public void test3() { MassTag massTag = new MassTag(); massTag.ID = 56488; massTag.MonoIsotopicMass = 2275.1694779; massTag.ChargeState = 3; massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649; massTag.NETVal = 0.3520239f; Run run = new XCaliburRun(xcaliburTestfile); ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); run.CurrentMassTag = massTag; Task peakChromGen = new PeakChromatogramGenerator(20); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(); Task chromPeakSel = new DeconTools.Backend.ProcessingTasks.ChromPeakSelector(1, 0.1); MSGeneratorFactory msgenFactory = new MSGeneratorFactory(); Task msgen = msgenFactory.CreateMSGenerator(run.MSFileType); peakChromGen.Execute(run.ResultCollection); smoother.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); chromPeakSel.Execute(run.ResultCollection); Console.WriteLine("Now generating MS...."); msgen.Execute(run.ResultCollection); Console.WriteLine("----------- RESULTS ----------------------\n"); TestUtilities.DisplayPeaks(run.PeakList); MassTagResultBase massTagResult = run.ResultCollection.MassTagResultList[massTag]; massTagResult.DisplayToConsole(); Assert.AreEqual(5512, massTagResult.ScanSet.PrimaryScanNumber); }
private Run setupRun(string runFile, string peaksFile) { RunFactory rf = new RunFactory(); Run run = rf.CreateRun(runFile); ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(peaksFile); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); return(run); }
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 --------------------------"); }
private void getAlignmentInfo(Run run) { ChromAlignerUsingVIPERInfo chromAligner = new ChromAlignerUsingVIPERInfo(); chromAligner.Execute(run); }
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(); }
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()); }