public void instiatateRunTest1() { Run run = new IMFRun(FileRefs.RawDataMSFiles.IMFStdFile1); Assert.AreEqual(Path.GetDirectoryName(FileRefs.RawDataMSFiles.IMFStdFile1), run.DataSetPath); Assert.AreEqual("50ugpmlBSA_CID_QS_16V_0000.Accum_1", run.DatasetName); }
public void GetMassSpectrumTest1() { Run run = new IMFRun(FileRefs.RawDataMSFiles.IMFStdFile1); var xydata = run.GetMassSpectrum(new ScanSet(233), 200, 2000); var numscans = run.GetNumMSScans(); Assert.AreEqual(600, numscans); var xvals = new float[1]; var yvals = new float[1]; xydata.GetXYValuesAsSingles(ref xvals, ref yvals); var sb = new StringBuilder(); for (var i = 0; i < xvals.Length; i++) { sb.Append(xvals[i]); sb.Append("\t"); sb.Append(yvals[i]); sb.Append(Environment.NewLine); } Console.Write(sb.ToString()); Assert.AreEqual(2595, xvals.Length); Assert.AreEqual(2595, yvals.Length); }
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 void GetSpectrumTypesTest1() { Run run = new IMFRun(FileRefs.RawDataMSFiles.IMFStdFile1); Assert.AreEqual(1, run.GetMSLevel(233)); //this function hasn't yet been implemented for IMF files Assert.AreEqual(1, run.GetMSLevel(234)); Assert.AreEqual(1, run.GetMSLevel(235)); }
public void examineIMFFile_Scan233MZ630() { Run run = new IMFRun(imfFilepath); run.MSParameters = new DeconTools.Backend.Parameters.MSParameters(); run.CurrentScanSet = new ScanSet(233, 229, 237); run.MSParameters.MinMZ = 100; run.MSParameters.MaxMZ = 631.5; int numPeaks = 0; for (double n = 629; n < 630; n = n + 0.01) { ResultCollection rc = new ResultCollection(run); Task msGen = new GenericMSGenerator(n, run.MSParameters.MaxMZ); msGen.Execute(rc); 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 zeroFiller = new DeconToolsZeroFiller(3); //zeroFiller.Execute(rc); Task peakDetector = new DeconToolsPeakDetector(detectorParams); peakDetector.Execute(rc); Task decon = new RapidDeconvolutor(); decon.Execute(rc); StringBuilder sb = new StringBuilder(); for (int i = 0; i < rc.ResultList.Count; i++) { IsosResult result = rc.ResultList[i]; if (result.IsotopicProfile.Peaklist[0].XValue > 629 && result.IsotopicProfile.Peaklist[0].XValue < 631) { sb.Append(n.ToString("0.00")); sb.Append("\t"); sb.Append(result.IsotopicProfile.Peaklist[0].XValue.ToString("0.00")); sb.Append("\t"); sb.Append(result.IsotopicProfile.Score.ToString("0.00")); sb.Append("\t"); sb.Append(result.Run.PeakList.Count); sb.Append("\t"); sb.Append(result.Run.XYData.Xvalues.Length); sb.Append("\n"); } } Console.Write(sb.ToString()); } }
public void MSGeneratorOnIMFFileTest1() { Run run = new IMFRun(imfFilepath); run.CurrentScanSet = new ScanSet(233, 229, 237); run.GetMassSpectrum(run.CurrentScanSet, 200, 2000); Assert.AreEqual(9908, run.XYData.Xvalues.Length); }
public void GetMassSpectrumAndSumAllTest() { Run run = new IMFRun(FileRefs.RawDataMSFiles.IMFStdFile1); var xydata = run.GetMassSpectrum(new ScanSet(10000, 1, 20000), 200, 2000); // this will sum scans 1 through 20000 (if <20000 scans, then will sum all available) var numscans = run.GetNumMSScans(); Assert.AreEqual(600, numscans); Assert.AreEqual(38326, xydata.Xvalues.Length); Assert.AreEqual(38326, xydata.Yvalues.Length); }
