public MercuryDistributionCreator() { avergineFormulaCreator = new DeconToolsV2.HornTransform.clsAveragine(); hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters(); decon2LSMercuryDistribution = new DeconToolsV2.clsMercuryIsotopeDistribution(); peakDetector = new DeconToolsPeakDetector(); }
public void exporterTest1() { Run run = new IMFRun(imfFilepath); run.CurrentScanSet = new ScanSet(233); ResultCollection results = new ResultCollection(run); Task msGen = new GenericMSGenerator(); msGen.Execute(results); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 3; detectorParams.ThresholdedData = false; Task peakDetector = new DeconToolsPeakDetector(detectorParams); peakDetector.Execute(results); DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); Task decon = new HornDeconvolutor(hornParams); decon.Execute(results); Exporter <ResultCollection> exporter = new BasicIsosExporter(exporterTest1OutputName); exporter.Export(results); }
public MercuryDistCollectionCreator() { this.hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters(); this.averagineFormula = this.hornParameters.AveragineFormula; this.tagFormula = this.hornParameters.TagFormula; }
public void fitterOnHornDataTest1() { Run run = new XCaliburRun(xcaliburTestfile); ResultCollection results = new ResultCollection(run); run.CurrentScanSet = new ScanSet(6067); Task msGen = new GenericMSGenerator(1154, 1158); msGen.Execute(results); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 0.5; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 3; detectorParams.ThresholdedData = false; Task peakDetector = new DeconToolsPeakDetector(detectorParams); peakDetector.Execute(results); DeconToolsV2.HornTransform.clsHornTransformParameters hornParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters(); hornParameters.PeptideMinBackgroundRatio = 2; Task decon = new HornDeconvolutor(hornParameters); decon.Execute(results); IsosResult result1 = results.ResultList[0]; MercuryDistributionCreator distcreator = new MercuryDistributionCreator(); double resolution = result1.IsotopicProfile.GetMZofMostAbundantPeak() / result1.IsotopicProfile.GetFWHM(); distcreator.CreateDistribution(result1.IsotopicProfile.MonoIsotopicMass, result1.IsotopicProfile.ChargeState, resolution); distcreator.OffsetDistribution(result1.IsotopicProfile); XYData theorXYData = distcreator.Data; StringBuilder sb = new StringBuilder(); TestUtilities.GetXYValuesToStringBuilder(sb, theorXYData.Xvalues, theorXYData.Yvalues); Console.WriteLine(sb.ToString()); AreaFitter areafitter = new AreaFitter(theorXYData, run.XYData, 10); double fitval = areafitter.getFit(); Console.WriteLine(result1.IsotopicProfile.Score + "\t" + fitval); Console.WriteLine((result1.IsotopicProfile.Score - fitval) / result1.IsotopicProfile.Score); Assert.AreEqual(0.0209385414928986, (decimal)fitval); //TODO: fix this test... i'm getting 0.0207350903681061m }
public void xcaliburFileMSMSDataTest1() { //exploring how only MSMS data is processed... Project.Reset(); Run run = new XCaliburRun(xcaliburTestfile, 6000, 6004); //only MS/MS data here ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1); sscc.Create(); Project project = Project.getInstance(); project.RunCollection.Add(run); Task msGen = new GenericMSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 1.3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 2; Task peakDetector = new DeconToolsPeakDetector(detectorParams); DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); hornparams.PeptideMinBackgroundRatio = 2; Task hornDecon = new HornDeconvolutor(hornparams); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(hornDecon); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new BasicTaskController(project.TaskCollection); controller.Execute(project.RunCollection); sw.Stop(); Assert.AreEqual(1, Project.getInstance().RunCollection.Count); Assert.AreEqual(3, project.TaskCollection.TaskList.Count); // Assert.AreEqual(21, project.RunCollection[0].ScanSetCollection.ScanSetList.Count); Assert.AreEqual(0, project.RunCollection[0].ResultCollection.ResultList.Count); Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds); Console.WriteLine("Scans analyzed = " + project.RunCollection[0].ScanSetCollection.ScanSetList.Count); Console.WriteLine("Features found = " + project.RunCollection[0].ResultCollection.ResultList.Count); }
