 = new LabelledIsotopicProfileScorer(minRelativeIntensityForScore); ChromatogramXYData = new XYData(); MassSpectrumXYData = new XYData(); ChromPeaksDetected = new List <ChromPeak>(); }
public void run_fullAnalysisTest1() { Run run = new BrukerRun(rsph_AOnly_28_run1File); MassTagCollection massTagColl = new MassTagCollection(); run.ResultCollection.MassTagResultType = DeconTools.Backend.Globals.MassTagResultType.N14N15_MASSTAG_RESULT; massTagColl.MassTagIDList = fourTestMTs; MassTagFromSqlDBImporter importer = new MassTagFromSqlDBImporter("MT_R_sphaeroides241_P513", "Albert"); importer.chargeStateFilterThreshold = 0.05; importer.Import(massTagColl); Assert.AreEqual(7, massTagColl.MassTagList.Count); ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(rsph_Aonly_28_run1_scans500_1000_peaks); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); Task peakChromGen = new PeakChromatogramGenerator(20); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(11, 11, 2); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(0.5, 0.5); Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.01, Globals.PeakSelectorMode.CLOSEST_TO_TARGET); MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); DeconToolsV2.Peaks.clsPeakProcessorParameters peakParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(2, 3, false, DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC); Task mspeakDet = new DeconToolsPeakDetector(peakParams); Task theorFeatureGen = new TomTheorFeatureGenerator(); N14N15TFFTask finder = new N14N15TFFTask(0.01); N14N15QuantifierTask quant = new N14N15QuantifierTask(1); IsotopicProfileFitScoreCalculator fitScoreCalc = new IsotopicProfileFitScoreCalculator(); List <long> timingResults = new List <long>(); foreach (MassTag mt in massTagColl.MassTagList) { run.CurrentMassTag = mt; mt.MZ = mt.MonoIsotopicMass / mt.ChargeState + Globals.PROTON_MASS; Console.WriteLine(); Console.WriteLine(); Console.WriteLine("------------------- MassTag = " + mt.ID + "---------------------------"); Console.WriteLine("monoMass = " + mt.MonoIsotopicMass.ToString("0.0000") + "; monoMZ = " + mt.MZ.ToString("0.0000") + "; ChargeState = " + mt.ChargeState + "; NET = " + mt.NETVal.ToString("0.000") + "; Sequence = " + mt.PeptideSequence + "\n"); Stopwatch sw = new Stopwatch(); sw.Start(); try { peakChromGen.Execute(run.ResultCollection); smoother.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); chromPeakSel.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); mspeakDet.Execute(run.ResultCollection); theorFeatureGen.Execute(run.ResultCollection); finder.Execute(run.ResultCollection); quant.Execute(run.ResultCollection); fitScoreCalc.Execute(run.ResultCollection); MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[mt]; massTagResult.DisplayToConsole(); Console.WriteLine("------------------------------ end --------------------------"); } catch (Exception ex) { Console.WriteLine("Task failed. Message: " + ex.Message + ex.StackTrace); } sw.Stop(); timingResults.Add(sw.ElapsedMilliseconds); } foreach (long tr in timingResults) { Console.WriteLine(tr); } Console.WriteLine("-------- Analysis time for all MTs = " + timingResults.Sum()); Console.WriteLine("-------- Average time for each MT = " + timingResults.Average()); Console.WriteLine(); }
public void smartChromPeakSelectorTest_noSumming() { var run = new RunFactory().CreateRun(xcaliburTestfile); run.Close(); run = new RunFactory().CreateRun(xcaliburTestfile); var massTagColl = new TargetCollection(); var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1); massTagColl = masstagImporter.Import(); var chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); var chromPeakDet = new ChromPeakDetector(0.5, 1); var smartchromParam = new SmartChromPeakSelectorParameters(); var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam); var basicChromParam = new ChromPeakSelectorParameters(); var basicChromPeakSelector = new BasicChromPeakSelector(basicChromParam); var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); var iterativeTff = new IterativeTFF(new IterativeTFFParameters()); var fitscoreCalc = new IsotopicProfileFitScoreCalculator(); var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt"; var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile); Assert.IsNotNull(xydata); run.XYData = xydata; // run.XYData.Display(); run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First(); Console.WriteLine("------MT = " + run.CurrentMassTag.ToString()); theorFeatureGen.Execute(run.ResultCollection); chromPeakDet.Execute(run.ResultCollection); var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag); //first run the standard peak selector basicChromPeakSelector.Execute(run.ResultCollection); Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue)); //now run the smart chrom peak selector run.XYData = xydata; chromPeakDet.Execute(run.ResultCollection); smartChromPeakSelector.Parameters.NETTolerance = 0.025f; smartChromPeakSelector.