public void ExportMultipleScansTest1() { Run run = new IMFRun(imfFilepath); ScanSetCollection scanSetCollection = new ScanSetCollection(); scanSetCollection.ScanSetList.Add(new ScanSet(232)); scanSetCollection.ScanSetList.Add(new ScanSet(233)); scanSetCollection.ScanSetList.Add(new ScanSet(234)); ResultCollection results = new ResultCollection(run); foreach (ScanSet scanset in scanSetCollection.ScanSetList) { run.CurrentScanSet = scanset; 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); Task decon = new RapidDeconvolutor(); decon.Execute(results); Task scanResultUpdater = new ScanResultUpdater(); scanResultUpdater.Execute(results); } Assert.AreEqual(3, results.ScanResultList.Count); Assert.AreEqual(92, results.ScanResultList[0].NumPeaks); Assert.AreEqual(82, results.ScanResultList[1].NumPeaks); Assert.AreEqual(72, results.ScanResultList[2].NumPeaks); Assert.AreEqual(11, results.ScanResultList[0].NumIsotopicProfiles); Assert.AreEqual(9, results.ScanResultList[1].NumIsotopicProfiles); Assert.AreEqual(9, results.ScanResultList[2].NumIsotopicProfiles); Assert.AreEqual(830.045752112968, (Decimal)results.ScanResultList[0].BasePeak.XValue); Assert.AreEqual(10438, results.ScanResultList[0].BasePeak.Height); Assert.AreEqual(0.09454554, (Decimal)results.ScanResultList[0].BasePeak.Width); Assert.AreEqual(434.9167, (Decimal)results.ScanResultList[0].BasePeak.SN); Exporter <ResultCollection> exporter = new BasicScansExporter(scansExporterTest1output); exporter.Export(results); }
public void MSGeneratorOnIMFFileTest2() { Run run = new IMFRun(imfFilepath); run.CurrentScanSet = new ScanSet(233, 229, 237); Task msgen = new GenericMSGenerator(); msgen.Execute(run.ResultCollection); Assert.AreEqual(9917, run.XYData.Xvalues.Length); Assert.AreEqual(1, run.GetMSLevel(run.CurrentScanSet.PrimaryScanNumber)); }
public void imfFile100ScansTest1() { Project.Reset(); Project project = Project.getInstance(); Run run = new IMFRun(imfFilepath, 200, 299); project.RunCollection.Add(run); 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); Task rapidDecon = new RapidDeconvolutor(); project.TaskCollection.TaskList.Add(msGen); project.TaskCollection.TaskList.Add(peakDetector); project.TaskCollection.TaskList.Add(rapidDecon); ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(run, run.MinScan, run.MaxScan, 1, 1); scanSetCreator.Create(); 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(100, project.RunCollection[0].ScanSetCollection.ScanSetList.Count); Assert.AreEqual(1070, 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 void FindMSPeaksTest1() { ParameterLoader loader = new ParameterLoader(); loader.LoadParametersFromFile(parameterFilename); Run run = new IMFRun(imfFilepath); run.CurrentScanSet = new ScanSet(1, 1, 100000); ResultCollection resultcollection = new ResultCollection(run); Task msgen = new GenericMSGenerator(); msgen.Execute(resultcollection); DeconToolsPeakDetector peakfinder = new DeconToolsPeakDetector(loader.PeakParameters); peakfinder.Execute(resultcollection); StringBuilder sb = new StringBuilder(); for (int i = 0; i < resultcollection.Run.PeakList.Count; i++) { MSPeak mspeak = (MSPeak)resultcollection.Run.PeakList[i]; sb.Append(resultcollection.Run.PeakList[i].XValue); sb.Append("\t"); sb.Append(resultcollection.Run.PeakList[i].Height); sb.Append("\t"); sb.Append(mspeak.SN); sb.Append("\t"); sb.Append(resultcollection.Run.PeakList[i].Width); sb.Append("\t"); sb.Append(Environment.NewLine); } Console.Write(sb.ToString()); Assert.AreEqual(2438, resultcollection.Run.PeakList.Count); Assert.AreEqual(547.316411323136, Convert.ToDecimal(resultcollection.Run.PeakList[982].XValue)); Assert.AreEqual(100385, resultcollection.Run.PeakList[982].Height); }
public void deconvoluteIMFDataTest1() { Run run = new IMFRun(imfFilepath); run.MSParameters = new DeconTools.Backend.Parameters.MSParameters(); 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); Task rapid = new RapidDeconvolutor(); rapid.Execute(results); Assert.AreEqual(9, results.ResultList.Count); Assert.AreEqual(582.820684517665, Convert.ToDecimal(results.ResultList[0].IsotopicProfile.Peaklist[0].XValue)); Assert.AreEqual(2984.0, results.ResultList[0].IsotopicProfile.Peaklist[0].Height); Assert.AreEqual(0.05905123, (decimal)results.ResultList[0].IsotopicProfile.Peaklist[0].Width); Assert.AreEqual(157.0526, (decimal)results.ResultList[0].IsotopicProfile.Peaklist[0].SN); Assert.AreEqual(4593, results.ResultList[0].IsotopicProfile.GetAbundance()); Assert.AreEqual(1, results.ResultList[8].IsotopicProfile.GetNumOfIsotopesInProfile()); Assert.AreEqual(2488.07303881522, Convert.ToDecimal(results.ResultList[8].IsotopicProfile.AverageMass)); Assert.AreEqual(3, results.ResultList[8].IsotopicProfile.ChargeState); Assert.AreEqual(18802, Convert.ToDecimal(results.ResultList[8].IsotopicProfile.IntensityAggregate)); Assert.AreEqual(2486.09777364184, Convert.ToDecimal(results.ResultList[8].IsotopicProfile.MonoIsotopicMass)); Assert.AreEqual(829.711934128853, Convert.ToDecimal(results.ResultList[8].IsotopicProfile.MonoPeakMZ)); }
public void UIMF_and_IMF_Nosumming_Test1() { Run uimfrun = new UIMFRun(uimfFilepath); Run imfRun = new IMFRun(imfFrame1200filepath); int startFrame = 1200; int stopFrame = 1200; int numFramesSummed = 1; int numScansSummed = 1; FrameSetCollectionCreator framesetCreator = new FrameSetCollectionCreator(uimfrun, startFrame, stopFrame, numFramesSummed, 1); framesetCreator.Create(); ScanSetCollectionCreator scanSetCreator = new ScanSetCollectionCreator(uimfrun, numScansSummed, 1); scanSetCreator.Create(); ResultCollection uimfResults = new ResultCollection(uimfrun); //first analyze the UIMF file.... foreach (FrameSet frameset in ((UIMFRun)uimfrun).FrameSetCollection.FrameSetList) { System.Diagnostics.Stopwatch sw = new System.Diagnostics.Stopwatch(); ((UIMFRun)uimfrun).CurrentFrameSet = frameset; foreach (ScanSet scanset in uimfrun.ScanSetCollection.ScanSetList) { uimfrun.CurrentScanSet = scanset; Task msgen = new UIMF_MSGenerator(0, 2000); msgen.Execute(uimfResults); Task peakDetector = new DeconToolsPeakDetector(); peakDetector.Execute(uimfResults); Task rapid = new RapidDeconvolutor(); rapid.Execute(uimfResults); Task scanResultUpdater = new ScanResultUpdater(); scanResultUpdater.Execute(uimfResults); } } //next analyze the IMF file for the corresponding frame scanSetCreator = new ScanSetCollectionCreator(imfRun, 0, 599, numScansSummed, 