public frmDecon2LS() { try { this.mMediator = new Decon2LSMediator(this); // // Required for Windows Form Designer support // InitializeComponent(); this.mMdiChildCloseHandler = new EventHandler(this.MdiChildClosed); // attach file viewer to mediator this.mFileTreeView.AttachTo(mMediator); // Initialize the categories that we always want to appear in the side view frmSpectra.InitializeCategories(mFileTreeView); frmMercury.InitializeCategories(mFileTreeView); frm2DPeakProcessing.InitializeCategories(mFileTreeView); } catch (Exception ex) { MessageBox.Show(ex.Message); } try { var paramLoader = new clsParameterLoader(); if (System.IO.File.Exists(Application.ExecutablePath + mstrDEFAULTPARAMFILE)) { mstrParamFile = Application.ExecutablePath + mstrDEFAULTPARAMFILE; paramLoader.LoadParametersFromFile(mstrParamFile); mobjPeakParameters = paramLoader.PeakParameters; mobjTransformParameters = paramLoader.TransformParameters; mobjFTICRRawPreProcessParameters = paramLoader.FTICRPreprocessOptions; mobjDTAGenerationParameters = paramLoader.DTAParameters; } else if (System.IO.File.Exists(Application.UserAppDataPath + mstrDEFAULTPARAMFILE)) { mstrParamFile = Application.UserAppDataPath + mstrDEFAULTPARAMFILE; paramLoader.LoadParametersFromFile(mstrParamFile); mobjPeakParameters = paramLoader.PeakParameters; mobjTransformParameters = paramLoader.TransformParameters; mobjFTICRRawPreProcessParameters = paramLoader.FTICRPreprocessOptions; mobjDTAGenerationParameters = paramLoader.DTAParameters; } else { // no default parameters found, loading defaults. MessageBox.Show(this, "No parameter file found. Loading defaults."); mobjPeakParameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); mobjTransformParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters(); mobjFTICRRawPreProcessParameters = new DeconToolsV2.Readers.clsRawDataPreprocessOptions(); mobjDTAGenerationParameters = new DeconToolsV2.DTAGeneration.clsDTAGenerationParameters(); mstrParamFile = Application.ExecutablePath + mstrDEFAULTPARAMFILE; } } catch (Exception ex) { Console.WriteLine(ex.Message + ex.StackTrace); mobjPeakParameters = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); mobjTransformParameters = new DeconToolsV2.HornTransform.clsHornTransformParameters(); mobjFTICRRawPreProcessParameters = new DeconToolsV2.Readers.clsRawDataPreprocessOptions(); mobjDTAGenerationParameters = new DeconToolsV2.DTAGeneration.clsDTAGenerationParameters(); } }
public void multiIMFFileDeconTest1() { imfFileList.Clear(); imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_1.IMF"); imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_QS_16V_0000.Accum_2.IMF"); imfFileList.Add("..\\..\\TestFiles\\50ugpmlBSA_CID_SQ_14V_0000.Accum_1.IMF"); Project.Reset(); Project project = Project.getInstance(); foreach (string strItem in imfFileList) { Run run = new IMFRun(strItem, 233, 233); project.RunCollection.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1); sscc.Create(); } Task msGen = new GenericMSGenerator(); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; detectorParams.SignalToNoiseThreshold = 3; detectorParams.ThresholdedData = false; Task peakDetector = new DeconToolsPeakDetector(detectorParams); DeconToolsV2.HornTransform.clsHornTransformParameters hornparams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); hornparams.PeptideMinBackgroundRatio = 5; Task hornDecon = new HornDeconvolutor(hornparams); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(hornDecon); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new BasicTaskController(project.TaskCollection); controller.Execute(project.RunCollection); sw.Stop(); Assert.AreEqual(3, Project.getInstance().RunCollection.Count); Assert.AreEqual(3, project.TaskCollection.TaskList.Count); Assert.AreEqual(1, project.RunCollection[0].ScanSetCollection.ScanSetList.Count); Assert.AreEqual(12, project.RunCollection[0].ResultCollection.ResultList.Count); int totalScans = 0; int totalFeatures = 0; for (int i = 0; i < project.RunCollection.Count; i++) { Console.WriteLine("Run name = " + project.RunCollection[i].Filename); Console.WriteLine("Scans analyzed = " + project.RunCollection[i].ScanSetCollection.ScanSetList.Count); Console.WriteLine("Features found = " + project.RunCollection[i].ResultCollection.ResultList.Count); totalFeatures += project.RunCollection[i].ResultCollection.ResultList.Count; totalScans += project.RunCollection[i].ScanSetCollection.ScanSetList.Count; } Console.WriteLine("------------------------------------------------"); Console.WriteLine("Total Features found = " + totalFeatures); Console.WriteLine("Total Scans = " + totalScans); Console.WriteLine("Total Time required (ms) = " + sw.ElapsedMilliseconds); }