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); iterativeTff.Execute(run.ResultCollection); TestUtilities.DisplayPeaks(run.PeakList); fitscoreCalc.Execute(run.ResultCollection); Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue)); //result.DisplayToConsole(); TestUtilities.DisplayIsotopicProfileData(result.Target.IsotopicProfile); }
public void smartChromPeakSelectorTest_withDynamicSumming() { var run = new RunFactory().CreateRun(xcaliburTestfile); var massTagColl = new TargetCollection(); var masstagImporter = new MassTagFromTextFileImporter(massTagTestList1); massTagColl = masstagImporter.Import(); var chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); var theorFeatureGen = new TomTheorFeatureGenerator(DeconTools.Backend.Globals.LabellingType.NONE, 0.005); var chromPeakDet = new ChromPeakDetector(0.5, 1); var smartchromParam = new SmartChromPeakSelectorParameters(); var smartChromPeakSelector = new SmartChromPeakSelector(smartchromParam); var basicChromPeakSelector = new BasicChromPeakSelector(new ChromPeakSelectorParameters()); var msgen = MSGeneratorFactory.CreateMSGenerator(run.MSFileType); var iterativeTff = new IterativeTFF(new IterativeTFFParameters()); var fitscoreCalc = new IsotopicProfileFitScoreCalculator(); var testChromatogramDataFile = @"\\protoapps\UserData\Slysz\DeconTools_TestFiles\TargetedWorkflowStandards\massTag635428_chromatogramData.txt"; var xydata = TestUtilities.LoadXYDataFromFile(testChromatogramDataFile); Assert.IsNotNull(xydata); run.XYData = new XYData(); run.XYData.Xvalues = xydata.Xvalues; run.XYData.Yvalues = xydata.Yvalues; // run.XYData.Display(); run.CurrentMassTag = massTagColl.TargetList.Where(p => p.ID == 635428).First(); Console.WriteLine("------MT = " + run.CurrentMassTag.ToString()); theorFeatureGen.Execute(run.ResultCollection); chromPeakDet.Execute(run.ResultCollection); //first run the standard peak selector basicChromPeakSelector.Execute(run.ResultCollection); var result = run.ResultCollection.GetTargetedResult(run.CurrentMassTag); Assert.AreEqual(10066, (int)Math.Round(result.ChromPeakSelected.XValue)); //now run the smart chrom peak selector run.XYData = new XYData(); run.XYData.Xvalues = xydata.Xvalues; run.XYData.Yvalues = xydata.Yvalues; chromPeakDet.Execute(run.ResultCollection); smartChromPeakSelector.Parameters.NETTolerance = 0.025f; smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51; smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC; smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 1; smartChromPeakSelector.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); iterativeTff.Execute(run.ResultCollection); fitscoreCalc.Execute(run.ResultCollection); Console.WriteLine(result.ScanSet); Assert.AreEqual(14, result.ScanSet.IndexValues.Count); Assert.AreEqual(0.0104m, (decimal)Math.Round(result.Score, 4)); Assert.AreEqual("9575 {9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624}", result.ScanSet.ToString()); run.XYData = new XYData(); run.XYData.Xvalues = xydata.Xvalues; run.XYData.Yvalues = xydata.Yvalues; chromPeakDet.Execute(run.ResultCollection); smartChromPeakSelector.Parameters.NETTolerance = 0.025f; smartChromPeakSelector.Parameters.MaxScansSummedInDynamicSumming = 51; smartChromPeakSelector.Parameters.SummingMode = SummingModeEnum.SUMMINGMODE_DYNAMIC; smartChromPeakSelector.Parameters.AreaOfPeakToSumInDynamicSumming = 2; smartChromPeakSelector.Execute(run.ResultCollection); msgen.Execute(run.ResultCollection); iterativeTff.Execute(run.ResultCollection); fitscoreCalc.Execute(run.ResultCollection); result.DisplayToConsole(); Assert.AreEqual(9579, (int)Math.Round(result.ChromPeakSelected.XValue)); Assert.AreEqual(0.025m, (decimal)(Math.Round(result.Score, 4))); //Console.WriteLine(result.ScanSet); Assert.AreEqual(26, result.ScanSet.IndexValues.Count); Assert.AreEqual("9575 {9493, 9500, 9506, 9513, 9520, 9527, 9534, 9540, 9547, 9554, 9561, 9568, 9575, 9582, 9589, 9596, 9603, 9610, 9617, 9624, 9631, 9638, 9645, 9652, 9658, 9665}", result.ScanSet.ToString()); }