1); scanSetCreator.Create(); ResultCollection imfResults = new ResultCollection(imfRun); foreach (ScanSet scanset in imfRun.ScanSetCollection.ScanSetList) { imfRun.CurrentScanSet = scanset; Task msgen = new GenericMSGenerator(0, 2000); msgen.Execute(imfResults); Task peakDetector = new DeconToolsPeakDetector(); peakDetector.Execute(imfResults); Task rapid = new RapidDeconvolutor(); rapid.Execute(imfResults); Task scanResultUpdater = new ScanResultUpdater(); scanResultUpdater.Execute(imfResults); } Console.WriteLine("imfScanSetCount = " + imfResults.Run.ScanSetCollection.ScanSetList.Count); Console.WriteLine("UIMFScanSetCount = " + uimfResults.Run.ScanSetCollection.ScanSetList.Count); Console.WriteLine("IMF scan0 peaks = " + imfResults.ScanResultList.Sum(p => p.NumPeaks)); Console.WriteLine("UIMF scan0 peaks = " + uimfResults.ScanResultList[0].NumPeaks); Console.WriteLine("imfResultCount = " + imfResults.ResultList.Count); Console.WriteLine("UIMFResultCount = " + uimfResults.ResultList.Count); for (int i = 0; i < uimfResults.ResultList.Count; i++) { Console.Write(getResultSummary(uimfResults.ResultList[i])); Console.Write(getResultSummary(imfResults.ResultList[i])); Console.Write("\n"); } }
public void compareUIMF_and_IMF_XYDataPoints2() { Run uimfRun = new UIMFRun(uimfFilepath2); ResultCollection uimfResults = new ResultCollection(uimfRun); Run imfRun = new IMFRun(imf2Frame391); ResultCollection imfResults = new ResultCollection(imfRun); FrameSet uimfFrame = new FrameSet(391); ((UIMFRun)uimfRun).CurrentFrameSet = uimfFrame; Task uimfMSGen = new UIMF_MSGenerator(); Task imfMSGen = new GenericMSGenerator(); ScanSetCollectionCreator scanSetCollectionCreator = new ScanSetCollectionCreator(uimfRun, 9, 1); scanSetCollectionCreator.Create(); scanSetCollectionCreator = new ScanSetCollectionCreator(imfRun, 9, 1); scanSetCollectionCreator.Create(); int scanStart = 200; int scanStop = 400; StringBuilder sb = new StringBuilder(); for (int n = scanStart; n < scanStop; n++) { uimfRun.CurrentScanSet = uimfRun.ScanSetCollection.ScanSetList[n]; imfRun.CurrentScanSet = imfRun.ScanSetCollection.ScanSetList[n + 1]; uimfMSGen.Execute(uimfResults); imfMSGen.Execute(imfResults); Assert.AreEqual(imfResults.Run.XYData.Xvalues.Length, uimfResults.Run.XYData.Xvalues.Length); double[] ppmDiffValues = new double[imfResults.Run.XYData.Xvalues.Length]; for (int i = 0; i < uimfResults.Run.XYData.Xvalues.Length; i++) { double imfXval = imfResults.Run.XYData.Xvalues[i]; double uimfXval = uimfResults.Run.XYData.Xvalues[i]; double imfYval = imfResults.Run.XYData.Yvalues[i]; double uimfYval = uimfResults.Run.XYData.Yvalues[i]; Assert.AreEqual(imfYval, uimfYval); Assert.AreEqual(Math.Round(imfXval, 8), Math.Round(uimfXval, 8)); //double ppmDiff = Math.Abs(imfXval - uimfXval) / imfXval * 1e6; //ppmDiffValues[i] = ppmDiff; //Assert.Less(ppmDiff, 0.25); } for (int i = 0; i < imfResults.Run.XYData.Xvalues.Length; i++) { sb.Append(n); sb.Append("\t"); sb.Append(imfResults.Run.XYData.Xvalues[i].ToString("0.00000")); sb.Append("\t"); sb.Append(uimfResults.Run.XYData.Xvalues[i].ToString("0.00000")); sb.Append("\t"); sb.Append(ppmDiffValues[i].ToString("0.00")); sb.Append("\t"); sb.Append(imfResults.Run.XYData.Yvalues[i]); sb.Append("\t"); sb.Append(uimfResults.Run.XYData.Yvalues[i]); sb.Append("\n"); } } Console.Write(sb.ToString()); }