public void multipleFrames_horn_test4() { Project.Reset(); //Project.getInstance().LoadOldDecon2LSParameters(uimfParameters1); UIMFRun run = new UIMFRun(uimfFilepath, 1202, 1202); Project.getInstance().RunCollection.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1); sscc.Create(); FrameSetCollectionCreator fscc = new FrameSetCollectionCreator(run, run.MinFrame, run.MaxFrame, 1, 1); fscc.Create(); Task msGen = new UIMF_MSGenerator(0, 5000); Task zeroFiller = new DeconToolsZeroFiller(3); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 4; detectorParams.SignalToNoiseThreshold = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; Task peakDetector = new DeconToolsPeakDetector(detectorParams); DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); hornParams.CompleteFit = true; hornParams.LeftFitStringencyFactor = 2.5; hornParams.RightFitStringencyFactor = 0.5; hornParams.PeptideMinBackgroundRatio = 4; hornParams.MaxFit = 0.4; hornParams.UseMZRange = false; hornParams.UseMercuryCaching = true; Task decon = new HornDeconvolutor(hornParams); Task scanResultsUpdater = new ScanResultUpdater(); Project.getInstance().TaskCollection.TaskList.Add(msGen); Project.getInstance().TaskCollection.TaskList.Add(zeroFiller); Project.getInstance().TaskCollection.TaskList.Add(peakDetector); Project.getInstance().TaskCollection.TaskList.Add(decon); Project.getInstance().TaskCollection.TaskList.Add(scanResultsUpdater); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new UIMF_TaskController(Project.getInstance().TaskCollection); controller.Execute(Project.getInstance().RunCollection); sw.Stop(); Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds); Console.WriteLine("Scans analyzed = " + Project.getInstance().RunCollection[0].ScanSetCollection.ScanSetList.Count); Console.WriteLine("Features found = " + Project.getInstance().RunCollection[0].ResultCollection.ResultList.Count); Console.WriteLine("Peaks found = " + Project.getInstance().RunCollection[0].ResultCollection.ScanResultList[0].NumPeaks); StringBuilder sb = new StringBuilder(); }
public void imf_multipleFrames_horn_test2() { List <Run> runCollection = new List <Run>(); Run run = new IMFRun(imfFilePath); runCollection.Add(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 9, 1); sscc.Create(); Task msGen = new GenericMSGenerator(0, 5000); Task zeroFiller = new DeconToolsZeroFiller(3); DeconToolsV2.Peaks.clsPeakProcessorParameters detectorParams = new DeconToolsV2.Peaks.clsPeakProcessorParameters(); detectorParams.PeakBackgroundRatio = 4; detectorParams.SignalToNoiseThreshold = 3; detectorParams.PeakFitType = DeconToolsV2.Peaks.PEAK_FIT_TYPE.QUADRATIC; Task peakDetector = new DeconToolsPeakDetector(detectorParams); DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); hornParams.CompleteFit = true; hornParams.LeftFitStringencyFactor = 2.5; hornParams.RightFitStringencyFactor = 0.5; hornParams.PeptideMinBackgroundRatio = 4; hornParams.MaxFit = 0.4; Task decon = new HornDeconvolutor(hornParams); Task scanResultsUpdater = new ScanResultUpdater(); TaskCollection tc = new TaskCollection(); tc.TaskList.Add(msGen); tc.TaskList.Add(zeroFiller); tc.TaskList.Add(peakDetector); tc.TaskList.Add(decon); tc.TaskList.Add(scanResultsUpdater); Stopwatch sw = new Stopwatch(); sw.Start(); TaskController controller = new BasicTaskController(tc); controller.Execute(runCollection); sw.Stop(); Console.WriteLine("Time required (ms) = " + sw.ElapsedMilliseconds); Console.WriteLine("Scans analyzed = " + runCollection[0].ScanSetCollection.ScanSetList.Count); Console.WriteLine("Features found = " + runCollection[0].ResultCollection.ResultList.Count); Console.WriteLine("Peaks found = " + runCollection[0].ResultCollection.ScanResultList.Sum(p => p.NumPeaks)); StringBuilder sb = new StringBuilder(); }
public void xcaliburSpeed_THRASH_Test1() { Run run = new XCaliburRun(xcaliburTestfile); int startScan = 6005; int stopScan = 6050; int numScansSummed = 1; ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, startScan, stopScan, numScansSummed, 1); scanSetCreator.Create(); ResultCollection results = new ResultCollection(run); List <timingResult> timingResults = new List <timingResult>(); System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch(); foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList) { if (results.Run.GetMSLevel(scanset.PrimaryScanNumber) != 1) { continue; } sw.Reset(); timingResult timeresult = new timingResult(); timeresult.frameNum = -1; timeresult.scanNum = scanset.PrimaryScanNumber; sw.Start(); run.CurrentScanSet = scanset; Task msgen = new GenericMSGenerator(); msgen.Execute(results); timeresult.msGenTime = sw.ElapsedMilliseconds; sw.Reset(); sw.Start(); Task peakDetector = new DeconToolsPeakDetector(); peakDetector.Execute(results); timeresult.peakDetectorTime = sw.ElapsedMilliseconds; sw.Reset(); sw.Start(); DeconToolsV2.HornTransform.clsHornTransformParameters hornParams = new DeconToolsV2.HornTransform.clsHornTransformParameters(); Task decon = new HornDeconvolutor(hornParams); decon.Execute(results); timeresult.deconTime = sw.ElapsedMilliseconds; sw.Reset(); sw.Start(); Task scanResultUpdater = new ScanResultUpdater(); scanResultUpdater.Execute(results); timeresult.resultUpdaterTime = sw.ElapsedMilliseconds; timingResults.Add(timeresult); } reportTimingEachScan(timingResults); /* * results on Gord's computer... 2009_11_18. * scanNum msgen peakDet decon updater * 6005 85 72 3013 3 * 6012 13 6 2661 0 * 6019 13 9 2908 0 * 6026 12 11 2560 0 * 6033 14 9 2778 0 * 6040 13 6 2558 0 * 6047 12 8 2753 0 * * Avg: 23.1 17.3 2747.3 0.4 */ }