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 void test2() { MassTag massTag = new MassTag(); massTag.ID = 56488; massTag.MonoIsotopicMass = 2275.1694779; massTag.ChargeState = 3; massTag.MZ = massTag.MonoIsotopicMass / massTag.ChargeState + 1.00727649; Run run = new XCaliburRun(xcaliburTestfile); PeakImporterFromText peakImporter = new DeconTools.Backend.Data.PeakImporterFromText(xcaliburPeakDataFile); peakImporter.ImportPeaks(run.ResultCollection.MSPeakResultList); run.CurrentMassTag = massTag; Task peakChromGen = new PeakChromatogramGenerator(10); Task smoother = new DeconTools.Backend.ProcessingTasks.Smoothers.DeconToolsSavitzkyGolaySmoother(2, 2, 2); Task peakDet = new DeconTools.Backend.ProcessingTasks.PeakDetectors.ChromPeakDetector(); peakChromGen.Execute(run.ResultCollection); smoother.Execute(run.ResultCollection); peakDet.Execute(run.ResultCollection); TestUtilities.DisplayPeaks(run.PeakList); TestUtilities.DisplayXYValues(run.ResultCollection); }
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); }
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(); }