public void imf_projectRef_horn_test2() { Project.Reset(); //Project.getInstance().RunCollection = new List<Run>(); Run run = new IMFRun(imfFilePath); Project.getInstance().RunCollection.Add(run); Project.getInstance().LoadOldDecon2LSParameters(imfParameters1); 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; hornParams.UseMZRange = false; hornParams.UseMercuryCaching = true; Task decon = new HornDeconvolutor(hornParams); HornDeconvolutor horn = (HornDeconvolutor)decon; 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(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.Sum(p => p.NumPeaks)); StringBuilder sb = new StringBuilder(); }
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 IMFcompareToCanonicalResults_noSumming() { //generate results using new framework int numScansSummed = 1; Run run = new IMFRun(imfFilepath); ResultCollection results = new ResultCollection(run); ScanSetCollectionCreator sscc = new ScanSetCollectionCreator(run, 231, 233, numScansSummed, 1, false); sscc.Create(); ParameterLoader loader = new ParameterLoader(); loader.LoadParametersFromFile(qtParameterfile1); foreach (ScanSet scanset in run.ScanSetCollection.ScanSetList) { run.CurrentScanSet = scanset; Task msgen = new GenericMSGenerator(); msgen.Execute(results); Task peakDetector = new DeconToolsPeakDetector(loader.PeakParameters); peakDetector.Execute(results); Task horndecon = new HornDeconvolutor(loader.TransformParameters); horndecon.Execute(results); Task scanResultUpdater = new ScanResultUpdater(); scanResultUpdater.Execute(results); } //read in results from canonical _isos List <IsosResult> canonIsos = readInIsos(canonIMFIsosFilename, Globals.MSFileType.PNNL_IMS); Assert.AreEqual(canonIsos.Count, results.ResultList.Count); //compare numbers StringBuilder sb = new StringBuilder(); for (int i = 0; i < results.ResultList.Count; i++) { sb.Append("scanmass\t"); sb.Append(results.ResultList[i].ScanSet.PrimaryScanNumber); sb.Append("\t"); sb.Append(canonIsos[i].ScanSet.PrimaryScanNumber); sb.Append("\n"); sb.Append("monoMass\t"); sb.Append(results.ResultList[i].IsotopicProfile.MonoIsotopicMass.ToString("0.0000")); sb.Append("\t"); sb.Append(canonIsos[i].IsotopicProfile.MonoIsotopicMass); sb.Append("\n"); sb.Append("intens\t"); sb.Append(results.ResultList[i].IsotopicProfile.IntensityAggregate); sb.Append("\t"); sb.Append(canonIsos[i].IsotopicProfile.IntensityAggregate); sb.Append("\n"); sb.Append("score\t"); sb.Append(results.ResultList[i].IsotopicProfile.Score.ToString("0.0000")); sb.Append("\t"); sb.Append(canonIsos[i].IsotopicProfile.Score); sb.Append("\n"); sb.Append("FWHM\t"); sb.Append(results.ResultList[i].IsotopicProfile.GetFWHM().ToString("0.0000")); sb.Append("\t"); sb.Append(canonIsos[i].IsotopicProfile.GetFWHM()); sb.Append("\n"); sb.Append("s/n\t"); sb.Append(results.ResultList[i].IsotopicProfile.GetSignalToNoise().ToString("0.0000")); sb.Append("\t"); sb.Append(canonIsos[i].IsotopicProfile.GetSignalToNoise()); sb.Append("\n"); sb.Append("\n"); } Console.Write(sb.ToString()); }